The density functional theory based molecular dynamics simulation method (“Car−Parrinello”) was applied in a numerical study of the electronic properties, hydrogen bonding, and infrared spectroscopy of the trans and cis isomer of N-methylacetamide in aqueous solution. A detailed analysis of the electronic structure of the solvated molecules, in terms of localized Wannier functions and Born atomic charges, is presented. Two schemes for the computation of the solute infrared absorption spectrum are investigated:  In the first method the spectrum is determined by Fourier transforming the time correlation function of the solute dipole as determined from the Wannier function analysis. The second method uses instead the molecular current−current correlation function computed from the Born charges and atomic velocities. The resulting spectral properties of trans- and cis-NMA are carefully compared to each other and to experimental results. We find that the two solvated isomers can be clearly distinguished by the...

Infrared Spectroscopy of N-Methylacetamide Revisited by ab Initio Molecular Dynamics Simulations

Absolute free energies of hydration (ΔG h y d ) have been computed for 25 diverse organic molecules using partial atomic charges derived from AM1 and PM3 wave functions via the CMI and CM3 procedures of Cramer, Truhlar, and coworkers. Comparisons are made with results using charges fit to the electrostatic potential surface (EPS) from ah initio 6-31G* wave functions and from the OPLS-AA force field. OPLS Lennard-Jones parameters for the organic molecules were used together with the TIP4P water model in Monte Carlo simulations with free energy perturbation theory. Absolute free energies of hydration were computed for OPLS united-atom and all-atom methane by annihilating the solutes in water and in the gas phase, and absolute ΔG h y d values for all other molecules were computed via transformation to one of these references. Optimal charge scaling factors were determined by minimizing the unsigned average error between experimental and calculated hydration free energies. The PM3-based charge models do not lead to lower average errors than obtained with the EPS charges for the subset of 13 molecules in the original study. However, improvement is obtained by scaling the CMIA partial charges by 1.14 and the CM3A charges by 1.15, which leads to average errors of 1.0 and 1.1 kcal/mol for the full set of 25 molecules. The scaled CMIA charges also yield the best results for the hydration of amides including the E/Z free-energy difference for N-methylacetamide in water.

Accuracy of free energies of hydration using CM1 and CM3 atomic charges.

The cation-enhanced formation of hydrophobic domains in aqueous humic acids has been shown to be a slow process, consistent with the evolution and disintegration of humic acid configurations over p...

Kinetic Aspects of Cation-Enhanced Aggregation in Aqueous Humic Acids

We have developed a polarizable intermolecular potential function (PIPF) for simulation of liquid amides. The PIPF potential includes a pairwise additive component, consisting of the familiar Lenna...

Simulation of Liquid Amides Using a Polarizable Intermolecular Potential Function

Temperature-dependent infrared spectra for liquid N-methylacetamide are calculated by the ab initio quantum cluster equilibrium (QCE) and Gaussian-94 methods and compared with experimental measurements. The calculations are based on standard ab initio self-consistent-field (SCF) methods at the 3-21G levels for five different molecular clusters. The cluster sizes vary from the monomer up to a five-membered linear structure. Strong cooperative effects are found in the molecular clusters and are reflected in the geometries and vibrational spectra for each species. The equilibrium populations of the clusters were calculated for the entire liquid range. At low temperatures the linear pentamer is the dominant species. At higher temperatures these clusters are replaced, primarily, by linear dimers and monomers. The calculated frequencies are in excellent agreement with the temperature behavior found in FT-IR experiments.

Stefania Balanicka

Papers

Dielectric properties and molecular structure of amide solutions. 1. N-Methylacetamide in carbon tetrachloride