Unified Approach for Molecular Dynamics and Density-Functional Theory

Car, Roberto; Parrinello, Michele

doi:10.1103/physrevlett.55.2471

Cited by 10,310 publications

(6,542 citation statements)

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“…Dynamical density funtional theory (DFT) calculations were carried out with the projector augmented-wave (PAW) method of Blöchl, 24 which is an implementation of the Car-Parrinello ab initio molecular dynamics. 25 The energy cutoff of the plane wave basis set was set to 30 Ry, and the calculations used the frozen-core approximation. All calculations employed the exchange correlation functional of the generalized gradient approximation with the local potential of Perdew and Zunger 26 To prevent electrostatic interactions between periodic images, a chargeisolation scheme was used.…”

Section: Computational Detailsmentioning

confidence: 99%

Conformational Pathways of Saturated Six-Membered Rings. A Static and Dynamical Density Functional Study

et al. 2005

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Vous avez des questions? Nous pouvons vous aider. Pour communiquer directement avec un auteur, consultez la première page de la revue dans laquelle son article a été publié afin de trouver ses coordonnées. Si vous n'arrivez pas à les repérer, communiquez avec nous à PublicationsArchive-ArchivesPublications@nrc-cnrc.gc.ca. Questions? Contact the NRC Publications Archive team atPublicationsArchive-ArchivesPublications@nrc-cnrc.gc.ca. If you wish to email the authors directly, please see the first page of the publication for their contact information. NRC Publications Archive Archives des publications du CNRCThis publication could be one of several versions: author's original, accepted manuscript or the publisher's version. / La version de cette publication peut être l'une des suivantes : la version prépublication de l'auteur, la version acceptée du manuscrit ou la version de l'éditeur. NRC Publications Record / Notice d'Archives des publications de CNRC:http://nparc.cisti-icist.nrc-cnrc.gc.ca/eng/view/object/?id=357c916e-19e7-4437-b461-25622e976464 http://nparc.cisti-icist.nrc-cnrc.gc.ca/fra/voir/objet/?id=357c916e-19e7-4437-b461-25622e976464 Wako-shi, Saitama 351, Japan ReceiVed: April 27, 2005; In Final Form: July 12, 2005 The conformation of the six-membered ring of pyranosyl sugars has pronounced effects on the physical and chemical properties of carbohydrates. We present a method to determine key features of the potential energy surfaces, such as transition states associated with the inversion pathways of the model compounds cyclohexane, tetrahydropyran, p-dioxane, m-dioxane, s-trioxane, and 2-oxanol. Finally, we make the first determination of the pathways for inversion of penta-O-methyl-R-D-glucopyranose and penta-O-methyl--D-glucopyranose. For both anomers, a transition state with five coplanar atoms with appreciable O E character was found. The method is based on constrained Car-Parrinello ab initio molecular dynamics, as implemented in the projector augmented-wave (PAW) method. The constraints are derived from the normal modes of six-membered rings and are described in terms of the canonical conformations 1 C 4 chair, 1,4 B boat, and O S 2 skew-boat. The PAW derived trajectories are in agreement with previous suggestions in the literature that pseudorotation is an important feature of such conformational interconversions. The dynamic nature as well as the internal coordinate-based constraints provide a method which can reliably accommodate pseudorotation. To determine semiquantitative energies, we recalculate key conformations using standard quantum mechanical calculations while keeping the ring dihedral angles frozen at their values found in the dynamics. In all cases where experimental barriers are known, our results are in excellent agreement.

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Section: Computational Detailsmentioning

confidence: 99%

Conformational Pathways of Saturated Six-Membered Rings. A Static and Dynamical Density Functional Study

et al. 2005

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“…The most rigorous approach would be ab initio Car-Parrinello simulations (CPMD). 27 Such an approach is not practical for very large systems such as proteins. Traditionally, protein dynamics are studied through classical MD simulations, and classical force fields such as CHARMM 22 and AMBER 21 are used extensively to study the structure and dynamics of proteins.…”

Section: Introductionmentioning

confidence: 99%

Modeling the Absorption Spectrum of Tryptophan in Proteins

et al. 2005

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We have applied time-dependent density functional theory (TDDFT) to study the valence π-π* excited states of the tryptophan chromophore in the environment of the proteins barnase and human serum albumin. The chromophore is represented by indole. Due to the approximate nature of TDDFT, in the gas phase the calculated vertical transition energies to the 1 L valence states are reordered with respect to experiment. The 1 L a state responds more than the 1 L b state to the local environment, described fully at the TDDFT level, and to bulk environment, described by a set of point charges. Nevertheless, the vertical transitions are readily identified. For human serum albumin, our calculations predict distinct spectral characteristics between structures with different tryptophan side chain torsion angles. The computational tractability of TDDFT relative to more accurate ab initio methods allows a large part of the surrounding protein environment (up to 100 atoms) to be explicitly included in the TDDFT calculations.

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“…This approach makes atomic forces trivial to implement. Lattice stresses are also straightforward to implement, making it applicable to both confined and extended systems, as well as Car-Parrinello molecular dynamics simulations 44 .…”

Section: Discussionmentioning

confidence: 99%

Parallel implementation of γ‐point pseudopotential plane‐wave DFT with exact exchange

et al. 2010

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Semi-local functionals commonly used in density functional theory (DFT) studies of solids usually fail to reproduce localized states such as trapped holes, polarons, excitons, and solitons. This failure is ascribed to self-interaction which creates a Coulomb barrier to localization. Pragmatic approaches in which the exchange correlation functionals are augmented with small amount of exact exchange (hybrid-DFT, e.g. B3LYP and PBE0) have shown promise in rectifying this type of failure, as well as producing more accurate band gaps and reaction barriers. The evaluation of exact exchange is challenging for large, solid state systems with periodic boundary conditions, especially when plane-wave basis sets are used. We have developed parallel algorithms for implementing exact exchange into pseudopotential plane-wave DFT program and we have implemented them in the NWChem program package. The technique developed can readily be employed in Γ-point plane-wave DFT programs. Furthermore, atomic forces and stresses are straightforward to implement, making it applicable to both confined and extended systems, as well as to Car-Parrinello ab initio molecular dynamic simulations. This method has been applied to several systems for which conventional DFT methods do not work well, including calculations for band gaps in oxides and the electronic structure of a charge trapped state in the Fe(II) containing mica, annite.2

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Unified Approach for Molecular Dynamics and Density-Functional Theory

Cited by 10,310 publications

References 9 publications

Conformational Pathways of Saturated Six-Membered Rings. A Static and Dynamical Density Functional Study

Conformational Pathways of Saturated Six-Membered Rings. A Static and Dynamical Density Functional Study

Modeling the Absorption Spectrum of Tryptophan in Proteins

Parallel implementation of γ‐point pseudopotential plane‐wave DFT with exact exchange

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