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Related Concept Videos

Reaction Quotient02:35

Reaction Quotient

The status of a reversible reaction is conveniently assessed by evaluating its reaction quotient (Q). For a reversible reaction described by m A + n B ⇌ x C + y D, the reaction quotient is derived directly from the stoichiometry of the balanced equation as
Reaction Mechanisms: The Steady-State Approximation01:26

Reaction Mechanisms: The Steady-State Approximation

The steady-state approximation, also referred to as the quasi-steady-state approximation to differentiate it from a true steady state, is a widely used method for simplifying calculations in complex reaction mechanisms. This approach is particularly useful when dealing with multi-step reactions that involve reverse reactions or several steps, which can significantly increase mathematical complexity and make the reactions nearly unsolvable analytically.The steady-state approximation operates on...
Reaction Mechanisms03:06

Reaction Mechanisms

Chemical reactions often occur in a stepwise fashion, involving two or more distinct reactions taking place in a sequence. A balanced equation indicates the reacting species and the product species, but it reveals no details about how the reaction occurs at the molecular level. The reaction mechanism (or reaction path) provides details regarding the precise, step-by-step process by which a reaction occurs.
For instance, the decomposition of ozone appears to follow a mechanism with two steps:
Reaction Mechanisms: Rate-limiting Step Approximation01:29

Reaction Mechanisms: Rate-limiting Step Approximation

The rate-determining step, or RDS, in a chemical reaction is the slowest step that determines the overall reaction rate. It is identified by using the observed rate law and typically involves approximation methods like the RDS approximation or the steady-state approximation.In the RDS approximation, also known as the rate-limiting-step or equilibrium approximation, the reaction mechanism consists of one or more reversible reactions near equilibrium, followed by a slower RDS, and then one or...
Free Energy Changes for Nonstandard States03:25

Free Energy Changes for Nonstandard States

The free energy change for a process taking place with reactants and products present under nonstandard conditions (pressures other than 1 bar; concentrations other than 1 M) is related to the standard free energy change according to this equation:
Multi-Step Reactions02:31

Multi-Step Reactions

Chemical reactions often occur in a stepwise fashion involving two or more distinct reactions taking place in a sequence. A balanced equation indicates the reacting species and the product species, but it reveals no details about how the reaction occurs at the molecular level. The reaction mechanism (or reaction path) provides details regarding the precise, step-by-step process by which a reaction occurs. Each of the steps in a reaction mechanism is called an elementary reaction. These...

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Related Experiment Video

Updated: Jul 14, 2026

Isotopic Effect in Double Proton Transfer Process of Porphycene Investigated by Enhanced QM/MM Method
05:51

Isotopic Effect in Double Proton Transfer Process of Porphycene Investigated by Enhanced QM/MM Method

Published on: July 19, 2019

Exploring SCC-DFTB paths for mapping QM/MM reaction mechanisms.

H Lee Woodcock1, Milan Hodoscek, Bernard R Brooks

  • 1Laboratory of Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA.

The Journal of Physical Chemistry. A
|June 9, 2007
PubMed
Summary

A new hybrid quantum mechanical/molecular mechanical (QM/MM) method, RPATh+RESD, efficiently locates transition structures. This method improves upon reaction coordinate driving (RCD) by eliminating path discontinuities and sequential calculation issues, advancing computational chemistry for reaction pathway analysis.

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Multiscale Sampling of a Heterogeneous Water/Metal Catalyst Interface using Density Functional Theory and Force-Field Molecular Dynamics
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Multiscale Sampling of a Heterogeneous Water/Metal Catalyst Interface using Density Functional Theory and Force-Field Molecular Dynamics

Published on: April 12, 2019

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Last Updated: Jul 14, 2026

Isotopic Effect in Double Proton Transfer Process of Porphycene Investigated by Enhanced QM/MM Method
05:51

Isotopic Effect in Double Proton Transfer Process of Porphycene Investigated by Enhanced QM/MM Method

Published on: July 19, 2019

Multiscale Sampling of a Heterogeneous Water/Metal Catalyst Interface using Density Functional Theory and Force-Field Molecular Dynamics
10:52

Multiscale Sampling of a Heterogeneous Water/Metal Catalyst Interface using Density Functional Theory and Force-Field Molecular Dynamics

Published on: April 12, 2019

Area of Science:

  • Computational Chemistry
  • Biophysical Chemistry
  • Biochemistry

Background:

  • Locating transition structures (TS) is crucial for understanding reaction mechanisms.
  • Standard reaction coordinate driving (RCD) methods suffer from hysteresis and sequential calculation limitations.
  • Hybrid quantum mechanical/molecular mechanical (QM/M M) potentials offer a balance of accuracy and computational efficiency.

Purpose of the Study:

  • To develop a novel first-order procedure for TS location using QM/MM potentials.
  • To enhance existing QM/MM reaction pathway methods (RPATh, NEB) by incorporating SCC-DFTB wave functions.
  • To apply and validate the new method (RPATh+RESD) to a biologically relevant enzymatic reaction.

Main Methods:

  • Development of the RPATh+RESD method, combining replica path (RPATh) and reaction coordinate driving (RCD) techniques.
  • Extension of CHARMM's QM/MM RPATh and nudged elastic band (NEB) methods to include SCC-DFTB wave functions.
  • Application to the chorismate mutase-catalyzed conversion of chorismate to prephenate.
  • Modification of the steepest descents (SD) minimizer for NEB to improve performance by uncoupling degrees of freedom.
  • Analysis of convergence behavior for RPATh and NEB with SCC-DFTB wave functions.

Main Results:

  • The RPATh+RESD method efficiently determines reaction barriers and eliminates RCD weaknesses.
  • Calculated barrier height (ΔE=5.7 kcal/mol) for chorismate mutase is in good agreement with prior studies.
  • RPATh and NEB methods mapped full reaction paths, showing good agreement with the RPATh+RESD transition state.
  • SCC-DFTB TS geometry closely approximates high-level QM/MM results, though barrier height is underestimated.
  • Modified NEB minimizer significantly improved performance.
  • RPATh and NEB generally converge at similar rates with SCC-DFTB, utilizing different minimization techniques.

Conclusions:

  • The new RPATh+RESD method provides an efficient and robust approach for locating transition structures using QM/MM.
  • Incorporating SCC-DFTB wave functions into RPATh and NEB extends their applicability.
  • The study highlights potential areas for SCC-DFTB parametrization improvement while validating the computational approach for enzymatic reactions.