Wrapping Up Hydrophobic Hydration: Locality Matters.

Water, being the universal solvent, acts as a competing agent in fundamental processes, such as folding, aggregation or biomolecular recognition. A molecular understanding of hydrophobic hydration is of central importance to understanding the subtle free energy differences, which dictate function. Ab initio and classical molecular dynamics simulations yield two distinct hydration water populations in the hydration shell of solvated tert-butanol noted as "HB-wrap" and "HB-hydration2bulk". The experimentally observed hydration water spectrum can be dissected into two modes, centered at 164 and 195 cm-1. By comparison to the simulations, these two bands are attributed to the "HB-wrap" and "HB-hydration2bulk" populations, respectively. We derive a quantitative correlation between the population in each of these two local water coordination motifs and the temperature dependence of the solvation entropy. The crossover from entropy to enthalpy dominated solvation at elevated temperatures, as predicted by theory and observed experimentally, can be rationalized in terms of the distinct temperature stability and thermodynamic signatures of "HB-wrap" and "HB-hydration2bulk".

Graph theory for automatic structural recognition in molecular dynamics simulations.

Graph theory algorithms have been proposed in order to identify, follow in time, and statistically analyze the changes in conformations that occur along molecular dynamics (MD) simulations. The atomistic granularity level of the MD simulations is maintained within the graph theoric algorithms proposed here, isomorphism is a key component together with keeping the chemical nature of the atoms. Isomorphism is used to recognize conformations and construct the graphs of transitions, and the reduction in complexity of the isomorphism has been achieved by the introduction of "orbits" and "reference snapshots." The proposed algorithms are applied to MD trajectories of gas phase molecules and clusters as well as condensed matter. The changes in conformations followed over time are hydrogen bond(s), proton transfer(s), coordination number(s), covalent bond(s), multiple fragmentation(s), and H-bonded membered rings. The algorithms provide an automatic analysis of multiple trajectories in parallel, and can be applied to ab initio and classical MD trajectories alike, and to more coarse grain representations.