scholarly journals Initial estimate for minimum energy pathways and transition states using velocities in internal coordinates

2020 ◽  
pp. 111046
Author(s):  
Mark C. Palenik
Keyword(s):  
Minimum Energy ◽  
Transition States ◽  
Initial Estimate ◽  
Internal Coordinates ◽  
Energy Pathways

scholarly journals Free energy pathways of a multistable liquid crystal device

Soft Matter ◽  
2015 ◽  
Vol 11 (24) ◽  
pp. 4809-4817 ◽  
Author(s):  
Halim Kusumaatmaja ◽  
Apala Majumdar
Keyword(s):  
Free Energy ◽  
Liquid Crystal ◽  
Energy Landscape ◽  
Minimum Energy ◽  
Transition States ◽  
Minimum Free Energy ◽  
Free Energy Landscape ◽  
Liquid Crystal Device ◽  
Energy Configurations ◽  
Energy Pathways

Understanding the free energy landscape of a multistable liquid crystal device in terms of its minimum free energy configurations, transition states, free energy barriers and minimum energy pathways.

Transition states and minimum energy pathways for the collapse of carbon nanotubes

2006 ◽  
Vol 73 (7) ◽  
Author(s):  
Sulin Zhang ◽  
Roopam Khare ◽  
Ted Belytschko ◽  
K. Jimmy Hsia ◽  
Steven L. Mielke ◽  
...  
Keyword(s):  
Carbon Nanotubes ◽  
Minimum Energy ◽  
Transition States ◽  
Energy Pathways

scholarly journals Rock climbing: A local-global algorithm to compute minimum energy and minimum free energy pathways

2017 ◽  
Vol 147 (15) ◽  
pp. 152718 ◽  
Author(s):  
Clark Templeton ◽  
Szu-Hua Chen ◽  
Arman Fathizadeh ◽  
Ron Elber
Keyword(s):  
Free Energy ◽  
Minimum Energy ◽  
Minimum Free Energy ◽  
Rock Climbing ◽  
Global Algorithm ◽  
Energy Pathways

scholarly journals Discovering minimum energy pathways via distortion symmetry groups

2018 ◽  
Vol 98 (8) ◽  
Author(s):  
Jason M. Munro ◽  
Hirofumi Akamatsu ◽  
Haricharan Padmanabhan ◽  
Vincent S. Liu ◽  
Yin Shi ◽  
...  
Keyword(s):  
Minimum Energy ◽  
Symmetry Groups ◽  
Energy Pathways

scholarly journals Ab initio study of the mechanism of the reaction ClO + O --> Cl + O2

2021 ◽  
Vol 66 (1) ◽  
Author(s):  
S. Naskar ◽  
G. Nandi ◽  
T. K. Ghosh
Keyword(s):  
Reaction Mechanism ◽  
Ab Initio ◽  
Minimum Energy ◽  
Transition States ◽  
Basis Set ◽  
Heat Of Reaction ◽  
Minimal Basis ◽  
Dissociation Energies ◽  
Correlation Consistent ◽  
Equilibrium Geometries

Abstract. Ab initio investigation on the reaction mechanism of ClO + O --> Cl + O2 reaction has been performed using correlation consistent triple zeta basis set. The geometry and frequency of the reactants, products, minimum energy geometries and transition states are obtained using MP2 method and energetics are obtained at the QCISD(T)//MP2 level of theory. Primarily, a possible reaction mechanism is obtained on the basis on IRC calculations using MP2 level of theory. To obtain true picture of the reaction path, we performed IRC calculations using CASSCF method with a minimal basis set 6-31G**. Some new equilibrium geometries and transition states have been identified at the CASSCF level. Energetics are also obtained at the QCISD(T)//CASSCF method. Possible reaction paths have been discussed, which are new in literature. Heat of reaction is found to be consistent with the experimental data. Bond dissociation energies to various dissociation paths are also reported.

scholarly journals Antisymmetry: Fundamentals and Applications

2020 ◽  
Vol 50 (1) ◽  
pp. 255-281 ◽  
Author(s):  
Hari Padmanabhan ◽  
Jason M. Munro ◽  
Ismaila Dabo ◽  
Venkatraman Gopalan
Keyword(s):  
Time Reversal ◽  
Minimum Energy ◽  
Chemical Species ◽  
Physical World ◽  
State Theory ◽  
Magnetic Structures ◽  
Structures And Properties ◽  
Point Groups ◽  
Arbitrary Dimensions ◽  
Energy Pathways

Symmetry is fundamental to understanding our physical world. An antisymmetry operation switches between two different states of a trait, such as two time states, position states, charge states, spin states, or chemical species. This review covers the fundamental concepts of antisymmetry and focuses on four antisymmetries, namely, spatial inversion in point groups, time reversal, distortion reversal, and wedge reversion. The distinction between classical and quantum mechanical descriptions of time reversal is presented. Applications of these antisymmetries—in crystallography, diffraction, determining the form of property tensors, classifying distortion pathways in transition state theory, finding minimum energy pathways, diffusion, magnetic structures and properties, ferroelectric and multiferroic switching, classifying physical properties in arbitrary dimensions, and antisymmetry-protected topological phenomena—are described.

Modeling reactivation of the phosphorylated human butyrylcholinesterase by QM(DFTB)/MM calculations

2015 ◽  
Vol 14 (07) ◽  
pp. 1550051 ◽  
Author(s):  
Anna Kulakova ◽  
Sofya Lushchekina ◽  
Bella Grigorenko ◽  
Alexander Nemukhin
Keyword(s):  
Minimum Energy ◽  
Hydrolysis Reaction ◽  
Chemical Transformations ◽  
Wild Type ◽  
General Base ◽  
Central Nerve System ◽  
Nerve System ◽  
Inhibited Enzyme ◽  
Human Butyrylcholinesterase ◽  
Energy Pathways

Human butyrylcholinesterase (BChE) is a bioscavenger that protects the enzyme which is critical for the central nerve system, acetylcholinesterase, from poisoning by organophosphorus agents. Elucidating the details of the hydrolysis reaction mechanism is important to understand how the phosphorylated BChE can be reactivated. Application of the QM(DFTB)/MM(AMBER) method to construct the minimum energy pathways for the hydrolysis reaction of the diethylphosphorylated BChE allowed us to suggest a mechanism of reactivation of the wild-type and the G117H mutated enzyme. Unlike previous approaches assuming that either His438 or His117 serves as a general base in the catalysis, in our proposal the Glu197 residue is responsible for activation of the nucleophilic water molecule (Wat) leading to the chemical transformations that restore the catalytic Ser198 residue in BChE. In agreement with the experimental data, it is shown that the G117H mutation facilitates the reactivation of the inhibited enzyme.

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