2024-03-28T13:21:08Zhttps://kuscholarworks.ku.edu/oai/requestoai:kuscholarworks.ku.edu:1808/84142019-04-12T14:46:40Zcom_1808_97col_1808_102
Wilson, George S.
Unruh, Jay R.
Gokulrangan, Giridharan
Lushington, Gerald H.
Johnson, Carey K.
2011-11-18T19:57:58Z
2011-11-18T19:57:58Z
2005-05
J.R. Unruh, G. Gokulrangan, G.H. Lushington, C.K. Johnson, and G.S. Wilson, Orientational Dynamics and Dye-DNA Interactions in a DNA Aptamer, Biophysical Journal. 88, 3455-3465 (2005). http://dx.doi.org/10.1529/biophysj.104.054148
http://hdl.handle.net/1808/8414
10.1529/biophysj.104.054148
https://orcid.org/0000-0003-3077-4990
We report the picosecond and nanosecond timescale rotational dynamics of a dye-labeled DNA oligonucleotide
or ‘‘aptamer’’ designed to bind specifically to immunoglobulin E. Rotational dynamics in combination with fluorescence lifetime
measurements provide information about dye-DNA interactions. Comparison of Texas Red (TR), fluorescein, and tetramethylrhodamine
(TAMRA)-labeled aptamers reveals surprising differences with significant implications for biophysical studies
employing such conjugates. Time-resolved anisotropy studies demonstrate that the TR- and TAMRA-aptamer anisotropy
decays are dominated by the overall rotation of the aptamer, whereas the fluorescein-aptamer anisotropy decay displays
a subnanosecond rotational correlation time much shorter than that expected for the overall rotation of the aptamer. Docking
and molecular dynamics simulations suggest that the low mobility of TR is a result of binding in the groove of the DNA helix.
Additionally, associated anisotropy analysis of the TAMRA-aptamer reveals both quenched and unquenched states that experience
significant coupling to the DNA motion. Therefore, quenching of TAMRA by guanosine must depend on the configuration
of the dye bound to the DNA. The strong coupling of TR to the rotational dynamics of the DNA aptamer, together with the
absence of quenching of its fluorescence by DNA, makes it a good probe of DNA orientational dynamics. The understanding of
the nature of dye-DNA interactions provides the basis for the development of bioconjugates optimized for specific biophysical
measurements and is important for the sensitivity of anisotropy-based DNA-protein interaction studies employing such
conjugates.
Dynamic Aspects of Chemical
Biology Training Grant (National Institutes of Health 5 T32 GM08545-09),
Support from the Petroleum Research Fund, administered by the American
Chemical Society.
en_US
Biophysical Society
Orientational Dynamics and Dye-DNA Interactions in a Dye-Labeled DNA Aptamer
Article
openAccess
Wilson, George S.
Johnson, Carey K.
Chemistry
Scholarly/refereed, publisher version
This item does not meet KU Open Access policy criteria.
oai:kuscholarworks.ku.edu:1808/328192024-01-16T16:12:07Zcom_1808_97col_1808_102
Aksenov, Nicolai A.
Aksenov, Alexander V.
Kurenkov, Igor A.
Kirillov, Nikita K.
Aksenov, Dmitrii A.
Arutiunov, Nikolai A.
Aksenova, Daria S.
Rubin, Michael
2022-07-11T18:43:27Z
2022-07-11T18:43:27Z
2022-04-28
Aksenov, N.A.; Aksenov, A.V.; Kurenkov, I.A.; Kirillov, N.K.; Aksenov, D.A.; Arutiunov, N.A.; Aksenova, D.S.; Rubin, M. One-Pot Synthesis of (E)-2-(3-Oxoindolin-2-ylidene)-2-arylacetonitriles. Molecules 2022, 27, 2808. https://doi.org/10.3390/molecules27092808
http://hdl.handle.net/1808/32819
10.3390/molecules27092808
https://orcid.org/ 0000-0002-7125-9066
https://orcid.org/ 0000-0002-0911-4093
https://orcid.org/ 0000-0002-1668-9311
PMC35566159
A highly efficient and expeditious one-pot approach towards 2-(3-oxoindolin-2-yl)acetonitriles was designed, which involves a base-assisted aldol reaction of ortho-nitroacetophenones, followed by hydrocyanation, triggering an unusual reductive cyclization reaction.
MDPI
© 2022 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license.
http://creativecommons.org/licenses/by/4.0/
openAccess
Nitroalkanes
Brønsted acid catalysis
Indoles
Rearrangements
Cascade transformations
One-Pot Synthesis of (E)-2-(3-Oxoindolin-2-ylidene)-2-arylacetonitriles
Article
Rubin, Michael
Chemistry
Scholarly/refereed, publisher version
This item meets KU Open Access policy criteria.
oai:kuscholarworks.ku.edu:1808/158602019-04-12T14:50:46Zcom_1808_97col_1808_102
Chu, Shih-I
Tietz, James V.
Datta, Krishna K.
2014-11-25T17:24:25Z
2014-11-25T17:24:25Z
1982-01-01
Chu, Shih-I., Tietz, James V., Datta, Krishna K. "Quantum dynamics of molecular multiphoton excitation in intense laser and static electric fields: Floquet theory, quasienergy spectra, and application to the HF molecule." The Journal of Chemical Physics 77, 2968 (1982); http://dx.doi.org/10.1063/1.444219.
http://hdl.handle.net/1808/15860
10.1063/1.444219
This is the published version, also available here: http://dx.doi.org/10.1063/1.444219.
The multiphoton excitationdynamics of vibration‐rotation states in diatomic molecules in intense laser and static electric fields is investigated. The Floquet matrix method is used to calculate the quasienergy and multiphoton absorptionspectra of the HF molecule as functions of field strengths and frequency. Nonlinear effects such as power broadening, dynamic Stark shift, Autler–Townes multiplet splitting, hole burning, and S‐hump behaviors, etc., are observed and discussed in terms of quasienergy diagrams. Many of the salient features in the spectral line shapes may be qualitatively understood in terms of an analytical three‐level model. The addition of a dc electric field removes the restriction of the rotational dipole selection rule and causes significant intermixing of the bare molecular vibrator states. Due to the greater number of strongly coupled nearby states in the dc field, nonlinear effects such as those mentioned above appear at a much lower ac field strength than they would in the absence of the dc field. The introduction of an external dc field, therefore, strongly enhances the multiphoton excitation probabilities and results in a much richer spectrum.
Elsevier
Multiphoton excitation
Field theory
Molecular dynamics
Molecular spectra
Static electric fields
Quantum dynamics of molecular multiphoton excitation in intense laser and static electric fields: Floquet theory, quasienergy spectra, and application to the HF molecule
Article
openAccess
Chu, Shih-I
Chemistry
na
Scholarly/refereed, publisher version
This item does not meet KU Open Access policy criteria.
oai:kuscholarworks.ku.edu:1808/319042021-10-22T19:45:38Zcom_1808_97col_1808_102
Moon, Hee-Jung
Finney, Joel
Ronnebaum, Trey
Mure, Minae
2021-10-05T20:30:06Z
2021-10-05T20:30:06Z
2014-08-01
Hee-Jung Moon, Joel Finney, Trey Ronnebaum, Minae Mure. Bioorg Chem. 2014 Dec; 57: 231–241. Published online 2014 Aug 1. doi: 10.1016/j.bioorg.2014.07.003
http://hdl.handle.net/1808/31904
10.1016/j.bioorg.2014.07.003
PMC6309629
This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.
Lysyl oxidase like-2 (LOXL2) belongs to the lysyl oxidase (LOX) family, which comprises Cu2+- and lysine tyrosylquinone (LTQ)-dependent amine oxidases. LOXL2 is proposed to function similarly to LOX in the extracellular matrix (ECM) by promoting crosslinking of collagen and elastin. LOXL2 has also been proposed to regulate extracellular and intracellular cell signaling pathways. Dysregulation of LOXL2 has been linked to many diseases, including cancer, pro-oncogenic angiogenesis, fibrosis and heart diseases. In this review, we will give an overview of the current understandings and hypotheses regarding the molecular functions of LOXL2.
Elsevier
Copyright © 2014 Elsevier Inc. All rights reserved.
http://creativecommons.org/licenses/by-nc-nd/4.0/
openAccess
Lysyl oxidase family
Lysyl oxidase like-2
Lysine tyrosylquinone (LTQ)
Cell signaling
Extracellular matrix
Tumor metastasis/invasion
Human lysyl oxidase-like 2
Article
Moon, Hee-Jung
Finney, Joel
Ronnebaum, Trey
Mure, Minae
Department of Chemistry
Scholarly/refereed, author accepted manuscript
This item meets KU Open Access policy criteria.
oai:kuscholarworks.ku.edu:1808/160112019-04-12T14:49:18Zcom_1808_97col_1808_102
Chu, Shih-I
2014-12-02T20:00:46Z
2014-12-02T20:00:46Z
1975-08-01
Chu, Shih-I. "Rotational excitation of symmetric-top molecular ions by electron impact." Phys. Rev. A 12, 396 – Published 1 August 1975. http://dx.doi.org/10.1103/PhysRevA.12.396.
http://hdl.handle.net/1808/16011
10.1103/PhysRevA.12.396
This is the publishers version, also available here: http://dx.doi.org/10.1103/PhysRevA.12.396.
The theory for the rotational excitation of symmetric-top molecular ions by electron impact is formulated within the Coulomb-Born approximation. Analytical expressions are derived for the rotational transitions induced by dipole and by quadrupole interactions. The cross sections are large and finite at threshold and decrease with increasing electron-impact energy. The validity of the present theory for the description of low-energy collisions is examined. Numerical calculations are reported for the excitation of the hydronium H3O+ ion.
American Physical Society
Rotational excitation of symmetric-top molecular ions by electron impact
Article
openAccess
Chu, Shih-I
Chemistry
na
Scholarly/refereed, publisher version
This item does not meet KU Open Access policy criteria.
oai:kuscholarworks.ku.edu:1808/159782019-04-12T14:46:53Zcom_1808_97col_1808_102
Telnov, Dmitry A.
Chu, Shih-I
2014-12-01T21:23:24Z
2014-12-01T21:23:24Z
2002-10-25
Telnov, Dmitry A.; Chu, Shih-I. (2002). "Multiphoton above-threshold detachment of Li-: Exterior-complex-scaling– generalized-pseudospectral method for calculations of complex-quasienergy resonances in Floquet formulation of time-dependent density-functional theory." Physical Review A, 66(4):043417. http://dx.doi.org/10.1103/PhysRevA.66.043417
1050-2947
http://hdl.handle.net/1808/15978
10.1103/PhysRevA.66.043417
This is the publisher's version, also available electronically from http://journals.aps.org/pra/abstract/10.1103/PhysRevA.66.043417.
We extend the exterior-complex-scaling–generalized-pseudospectral (ECSGPS) method [D. A. Telnov and S. I. Chu, Phys. Rev. A 59, 2864 (1999)] to the nonperturbative calculations of complex-quasienergy resonances of many-electron quantum systems within the Floquet formulation of time-dependent density-functional theory (TDDFT) [D. A. Telnov and S. I. Chu, Chem. Phys. Lett. 264, 466 (1997)]. The ECSGPS technique appears very useful in TDDFT-Floquet calculations where the exchange-correlation potentials may exhibit quite complicated behavior as functions of the electron coordinates and cannot be easily treated by means of the uniform-complex-scaling techniques. We have applied this procedure to the study of one-photon detachment and two-photon dominant above-threshold detachment of Li- negative ions. In the one-photon case, the photodetachment cross section has been calculated as a function of the photon energy with results in good agreement with the experimental data. In the two-photon case, both the partial detachment rates and electron angular distributions for the dominant and above-threshold channels are presented for a range of laser field frequencies and intensities. Dramatic transformations of the angular distributions in the vicinity of the two-photon threshold are observed and analyzed.
American Physical Society
Multiphoton above-threshold detachment of Li-: Exterior-complex-scaling– generalized-pseudospectral method for calculations of complex-quasienergy resonances in Floquet formulation of time-dependent density-functional theory
Article
openAccess
Telnov, Dmitry A.
Chemistry
Scholarly/refereed, publisher version
This item does not meet KU Open Access policy criteria.
oai:kuscholarworks.ku.edu:1808/251022018-07-17T16:18:08Zcom_1808_97col_1808_102
Ulapane, Kavisha R.
On, Ngoc
Kiptoo, Paul
Williams, Todd D.
Miller, Donald W.
Siahaan, Teruna J.
2017-10-09T17:50:54Z
2017-10-09T17:50:54Z
2017-06-08
Ulapane, K. R., On, N., Kiptoo, P., Williams, T. D., Miller, D. W., & Siahaan, T. J. (2017). Improving Brain Delivery of Biomolecules via BBB Modulation in Mouse and Rat: Detection using MRI, NIRF, and Mass Spectrometry. Nanotheranostics, 1(2), 217–231. http://doi.org/10.7150/ntno.19158
http://hdl.handle.net/1808/25102
10.7150/ntno.19158
PMC5588751
There is an urgent need to develop new and alternative methods to deliver functional biomolecules to the brain for diagnosis and treatment of brain diseases. The goal of this study was to evaluate the activity of blood-brain barrier (BBB) modulators (i.e., HAV and ADT peptides) to deliver functional biomolecules (i.e., galbumin, IRdye800cw-cLABL, and cIBR7) to the brains of mice and rats. HAV6, cHAVc3, and ADTC5 peptides but not HAV4 peptide significantly enhanced the brain delivery of 65 kDa galbumin compared to control in Balb/c mice as quantified by magnetic resonance imaging (MRI). Ten-minute pretreatment with ADTC5 peptide still significantly increased brain delivery of galbumin; however, no enhancement was observed after 10-min pretreatment with HAV6. There was no enhancement of galbumin deposition following 40-min pretreatment with ADTC5 or HAV6, suggesting a short duration of the BBB opening for large molecules. ADTC5 peptide also improved the brain delivery of IRdye800cw-cLABL peptide about 3.5-fold compared to control in Balb/c mice as detected by near infrared fluorescence (NIRF). The BBB modulator activity of ADTC5 to deliver cIBR7 peptide was also evaluated in vivo using Sprague-Dawley rats. The amount of cIBR7 in the brain was detected by LC-MS/MS. ADTC5 peptide enhanced the delivery of cIBR7 peptide into rat brain about 4-fold compared to control and the intact cIBR7 can be efficiently extracted and detected in rat brain. In conclusion, HAV and ADT peptides enhance the brain delivery of functional peptides (e.g., cLABL and cIBR7) and protein (e.g., 65 kDa galbumin) in two animal models, and the duration of the BBB opening for a large molecule (e.g., galbumin) was short.
Ivyspring International Publisher
© Ivyspring International Publisher. This is an open access article distributed under the terms of the Creative Commons Attribution (CC BY-NC) license. See http://ivyspring.com/terms for full terms and conditions.
https://creativecommons.org/licenses/by-nc/4.0/
openAccess
Blood-brain barrier
BBB
Brain delivery
Cadherin peptides
HAV peptide
ADT peptide
Paracellular diffusion
Tight junction
Adherens junction
BBB modulation
Improving Brain Delivery of Biomolecules via BBB Modulation in Mouse and Rat: Detection using MRI, NIRF, and Mass Spectrometry
Article
Ulapane, Kavisha R.
Siahaan, Teruna J.
Kiptoo, Paul
Williams, Todd D.
Chemistry
Pharmaceutical Chemistry
Mass Spectrometry Laboratory
Scholarly/refereed, publisher version
This item meets KU Open Access policy criteria.
oai:kuscholarworks.ku.edu:1808/160942019-04-12T14:45:57Zcom_1808_97col_1808_102
Hierl, Peter M.
Pacak, V.
Herman, Z.
2014-12-15T17:02:13Z
2014-12-15T17:02:13Z
1977-01-01
Hierl, Peter M.; Pacak, V.; Herman, Z. (1977). "Kinematics of charge transfer: Ar^++H2." Jounal of Chemical Physics, 67:2678-2686. http://dx.doi.org/10.1063/1.435181
0021-9606
http://hdl.handle.net/1808/16094
10.1063/1.435181
This is the publisher's version, also available electronically from http://scitation.aip.org/content/aip/journal/jcp/67/6/10.1063/1.435181.
Product angular and velocity vector distributions have been measured in a crossed beam experiment for the charge transfer process Ar++H2→Ar+H2 + at relative collision energies of 0.13, 0.48, and 3.44 eV. Charge transfer was found to occur by two distinct mechanisms: (1) a simple electron‐jump mechanism which preserves the quasirectilinear trajectories of the colliding species and which selectively produces H2 + in the vibrational state most nearly resonant with the reactant ion, and (2) an intimate‐collision mechanism which results in large‐angle scattering and which produces H2 + in a broad range of vibrational states.
American Institute of Physics
Kinematics of charge transfer: Ar^++H2
Article
openAccess
Hierl, Peter M.
Chemistry
Scholarly/refereed, publisher version
This item does not meet KU Open Access policy criteria.
oai:kuscholarworks.ku.edu:1808/161652019-04-12T14:46:22Zcom_1808_97col_1808_102
Laird, Brian Bostian
McCoy, John D.
Haymet, A. D. J.
2014-12-17T22:28:26Z
2014-12-17T22:28:26Z
1987-09-01
Laird, Brian Bostian; McCoy, John D.; Haymet, A. D. J. (1987). "Density functional theory of freezing: Analysis of crystal density." The Journal of Chemical Physics, 87(9):5449-5456. http://dx.doi.org/10.1063/1.453663
0021-9606
http://hdl.handle.net/1808/16165
10.1063/1.453663
This is the publisher's version, also available electronically from http://scitation.aip.org/content/aip/journal/jcp/87/9/10.1063/1.453663
The density functional theory of freezing is used to study the liquid to crystal phase transition in the hardsphere and Lennard‐Jones systems. An important step in the calculation is the parametrization of the solid phase average single particle density ρ(r). In this work two popular parametrizations are compared. The first method is a general Fourier decomposition of the periodic solid density in which the amplitude of each (non‐symmetry‐related) Fourier component is treated as an independent parameter. The second parametrization, which is more restrictive but easier to implement, approximates the solid density as a sum of Gaussian peaks centered at the sites of a periodic lattice. The two methods give essentially identical results for the phase diagrams for the two systems studied, but the crystal density predicted by the Fourier method exhibits significant anisotropies which are excluded from the Gaussian representation by construction.
American Institute of Physics
Density functional theory of freezing: Analysis of crystal density
Article
openAccess
Laird, Brian Bostian
Chemistry
Scholarly/refereed, publisher version
This item does not meet KU Open Access policy criteria.
oai:kuscholarworks.ku.edu:1808/160222019-04-12T14:49:37Zcom_1808_97col_1808_102
Birnbaum, George
Chu, Shih-I
Dalgarno, A.
Frommhold, Lothar
Wright, E. L.
2014-12-03T18:58:11Z
2014-12-03T18:58:11Z
1984-02-01
Birnbaum, George., Chu, Shih-I., Dalgarno, A., Frommhold, Lothar., Wright, E. L. "Theory of collision-induced translation-rotation spectra: H2-He." Phys. Rev. A 29, 595 – Published 1 February 1984. http://dx.doi.org/10.1103/PhysRevA.29.595.
http://hdl.handle.net/1808/16022
10.1103/PhysRevA.29.595
This is the published version, also available here: http://dx.doi.org/10.1103/PhysRevA.29.595.
An adiabatic quantal theory of spectral line shapes in collision-induced absorption and emission is presented which incorporates the induced translation-rotation and translation-vibration spectra. The generalization to account for the anisotropy of the scattering potential is given. Calculations are carried out of the collision-induced absorption spectra of He in collisions with H2 with ab initio electric dipole functions and realistic potentials. The anisotropy of the interaction potential is small and is not included in the calculations. The predicted spectra are in satisfactory agreement with experimental data though some deviations occur which may be significant. The rotational line shapes have exponential wings and are not Lorentzian. The connection between the quantal and classical theories is written out explicitly for the isotropic overlap induction.
American Physical Society
Theory of collision-induced translation-rotation spectra: H2-He
Article
openAccess
Chu, Shih-I
Chemistry
na
Scholarly/refereed, publisher version
This item does not meet KU Open Access policy criteria.
oai:kuscholarworks.ku.edu:1808/161062019-04-12T14:46:05Zcom_1808_97col_1808_102
Hierl, Peter M.
Franklin, J. L.
2014-12-15T18:57:51Z
2014-12-15T18:57:51Z
1967-01-01
Hierl, Peter M.; Franklin, J. L. (1967). "Appearance Potentials and Kinetic Energies of Ions from N2, CO, and NO." Jounal of Chemical Physics, 47:3154-3161. http://dx.doi.org/10.1063/1.1712367
0021-9606
http://hdl.handle.net/1808/16106
10.1063/1.1712367
This is the publisher's version, also available electronically from http://scitation.aip.org/content/aip/journal/jcp/47/9/10.1063/1.1712367
A recently developed method has permitted the measurement of excess translational energy of ions formed in a time‐of‐flight mass spectrometer. The method, in conjunction with the RPD technique for determining appearance potentials, has been applied to the electron‐impact study of nitrogen, carbon monoxide, and nitric oxide. A total of 31 different ionization processes have been observed and identified, several of which had not been previously reported in the literature.
American Institute of Physics
Appearance Potentials and Kinetic Energies of Ions from N2, CO, and NO
Article
openAccess
Hierl, Peter M.
Chemistry
Scholarly/refereed, publisher version
This item does not meet KU Open Access policy criteria.
oai:kuscholarworks.ku.edu:1808/160282019-04-12T14:31:53Zcom_1808_97col_1808_102
Zhou, Zhongyuan
Chu, Shih-I
2014-12-04T17:20:09Z
2014-12-04T17:20:09Z
2009-05-13
Zhou, Zhongyuan & Chu, Shih-I. "Time-dependent localized Hartree-Fock density-functional linear response approach for photoionization of atomic excited states." Phys. Rev. A 79, 053412 – Published 13 May 2009. http://dx.doi.org/10.1103/PhysRevA.79.053412.
http://hdl.handle.net/1808/16028
10.1103/PhysRevA.79.053412
This is the published version, also available here: http://dx.doi.org/10.1103/PhysRevA.79.053412.
We present a time-dependent localized Hartree-Fock density-functional linear response approach for the treatment of photoionization of atomic systems. This approach employs a spin-dependent localized Hartree-Fock exchange potential to calculate electron orbitals and kernel functions, and thus can be used to study the photoionization from atomic excited states. We have applied the approach to the calculation of photoionization cross sections of Ne ground state. The results are in agreement with available experimental data and have comparable accuracies with other ab initio theoretical results. We have also extended the approach to explore the photoionization from Ne excited states and obtained some results for the photoionization from outer-shell and inner-shell excited states.
American Physical Society
Time-dependent localized Hartree-Fock density-functional linear response approach for photoionization of atomic excited states
Article
openAccess
Zhou, Zhongyuan
Chu, Shih-I
Chemistry
fullparticipation
Scholarly/refereed, publisher version
This item meets KU Open Access policy criteria.
oai:kuscholarworks.ku.edu:1808/255362017-12-01T09:01:25Zcom_1808_97col_1808_102
de Vries, Thomas A.
Hollenbeck, John R.
Davison, Robert B.
Walter, Frank
van der Vegt, Gerben S.
2017-11-30T22:47:27Z
2017-11-30T22:47:27Z
2016
De Vries, T. A., Hollenbeck, J. R., Davison, R. B., Walter, F., & Van Der Vegt, G. S. (2016). Managing coordination in multiteam systems: Integrating micro and macro perspectives. Academy of Management Journal, 59(5), 1823-1844.
http://hdl.handle.net/1808/25536
10.5465/amj.2014.0385
Multiteam systems (i.e., teams of teams) are frequently used to deal with complex and demanding challenges that require several teams’ joint efforts. However, achieving effective horizontal coordination across component teams in these systems remains difficult. Using insights from organizational behavior research, we argue that horizontal coordination between component teams can benefit if a multiteam system is composed of generalist members who are acquainted with the multiple functions present in the overall system (i.e., high intrapersonal functional diversity [IFD]). At the same time, however, such IFD may have detrimental side effects because generalists’ broad focus may distract them from high-impact, specialized activities (i.e., aspirational behavior). Building on insights from organization theory, we propose that coordination across a multiteam system’s hierarchical layers (i.e., vertical coordinated action between a team tasked with system-wide integration and task-specialized component teams) is critical for reaping IFD’s benefits while avoiding its costs. These notions are supported in a sample of 236 14-person multiteam systems engaged in a realistic decision-making simulation. Our findings illustrate how combining insights from organizational behavior and organization theory can advance academic knowledge on multiteam systems and offer practical solutions for managing such systems.
Academy of Management
This is an open access article under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs License 4.0 (CC BY-NC-ND 4.0), which permits use and distribution in any medium, provided the original work is properly cited, the use is non-commercial and no modifications or adaptations are made.
http://creativecommons.org/licenses/by-nc-nd/4.0/
openAccess
Aspirational behavior
Integrative leadership
Horizontal coordination
Intrapersonal functional diversity
Multiteam systems
Vertical coordinated action
Managing Coordination in Multiteam Systems: Integrating Micro and Macro Perspectives
Article
Chemistry
Scholarly/refereed, publisher version
This item meets KU Open Access policy criteria.
oai:kuscholarworks.ku.edu:1808/160042019-04-12T14:29:24Zcom_1808_97col_1808_102
Chu, Shih-I
Zhou, Zhongyuan
2014-12-02T19:22:24Z
2014-12-02T19:22:24Z
2011-01-19
Zhou, Zhongyuan & Chu, Shih-I. "Precision calculation of above-threshold multiphoton ionization in intense short-wavelength laser fields: The momentum-space approach and time-dependent generalized pseudospectral method." Phys. Rev. A 83, 013405 – Published 19 January 2011. http://dx.doi.org/10.1103/PhysRevA.83.013405.
http://hdl.handle.net/1808/16004
10.1103/PhysRevA.83.013405
This is the published version, also available here: http://dx.doi.org/10.1103/PhysRevA.83.013405.
We present an approach in momentum (P) space for the accurate study of multiphoton and above-threshold ionization (ATI) dynamics of atomic systems driven by intense laser fields. In this approach, the electron wave function is calculated by solving the P-space time-dependent Schrödinger equation (TDSE) in a finite P-space volume under a simple zero asymptotic boundary condition. The P-space TDSE is propagated accurately and efficiently by means of the time-dependent generalized pseudospectral method with optimal momentum grid discretization and a split-operator time propagator in the energy representation. The differential ionization probabilities are calculated directly from the continuum-state wave function obtained by projecting the total electron wave function onto the continuum-state subspace using the projection operator constructed by the continuum eigenfunctions of the unperturbed Hamiltonian. As a case study, we apply this approach to the nonperturbative study of the multiphoton and ATI dynamics of a hydrogen atom exposed to intense short-wavelength laser fields. High-resolution photoelectron energy-angular distribution and ATI spectra have been obtained. We find that with the increase of the laser intensity, the photoelectron energy-angular distribution changes from circular to dumbbell shaped and is squeezed along the laser field direction. We also explore the change of the maximum photoelectron energy with laser intensity and strong-field atomic stabilization phenomenon in detail.
American Physical Society
Precision calculation of above-threshold multiphoton ionization in intense short-wavelength laser fields: The momentum-space approach and time-dependent generalized pseudospectral method
Article
openAccess
Chu, Shih-I
Zhou, Zhongyuan
Chemistry
fullparticipation
Scholarly/refereed, publisher version
This item meets KU Open Access policy criteria.
oai:kuscholarworks.ku.edu:1808/189702019-04-12T14:54:47Zcom_1808_97col_1808_102
Rogers, Steven A.
2015-11-20T23:04:54Z
2015-11-20T23:04:54Z
2010-07-08
Rogers, Steven A., Daniel C. Whitehead, Trey Mullikin, and Christian Melander. "Synthesis and Bacterial Biofilm Inhibition Studies of Ethyl N-(2-phenethyl) Carbamate Derivatives." Organic & Biomolecular Chemistry Org. Biomol. Chem. 8.17 (2010): 3857. DOI:10.1039/C0OB00063A
http://hdl.handle.net/1808/18970
10.1039/C0OB00063A
This is the published version. Copyright Royal Society of Chemistry
An 88 member library based upon the marine bacterial metabolite ethyl N-(2-phenethyl) carbamate was evaluated for bacterial biofilm inhibition against a panel of medically relevant strains. These studies culminated in the discovery of a new class of molecules capable of inhibiting the formation of S. aureus biofilms with low micromolar IC50 values.
Royal Society of Chemistry
Synthesis and bacterial biofilm inhibition studies of ethyl N-(2-phenethyl) carbamate derivatives
Article
openAccess
Rogers, Steven A.
Chemistry
Scholarly/refereed, publisher version
This item meets KU Open Access policy criteria.
oai:kuscholarworks.ku.edu:1808/297352019-12-06T21:09:02Zcom_1808_97col_1808_102
Maslivetc, Vladimir A.
Frolova, Liliya V.
Rogelj, Snezna
Maslivetc, Anna A.
Rubina, Marina
Rubin, Michael
2019-11-07T22:08:53Z
2019-11-07T22:08:53Z
2018-10-24
Maslivetc, V. A., Frolova, L. V., Rogelj, S., Maslivetc, A. A., Rubina, M., & Rubin, M. (2018). Metal-Templated Assembly of Cyclopropane-Fused Diazepanones and Diazecanones via exo- trig Nucleophilic Cyclization of Cyclopropenes with Tethered Carbamates. The Journal of organic chemistry, 83(22), 13743–13753. doi:10.1021/acs.joc.8b02062
http://hdl.handle.net/1808/29735
10.1021/acs.joc.8b02062
https://orcid.org/0000-0003-1673-6365
https://orcid.org/0000-0002-1668-9311
PMC6667834
This document is the Accepted Manuscript version of a Published Work that appeared in final form in The Journal of Organic Chemistry, copyright © American Chemical Society after peer review and technical editing by the publisher. To access the final edited and published work see http://doi.org/10.1021/acs.joc.8b02062.
A strain-release-driven, cation-templated nucleophilic 7- and 8-exo-trig-cyclization of tethered Boc-protected amines to cyclopropenes is described. The featured reaction proceeds in diastereo- and regioselective fashion and allows for preparation of the corresponding 2,5-diazabicyclo[5.1.0]octan-6-ones and 2,6-diazabicyclo[6.1.0]nonan-7-ones as sole products in high yields. Preliminary studies on anticancer activities of these novel cyclopropane-fused medium heterocycles were performed.
American Chemical Society
Copyright © 2018 American Chemical Society
openAccess
Metal-Templated Assembly of Cyclopropane-Fused Diazepanones and Diazecanones via exo-trig Nucleophilic Cyclization of Cyclopropenes with Tethered Carbamates
Article
Maslivetc, Vladimir A.
Maslivetc, Anna A.
Rubina, Rubina
Rubin, Michael
Chemistry
Scholarly/refereed, author accepted manuscript
This item meets KU Open Access policy criteria.
oai:kuscholarworks.ku.edu:1808/161802019-04-12T14:46:33Zcom_1808_97col_1808_102
Thompson, Ward H.
Karlsson, Hans O.
Miller, William H.
2014-12-18T17:10:11Z
2014-12-18T17:10:11Z
1996-09-01
Thompson, Ward H.; Karlsson, Hans O.; Miller, William H. (1996). "Theoretical calculation of photodetachment intensities for H3O−." The Journal of Chemical Physics, 105(13):5387-5396. http://dx.doi.org/10.1063/1.472380
0021-9606
http://hdl.handle.net/1808/16180
10.1063/1.472380
This is the publisher's version, also available electronically from http://scitation.aip.org/content/aip/journal/jcp/105/13/10.1063/1.472380.
We have calculated total and arrangement‐selected photodetachment intensities for the H3O− anion (and its deuterated form, D3O−) using a Green’s function in a discrete variable representation with absorbing boundary conditions. A multiply‐shifted quasiminimal residual method is used to obtain the Green’s function for many energies at once. We present spectra obtained by explicitly treating two and four degrees of freedom. Comparison with experiment indicates that the bending angles in the anion and neutral are more similar than in the current potential energy surfaces. The calculated spectra are also consistent with the suggestion that the barrier should be ‘‘earlier.’’
American Institute of Physics
Theoretical calculation of photodetachment intensities for H3O−
Article
openAccess
Thompson, Ward H.
Chemistry
Scholarly/refereed, publisher version
This item does not meet KU Open Access policy criteria.
oai:kuscholarworks.ku.edu:1808/236442019-04-12T14:13:36Zcom_1808_97col_1808_102
Painter, Thomas O.
Bunn, Jonathon R.
Schoenen, Frank J.
Douglas, Justin T.
Day, Victor W.
Santini, Conrad
2017-04-12T18:50:03Z
2017-04-12T18:50:03Z
2013-04-13
Painter, T. O., Bunn, J. R., Schoenen, F. J., Douglas, J. T., Day, V. W., & Santini, C. (2013). Skeletal Diversification via Heteroatom Linkage Control: Preparation of Bicyclic and Spirocyclic Scaffolds from N-Substituted Homopropargyl Alcohols. The Journal of Organic Chemistry, 78(8), 3720–3730. http://doi.org/10.1021/jo400077m
http://hdl.handle.net/1808/23644
10.1021/jo400077m
The discovery and application of a new branching pathway synthesis strategy that rapidly produces skeletally diverse scaffolds is described. Two different scaffold types, one a bicyclic iodo-vinylidene tertiary amine/tertiary alcohol and the other, a spirocyclic 3-furanone, are each obtained using a two-step sequence featuring a common first step. Both scaffold types lead to intermediates that can be orthogonally diversified using the same final components. One of the scaffold types was obtained in sufficiently high yield that it was immediately used to produce a 97-compound library.
American Chemical Society
This document is the Accepted Manuscript version of a Published Work that appeared in final form in the Journal of Organic Chemistry, copyright © American Chemical Society after peer review and technical editing by the publisher. To access the final edited and published work see http://dx.doi.org/10.1021/jo400077m.
openAccess
Skeletal Diversification via Heteroatom Linkage Control: Preparation of Bicyclic and Spirocyclic Scaffolds from NSubstituted Homopropargyl Alcohols
Article
Painter, Thomas O.
Bunn, Jonathon R.
Schoenen, Frank J.
Douglas, Justin T.
Day, Victor W.
Santini, Conrad
Chemistry
Scholarly/refereed, author accepted manuscript
This item meets KU Open Access policy criteria.
oai:kuscholarworks.ku.edu:1808/135462018-07-13T15:43:49Zcom_1808_97col_1808_102
Loh, Joanna K.
Yoon, Sun Young
Samarakoon, Thiwanka Bandara
Rolfe, Alan
Porubsky, Patrick R.
Neuenswander, Benjamin
Lushington, Gerald H.
Hanson, Paul R.
2014-04-17T21:03:56Z
2014-04-17T21:03:56Z
2012-08-15
Loh, Joanna K, Sun Young Yoon, Thiwanka B Samarakoon, Alan Rolfe, Patrick Porubsky, Benjamin Neuenswander, Gerald H Lushington, and Paul R Hanson. 2012. “Exploring Chemical Diversity via a Modular Reaction Pairing Strategy.” Beilstein Journal of Organic Chemistry 8 : 1293–1302. http://dx.doi.org/10.3762/bjoc.8.147
http://hdl.handle.net/1808/13546
10.3762/bjoc.8.147
The efficient synthesis of an 80-member library of unique benzoxathiazocine 1,1-dioxides by a microwave-assisted, intermolecular nucleophilic aromatic substitution (SNAr) diversification pathway is reported. Eight benzofused sultam cores were generated by means of a sulfonylation/SNAr/Mitsunobu reaction pairing protocol, and subsequently diversified by intermolecular SNAr with ten chiral, non-racemic amine/amino alcohol building blocks. Computational analyses were employed to explore and evaluate the chemical diversity of the library.
Financial support of this work was provided by the National Institute of General Medical Sciences and is gratefully acknowledged (P50-GM069663 and P41-GM076302). In addition, funding from The University of Kansas for an Undergraduate Research Award (S.Y.) is gratefully acknowledged.
Beilstein-Institut
This is an Open Access article under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
The license is subject to the Beilstein Journal of Organic Chemistry terms and conditions: (http://www.beilstein-journals.org/bjoc)
http://creativecommons.org/licenses/by/2.0
openAccess
Benzoxathiazocine 1
1- Dioxides
Chemical Diversity
Informatics
Nucleophilic Aromatic Substitution
Sultams
Exploring chemical diversity via a modular reaction pairing strategy
Article
Loh, Joanna K.
Yoon, Sung Young
Samarakoon, Thiwanka B.
Rolfe, Alan
Porubsky, Patrick
Neuenswander, Benjamin
Lushington, Gerald H.
Hanson, Paul R.
Department of Chemisty
fullparticipation
Scholarly/refereed, publisher version
This item meets KU Open Access policy criteria.
oai:kuscholarworks.ku.edu:1808/237452018-07-17T15:29:40Zcom_1808_97col_1808_102
Rolfe, Alan
Hanson, Paul R.
2017-04-19T20:44:14Z
2017-04-19T20:44:14Z
2009-12-16
Rolfe, Alan, and Paul R. Hanson. “Microwave-Assisted Sequential One-Pot Protocol to Benzothiadiazin-3-One-1,1-Dioxides via a Copper-Catalyzed N-Arylation Strategy.” Tetrahedron letters 50.50 (2009): 6935–6937.
http://hdl.handle.net/1808/23745
10.1016/j.tetlet.2009.09.090
A microwave-assisted, sequential, one-pot protocol has been developed for the synthesis of a variety of benzothiadiazin-3-one-1,1-dioxides. This protocol utilizes a copper-catalyzed N-arylation of α-bromo-benzenesulfonamides with a number of amines to generate the corresponding 2-aminobenzenesulfonamides, which undergo cyclization to the desired sultams using carbonyl diimidazole (CDI). A range of conditions was evaluated for the key C–N bond formation step with tolerance toward functionalized amines.
Elsevier
This is an open access article under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs License 3.0 (CC BY-NC-ND 3.0 US), which permits use and distribution in any medium, provided the original work is properly cited, the use is non-commercial and no modifications or adaptations are made.
http://creativecommons.org/licenses/by-nc-nd/3.0/
openAccess
Microwave-assisted sequential one-pot protocol to benzothiadiazin-3-one-1,1-dioxides via a copper-catalyzed N-arylation strategy
Article
Hanson, Paul R.
Chemistry
Scholarly/refereed, author accepted manuscript
This item meets KU Open Access policy criteria.
oai:kuscholarworks.ku.edu:1808/243862019-04-12T14:18:41Zcom_1808_97col_1808_102
Yao, Huili
Wang, Yan
Lovell, Scott
Kumar, Ritesh
Ruvinsky, Anatoly M.
Battaile, Kevin P.
Vakser, Ilya A.
Rivera, Mario
2017-06-06T18:31:40Z
2017-06-06T18:31:40Z
2012-08-15
Yao, H., Wang, Y., Lovell, S., Kumar, R., Ruvinsky, A. M., Battaile, K. P., … Rivera, M. (2012). The structure of the BfrB-Bfd complex reveals protein-protein interactions enabling iron release from bacterioferritin. Journal of the American Chemical Society, 134(32), 13470–13481. http://doi.org/10.1021/ja305180n
http://hdl.handle.net/1808/24386
10.1021/ja305180n
PMC3428730
This document is the Accepted Manuscript version of a Published Work that appeared in final form in the Journal of the American Chemical Society, copyright © American Chemical Society after peer review and technical editing by the publisher. To access the final edited and published work see http://doi.org/10.1021/ja305180n.
Ferritin-like molecules are unique to cellular iron homeostasis because they can store iron at concentrations much higher than those dictated by the solubility of Fe3+. Very little is known about the protein interactions that deliver iron for storage, or promote the mobilization of stored iron from ferritin-like molecules. Here, we report the X-ray crystal structure of Pseudomonas aeruginosa bacterioferritin (Pa-BfrB) in complex with bacterioferritin-associated ferredoxin (Pa-Bfd) at 2.0 Å resolution. As the first example of a ferritin-like molecule in complex with a cognate partner, the structure provides unprecedented insight into the complementary interface that enables the [2Fe-2S] cluster of Pa-Bfd to promote heme-mediated electron transfer through the BfrB protein dielectric (~18 Å), a process that is necessary to reduce the core ferric mineral and facilitate mobilization of Fe2+. The Pa-BfrB-Bfd complex also revealed the first structure of a Bfd, thus providing a first view to what appears to be a versatile metal binding domain ubiquitous to the large Fer2_BFD family of proteins and enzymes with diverse functions. Residues at the Pa-BfrB-Bfd interface are highly conserved in Bfr and Bfd sequences from a number of pathogenic bacteria, suggesting that the specific recognition between Pa-BfrB and Pa-Bfd is of widespread significance to the understanding of bacterial iron homeostasis.
American Chemical Society
The structure of the BfrB-Bfd complex reveals protein-protein interactions enabling iron release from bacterioferritin
Article
openAccess
Yao, Huili
Wang, Yan
Lovell, Scott
Kumar, Ritesh
Ruvinsky, Anatoly M.
Battaile, Kevin P.
Vasker, Ilya A.
Rivera, Mario
Chemistry
Scholarly/refereed, publisher version
This item meets KU Open Access policy criteria.
oai:kuscholarworks.ku.edu:1808/160382019-04-12T14:49:31Zcom_1808_97col_1808_102
Telnov, Dmitry A.
Chu, Shih-I
2014-12-04T21:15:03Z
2014-12-04T21:15:03Z
2000-12-13
Telnov, Dmitry A. and Shih-I Chu. "Exact relations of the quasienergy functional and the exchange-correlation potential from the Floquet formulation of time-dependent density functional theory" Phys. Rev. A 63, 012514 – Published 13 December 2000. http://dx.doi.org/10.1103/PhysRevA.63.012514
http://hdl.handle.net/1808/16038
10.1103/PhysRevA.63.012514
In the framework of the Floquet formulation of time-dependent density functional theory we present several
exact relations involving different parts of the quasienergy functional. These relations hold when the exact
densities and exchange-correlation energy functional are employed. They can be used as useful constraints and
tests when searching for the approximate forms of the time-dependent exchange-correlation functionals. The
general results are illustrated on an exactly soluble model, Hooke’s atom in a linearly polarized monochromatic
laser field.
American Physical Society
Exact relations of the quasienergy functional and the exchange-correlation potential from the Floquet formulation of time-dependent density functional theory
Article
openAccess
Telnov, Dmitry A.
Chu, Shih-I
Department of Chemistry
na
Scholarly/refereed, publisher version
This item does not meet KU Open Access policy criteria.
oai:kuscholarworks.ku.edu:1808/158732019-04-12T14:50:55Zcom_1808_97col_1808_102
Chu, Shih-I
Wang, Kwanghsi
Layton, Eric
2014-11-25T18:27:17Z
2014-11-25T18:27:17Z
1990-01-01
Shih-I Chu, Kwanghsi Wang, and Eric Layton, "Nonperturbative treatments of level shifts of excited states and high-order harmonic generation in strong fields," J. Opt. Soc. Am. B 7, 425-432 (1990) http://dx.doi.org/10.1364/JOSAB.7.000425.
http://hdl.handle.net/1808/15873
10.1364/JOSAB.7.000425
This is the published version, also available here: http://dx.doi.org/10.1364/JOSAB.7.000425.
In this paper we accomplish three goals. First, we present new nonperturbative results of complex quasi-energies (shifts and widths) for several low-lying excited states of atomic H in strong fields, using the L2 non-Hermitian Floquet matrix technique. Second, we present a new nonperturbative L2 technique for the treatment of ac Stark shifts of arbitrary excited states. We found that all the Rydberg states in weak fields are upshifted and closely follow the quadratic field dependence described by the ponderomotive potential e2F2/4mω2. Large deviation from the ponderomotive shift and intricate level-shift behaviors, however, occur in strong fields. Finally, we present a classical nonperturbative treatment of the electronic motion in intense laser fields. We show that the spectral analysis of classical trajectories can provide detailed insights regarding the mechanisms responsible for the multiple-harmonic generation recently observed in high-intensity experiments.
Optical Society of America
Nonperturbative treatments of level shifts of excited states and high-order harmonic generation in strong fields
Article
openAccess
Chu, Shih-I
Wang, Kwanghsi
Layton, Eric
Chemistry
na
Scholarly/refereed, publisher version
This item does not meet KU Open Access policy criteria.
oai:kuscholarworks.ku.edu:1808/159652019-04-12T14:39:19Zcom_1808_97col_1808_102
Chu, Shih-I
Ng, H. T.
2014-12-01T20:32:50Z
2014-12-01T20:32:50Z
2012-02-27
Chu, Shih-I & Ng, H. T. "Coherent control of atomic spin currents in a double well." Phys. Rev. A 85, 023636 – Published 27 February 2012. http://dx.doi.org/10.1103/PhysRevA.85.023636.
http://hdl.handle.net/1808/15965
10.1103/PhysRevA.85.023636
This is the published version, also available here: http://dx.doi.org/10.1103/PhysRevA.85.023636.
We propose a method for controlling the atomic currents of a two-component Bose-Einstein condensate in a double well by applying an external field to the atoms in one of the potential wells. We study the ground-state properties of the system and show that the directions of spin currents and net-particle tunneling can be manipulated by adiabatically varying the coupling strength between the atoms and the field. This system can be used to study spin and tunneling phenomena across a wide range of interaction parameters. In addition, spin-squeezed states can be generated. It is useful for quantum information processing and quantum metrology.
American Physical Society
Coherent control of atomic spin currents in a double well
Article
openAccess
Chu, Shih-I
Chemistry
fullparticipation
Scholarly/refereed, publisher version
This item meets KU Open Access policy criteria.
oai:kuscholarworks.ku.edu:1808/310462021-01-07T09:00:58Zcom_1808_97col_1808_102
Zhang, Peng
Zhou, Xin
Zeng, Yong
2021-01-06T19:53:59Z
2021-01-06T19:53:59Z
2019-04-22
Chem. Sci., 2019, 10, 5495
http://hdl.handle.net/1808/31046
10.1039/C9SC00961B
https://orcid.org/0000-0003-0537-109X
This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.
Circulating exosomes have been studied as a promising biomarker for non-invasive cancer diagnosis, as they are implicated in tumor initiation, progression, and metastasis. However, the clinical significance of circulating exosomes has not been revealed thoroughly, due to the technical limitation in sensitive and multiplexed detection of cargoes on exosomes, such as proteins and nucleic acids. Herein we developed an integrated exosome profiling platform (ExoProfile chip) to afford superior sensitivity and multiplexed capability for quantitative detection of a panel of surface protein markers on exosomes. To achieve this goal, we innovatively constructed 3D porous serpentine nanostructures via patterned colloidal self-assembly to provide enormous reaction sites and improve biosensing efficiency of exosomes. Meanwhile, the switchable microfluidic design enabled the simultaneous detection of eight markers on single addition of exosome samples. The ExoProfile chip was validated with purified exosomes from SKOV3 cells, which yielded a limit of detection of 21 exosomes per μL. We applied the ExoProfile chip to clinical analysis of circulating exosomes using only 10 μL ovarian cancer plasma and completing the analysis within 3 h. The diagnostic power of seven markers (EGFR, HER2, CA125, FRα, CD24, EpCAM, and CD9 plus CD63) were evaluated with receiver operator characteristic curve and heatmap clustering. Compared to single biomarker, the combined assessment of a biomarker panel was demonstrated to display improved accuracy in distinguishing early and late stage cancer. The results suggested the ExoProfile chip as a promising platform for molecular fingerprinting of circulating exosomes towards early cancer diagnosis.
Royal Society of Chemistry
© The Royal Society of Chemistry 2019.
http://creativecommons.org/licenses/by-nc/4.0/
openAccess
Multiplexed immunophenotyping of circulating exosomes on nano-engineered ExoProfile chip towards early diagnosis of cancer
Article
Zhang, Peng
Zeng, Yong
Chemistry
Scholarly/refereed, publisher version
This item meets KU Open Access policy criteria.
oai:kuscholarworks.ku.edu:1808/127122018-02-23T18:45:44Zcom_1808_97com_1808_11673col_1808_102col_1808_11675
Gong, Maogang
Kirkeminde, Alec
Ren, Shenqiang
2014-01-13T17:46:40Z
2014-01-13T17:46:40Z
2013-06-28
Gong, M., Kirkeminde, A., & Ren, S. (2013). Symmetry-Defying Iron Pyrite (FeS2) Nanocrystals through Oriented Attachment. Scientific reports, 3. http://dx/doi.org/10.1038/srep02092
http://hdl.handle.net/1808/12712
10.1038/srep02092
A grant from the One-University Open Access Fund at the University of Kansas was used to defray the author’s publication fees in this Open Access journal. The Open Access Fund, administered by librarians from the KU, KU Law, and KUMC libraries, is made possible by contributions from the offices of KU Provost, KU Vice Chancellor for Research & Graduate Studies, and KUMC Vice Chancellor for Research. For more information about the Open Access Fund, please see http://library.kumc.edu/authors-fund.xml.
Iron pyrite (fool's gold, FeS2) is a promising earth abundant and environmentally benign semiconductor material that shows promise as a strong and broad absorber for photovoltaics and high energy density cathode material for batteries. However, controlling FeS2 nanocrystal formation (composition, size, shape, stoichiometry, etc.) and defect mitigation still remains a challenge. These problems represent significant limitations in the ability to control electrical, optical and electrochemical properties to exploit pyrite's full potential for sustainable energy applications. Here, we report a symmetry-defying oriented attachment FeS2 nanocrystal growth by examining the nanostructure evolution and recrystallization to uncover how the shape, size and defects of FeS2 nanocrystals changes during growth. It is demonstrated that a well-controlled reaction temperature and annealing time results in polycrystal-to-monocrystal formation and defect annihilation, which correlates with the performance of photoresponse devices. This knowledge opens up a new tactic to address pyrite's known defect problems.
Nature Publishing Group
This work is licensed under a Creative Commons Attribution 3.0 Unported License. To view a copy of this license, visit http://creativecommons.org/licenses /by/3.0/
http://creativecommons.org/licenses/by/3.0/
openAccess
Nanoparticles
Optical Sensors
Colloids
Synthesis And Processing
Symmetry-Defying Iron Pyrite (FeS2) Nanocrystals through Oriented Attachment
Article
Gong, Maogang
Kirkeminde, Alec
Ren, Shenqiang
Chemistry
fullparticipation
Scholarly/refereed, publisher version
This item meets KU Open Access policy criteria.
oai:kuscholarworks.ku.edu:1808/238472019-04-12T14:16:00Zcom_1808_97col_1808_102
Price, E. Shane
Aleksiejew, Marek
Johnson, Carey K.
2017-04-27T19:15:54Z
2017-04-27T19:15:54Z
2011-07-28
Price, E. S., Aleksiejew, M., & Johnson, C. K. (2011). FRET-FCS Detection of Intra-Lobe Dynamics in Calmodulin. The Journal of Physical Chemistry. B, 115(29), 9320–9326. http://doi.org/10.1021/jp203743m
http://hdl.handle.net/1808/23847
10.1021/jp203743m
PMC3151148
Fluorescence correlation spectroscopy (FCS) can be coupled with Förster resonance energy transfer (FRET) to detect intramolecular dynamics of proteins on the microsecond time scale. Here we describe application of FRET-FCS to detect fluctuations within the N-terminal and C-terminal domains of the Ca2+-signaling protein calmodulin. Intramolecular fluctuations were resolved byglobal fitting of the two fluorescence autocorrelation functions (green-green and red-red) together with the two cross-correlation functions (green-red and red-green). To match the Förster radius forFRET to the dimensions of the N-terminal and C-terminal domains, a near-infrared acceptor fluorophore (Atto 740) was coupled with a green-emitting donor (Alexa Fluor 488). Fluctuations were detected in both domains on the time scale of 30 to 40 μs. In the N-terminal domain, the amplitude of the fluctuations was dependent on occupancy of Ca2+ binding sites. A high amplitude of dynamics in apo-calmodulin (in the absence of Ca2+) was nearly abolished at a high Ca2+ concentration. For the C-terminal domain the dynamic amplitude changed little with Ca2+ concentration. The Ca2+ dependence of dynamics for the N-terminal domain suggests that the fluctuations detected by FCS in the N-terminal domain are coupled to the opening and closing of the EF-hand Ca2+-binding loops.
American Chemical Society
This document is the Accepted Manuscript version of a Published Work that appeared in final form in the Journal of Physical Chemistry B, copyright © American Chemical Society after peer review and technical editing by the publisher. To access the final edited and published work see http://dx.doi.org/10.1021/jp203743m.
openAccess
Calmodulin
Fluorescence correlation spectroscopy
FRET
Protein dynamics
FRET-FCS Detection of Intra-Lobe Dynamics in Calmodulin
Article
Price, E. Shane
Marek, Aleksiejaw
Johnson, Carey K.
Chemistry
Scholarly/refereed, author accepted manuscript
This item meets KU Open Access policy criteria.
oai:kuscholarworks.ku.edu:1808/308802020-11-20T09:00:50Zcom_1808_97col_1808_102
Zhang, Peng
Zhou, Xin
Zeng, Yong
2020-11-19T15:03:03Z
2020-11-19T15:03:03Z
2019-04-22
Zhang, P., Zhou, X., & Zeng, Y. (2019). Multiplexed immunophenotyping of circulating exosomes on nano-engineered ExoProfile chip towards early diagnosis of cancer. Chemical science, 10(21), 5495–5504. https://doi.org/10.1039/c9sc00961b
http://hdl.handle.net/1808/30880
10.1039/c9sc00961b
https://orcid.org/0000-0003-0537-109X
PMC6544119
This work is licensed under a Creative Commons Attribution-NoDerivatives 3.0 Unported License.
Circulating exosomes have been studied as a promising biomarker for non-invasive cancer diagnosis, as they are implicated in tumor initiation, progression, and metastasis. However, the clinical significance of circulating exosomes has not been revealed thoroughly, due to the technical limitation in sensitive and multiplexed detection of cargoes on exosomes, such as proteins and nucleic acids. Herein we developed an integrated exosome profiling platform (ExoProfile chip) to afford superior sensitivity and multiplexed capability for quantitative detection of a panel of surface protein markers on exosomes. To achieve this goal, we innovatively constructed 3D porous serpentine nanostructures via patterned colloidal self-assembly to provide enormous reaction sites and improve biosensing efficiency of exosomes. Meanwhile, the switchable microfluidic design enabled the simultaneous detection of eight markers on single addition of exosome samples. The ExoProfile chip was validated with purified exosomes from SKOV3 cells, which yielded a limit of detection of 21 exosomes per μL. We applied the ExoProfile chip to clinical analysis of circulating exosomes using only 10 μL ovarian cancer plasma and completing the analysis within 3 h. The diagnostic power of seven markers (EGFR, HER2, CA125, FRα, CD24, EpCAM, and CD9 plus CD63) were evaluated with receiver operator characteristic curve and heatmap clustering. Compared to single biomarker, the combined assessment of a biomarker panel was demonstrated to display improved accuracy in distinguishing early and late stage cancer. The results suggested the ExoProfile chip as a promising platform for molecular fingerprinting of circulating exosomes towards early cancer diagnosis.
National Cancer Institute Cancer Center Support Grant (P30 CA168524)
NIH 1R21CA186846
NIH 1R21CA207816
NIH 1R21EB024101
NIH 1R33CA214333
NIH P20GM103638
NIH/NIGMS P20GM103418
Royal Society of Chemistry
© The Royal Society of Chemistry 2019
https://creativecommons.org/licenses/by-nc/3.0/
openAccess
Multiplexed immunophenotyping of circulating exosomes on nano-engineered ExoProfile chip towards early diagnosis of cancer
Article
Zhang, Peng
Zhou, Xin
Zeng, Yong
Chemistry
Scholarly/refereed, publisher version
This item meets KU Open Access policy criteria.
oai:kuscholarworks.ku.edu:1808/161372019-04-12T14:46:09Zcom_1808_97col_1808_102
Davidchack, Ruslan L.
Laird, Brian Bostian
2014-12-16T22:28:02Z
2014-12-16T22:28:02Z
2003-04-11
Davidchack, Ruslan L.; Laird, Brian Bostian. (2003). "Direct calculation of the crystal–melt interfacial free energies for continuous potentials: Application to the Lennard-Jones system." The Journal of Chemical Physics, 118(16):7651. http://dx.doi.org/10.1063/1.1563248
0021-9606
http://hdl.handle.net/1808/16137
10.1063/1.1563248
https://orcid.org/0000-0001-9418-5322
This is the publishers' version, also available electronically from http://scitation.aip.org/content/aip/journal/jcp/118/16/10.1063/1.1563248.
Extending to continuous potentials a cleaving wall molecular dynamics simulation method recently developed for the hard-sphere system [Phys. Rev. Lett. 85, 4751 (2000)], we calculate the crystal–melt interfacial free energies, γ, for a Lennard-Jones system as functions of both crystal orientation and temperature. At the triple point, T*=0.617, the results are consistent with an earlier cleaving potential calculation by Broughton and Gilmer [J. Chem. Phys. 84, 5759 (1986)], however, the greater precision of the current calculation allows us to accurately determine the anisotropy of γ. From our data we find that, at all temperatures studied, γ111<γ110<γ100. A comparison is made to the results from our previous hard-sphere calculation and to recent results for Ni by Asta, Hoyt, and Karma [Phys. Rev. B 66 100101(R) (2002)].
American Institute of Physics
Direct calculation of the crystal–melt interfacial free energies for continuous potentials: Application to the Lennard-Jones system
Article
openAccess
Laird, Brian B.
Chemistry
Scholarly/refereed, publisher version
This item does not meet KU Open Access policy criteria.
oai:kuscholarworks.ku.edu:1808/236232018-07-17T15:25:02Zcom_1808_97col_1808_102
Chegondi, Rambabu
Hanson, Paul R.
2017-04-10T20:55:25Z
2017-04-10T20:55:25Z
2015-06-03
Chegondi, Rambabu, and Paul R. Hanson. “Synthetic Studies to Lyngbouilloside: A Phosphate Tether-Mediated Synthesis of the Macrolactone Core.” Tetrahedron letters 56.23 (2015): 3330–3333.
http://hdl.handle.net/1808/23623
10.1016/j.tetlet.2015.01.109
A concise synthetic pathway to the originally assigned structure of lyngbouilloside macrolactone (3) is reported. The core macrocycle 3 was synthesized via a phosphate tether-mediated, one-pot, sequential RCM/CM/chemoselective hydrogenation reaction, Roskamp homologation, and a high yielding Boeckman acylketene cyclization.
Elsevier
This is an open access article under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs License 3.0 (CC BY-NC-ND 3.0 US), which permits use and distribution in any medium, provided the original work is properly cited, the use is non-commercial and no modifications or adaptations are made.
http://creativecommons.org/licenses/by-nc-nd/3.0/
openAccess
Phosphate tether
(-)-Lyngbouilloside
Total synthesis
Metathesis
Synthetic Studies to Lyngbouilloside: A Phosphate Tether-Mediated Synthesis of the Macrolactone Core
Article
Hanson, Paul R.
Chemistry
Scholarly/refereed, author accepted manuscript
This item meets KU Open Access policy criteria.
oai:kuscholarworks.ku.edu:1808/226242019-04-12T14:17:25Zcom_1808_97col_1808_102
Woodin, Carrie L.
Maxon, Morgan
Desaire, Heather
2017-01-12T20:00:20Z
2017-01-12T20:00:20Z
2014-05-21
Woodin, Carrie L., Morgan Maxon, and Heather Desaire. "Software for Automated Interpretation of Mass Spectrometry Data from Glycans and Glycopeptides." The Analyst 138.10 (2013): 2793.
http://hdl.handle.net/1808/22624
10.1039/c2an36042j
The purpose of this review is to provide those interested in glycosylation analysis with the most updated information on the availability of automated tools for MS characterization of N-linked and O-linked glycosylation types. Specifically, this review describes software tools that facilitate elucidation of glycosylation from MS data on the basis of mass alone, as well as software designed to speed the interpretation of glycan and glycopeptide fragmentation from MS/MS data. This review focuses equally on software designed to interpret the composition of released glycans and on tools to characterize N-linked and O-linked glycopeptides. Several websites have been compiled and described that will be helpful to the reader who is interested in further exploring the described tools.
Royal Society of Chemistry
Software for Automated Interpretation of Mass Spectrometry Data from Glycans and Glycopeptides
Article
openAccess
Desaire, Heather
Chemistry
Scholarly/refereed, author accepted manuscript
This item meets KU Open Access policy criteria.
oai:kuscholarworks.ku.edu:1808/84162019-04-12T14:38:17Zcom_1808_97col_1808_102
Wilson, George S.
Ammam, Malika
Zakai, Uzma I.
Glass, Richard S.
2011-11-18T19:58:30Z
2011-11-18T19:58:30Z
2010-02
Ammam, M., Zakai, U.I., Wilson, G.S., Glass, R.S., Anodic Oxidation of m-terphenyl thio-, seleno-and telluroethers: Lowered oxidation potentials due to chalcogen.•••π interaction,. Pure and Applied Chemistry, 82, 555-563 (2010)
http://hdl.handle.net/1808/8416
The electrochemistry of m-terphenylthio-, seleno-, and telluroethers was studied
using cyclic voltammetry in acetonitrile. All of the compounds studied showed irreversible
oxidations. The first oxidation potentials for the thio- and selenoethers are less positive than
expected. This facilitation in oxidation is ascribed to through-space S···π and Se···π interaction,
respectively, on removal of an electron. No evidence for a comparable effect was
found for the phenyltelluro-ethers studied.
en_US
International Union of Pure and Applied Chemistry
http://www.iupac.org/publications/pac/pdf/2010/pdf/8203x0555.pdf
Anodic Oxidation of m-terphenyl thio-, seleno-and telluroethers: Lowered oxidation potentials due to chalcogen.•••π interaction
Article
openAccess
Wilson, George S.
Chemistry
fullparticipation
Scholarly/refereed, publisher version
This item meets KU Open Access policy criteria.
oai:kuscholarworks.ku.edu:1808/161002019-04-12T14:46:04Zcom_1808_97col_1808_102
Wyatt, J. R.
Strattan, L. W.
Hierl, Peter M.
2014-12-15T18:01:12Z
2014-12-15T18:01:12Z
1975-01-01
Wyatt, J. R.; Strattan, L. W.; Hierl, P. M. (1975). "Role of impact parameter in branching reactions." Jounal of Chemical Physics, 63:5044-5045. http://dx.doi.org/10.1063/1.431205
0021-9606
http://hdl.handle.net/1808/16100
10.1063/1.431205
This is the publisher's version, also available electronically from http://scitation.aip.org/content/aip/journal/jcp/63/11/10.1063/1.431205.
American Institute of Physics
Role of impact parameter in branching reactions
Article
openAccess
Wyatt, J. R.
Strattan, L. W.
Hierl, Peter M.
Chemistry
Scholarly/refereed, publisher version
This item does not meet KU Open Access policy criteria.
oai:kuscholarworks.ku.edu:1808/160012019-04-12T14:51:14Zcom_1808_97com_1808_8219col_1808_102col_1808_8220
Chu, Xi
Chu, Shih-I
2014-12-02T19:06:31Z
2014-12-02T19:06:31Z
2001-07-13
Chu, Shih-I. & Xi, Chu. "Optimization of high-order harmonic generation by genetic algorithm and wavelet time-frequency analysis of quantum dipole emission." Phys. Rev. A 64, 021403(R) – Published 13 July 2001. http://dx.doi.org/10.1103/PhysRevA.64.021403.
http://hdl.handle.net/1808/16001
10.1103/PhysRevA.64.021403
This is the published version, also available here: http://dx.doi.org/10.1103/PhysRevA.64.021403.
We present an ab initio three-dimensional quantum study of the coherent control of high-order harmonic generation (HHG) processes in intense pulsed laser fields by means of the genetic algorithm optimization of the laser-pulse amplitude and phase. Accurate time-dependent wavefunction and HHG power spectrum are obtained by the time-dependent generalized pseudospectral method and wavelet transform is used to obtain the dynamical phase associated with the dipole-emission time profile. It is shown that “intra-atomic” dynamical phase matching on the sub-optical cycle, attosecond, time scale can be achieved, leading to nearly perfect constructive interference between different returning electronic wave packets and marked improvement in both emission intensity and purity of a given harmonic order.
American Physical Society
Optimization of high-order harmonic generation by genetic algorithm and wavelet time-frequency analysis of quantum dipole emission
Article
openAccess
Chu, Shih-I
Chu, Xi
Chemistry
na
Scholarly/refereed, publisher version
This item does not meet KU Open Access policy criteria.
oai:kuscholarworks.ku.edu:1808/345882023-07-12T06:05:55Zcom_1808_97col_1808_102
Hu, Mengjia
Brown, Virginia
Jackson, Joshua M.
Wijerathne, Harshani
Pathak, Harsh
Koestler, Devin C.
Nissen, Emily
Hupert, Mateusz L.
Muller, Rolf
Godwin, Andrew K.
Witek, Malgorzata A.
Soper, Steven A.
2023-07-11T16:05:24Z
2023-07-11T16:05:24Z
2023
Hu, M., Brown, V., Jackson, J. M., Wijerathne, H., Pathak, H., Koestler, D. C., Nissen, E., Hupert, M. L., Muller, R., Godwin, A. K., Witek, M. A., & Soper, S. A. (2023). Assessing Breast Cancer Molecular Subtypes Using Extracellular Vesicles' mRNA. Analytical chemistry, 95(19), 7665–7675. https://doi.org/10.1021/acs.analchem.3c00624
https://hdl.handle.net/1808/34588
10.1021/acs.analchem.3c00624
PMC10243595
This document is the Accepted Manuscript version of a Published Work that appeared in final form in Analytical Chemistry, copyright © 2023 American Chemical Society after peer review and technical editing by the publisher. To access the final edited and published work see https://doi.org/10.1021/acs.analchem.3c00624.
Extracellular vesicles (EVs) carry RNA cargo that is believed to be associated with the cell-of-origin and thus have the potential to serve as a minimally invasive liquid biopsy marker for supplying molecular information to guide treatment decisions (i.e., precision medicine). We report the affinity isolation of EV subpopulations with monoclonal antibodies attached to the surface of a microfluidic chip that is made from a plastic to allow for high-scale production. The EV microfluidic affinity purification (EV-MAP) chip was used for the isolation of EVs sourced from two-orthogonal cell types and was demonstrated for its utility in a proof-of-concept application to provide molecular subtyping information for breast cancer patients. The orthogonal selection process better recapitulated the epithelial tumor microenvironment by isolating two subpopulations of EVs: EVEpCAM (epithelial cell adhesion molecule, epithelial origin) and EVFAPα (fibroblast activation protein α, mesenchymal origin). The EV-MAP provided recovery >80% with a specificity of 99 ± 1% based on exosomal mRNA (exo-mRNA) and real time–droplet digital polymerase chain reaction results. When selected from the plasma of healthy donors and breast cancer patients, EVs did not differ in size or total RNA mass for both markers. On average, 0.5 mL of plasma from breast cancer patients yielded ∼2.25 ng of total RNA for both EVEpCAM and EVFAPα, while in the case of cancer-free individuals, it yielded 0.8 and 1.25 ng of total RNA from EVEpCAM and EVFAPα, respectively. To assess the potential of these two EV subpopulations to provide molecular information for prognostication, we performed the PAM50 test (Prosigna) on exo-mRNA harvested from each EV subpopulation. Results suggested that EVEpCAM and EVFAPα exo-mRNA profiling using subsets of the PAM50 genes and a novel algorithm (i.e., exo-PAM50) generated 100% concordance with the tumor tissue.
American Chemical Society
Copyright © 2023 American Chemical Society
embargoedAccess
Assays
Biopolymers
Genetics
Immunology
Peptides and proteins
Assessing Breast Cancer Molecular Subtypes Using Extracellular Vesicles’ mRNA
Article
Hu, Mengjia
Brown, Virginia
Jackson, Joshua M.
Wijerathne, Harshani
Godwin, Andrew K.
Witek, Malgorzata A.
Soper, Steven A.
Chemistry
Scholarly/refereed, author accepted manuscript
This item meets KU Open Access policy criteria.
oai:kuscholarworks.ku.edu:1808/159742019-04-12T14:51:09Zcom_1808_97col_1808_102
Chu, Shih-I
Tong, Xiao-Min
2014-12-01T21:06:01Z
2014-12-01T21:06:01Z
1997-05-01
Chu, Shih-I. & Tong, Xiao-Min. "Density-functional theory with optimized effective potential and self-interaction correction for ground states and autoionizing resonances." Phys. Rev. A 55, 3406 – Published 1 May 1997. http://dx.doi.org/10.1103/PhysRevA.55.3406.
http://hdl.handle.net/1808/15974
10.1103/PhysRevA.55.3406
This is the published version, also available here: http://dx.doi.org/10.1103/PhysRevA.55.3406.
We present a self-interaction-free density-functional theory (DFT) for the treatment of both the static properties of the ground states and the photoionization processes of many-electron systems. The method is based on the Krieger-Li-Iafrate (KLI) treatment of the optimized effective potential (OEP) theory and the incorporation of an explicit self-interaction correction (SIC) term. Such an extended OEP–KLI-SIC method uses only orbital-independent single-particle local potentials and is thus computationally more efficient and yet maintains good accuracy. The usefulness of the procedure is examined by the studies of the static properties of the ground states of atoms (Z⩽18) and the dynamical photoionization processes involving autoionizing resonances. Both the energy functionals of the local spin-density approximation (LSDA) and Becke's exchange energy functional and the correlation energy functional of Lee-Yang-Parr (BLYP) are used as the input to the KLI-SIC calculations. It is found that the implementation of the KLI-SIC procedure gives rise to optimized effective potentials that possess the correct behavior in both short-range and long-range regimes. As a consequence, the LSDA and BLYP ionization potentials are significantly improved. For higher-Z atoms, the improvement of the LSDA total energies and the ionization potentials are particularly remarkable, approaching the experimental or exact values. As another test of the KLI-SIC method, we have performed the calculation of the photoionization cross sections of the Ne atom using both the time-independent and time-dependent LSDA (TDLSDA) methods. We found that the TDLSDA results agree closely with the experimental data in the broad peak region, followed by a series of sharp resonances due to the 2s→np resonant transitions. The calculated linewidths and resonance line profile parameters are in reasonable agreement with both the experimental and the configuration-interaction (R-matrix) results, demonstrating the usefulness of the KLI-SIC procedure for achieving accurate DFT calculations in both static properties and dynamical processes.
American Physical Society
Density-functional theory with optimized effective potential and self-interaction correction for ground states and autoionizing resonances
Article
openAccess
Tong, Xiao-Min
Chu, Shih-I
Chemistry
na
Scholarly/refereed, publisher version
This item does not meet KU Open Access policy criteria.
oai:kuscholarworks.ku.edu:1808/159952019-04-12T14:51:12Zcom_1808_97col_1808_102
Chu, Shih-I
Yang, Chui-Ping
Han, Siyuan
2014-12-02T17:45:13Z
2014-12-02T17:45:13Z
2002-09-04
Yang, Chui-Ping., Chu, Shih-I., Han, Siyuan. "Error-prevention scheme with two pairs of qubits." Phys. Rev. A 66, 034301 – Published 4 September 2002. http://dx.doi.org/10.1103/PhysRevA.66.034301.
http://hdl.handle.net/1808/15995
10.1103/PhysRevA.66.034301
This is the published version, also available here: http://dx.doi.org/10.1103/PhysRevA.66.034301.
A scheme is presented for protecting one-qubit quantum information against decoherence due to a general environment and local exchange interactions. The scheme operates essentially by distributing information over two pairs of qubits and through error-prevention procedures. In the scheme, quantum information is encoded through a decoherence-free subspace for collective phase errors and exchange errors affecting the qubits in pairs; leakage out of the encoding space due to amplitude damping is reduced by quantum Zeno effect. In addition, how to construct decoherence-free states for n-qubit information against phase and exchange errors is discussed.
American Physical Society
Error-prevention scheme with two pairs of qubits
Article
openAccess
Yang, Chui-Ping
Chu, Shih-I
Han, Siyuan
Chemistry
Physics and Astronomy
na
Scholarly/refereed, publisher version
This item does not meet KU Open Access policy criteria.
oai:kuscholarworks.ku.edu:1808/146922018-07-11T17:29:26Zcom_1808_97col_1808_102
Goller, Carlos C.
Arshad, Mehreen
Noah, James W.
Ananthan, Subramaniam
Evans, Carrie W.
Nebane, N. Miranda
Rasmussen, Lynn
Sosa, Melinda
Tower, Nichole A.
White, E. Lucile
Neuenswander, Benjamin
Porubsky, Patrick R.
Maki, Brooks E.
Rogers, Steven A.
Schoenen, Frank J.
Seed, Patrick C.
2014-07-10T18:32:53Z
2014-07-10T18:32:53Z
2014-07-01
Goller CC, Arshad M, Noah JW, Ananthan S, Evans CW, et al. (2014) Lifting the Mask: Identification of New Small Molecule Inhibitors of Uropathogenic Escherichia coli Group 2 Capsule Biogenesis. PLoS ONE 9(7): e96054. http://dx.doi.org/10.1371/journal.pone.0096054
http://hdl.handle.net/1808/14692
10.1371/journal.pone.0096054
Uropathogenic Escherichia coli (UPEC) is the leading cause of community-acquired urinary tract infections (UTIs), with over 100 million UTIs occurring annually throughout the world. Increasing antimicrobial resistance among UPEC limits ambulatory care options, delays effective treatment, and may increase overall morbidity and mortality from complications such as urosepsis. The polysaccharide capsules of UPEC are an attractive target a therapeutic, based on their importance in defense against the host immune responses; however, the large number of antigenic types has limited their incorporation into vaccine development. The objective of this study was to identify small-molecule inhibitors of UPEC capsule biogenesis. A large-scale screening effort entailing 338,740 compounds was conducted in a cell-based, phenotypic screen for inhibition of capsule biogenesis in UPEC. The primary and concentration-response assays yielded 29 putative inhibitors of capsule biogenesis, of which 6 were selected for further studies. Secondary confirmatory assays identified two highly active agents, named DU003 and DU011, with 50% inhibitory concentrations of 1.0 µM and 0.69 µM, respectively. Confirmatory assays for capsular antigen and biochemical measurement of capsular sugars verified the inhibitory action of both compounds and demonstrated minimal toxicity and off-target effects. Serum sensitivity assays demonstrated that both compounds produced significant bacterial death upon exposure to active human serum. DU011 administration in mice provided near complete protection against a lethal systemic infection with the prototypic UPEC K1 isolate UTI89. This work has provided a conceptually new class of molecules to combat UPEC infection, and future studies will establish the molecular basis for their action along with efficacy in UTI and other UPEC infections.
This work was supported by NIH grant R03MH090791 (PI, Seed) and the NIH Molecular Libraries Probe Production Centers Network grant 5U54HG005031 (PI, Jeffrey Aubé). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Public Library of Science
© 2014 Goller et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
http://creativecommons.org/licenses/by/4.0/
openAccess
Antigen Encapsulation
Bacterial Pathogens
Bacteriophages
Biosynthesis
Escherichia Coli Infections
Lysis (medicine)
Polysaccharides
Renal System
Lifting the Mask: Identification of New Small Molecule Inhibitors of Uropathogenic Escherichia coli Group 2 Capsule Biogenesis
Article
Neuenswander, Benjamin
Porubsky, Patrick
Maki, Brooks E.
Rogers, Steven A.
Schoenen, Frank
University of Kansas Specialized Chemistry Center
fullparticipation
Scholarly/refereed, publisher version
This item meets KU Open Access policy criteria.
oai:kuscholarworks.ku.edu:1808/162272019-04-12T14:46:37Zcom_1808_97col_1808_102
Calef, Daniel F.
Friesner, Richard
Korzeniewski, Gregory
Laird, Brian Bostian
Silbey, Robert
2015-01-12T15:53:59Z
2015-01-12T15:53:59Z
1984-05-01
Calef, Daniel F. et al. (1984). "Calculation of the Green's function from high- and low-density series expansions for disordered transport." Physical Review A, 29:2963(R). http://dx.doi.org/10.1103/PhysRevA.29.2963
1050-2947
http://hdl.handle.net/1808/16227
10.1103/PhysRevA.29.2963
This is the publisher's version, also available electronically from http://journals.aps.org/pra/abstract/10.1103/PhysRevA.29.2963
We investigate density expansions for the configurationally averaged Green's function for a random walk on a (site) disordered lattice. Two-point Padé summation techniques are used in conjunction with scaling arguments to examine behavior near the percolation density. Recent proposals for the structure of the percolation cluster are discussed in light of the results.
American Physical Society
Calculation of the Green's function from high- and low-density series expansions for disordered transport
Article
openAccess
Laird, Brian Bostian
Chemistry
Scholarly/refereed, publisher version
This item does not meet KU Open Access policy criteria.
oai:kuscholarworks.ku.edu:1808/343502023-06-14T06:05:41Zcom_1808_97col_1808_102
Weerasekara, Dhanushka B.
Lunte, Susan M.
2023-06-13T15:54:07Z
2023-06-13T15:54:07Z
2021-12-31
Weerasekara, D. B., & Lunte, S. M. (2022). Separation and Detection of Tyrosine and Phenylalanine-derived Oxidative Stress Biomarkers Using Microchip Electrophoresis with Electrochemical Detection. Electroanalysis, 34(12), 1913–1927. https://doi.org/10.1002/elan.202100580
https://hdl.handle.net/1808/34350
10.1002/elan.202100580
https://orcid.org/0000-0002-1195-0314
PMC10202003
This is the peer reviewed version of the following article: D. B. Weerasekara, S. M. Lunte, Electroanalysis 2022, 34, 1913, which has been published in final form at https://doi.org/10.1002/elan.202100580. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Use of Self-Archived Versions. This article may not be enhanced, enriched or otherwise transformed into a derivative work, without express permission from Wiley or by statutory rights under applicable legislation. Copyright notices must not be removed, obscured or modified. The article must be linked to Wiley’s version of record on Wiley Online Library and any embedding, framing or otherwise making available the article or pages thereof by third parties from platforms, services and websites other than Wiley Online Library must be prohibited.
A method for the determination of selected aromatic amino acid biomarkers of oxidative stress using microchip electrophoresis with electrochemical detection is described. The separation of the major reaction products of phenylalanine and tyrosine with reactive nitrogen and oxygen species was accomplished using ligand exchange micellar electrokinetic chromatography with a PDMS/glass hybrid chip. Electrochemical detection was achieved using a pyrolyzed photoresist film working electrode. The system was evaluated for the analysis of the products of the Fenton reaction with tyrosine and phenylalanine, and the reaction of peroxynitrite with tyrosine.
Wiley
© 2022 Wiley-VCH GmbH
openAccess
Reactive nitrogen and oxygen species
Microchip electrophoresis with electrochemical detection
Hydroxyl radical
Peroxynitrite
Tyrosine
Separation and Detection of Tyrosine and Phenylalanine-derived Oxidative Stress Biomarkers Using Microchip Electrophoresis with Electrochemical Detection
Article
Scholarly/refereed, author accepted manuscript
This item meets KU Open Access policy criteria.
oai:kuscholarworks.ku.edu:1808/239072019-04-12T14:16:22Zcom_1808_97col_1808_102
Go, Eden P.
Liao, Hua-Xin
Alam, S. Munir
Hua, David C.
Haynes, Barton F.
Desaire, Heather
2017-05-05T17:08:55Z
2017-05-05T17:08:55Z
2013-03-01
Go, E. P., Liao, H.-X., Alam, S. M., Hua, D., Haynes, B. F., & Desaire, H. (2013). Characterization of Host-Cell Line Specific Glycosylation Profiles of Early Transmitted/Founder HIV-1 gp120 Envelope Proteins. Journal of Proteome Research, 12(3), 1223–1234. http://doi.org/10.1021/pr300870t
http://hdl.handle.net/1808/23907
10.1021/pr300870t
PMC3674872
Glycosylation plays an essential role in regulating protein function by modulating biological, structural, and therapeutic properties. However, due to its inherent heterogeneity and diversity, the comprehensive analysis of protein glycosylation remains a challenge. As part of our continuing effort in the analysis of glycosylation profiles of recombinant HIV-1 envelope-based immunogens, we evaluated and compared the host-cell specific glycosylation pattern of recombinant HIV-1 surface glycoprotein, gp120, derived from clade C transmitted/founder virus 1086.C expressed in Chinese hamster ovary (CHO) and human embryonic kidney containing T antigen (293T) cell lines. We used an integrated glycopeptide-based mass mapping workflow that includes a partial deglycosylation step described in our previous study1 with the inclusion of the fragmentation technique, electron transfer dissociation (ETD), to complement collision induced dissociation (CID). The inclusion of ETD facilitated the analysis by providing additional validation for glycopeptide identification and expanding the identified glycopeptides to include coverage of O-linked glycosylation. The site-specific glycosylation analysis shows that the transmitted/founder 1086.C gp120 expressed in CHO and 293T displayed distinct similarities and differences. For N-linked glycosylation, two sites (N386 and N392), in the V4 region were populated with high mannose glycans in the CHO cell-derived 1086.C gp120, while these sites had a mixture of high mannose and processed glycans in the 293T cell-derived 1086.C gp120. Compositional analysis of O-linked glycans revealed that 293T cell-derived 1086.C gp120 consisted of cores 1, 2, and 4 type O-linked glycans while CHO cell-derived 1086.C exclusively consisted of core 1 type O-linked glycans. Overall, glycosylation site occupancy of the CHO and 293T cell-derived 1086.C gp120 show high degree of similarity except for one site at N88 in the C1 region. This site was partially occupied in 293T-gp120 but fully occupied in CHO-gp120. Site-specific glycopeptide analysis of transmitted/founder 1086.C gp120 expressed in CHO cells revealed the presence of phosphorylated glycans while 293T cell produced 1086.C gp120 glycans were not phosphorylated. While the influence of phosphorylated glycans on immunogenicity is unclear, distinguishing host-cell specific variations in glycosylation profiles provides insights into the similarity (or difference) in recombinant vaccine products. While these differences had minimal effect on envelope antigenicity, they may be important in considering immunogenicity and functional capacities of recombinant envelope proteins produced in different expression systems.
American Chemical Society
This document is the Accepted Manuscript version of a Published Work that appeared in final form in the Journal of Proteome Research, copyright © American Chemical Society after peer review and technical editing by the publisher. To access the final edited and published work see http://dx.doi.org/10.1021/pr300870t.
openAccess
Characterization of Host-Cell Line Specific Glycosylation Profiles of Early Transmitted/Founder HIV-1 gp120 Envelope Proteins
Article
Go, Eden P.
Hua, David
Desaire, Heather
Chemistry
Scholarly/refereed, author accepted manuscript
This item meets KU Open Access policy criteria.
oai:kuscholarworks.ku.edu:1808/160292019-04-12T14:49:38Zcom_1808_97col_1808_102
Telnov, Dmitry A.
Wang, Jingyan
Chu, Shih-I
2014-12-04T17:23:25Z
2014-12-04T17:23:25Z
1995-11-01
Telnov, Dmitry A., Wang, Jingyan., Chu, Shih-I. "Two-color phase control of high-order harmonic generation in intense laser fields." Phys. Rev. A 52, 3988 – Published 1 November 1995. http://dx.doi.org/10.1103/PhysRevA.52.3988.
http://hdl.handle.net/1808/16029
10.1103/PhysRevA.52.3988
This is the published version, also available here: http://dx.doi.org/10.1103/PhysRevA.52.3988.
We present a time-independent generalized Floquet approach for nonperturbative treatment of high-order harmonic generation (HG) in intense onea (i) determination of the complex quasienergy eigenvalue and eigenfunction by means of the non-Hermitian Floquet formalism, wherein the Floquet Hamiltonian is discretized by the complex-scaling generalized pseudospectral technique [Wang, Chu, and Laughlin, Phys. Rev. A 50, 3208 (1994)], and (ii) calculation of the HG rates based on the approach that implies the classical treatment of the electromagnetic field and quantal treatment of the atom. The method is applied to the nonperturbative study of HG by the hydrogen atom in strong laser fields with the fundamental frequencies 532 and 775 nm and their third harmonics. The results show a strong dependence on the relative phase δ between the fundamental frequency field and its harmonic. For the intensities used in calculations (1×1013 and 5×1013 W/cm2 for the fundamental frequency 532 nm and 1×1013 and 3×1013 W/cm2 for the fundamental frequency 775 nm, the harmonic intensity being 10 and 100 times weaker), the total photon emission rate has its maximum at δ=0 and minimum at δ=π. However, this tendency, while valid for the first several HG peaks, is reversed for the higher HG peaks. The HG spectrum for δ=π is broader and the peak heights decrease more slowly compared to the case of δ=0. These results have their analog in the multiphoton above-threshold detachment study performed recently for H- ions [Telnov, Wang, and Chu, Phys. Rev. A 51, 4797 (1995)].
American Physical Society
Two-color phase control of high-order harmonic generation in intense laser fields
Article
openAccess
Telnov, Dmitry A.
Wang, Jingyan
Chu, Shih-I
Chemistry
na
Scholarly/refereed, publisher version
This item does not meet KU Open Access policy criteria.
oai:kuscholarworks.ku.edu:1808/309332020-12-01T09:00:59Zcom_1808_97col_1808_102
Hageman, Tyler
Wei, Hui
Kuehne, Patrick
Fu, Jinmei
Ludwig, Richard
Tao, Li
Leone, Anthony
Zocher, Marcel
Das, Tapan K.
2020-11-30T14:44:46Z
2020-11-30T14:44:46Z
2018-12-10
Hageman, T., Wei, H., Kuehne, P., Fu, J., Ludwig, R., Tao, L., Leone, A., Zocher, M., & Das, T. K. (2018). Impact of Tryptophan Oxidation in Complementarity-Determining Regions of Two Monoclonal Antibodies on Structure-Function Characterized by Hydrogen-Deuterium Exchange Mass Spectrometry and Surface Plasmon Resonance. Pharmaceutical research, 36(1), 24. https://doi.org/10.1007/s11095-018-2545-8
http://hdl.handle.net/1808/30933
10.1007/s11095-018-2545-8
https://orcid.org/0000-0002-0954-7518
PMC6290686
This work is licensed under a Creative Commons Attribution 4.0 International License.
Purpose
Tryptophan’s (Trp) unique hydrophobic and structural properties make it an important antigen binding motif when positioned in complementarity-determining regions (CDRs) of monoclonal antibodies (mAbs). Oxidation of Trp residues within the CDR can deleteriously impact antigen binding, particularly if the CDR conformation is altered. The goal of this study was to evaluate the conformational and functional impact of Trp oxidation for two mAb subtypes, which is essential in determining the structure-function relationship and establishing appropriate analytical control strategies during protein therapeutics development.
Methods
Selective Trp oxidation was induced by 2,2′-Azobis(2-amidinopropane) dihydrochloride (AAPH) treatment in the presence of free methionine (Met). The native and chemically oxidized mAbs were characterized by hydrogen-deuterium exchange mass spectrometry (HDX-MS) for conformational changes and surface plasmon resonance (SPR) for antigen-antibody binding.
Results
Treatment of mAbs with AAPH selectively oxidized solvent accessible Trp residues. Oxidation of Trp within or in proximity of CDRs increased conformational flexibility in variable domains and disrupted antigen binding.
Conclusions
Trp oxidation in CDRs can adversely impact mAbs’ conformation and antigen binding. Trp oxidation should be carefully evaluated as part of critical quality attribute assessments. Oxidation susceptible Trp should be closely monitored during process development for mAbs to establish appropriate analytical control for manufacturing of drug substance and drug product.
Springer
Copyright © 2018, The Author(s)
http://creativecommons.org/licenses/by/4.0/
openAccess
Tryptophan oxidation
Complementarity-determining region
Monoclonal antibody
Hydrogen-deuterium exchange mass spectrometry
Surface plasmon resonance
Impact of Tryptophan Oxidation in Complementarity-Determining Regions of Two Monoclonal Antibodies on Structure-Function Characterized by Hydrogen-Deuterium Exchange Mass Spectrometry and Surface Plasmon Resonance
Article
Hageman, Tyler
Chemistry
Scholarly/refereed, publisher version
This item meets KU Open Access policy criteria.
oai:kuscholarworks.ku.edu:1808/160652019-04-12T14:45:43Zcom_1808_97col_1808_102
Telnov, Dmitry A.
Chu, Shih-I
2014-12-10T16:53:41Z
2014-12-10T16:53:41Z
1999-12-14
Telnov, Dmitry A.; Chu, Shih-I. (1999). "High-order perturbation expansion of non-Hermitian Floquet theory for multiphoton and above-threshold ionization processes." Physical Review A, 61(01):013408. http://dx.doi.org/10.1103/PhysRevA.61.013408.
1050-2947
http://hdl.handle.net/1808/16065
10.1103/PhysRevA.61.013408
This is the publisher's version, also available electronically from http://journals.aps.org/pra/abstract/10.1103/PhysRevA.61.013408
A high-order perturbation theory is presented for efficient and accurate computation of multiphoton and above-threshold ionization cross sections of atoms and molecules in weak to medium strength laser fields. The procedure is based on a Raleigh-Schrödinger perturbative expansion of the time-independent non-Hermitian Floquet Hamiltonian. The reduced Green function and generalized pseudospectral discretization techniques are extended to facilitate the calculation of complex quasienergy resonance states without the need of diagonalizing the full Floquet Hamiltonian. Explicit expressions are presented for the determination of intensity-dependent total and partial rates and electron angular distributions. The theory is applied to a case study of multiphoton detachment of H- for a range of laser frequencies (corresponding to the absorption of a minimum of two photons) and laser intensities from 107 to 10(12)W/cm(2). It is found that a 16th-order perturbative Floquet procedure provides an excellent description of the two-photon-dominant detachment processes for laser intensity up to 2×10(11)W/cm(2). The predicted electron angular distributions are in good agreement with recent experimental data.
American Physical Society
High-order perturbation expansion of non-Hermitian Floquet theory for multiphoton and above-threshold ionization processes
Article
openAccess
Telnov, Dmitry A.
Chu, Shih-I
Chemistry
Scholarly/refereed, publisher version
This item does not meet KU Open Access policy criteria.
oai:kuscholarworks.ku.edu:1808/239082019-04-12T14:16:23Zcom_1808_97col_1808_102
Go, Eden P.
Chang, Qing
Liao, Hua-Xin
Sutherland, Laura L.
Alam, S. Munir
Haynes, Barton F.
Desaire, Heather
2017-05-05T17:22:42Z
2017-05-05T17:22:42Z
2009-09
Go, E. P., Chang, Q., Liao, H.-X., Sutherland, L. L., Alam, S. M., Haynes, B. F., & Desaire, H. (2009). Glycosylation Site-Specific Analysis of Clade C HIV-1 Envelope Proteins. Journal of Proteome Research, 8(9), 4231–4242. http://doi.org/10.1021/pr9002728
http://hdl.handle.net/1808/23908
10.1021/pr9002728
PMC2756219
The extensive glycosylation of HIV-1 envelope proteins (Env), gp120/gp41, is known to play an important role in evasion of host immune response by masking key neutralization epitopes and presenting the Env glycosylation as “self” to the host immune system. The Env glycosylation is mostly conserved but continues to evolve to modulate viral infectivity. Thus, profiling Env
glycosylation and distinguishing interclade and intraclade glycosylation variations are necessary components in unraveling the effects of glycosylation on Env’s immunogenicity. Here, we describe a mass spectrometry-based approach to characterize the glycosylation profiles of two rVV-expressed clade C Envs by identifying the glycan motifs on each glycosylation site and determining the degree of glycosylation site occupancy. One Env is a wild-type Env, while the other is a synthetic “consensus” sequence (C.CON). The observed differences in the glycosylation profiles between the two clade C Envs show that C.CON has more unutilized sites and high levels of high mannose glycans; these features mimic the glycosylation profile of a Group M consensus immunogen, CONS. Our results also reveal a clade-specific glycosylation pattern. Discerning interclade and intraclade glycosylation variations could provide valuable information in understanding the molecular differences among the different HIV-1 clades and in designing new Env-based immunogens.
American Chemical Society
This document is the Accepted Manuscript version of a Published Work that appeared in final form in the Journal of Proteome Research, copyright © American Chemical Society after peer review and technical editing by the publisher. To access the final edited and published work see http://dx.doi.org/10.1021/pr9002728.
openAccess
HIV
Envelope glycoprotein
Glycosylation;
Vaccine
Mass spectrometry
Glycosylation Site-Specific Analysis of Clade C HIV-1 Envelope Proteins
Article
Go, Eden P.
Chang, Qing
Desaire, Heather
Chemistry
Scholarly/refereed, author accepted manuscript
This item meets KU Open Access policy criteria.
oai:kuscholarworks.ku.edu:1808/305182020-06-17T08:00:51Zcom_1808_97col_1808_102
Weerakoon-Ratnayake, Kumuditha M.
Vaidyanathan, Swarnagowri
Larkey, Nicholas
Dathathreya, Kavya
Hu, Mengjia
Jose, Jilsha
Mog, Shalee
August, Keith
Godwin, Andrew K.
Hupert, Mateusz L.
Witek, Malgorzata A.
Soper, Steven A.
2020-06-16T20:37:05Z
2020-06-16T20:37:05Z
2020-02-24
M Weerakoon-Ratnayake, K., Vaidyanathan, S., Larky, N., Dathathreya, K., Hu, M., Jose, J., Mog, S., August, K., K Godwin, A., L Hupert, M., A Witek, M., & A Soper, S. (2020). Microfluidic Device for On-Chip Immunophenotyping and Cytogenetic Analysis of Rare Biological Cells. Cells, 9(2), 519. https://doi.org/10.3390/cells9020519
http://hdl.handle.net/1808/30518
10.3390/cells9020519
https://orcid.org/0000-0002-6839-4515
https://orcid.org/0000-0003-0397-5543
https://orcid.org/0000-0002-3987-9580
PMC7072755
This work is licensed under a Creative Commons Attribution 4.0 International License.
The role of circulating plasma cells (CPCs) and circulating leukemic cells (CLCs) as biomarkers for several blood cancers, such as multiple myeloma and leukemia, respectively, have recently been reported. These markers can be attractive due to the minimally invasive nature of their acquisition through a blood draw (i.e., liquid biopsy), negating the need for painful bone marrow biopsies. CPCs or CLCs can be used for cellular/molecular analyses as well, such as immunophenotyping or fluorescence in situ hybridization (FISH). FISH, which is typically carried out on slides involving complex workflows, becomes problematic when operating on CLCs or CPCs due to their relatively modest numbers. Here, we present a microfluidic device for characterizing CPCs and CLCs using immunofluorescence or FISH that have been enriched from peripheral blood using a different microfluidic device. The microfluidic possessed an array of cross-channels (2–4 µm in depth and width) that interconnected a series of input and output fluidic channels. Placing a cover plate over the device formed microtraps, the size of which was defined by the width and depth of the cross-channels. This microfluidic chip allowed for automation of immunofluorescence and FISH, requiring the use of small volumes of reagents, such as antibodies and probes, as compared to slide-based immunophenotyping and FISH. In addition, the device could secure FISH results in <4 h compared to 2–3 days for conventional FISH.
MDPI
© 2020 by the authors.
http://creativecommons.org/licenses/by/4.0/
openAccess
Microfluidics
Immunophenotyping
Fish
Liquid biopsy
Circulating leukemia cells
Circulating plasma cells
Microfluidic Device for On-Chip Immunophenotyping and Cytogenetic Analysis of Rare Biological Cells
Article
Weerakoon-Ratnayake, Kumuditha M.
Vaidyanathan, Swarnagowri
Larkey, Nicholas
Dathathreya, Kavya
Hu, Mengjia
Jose, Jilsha
Mog, Shalee
Hupert, Mateusz L.
Witek, Malgorzata A.
Soper, Steven A.
Chemistry
Center of BioModular Multiscale Systems for Precision Medicine
Bioengineering
Pathology & Laboratory Medicine
BioFluidica Research Laboratory
Mechanical Engineering
Scholarly/refereed, publisher version
This item meets KU Open Access policy criteria.
oai:kuscholarworks.ku.edu:1808/244862019-04-12T14:19:28Zcom_1808_97col_1808_102
Krause, Mary Elizabeth
Glass, Amanda M.
Jackson, Timothy A.
Laurence, Jennifer S.
2017-06-13T17:00:01Z
2017-06-13T17:00:01Z
2010-01-18
Krause, M. E., Glass, A. M., Jackson, T. A., & Laurence, J. S. (2010). A novel tripeptide model of nickel superoxide dismutase. Inorganic Chemistry, 49(2), 362–364. http://doi.org/10.1021/ic901828m.
http://hdl.handle.net/1808/24486
10.1021/ic901828m
PMC2810650
This document is the Accepted Manuscript version of a Published Work that appeared in final form in the Inorganic Chemistry, copyright © American Chemical Society after peer review and technical editing by the publisher. To access the final edited and published work see http://doi.org/10.1021/ic901828m.
Nickel superoxide dismutase (Ni-SOD) catalyzes the disproportionation of superoxide to molecular oxygen and hydrogen peroxide, but the overall reaction mechanism has yet to be determined. Peptide-based models of the 2N:2S nickel coordination sphere of Ni-SOD have provided some insight into the mechanism of this enzyme. Here we show that the coordination sphere of Ni-SOD can be mimicked using the tripeptide asparagine-cysteine-cysteine (NCC). NCC binds nickel with extremely high affinity at physiological pH with 2N:2S geometry, as demonstrated by electronic absorption and circular dichroism (CD) data. Like Ni-SOD, Ni-NCC has mixed amine/amide ligation that favors metal-based oxidation over ligand-based oxidation. Electronic absorption, CD, and magnetic CD data (MCD) collected for Ni-NCC are consistent with a diamagnetic Ni(II) center bound in square planar geometry. Ni-NCC is quasi-reversibly oxidized with a midpoint potential of 0.72(2) V (versus Ag/AgCl) and breaks down superoxide in an enzyme-based assay, supporting its potential use as a model for Ni-SOD chemistry.
American Chemical Society
A novel tripeptide model of nickel superoxide dismutase
Article
openAccess
Krause, Mary E.
Glass, Amanda M.
Jackson, Timothy A.
Laurence, Jennifer S.
Chemistry
Scholarly/refereed, author accepted manuscript
This item meets KU Open Access policy criteria.
oai:kuscholarworks.ku.edu:1808/160322019-04-12T14:30:50Zcom_1808_97col_1808_102
Ho, Tak-San
Hung, Shih-Han
Chen, Hsing-Ta
Chu, Shih-I
2014-12-04T17:37:50Z
2014-12-04T17:37:50Z
2009-06-22
Ho, Tak-San., Hung, Shih-Han., Chen, Hsing-Ta., Chu, Shih-I. "Memory effect on the multiphoton coherent destruction of tunneling in the electron transport of nanoscale systems driven by a periodic field: A generalized Floquet approach." Phys. Rev. B 79, 235323 – Published 22 June 2009. http://dx.doi.org/10.1103/PhysRevB.79.235323.
http://hdl.handle.net/1808/16032
10.1103/PhysRevB.79.235323
This is the published version, also available here: http://dx.doi.org/10.1103/PhysRevB.79.235323.
Time-dependent electron-transport processes are often studied in the wide-band limit. In this paper, a generalized Floquet approach beyond the wide-band limit is developed for the general treatment of memory effect on the virtually unexplored multiphoton (MP) coherent destruction of tunneling (CDT) phenomenon of periodically driven electrode-wire-electrode nanoscale systems. As a case study, we apply the approach for a detailed analysis of the electron-transport dc current in the electrode-quantum double dot-electrode system, showing the significance of memory effect as well as illustrating the origin of the MP-CDT phenomenon.
American Physical Society
Memory effect on the multiphoton coherent destruction of tunneling in the electron transport of nanoscale systems driven by a periodic field: A generalized Floquet approach
Article
openAccess
Chu, Shih-I
Chemistry
fullparticipation
Scholarly/refereed, publisher version
This item meets KU Open Access policy criteria.
oai:kuscholarworks.ku.edu:1808/328312024-01-16T16:12:07Zcom_1808_97col_1808_102
Aksenov, Nicolai A.
Aksenov, Alexander V.
Kornienko, Alexander
De Carvalho, Annelise
Mathieu, Véronique
Aksenov, Dmitrii A.
Ovcharov, Sergei N.
Griaznov, Georgii D.
Rubin, Michael
2022-07-12T18:21:28Z
2022-07-12T18:21:28Z
2018-11-01
Aksenov NA, Aksenov AV, Kornienko A, De Carvalho A, Mathieu V, Aksenov DA, Ovcharov SN, Griaznov GD, Rubin M. A nitroalkane-based approach to one-pot three-component synthesis of isocryptolepine and its analogs with potent anti-cancer activities. RSC Adv. 2018 Nov 1;8(64):36980-36986. doi: 10.1039/c8ra08155g. PMID: 35558925; PMCID: PMC9089289.
http://hdl.handle.net/1808/32831
10.1039/c8ra08155g
https://orcid.org/ 0000-0002-7125-9066
https://orcid.org/ 0000-0002-6644-9949
https://orcid.org/ 0000-0003-2041-7367
https://orcid.org/ 0000-0002-1668-9311
PMC35558925
A second generation polyphosphoric acid-mediated one-pot three-component synthesis of indoloquinoline scaffold is developed. This improved version of the process involves electrophilically activated nitroalkanes for the installation of strategic C–C and C–N bonds and ring C assembly. This modification allows the elimination of unnecessary solvent change operations and all steps are carried out in a true, uninterrupted one-pot manner. A further improvement involves the possibility to install an ortho-amino group in situ. A synthetic application of this method is showcased by the concise synthesis of an isocryptolepine alkaloid and its synthetic analogs with potent anticancer activities.
Royal Society of Chemistry
This article is licensed under a Creative Commons Attribution-NonCommercial 3.0 Unported License. © The Royal Society of Chemistry 2018.
https://creativecommons.org/licenses/by-nc/4.0/
openAccess
A nitroalkane-based approach to one-pot three-component synthesis of isocryptolepine and its analogs with potent anti-cancer activities
Article
Rubin, Michael
Chemistry
Scholarly/refereed, publisher version
This item meets KU Open Access policy criteria.
oai:kuscholarworks.ku.edu:1808/159982019-04-12T14:51:14Zcom_1808_97col_1808_102
Chu, Shih-I
Wang, Jingyan
Laughlin, Cecil
2014-12-02T18:37:48Z
2014-12-02T18:37:48Z
1994-10-01
Chu, Shih-I., Wang, Jingyan., Laughlin, Cecil. "Multiphoton detachment of H-. II. Intensity-dependent photodetachment rates and threshold behavior—complex-scaling generalized pseudospectral method." Phys. Rev. A 50, 3208 – Published 1 October 1994. http://dx.doi.org/10.1103/PhysRevA.50.3208.
http://hdl.handle.net/1808/15998
10.1103/PhysRevA.50.3208
This is the published version, also available here: http://dx.doi.org/10.1103/PhysRevA.50.3208.
We extend our previous perturbative study of the multiphoton detachment of H- [Phys. Rev. A 48, 4654 (1993)] to stronger fields by considering the intensity-dependent photodetachment rates and threshold behavior. An accurate one-electron model potential, which reproduces exactly the known H- binding energy and the low-energy e-H(1s) elastic-scattering phase shifts, is employed. A computational technique, the complex-scaling generalized pseudospectral method, is developed for accurate and efficient treatment of the time-independent non-Hermitian Floquet Hamiltonian H^F. The method is simple to implement, does not require the computation of potential matrix elements, and is computationally more efficient than the traditional basis-set-expansion–variational method. We present detailed nonperturbative results of the intensity- and frequency-dependent complex quasienergies (ER,-Γ/2), the complex eigenvalues of H^F, providing directly the ac Stark shifts and multiphoton detachment rates of H-. The laser intensity considered ranges from 1 to 40 GW/cm2 and the laser frequency covers 0.20–0.42 eV (in the c.m. frame). Finally we perform a simulation of intensity-averaged multiphoton detachment rates by considering the experimental conditions of the laser and H- beams. The results (without any free parameters) are in good agreement with experimental data, both in absolute magnitude and in the threshold behavior.
American Physical Society
Multiphoton detachment of H-. II. Intensity-dependent photodetachment rates and threshold behavior—complex-scaling generalized pseudospectral method
Article
openAccess
Chu, Shih-I
Wang, Jingyan
Chemistry
na
Scholarly/refereed, publisher version
This item does not meet KU Open Access policy criteria.
oai:kuscholarworks.ku.edu:1808/342392023-05-31T06:05:39Zcom_1808_97col_1808_102
Priviter, Anna
Cardaci, Vincenzo
Weerasekara, Dhanushka
Saab, Miriam Wissam
Diolosà, Lidia
Fidilio, Annamaria
Jolivet, Renaud Blaise
Lazzarino, Giuseppe
Amorini, Angela Maria
Camarda, Massimo
Lunte, Susan Marie
Caraci, Filippo
Caruso, Giuseppe
2023-05-30T21:20:10Z
2023-05-30T21:20:10Z
2023-03-29
Privitera, A., Cardaci, V., Weerasekara, D., Saab, M. W., Diolosà, L., Fidilio, A., Jolivet, R. B., Lazzarino, G., Amorini, A. M., Camarda, M., Lunte, S. M., Caraci, F., & Caruso, G. (2023). Microfluidic/HPLC combination to study carnosine protective activity on challenged human microglia: Focus on oxidative stress and energy metabolism. Frontiers in pharmacology, 14, 1161794. https://doi.org/10.3389/fphar.2023.1161794
https://hdl.handle.net/1808/34239
10.3389/fphar.2023.1161794
PMC10095171
Carnosine (β-alanyl-L-histidine) is a naturally occurring endogenous peptide widely distributed in excitable tissues such as the brain. This dipeptide possesses well-demonstrated antioxidant, anti-inflammatory, and anti-aggregation properties, and it may be useful for treatment of pathologies characterized by oxidative stress and energy unbalance such as depression and Alzheimer’s disease (AD). Microglia, the brain-resident macrophages, are involved in different physiological brain activities such synaptic plasticity and neurogenesis, but their dysregulation has been linked to the pathogenesis of numerous diseases. In AD brain, the activation of microglia towards a pro-oxidant and pro-inflammatory phenotype has found in an early phase of cognitive decline, reason why new pharmacological targets related to microglia activation are of great importance to develop innovative therapeutic strategies. In particular, microglia represent a common model of lipopolysaccharides (LPS)-induced activation to identify novel pharmacological targets for depression and AD and numerous studies have linked the impairment of energy metabolism, including ATP dyshomeostasis, to the onset of depressive episodes. In the present study, we first investigated the toxic potential of LPS + ATP in the absence or presence of carnosine. Our studies were carried out on human microglia (HMC3 cell line) in which LPS + ATP combination has shown the ability to promote cell death, oxidative stress, and inflammation. Additionally, to shed more light on the molecular mechanisms underlying the protective effect of carnosine, its ability to modulate reactive oxygen species production and the variation of parameters representative of cellular energy metabolism was evaluated by microchip electrophoresis coupled to laser-induced fluorescence and high performance liquid chromatography, respectively. In our experimental conditions, carnosine prevented LPS + ATP-induced cell death and oxidative stress, also completely restoring basal energy metabolism in human HMC3 microglia. Our results suggest a therapeutic potential of carnosine as a new pharmacological tool in the context of multifactorial disorders characterize by neuroinflammatory phenomena including depression and AD.
Frontiers Media
© 2023 Privitera, Cardaci, Weerasekara, Saab, Diolosà, Fidilio, Jolivet, Lazzarino, Amorini, Camarda, Lunte, Caraci and Caruso. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY).
http://creativecommons.org/licenses/by/4.0/
openAccess
Carnosine
Human microglia
Inflammation
Oxidative stress
Energy metabolism
Depression
Microfluidics
HPLC
Microfluidic/HPLC combination to study carnosine protective activity on challenged human microglia: Focus on oxidative stress and energy metabolism
Article
Weerasekara, Dhanushka
Lunte, Susan Marie
Ralph N. Adams Institute for Bioanalytical Chemistry
Pharmaceutical Chemistry
Chemistry
Scholarly/refereed, publisher version
This item meets KU Open Access policy criteria.
oai:kuscholarworks.ku.edu:1808/134672018-07-13T15:29:48Zcom_1808_97col_1808_102
Chini, Michael
Wang, Xiaowei
Cheng, Yan
Wu, Yi
Zhao, Di
Telnov, Dmitry A.
Chu, Shih-I
Chang, Zenghu
2014-04-11T20:33:42Z
2014-04-11T20:33:42Z
2013-01-22
Chini, Michael, Xiaowei Wang, Yan Cheng, Yi Wu, Di Zhao, Dmitry A Telnov, Shih-I Chu, and Zenghu Chang. 2013. “Sub-Cycle Oscillations in Virtual States Brought to Light.” Scientific Reports 3 . http://dx.doi.org/10.1038/srep01105 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3551229/
http://hdl.handle.net/1808/13467
10.1038/srep01105
Understanding and controlling the dynamic evolution of electrons in matter is among the most fundamental goals of attosecond science. While the most exotic behaviors can be found in complex systems, fast electron dynamics can be studied at the fundamental level in atomic systems, using moderately intense (≲103 W/cm2) lasers to control the electronic structure in proof-of-principle experiments. Here, we probe the transient changes in the absorption of an isolated attosecond extreme ultraviolet (XUV) pulse by helium atoms in the presence of a delayed, few-cycle near infrared (NIR) laser pulse, which uncovers absorption structures corresponding to laser-induced “virtual” intermediate states in the two-color two-photon (XUV+NIR) and three-photon (XUV+NIR+NIR) absorption process. These previously unobserved absorption structures are modulated on half-cycle (~1.3 fs) and quarter-cycle (~0.6 fs) timescales, resulting from quantum optical interference in the laser-driven atom.
Macmillan Publishers Limited
This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivs 3.0 Unported License. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-nd/3.0/.
http://creativecommons.org/licenses/by-nc-nd/3.0/
openAccess
Ultrafast Lasers
Atomic And Molecular Interactions With Photons
Electronic Structure Of Atoms And Molecules
Ultrafast Photonics
Sub-cycle Oscillations in Virtual States Brought to Light
Article
Zhao, Di
Telnov, Dmitry A.
Chu, Shih-I
Chemistry
fullparticipation
Scholarly/refereed, publisher version
This item meets KU Open Access policy criteria.
oai:kuscholarworks.ku.edu:1808/314412021-02-18T09:01:00Zcom_1808_97col_1808_102
Jas, Gouri S.
Childs, Ed W.
Kuczera, Krzysztof
2021-02-17T22:58:12Z
2021-02-17T22:58:12Z
2019-02-21
J. Chem. Phys. 150, 074902 (2019); https://doi.org/10.1063/1.5082192
http://hdl.handle.net/1808/31441
10.1063/1.5082192
https://orcid.org/0000-0002-0774-012X
https://orcid.org/0000-0003-2358-1349
This article may be downloaded for personal use only. Any other use requires prior permission of the author and AIP Publishing. This article appeared in J. Chem. Phys. 150, 074902 (2019); https://doi.org/10.1063/1.5082192 and may be found at https://aip.scitation.org/doi/full/10.1063/1.5082192
Thermodynamically stable conformers of secondary structural elements make a stable tertiary/quaternary structure that performs its proper biological function efficiently. Formation mechanisms of secondary and tertiary/quaternary structural elements from the primary structure are driven by the kinetic properties of the respective systems. Here we have carried out thermodynamic and kinetic characterization of an alpha helical heteropeptide in two protonation states, created with the addition and removal of a proton involving a single histidine residue in the primary structure. Applying far-UV circular dichroism spectroscopy, the alpha helix is observed to be significantly more stable in the deprotonated state. Nanosecond laser temperature jump spectroscopy monitoring time-resolved tryptophan fluorescence on the protonated conformer is carried out to measure the kinetics of this system. The measured relaxation rates at a final temperature between 296K and 314 K generated a faster component of 20 ns–11 ns and a slower component of 314 ns–198 ns. Atomically detailed characterization of the helix-coil kinetic pathways is performed based on all-atom molecular dynamics trajectories of the two conformers. Application of clustering and kinetic coarse-graining with optimum dimensionality reduction produced description of the trajectories in terms of kinetic models with two to five states. These models include aggregate states corresponding to helix, coil, and intermediates. The “coil” state involves the largest number of conformations, consistent with the expected high entropy of this structural ensemble. The “helix” aggregate states are found to be mixed with the full helix and partially folded forms. The experimentally observed higher helix stability in the deprotonated form of the alpha helical heteropeptide is reflected in the nature of the “helix” aggregate state arising from the kinetic model. In the protonated form, the “coil” state exhibits the lowest free energy and longest lifetime, while in the deprotonated form, it is the “helix” that is found to be most stable. Overall, the coarse grained models suggest that the protonation of a single histidine residue in the primary structure induces significant changes in the free energy landscape and kinetic network of the studied helix-forming heteropeptide.
American Institute of Physics
© 2019 Author(s).
openAccess
Kinetic pathway analysis of an α-helix in two protonation states: Direct observation and optimal dimensionality reduction
Article
Kuczera, Krzysztof
Chemistry
Molecular Biosciences
Scholarly/refereed, publisher version
This item meets KU Open Access policy criteria.
oai:kuscholarworks.ku.edu:1808/255202018-07-24T18:11:43Zcom_1808_97col_1808_102
Davidchack, Ruslan L.
Laird, Brian Bostian
Roth, R.
2017-11-29T23:23:57Z
2017-11-29T23:23:57Z
2016
Davidchack, R. L., Laird, B. B., & Roth, R. (2016). Hard spheres at a planar hard wall: Simulations and density functional theory. arXiv preprint arXiv:1603.06906.
http://hdl.handle.net/1808/25520
10.5488/CMP.19.23001
https://orcid.org/0000-0001-9418-5322
Hard spheres are a central and important model reference system for both homogeneous and inhomogeneous fluid systems. In this paper we present new high-precision molecular-dynamics computer simulations for a hard sphere fluid at a planar hard wall. For this system we present benchmark data for the density profile ρ(z) at various bulk densities, the wall surface free energy γ, the excess adsorption Γ, and the excess volume vex, which is closely related to Γ. We compare all benchmark quantities with predictions from state-of-the-art classical density functional theory calculations within the framework of fundamental measure theory. While we find overall good agreement between computer simulations and theory, significant deviations appear at sufficiently high bulk densities.
Institute for Condensed Matter Physics
All papers in Condensed Matter Physics journal are published under the terms of the Creative Commons Attribution 4.0 International License (CC-BY) with the authors retaining a copyright to their articles. This license permits anyone to copy, distribute, transmit, and adapt an article’s content, without obtaining permission from the author(s) or CMP journal, provided a proper attribution is given to the author(s) and to the source of the material. Please check full license terms and requirements at https://creativecommons.org/licenses/by/4.0/.
https://creativecommons.org/licenses/by/4.0
openAccess
Inhomogeneous fluids
Solid-liquid interfaces
Surface thermodynamics
Classical density functional theory
Molecular-dynamics simulation
Hard spheres at a planar hard wall: Simulations and density functional theory
Article
Laird, Brian Bostian
Chemistry
Scholarly/refereed, publisher version
This item meets KU Open Access policy criteria.
oai:kuscholarworks.ku.edu:1808/273002018-11-13T09:01:46Zcom_1808_97col_1808_102
Aksenov, Alexander V.
Ovcharov, Dmitrii S.
Aksenov, Nicolai A.
Aksenov, Dmitrii A.
Nadein, Oleg N.
Rubin, Michael
2018-11-12T20:29:33Z
2018-11-12T20:29:33Z
2017-06-08
Aksenov, A. V., Ovcharov, D. S., Aksenov, N. A., Aksenov, D. A., Nadein, O. N., & Rubin, M. (2017). Dual role of polyphosphoric acid-activated nitroalkanes in oxidative peri-annulations: efficient synthesis of 1, 3, 6, 8-tetraazapyrenes. RSC Advances, 7(48), 29927-29932.
http://hdl.handle.net/1808/27300
10.1039/C7RA04751G
A highly efficient synthetic method for expeditious and selective assembly of tetraazopyrenes (TAPy) is reported, based on the novel reaction of electrophilically activated nitroalkanes with aromatic amines. Remarkably, the nitroalkanes play a dual role in this process, also serving as mild and efficient oxidants promoting aromatization of the final product and allowing for the exclusion of a poorly controllable aerobic treatment.
Royal Society of Chemistry
© The Royal Society of Chemistry 2017. This article is licensed under a Creative Commons Attribution-NonCommercial 3.0 Unported Licence.
https://creativecommons.org/licenses/by-nc/3.0/us/
openAccess
Dual role of polyphosphoric acid-activated nitroalkanes in oxidative peri-annulations: efficient synthesis of 1,3,6,8-tetraazapyrenes
Article
Rubin, Michael
Chemistry
Scholarly/refereed, publisher version
This item meets KU Open Access policy criteria.
oai:kuscholarworks.ku.edu:1808/241142019-04-12T14:17:11Zcom_1808_97col_1808_102
Lopez-Sambrooks, Cecilia
Shrimal, Shiteshu
Khodier, Carol
Flaherty, Daniel P.
Rinis, Natalie
Charest, Jonathan C.
Gao, Ningguo
Zhao, Peng
Wells, Lance
Lewis, Timothy A.
Lehrman, Mark A.
Gilmore, Reid
Golden, Jennifer E.
2017-05-12T15:20:42Z
2017-05-12T15:20:42Z
2016-12
Lopez-Sambrooks, C., Shrimal, S., Khodier, C., Flaherty, D. P., Rinis, N., Charest, J. C., … Contessa, J. N. (2016). Oligosaccharyltransferase Inhibition Induces Senescence in RTK-Driven Tumor Cells. Nature Chemical Biology, 12(12), 1023–1030. http://doi.org/10.1038/nchembio.2194
http://hdl.handle.net/1808/24114
10.1038/nchembio.2194
https://orcid.org/0000-0002-8305-0606
https://orcid.org/0000-0002-6813-3710
PMC5393272
Asparagine (N)-linked glycosylation is a protein modification critical for glycoprotein folding, stability, and cellular localization. To identify small molecules that inhibit new targets in this biosynthetic pathway, we initiated a cell-based high throughput screen and lead compound optimization campaign that delivered a cell permeable inhibitor (NGI-1). NGI-1 targets the oligosaccharyltransferase (OST), a hetero-oligomeric enzyme that exists in multiple isoforms and transfers oligosaccharides to recipient proteins. In non-small cell lung cancer cells NGI-1 blocks cell surface localization and signaling of the EGFR glycoprotein, but selectively arrests proliferation in only those cell lines that are dependent on EGFR (or FGFR) for survival. In these cell lines OST inhibition causes cell cycle arrest accompanied by induction of p21, autofluorescence, and changes in cell morphology; all hallmarks of senescence. These results identify OST inhibition as a potential therapeutic approach for treating receptor tyrosine kinase-dependent tumors and provides a chemical probe for reversibly regulating N-linked glycosylation in mammalian cells.
Nature Publishing Group
Oligosaccharyltransferase Inhibition Induces Senescence in RTK-Driven Tumor Cells
Article
openAccess
Flaherty, Daniel P.
Golden, Jennifer E.
Chemistry
Scholarly/refereed, author accepted manuscript
This item meets KU Open Access policy criteria.
oai:kuscholarworks.ku.edu:1808/264992018-06-14T08:01:08Zcom_1808_97col_1808_102
Tang, Yu
Li, Yuting
Fung, Victor
Jiang, De-en
Huang, Weixin
Zhang, Shiran
Iwasawa, Yasuhiro
Sakata, Tomohiro
Nguyen, Luan
Zhang, Xiaoyan
Frenkel, Anatoly I.
Tao, Franklin Feng
2018-06-13T16:45:59Z
2018-06-13T16:45:59Z
2018-03-26
Tang, Y., Li, Y., Fung, V., Jiang, D., Huang, W., Zhang, S., … Tao, F. (Feng). (2018). Single rhodium atoms anchored in micropores for efficient transformation of methane under mild conditions. Nature Communications, 9, 1231. http://doi.org/10.1038/s41467-018-03235-7
http://hdl.handle.net/1808/26499
10.1038/s41467-018-03235-7
Catalytic transformation of CH4 under a mild condition is significant for efficient utilization of shale gas under the circumstance of switching raw materials of chemical industries to shale gas. Here, we report the transformation of CH4 to acetic acid and methanol through coupling of CH4, CO and O2 on single-site Rh1O5 anchored in microporous aluminosilicates in solution at ≤150 °C. The activity of these singly dispersed precious metal sites for production of organic oxygenates can reach about 0.10 acetic acid molecules on a Rh1O5 site per second at 150 °C with a selectivity of ~70% for production of acetic acid. It is higher than the activity of free Rh cations by >1000 times. Computational studies suggest that the first C–H bond of CH4 is activated by Rh1O5 anchored on the wall of micropores of ZSM-5; the formed CH3 then couples with CO and OH, to produce acetic acid over a low activation barrier.
Nature Publishing Group
Copyright © The Author(s) 2018 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
http://creativecommons.org/licenses/by/4.0/
openAccess
Single rhodium atoms anchored in micropores for efficient transformation of methane under mild conditions
Article
Tang, Yu
Li, Yuting
Huang, Weixin
Zhang, Shiran
Nguyen, Luan
Zhang, Xiaoyan
Tao, Franklin Feng
Chemistry
Scholarly/refereed, publisher version
This item meets KU Open Access policy criteria.
oai:kuscholarworks.ku.edu:1808/243882019-04-12T14:18:28Zcom_1808_97col_1808_102
Zhu, Zhikai
Go, Eden P.
Desaire, Heather
2017-06-06T18:55:19Z
2017-06-06T18:55:19Z
2014-06
Zhu, Z., Go, E. P., & Desaire, H. (2014). Absolute Quantitation of Glycosylation Site Occupancy Using Isotopically Labeled Standards and LC-MS. Journal of the American Society for Mass Spectrometry, 25(6), 1012–1017. http://doi.org/10.1007/s13361-014-0859-2
http://hdl.handle.net/1808/24388
10.1007/s13361-014-0859-2
PMC4458369
This document is the Accepted Manuscript version of a Published Work that appeared in final form in the Journal of the American Chemical Society, copyright © American Chemical Society after peer review and technical editing by the publisher. To access the final edited and published work see http://doi.org/10.1007/s13361-014-0859-2.
N-linked glycans are required to maintain appropriate biological functions on proteins. Underglycosylation leads to many diseases in plants and animals; therefore, characterizing the extent of glycosylation on proteins is an important step in understanding, diagnosing, and treating diseases. To determine the glycosylation site occupancy, protein N-glycosidase F (PNGase F) is typically used to detach the glycan from the protein, during which the formerly glycosylated asparagine undergoes deamidation to become an aspartic acid. By comparing the abundance of the resulting peptide containing aspartic acid against the one containing non-glycosylated asparagine, the glycosylation site occupancy can be evaluated. However, this approach can give inaccurate results when spontaneous chemical deamidation of the non-glycosylated asparagine occurs. To overcome this limitation, we developed a new method to measure the glycosylation site occupancy that does not rely on converting glycosylated peptides to their deglycosylated forms. Specifically, the overall protein concentration and the non-glycosylated portion of the protein are quantified simultaneously by using heavy isotope-labeled internal standards coupled with LC-MS analysis, and the extent of site occupancy is accurately determined. The efficacy of the method was demonstrated by quantifying the occupancy of a glycosylation site on bovine fetuin. The developed method is the first work that measures the glycosylation site occupancy without using PNGase F, and it can be done in parallel with glycopeptide analysis because the glycan remains intact throughout the workflow.
American Chemical Society
N-linked glycosylation
Site occupancy
PNGase F
Liquid chromatography/mass spectrometry
Chemical deamidation
Absolute Quantitation of Glycosylation Site Occupancy Using Isotopically Labeled Standards and LC-MS
Article
openAccess
Zhu, Zhikai
Go, Eden P.
Desaire, Heather
Chemistry
Scholarly/refereed, author accepted manuscript
This item meets KU Open Access policy criteria.
oai:kuscholarworks.ku.edu:1808/335502022-09-21T08:01:04Zcom_1808_97col_1808_102
Wijerathne, Harshani
Witek, Malgorzata A.
Jackson, Joshua M.
Brown, Virginia
Hupert, Mateusz L.
Herrera, Kristina
Kramer, Cameron
Davidow, Abigail E.
Li, Yan
Baird, Alison E.
Murphy, Michael C.
Soper, Steven A.
2022-09-20T18:23:07Z
2022-09-20T18:23:07Z
2020-10-26
Wijerathne, H., Witek, M.A., Jackson, J.M. et al. Affinity enrichment of extracellular vesicles from plasma reveals mRNA changes associated with acute ischemic stroke. Commun Biol 3, 613 (2020). https://doi.org/10.1038/s42003-020-01336-y
http://hdl.handle.net/1808/33550
10.1038/s42003-020-01336-y
https://orcid.org/0000-0002-2802-7235
https://orcid.org/0000-0002-8292-7058
Currently there is no in vitro diagnostic test for acute ischemic stroke (AIS), yet rapid diagnosis is crucial for effective thrombolytic treatment. We previously demonstrated the utility of CD8(+) T-cells’ mRNA expression for AIS detection; however extracellular vesicles (EVs) were not evaluated as a source of mRNA for AIS testing. We now report a microfluidic device for the rapid and efficient affinity-enrichment of CD8(+) EVs and subsequent EV’s mRNA analysis using droplet digital PCR (ddPCR). The microfluidic device contains a dense array of micropillars modified with anti-CD8α monoclonal antibodies that enriched 158 ± 10 nm sized EVs at 4.3 ± 2.1 × 109 particles/100 µL of plasma. Analysis of mRNA from CD8(+) EVs and their parental T-cells revealed correlation in the expression for AIS-specific genes in both cell lines and healthy donors. In a blinded study, 80% test positivity for AIS patients and controls was revealed with a total analysis time of 3.7 h.
Nature Research
© The Author(s) 2020. This article is licensed under a Creative Commons Attribution 4.0 International License.
http://creativecommons.org/licenses/by/4.0/
openAccess
Mechanisms of disease
Microfluidics
Stroke
Affinity enrichment of extracellular vesicles from plasma reveals mRNA changes associated with acute ischemic stroke
Article
Wijerathne, Harshani
Witek, Malgorzata A.
Jackson, Joshua M.
Brown, Virginia
Kramer, Cameron
Davidow, Abigail E.
Murphy, Michael C.
Soper, Steven A.
Chemistry
Center of BioModular Multiscale Systems for Precision Medicine
Bioengineering Program
Mechanical Engineering
Scholarly/refereed, publisher version
This item meets KU Open Access policy criteria.
oai:kuscholarworks.ku.edu:1808/160452019-04-12T14:45:40Zcom_1808_97col_1808_102
Hollars, Christopher W.
Dunn, Robert C.
2014-12-05T16:06:02Z
2014-12-05T16:06:02Z
1998-01-01
Hollars, Christoper W. & Dunn, Robert C. "Evaluation of thermal evaporation conditions used in coating aluminum on near-field fiber-optic probes." Rev. Sci. Instrum. 69, 1747 (1998). http://dx.doi.org/10.1063/1.1148836.
http://hdl.handle.net/1808/16045
10.1063/1.1148836
This is the published version, also available here: http://dx.doi.org/10.1063/1.1148836.
The effects that the thermal evaporation conditions have on the roughness of aluminum-coated near-field fiber-optic probes were investigated using the high-resolution capabilities of atomic force microscopy. The coating conditions studied include the effects of background gas composition, base vacuum pressure, and aluminum evaporation rate. The effects of aging on the aluminum-coated tips were also evaluated. The results from topography measurements of the resulting aluminumfilm indicated that the most dramatic improvements in the tip coatings can be achieved using high aluminum evaporation rates at base vacuum pressures below 10−5 Torr. These results agree with other studies on thin aluminumfilms and reflect a decrease in oxide formation. For demanding applications of near-field microscopy requiring maximal resolution, the results presented here indicate that it may also be necessary to reduce oxygen and/or water from the vacuum chamber prior to coating.
American Institute of Physics
Aluminium
Thin films
Atomic force microscopy
High pressure
Near-field scanning optical microscopy
Evaluation of thermal evaporation conditions used in coating aluminum on near-field fiber-optic probes
Article
openAccess
Hollars, Christopher W.
Dunn, Robert C.
Chemistry
Scholarly/refereed, publisher version
This item does not meet KU Open Access policy criteria.
oai:kuscholarworks.ku.edu:1808/160832019-04-12T14:49:43Zcom_1808_97col_1808_102
Geibel, Sven
Barth, Andreas
Amslinger, Sabine
Jung, Andreas H.
Burzik, Christiane
Clarke, Ronald J.
Givens, Richard S.
Fendler, Klaus
2014-12-12T17:09:18Z
2014-12-12T17:09:18Z
2000-09-01
Geibel, Sven., Barth, Andreas., Amslinger, Sabine., Jung, Andreas H., Burzik, Christiane., Clarke, Ronald J., Givens, Richard S., Fendler, Klaus. "P3-[2-(4-hydroxyphenyl)-2-oxo]ethyl ATP for the Rapid Activation of the Na+,K+-ATPase."
Biophysical Journal. Volume 79, Issue 3, September 2000, Pages 1346–1357. http://dx.doi.org/10.1016/S0006-3495(00)76387-9.
http://hdl.handle.net/1808/16083
10.1016/S0006-3495(00)76387-9
This is the published version, also available here: http://dx.doi.org/10.1016/S0006-3495(00)76387-9.
P3-[2-(4-hydroxyphenyl)-2-oxo]ethyl ATP (pHP-caged ATP) has been investigated for its application as a phototrigger for the rapid activation of electrogenic ion pumps. The yield of ATP after irradiation with a XeCl excimer laser (λ = 308 nm) was determined at pH 6.0–7.5. For comparison, the photolytic yields of P3-[1-(2-nitrophenyl)]ethyl ATP (NPE-caged ATP) and P3-[1,2-diphenyl-2-oxo]ethyl ATP (desyl-caged ATP) were also measured. It was shown that at λ = 308 nm pHP-caged ATP is superior to the other caged ATP derivatives investigated in terms of yield of ATP after irradiation. Using time-resolved single-wavelength IR spectroscopy, we determined a lower limit of 106 s−1 for the rate constant of release of ATP from pHP-caged ATP at pH 7.0. Like NPE-caged ATP, pHP-caged ATP and desyl-caged ATP bind to the Na+,K+-ATPase and act as competitive inhibitors of ATPase function. Using pHP-caged ATP, we investigated the charge translocation kinetics of the Na+,K+-ATPase at pH 6.2–7.4. The kinetic parameters obtained from the electrical measurements are compared to those obtained with a technique that does not require caged ATP, namely parallel stopped-flow experiments using the voltage-sensitive dye RH421. It is shown that the two techniques yield identical results, provided the inhibitory properties of the caged compound are taken into account. Our results demonstrate that under physiological (pH 7.0) and slightly basic (pH 7.5) or acidic (pH 6.0) conditions, pHP-caged ATP is a rapid, effective, and biocompatible phototrigger for ATP-driven biological systems.
Biophysical Society
P3-[2-(4-hydroxyphenyl)-2-oxo]ethyl ATP for the Rapid Activation of the Na+,K+-ATPase
Article
openAccess
Jung, Andreas H.
Amslinger, Sabine
Givens, Richard S.
Chemistry
na
Scholarly/refereed, publisher version
This item does not meet KU Open Access policy criteria.
oai:kuscholarworks.ku.edu:1808/221252019-04-12T14:26:12Zcom_1808_97col_1808_102
Ringe, Rajesh P.
Yasmeen, Anila
Ozorowski, Gabriel
Go, Eden P.
Pritchard, Laura K.
Guttman, Miklos
Ketas, Thomas A.
Cottrell, Christopher A.
Wilson, Ian A.
Sanders, Rogier W.
Desaire, Heather
2016-12-02T20:56:24Z
2016-12-02T20:56:24Z
2015-08-26
Ringe RP, Yasmeen A, Ozorowski G, Go EP, Pritchard LK, Guttman M, Ketas TA, Cottrell CA, Wilson IA, Sanders RW, Cupo A, Crispin M, Lee KK, Desaire H, Ward AB, Klasse PJ, Moore JP. 2015. Influences on the design and purification of soluble, recombinant native-like HIV-1 envelope glycoprotein trimers. J Virol 89:12189 –12210. doi:10.1128/JVI.01768-15.
http://hdl.handle.net/1808/22125
10.1128/JVI.01768-15
We have investigated factors that influence the production of native-like soluble, recombinant trimers based on the env genes of two isolates of human immunodeficiency virus type 1 (HIV-1), specifically 92UG037.8 (clade A) and CZA97.012 (clade C). When the recombinant trimers based on the env genes of isolates 92UG037.8 and CZA97.012 were made according to the SOSIP.664 design and purified by affinity chromatography using broadly neutralizing antibodies (bNAbs) against quaternary epitopes (PGT145 and PGT151, respectively), the resulting trimers are highly stable and they are fully native-like when visualized by negative-stain electron microscopy. They also have a native-like (i.e., abundant) oligomannose glycan composition and display multiple bNAb epitopes while occluding those for nonneutralizing antibodies. In contrast, uncleaved, histidine-tagged Foldon (Fd) domain-containing gp140 proteins (gp140UNC-Fd-His), based on the same env genes, very rarely form native-like trimers, a finding that is consistent with their antigenic and biophysical properties and glycan composition. The addition of a 20-residue flexible linker (FL20) between the gp120 and gp41 ectodomain (gp41ECTO) subunits to make the uncleaved 92UG037.8 gp140-FL20 construct is not sufficient to create a native-like trimer, but a small percentage of native-like trimers were produced when an I559P substitution in gp41ECTO was also present. The further addition of a disulfide bond (SOS) to link the gp120 and gp41 subunits in the uncleaved gp140-FL20-SOSIP protein increases native-like trimer formation to ∼20 to 30%. Analysis of the disulfide bond content shows that misfolded gp120 subunits are abundant in uncleaved CZA97.012 gp140UNC-Fd-His proteins but very rare in native-like trimer populations. The design and stabilization method and the purification strategy are, therefore, all important influences on the quality of trimeric Env proteins and hence their suitability as vaccine components.
Science Publications
Influences on the Design and Purification of Soluble, Recombinant Native-Like HIV-1 Envelope Glycoprotein Trimers
Article
openAccess
Desaire, Heather
Chemistry
Scholarly/refereed, publisher version
This item meets KU Open Access policy criteria.
oai:kuscholarworks.ku.edu:1808/161792019-04-12T14:46:33Zcom_1808_97col_1808_102
Wang, Haobin
Thompson, Ward H.
Miller, William H.
2014-12-18T17:02:54Z
2014-12-18T17:02:54Z
1997-08-01
Wang, Haobin; Thompson, Ward H.; Miller, William H. (1997). "Thermal rate constant calculation using flux–flux autocorrelation functions: Application to Cl+H2→HCl+H reaction." The Journal of Chemical Physics, 107(18):7194-7201. http://dx.doi.org/10.1063/1.474959
0021-9606
http://hdl.handle.net/1808/16179
10.1063/1.474959
This is the publisher's version, also available electronically from http://scitation.aip.org/content/aip/journal/jcp/107/18/10.1063/1.474959.
An efficient method was recently introduced by Thompson and Miller [J. Chem. Phys. 106, 142 (1997)] for calculating thermal rate constants using the flux–flux autocorrelation function with absorbing boundary conditions. The method uses an iterative method to exploit the low rank feature of the Boltzmannized flux operator and subsequently only propagates the eigenvectors that have significant contributions to the rate constant. In the present article, this method is used to calculate the thermal rate constants of the Cl+H2→HCl+Hreaction in the temperature range of 200–1500 °K. Total angular momentum is treated by employing the body-fixed axis frame, both exactly and also via various approximations. Comparisons with previous exact and approximate theoretical results are made.
American Institute of Physics
Thermal rate constant calculation using flux–flux autocorrelation functions: Application to Cl+H2→HCl+H reaction
Article
openAccess
Wang, Haobin
Thompson, Ward H.
Miller, William H.
Chemistry
Scholarly/refereed, publisher version
This item does not meet KU Open Access policy criteria.
oai:kuscholarworks.ku.edu:1808/252532017-12-19T14:41:09Zcom_1808_97col_1808_102
Biancardi, Alessandro
Barnes, Jeremy
Caricato, Marco
2017-11-03T18:33:09Z
2017-11-03T18:33:09Z
2016-12-15
Biancardi, A., Barnes, J., & Caricato, M. (2016). Point charge embedding for ONIOM excited states calculations. The Journal of Chemical Physics, 145(22), 224109. doi:10.1063/1.4972000
http://hdl.handle.net/1808/25253
10.1063/1.4972000
Hybrid quantum mechanical methods can assist in the interpretation and prediction of the electronic spectra of large molecular structures. In this work, we study the performance of the ONIOM (Our own N-layered Integrated molecular Orbital molecular Mechanics) hybrid method for the calculation of transition energies and oscillator strengths by embedding the core region in a field of fixed point charges. These charges introduce polarization effects from the substituent groups to the core region. We test various charge definitions, with particular attention to the issue of overpolarization near the boundary between layers. To minimize this issue, we fit the charges on the electrostatic potential of the entire structure in the presence of the link atoms used to cap dangling bonds. We propose two constrained fitting strategies: one that produces an average set of charges common to both model system calculations, EE(L1), and one that produces two separate sets of embedding charges, EE(L2). The results from our tests show that indeed electronic embedding with constrained-fitted charges tends to improve the performance of ONIOM compared to non-embedded calculations. However, the EE(L2) charges work best for transition energies, and the EE(L1) charges work best for oscillator strengths. This may be an indication that fixed point charges do not have enough flexibility to adapt to each system, and other effects (e.g., polarization of the embedding field) may be necessary.
AIP Publishing
http://aip.scitation.org/doi/10.1063/1.4972000
© The Authors 2016
openAccess
Point charge embedding for ONIOM excited states calculations
Article
Biancardi, Alessandro
Barnes, Jeremy
Caricato, Marco
Chemistry
Scholarly/refereed, publisher version
This item meets KU Open Access policy criteria.
oai:kuscholarworks.ku.edu:1808/226172019-04-12T14:17:30Zcom_1808_97col_1808_102
Linz, Thomas H.
Lunte, Susan M.
2017-01-12T19:27:47Z
2017-01-12T19:27:47Z
2015-06-21
Linz, Thomas H., and Susan M. Lunte. "Determination of Methylarginines in Infant Plasma by CE-LIF." Anal. Methods 6.12 (2014): 3990-994.
http://hdl.handle.net/1808/22617
10.1039/C4AY00340C
Methylarginines (MAs) are a class of nitric oxide synthase inhibitors that have been implicated in respiratory complications of critically ill infants. This paper describes the development of an analytical method to measure these compounds in the plasma of newborns using capillary electrophoresis (CE). The CE separation method was optimized to enable complete baseline resolution of the four MA analogues of interest. Sample preparation concerns for infant-derived samples were addressed by validating a heat-assisted extraction method for the analysis of low volume (≤100 µL) samples from a plasma matrix. It was determined that the sample matrix (plasma versus serum) did not affect the measured MA concentrations, while extracting smaller volumes of plasma that underwent heat-induced gelation afforded higher MA recoveries than larger volume samples. These methods were then applied to blood samples collected from infants housed in the neonatal intensive care unit. It was discovered that these newborns had significantly elevated concentrations of MAs at younger ages (< 6 months) while amounts were similar between infants 6 months old and adults. The data are preliminary, but demonstrate an interesting age dependence on the concentrations of these nitric oxide inhibitors, which has not been previously reported.
Royal Society of Chemistry
Determination of Methylarginines in Infant Plasma by CE-LIF
Article
openAccess
Lunte, Susan M.
Chemistry
Scholarly/refereed, author accepted manuscript
This item meets KU Open Access policy criteria.
oai:kuscholarworks.ku.edu:1808/309262020-11-26T09:00:51Zcom_1808_97com_1808_80col_1808_102col_1808_81
Angalakurthi, Siva Krishna
Vance, David J.
Rong, Yinghui
Nguyen, Chi My Thi
Rudolph, Michael J.
Volkin, David
Middaugh, C. Russell
Weis, David D.
Mantis, Nicholas J.
2020-11-25T15:03:38Z
2020-11-25T15:03:38Z
2018-12-17
Angalakurthi, S. K., Vance, D. J., Rong, Y., Nguyen, C., Rudolph, M. J., Volkin, D., Middaugh, C. R., Weis, D. D., & Mantis, N. J. (2018). A Collection of Single-Domain Antibodies that Crowd Ricin Toxin's Active Site. Antibodies (Basel, Switzerland), 7(4), 45. https://doi.org/10.3390/antib7040045
http://hdl.handle.net/1808/30926
10.3390/antib7040045
https://orcid.org/0000-0002-9913-7722
https://orcid.org/0000-0003-3032-1211
https://orcid.org/0000-0002-5083-8640
PMC6374049
This work is licensed under a Creative Commons Attribution 4.0 International License.
In this report, we used hydrogen exchange-mass spectrometry (HX-MS) to identify the epitopes recognized by 21 single-domain camelid antibodies (VHHs) directed against the ribosome-inactivating subunit (RTA) of ricin toxin, a biothreat agent of concern to military and public health authorities. The VHHs, which derive from 11 different B-cell lineages, were binned together based on competition ELISAs with IB2, a monoclonal antibody that defines a toxin-neutralizing hotspot (“cluster 3”) located in close proximity to RTA’s active site. HX-MS analysis revealed that the 21 VHHs recognized four distinct epitope subclusters (3.1–3.4). Sixteen of the 21 VHHs grouped within subcluster 3.1 and engage RTA α-helices C and G. Three VHHs grouped within subcluster 3.2, encompassing α-helices C and G, plus α-helix B. The single VHH in subcluster 3.3 engaged RTA α-helices B and G, while the epitope of the sole VHH defining subcluster 3.4 encompassed α-helices C and E, and β-strand h. Modeling these epitopes on the surface of RTA predicts that the 20 VHHs within subclusters 3.1–3.3 physically occlude RTA’s active site cleft, while the single antibody in subcluster 3.4 associates on the active site’s upper rim.
National Institutes of Allergy and Infectious Diseases, National Institutes of Health (HHSN272201400021C)
MDPI
© 2018 by the authors. Licensee MDPI, Basel, Switzerland.
http://creativecommons.org/licenses/by/4.0/
openAccess
Toxin
Antibody
Camelid
Vaccine
Biodefense
Hydrogen exchange-mass spectrometry
A Collection of Single-Domain Antibodies that Crowd Ricin Toxin’s Active Site
Article
Angalakurthi, Siva Krishna
Volkin, David
Middaugh, C. Russell
Weis, David D.
Pharmaceutical Chemistry
Chemistry
Scholarly/refereed, publisher version
This item meets KU Open Access policy criteria.
oai:kuscholarworks.ku.edu:1808/159762019-04-12T14:39:46Zcom_1808_97col_1808_102
Son, Sang-Kil
Chu, Shih-I
2014-12-01T21:15:28Z
2014-12-01T21:15:28Z
2009-07-24
Son, Sang-Kil; Chu, Shih-I. (2009). "Multielectron effects on the orientation dependence and photoelectron angular distribution of multiphoton ionization of CO2 in strong laser fields." Physical Review A, 80(1)011403(R). http://dx.doi.org/10.1103/PhysRevA.80.011403.
1050-2947
http://hdl.handle.net/1808/15976
10.1103/PhysRevA.80.011403
This is the publisher's version, also available electronically from http://journals.aps.org/pra/abstract/10.1103/PhysRevA.80.011403.
We perform an ab initio study of multiphoton ionization (MPI) of carbon dioxide in intense linearly polarized laser pulses with arbitrary molecular orientation by means of a time-dependent density-functional theory (TDDFT) with proper long-range potential. We develop a time-dependent Voronoi-cell finite difference method with highly adaptive molecular grids for accurate solution of the TDDFT equations. Our results demonstrate that the orientation dependence of MPI is determined by multiple orbital contributions and that the electron correlation effects are significant. The maximum peak of MPI is predicted to be at 40° in good agreement with recent experimental data. Photoelectron angular distribution reveals the delicate relation between the orientation dependence and the molecular orbital symmetry.
American Physical Society
Multielectron effects on the orientation dependence and photoelectron angular distribution of multiphoton ionization of CO2 in strong laser fields
Article
openAccess
Chu, Shih-I
Chemistry
fullparticipation
Scholarly/refereed, publisher version
This item meets KU Open Access policy criteria.
oai:kuscholarworks.ku.edu:1808/234722019-04-12T14:25:00Zcom_1808_97col_1808_102
Rolfe, Alan
Samarakoon, Thiwanka Bandara
Hanson, Paul R.
2017-03-23T16:03:51Z
2017-03-23T16:03:51Z
2010-03-19
Rolfe, A., Samarakoon, T. B., & Hanson, P. R. (2010). Formal [4+3] Epoxide Cascade Reaction via a Complementary Ambiphilic Pairing Strategy. Organic Letters, 12(6), 1216–1219. http://doi.org/10.1021/ol100035e
http://hdl.handle.net/1808/23472
10.1021/ol100035e
A formal [4+3] epoxide cascade protocol utilizing ambiphilic sulfonamides and a variety of epoxides (masked ambiphiles) has been developed for the generation of benzothiaoxazepine-1,1′-dioxides and oxathiazepine-1,1′-dioxides. This protocol combines an epoxide ring-opening with either an SNAr or oxa-Michael cyclization pathway.
American Chemical Society
This document is the Accepted Manuscript version of a Published Work that appeared in final form in Organic Letters, copyright © American Chemical Society after peer review and technical editing by the publisher. To access the final edited and published work see http://dx.doi.org/10.1021/ol100035e
openAccess
Formal [4+3] Epoxide Cascade Reaction via a Complementary Ambiphilic Pairing Strategy
Article
Rolfe, Alan
Samarakoon, Thiwanka Bandara
Chemistry
Scholarly/refereed, author accepted manuscript
This item meets KU Open Access policy criteria.
oai:kuscholarworks.ku.edu:1808/158682019-04-12T14:50:54Zcom_1808_97col_1808_102
Chu, Shih-I
Datta, Krishna K.
2014-11-25T18:05:35Z
2014-11-25T18:05:35Z
1982-01-01
Chu, Shih-I. & Datta, Krishna K. "Studies of multichannel rotational predissociation of Ar–H2 van der Waals molecule by the complex‐coordinate coupled‐channel formalism." e Journal of Chemical Physics 76, 5307 (1982); http://dx.doi.org/10.1063/1.442929.
http://hdl.handle.net/1808/15868
10.1063/1.442929
This is the published version, also available here: http://dx.doi.org/10.1063/1.442929.
The complex‐coordinate coupled‐channel (CCCC) formalism previously developed [J. Chem. Phys. 72, 4772 (1980)] is applied to the accurate determination of the level widths (lifetimes) and energies of rotationally predissociating metastable Ar⋅⋅⋅H2 van der Waals molecules. Calculations are performed using several realistic anisotropic potentials obtained recently by experiments, including Lennard‐Jones (LJ), Buckingham–Corner (BC) type potentials, as well as the semiempirical potential of Tang–Toennies (TT). New numerical methods are introduced here to deal with the complex rotations of piecewise inhomogeneous potentials such as those of BC and TT. It is found that the CCCC method is capable of providing reliable results for any given potential surface. Furthermore, the CCCC results are sensitive to the potential surfaces used. For example, the linewidths predicted for different LJ potential surfaces considered here vary by a factor as large as 4. However, the agreement among more recent potentials, namely, the BC potential of Zandee and Reuss and that of Le Roy and Carley as well as the potential of Tang and Toennies, is much closer: the resonance energies agree to within 1 cm−1 and the linewidths to within 30%.
Elsevier
Semi empirical calculations
Predissociation
Anisotropy
Linewidths
Potential energy surfaces
Studies of multichannel rotational predissociation of Ar–H2 van der Waals molecule by the complexcoordinate coupledchannel formalism
Article
openAccess
Chu, Shih-I
Chemistry
na
Scholarly/refereed, publisher version
This item does not meet KU Open Access policy criteria.
oai:kuscholarworks.ku.edu:1808/160532019-04-12T14:45:43Zcom_1808_97col_1808_102
Hollars, Christopher W.
Dunn, Robert C.
2014-12-05T16:57:41Z
2014-12-05T16:57:41Z
2000-02-01
Hollars, Christopher W. & Dunn, Robert C. "Probing single molecule orientations in model lipid membranes with near-field scanning optical microscopy." J. Chem. Phys. 112, 7822 (2000); http://dx.doi.org/10.1063/1.481367.
http://hdl.handle.net/1808/16053
10.1063/1.481367
This is the published version, also available here: http://dx.doi.org/10.1063/1.481367.
Single molecule near-field fluorescence measurements are utilized to characterize the molecular level structure in Langmuir–Blodgett monolayers of L-α-dipalmitoylphosphatidylcholine (DPPC).Monolayers incorporating 3×10−4 mol % of the fluorescent lipid analog N-(6-tetramethylrhodaminethiocarbamoyl)-1,2-dihexadecanoyl-sn- glycero-3-phosphoethanolamine, triethylammonium salt (TRITC–DHPE) are transferred onto a freshly cleaved mica surface at low (π=8 mN/m) and high (π=30 mN/m)surfacepressures. The near-field fluorescence images exhibit shapes in the single molecule images that are indicative of the lipid analog probe orientation within the films. Modeling the fluorescence patterns yields the single molecule tilt angle distribution in the monolayers which indicates that the majority of the molecules are aligned with their absorption dipole moment pointed approximately normal to the membrane plane. Histograms of the data indicate that the average orientation of the absorption dipole moment is 2.2° (σ=4.8°) in monolayers transferred at π=8 mN/m and 2.4° (σ=5.0°) for monolayers transferred at π=30 mN/m. There is no statistical difference in the mean tilt angle or distribution for the two monolayer conditions studied. The insensitivity of tilt angle to filmsurfacepressure may arise from small chromophore doped domains of trapped liquid-expanded lipid phase remaining at high surfacepressure. There is no evidence in the near-field fluorescence images for probe molecules oriented with their dipole moment aligned parallel with the membrane plane. We do, however, find a small but significant population of probe molecules (∼13%) with tilt angles greater than 16°. Comparison of the simultaneously collected near-field fluorescence and force images suggests that these large angle orientations are not the result of significant defects in the films. Instead, this small population may represent a secondary insertion geometry for the probe molecule into the lipidmonolayer.
American Institute of Physics
Monolayers
Fluorescence
Lipids
Electric dipole moments
High pressure
Probing single molecule orientations in model lipid membranes with near-field scanning optical microscopy
Article
openAccess
Hollars, Christopher W.
Dunn, Robert C.
Chemistry
Scholarly/refereed, publisher version
This item does not meet KU Open Access policy criteria.
oai:kuscholarworks.ku.edu:1808/237272019-04-12T14:15:16Zcom_1808_97col_1808_102
Aksenov, Alexander V.
Smirnov, Alexander N.
Magedov, Igor V.
Reisenauer, Mary R.
Aksenov, Nicolai A.
Aksenova, Inna V.
Pendleton, Alexander L.
Nguyen, Gina
Johnston, Robert K.
Rubin, Michael
De Carvalho, Annelise
Kiss, Robert
Mathieu, Véronique
Lefranc, Florence
Correa, Jaime
Cavazos, David A.
Brenner, Andrew J.
Bryan, Brad A.
Rogelj, Snezna
Kornienko, Alexander
Frolova, Liliya V.
2017-04-18T17:31:19Z
2017-04-18T17:31:19Z
2015-03-12
Aksenov, A. V., Smirnov, A. N., Magedov, I. V., Reisenauer, M. R., Aksenov, N. A., Aksenova, I. V., … Frolova, L. V. (2015). Activity of 2-Aryl-2-(3-indolyl)acetohydroxamates Against Drug-Resistant Cancer Cells. Journal of Medicinal Chemistry, 58(5), 2206–2220. http://doi.org/10.1021/jm501518y
http://hdl.handle.net/1808/23727
10.1021/jm501518y
https://orcid.org/0000-0002-1668-9311
Many types of tumor, including glioma, melanoma, non-small cell lung, esophageal, head and neck cancer, among others, are intrinsically resistant to apoptosis induction and poorly responsive to current therapies with proapoptotic agents. In addition, tumors often develop multi-drug resistance based on the cellular efflux of chemotherapeutic agents. Thus, novel anticancer agents capable of overcoming these intrinsic or developed tumor resistance mechanisms are urgently needed. We describe a series of 2-aryl-2-(3-indolyl)acetohydroxamic acids, which are active against apoptosis- and multidrug-resistant cancer cells as well as glioblastoma neurosphere stem-like cell cultures derived from patients. Thus, the described compounds serve as a novel chemical scaffold for the development of potentially highly effective clinical cancer drugs.
American Chemical Society
This document is the Accepted Manuscript version of a Published Work that appeared in final form in the Journal of Medicinal Chemistry, copyright © American Chemical Society after peer review and technical editing by the publisher. To access the final edited and published work see http://dx.doi.org/10.1021/jm501518y.
openAccess
Activity of 2-Aryl-2-(3-indolyl)acetohydroxamates Against Drug-Resistant Cancer Cells
Article
Rubin, Michael
Chemistry
Scholarly/refereed, author accepted manuscript
This item meets KU Open Access policy criteria.
oai:kuscholarworks.ku.edu:1808/161412019-04-12T14:46:10Zcom_1808_97col_1808_102
Sibug-Aga, Rachel
Laird, Brian Bostian
2014-12-17T15:39:09Z
2014-12-17T15:39:09Z
2002-10-15
Sibug-Aga, Rachel; Laird, Brian Bostian. (2002). "Structure and dynamics of the interface between a binary hard-sphere crystal of NaCl type and its coexisting binary fluid." Physical Review B, 66(14):14106. http://dx.doi.org/10.1103/PhysRevB.66.144106.
1098-0124
http://hdl.handle.net/1808/16141
10.1103/PhysRevB.66.144106
This is the publisher's version, also available electronically from http://journals.aps.org/prb/abstract/10.1103/PhysRevB.66.144106.
Molecular-dynamics simulations are performed to study the [100] and [111] orientations of the crystal-melt interface between an ordered two-component hard sphere with an NaCl structure and its coexisting binary hard-sphere fluid. The diameter ratio of the two types of hard spheres making up the mixture is α=0.414. This work complements our earlier interface simulations [J. Chem. Phys. 116, 3410 (2002)] for the same diameter ratio at lower pressures where the smaller component is immiscible in the solid and the fluid mixture coexists with a pure fcc crystal of large particles. Density profiles and diffusion coefficient profiles are presented for the AB interfacial system. We find that for this system, the transition from crystallike to fluidlike behavior of both the density and diffusion constant profiles occurs over a narrower region than that seen in our previous studies of the fcc/binary fluid system. But similar to what was found in the fcc/binary fluid interface the transition region for the large particle diffusion constant is shifted about 1.0σA toward the fluid phase relative to that for the small particles.
American Physical Society
Structure and dynamics of the interface between a binary hard-sphere crystal of NaCl type and its coexisting binary fluid
Article
openAccess
Sibug-Aga, Rachel
Laird, Brian Bostian
Chemistry
Scholarly/refereed, publisher version
This item does not meet KU Open Access policy criteria.
oai:kuscholarworks.ku.edu:1808/236962019-04-12T14:14:00Zcom_1808_97col_1808_102
Chang, Cindy M.
Klema, Valerie J.
Johnson, Bryan J.
Mure, Minae
Klinman, Judith P.
Wilmont, Carrie M.
2017-04-13T17:45:11Z
2017-04-13T17:45:11Z
2010-03-23
Chang, C. M., Klema, V. J., Johnson, B. J., Mure, M., Klinman, J. P., & Wilmot, C. M. (2010). Kinetic and Structural Analysis of Substrate Specificity in Two Copper Amine Oxidases from Hansenula polymorpha,. Biochemistry, 49(11), 2540–2550. http://doi.org/10.1021/bi901933d
http://hdl.handle.net/1808/23696
10.1021/bi901933d
The structural underpinnings of enzyme substrate specificity are investigated in a pair of copper amine oxidases (CAOs) from Hansenula polymorpha (HPAO-1 and HPAO-2). The X-ray crystal structure (to 2.0 Å resolution) and steady state kinetic data of the second copper amine oxidase (HPAO-2) are presented for comparison to HPAO-1. Despite 34 % sequence identity and superimposable active site residues implicated in catalysis, the enzymes vary considerably in their substrate entry channel. The previously studied CAO, HPAO-1, has a narrow substrate channel. In contrast HPAO-2 has a wide funnel-shaped substrate channel, which also contains a side-chamber. In addition, there are a number of amino acid changes within the channels of HPAO-2 and HPAO-1 that may sterically impact the ability of substrates to form covalent Schiff base catalytic intermediates and to initiate chemistry. These differences can partially explain the greatly different substrate specificities as characterized by kcat/Km value differences: in HPAO-1, the kcat/Km for methylamine is 330-fold greater than for benzylamine, whereas in HPAO-2 it is benzylamine that is the better substrate by 750-fold. In HPAO-2 an inflated Dkcat/Km(methylamine) in relation to Dkcat/Km(benzylamine) indicates that proton abstraction has been impeded more than substrate release. In HPAO-1, Dkcat/Km(S) changes little with the slow substrate, and indicates a similar increase in the energy barriers that control both substrate binding and subsequent catalysis. In neither case is kcat/Km for the second substrate, O2, significantly altered. These results reinforce the modular nature of the active sites of CAOs and show that multiple factors contribute to substrate specificity and catalytic efficiency. In HPAO-1, the enzyme with the smaller substrate binding pocket, both initial substrate binding and proton loss are affected by an increase in substrate size, while in HPAO-2, the enzyme with the larger substrate binding pocket, the rate of proton loss is differentially affected when a phenyl substituent in substrate is reduced to the size of a methyl group.
ACS
Copyright © 2010 American Chemical Society
openAccess
Kinetic and Structural Analysis of Substrate Specificity in Two Copper Amine Oxidases from Hansenula polymorpha
Article
Mure, Minae
Chemistry
Scholarly/refereed, author accepted manuscript
This item meets KU Open Access policy criteria.
oai:kuscholarworks.ku.edu:1808/236832019-04-12T14:13:55Zcom_1808_97col_1808_102
Culpepper, Megen A.
Scott, Emily E.
Limburg, Julian
2017-04-13T16:00:47Z
2017-04-13T16:00:47Z
2010-01-12
Culpepper, M. A., Scott, E. E., & Limburg, J. (2010). CRYSTAL STRUCTURE OF PROLYL 4-HYDROXYLASE FROM BACILLUS ANTHRACIS. Biochemistry, 49(1), 124–133. http://doi.org/10.1021/bi901771z
http://hdl.handle.net/1808/23683
10.1021/bi901771z
Prolyl 4-hydroxylases (P4H) catalyze the posttranslational hydroxylation of proline residues and play a role in collagen production, hypoxia response, and cell wall development. P4Hs belong to the Fe(II)/αKG oxygenases and require Fe(II), α-ketoglutarate (αKG), and O2 for activity. We report the 1.40 Å structure of a P4H from Bacillus anthracis, the causative agent of anthrax, whose immunodominant exosporium protein BclA contains collagen-like repeat sequences. The structure reveals the double stranded β-helix core fold characteristic of Fe(II)/αKG oxygenases. This fold positions Fe-binding and αKG-binding residues in what is expected to be catalytically-competent orientations and is consistent with proline peptide substrate binding at the active site mouth. Comparisons of the anthrax-P4H structure with Cr-P4H-1 structures reveal similarities in a peptide surface groove. However, sequence and structural comparisons suggest differences in conformation of adjacent loops may change the interaction with peptide substrates. These differences may be the basis of substantial disparity between the KM values for the Cr-P4H-1 vs. the anthrax and human P4H enzymes. Additionally, while previous structures of P4H enzymes are monomers, Bacillus anthracis P4H forms an α2 homodimer and suggests residues important for interactions between the α2 subunits of the α2β2 human collagen P4H. Thus the anthrax-P4H structure provides insight into the structure and function of the α subunit of human-P4H, which may aid in the development of selective inhibitors of the human-P4H enzyme involved in fibrotic disease.
ACS
Copyright © 2009 American Chemical Society
openAccess
Crystal Structure of Prolyl 4-Hydroxylase from Bacillus anthracis
Article
Culpepper, Megan A.
Scott, Emily E.
Limburg, Julian
Chemistry
Medicinal Chemistry
Scholarly/refereed, author accepted manuscript
This item meets KU Open Access policy criteria.
oai:kuscholarworks.ku.edu:1808/133922018-11-15T16:34:23Zcom_1808_97col_1808_102
Desaire, Heather
Haynes, Barton F.
Go, Eden P.
Liao, Hua-Xin
Sutherland, Laura L.
Chang, Qing
Zhang, Ying
Irungu, Janet W.
Alam, S. Munir
2014-04-02T15:20:45Z
2014-04-02T15:20:45Z
2009-10-22
Desaire, H, BF Haynes, EP Go, H Liao, LL Sutherland, Q Chang, Y Zhang, J Irungu, and SM Alam. 2009. “P20-08. Glycosylation: An Important Factor in Env Diversity.” Retrovirology 6:P378. http://dx.doi.org/10.1186/1742-4690-6-S3-P378.
http://hdl.handle.net/1808/13392
10.1186/1742-4690-6-S3-P378
Supported by a CAVD Grant from the Bill and Melinda Gates Foundation.
BioMed Central
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
http://creativecommons.org/licenses/by/2.0
openAccess
P20-08. Glycosylation: an important factor in Env diversity
Article
Desaire, Heather
Go, Eden P.
Chang, Q
Zhang, Y
Irungu, J
Department of Chemistry
Scholarly/refereed, publisher version
This item meets KU Open Access policy criteria.
oai:kuscholarworks.ku.edu:1808/232252019-04-12T14:22:14Zcom_1808_97col_1808_102
Asad, Naeem
Hanson, Paul R.
Long, Toby R.
Rayabarapu, Dinesh Kumar
Rolfe, Alan
2017-02-22T21:04:59Z
2017-02-22T21:04:59Z
2012-09-07
Asad, Naeem, Paul R. Hanson, Toby R. Long, Dinesh K. Rayabarapu, and Alan Rolfe. "Synthesis of Epoxybenzo[d]isothiazole 1,1-dioxides via a Reductive-Heck, Metathesis-sequestration Protocol." Chemical Communications 47.33 (2011): 9528.
http://hdl.handle.net/1808/23225
10.1039/c1cc12503f
https://orcid.org/0000-0001-6871-5270
An atom-economical purification protocol, using solution phase processing via ring-opening metathesis polymerization (ROMP) has been developed for the synthesis of tricyclic sultams. This chromatography-free method allows for convenient isolation of reductive-Heck products and reclamation of excess starting material via sequestration involving metathesis catalysts and a catalyst-armed Si-surface.
Royal Society of Chemistry
Synthesis of epoxybenzo[d]isothiazole 1,1-dioxides via a reductive-Heck, metathesis-sequestration protocol
Article
openAccess
Hanson, Paul R.
Chemistry
Scholarly/refereed, author accepted manuscript
This item meets KU Open Access policy criteria.
oai:kuscholarworks.ku.edu:1808/235002019-04-12T14:25:15Zcom_1808_97col_1808_102
Kusuma, Bhaskar Reddy
Brandt, Gary E. L.
Blagg, Brian S. J.
2017-03-28T18:06:05Z
2017-03-28T18:06:05Z
2012-12-21
Kusuma, B. R., Brandt, G. E. L., & Blagg, B. S. J. (2012). Synthesis of Cruentaren A. Organic Letters, 14(24), 6242–6245. http://doi.org/10.1021/ol302999v
http://hdl.handle.net/1808/23500
10.1021/ol302999v
Cruentaren A, an antifungal benzolactone produced by the myxobacterium Byssovorax cruenta, is highly cytotoxic against various human cancer cell lines and a highly selective inhibitor of mitochondrial F-ATPase. A convergent and efficient synthesis of cruentaren A is reported, based upon a diastereoselective alkylation, a series of stereoselective aldol reactions utilizing Myers’ pseudoephedrine propionamide, an acyl bromide–mediated esterification and a ring-closing metathesis (RCM) as the key steps. The RCM reaction was applied for the first time towards the total synthesis of cruentaren A, which led to a convergent and efficient synthesis of the natural product.
American Chemical Society
This document is the Accepted Manuscript version of a Published Work that appeared in final form in Organic Letters, copyright © American Chemical Society after peer review and technical editing by the publisher. To access the final edited and published work see http://dx.doi.org/10.1021/ol302999v.
openAccess
Synthesis of Cruentaren A
Article
Kusuma, Bhaskar Reddy
Brandt, Gary E. L.
Blagg, Brain S. J.
Chemistry
Scholarly/refereed, author accepted manuscript
This item meets KU Open Access policy criteria.
oai:kuscholarworks.ku.edu:1808/235622019-04-12T14:25:12Zcom_1808_97col_1808_102
Clark, Daniel Forrest
Go, Eden P.
Desaire, Heather
2017-03-31T20:56:15Z
2017-03-31T20:56:15Z
2013-01-03
Clark, D. F., Go, E. P., & Desaire, H. (2013). A Simple Approach to Assign Disulfide Connectivity Using Extracted Ion Chromatograms of Electron Transfer Dissociation Spectra. Analytical Chemistry, 85(2), 1192–1199. http://doi.org/10.1021/ac303124w
http://hdl.handle.net/1808/23562
10.1021/ac303124w
Increasing interest in production of protein-based pharmaceuticals (biotherapeutics) is accompanied by an increased need for verification of protein folding and correct disulfide bonding. Recombinant protein expression may produce aberrant disulfide bonds and could result in safety concerns or decreased efficacy. Thus, the thorough analysis of disulfide bonding is a necessity for protein therapeutics. The use of ETD facilitates this analysis because disulfide bonds are preferentially cleaved when subjected to ETD. Here, we make use of this well-characterized reaction to assign disulfide bonding networks by coupling the use of extracted ion chromatograms (XICs) of cysteine-containing peptides with ETD analysis to produce an efficient assignment approach for disulfide bonding. This method can be used to assign a disulfide pattern in a de novo fashion, to detect disulfide shuffling, and to provide information on heterogeneity, when more than one disulfide bonding pattern is present. The method was applied for assigning the disulfide-bonding network of a recombinant monomer of the HIV envelope protein gp120. It was found that one region of the protein, the V1/V2 loops, had significant heterogeneity in the disulfide bonds.
American Chemistry Society
© 2012 American Chemical Society
openAccess
A Simple Approach to Assign Disulfide Connectivity Using Extracted Ion Chromatograms of Electron Transfer Dissociation Spectra
Article
Go, Eden
Desaire, Heather
Chemistry
Scholarly/refereed, author accepted manuscript
This item meets KU Open Access policy criteria.
oai:kuscholarworks.ku.edu:1808/244812018-12-06T19:38:46Zcom_1808_97col_1808_102
Zang, Qin
Javed, Salim
Zhou, Aihua
Knudtson, Christopher Anton
Bi, Danse
Basha, Fatima Z.
Hanson, Paul R.
2017-06-13T15:41:32Z
2017-06-13T15:41:32Z
2012-12-31
Zang, Q., Javed, S., Zhou, A., Knudtson, C. A., Bi, D., Basha, F. Z., & Hanson, P. R. (2012). Synthesis of a Library of 1,5,2-Dithiazepine 1,1-Dioxides. Part 2: Routes to Bicyclic Sultams. Heterocycles, 86(2), 10.3987/COM–12–S(N)122. http://doi.org/10.3987/COM-12-S(N)122
http://hdl.handle.net/1808/24481
10.3987/COM-12-S(N)122.
PMC3873775
The synthesis of a library of bicyclic sultams incorporating the 1,5,2-dithiazepine 1,1-dioxide moiety is reported. Following scaffold synthesis via a one-pot sulfonylation/intramolecular thia-Michael protocol, several additional cyclization strategies have been realized enabling access to new bicyclic sultams.
Elsevier
This is an open access article under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs License 4.0 (CC BY-NC-ND 4.0), which permits use and distribution in any medium, provided the original work is properly cited, the use is non-commercial and no modifications or adaptations are made.
http://creativecommons.org/licenses/by-nc-nd/4.0/
openAccess
Synthesis of a Library of 1,5,2-Dithiazepine 1,1-Dioxides. Part 2: Routes to Bicyclic Sultams
Article
Zang, Qin
Javed, Salim
Zhou, Aihua
Knudtson, Chris A.
Bi, Danse
Hanson, Paul R.
Chemistry
Scholarly/refereed, author accepted manuscript
This item meets KU Open Access policy criteria.
oai:kuscholarworks.ku.edu:1808/234952018-12-18T19:48:58Zcom_1808_97col_1808_102
Rumi-Masante, Julie
Rusinga, Farai Ivan
Lester, Terrence E.
Dunlap, Tori B.
Williams, Todd D.
Dunker, A. Keith
Weis, David D.
Creamer, Trevor P.
2017-03-27T21:23:22Z
2017-03-27T21:23:22Z
2011-11-12
Rumi-Masante, Julie, Farai I. Rusinga, Terrence E. Lester, Tori B. Dunlap, Todd D. Williams, A. Keith Dunker, David D. Weis, and Trevor P. Creamer. "Structural Basis for Activation of Calcineurin by Calmodulin." Journal of Molecular Biology 415.2 (2012): 307-17.
http://hdl.handle.net/1808/23495
10.1016/j.jmb.2011.11.008
The highly conserved phosphatase calcineurin plays vital roles in numerous processes including T-cell activation, development and function of the central nervous system, and cardiac growth. It is activated by the calcium sensor calmodulin. Calmodulin binds to a regulatory domain within calcineurin, causing a conformational change that displaces an autoinhibitory domain from the active site, resulting in activation of the phosphatase. This is the same general mechanism by which calmodulin activates calmodulin-dependent protein kinases. Previously published data has hinted that the regulatory domain of calcineurin is intrinsically disordered. In this work we demonstrate that the regulatory domain is unstructured and that it folds upon binding calmodulin, ousting the autoinhibitory domain from the catalytic site. The regulatory domain is 95 residues long, with the autoinhibitory domain attached to its C-terminal end and the 24 residue calmodulin binding region towards the N-terminal end. This is unlike the calmodulin-dependent protein kinases which have calmodulin binding sites and autoinhibitory domains immediately adjacent in sequence. Our data demonstrate that not only does the calmodulin binding region fold, but that an ~25-30 residue region between it and the autoinhibitory domain also folds, resulting in over half of the regulatory domain adopting α-helical structure. This appears to be the first observation of calmodulin inducing folding of this scale outside of its binding site on a target protein.
Elsevier
This is an open access article under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs License 3.0 (CC BY-NC-ND 3.0 US), which permits use and distribution in any medium, provided the original work is properly cited, the use is non-commercial and no modifications or adaptations are made.
http://creativecommons.org/licenses/by-nc-nd/3.0/
openAccess
Structural basis for activation of calcineurin by calmodulin
Article
Weis, David D.
Chemistry
Scholarly/refereed, author accepted manuscript
This item meets KU Open Access policy criteria.
oai:kuscholarworks.ku.edu:1808/160722019-04-12T14:45:55Zcom_1808_97col_1808_102
Ho, Tak-San
Laughlin, Cecil
Chu, Shih-I
2014-12-10T17:55:53Z
2014-12-10T17:55:53Z
1985-07-01
Ho, Tak-San; Laughlin, Cecil; Chu, Shih-I. (1985). "Laser-assisted charge-transfer reactions (Li(3)(+)+H): Coupled dressed-quasimolecular-state approach." Physical Review A, 32(01):122. http://dx.doi.org/10.1103/PhysRevA.32.122
1050-2947
http://hdl.handle.net/1808/16072
10.1103/PhysRevA.32.122
This is the publisher's version, also available electronically from http://journals.aps.org/pra/abstract/10.1103/PhysRevA.32.122.
A semiclassical coupled dressed-quasimolecular-states (DQMS) approach is presented for nonperturbative treatment of multichannel charge-transfer reactions at low collision velocities and high laser intensities, incorporating the implementation of the generalized Van Vleck (GVV) nearly degenerate perturbation theory. The GVV technique allows block partitioning of the infinite-dimensional Floquet Hamiltonian into a finite-dimensional model DQMS space, and thereby reduces greatly the number of effective coupled channels. Further, the GVV-Floquet basis allows minimization of the (usually large in amplitude) field-induced nonadiabatic radial couplings without the need to explicitly construct the transformation between the adiabatic and diabatic DQMS basis. This yields a new set of coupled GVV-DQMS equations (neither adiabatic nor diabatic) which are particularly convenient for multichannel calculations. The method is applied to the study of the laser-assisted charge-transfer process: Li(3+)+H(1s)+ħω→Li(2)+(n= 3)+H(+), using 2-, 5-, and 15- GVV-DQMS basis. It is found that while the 5-state results agree well with the 15-state calculations even up to very high intensities for the (LiH)3+ system, the 2-state basis is inadequate at high-intensity and lower-wavelength regimes. Detailed results and nonlinear dynamical features are presented for the process at small impact velocity 10(7) cm/s and strong laser fields with intensity ranging from 1 to 100 TW/cm(2) and wavelengths from 1500 to 3000 Å.
American Physical Society
Laser-assisted charge-transfer reactions (Li(3)(+)+H): Coupled dressed-quasimolecular-state approach
Article
openAccess
Ho, Tak-San
Laughlin, Cecil
Chu, Shih-I
Chemistry
Scholarly/refereed, publisher version
This item does not meet KU Open Access policy criteria.
oai:kuscholarworks.ku.edu:1808/240792018-11-01T15:58:15Zcom_1808_97col_1808_102
Frankowski, Kevin J.
Slauson, Stephen R.
Movell, Kimberly M.
Phillips, Angela M.
Streicher, John M.
Zhou, Lei
Whipple, David A.
Schoenen, Frank J.
Prisinzano, Thomas E.
Bohn, Laura M.
Aubé, Jeffrey
2017-05-10T18:26:15Z
2017-05-10T18:26:15Z
2015-07-15
Frankowski, K. J., Slauson, S. R., Lovell, K. M., Phillips, A. M., Streicher, J. M., Zhou, L., … Aubé, J. (2015). Potency enhancement of the κ-opioid receptor antagonist probe ML140 through sulfonamide constraint utilizing a tetrahydroisoquinoline motif. Bioorganic & Medicinal Chemistry, 23(14), 3948–3956. http://doi.org/10.1016/j.bmc.2014.12.033
http://hdl.handle.net/1808/24079
10.1016/j.bmc.2014.12.033
https://orcid.org/0000-0003-1049-5767
https://orcid.org/0000-0002-2811-2894
PMC4468036
Optimization of the sulfonamide-based kappa opioid receptor (KOR) antagonist probe molecule ML140 through constraint of the sulfonamide nitrogen within a tetrahydroisoquinoline moiety afforded a marked increase in potency. This strategy, when combined with additional structure-activity relationship exploration, has led to a compound only six-fold less potent than norBNI, a widely utilized KOR antagonist tool compound, but significantly more synthetically accessible. The new optimized probe is suitably potent for use as an in vivo tool to investigate the therapeutic potential of KOR antagonists.
Elsevier
This article is made available under a Creative Commons Attribution-NonCommercial-NoDerivs 3.0 Unported (CC BY-NC-ND 3.0) License.
https://creativecommons.org/licenses/by-nc-nd/3.0/
openAccess
Kappa Opioid Receptor
Antagonist
Molecular constraint
Potency enhancement
Tetrahydroisoquinoline
Potency enhancement of the κ-opioid receptor antagonist probe ML140 through sulfonamide constraint utilizing a tetrahydroisoquinoline motif
Article
Frankowski, Kevin J.
Slauson, Stephen R.
Whipple, David A.
Schoenen, Frank J.
Prisinzano, Thomas E.
Aubé, Jeffrey
Specialized Chemistry Center
Scholarly/refereed, author accepted manuscript
This item meets KU Open Access policy criteria.
oai:kuscholarworks.ku.edu:1808/157292019-04-12T14:45:40Zcom_1808_97com_1808_8219col_1808_102col_1808_8220
Hossain, Alamgir
Powell, Douglas R.
Bowman-James, Kristin
2014-11-12T21:00:43Z
2014-11-12T21:00:43Z
2003-01-17
Hossain, Md. A., Powell, D. R. and Bowman-James, K. (2003), A potassium crown ether complex with dichloroaurate(I). Acta Crystallographica E, 59: m57–m58. http://dx.doi.org/10.1107/S1600536803000813.
http://hdl.handle.net/1808/15729
10.1107/S1600536803000813
https://orcid.org/0000-0001-7133-468X
This is the published version, also available here: http://dx.doi.org/10.1107/S1600536803000813.
The title compound, (1,4,7,10,13,16-hexaoxacyclooctane)potassium dichloroaurate(I), [K(C12H24O6)][AuCl2], consists of potassium ion encapsulated by the 18-membered crown ether 1,4,7,10,13,16-hexaoxacyclooctane and a linear dichloroaurate(I) monoanion. The potassium occupies a crystallographic center of symmetry with a ring coordination number of six, and two chlorides in axial sites at a distance of 3.2306 (5) Å. The linear anionic species sits on another crystallographic center of symmetry.
International Union of Crystallography
Single-crystal X-ray Study
T = 100 K
Mean (c±c) = 0.002aê
R Factor = 0.017
Wr Factor = 0.047
Data-to-parameter Ratio = 27.2
A potassium crown ether complex with dichloroaurate(I)
Article
openAccess
Hossain, Almgir
Powell, Douglas R.
Bowman-James, Kristin
Chemistry
Scholarly/refereed, publisher version
This item does not meet KU Open Access policy criteria.
oai:kuscholarworks.ku.edu:1808/158392019-04-12T14:50:43Zcom_1808_97col_1808_102
Chu, Shih-I
Wang, Kwanghsi
2014-11-21T18:46:25Z
2014-11-21T18:46:25Z
1987-08-15
Wang, Kwanghsi & Chu, Shih-I. "Floquet–Liouville supermatrix approach. II. Intensity‐dependent generalized nonlinear optical susceptibilities." The Journal of Chemical Physics 86, 3225 (1987); http://dx.doi.org/10.1063/1.451981.
http://hdl.handle.net/1808/15839
10.1063/1.451981
This is the published version, also available here: http://dx.doi.org/10.1063/1.451981
We present a practical n o n p e r t u r b a t i v e method for e x a c t treatment of i n t e n s i t y‐d e p e n d e n t generalized nonlinear optical susceptibilities χ(ω) in intense polychromatic fields, valid for arbitrary laser intensities, detunings, and relaxation. By means of the many‐mode Floquet theory, the time‐dependent Liouville equation can be transformed into an equivalent t i m e‐i n d e p e n d e n t infinite‐dimensional Floquet–Liouville supermatrix (FLSM) eigenvalue problem. It is then shown that the nonlinear optical susceptibilities χ(ω) can be completely determined simply from the supereigenvalues and eigenfunctions of the Floquet–Liouvillian L̂ F . In addition to this exact FLSM approach, we have also presented higher‐order perturbative results, based on the extension of the Salwen’s nearly degenerate perturbation theory, appropriate for somewhat weaker fields and near‐resonant multiphoton processes, but beyond the conventional perturbative or rotating wave approximation (RWA). In the case of two‐level systems, for example, the implementation of Salwen’s method in the time‐independent L̂ F allows the reduction of the infinite‐dimensional FLSM into a 4×4 dimensional effective Hamiltonian, from which essential a n a l y t i c a l formulas for intensity‐dependent χ(ω) can be obtained. These methods are applied to a detailed study of intensity‐dependent spectralline shapes (such as hole burning and extra resonance peaks at the line center, and the effects of saturation, detuning, and radiative and collisional damping, etc.) and subharmonic structures in nonlinear multiple wave mixings χ[(m+1)ω1−mω2] for two‐level systems in intense linearly polarized bichromatic fields.
AIP Publishing
Nonlinear optical susceptibility
Atomic line shapes
Eigenvalues
Multiphoton processes
Multiple resonance spectra
Floquet–Liouville supermatrix approach. II. Intensity‐dependent generalized nonlinear optical susceptibilities
Article
openAccess
Chu, Shih-I
Chemistry
na
Scholarly/refereed, publisher version
This item does not meet KU Open Access policy criteria.
oai:kuscholarworks.ku.edu:1808/231962018-07-16T17:41:10Zcom_1808_97col_1808_102
Ortiz, Andrea Naomi
Kurth, Benjamin J.
Osterhaus, Gregory L.
Johnson, Michael A.
2017-02-16T20:17:08Z
2017-02-16T20:17:08Z
2011-03-29
Ortiz, A. N., Kurth, B. J., Osterhaus, G. L., & Johnson, M. A. (2011). Impaired dopamine release and uptake in R6/1 Huntington’s disease model mice. Neuroscience Letters, 492(1), 11–14. http://doi.org/10.1016/j.neulet.2011.01.036
http://hdl.handle.net/1808/23196
10.1016/j.neulet.2011.01.036
Huntington’s disease (HD) is a progressive, neurodegenerative movement disorder. Here, we used fast-scan cyclic voltammetry to measure dopamine release and uptake in striatal brain slices from R6/1 HD model mice. Peak dopamine release ([DA]max) was significantly diminished in R6/1 mice (52% of wild-type at 24 weeks of age). Similarly, dopamine released per locally applied electrical stimulus pulse ([DA]p), which is [DA]max corrected for uptake and electrode performance, was also diminished in R6/1 mice (43% of wild-type by 24 weeks of age). Moreover, Vmax, the maximum rate of dopamine uptake, obtained by modeling the stimulated release plots, was decreased at 16 and 24 weeks of age in R6/1 mice (51 and 48% of wild-type, respectively). Thus, impairments in both dopamine release and uptake appear to progress in an age-dependent manner in R6/1 mice.
Elsevier
This is an open access article under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs License 3.0 (CC BY-NC-ND 3.0 US), which permits use and distribution in any medium, provided the original work is properly cited, the use is non-commercial and no modifications or adaptations are made.
http://creativecommons.org/licenses/by-nc-nd/4.0/
openAccess
Dopamine
Voltammetry
Huntington’s disease
R6/1 mice
Release
Uptake
Impaired dopamine release and uptake in R6/1 Huntington's disease model mice
Article
Ortiz, Andrea N.
Kurth, Benjamin J.
Osterhaus, Gregory L.
Johnson, Michael A.
Chemistry
Scholarly/refereed, author accepted manuscript
This item meets KU Open Access policy criteria.
oai:kuscholarworks.ku.edu:1808/222672019-04-12T14:16:28Zcom_1808_97col_1808_102
Harvey, Jacob A.
Thompson, Ward H.
2016-12-19T21:23:07Z
2016-12-19T21:23:07Z
2015-07
Harvey, J. A., & Thompson, W. H. (2015). Solute location in a nanoconfined liquid depends on charge distribution. J. Chem. Phys., 143(4), 044701. doi:10.1063/1.4926936
http://hdl.handle.net/1808/22267
10.1063/1.4926936
Nanostructured materials that can confine liquids have attracted increasing attention for their diverse properties and potential applications. Yet, significant gaps remain in our fundamental understanding of such nanoconfined liquids. Using replica exchange molecular dynamics simulations of a nanoscale, hydroxyl-terminated silica pore system, we determine how the locations explored by a coumarin 153 (C153) solute in ethanol depend on its charge distribution, which can be changed through a charge transfer electronic excitation. The solute position change is driven by the internal energy, which favors C153 at the pore surface compared to the pore interior, but less so for the more polar, excited-state molecule. This is attributed to more favorable non-specific solvation of the large dipole moment excited-state C153 by ethanol at the expense of hydrogen-bonding with the pore. It is shown that a change in molecule location resulting from shifts in the charge distribution is a general result, though how the solute position changes will depend upon the specific system. This has important implications for interpreting measurements and designing applications of mesoporous materials.
AIP Publishing
© 2015 AIP Publishing LLC
openAccess
Excited States
Free Energy
Ground States
Solvents
Hydrogen Bonding
Solute location in a nanoconfined liquid depends on charge distribution
Article
Harvey, Jacob A.
Thompson, Ward H.
Chemistry
Scholarly/refereed, publisher version
This item meets KU Open Access policy criteria.
oai:kuscholarworks.ku.edu:1808/167382018-07-13T16:37:46Zcom_1808_97col_1808_102
Sheu, Yae-Lin
Hsu, Liang-Yan
Wu, Hau-tieng
Li, Peng-Cheng
Chu, Shih-I
2015-02-20T19:30:13Z
2015-02-20T19:30:13Z
2014-11-26
Sheu, Y., Hsu, L.-Y., Wu, H., Li, P.-C., & Chu, S.-I. (2014). A new time-frequency method to reveal quantum dynamics of atomic hydrogen in intense laser pulses: Synchrosqueezing transform. AIP Advances, 4(11), 117138.
http://dx.doi.org/10.1063/1.4903164
http://hdl.handle.net/1808/16738
10.1063/1.4903164
This study introduces a new adaptive time-frequency (TF) analysis technique, the synchrosqueezing transform (SST), to explore the dynamics of a laser-driven hydrogen atom at an ab initio level, upon which we have demonstrated its versatility as a new viable venue for further exploring quantum dynamics. For a signal composed of oscillatory components which can be characterized by instantaneous frequency, the SST enables rendering the decomposed signal based on the phase information inherited in the linear TF representation with mathematical support. Compared with the classical type of TF methods, the SST clearly depicts several intrinsic quantum dynamical processes such as selection rules, AC Stark effects, and high harmonic generation.
This work was supported by the National Science Council and National Taiwan University (Grant No. 103R8700-2 and 103R104021). The authors would also like to thank Dr. Han-Chih Chang from Department of Physics in University ofWashington at Seattle for their valuable suggestions.
AIP publishing
C 2014 Author(s). All article content, except where otherwise noted, is licensed under a Creative Commons Attribution 3.0 Unported License.
http://creativecommons.org/licenses/by/3.0/
openAccess
A new time-frequency method to reveal quatum dynamics of atomic hydrogen in intense laser pulses: Synchrosqueezing transform
Article
Chu, Shih-I
Department of Chemistry
Scholarly/refereed, publisher version
This item meets KU Open Access policy criteria.
oai:kuscholarworks.ku.edu:1808/309932020-12-23T09:00:51Zcom_1808_97col_1808_102
Caruso, Giuseppe
Fresta, Claudia G.
Fidilio, Annamaria
O’Donnell, Fergal
Musso, Nicolò
Lazzarino, Giacomo
Grasso, Margherita
Amorini, Angela M.
Tascedda, Fabio
Bucolo, Claudio
Drago, Filippo
Tavazzi, Barbara
Lazzarino, Giuseppe
Lunte, Susan M.
Caraci, Filippo
2020-12-22T19:52:26Z
2020-12-22T19:52:26Z
2019-08-06
Caruso, G.; Fresta, C.G.; Fidilio, A.; O’Donnell, F.; Musso, N.; Lazzarino, G.; Grasso, M.; Amorini, A.M.; Tascedda, F.; Bucolo, C.; Drago, F.; Tavazzi, B.; Lazzarino, G.; Lunte, S.M.; Caraci, F. Carnosine Decreases PMA-Induced Oxidative Stress and Inflammation in Murine Macrophages. Antioxidants 2019, 8, 281.
http://hdl.handle.net/1808/30993
10.3390/antiox8080281
https://orcid.org/0000-0003-1571-5327
https://orcid.org/0000-0003-2451-1158
https://orcid.org/0000-0003-3525-9955
https://orcid.org/0000-0002-0958-7333
https://orcid.org/0000-0001-8743-0895
https://orcid.org/0000-0002-5917-7279
This work is licensed under a Creative Commons Attribution 4.0 International License.
Carnosine is an endogenous dipeptide composed of β-alanine and L-histidine. This naturally occurring molecule is present at high concentrations in several mammalian excitable tissues such as muscles and brain, while it can be found at low concentrations in a few invertebrates. Carnosine has been shown to be involved in different cellular defense mechanisms including the inhibition of protein cross-linking, reactive oxygen and nitrogen species detoxification as well as the counteraction of inflammation. As a part of the immune response, macrophages are the primary cell type that is activated. These cells play a crucial role in many diseases associated with oxidative stress and inflammation, including atherosclerosis, diabetes, and neurodegenerative diseases. In the present study, carnosine was first tested for its ability to counteract oxidative stress. In our experimental model, represented by RAW 264.7 macrophages challenged with phorbol 12-myristate 13-acetate (PMA) and superoxide dismutase (SOD) inhibitors, carnosine was able to decrease the intracellular concentration of superoxide anions (O2−•) as well as the expression of Nox1 and Nox2 enzyme genes. This carnosine antioxidant activity was accompanied by the attenuation of the PMA-induced Akt phosphorylation, the down-regulation of TNF-α and IL-6 mRNAs, and the up-regulation of the expression of the anti-inflammatory mediators IL-4, IL-10, and TGF-β1. Additionally, when carnosine was used at the highest dose (20 mM), there was a generalized amelioration of the macrophage energy state, evaluated through the increase both in the total nucleoside triphosphate concentrations and the sum of the pool of intracellular nicotinic coenzymes. Finally, carnosine was able to decrease the oxidized (NADP+)/reduced (NADPH) ratio of nicotinamide adenine dinucleotide phosphate in a concentration dependent manner, indicating a strong inhibitory effect of this molecule towards the main source of reactive oxygen species in macrophages. Our data suggest a multimodal mechanism of action of carnosine underlying its beneficial effects on macrophage cells under oxidative stress and inflammation conditions.
MDPI
© 2019 by the authors. Licensee MDPI, Basel, Switzerland.
http://creativecommons.org/licenses/by/4.0/
openAccess
Carnosine
Macrophages
Superoxide
Oxidative stress
Inflammation
Antioxidants
Carnosine Decreases PMA-Induced Oxidative Stress and Inflammation in Murine Macrophages
Article
Fresta, Claudia G.
Lunte, Susan M.
Ralph N. Adams Institute for Bioanalytical Chemistry
Pharmaceutical Chemistry
Scholarly/refereed, publisher version
This item meets KU Open Access policy criteria.
oai:kuscholarworks.ku.edu:1808/160792019-04-12T14:45:58Zcom_1808_97col_1808_102
Elles, Christopher G.
Bingemann, Dieter
Heckscher, Max M.
Crim, F. Fleming
2014-12-10T18:56:12Z
2014-12-10T18:56:12Z
2003-03-07
Elles, Christopher G.; Bingemann, Dieter; Heckscher, Max M.; Crim, F. Fleming. (2003). "Vibrational relaxation of CH(2)I(2) in solution: Excitation level dependence." The Journal of Chemical Physics, 118:5587. http://dx.doi.org/10.1063/1.1554396.
0021-9606
http://hdl.handle.net/1808/16079
10.1063/1.1554396
This is the publisher's version, also available electronically from http://scitation.aip.org/content/aip/journal/jcp/118/12/10.1063/1.1554396.
Transient electronic absorption monitors the flow of vibrational energy in methylene iodide (CH(2)I(2)) following excitation of five C–H stretch and stretch–bend modes ranging in energy from 3000 to 9000 cm(−1). Intramolecular vibrational relaxation (IVR) occurs through a mechanism that is predominantly state-specific at the C–H stretch fundamental but closer to the statistical limit at higher excitation levels. The IVR times change with the excitation energy between the fundamental and first C–H stretch overtone but are constant above the overtone. The intermolecular energy transfer (IET) times depend only weakly on the initial excitation level. Both the IVR and the IET times depend on the solvent[CCl(4), CDCl(3), C(6)D(6), C(6)H(6), or (CD(3))(2)CO] and its interaction strength, yet there is no energy level dependence of the solvent influence.
American Institute of Physics
Vibrational relaxation of CH(2)I(2) in solution: Excitation level dependence
Article
openAccess
Elles, Christopher G.
Chemistry
Scholarly/refereed, publisher version
This item does not meet KU Open Access policy criteria.
oai:kuscholarworks.ku.edu:1808/305332020-06-18T08:00:58Zcom_1808_97col_1808_102
Fresta, Claudia G.
Fidilio, Annamaria
Lazzarino, Giacomo
Musso, Nicolò
Grasso, Margherita
Merlo, Sara
Amorini, Angela M.
Bucolo, Claudio
Tavazzi, Barbara
Lazzarino, Giuseppe
Lunte, Susan M.
Caraci, Filippo
Caruso, Giuseppe
2020-06-17T19:01:22Z
2020-06-17T19:01:22Z
2020-01-25
Fresta, C. G., Fidilio, A., Lazzarino, G., Musso, N., Grasso, M., Merlo, S., Amorini, A. M., Bucolo, C., Tavazzi, B., Lazzarino, G., Lunte, S. M., Caraci, F., & Caruso, G. (2020). Modulation of Pro-Oxidant and Pro-Inflammatory Activities of M1 Macrophages by the Natural Dipeptide Carnosine. International journal of molecular sciences, 21(3), 776. https://doi.org/10.3390/ijms21030776
http://hdl.handle.net/1808/30533
10.3390/ijms21030776
https://orcid.org/0000-0002-6558-9800
https://orcid.org/0000-0003-3525-9955
https://orcid.org/0000-0001-8743-0895
https://orcid.org/0000-0002-5917-7279
https://orcid.org/0000-0003-1571-5327
PMC7038063
This work is licensed under a Creative Commons Attribution 4.0 International License.
Carnosine is a natural endogenous dipeptide widely distributed in mammalian tissues, existing at particularly high concentrations in the muscles and brain and possesses well-characterized antioxidant and anti-inflammatory activities. In an in vitro model of macrophage activation, induced by lipopolysaccharide + interferon-gamma (LPS + IFN-γ), we here report the ability of carnosine to modulate pro-oxidant and pro-inflammatory activities of macrophages, representing the primary cell type that is activated as a part of the immune response. An ample set of parameters aimed to evaluate cytotoxicity (MTT assay), energy metabolism (HPLC), gene expressions (high-throughput real-time PCR (qRT-PCR)), protein expressions (western blot) and nitric oxide production (qRT-PCR and HPLC), was used to assess the effects of carnosine on activated macrophages challenged with a non cytotoxic LPS (100 ng/mL) + IFN-γ (600 U/mL) concentration. In our experimental model, main carnosine beneficial effects were: (1) the modulation of nitric oxide production and metabolism; (2) the amelioration of the macrophage energy state; (3) the decrease of the expressions of pro-oxidant enzymes (Nox-2, Cox-2) and of the lipid peroxidation product malondialdehyde; (4) the restoration and/or increase of the expressions of antioxidant enzymes (Gpx1, SOD-2 and Cat); (5) the increase of the transforming growth factor-β1 (TGF-β1) and the down-regulation of the expressions of interleukins 1β and 6 (IL-1β and IL-6) and 6) the increase of the expressions of Nuclear factor (erythroid-derived 2)-like 2 (Nrf2) and heme oxygenase-1 (HO-1). According to these results carnosine is worth being tested in the treatment of diseases characterized by elevated levels of oxidative stress and inflammation (atherosclerosis, cancer, depression, metabolic syndrome, and neurodegenerative diseases).
MDPI
© 2020 by the authors.
http://creativecommons.org/licenses/by/4.0/
openAccess
Carnosine
M1 macrophages
Nitric oxide
Oxidative stress
Inflammation
Antioxidants
Energy metabolism
Modulation of Pro-Oxidant and Pro-Inflammatory Activities of M1 Macrophages by the Natural Dipeptide Carnosine
Article
Fresta, Claudia G.
Lunte, Susan M.
Ralph N. Adams Institute for Bioanalytical Chemistry
Pharmaceutical Chemistry
Chemistry
Scholarly/refereed, publisher version
This item meets KU Open Access policy criteria.
oai:kuscholarworks.ku.edu:1808/233622019-04-12T14:24:27Zcom_1808_97col_1808_102
Jayasinghe, Susanthi
Venukadasula, Phanindra K. M.
Hanson, Paul R.
2017-03-08T19:43:52Z
2017-03-08T19:43:52Z
2014-01-03
Jayasinghe, S., Venukadasula, P. K. M., & Hanson, P. R. (2014). An Efficient, Modular Approach for the Synthesis of (+)-Strictifolione and a Related Natural Product. Organic Letters, 16(1), 122–125. http://doi.org/10.1021/ol403110p
http://hdl.handle.net/1808/23362
10.1021/ol403110p
An efficient, library amenable, “pot economical” total synthesis of (+)-strictifolione and the related natural product, (6R)-6[(E,4R,6R)-4,6-dihydroxy-10-phenyl-1-decenyl]-5,6-dihydro-2H-2-pyrone are reported. This modular approach takes advantage of two consecutive phosphate tether-mediated, one-pot, sequential protocols, followed by a final cross metathesis to deliver both antifungal natural products in a three-pot process from the respective enantiomeric (R,R)- and (S,S)-trienes with minimal purification. A salient feature of this route is that additional protecting groups are not required as a result of the orthogonal protecting- and leaving-group properties innate to phosphate triesters.
American Chemical Society
This document is the Accepted Manuscript version of a Published Work that appeared in final form in Organic Letters, copyright © American Chemical Society after peer review and technical editing by the publisher. To access the final edited and published work see http://dx.doi.org/10.1021/ol403110p
openAccess
An Efficient, Modular Approach for the Synthesis of (+)-Strictifolione and a Related Natural Product
Article
Jayasinghe, Susanthi
Venukadasula, Phanindra K. M.
Hanson, Paul R.
Chemistry
Scholarly/refereed, author accepted manuscript
This item meets KU Open Access policy criteria.
oai:kuscholarworks.ku.edu:1808/346612023-07-28T06:05:53Zcom_1808_97com_1808_7165col_1808_102col_1808_7166
Sun, Shuai
Kaiser, John
Meier, Alex
2023-07-27T23:20:02Z
2023-07-27T23:20:02Z
2023-07
https://hdl.handle.net/1808/34661
https://orcid.org/0000-0003-4544-8506
This book is being made available in both PDF and ePub formats for the convenience of the reader.
The field of chemistry has long been associated with the pursuit of objective facts and the uncovering of the building blocks of our universe. However, this view can often exclude the important role that diversity, equity, and inclusion (DEI) play in the advancement of scientific knowledge. By highlighting the contributions of minority chemists and integrating DEI principles into chemistry education, we can promote a more inclusive environment and foster greater understanding of the complex connections between chemistry and society.
In the first section, we provide a biography of each chemist, discussing their personal and professional lives and how their minority identity has interacted with their careers. The second section summarizes their research and accomplishments in the field of chemistry, emphasizing the importance of their work and the implications it has had on the broader scientific community. Finally, the third section explores how their research is related to the topics and contents taught in general chemistry, creating a connection between the material students learn in the classroom and the real-world applications of chemistry.
In recent years, there has been a growing recognition of the need to incorporate DEI into STEM education, and chemistry is no exception. Despite this, there remains a scarcity of learning materials that directly introduce diversity and equality in chemistry education. As a result, students may view chemistry as an isolated discipline that is removed from the broader community.
This book aims to challenge that perception by introducing readers to minority chemists, their research, and the ways in which their work is related to topics taught in general chemistry courses. By exploring the lives and research of chemists who come from diverse backgrounds, we hope to showcase the importance of diverse perspectives in the advancement of the field and inspire a new generation of scientists who embrace and promote DEI in their own work. Each chapter of this book is divided into three main sections, highlighting the personal and professional lives of these extraordinary individuals and demonstrating the impact their work has had on the field.
University of Kansas
https://opentext.ku.edu/deichemistry/
Copyright 2023 Shuai Sun; John Kaiser; and Alex Meier. This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License, except where otherwise noted.
https://creativecommons.org/licenses/by-nc/4.0/
openAccess
Chemistry
Diversity
Equity
Inclusion
Breaking Barriers: Diversity and Equity in Chemistry
Book
Sun, Shuai
Chemistry
oai:kuscholarworks.ku.edu:1808/318692021-08-23T21:30:48Zcom_1808_97col_1808_102
Field, Thomas M.
Shin, Mimi
Stucky, Chase S.
Loomis, Joseph
Johnson, Michael A.
2021-08-23T21:30:48Z
2021-08-23T21:30:48Z
2018-03-23
T. M. Field, M. Shin, C. S. Stucky, J. Loomis, M. A. Johnson, ChemPhysChem 2018, 19, 1192.
http://hdl.handle.net/1808/31869
10.1002/cphc.201701357
https://orcid.org/0000-0001-5078-9896
This is the peer reviewed version of the following article: T. M. Field, M. Shin, C. S. Stucky, J. Loomis, M. A. Johnson, ChemPhysChem 2018, 19, 1192., which has been published in final form at https://doi.org/10.1002/cphc.201701357. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Use of Self-Archived Versions. This article may not be enhanced, enriched or otherwise transformed into a derivative work, without express permission from Wiley or by statutory rights under applicable legislation. Copyright notices must not be removed, obscured or modified. The article must be linked to Wiley’s version of record on Wiley Online Library and any embedding, framing or otherwise making available the article or pages thereof by third parties from platforms, services and websites other than Wiley Online Library must be prohibited.
Post-chemotherapy cognitive impairment, also known as ‘chemobrain,’ is a neurological condition in which cognitive function is impaired as a result of cancer chemotherapy treatment. In this work, we used fast-scan cyclic voltammetry (FSCV) to measure electrically evoked dopamine release and uptake in whole brain preparations from zebrafish that have been treated with carboplatin, an agent associated with chemobrain. We administered carboplatin by addition to the fish's tank water or their food. One week of treatment with 100 μM carboplatin in the water was needed to significantly impair dopamine release (∼40 % of control); however, only one day of treatment through the zebrafish's food was needed to cause a similar impairment. Atomic absorption spectroscopy measurements suggested that administration through food resulted in higher initial levels of carboplatin compared to water administration, but water administration resulted in an increase over time. Uptake, determined by modeling stimulated release plots, was unaffected. These results are consistent with our previous findings of diminished neurotransmitter release in rats and support a role for zebrafish in chemobrain-related studies.
Wiley
© 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.
openAccess
Brain
Dopamine
Electrochemistry
Voltammetry
Zebrafish
Electrochemical Measurement of Dopamine Release and Uptake in Zebrafish Following Treatment with Carboplatin
Article
Field, Thomas M.
Shin, Mimi
Stucky, Chase S.
Loomis, Joseph
Johnson, Michael A.
Chemistry
Graduate Program in Neuroscience
Scholarly/refereed, author accepted manuscript
This item meets KU Open Access policy criteria.
oai:kuscholarworks.ku.edu:1808/224582019-04-12T14:17:13Zcom_1808_97col_1808_102
Weaver, Jimmie D.
Morris, David K.
Tunge, Jon A.
2017-01-05T17:58:53Z
2017-01-05T17:58:53Z
2009-09-08
Tunge, Jon, Jimmie Weaver, and David Morris. "Synthesis of Chiral Nonracemic Tertiary α-Thio and α-Sulfonyl Acetic Esters via SN2 Reactions of Tertiary Mesylates." Synlett 2010.03 (2010): 470-74.
http://hdl.handle.net/1808/22458
10.1055/s-0029-1219186
Syntheses of enantioenriched sulfides and sulfones via substitution of tertiary mesylate with thiolate nucleophile were achieved with modest to excellent success.
Thieme Publishing
https://www.thieme-connect.de/products/ejournals/html/10.1055/s-0029-1219186
Sulfide
Sulfone
Sn2 reaction
Synthesis of Chiral Nonracemic Tertiary α-Thio and α-Sulfonyl Acetic Esters via SN2 Reactions of Tertiary Mesylates
Article
openAccess
Tunge, Jon A.
Chemistry
Scholarly/refereed, publisher version
This item meets KU Open Access policy criteria.
oai:kuscholarworks.ku.edu:1808/160142019-04-12T14:49:21Zcom_1808_97col_1808_102
Chu, Shih-I
Ho, Tak-San
2014-12-02T20:13:36Z
2014-12-02T20:13:36Z
1985-07-01
Ho, Tak-San & Chu, Shih-I. "Semiclassical many-mode Floquet theory. IV. Coherent population trapping and SU(3) dynamical evolution of dissipative three-level systems in intense bichromatic fields." Phys. Rev. A 32, 377 – Published 1 July 1985. http://dx.doi.org/10.1103/PhysRevA.32.377.
http://hdl.handle.net/1808/16014
10.1103/PhysRevA.32.377
This is the published version, also available here: http://dx.doi.org/10.1103/PhysRevA.32.377.
The many-mode Floquet theory (MMFT) recently developed by authors is extended to incorporate the irreversible damping mechanisms for the nonperturbative treatment of the dynamical evolution of dissipative three-level systems at two-photon or multiphoton coherent resonance trapping conditions induced by two strong linearly polarized monochromatic fields. It has been recently shown by several workers that under the rotating-wave approximation (RWA), population may be permanently trapped in the three-level system if the coherent monochromatic fields are exactly two-photon resonant with the initial and final states, decoupled from the intermediate decaying level. In practice, the inclusion of the non-RWA terms necessarily modifies the resonant trapping conditions and behavior. In this paper we extend the generalized Van Vleck (GVV) nearly degenerate perturbation theory to an analytical treatment of the non-Hermitian two-mode Floquet Hamiltonian. This reduces the infinite-dimensional time-independent non-Hermitian Floquet Hamiltonian to a 3×3 effective Hamiltonian, from which essential properties of the coherent population-trapping behavior as well as the dynamical evolution of the dissipative SU(3) coherence vector S→(t) can be readily obtained and expressed in terms of only three complex quasienergy eigenvalues and eigenvectors. The MMFT-GVV studies show that the RWA two-photon resonant trapping condition is substantially modified by the effects of non-RWA terms, and that the system can be ‘‘quasitrapped’’ for only a finite amount of time characterized by a small imaginary energy (width) associated with a coherent superposition state of the initial and final levels. Furthermore, it is found that the initially eight-dimensional coherence vector S→(t) evolves predominantly to a one-dimensional scalar at the two-photon or multiphoton resonant quasitrapping conditions. Detailed results and pictorial representations of the population trapping and SU(3) dissipative dynamical evolution are presented.
American Physical Society
Semiclassical many-mode Floquet theory. IV. Coherent population trapping and SU(3) dynamical evolution of dissipative three-level systems in intense bichromatic fields
Article
openAccess
Chu, Shih-I
Ho, Tak-San
Chemistry
na
Scholarly/refereed, publisher version
This item does not meet KU Open Access policy criteria.
oai:kuscholarworks.ku.edu:1808/161502019-04-12T14:46:17Zcom_1808_97col_1808_102
Bembenek, Scott D.
Laird, Brian Bostian
2014-12-17T17:35:34Z
2014-12-17T17:35:34Z
1996-01-01
Bembenek, Scott D.; Laird, Brian B. (1996). "The role of localization in glasses and supercooled liquids." The Journal of Chemical Physics, 104(13):5499-5208. http://dx.doi.org/10.1063/1.471147.
0021-9606
http://hdl.handle.net/1808/16150
10.1063/1.471147
This is the publisher's version, also available electronically from http://scitation.aip.org/content/aip/journal/jcp/104/13/10.1063/1.471147.
Localized excitations (tunneling modes, soft harmonic vibrations) are believed to play a dominant role in the thermodynamics and transport properties of glasses at low temperature. Using instantaneous normal‐mode (INM) analysis, we explore the role that such localization plays in determining the behavior of such systems in the vicinity of the glass transition. Building on our previous study [Phys. Rev. Lett. 74, 936 (1995)] we present evidence that the glass transition in two simple model systems is associated with a transition temperature below which all un‐ stable INM’s become localized. This localization transition is a possible mechanism for the change in diffusion mechanism from continuous flow to localized hopping that is believed to occur in fragile glass formers at a temperature just above T g .
American Institute of Physics
The role of localization in glasses and supercooled liquids
Article
openAccess
Bembenek, Scott D.
Laird, Brian Bostian
Chemistry
Scholarly/refereed, publisher version
This item does not meet KU Open Access policy criteria.
oai:kuscholarworks.ku.edu:1808/160232019-04-12T14:49:25Zcom_1808_97col_1808_102
Chu, Shih-I
Cooper, J.
2014-12-03T20:03:28Z
2014-12-03T20:03:28Z
1985-11-01
Chu, Shih-I. & Cooper, J. "Threshold shift and above-threshold multiphoton ionization of atomic hydrogen in intense laser fields." Phys. Rev. A 32, 2769 – Published 1 November 1985. http://dx.doi.org/10.1103/PhysRevA.32.2769.
http://hdl.handle.net/1808/16023
10.1103/PhysRevA.32.2769
This is the published version, also available here: http://dx.doi.org/10.1103/PhysRevA.32.2769.
Accurate ab initio nonperturbative L2 non-Hermitian Floquet calculations for intensity-dependent threshold shifts and ground-state total ionization widths (rates) for one-, two-, and three-photon-dominant intense-field ionization of atomic hydrogen are presented. The results show the importance of both the ac Stark shift and the pondermotive potential in the determination of the net threshold shift. In addition, branching ratios to individual continua have been estimated, yielding physical insights regarding the general features and mechanisms of the frequency- and intensity-dependent continuum-continuum transitions and ‘‘peak switching’’ phenomena in the above-threshold ionization processes.
American Physical Society
Threshold shift and above-threshold multiphoton ionization of atomic hydrogen in intense laser fields
Article
openAccess
Chu, Shih-I
Chemistry
na
Scholarly/refereed, publisher version
This item does not meet KU Open Access policy criteria.
oai:kuscholarworks.ku.edu:1808/162072019-04-12T14:31:54Zcom_1808_97col_1808_102
Liao, Sheng-Lun
Ho, Tak-San
Chu, Shih-I
Rabitz, Herschel
2015-01-09T17:28:19Z
2015-01-09T17:28:19Z
2011-09-07
Liao, Sheng-Lun., Ho, Tak-San., Chu, Shih-I., Rabitz, Herschel. "Fast-kick-off monotonically convergent algorithm for searching optimal control fields." Phys. Rev. A 84, 031401(R) – Published 7 September 2011. http://dx.doi.org/10.1103/PhysRevA.84.031401.
http://hdl.handle.net/1808/16207
10.1103/PhysRevA.84.031401
This is the published version, also available here: http://dx.doi.org/10.1103/PhysRevA.84.031401.
This Rapid Communication presents a fast-kick-off search algorithm for quickly finding optimal control fields in the state-to-state transition probability control problems, especially those with poorly chosen initial control fields. The algorithm is based on a recently formulated monotonically convergent scheme [T.-S. Ho and H. Rabitz, Phys. Rev. E 82, 026703 (2010)]. Specifically, the local temporal refinement of the control field at each iteration is weighted by a fractional inverse power of the instantaneous overlap of the backward-propagating wave function, associated with the target state and the control field from the previous iteration, and the forward-propagating wave function, associated with the initial state and the concurrently refining control field. Extensive numerical simulations for controls of vibrational transitions and ultrafast electron tunneling show that the new algorithm not only greatly improves the search efficiency but also is able to attain good monotonic convergence quality when further frequency constraints are required. The algorithm is particularly effective when the corresponding control dynamics involves a large number of energy levels or ultrashort control pulses.
American Physical Society
Fast-kick-off monotonically convergent algorithm for searching optimal control fields
Article
openAccess
Chu, Shih-I
Chemistry
fullparticipation
Scholarly/refereed, publisher version
This item meets KU Open Access policy criteria.
oai:kuscholarworks.ku.edu:1808/159732019-04-12T14:51:09Zcom_1808_97col_1808_102
Chu, Shih-I
Roy, Amlan K.
2014-12-01T21:01:21Z
2014-12-01T21:01:21Z
2002-05-07
Chu, Shih-I. & Roy, Amlan K. "Density-functional calculations on singly and doubly excited Rydberg states of many-electron atoms." Phys. Rev. A 65, 052508 – Published 7 May 2002. http://dx.doi.org/10.1103/PhysRevA.65.052508.
http://hdl.handle.net/1808/15973
10.1103/PhysRevA.65.052508
This is the published version, also available here: http://dx.doi.org/10.1103/PhysRevA.65.052508.
Nearly 100 low-, moderately high-, and high-lying singly and doubly excited states of He, Li, and Be have been calculated using a nonvariational, work-function-based exchange potential within the nonrelativistic Hohenberg-Kohn-Sham density-functional theory (DFT). The nonlinear gradient included in the Lee-Yang-Parr correlation functional is used to incorporate the correlation potential. The generalized pseudospectral method is used for nonuniform and optimal spatial grid discretization and solution of the Kohn-Sham equation to obtain accurate eigenvalues, expectation values, and radial densities for both ground and excited states. The results are compared with the available theoretical and experimental data. The discrepancy in the calculated singly excited state energies is within about 0.01% for He (for other atoms, it is less than 0.2%), while that for the doubly excited states of He is well within 3.6%. The deviations in the calculated single- and double-excitation energies for 31 selected states are in the error ranges 0.009–0.632 % and 0.085–1.600 %, respectively. The overall agreement of the present results is quite gratifying, especially in the light of DFT’s difficulties in dealing with excited states. The exchange-only results are practically of Hartree-Fock quality, and the correlation-included results are usually slightly overestimated. The present method offers a simple, computationally efficient and general scheme for accurate calculation of multiply excited Rydberg states within DFT.
American Physical Society
Density-functional calculations on singly and doubly excited Rydberg states of many-electron atoms
Article
openAccess
Chu, Shih-I
Roy, Amlan K.
Chemistry
na
Scholarly/refereed, publisher version
This item does not meet KU Open Access policy criteria.
oai:kuscholarworks.ku.edu:1808/161342019-04-12T14:46:11Zcom_1808_97col_1808_102
Feng, Xiaobing
Laird, Brian Bostian
2014-12-16T21:50:59Z
2014-12-16T21:50:59Z
2006-01-30
Feng, Xiaobing; Laird, Brian Bostian. (2006). "Calculation of the crystal-melt interfacial free energy of succinonitrile from molecular simulation." The Journal of Chemical Physics, 124(4):044707. http://dx.doi.org/10.1063/1.2149859
0021-9606
http://hdl.handle.net/1808/16134
10.1063/1.2149859
This is the publisher's version, also available electronically from http://scitation.aip.org/content/aip/journal/jcp/124/4/10.1063/1.2149859.
American Institute of Physics
Calculation of the crystal-melt interfacial free energy of succinonitrile from molecular simulation
Article
openAccess
Feng, Xiaobing
Laird, Brian Bostian
Chemistry
Scholarly/refereed, publisher version
This item does not meet KU Open Access policy criteria.
dim///col_1808_102/100