Multipole moments for embedding potentials: Exploring different atomic allocation algorithms
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We review the state-of-the-art in computational molecular simulations for biological systems. We limit our discussion to three fields: all-atom simulations, coarse-grained models, and novel multiscale approaches. While molecular dynamics simulations are br ...
Chemoselective autoxidation of 4-imino-1,5-dimethyl-3-(4-nitrophenyl) imidazolidin-2-one (1b) to its 5-hydroxy derivative 2 occurred in solutions of DMSO-d(6), acetonitrile-d(3) or refluxing ethanol. Also bis(imidazolidin-5-yl) peroxide 5 was isolated as a ...
The need to perform large-scale molecular dynamics simulations of radiation defects in ferritic steels has stimulated the recent development of a 'magnetic' interatomic potential for body-centred cubic alpha-iron [1,2]. Here we describe the first applicati ...
In a recent work [Laio, A., VandeVondele, J., Rothlisberger, U. J. Phys. Chem. B 2002 106, 7300] a novel method has been proposed to define dynamical electrostatic potential derived (D-RESP) charges for systems described within a quantum mechanics/mol. mec ...
yWe develop a semi-empirical many-body interatomic potential suitable for large scale molecular dynamics simulations of magnetic a-iron. The functional form of the embedding part of the potential is derived using a combination of the Stoner and the Ginzbur ...
We propose a definition for the dipole of an individual molecule in a molecular solid or fluid. This problem is currently dealt with by partitioning-according to some prescription-the continuous electron density of the condensed phase. Instead, here we foc ...
Almost half of the proteome of living organisms is constituted of metalloproteins. Unfortunately, the ability of the current generation of molecular dynamics pairwise-additive forcefields to properly describe metal pockets is severely lacking due to the in ...
This thesis describes the application of the quantum mechanics/molecular mechanics (QM/MM) Car-Parrinello methodology to two systems of high biological interest: (a) The potassium channel KcsA from Streptomyces lividans and (b) The DNA repair enzyme EndoIV ...
Good things come in small packages: For its moderate molecular weight, the metallostar complex [Fe{Gd2L(H2O)4}3]4− (see picture; L is a bipyridine–poly(aminocarboxylate) derivative) displays exceptionally high proton relaxivity, which is explained in terms ...
A computational method for multiscale modeling of plasticity is presented wherein each dislocation is treated as either an atomistic or continuum entity within a single computational framework. The method divides space into atomistic and continuum regions ...