Molecular Modeling of Trifluoromethanesulfonic Acid for Solvation Theory

Molecular dynamics study of solvation effects on acid dissociation in aprotic media

Acid ionization in aprotic media is studied using Molecular Dynamics techniques. In particular, models for HCl ionization in acetonitrile and dimethylsulfoxide are investigated. The proton is treated quantum mechanically using Feynman path integral methods and the remaining molecules are treated classically. Quantum effects are shown to be essential for the proper treatment of the ionization. The potential of mean force is computed as a function of the ion pair separation and the local solvent structure is examined. The computed dissociation constants in both solvents differ by several orders …

Modeling Charge-Sign Asymmetric Solvation Free Energies With Nonlinear Boundary Conditions

We show that charge-sign-dependent asymmetric hydration can be modeled accurately using linear Poisson theory but replacing the standard electric-displacement boundary condition with a simple nonlinear boundary condition. Using a single multiplicative scaling factor to determine atomic radii from molecular dynamics Lennard-Jones parameters, the new model accurately reproduces MD free-energy calculations of hydration asymmetries for (i) monatomic ions, (ii) titratable amino acids in both their protonated and unprotonated states, and (iii) the Mobley "bracelet" and "rod" test problems [J. Phys. …

Review: Multifield mediation of the hydrogen-bonding network and properties of the deionized water and the monovalent Lewis-Hofmeister solutions

Charge injection in terms of anions, cations, electrons, lone pairs, protons, and molecular dipoles by acid,base, salt and organic molecular solvation mediates the O:HO bonding network and properties of the solution through O:H formation, HH fragillization, O:=:O compression, electrostatic polarization, H2O dipolar shielding, and solute/solute interaction

Multimodel Approach to the Optical Properties of Molecular Dyes in Solution

We introduce a multimodel approach to the simulation of the optical properties of molecular dyes in solution, whereby the effects of thermal fluctuations and of dielectric screening on the absorption spectra are accounted for by explicit and implicit solvation models, respectively. Thermal effects are treated by averaging the spectra of molecular configurations generated by an ab initio molecular-dynamics simulation where solvent molecules are treated explicitly. Dielectric effects are then dealt with implicitly by computing the spectra upon removal of the solvent molecules and their replaceme…

Dynamical coupling between protein conformational fluctuation and hydration water: Heterogeneous dynamics of biological water

We investigate dynamical coupling between water and amino acid side-chain residues in solvation dynamics by selecting residues often used as natural probes, namely tryptophan, tyrosine and histidine, located at different positions on protein surface and having various degrees of solvent exposure. Such differently placed residues are found to exhibit different timescales of relaxation. The total solvation response, as measured by the probe is decomposed in terms of its interactions with (i) protein core, (ii) side-chain atoms and (iii) water molecules. Significant anti cross-correlations among …

单单价离子在参考相互作用位模型中的优化参数集开发

Development of an Optimized Parameter Set for Monovalent Ions in the Reference Interaction Site Model of Solvation

本文通过优化Lennard-Jones 12-6模型参数，提升了1D-RISM在单单价离子水合自由能、离子-氧距离和平均活度系数的准确性，并验证了其在不同盐浓度下的有效性。