Comment on "Using quaternions to calculate RMSD" [J. Comp. Chem. 25, 1849 (2004)

Coutsias et al. have recently published a method to find the optimal rotational superposition of two molecular structures, which is based on a representation of rotations by quaternions (J. Comp. Chem. 25(15), 1849 (2004)). The method, which has been suggested by other authors before, is compared to the one by Kabsch, where the elements of the rotation matrix are directly used as variables of the optimization problem. The statement that the two methods are equivalent is misleading in the sense that the Kabsch method may yield an improper optimal rotation, which must be explicitly checked for, whereas the quaternion method does not mix proper and improper rotations. Nevertheless, both types of solutions can be considered by solving the same eigenvector problem. The relation between the two types of solutions is briefly discussed and bounds for the eigenvalues are given.     

Coherent dynamics of meta-toluidine investigated by quasielastic neutron scattering

The coherent dynamics of a typical fragile glass former, meta-toluidine, was investigated at the molecular level using quasielastic neutron scattering, with time-of-flight and neutron spin echo spectrometers. It is well known that the static structure factor of meta-toluidine shows a prepeak originating from clustering of the molecules through hydrogen bonding between the amine groups. The dynamics of meta-toluidine was measured for several values of the wavevector transfer Q, which is equivalent to an inverse length scale, in a range encompassing the prepeak and the structure factor peak. Data were collected in the temperature range corresponding to the liquid and supercooled states, down to the glass transition. At least two dynamical processes were identified. This paper focuses on the slowest relaxation process in the system, the α-relaxation, which was found to scale with the macroscopic shear viscosity at all the investigated Q values. No evidence of "de Gennes" narrowing associated with the prepeak was observed, in contrast with what happens at the Q value corresponding to the interparticle distance. Moreover, using partially deuterated samples, the dynamics of the clusters was found to be correlated to the single-particle dynamics of the meta-toluidine molecules.     

nMoldyn 3: Using task farming for a parallel spectroscopy‐oriented analysis of molecular dynamics simulations

We present a new version of the program package nMoldyn, which has been originally developed for a neutron‐scattering oriented analysis of molecular dynamics simulations of macromolecular systems (Kneller et al., Comput. Phys. Commun. 1995, 91, 191) and was later rewritten to include in‐depth time series analyses and a graphical user interface (Rog et al., J. Comput. Chem. 2003, 24, 657). The main improvement in this new version and the focus of this article are the parallelization of all the analysis algorithms for use on multicore desktop computers as well as distributed‐memory computing clusters. The parallelization is based on a task farming approach which maintains a simple program structure permitting easy modification and extension of the code to integrate new analysis methods. © 2012 Wiley Periodicals, Inc.     

Concerted and stepwise proton-coupled electron transfers in aquo/hydroxo complex couples in water: oxidative electrochemistry of [Os(II)(bpy)(2)(py)(OH(2))](2+)

Successive oxidation of transition metal(II) aqua complexes (M(II)OH(2) to M(III)OH) is a domain in which proton-coupled electron transfer reactions are extremely common. The mechanism of these PCET reactions-concerted or stepwise-is an important issue in the understanding and design of natural or artificial systems catalyzing the formation of dioxygen by four-electron oxidation of water. Concerted proton-coupled electron transfer from an aqua metal(II) to a hydroxo metal(III) complex requires the close proximity of a proton-accepting group with a pK value between those of the aqua complexes. Otherwise, stepwise electron-proton or proton-electron pathways involving high-energy intermediates are followed. Concerted proton-electron pathways involving water as proton-acceptor or proton-donor group are inefficient. Cyclic voltammetry of the title complex in buffered aqueous solution and re-examination of previous results for the same complex attached to an electrode surface are used to establish these conclusions, which provide a starting point on the route to higher degrees of oxidation, such as those involved in the catalysis of water oxidation.     

The numerical integration of relative equilibrium solutions. The nonlinear Schrodinger equation

We analyse different error propagation mechanisms for conservativeand nonconservative time-integrators of nonlinear Schrödingerequations. We use a geometric approach based on interpretingwaves as relative equilibria.     

Quasielastic neutron scattering and relaxation processes in proteins: analytical and simulation-based models

The present article gives an overview of analytical and simulation approaches to describe the relaxation dynamics of proteins. Particularly emphasised are recent developments of theoretical models, such as fractional Brownian dynamics. The latter connects dynamical events seen on the pico- to nanosecond time scale, accessible to quasielastic neutron scattering, and functional dynamics of proteins on much longer time scales.