scholarly journals An Integrated Path Integral and Free-Energy Perturbation−Umbrella Sampling Method for Computing Kinetic Isotope Effects of Chemical Reactions in Solution and in Enzymes

2007 ◽  
Vol 3 (3) ◽  
pp. 949-960 ◽  
Author(s):  
Dan Thomas Major ◽  
Jiali Gao
Keyword(s):  
Free Energy ◽  
Chemical Reactions ◽  
Path Integral ◽  
Sampling Method ◽  
Isotope Effects ◽  
Kinetic Isotope Effects ◽  
Umbrella Sampling ◽  
Free Energy Perturbation ◽  
Kinetic Isotope ◽  
Energy Perturbation

Chapter 5. Kinetic Isotope Effects from Hybrid Classical and Quantum Path Integral Computations

2009 ◽  
pp. 105-131 ◽  
Author(s):  
Jiali Gao ◽  
Kin-Yiu Wong ◽  
Dan T. Major ◽  
Alessandro Cembran ◽  
Lingchun Song ◽  
...  
Keyword(s):  
Path Integral ◽  
Isotope Effects ◽  
Kinetic Isotope Effects ◽  
Kinetic Isotope

scholarly journals Rate Coefficients and Kinetic Isotope Effects of the Cl + XCl  XCl + Cl (X=H, D, Mu) Reactions from Ring Polymer Molecular Dynamics

2020 ◽  
Author(s):  
junhua fang ◽  
Wenbin Fan ◽  
Hui Yang ◽  
Jianing Song ◽  
Yongle Li
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Energy Surface ◽  
Isotope Effects ◽  
Kinetic Isotope Effects ◽  
Rate Coefficients ◽  
Theoretical Methods ◽  
Kinetic Isotope ◽  
Ring Polymer ◽  
Experimental Values

<p>The ring-polymer molecular dynamics (RPMD) was used to calculate the thermal rate coefficients and kinetic isotope effects of the heavy-light-heavy abstract reaction Cl + XCl ® XCl + Cl (X=H, D, Mu). For the Cl + HCl reaction, the excellent agreement between the RPMD and experimental values provides a strong proof for the accuracy of the RPMD theory. And the RPMD results also consistent with results from other theoretical methods including improved-canonical-variational-theory and quantum dynamics. The most novel finding is there is a double peak in Cl + MuCl reaction near the transition state, leaving a free energy well. It comes from the mode softening of the reaction system at the peak of the potential energy surface. Such an explicit free energy well suggests strongly there is an observable resonance. And for the Cl + DCl reaction, the RPMD rate coefficient again gives very accurate results comparing with experimental values. The only exception is at the temperature of 312.5 K, at this temperature, results from RPMD and all other theoretical methods are close to each other but slightly lower than the experimental value, which indicates experimental or potential energy surface deficiency.</p><div><br></div>

scholarly journals Rate Coefficients and Kinetic Isotope Effects of the XCl + Cl (X=H, D, Mu) Reactions from Ring Polymer Molecular Dynamics

2020 ◽  
Author(s):  
junhua fang ◽  
Wenbin Fan ◽  
Hui Yang ◽  
Jianing Song ◽  
Yongle Li
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Energy Surface ◽  
Isotope Effects ◽  
Kinetic Isotope Effects ◽  
Rate Coefficients ◽  
Theoretical Methods ◽  
Kinetic Isotope ◽  
Ring Polymer ◽  
Experimental Values

<p>The ring-polymer molecular dynamics (RPMD) was used to calculate the thermal rate coefficients and kinetic isotope effects of the heavy-light-heavy abstract reaction Cl + XCl ® XCl + Cl (X=H, D, Mu). For the Cl + HCl reaction, the excellent agreement between the RPMD and experimental values provides a strong proof for the accuracy of the RPMD theory. And the RPMD results also consistent with results from other theoretical methods including improved-canonical-variational-theory and quantum dynamics. The most novel finding is there is a double peak in Cl + MuCl reaction near the transition state, leaving a free energy well. It comes from the mode softening of the reaction system at the peak of the potential energy surface. Such an explicit free energy well suggests strongly there is an observable resonance. And for the Cl + DCl reaction, the RPMD rate coefficient again gives very accurate results comparing with experimental values. The only exception is at the temperature of 312.5 K, at this temperature, results from RPMD and all other theoretical methods are close to each other but slightly lower than the experimental value, which indicates experimental or potential energy surface deficiency.</p><div><br></div>

Mutation L1196M-induced conformational changes and the drug resistant mechanism of anaplastic lymphoma kinase studied by free energy perturbation and umbrella sampling

2017 ◽  
Vol 19 (44) ◽  
pp. 30239-30248 ◽  
Author(s):  
Jianzhong Chen ◽  
Jinan Wang ◽  
Weiliang Zhu
Keyword(s):  
Free Energy ◽  
Conformational Changes ◽  
Anaplastic Lymphoma Kinase ◽  
Drug Target ◽  
Umbrella Sampling ◽  
Free Energy Perturbation ◽  
Drug Resistant ◽  
Anaplastic Lymphoma ◽  
Energy Perturbation ◽  
Different Levels

Anaplastic lymphoma kinase (ALK) has been regarded as a promising drug target in the treatment of tumors and the mutation L1196M induces different levels of drug resistance toward the existing inhibitors.

Linear free energy relationship and kinetic isotope effects as measures for the transition-state variation — A case of the neophyl system

2005 ◽  
Vol 83 (9) ◽  
pp. 1606-1614 ◽  
Author(s):  
Salai Cheettu Ammal ◽  
Hiroshi Yamataka
Keyword(s):  
Free Energy ◽  
Transition State ◽  
Density Functional ◽  
Isotope Effects ◽  
Kinetic Isotope Effects ◽  
Single Step ◽  
Linear Free Energy Relationship ◽  
Linear Free Energy ◽  
Kinetic Isotope ◽  
State Variation

Ab initio calculations at the MP2/6-31G* level and density functional theory (B3LYP/6-311+G**) calculations have been performed on acid-catalyzed ionizations of substituted neophyl alcohols to investigate whether a variation of the transition-state (TS) structure is reflected in the kinetic isotope effects (KIE) and linear free energy relationship. The effect of substituents on KIEs, TS structures, and activation and reaction energies was calculated. This study revealed that a curved Brønsted-type plot could arise for a single-step process from the variation of TS structure with the substituent, whereas the Hammett plots with a dual-parameter treatment can not detect such TS variation. The variation of KIEs at various positions of neophyl alcohol reflects the variation of TS structures in a manner consistent with the More O'Ferrall – Jencks type reaction diagram analyses.Key words: transition-state variation, substituent effect, kinetic isotope effect, linear free energy relationship.

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