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Dynamical properties of liquid water were studied using Car-Parrinello [Phys. Rev. Lett. 55, 2471 (1985)] ab initio molecular dynamics (AIMD) simulations within the Kohn-Sham (KS) density functional theory employing the Becke-Lee-Yang-Parr exchange-correlation functional for the electronic structure. The KS orbitals were expanded in a discrete variable representation basis set, wherein the complete basis set limit can be easily reached and which, therefore, provides complete convergence of ionic forces. In order to minimize possible nonergodic behavior of the simulated water system in a constant energy (NVE) ensemble, a long equilibration run (30 ps) preceded a 60 ps long production run. The temperature drift during the entire 60 ps trajectory was found to be minimal. The diffusion coefficient [0.055 Å2/ps] obtained from the present work for 32 D2O molecules is a factor of 4 smaller than the most up to date experimental value, but significantly larger than those of other recent AIMD studies. Adjusting the experimental result so as to match the finite-sized system used in the present study brings the comparison between theory and experiment to within a factor of 3. More importantly, the system is not observed to become “glassy” as has been reported in previous AIMD studies. The computed infrared spectrum is in good agreement with experimental data, especially in the low frequency regime where the translational and librational motions of water are manifested. The long simulation length also made it possible to perform detailed studies of hydrogen bond dynamics. The relaxation dynamics of hydrogen bonds observed in the present AIMD simulation is slower than those of popular force fields, such as the TIP4P potential, but comparable to that of the TIP5P potential. [ABSTRACT FROM AUTHOR]

We present a rigorous description of chemical space within a molecular grand-canonical ensemble multi-component density functional theory framework. A total energy density functional for chemical compounds in contact with an electron and a proton bath is introduced using Lagrange multipliers which correspond to the energetic response to changes of the elementary particle densities. From a generalized Gibbs-Duhem equation analog, reactivity indices such as the nuclear hardness and a molecular Fukui function, which couples the grand-canonical electronic and nuclear degrees of freedom, are obtained. Maxwell relations between composition particles, ionic displacements, and the external potential are discussed. Numerical results for the molecular Fukui function are presented as well as finite temperature estimates for the oxidation of ammonia. [ABSTRACT FROM AUTHOR]

Structural properties of liquid water at ambient temperature were studied using Car-Parrinello [Phys. Rev. Lett. 55, 2471 (1985)] ab initio molecular dynamics (CPAIMD) simulations combined with the Kohn-Sham (KS) density functional theory and the BLYP exchange-correlation functional for the electronic structure. Unlike other recent work on the same subject, where plane-wave (PW) or hybrid Gaussian/plane-wave basis sets were employed, in the present paper, a discrete variable representation (DVR) basis set is used to expand the KS orbitals, so that with the real-space grid adapted in the present work, the properties of liquid water could be obtained very near the complete basis set limit. Structural properties of liquid water were extracted from a 30 ps CPAIMD-BLYP/DVR trajectory at 300 K. The radial distribution functions (RDFs), spatial distribution functions, and hydrogen bond geometry obtained from the CPAIMD-BLYP/DVR simulation are generally in good agreement with the most up to date experimental measurements. Compared to recent ab initio MD simulations based on PW basis sets, less significant overstructuring was found in the RDFs and the distributions of hydrogen bond angles, suggesting that previous plane-wave and Gaussian basis set calculations have exaggerated the tendency toward overstructuring. [ABSTRACT FROM AUTHOR]

The ab initio molecular-dynamics formalism of Car and Parrinello is extended to preserve the locality of the orbitals. The supplementary term in the Lagrangian does not affect the nuclear dynamics, but ensures “on the fly” localization of the electronic orbitals within a periodic supercell in the Γ-point approximation. The relationship between the resulting equations of motion and the formation of a gauge-invariant Lagrangian combined with a gauge-fixing procedure is briefly discussed. The equations of motion can be used to generate a very stable and easy to implement numerical integration algorithm. It is demonstrated that this algorithm can be used to compute the trajectory of the maximally localized orbitals, known as Wannier orbitals, in ab initio molecular dynamics with only a modest increase in the overall computer time. In the present paper, the new method is implemented within the generalized gradient approximation to Kohn–Sham density-functional theory employing plane wave basis sets and atomic pseudopotentials. In the course of the presentation, we briefly discuss how the present approach can be combined with localized basis sets to design fast linear scaling ab initio molecular-dynamics methods. © 2004 American Institute of Physics. [ABSTRACT FROM AUTHOR]

A new formalism designed to treat long range interactions on surfaces, systems which are infinitely replicated in two spatial directions but have finite extent in the third, is developed. The new formalism is based in reciprocal space and, thus, permits the facile extension of standard plane-wave based density functional theory, Ewald summation, and smooth particle-mesh Ewald methods to handle surfaces efficiently. The method is tested on both model (body centered cubic lattices) and realistic problems (an ice surface with a defect and the 2 x 1 surface reconstruction of silicon) and found to be accurate, efficient, and a marked improvement on existing formulations in speed, accuracy, and utility. [ABSTRACT FROM AUTHOR]

Presents a reciprocal space based formalism for treating long range forces in clusters. Incorporation of the formalism into plane-wave based density function theory calculations, Ewald summation calculations and smooth particle-mesh Ewald calculations to yield accurate and numerically efficient descriptions of long range interactions in cluster systems.

Mixed quantum mechanical/molecular mechanical (QM/MM) models, in which one part of a system is treated at an ab initio level while the rest is described by an empirical force field, are becoming increasingly popular. In this Letter, we describe a simple QM/MM model for methanol (CH3OH) in which the OH constitutes the ab initio region and is treated within a density functional representation, while the methyl group, the MM region, is treated using the AMBER force field. The model is used to study the structure of the bulk liquid and is shown to compare favorably with the experimental structure. [Copyright &y& Elsevier]

The article examines the process of characterizing the catalic mechanism of histone deacetylases by usingdensity functional theory quantum mechanical and molecular mechanical (QM/MM) studies by histone-deacetylase-like protein. The calculations are based on the pseudobond ab initio QM/MM approach. The quantum mechanical subsystem is treated by the hybrid B3LYP functional with a Stuttgart ECP/basis set.