Stress decomposition of a wave pulse traveling left to right through graphene nanotubes either in the armchair (upper) or zigzag (lower) configurations.

<p>Data are shown for the 450 fs time-point.</p

The delta in residue-averaged hydrostatic pressure between clusters 1 and 2 (solid, blue line) and the associated standard error of the mean (dashed, red line) for all 58 residues of BPTI.

<p>Residues with large (greater in magnitude than 500 bar) are labeled.</p

Residue-averaged differences in stress between clusters 1 and 2 (cluster 1 minus cluster 2).

<p>The left color spectrum applies to the total stress, and the right color spectrum applies to all of the stress components.</p

Mean square fluctuations of the residue-averaged stresses computed from the 1 ms BPTI trajectory.

<p>(Left) Cluster 2; values range from 1.50 to 5.08 Mbar. (Right) Difference between cluster 1 and 2 (cluster 1 minus cluster 2); values range from −90.3 to 63.6 kbar. Purple (negative) and orange (positive) indicate regions where cluster 1 has less or more stress fluctuations than cluster 2, respectively.</p

Formulae for mean principal stress (negative hydrostatic pressure) associated with potential terms in common classical force-fields.

<p>Formulae for mean principal stress (negative hydrostatic pressure) associated with potential terms in common classical force-fields.</p

Charge Hydration Asymmetry: The Basic Principle and How to Use It to Test and Improve Water Models

Charge hydration asymmetry (CHA) manifests itself in the experimentally observed strong dependence of free energy of ion hydration on the sign of the ion charge. This asymmetry is not consistently accounted for by popular models of solvation; its magnitude varies greatly between the models. While it is clear that CHA is somehow related to charge distribution within a water molecule, the exact nature of this relationship is unknown. We propose a simple, yet general and rigorous criterion that relates rotational and charge inversion properties of a water molecule’s charge distribution with its ability to cause CHA. We show which electric multipole components of a water molecule are key to explain its ability for asymmetric charge hydration. We then test several popular water models and explain why specific models show none, little, or strong CHA in simulations. We use the gained insight to derive an analogue of the Born equation that includes the missing physics necessary to account for CHA and does not rely on redefining the continuum dielectric boundary. The proposed formula is as simple as the original, does not contain any fitting parameters, and predicts hydration free energies and entropies of spherical cations and anions within experimental uncertainty. Our findings suggest that the gap between the practical continuum electrostatics framework and the more fundamental explicit solvent treatment may be reduced considerably by explicitly introducing CHA into the existing continuum framework

Bridging Calorimetry and Simulation through Precise Calculations of Cucurbituril–Guest Binding Enthalpies

We used microsecond time scale molecular dynamics simulations to compute, at high precision, binding enthalpies for cucurbit[7]­uril (CB7) with eight guests in aqueous solution. The results correlate well with experimental data from previously published isothermal titration calorimetry studies, and decomposition of the computed binding enthalpies by interaction type provides plausible mechanistic insights. Thus, dispersion interactions appear to play a key role in stabilizing these complexes, due at least in part to the fact that their packing density is greater than that of water. On the other hand, strongly favorable Coulombic interactions between the host and guests are compensated by unfavorable solvent contributions, leaving relatively modest electrostatic contributions to the binding enthalpies. The better steric fit of the aliphatic guests into the circular host appears to explain why their binding enthalpies tend to be more favorable than those of the more planar aromatic guests. The present calculations also bear on the validity of the simulation force field. Somewhat unexpectedly, the TIP3P water yields better agreement with experiment than the TIP4P-Ew water model, although the latter is known to replicate the properties of pure water more accurately. More broadly, the present results demonstrate the potential for computational calorimetry to provide atomistic explanations for thermodynamic observations