Thermal stability of water polyhedra with square faces

The ability to form numerous crystalline modifications of ice and gas hydrate frameworks is a characteristic feature of water. In fact, this structural variety is much wider due to the proton disorder. Configurations with different arrangements of hydrogen atoms (protons) in hydrogen bonds are not equivalent in their properties. Polyhedral water clusters are convenient objects for studying the effect of proton disorder on the properties of ice-like systems. It was previously established that the stability of water polyhedra is determined by the competition of two factors. The geometric factor gives preference to tetrahedrally coordinated structures with a large number of pentagonal faces. The topological factor takes into account the number of energetically most favorable types of H-bonds. This number increases with the number of square faces. It was found that tetrahedrally coordinated structures are not the most stable. However, these calculations were performed without taking thermal effects into account [Kirov M. V., J. Phys. Chem. A, 2020, 124, 4463−4470]. The purpose of the present article is to study the structural stability of various water polyhedra at different temperatures. In the course of modeling, using the Amoeba force field, the advantage of configurations with a large number of square faces is demonstrated. The structure and energetics of surface defects are studied. Several very stable structures of unusual shape were found, including polyhedra which contain 4-coordinated molecules and polyhedra whose O–H groups are directed to the cluster center. The comparative analysis of cluster stability includes the temperature intervals of melting-like transitions.

Implicit Solvents for the Polarizable Atomic Multipole AMOEBA Force Field

Computational protein design, ab initio protein/RNA folding, and protein-ligand screening can be too computationally demanding for explicit treatment of solvent. For these applications, implicit solvent offers a compelling alternative, which we describe here for the polarizable atomic multipole AMOEBA force field based on three treatments of continuum electrostatics: numerical solutions to the Poisson-Boltzmann equation (PBE), the domain-decomposition Conductor-like Screening Model (ddCOSMO) approximation to the PBE, and the analytic generalized Kirkwood (GK) approximation. The continuum electrostatic models are combined with a nonpolar estimator based on novel cavitation and dispersion terms. Electrostatic model parameters are numerically optimized using a least squares style target function based on a library of 103 small molecule solvation free energy differences. Mean signed errors for the APBS, ddCOSMO, and GK models are 0.05, 0.00, and 0.00 kcal/mol, respectively, while the mean unsigned errors are 0.70, 0.63, and 0.51 kcal/mol, respectively. Validation of the electrostatic response of the resulting implicit solvents, which are available in the Tinker (or Tinker-HP), OpenMM, and Force Field X software packages, is based on comparisons to explicit solvent simulations for a series of proteins and nucleic acids. Overall, the emergence of performative implicit solvent models for polarizable force fields will open the door to their use for folding and design applications.<br>

Implicit Solvents for the Polarizable Atomic Multipole AMOEBA Force Field

Computational protein design, ab initio protein/RNA folding, and protein-ligand screening can be too computationally demanding for explicit treatment of solvent. For these applications, implicit solvent offers a compelling alternative, which we describe here for the polarizable atomic multipole AMOEBA force field based on three treatments of continuum electrostatics: numerical solutions to the Poisson-Boltzmann equation (PBE), the domain-decomposition Conductor-like Screening Model (ddCOSMO) approximation to the PBE, and the analytic generalized Kirkwood (GK) approximation. The continuum electrostatic models are combined with a nonpolar estimator based on novel cavitation and dispersion terms. Electrostatic model parameters are numerically optimized using a least squares style target function based on a library of 103 small molecule solvation free energy differences. Mean signed errors for the APBS, ddCOSMO, and GK models are 0.05, 0.00, and 0.00 kcal/mol, respectively, while the mean unsigned errors are 0.70, 0.63, and 0.51 kcal/mol, respectively. Validation of the electrostatic response of the resulting implicit solvents, which are available in the Tinker (or Tinker-HP), OpenMM, and Force Field X software packages, is based on comparisons to explicit solvent simulations for a series of proteins and nucleic acids. Overall, the emergence of performative implicit solvent models for polarizable force fields will open the door to their use for folding and design applications.<br>

Excited state Born–Oppenheimer molecular dynamics through coupling between time dependent DFT and AMOEBA

We present the implementation of excited state Born–Oppenheimer molecular dynamics (BOMD) using a polarizable QM/MM approach based on time-dependent density functional theory (TDDFT) formulation and the AMOEBA force field.