Quantum chemical benchmark databases of gold-standard dimer interaction energies.

Advances in computational chemistry create an ongoing need for larger and higher-quality datasets that characterize noncovalent molecular interactions. We present three benchmark collections of quantum mechanical data, covering approximately 3,700 distinct types of interacting molecule pairs. The first collection, which we refer to as DES370K, contains interaction energies for more than 370,000 dimer geometries.

Improving the accuracy of Møller-Plesset perturbation theory with neural networks.

Noncovalent interactions are of fundamental importance across the disciplines of chemistry, materials science, and biology. Quantum chemical calculations on noncovalently bound complexes, which allow for the quantification of properties such as binding energies and geometries, play an essential role in advancing our understanding of, and building models for, a vast array of complex processes involving molecular association or self-assembly. Because of its relatively modest computational cost, second-order Møller-Plesset perturbation (MP2) theory is one of the most widely used methods in quantum chemistry for studying noncovalent interactions.

Water dispersion interactions strongly influence simulated structural properties of disordered protein states.

Many proteins can be partially or completely disordered under physiological conditions. Structural characterization of these disordered states using experimental methods can be challenging, since they are composed of a structurally heterogeneous ensemble of conformations rather than a single dominant conformation. Molecular dynamics (MD) simulations should in principle provide an ideal tool for elucidating the composition and behavior of disordered states at an atomic level of detail.

Application of a polarizable force field to calculations of relative protein-ligand binding affinities.

An explicitly polarizable force field based exclusively on quantum data is applied to calculations of relative binding affinities of ligands to proteins. Five ligands, differing by replacement of an atom or functional group, in complexes with three serine proteases-trypsin, thrombin, and urokinase-type plasminogen activator-with available experimental binding data are used as test systems. A special protocol of thermodynamic integration was developed and used to provide sufficiently low levels of systematic error along with high numerical efficiency and statistical stability.

Nonadditive effects in ternary H2-cation-PAH systems.

This article reports state-of-the-art ab initio calculations at the second order of Møller-Plesset perturbation theory of molecular hydrogen binding in its ternary complexes with lightweight alkali cations (M = Li or Na) and polycyclic aromatic hydrocarbons (PAHs) up to coronene. The study revealed a substantial nonadditive contribution to the H(2) stabilization energy. In the most stable conformation, the nonadditive contribution weakens the H(2) binding by a factor of nearly 1.

Assessment of performance of the general purpose polarizable force field QMPFF3 in condensed phase.

The recently introduced force field (FF) QMPFF3 is thoroughly validated in gas, liquid, and solid phases. For the first time, it is demonstrated that a physically well-grounded general purpose FF fitted exclusively to a comprehensive set of high level vacuum quantum mechanical data applied as it is to simulation of condensed phase provides high transferability for a wide range of chemical compounds. QMPFF3 demonstrates accuracy comparable with that of the FFs explicitly fitted to condensed phase data, but due to high transferability it is expected to be successful in simulating large molecular complexes.

Contribution of quantum molecular flexibility to the second virial coefficient of water vapor.

The contribution of essentially quantum internal molecular motions to the second virial coefficient B2 of water vapor is analyzed in the framework of the path integral approach. A general purpose ab initio polarizable force field QMPFF2 or a nonpolarizable three-site water model are used with oscillator and Morse valence potentials. It is demonstrated that the contribution may be significant but depends strongly on the form of the intramolecular potential.