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Radu Iftimie

Publications and source records attributed to Radu Iftimie.

6 recordsLinked to original sources
PubMed2006

Ab initio and empirical model MD simulation studies of solvent effects on the properties of N-methylacetamide along a cis-trans isomerization pathway.

The properties of N-methylacetamide along a cis-trans isomerization pathway described by twisting about the C(O)-N bond are examined at finite temperature both in vacuo and in explicit water solvent. Two distinctly different theoretical descriptions, an ab initio (DFT-BLYP) and an empirical (CHARMM22) model, are studied in order to permit an assessment of the dominant forces active in the system. An analysis of the solvent structure at equilibrium and changes in solvation structure accompanying isomerization is, therefore, given for each model. Many-body polarization effects absent under CHARMM22 but present in the ab initio model are found to have a profound influence on the system. The electronic structure of the NMA molecule predicted by the ab initio method along the reaction coordinate is examined in order to shed further light on changes in peptide "partial-double" bond character [C(O)-N] as isomerization takes place. A new statistical-mechanical interpretation of the entropy change during a chemical reaction is presented to help interpret the thermochemistry of the simple reaction.

Acetamides↗
PubMed2005

Decomposing total IR spectra of aqueous systems into solute and solvent contributions: a computational approach using maximally localized Wannier orbitals.

The theoretical principles underpinning the calculation of infrared spectra for condensed-phase systems in the context of ab initio molecular dynamics have been recently developed in literature. At present, most ab initio molecular dynamics calculations are restricted to relatively small systems and short simulation times. In this paper we devise a method that allows well-converged results for infrared spectra from ab initio molecular dynamics simulations using small systems and short trajectories characteristic of simulations typically performed in practice. We demonstrate the utility of our approach by computing the imaginary part of the dielectric constant epsilon"(omega) for H2O and D2O in solid and liquid phases and show that it compares well with experimental data. We further demonstrate that maximally localized Wannier orbitals can be used to separate the individual contributions of different molecular species to the linear spectrum of complex systems. The new spectral decomposition method is shown to be useful in present-day ab initio molecular dynamics calculations to compute the magnitude of the "continuous absorption" generated by excess protons in aqueous solutions with good accuracy even when other species present in the solutions absorb strongly in the same frequency window.

Journal Article↗
PubMed2005

Ab initio molecular dynamics: concepts, recent developments, and future trends.

The methodology of ab initio molecular dynamics, wherein finite-temperature dynamical trajectories are generated by using forces computed "on the fly" from electronic structure calculations, has had a profound influence in modern theoretical research. Ab initio molecular dynamics allows chemical processes in condensed phases to be studied in an accurate and unbiased manner, leading to new paradigms in the elucidation of microscopic mechanisms, rationalization of experimental data, and testable predictions of new phenomena. The purpose of this work is to give a brief introduction to the technique and to review several important recent developments in the field. Several illustrative examples showing the power of the technique have been chosen. Perspectives on future directions in the field also will be given.

Biophysics↗
PubMed2004

On-the-fly localization of electronic orbitals in Car-Parrinello molecular dynamics.

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 Gamma-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.

Journal Article↗