Empirical Valence Bond Simulations of Biological Systems

Research output: Chapter in Book/Report/Conference proceedingChapter

Abstract

Summary The empirical valence bond (EVB) approach is a unique hybrid quantum mechanical molecular mechanical (QM/MM) approach with various clear advantages. It facilitates the understanding of reaction mechanisms in biological systems; the calibration of the approach together with its comparative nature often guarantees more accurate results. Furthermore, the simplicity of the potential energy surface enables highly efficient sampling, which is important when particularly large systems or averages over considerably large configuration ensembles are of interest. The EVB approach also provides simple definition of the reaction coordinate, which includes all the system's degrees of freedom. Finally, the method benefits from the valence bond character of the wavefunction, which includes easily accessible chemical insight. As such the EVB contributes considerably to our understanding of complex biological problems. In this review we will discuss these different capabilities of the method while highlighting the advantages of the method over other standard (MO based) QM/MM approaches.
Original languageEnglish
Title of host publicationTheory and Applications of the Empirical Valence Bond Approach
PublisherJohn Wiley & Sons, Ltd
Chapter6
Pages145-171
Number of pages27
ISBN (Electronic)9781119245544
ISBN (Print)9781119245391
DOIs
StatePublished - Feb 2017

Keywords

  • valence bond
  • enzyme reactivity
  • g-proteins
  • copper chaperones
  • enzyme design
  • paradynamics
  • entropy calculations
  • reaction coordinate

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