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Special Issue "Advances in Density Functional Theory"

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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Physical Chemistry, Theoretical and Computational Chemistry".

Deadline for manuscript submissions: closed (30 April 2012)

Special Issue Editor

Guest Editor
Dr. Jaime Ferrer

Departamento de Física, Universidad de Oviedo, 33007 Oviedo, Spain
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Special Issue Information

Dear Colleagues,

Density Functional Theory (DFT) has enabled the ability to determine the properties of molecules, nanostructures, bulk materials and biological matter from quantum mechanics. The Local Density Approximation to the exchange and correlation potential of the Jellium model performs remarkably well for a large majority of quantum systems. Its accuracy has even been improved by including density gradient corrections, exact exchange, hybrid functionals, self-interaction corrections, LDA+U or Dynamical Mean Field Theory approaches. DFT has even been proposed for tight-binding models of strongly correlated electrons. The practical limits of DFT are being pushed continually to larger length- and time-scales by the delivery of clever algorithms, the use of more powerful computer resources, or the recent deployment of GPU-based codes.

DFT is nowadays an essential tool box for the understanding of the physical mechanisms underlying the properties of matter. It has reached such a level of maturity that many experimental advances are brough hand in hand with, or at least followed shortly thereafter by a series on ab-initio simulations. This level of maturity has lead to a vast array of multidisciplinary collaborations between experimental and theoretical physicists, chemists, mineralogists and biologists.

This monographic issue will bring a flavor of some of the recent methodological advances. Examples include the development of new multi-scale algorithms that allow a smooth bridging between DFT and atomistic or continuum models, or the proposal of new approaches to describe sophisticated phenomena in strongly correlated materials. We also wellcome papers describing simulations where new grounds beyond the conventional realm of DFT are explored.

Dr. Jaime Ferrer
Guest Editor

Keywords

  • nanostructured materials
  • nanomagnetism
  • nanoelectronics
  • biophysics
  • graphene
  • topological insulators
  • multi-scale approaches
  • strong correlations
  • time-dependent phenomena

Published Papers (4 papers)

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Research

Open AccessArticle A Density Functional Theory Study on the Deformation Behaviors of Fe-Si-B Metallic Glasses
Int. J. Mol. Sci. 2012, 13(8), 10401-10409; doi:10.3390/ijms130810401
Received: 4 June 2012 / Revised: 3 August 2012 / Accepted: 13 August 2012 / Published: 21 August 2012
Cited by 2 | PDF Full-text (1683 KB) | HTML Full-text | XML Full-text
Abstract
Density functional theory has been employed to investigate the deformation behaviors of glassy Fe-Si-B model systems prepared by ab initio molecular dynamics. The atomistic deformation defects which are closely related to the local dilation volumes or excess volumes and unstable bonding have been
[...] Read more.
Density functional theory has been employed to investigate the deformation behaviors of glassy Fe-Si-B model systems prepared by ab initio molecular dynamics. The atomistic deformation defects which are closely related to the local dilation volumes or excess volumes and unstable bonding have been systematically analyzed. It has been found that the icosahedral structures are relatively stable under shear deformation until fracture occurs. Plastic flow is indicated by interruption of percolating icosahedral structures, caused by unstable Fe-Si bonding of p-s hybridization in nature. Full article
(This article belongs to the Special Issue Advances in Density Functional Theory)
Open AccessArticle A Promising Tool to Achieve Chemical Accuracy for Density Functional Theory Calculations on Y-NO Homolysis Bond Dissociation Energies
Int. J. Mol. Sci. 2012, 13(7), 8051-8070; doi:10.3390/ijms13078051
Received: 25 May 2012 / Revised: 19 June 2012 / Accepted: 25 June 2012 / Published: 28 June 2012
Cited by 2 | PDF Full-text (608 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
A DFT-SOFM-RBFNN method is proposed to improve the accuracy of DFT calculations on Y-NO (Y = C, N, O, S) homolysis bond dissociation energies (BDE) by combining density functional theory (DFT) and artificial intelligence/machine learning methods, which consist of self-organizing feature mapping neural
[...] Read more.
A DFT-SOFM-RBFNN method is proposed to improve the accuracy of DFT calculations on Y-NO (Y = C, N, O, S) homolysis bond dissociation energies (BDE) by combining density functional theory (DFT) and artificial intelligence/machine learning methods, which consist of self-organizing feature mapping neural networks (SOFMNN) and radial basis function neural networks (RBFNN). A descriptor refinement step including SOFMNN clustering analysis and correlation analysis is implemented. The SOFMNN clustering analysis is applied to classify descriptors, and the representative descriptors in the groups are selected as neural network inputs according to their closeness to the experimental values through correlation analysis. Redundant descriptors and intuitively biased choices of descriptors can be avoided by this newly introduced step. Using RBFNN calculation with the selected descriptors, chemical accuracy (≤1 kcal·mol−1) is achieved for all 92 calculated organic Y-NO homolysis BDE calculated by DFT-B3LYP, and the mean absolute deviations (MADs) of the B3LYP/6-31G(d) and B3LYP/STO-3G methods are reduced from 4.45 and 10.53 kcal·mol−1 to 0.15 and 0.18 kcal·mol−1, respectively. The improved results for the minimal basis set STO-3G reach the same accuracy as those of 6-31G(d), and thus B3LYP calculation with the minimal basis set is recommended to be used for minimizing the computational cost and to expand the applications to large molecular systems. Further extrapolation tests are performed with six molecules (two containing Si-NO bonds and two containing fluorine), and the accuracy of the tests was within 1 kcal·mol−1. This study shows that DFT-SOFM-RBFNN is an efficient and highly accurate method for Y-NO homolysis BDE. The method may be used as a tool to design new NO carrier molecules. Full article
(This article belongs to the Special Issue Advances in Density Functional Theory)
Open AccessArticle Density Functional Theory (DFT) Study of Triphenylamine-Based Dyes for Their Use as Sensitizers in Molecular Photovoltaics
Int. J. Mol. Sci. 2012, 13(4), 4418-4432; doi:10.3390/ijms13044418
Received: 6 February 2012 / Revised: 4 March 2012 / Accepted: 20 March 2012 / Published: 10 April 2012
Cited by 13 | PDF Full-text (606 KB) | HTML Full-text | XML Full-text
Abstract
In this work we studied three dyes which are proposed for potential photovoltaic applications and named Dye7, Dye7-2t and Dye7-3t. The Density Functional Theory (DFT) was utilized, using the M05-2X hybrid meta-GGA functional and the 6–31+G(d,p) basis set. This level of calculation was
[...] Read more.
In this work we studied three dyes which are proposed for potential photovoltaic applications and named Dye7, Dye7-2t and Dye7-3t. The Density Functional Theory (DFT) was utilized, using the M05-2X hybrid meta-GGA functional and the 6–31+G(d,p) basis set. This level of calculation was used to find the optimized molecular structure and to predict the main molecular vibrations, the absorption and emission spectra, the molecular orbitals energies, dipole moment, isotropic polarizability and the chemical reactivity parameters that arise from Conceptual DFT. Also, the pKa values were calculated with the semi-empirical PM6 method. Full article
(This article belongs to the Special Issue Advances in Density Functional Theory)
Open AccessArticle Toward the Understanding of the Metabolism of Levodopa I. DFT Investigation of the Equilibrium Geometries, Acid-Base Properties and Levodopa-Water Complexes
Int. J. Mol. Sci. 2012, 13(4), 4321-4339; doi:10.3390/ijms13044321
Received: 9 January 2012 / Revised: 13 March 2012 / Accepted: 26 March 2012 / Published: 2 April 2012
Cited by 4 | PDF Full-text (1980 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Levodopa (LD) is used to increase dopamine level for treating Parkinson’s disease. The major metabolism of LD to produce dopamine is decarboxylation. In order to understand the metabolism of LD; the electronic structure of levodopa was investigated at the Density Functional DFT/B3LYP level
[...] Read more.
Levodopa (LD) is used to increase dopamine level for treating Parkinson’s disease. The major metabolism of LD to produce dopamine is decarboxylation. In order to understand the metabolism of LD; the electronic structure of levodopa was investigated at the Density Functional DFT/B3LYP level of theory using the 6-311+G** basis set, in the gas phase and in solution. LD is not planar, with the amino acid side chain acting as a free rotator around several single bonds. The potential energy surface is broad and flat. Full geometry optimization enabled locating and identifying the global minimum on this Potential energy surface (PES). All possible protonation/deprotonation forms of LD were examined and analyzed. Protonation/deprotonation is local in nature, i.e., is not transmitted through the molecular framework. The isogyric protonation/deprotonation reactions seem to involve two subsequent steps: First, deprotonation, then rearrangement to form H-bonded structures, which is the origin of the extra stability of the deprotonated forms. Natural bond orbital (NBO) analysis of LD and its deprotonated forms reveals detailed information of bonding characteristics and interactions across the molecular framework. The effect of deprotonation on the donor-acceptor interaction across the molecular framework and within the two subsystems has also been examined. Attempts to mimic the complex formation of LD with water have been performed. Full article
(This article belongs to the Special Issue Advances in Density Functional Theory)

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