| dc.description.abstract | Molecular reorientation of the four isomeric butanols are investigated with molecular dynamics simulations. The purpose of this study is to probe how alcohol reorientational and hydrogen-bond (H-bond) dynamics is influenced by the arrangement of the steric bulk of the isomeric butanols in their liquid state. The OH reorientation times are explained with the extended jump model in which the OH reorientation is broken down into contributions due to ``jumps'' between H-bond partners and ``frame'' reorientation of the intact H-bonded pair. In the case of the isomeric butanols, the model provides a quantitative description of the OH reorientation times. Our results show that reorientation is fastest in iso-butanol and slowest in tert-butanol, while sec- and n-butanol have similar reorientation times. Similar reorientation times for sec- and n-butanol is due to the unpredictable cancellation between the jump and frame reorientation in the two alcohols. Entropic, enthalpic and dynamical factors that include transition state recrossing effects are seen to contribute to the jump reorientation times. Finally, a model that is based on the liquid structure is offered to evaluate the enthalpic and entropic contributions to the jump time. This study represents the foundation for a model that predicts OH reorientation times in alcohols even though further work is needed for a better prediction of frame reorientation times and the transition state recrossing effects. An estimation of the activation energy of chemical reactions like jump reorientation of OH groups in alcohols from molecular dynamics simulations has always required numerous simulations at several temperatures. In this work, several methods for calculating the activation energies at a single temperature have been explored. The applications explored include classical and quantum systems and the activation energy is evaluated using the same time correlation functions that are used to evaluate rate constants from molecular or quantum dynamics trajectories. The use of these time correlation functions show that the activation energy can be evaluated with no extra computational cost. In addition to an analysis of molecular dynamics trajectories, vibrational spectroscopy is a very useful tool for probing structure and dynamics in liquids and the simulation of spectra can be achieved in a variety of ways. Empirical maps for spectroscopic quantities required for the simulation of spectra of OH stretching vibrations are related to the electric field on the hydrogen atom due to the surrounding liquid molecules. Upon the analysis of the four lowest linear alcohols, methanol, ethanol, n-propanol, and n-butanol, it is shown that a single (``universal") map can be used for alcohols with different alkyl groups. Spectra of the OH stretch simulated for the four lowest linear alcohols with this ``universal" map is in very good agreement with those that are simulated using maps that have been optimized for the individual alcohols. However, the spectra resulting from this map differs from that simulated using maps developed for water. The simulated spectra suggest that it may be possible to use one map to simulate OH stretching vibration in other alcohols that are not part of the study. The simulated spectra are very similar to available experimental spectra and the role of non-Condon effects, reorientation dynamics, hydrogen bonding, and spectral diffusion in the simulated spectra are discussed. The Empirical maps developed for the OH stretching vibration of alcohols were used to simulate the IR, Raman, and 2D-IR photon echo spectra of isotopically dilute isomeric butanols. Raman spectra shows that the branched isomers have more weakly bonded alcohols compared to linear alcohols. While the simulation of the vibrational spectra of the OH stretch of isotopically dilute alcohols is relatively straightforward, the accurate simulation of vibrational spectra of the OH stretch in the neat liquids requires a good estimate of intermolecular vibrational coupling. The discrete variable representation method is used to calculate intermolecular vibrational coupling of OH and OD bonds in water. Intermolecular vibrational coupling decreases on H to D substitution and the transition dipole coupling approximation is seen to accurately predict the intermolecular vibrational coupling constant at long intermolecular distances. | |
