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Related Concept Videos

Electrostatic Boundary Conditions01:16

Electrostatic Boundary Conditions

Consider an external electric field propagating through a homogeneous medium. When the electric field crosses the surface boundary of the medium, it undergoes a discontinuity. The electric field can be resolved into normal and tangential components. The amount by which the field changes at any boundary is given by the difference between the field components above and below the surface boundary.
The surface integral of an electric field is given by Gauss's law in integral form and is related to...
Electrostatic Boundary Conditions in Dielectrics01:27

Electrostatic Boundary Conditions in Dielectrics

When an electric field passes from one homogeneous medium to another, crossing the boundary between the two mediums imparts a discontinuity in the electric field. This results in electrostatic boundary conditions that depend on the type of mediums the field propagates through.
Consider a case where both the mediums across a boundary are two different dielectric materials. Recall that the electric field and electric displacement are proportional and related through the material's permittivity.
Spin–Spin Coupling: Three-Bond Coupling (Vicinal Coupling)01:22

Spin–Spin Coupling: Three-Bond Coupling (Vicinal Coupling)

Vicinal or three-bond coupling is commonly observed between protons attached to adjacent carbons. Here, nuclear spin information is primarily transferred via electron spin interactions between adjacent C‑H bond orbitals. This generally favors the antiparallel arrangement of spins, so 3J values are usually positive.
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Hybridization of Atomic Orbitals I03:24

Hybridization of Atomic Orbitals I

The mathematical expression known as the wave function, ψ, contains information about each orbital and the wavelike properties of electrons in an isolated atom. When atoms are bound together in a molecule, the wave functions combine to produce new mathematical descriptions that have different shapes. This process of combining the wave functions for atomic orbitals is called hybridization and is mathematically accomplished by the linear combination of atomic orbitals. The new orbitals that...
Hybridization of Atomic Orbitals II03:35

Hybridization of Atomic Orbitals II

sp3d and sp3d 2 Hybridization
Van der Waals Equation01:10

Van der Waals Equation

The ideal gas law is an approximation that works well at high temperatures and low pressures. The van der Waals equation of state (named after the Dutch physicist Johannes van der Waals, 1837−1923) improves it by considering two factors.
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Density embedded VB/MM: a hybrid ab initio VB/MM with electrostatic embedding.

Avital Sharir-Ivry1, Hadar A Crown, Wei Wu

  • 1Department of Medicinal Chemistry and Natural Products, The Lise Meitner-Minerva Center for Computational Quantum Chemistry, School of Pharmacy, The Hebrew University of Jerusalem, Jerusalem 91120, Israel. avitalsh@ekmd.huji.ac.il

The Journal of Physical Chemistry. A
|February 26, 2008
PubMed
Summary

A new hybrid quantum mechanics/molecular mechanics (QM/MM) method, density embedded valence-bond/molecular mechanics (DE-VB/MM), enables accurate calculations of reactions in large biological systems. This approach enhances understanding of chemical reactivity in complex environments.

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Area of Science:

  • Computational Chemistry
  • Quantum Chemistry
  • Biochemistry

Background:

  • Accurate modeling of chemical reactions in biological systems is crucial for understanding complex biological processes.
  • Existing methods may face limitations in describing the interplay between reactive fragments and their surrounding environment.
  • Hybrid quantum mechanics/molecular mechanics (QM/MM) approaches offer a promising avenue for studying large systems.

Purpose of the Study:

  • To introduce and validate a novel hybrid QM/MM method, density embedded valence-bond/molecular mechanics (DE-VB/MM).
  • To enable accurate quantum mechanical calculations of chemical reactions within large biological systems.
  • To improve the description of electrostatic interactions between reactive centers and their environment.

Main Methods:

  • Development of the density embedded valence-bond/molecular mechanics (DE-VB/MM) method, combining ab initio valence-bond (VB) theory with molecular mechanics (MM).
  • Incorporation of electrostatic embedding to account for wave function polarization of reactive fragments due to the environment.
  • Application of the DE-VB/MM method to study the identity SN2 reaction of chloride anion with methyl chloride in aqueous solution.

Main Results:

  • The DE-VB/MM method successfully calculates adiabatic ground state reaction profiles, diabatic VB configurations, and VB state correlation diagrams.
  • Results for the model SN2 reaction show excellent agreement with experimental and other computational data.
  • The method overcomes limitations of previous VB/MM approaches regarding electrostatic interactions.

Conclusions:

  • The DE-VB/MM method provides a robust framework for investigating chemical reactivity in complex biological systems.
  • Accurate modeling of electrostatic interactions and wave function polarization is key to its success.
  • DE-VB/MM is a valuable tool for advancing our understanding of biochemical reaction mechanisms.