Partition coefficients of methylated DNA bases obtained from free energy calculations with molecular electron density derived atomic charges

Partition coefficients serve in various areas as pharmacology and environmental sciences to predict the hydrophobicity of different substances. Recently, they have also been used to address the accuracy of force fields for various organic compounds and specifically the methylated DNA bases. In this study, atomic charges were derived by different partitioning methods (Hirshfeld and Minimal Basis Iterative Stockholder) directly from the electron density obtained by electronic structure calculations in a vacuum, with an implicit solvation model or with explicit solvation taking the dynamics of the solute and the solvent into account. To test the ability of these charges to describe electrostatic interactions in force fields for condensed phases, the original atomic charges of the AMBER99 force field were replaced with the new atomic charges and combined with different solvent models to obtain the hydration and chloroform solvation free energies by molecular dynamics simulations. Chloroform-water partition coefficients derived from the obtained free energies were compared to experimental and previously reported values obtained with the GAFF or the AMBER-99 force field. The results show that good agreement with experimental data is obtained when the polarization of the electron density by the solvent has been taken into account, and when the energy needed to polarize the electron density of the solute has been considered in the transfer free energy. These results were further confirmed by hydration free energies of polar and aromatic amino acid side chain analogs. Comparison of the two partitioning methods, Hirshfeld-I and Minimal Basis Iterative Stockholder (MBIS), revealed some deficiencies in the Hirshfeld-I method related to the unstable isolated anionic nitrogen pro-atom used in the method. Hydration free energies and partitioning coefficients obtained with atomic charges from the MBIS partitioning method accounting for polarization by the implicit solvation model are in good agreement with the experimental values. © 2018 Wiley Periodicals, Inc.

Charge separation and isolation in strong water droplet impacts

Charge separation in condensed matter after strong impacts is a general and intriguing phenomenon in nature, which is often identified and described but not necessarily well understood in terms of a quantitative mechanistic picture. Here we show that charge separation naturally occurs if water droplets/clusters or ice particles with embedded charge carriers, e.g., ions, encounter a high energy impact with subsequent dispersion - even if the involved kinetic energy is significantly below the molecular ionization energy. We find that for low charge carrier concentrations (c < 0.01 mol L(-1)) a simple statistical Poisson model describes the charge distribution in the resulting molecular "fragments" or aggregates. At higher concentrations Coulomb interactions between the charge carriers become relevant, which we describe by a Monte Carlo approach. Our models are compared to experimental data for strong (laser) impacts on liquid micro beams and discussed for the charge generation in cluster-impact mass spectrometry on cosmic dust detectors where particle kinetic energies are below the plasma threshold. Taken together, a simple and intuitive but quantitative microscopic model is obtained, which may contribute to the understanding of a larger range of phenomena related to charge generation and separation in nature.

Hydrogen bond dynamics of superheated water and methanol by ultrafast IR-pump and EUV-photoelectron probe spectroscopy

Snapshot of superheated water 40 ps after fs-IR laser excitation; representative aggregates formed during the simulation (close-up) compared to one obtained from superheated methanol phase (inset).

Water Catalysis of a Radical-Molecule Gas-Phase Reaction

There has been considerable speculation about the role of water and water complexes in chemical gas-phase reactions, including the conjecture that water may act as a molecular catalyst through its ability to form hydrogen bonds. Here, we present kinetic studies in which the effect of water on the rate of the reaction between hydroxyl radicals and acetaldehyde has been measured directly in Laval nozzle expansions at low temperatures. An increasing enhancement of the reaction rate by added water was found with decreasing temperatures between 300 and 60 kelvin. Quantum chemical calculations and statistical rate theory support our conclusions that this observation is due to the reduction of an intrinsic reaction barrier caused by specific water aggregation. The results suggest that even single water molecules can act as catalysts in radical-molecule reactions.