Ab initio calculations are used to calculate the atomic charges in the selectivity filter part of KcsA potassium channel according to the Merz–Kollman–Singh scheme. On the basis of a long molecular dynamics simulation, we show that these charges deviate significantly from the values usually implemented in the most common force fields. These consequent changes may considerably influence our view...

The fragmentation of multiply charged atomic sodium clusters of mass 200 is investigated using the Micro-canonical Metropolis Monte Carlo (MMMC) statistical technique for excitation energies up to 200 eV and for cluster charges up to +9e. In this work we present caloric curves and charged and uncharged fragment mass distributions for clusters with charges 0, 2, and 4. The caloric curves show a ...

The ability of insulating materials to trap charges is a phenomenon of interest in many technological fields such as information storage, electron beam lithography and formation of electrets for instance. However, charge-trapping characteristics are not well understood in spite of a large amount of studies carried out mainly by scanning electron microscopy (SEM) [1,2] and more recently by atomi...

We have studied the transferability of atomic charges for proteins, fitted to the quantum mechanical electrostatic potential and extensively averaged over a set of structures sampled by molecular dynamics (MD) and over all residue of the same kind in the protein sequence (xAvESP). Previously, such charges were obtained for one single protein (avidin). In this study, we employ five additional pr...

A simple but accurate approach, the charge-on-site scheme, is introduced to calculate coupling matrix elements for electron transfer (ET) in donor–bridge–acceptor (d–b–a) systems. The electronic coupling is explicitly expressed through energies of relevant adiabatic states and charges on the donor and acceptor sites. The method is formulated within twoand multistate models. The proposed scheme ...

The conformational properties of conjugated heteroaromatic bipyridines, pyridyl-pyridiniums and bipyridinium have been investigated using density functional theory (DFT). The molecules studied were neutral 2,20-bipyridine (2,20-bpy), 2,30bipyridine (2,30-bpy) and 3,30-bipyridine (3,30-bpy) and the singly protonated 3-pyridyl-20-pyridinium (3-py-20-pyH) and 2pyridyl-20-pyridinium (2-py-20-pyH) a...

Combined quantum mechanics/molecular mechanics (QM/MM) methods are increasingly important for the study of chemical reactions and systems in condensed phases. Here, we have tested the accuracy of a density functional theory-based QM/MM implementation (B3LYP/6-311+G(d,p)/CHARMM27) on a set of biologically relevant interactions by comparison with full QM calculations. Intermolecular charge transf...

The Gibbs energy of hydration is an important quantity to understand the molecular behavior in aqueous systems at constant temperature and pressure. In this work we review the performance of some popular force fields, namely TraPPE, OPLS-AA and Gromos, in reproducing the experimental Gibbs energies of hydration of several alkyl-aromatic compounds--benzene, mono-, di- and tri-substituted alkylbe...

Gaussian-3 total energies has been approximated using single-point Hartree-Fock-self-consistent field (HFSCF) total energies plus the correlation energy corrections calculated from the HF-SCF partial atomic charges according to the rapid estimation of correlation energy from partial charges (RECEP) method (Chem. Phys. Lett. 1999, 307, 469). Sixty-five closed-shell neutral molecules (composed of...

The pairwise descreening approximation provides a rapid computational algorithm for the evaluation of solute shape effects on electrostatic contributions to solvation energies. In this article we show that solvation models based on this algorithm are useful for predicting free energies of solvation across a wide range of solute functionalities, and we present six new general parametrizations of...