J. Chem. Theory Comput. 2014, 10 (11), 5113−5124. DOI:10.1021/ct500569b In our paper we did not properly acknowledge the contribution by Head-Gordon and co-workers (ref 41 of our manuscript). These authors used a similar modification of the mixing rules for protein−water interactions, although the correction was applied on a per-atom basis to both the characteristic distance (sigma) and energy ...

The excited states of a flavin-related compound, lumiflavin, were studied by the symmetry-adapted cluster (SAC)-configuration interaction (CI) ethod. The absorption peaks observed in the experimental spectrum were theoretically assigned. Transition energy of some low-lying n– * states ere obtained. The energy minimum structures of the first singlet and triplet excited states were calculated by ...

Small molecule permeability through cellular membranes is critical to a better understanding of pharmacodynamics and the drug discovery endeavor. Such permeability may be estimated as a function of the free energy change of barrier crossing by invoking the barrier domain model, which posits that permeation is limited by passage through a single "barrier domain" and assumes diffusivity differenc...

Tetrahydroimidazo-[4,5,l-jk][1,4]-benzodiazepin-2-(1H)-one (TIBO) derivatives are important nonnucleoside human immunodeficiency virus-1 reverse transcriptase inhibitors (NNRTI). Several TIBO derivatives have shown high potency to inhibit reverse transcriptase (RT) and one (Tivirapine) has entered into clinical trials. The free energy of binding (FEB) is a numerical way to express the binding a...

Naproxen was studied by classical thermoanalytical methods, namely sublimation calorimetry, solution calorimetry and the solubility method. Temperature dependence of a saturated vapor pressure was obtained and the sublimation enthalpy, deltaHsub(0) and entropy, deltaSsub(0) and their relative fraction of the total process were calculated. These parameters yielded for naproxen were compared to t...

In this study, we have attempted to explore the molecular mechanism associated with a diffusion controlled reaction at a polymer hydration region by monitoring temperature-dependent solvolysis reaction of benzoyl chloride (BzCl) in water-poly(ethylene glycol) mixture at low water concentration. BzCl being highly hydrophobic resides in the vicinity of the PEG surface and the reaction takes place...

We present a method called MOPED for optimizing energetic and structural parameters in computational models, including all-atom energy functions, when native structures and decoys are given. The present method goes beyond previous approaches in treating energy functions that are nonlinear in the parameters and continuous in the degrees of freedom. We illustrate the method by improving solvation...

Rigorously continuous and smooth potential energy surfaces, as well as exact analytic gradients, are obtained for a conductorlike screening solvation model (CPCM, a variant of the general COSMO) with Hartree-Fock (RHF, ROHF, UHF, and MCSCF) and density functional theory (R-DFT, RO-DFT, and U-DFT) methods using a new tessellation scheme, fixed points with variable areas (FIXPVA). In FIXPVA, sphe...

Recently, the combination of state-of-the-art molecular mechanical force fields with continuum solvation models enables us to make relatively accurate predictions of both structures and free energies for macromolecules from molecular dynamics trajectories. The first part of this review is focused on the history and basic theory of free energy calculations based on physically effective energy fu...