scholarly journals Transition state geometry of driven chemical reactions on time-dependent double-well potentials

2016 ◽  
Vol 18 (44) ◽  
pp. 30270-30281 ◽  
Author(s):  
Andrej Junginger ◽  
Galen T. Craven ◽  
Thomas Bartsch ◽  
F. Revuelta ◽  
F. Borondo ◽  
...  
Keyword(s):  
Transition State ◽  
Invariant Manifold ◽  
Chemical Reactions ◽  
Time Dependent ◽  
Transition State Geometry

The minimum contour in the forward Lagrangian descriptor overlaps the invariant manifold (in green) dividing reactant and product regions.

scholarly journals Time-dependent communication between multiple amino acids during protein folding

2021 ◽  
Vol 12 (16) ◽  
pp. 5944-5951
Author(s):  
Song-Ho Chong ◽  
Sihyun Ham
Keyword(s):  
Amino Acids ◽  
Protein Folding ◽  
Transition State ◽  
Time Dependent ◽  
Transition Path ◽  
Contact Formation ◽  
Molecular Origin

Cooperativity in contact formation among multiple amino acids starts to develop upon entering the folding transition path and attains a maximum at the folding transition state, providing the molecular origin of the two-state folding behavior.

On the Calculation of Transition State Activity Coefficient and Solvent Effects on Chemical Reactions

1998 ◽  
Vol 63 (12) ◽  
pp. 1969-1976 ◽  
Author(s):  
Alvaro Domínguez ◽  
Rafael Jimenez ◽  
Pilar López-Cornejo ◽  
Pilar Pérez ◽  
Francisco Sánchez
Keyword(s):  
Activity Coefficient ◽  
Transition State ◽  
Chemical Reactions ◽  
Solvent Effects ◽  
Transition State Theory ◽  
Reaction Medium ◽  
State Theory ◽  
Precursor Complex ◽  
State Activity ◽  
Classical Transition

Solvent effects, when the classical transition state theory (TST) holds, can be interpreted following the Brønsted equation. However, when calculating the activity coefficient of the transition state, γ# it is important to take into account that this coefficient is different from that of the precursor complex, γPC. The activity coefficient of the latter is, in fact, that calculated in classical treatments of salt and solvent effects. In this paper it is shown how the quotients γ#/γPC change when the reaction medium changes. Therefore, the conclusions taken on the basis of classical treatments may be erroneous.

scholarly journals Advances in Automated Transition State Theory Calculations: Improvements on the AutoTST Framework

2020 ◽  
Author(s):  
Nathan Harms ◽  
Carl Underkoffler ◽  
Richard West
Keyword(s):  
Transition State ◽  
Kinetic Parameters ◽  
Transition State Theory ◽  
Vibrational Analysis ◽  
Chemical Kinetic ◽  
State Theory ◽  
Combustion Chemistry ◽  
Transition State Geometry ◽  
Substantial Progress ◽  
Symmetry Number

<div>Kinetic modeling of combustion chemistry has made substantial progress in recent years with the development of increasingly detailed models. However, many of the chemical kinetic parameters utilized in detailed models are estimated, often inaccurately. To help replace rate estimates with more accurate calculations, we have developed AutoTST, an automated Transition State Theory rate calculator. This work describes improvements to AutoTST, including: a systematic conformer search to find an ensemble of low energy conformers, vibrational analysis to validate transition state geometries, more accurate symmetry number calculations, and a hindered rotor treatment when deriving kinetics. These improvements resulted in location of transition state geometry for 93% of cases and generation of kinetic parameters for 74% of cases. Newly calculated parameters agree well with benchmark calculations and perform well when used to replace estimated parameters in a detailed kinetic model of methanol combustion.</div>

Compressible Flow Simulations on a Massively Parallel Computer

1991 ◽  
Vol 02 (01) ◽  
pp. 430-436
Author(s):  
ELAINE S. ORAN ◽  
JAY P. BORIS
Keyword(s):  
Compressible Flow ◽  
Chemical Reactions ◽  
Large Scale ◽  
Model Development ◽  
Time Dependent ◽  
Parallel Computer ◽  
Massively Parallel ◽  
Parallel Solution ◽  
Flow Simulations ◽  
Connection Machine

This paper describes model development and computations of multidimensional, highly compressible, time-dependent reacting on a Connection Machine (CM). We briefly discuss computational timings compared to a Cray YMP speed, optimal use of the hardware and software available, treatment of boundary conditions, and parallel solution of terms representing chemical reactions. In addition, we show the practical use of the system for large-scale reacting and nonreacting flows.

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