Anisotropic nonadditive ab initio force field for noncovalent interactions of H2

Spherical harmonics representation of the potential energy surface for the H2⋯H2 van der Waals complex

We perform a study of the molecular anisotropy for the H₂⋯H₂ van der Waals system using a spherical harmonics expansion. We use six leading stable configurations to construct our analytical potential energy surface (PES) from ab initio calculations guided qualitatively by the symmetry-adapted perturbation theory (SAPT) analyses. We extrapolate the energies of the PES performed at the CCSD(T)/aug-cc-pVnZ (n = 2 and 3) levels to the complete basis set (CBS) limit. To best fit the shallow potential energy surface of each leading configuration with the intermolecular distance, it was employed an extended version of the Rydberg potential. To assess the quality of our extrapolated analytical PES, we calculate the second virial coefficients, which are in relatively good agreement with the experimental data. As a result, the spherical harmonics coefficients obtained might be of considerable relevance in spectroscopy and dynamics applications.

Visualizing the Geometry of Hydrogen Dimers

The simplest molecular dimer, H₂-H₂, poses a challenge to both experiment and theory as a system with a multidimensional energy surface that supports only a single weakly bound quantum state. Here, we provide a direct experimental image of the structure of hydrogen dimers [(H₂)₂, H₂-D₂, and (D₂)₂] obtained via femtosecond laser-induced Coulomb explosion imaging. Our results indicate that hydrogen dimers are not restricted to a particular geometry but rather occur as a mixture of all possible configurations. The measured intermolecular distance distributions were used to deduce the isotropic intermolecular potential as well as the binding energies of the dimers.

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. Unfortunately, MD simulations using current physics-based models tend to produce disordered-state ensembles that are structurally too compact relative to experiments. We find that the water models typically used in MD simulations significantly underestimate London dispersion interactions, and speculate that this may be a possible reason for these erroneous results. To test this hypothesis, we create a new water model, TIP4P-D, that approximately corrects for these deficiencies in modeling water dispersion interactions while maintaining compatibility with existing physics-based models. We show that simulations of solvated proteins using this new water model typically result in disordered states that are substantially more expanded and in better agreement with experiment. These results represent a significant step toward extending the range of applicability of MD simulations to include the study of (partially or fully) disordered protein states.

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 1.5 and 1.3 for Li and Na cations, respectively, as compared with the pairwise sum of direct H(2)-M(+) and H(2)-PAH contributions. In the Li case, the presence of PAH not only does not promote H(2) binding but has a large (approximately 20%) weakening effect in comparison with the initial H(2)-Li(+) interaction. In the Na case, the presence of PAH has the usual stabilizing influence on the hydrogen binding. A careful analysis of the physical components of the nonadditive effect on the example of H(2)-M(+)-benzene complexes revealed the dominating role of the induction nonadditivity.

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. The calculated results are in excellent quantitative (rmsd = 1.0 kcal/mol) and qualitative (R(2) = 0.90) agreement with experimental data. The potential of the methodology to explain the observed differences in the ligand affinities is also demonstrated.

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.