Journal of Computational Chemistry

On page 996 (DOI: 10.1002/jcc.23899), Elmar Krieger and Gert Vriend describe a collection of algorithms to accelerate molecular dynamics simulations. The validation of the protocol includes simulations of the enzyme dihydrofolate reductase (shown at the back) and a capped alanine dipeptide (shown at the front). The phi/psi dihedral angle distribution extracted from the latter simulation is depicted as a free energy landscape in shades of blue. One of the acceleration methods involves the LINCS algorithm, tuned to constrain not only bonds but also selected angles formed by hydrogen atoms. These constraints are shown in bright orange for the alanine dipeptide, and for a larger peptide with sequence AIAFAWARATA in the middle.

Charge transfer among individual atoms is the key concept in modern electronic theory of chemical bonding. On page 1008 (DOI: 10.1002/jcc.23880), Yi Wang, William Yi Wang, Long-Qing Chen and Zi-Kui Liu present a first-principles approach to calculating the charge transfer. Based on the effects of perturbations of an individual atom or a group of atoms on the electron charge density, the amount of electron charge associated with a particular atom or a group of atoms is determined. The topological electron loss versus gain is demonstrated using ethylene, graphene, MgO, and SrTiO₃ as examples.

In nanopore force spectroscopy (NFS), a charged polymer is threaded through a channel of molecular dimensions. When an electric field is applied across the insulating membrane, the ionic current through the nanopore reports on polymer translocation, unzipping, dissociation, and so forth. A new model is presented that can be applied in molecular dynamics simulations of NFS. Although simplified, it does reproduce experimental trends and all-atom simulations. The model was applied to simulations of DNA hairpin unzipping in nanopores.

General approach to the phonon symmetry analysis for nanowires and nanotubes is outlined. It is illustrated on the example of TiO₂ rutile-based nanorods and TiO₂ anatase-based nanotubes with the hexagonal and rectangular morphology, respectively. The number and symmetry of Infrared active, Raman active, and silent modes is found, which is important for the vibrational spectra interpretations of the systems in consideration. There are four acoustic modes with zero frequencies for k = 0: three longitudinal acoustic and one twisting.

Mg²⁺ ions are essential for nucleic acid structure and function and this has motivated the development of several Mg²⁺ models for use in molecular simulations. As a first step in developing improved Mg²⁺ models for biomolecular simulations, we focus on the ability to which 17 different pairwise potential Mg²⁺ models, which belong to the most mature force fields for modeling nucleic acid dynamics, can simultaneously reproduce structural, thermodynamic, kinetic and mass transport properties in aqueous solution. These represent a balanced set of solution properties that serve as a useful departure point from which robust models for molecular dynamics simulations of biological processes can be developed by tuning pairwise interaction parameters.

A method is developed to study protein complexation in a system governed by specific and nonspecific interactions. Strong associations lead to narrow distributions in the configuration space; weak and ultraweak associations lead instead to broader distributions, a manifestation of nonspecific sparsely populated binding modes. The method can be used to explore alternative pathways of complexation with statistical significance and can be integrated into a general algorithm to study protein interaction networks in concentrated multispecies, multiprotein systems.

Molecular simulations with empirical force fields were originally a task for experts with huge computer clusters, but have nowadays become easily accessible for all interested scientists on their personal computers. The long simulation time scales needed to draw useful conclusions can be reached with faster hardware or faster software. This article concentrates on the latter and describes algorithms to speed up simulations, implemented in the molecular modeling program YASARA.

Charge transfer among individual atoms is the key concept in modern electronic theory of chemical bonding. A first-principles approach to calculating the charge transfer is presented. Based on the effects of perturbations of an individual atom or a group of atoms on the electron charge density, the amount of electron charge associated with a particular atom or a group of atoms is determined. The topological electron loss versus gain is demonstrated using ethylene, graphene, MgO, and SrTiO3 as examples.

QuickFF is a software package to derive accurate force fields for isolated and complex molecular systems in a quick and easy manner. Apart from its general applicability, the program has been designed to generate force fields for metal-organic frameworks in an automated fashion. The force field parameters for the covalent terms are derived from ab initio data. As a result, accurate force fields are generated with minimal effort.