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Coordination compounds and complexes exhibit different colors, geometries, and magnetic behavior, depending on the metal atom/ion and ligands from which they are composed. In an attempt to explain the bonding and structure of coordination complexes, Linus Pauling proposed the valence bond theory, or VBT, using the concepts of hybridization and the overlapping of the atomic orbitals. According to VBT, the central metal atom or ion (Lewis acid) hybridizes to provide empty orbitals of suitable...
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According to valence bond theory, a covalent bond results when: (1) an orbital on one atom overlaps an orbital on a second atom, and (2) the single electrons in each orbital combine to form an electron pair. The strength of a covalent bond depends on the extent of overlap of the orbitals involved. Maximum overlap is possible when the orbitals overlap on a direct line between the two nuclei.
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Bond energy is the energy required to break a bond homolytically. These values are usually expressed in units of kcal/mol or kJ/mol and are referred to as bond dissociation energies when given for specific bonds or average bond energies when indicated for a given type of bond over many compounds. Firstly, the bond dissociation energy for a single bond is weaker than that of a double bond, which in turn is weaker than that of a triple bond. Secondly, hydrogen forms relatively strong bonds with...
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Author Spotlight: Streamlining Visual Dynamics to Simplify Molecular Dynamics Simulations Using Gromacs
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Efficient Empirical Valence Bond Simulations with GROMACS.

Gabriel Oanca1, Florian van der Ent1, Johan Åqvist1

  • 1Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, Uppsala SE-751 24, Sweden.

Journal of Chemical Theory and Computation
|August 25, 2023
PubMed
Summary

We present a new protocol for empirical valence bond (EVB) simulations in GROMACS. This method accurately calculates reaction free-energy profiles in complex systems like enzymes, offering a robust and efficient approach for biochemical research.

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Area of Science:

  • Computational chemistry
  • Biochemistry
  • Molecular dynamics

Background:

  • Empirical valence bond (EVB) simulations are crucial for understanding reaction mechanisms in complex biological systems.
  • Classical force fields are often used to represent chemical reactions within these simulations.
  • Accurate free-energy calculations are essential for determining reaction profiles.

Purpose of the Study:

  • To introduce and validate a protocol for performing empirical valence bond (EVB) simulations using GROMACS software.
  • To demonstrate the efficiency and reliability of the GROMACS implementation for EVB simulations.
  • To enable the study of reaction free-energy profiles in large and complex systems, such as enzymes.

Main Methods:

  • Implementation of the empirical valence bond (EVB) method within the GROMACS simulation package.
  • Utilization of classical force fields to model chemical reactions.
  • Application of standard free-energy calculation techniques to map reaction pathways.
  • Validation through replication of two previously published enzyme simulation cases.

Main Results:

  • The GROMACS implementation of EVB simulations provides results virtually identical to specialized EVB software.
  • The protocol successfully decomposes activation free energy into enthalpic and entropic components.
  • The catalytic effect of enzymes can be accurately calculated and compared to reactions in aqueous solution.
  • The method proves robust and scalable for very large biological systems.

Conclusions:

  • The developed GROMACS protocol offers a fast, reliable, and robust method for empirical valence bond (EVB) simulations.
  • This implementation facilitates the accurate calculation of reaction free-energy profiles in complex systems, including enzymes.
  • The GROMACS EVB protocol is suitable for large-scale simulations, advancing computational studies in biochemistry and molecular dynamics.