A first principles molecular dynamics study of vibrational spectral diffusion and hydrogen bond dynamics in liquid methanol

Effect of the Hydration Shell on the Carbonyl Vibration in the Ala-Leu-Ala-Leu Peptide

The vibrational spectrum of the Ala-Leu-Ala-Leu peptide in solution, computed from first-principles simulations, shows a prominent band in the amide I region that is assigned to stretching of carbonyl groups. Close inspection reveals combined but slightly different contributions by the three carbonyl groups of the peptide. The shift in their exact vibrational signature is in agreement with the different probabilities of these groups to form hydrogen bonds with the solvent. The central carbonyl group has a hydrogen bond probability intermediate to the other two groups due to interchanges between different hydrogen-bonded states. Analysis of the interaction energies of individual water molecules with that group shows that shifts in its frequency are directly related to the interactions with the water molecules in the first hydration shell. The interaction strength is well correlated with the hydrogen bond distance and hydrogen bond angle, though there is no perfect match, allowing geometrical criteria for hydrogen bonds to be used as long as the sampling is sufficient to consider averages. The hydrogen bond state of a carbonyl group can therefore serve as an indicator of the solvent's effect on the vibrational frequency.

Efficiently Calculating Anharmonic Frequencies of Molecular Vibration by Molecular Dynamics Trajectory Analysis

Two efficient methods, the Eckart frame algorithm and the multiorder derivative algorithm, for vibrational frequency calculation directly based on the raw data of atomic trajectory from the state-of-the-art first-principles molecular dynamics simulation are presented. The Eckart frame approach is robust to retrieve the full set of anharmonic fundamental frequencies of any molecule from the atomic trajectory for a sufficiently long molecular dynamics simulation at a temperature close to 0 K. In addition to the fundamental vibrational frequencies, the multiorder derivative approach is universal for the calculations of vibrational frequencies based on the molecular dynamics result in a wide range of temperatures. The accuracy, efficiency, and applicability of these two methods are demonstrated through several successful examples in calculating the anharmonic fundamental vibrational frequencies of methane, ethylene, water, and cyclobutadiene.

A "Universal" Spectroscopic Map for the OH Stretching Mode in Alcohols

Empirical maps are presented for the OH stretching vibrations in neat alcohols in which the relevant spectroscopic quantities are expressed in terms of the electric field exerted on the hydrogen atom by the surrounding liquid. It is found, by examination of the four lowest linear alcohols, methanol, ethanol, n-propanol, and n-butanol, that a single map can be used for alcohols with different alkyl groups. This "universal" map is in very good agreement with maps optimized for the individual alcohols but differs from those previously developed for water. This suggests that one map can be used for all alcohols, perhaps even those not examined in the present study. The universal map gives IR lineshapes in good agreement with measured spectra for isotopically dilute methanol and ethanol, while the two-dimensional IR photon echo spectra give results that differ from experiments. The role of non-Condon effects, reorientation dynamics, hydrogen bonding, and spectral diffusion is discussed.

Probing the dynamics of N-methylacetamide in methanol via ab initio molecular dynamics

Two-dimensional infrared (2D IR) spectroscopy of amide 1 vibrational bands provides a valuable probe of proteins as well as molecules such as N-methylacetamide (NMA), which present peptide-like H-bonding possibilities to a solvent.