The methodology of ab initio molecular dynamics, wherein finite-temperature dynamical trajectories are generated by using forces computed ''on the fly'' from electronic structure calculations, has had a profound influence in modern theoretical research. Ab initio molecular dynamics allows chemical processes in condensed phases to be studied in an accurate and unbiased manner, leading to new paradigms in the elucidation of microscopic mechanisms, rationalization of experimental data, and testable predictions of new phenomena. The purpose of this work is to give a brief introduction to the technique and to review several important recent developments in the field. Several illustrative examples showing the power of the technique have been chosen. Perspectives on future directions in the field also will be given.M odern theoretical methodology, aided by the advent of high speed and massively parallel computing, has advanced to a level that the microscopic details of chemical processes in condensed phases can now be treated on a relatively routine basis. One of the most commonly used theoretical approaches for such studies is the molecular dynamics (MD) method, in which the classical Newtonian equations of motion for a system are solved numerically starting from a prespecified initial state and subject to a set of boundary conditions appropriate to the problem. MD methodology allows both equilibrium thermodynamic and dynamical properties of a system at finite temperature to be computed. The quality of a MD calculation rests largely on the method by which the forces are specified. In many applications, these forces are computed from an empirical model or ''force field,'' an approach that has enjoyed tremendous success in the treatment of systems ranging from simple liquids and solids to polymers and biological systems including proteins, membranes, and nucleic acids. Since most force fields do not include electronic polarization effects (see, however, ref. 1) and can treat chemical reactivity only through specialized techniques (see, e.g., ref.2), it is often necessary to turn to the methodology of ab initio MD (AIMD).AIMD is a rapidly evolving and growing technique that constitutes one of the most important theoretical tools developed in the last decades. In an AIMD calculation, finite-temperature dynamical trajectories are generated by using forces obtained directly from electronic structure calculations performed ''on the fly'' as the simulation proceeds. Thus, AIMD permits chemical bond breaking and forming events to occur and accounts for electronic polarization effects (3, 4). AIMD has been successfully applied to a wide variety of important problems in physics and chemistry and is now beginning to influence biology as well. In numerous studies, new physical phenomena have been revealed and microscopic mechanisms elucidated that could not have been uncovered by using empirical methods, often leading to new interpretations of experimental data and even suggesting new experiments to perform.In its most ideal form,...

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The theoretical principles underpinning the calculation of infrared spectra for condensed-phase systems in the context of ab initio molecular dynamics have been recently developed in literature. At present, most ab initio molecular dynamics calculations are restricted to relatively small systems and short simulation times. In this paper we devise a method that allows well-converged results for infrared spectra from ab initio molecular dynamics simulations using small systems and short trajectories characteristic of simulations typically performed in practice. We demonstrate the utility of our approach by computing the imaginary part of the dielectric constant epsilon"(omega) for H2O and D2O in solid and liquid phases and show that it compares well with experimental data. We further demonstrate that maximally localized Wannier orbitals can be used to separate the individual contributions of different molecular species to the linear spectrum of complex systems. The new spectral decomposition method is shown to be useful in present-day ab initio molecular dynamics calculations to compute the magnitude of the "continuous absorption" generated by excess protons in aqueous solutions with good accuracy even when other species present in the solutions absorb strongly in the same frequency window.

In this paper the ab initio potential of mean force for the formic acid-water system is calculated in a Monte Carlo simulation using a classical fluctuating charge molecular mechanics potential to guide Monte Carlo updates. The ab initio energies in the simulation are calculated using density-functional theory ͑DFT͒ methods recently developed by Salahub et al. ͓J. Chem. Phys. 107, 6770 ͑1997͔͒ to describe hydrogen-bonded systems. Importance sampling methods are used to investigate structural changes and it is demonstrated that using a molecular mechanics importance function can improve the efficiency of a DFT simulation by several orders of magnitude. Monte Carlo simulation of the system in a canonical ensemble at Tϭ300 K reveals two chemical processes at intermediate time scales: The rotation of the H 2 O bonded to HCOOH, which takes place on a time scale of 3 ps, and the dissociation of the complex which occurs in 24 ps. It is shown that these are the only important structural ''reactions'' in the formic acid-water cluster which take place on a time scale shorter than the double transfer of the proton.

The existence of a broad, mid-infrared absorption ranging from 1000 to 3000 cm(-1) is usually interpreted as a signature for the existence of protonated water networks. Herein, we use cryogenic mixtures of water and hydrogen fluoride (HF) and show experimental and computational evidence that similarly wide absorptions can be generated by a broad distribution of proton-shared and ion pair complexes. In the present case, we demonstrate that the broadening is mainly inhomogeneous, reflecting the fact that the topology of the first solvation shell determines the local degree of ionization and the shared-proton asymmetric stretching frequency within H2O x HF complexes. The extreme sensitivity of the proton transfer potential energy hypersurface to local hydrogen bonding topologies modulates its vibrational frequency from 2800 down to approximately 1300 cm(-1), the latter value being characteristic of solvation geometries that yield similar condensed-phase proton affinities for H2O and fluoride. By linking the local degree of ionization to the solvation pattern, we are able to propose a mechanism of ionization for HF in aqueous solutions and to explain some of their unusual properties at large concentrations. However, an important conclusion of broad scientific interest is our prediction that spectral signatures that are normally attributed to protonated water networks could also reveal the presence of strong hydrogen bonds between un-ionized acids and water molecules, with important consequences to spectroscopic investigations of biologically relevant proton channels and pumps.

A novel approach for representing the intramolecular polarizability as a continuum dielectric is introduced to account for molecular electronic polarization. It is shown, using a finite-difference solution to the Poisson equation, that the Electronic Polarization from Internal Continuum (EPIC) model yields accurate gas-phase molecular polarizability tensors for a test set of 98 challenging molecules composed of heteroaromatics, alkanes and diatomics. The electronic polarization originates from a high intramolecular dielectric that produces polarizabilities consistent with B3LYP/aug-cc-pVTZ and experimental values when surrounded by vacuum dielectric. In contrast to other approaches to model electronic polarization, this simple model avoids the polarizability catastrophe and accurately calculates molecular anisotropy with the use of very few fitted parameters and without resorting to auxiliary sites or anisotropic atomic centers. On average, the unsigned error in the average polarizability and anisotropy compared to B3LYP are 2% and 5%, respectively. The correlation between the polarizability components from B3LYP and this approach lead to a R2 of 0.990 and a slope of 0.999. Even the F2 anisotropy, shown to be a difficult case for existing polarizability models, can be reproduced within 2% error. In addition to providing new parameters for a rapid method directly applicable to the calculation of polarizabilities, this work extends the widely used Poisson equation to areas where accurate molecular polarizabilities matter.

The cis-trans isomerization of N-methylacetamide, a molecular model of the polypeptide chain, is examined via umbrella sampling Car-Parrinello MD and classical MD, in both gas and solution phases at 300 K. A new analysis of the C(O)-N bond interconversion and a full examination of the solvent shell structure are presented.

The origin of the continuum region ($\tilde \nu $=1000–3000 cm−1) in the IR absorption spectra of solutions of strong acids is well understood, but in weak acids, it has remained a mystery until now. An ab initio molecular dynamics approach is used to explain the molecular origin of this continuum for aqueous solutions of the weak acid HF and identify the structure and chemical nature of the dominant species (see picture).