Recent Progress in Density Functional Methodology for Biomolecular Modeling

  • Dennis R. Salahub
  • Aurélien de la Lande
  • Annick Goursot
  • Rui Zhang
  • Yue Zhang
Chapter
Part of the Structure and Bonding book series (STRUCTURE, volume 150)

Abstract

Density Functional Theory (DFT) has become the workhorse of applied computational chemistry. DFT has grown in a number of different directions depending on the applications concerned. In this chapter, we provide a broad review of a number of DFT and DFT-based methods, having in mind the accurate description of biological systems and processes. These range from pure “cluster” DFT studies of the structure, properties, and reactions of biochemical species (such as enzymatic catalysts) using either straight DFT or dispersion-corrected functionals (DFT-D), to Born–Oppenheimer-DFT dynamics of systems containing up to a hundred atoms or more (such as glycero-lipids), to hybrid DFT/Molecular Mechanical Molecular Dynamics methods which include protein and solvent environments (for enzymes or ion channels, for example), to constrained-DFT (working within the Marcus framework for electron-transfer reactions), to Interpretational-DFT (which provides the interpretational benefits of the Kohn–Sham DFT methodology).

Graphical Abstract

Keywords

Biomolecular modeling Born–Oppenheimer molecular dynamics Constrained DFT Density Functional Theory Dispersion-corrected DFT Interpretational DFT QM/MM methodology 

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Copyright information

© Springer-Verlag Berlin Heidelberg 2013

Authors and Affiliations

  • Dennis R. Salahub
    • 1
  • Aurélien de la Lande
    • 2
  • Annick Goursot
    • 3
  • Rui Zhang
    • 1
  • Yue Zhang
    • 4
  1. 1.Department of Chemistry, Institute for Biocomplexity and InformaticsUniversity of CalgaryCalgaryCanada
  2. 2.Laboratoire de Chimie PhysiqueUMR 8000, CNRS. Université Paris SudOrsayFrance
  3. 3.ICGM, UMR 5253 CNRSEcole de Chimie de MontpellierMontpellierFrance
  4. 4.Key Laboratory for Macromolecular Science of Shaanxi Province, School of Chemistry & MaterialsShaanxi Normal UniversityXi’anChina

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