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 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 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.

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.

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.

scholarly journals The Key Role of the Latent N-H Group in Milstein's Catalyst for Ester Hydrogenation

2021 ◽  
Author(s):  
John Pham ◽  
Cole Jarczyk ◽  
Eamon Reynolds ◽  
Sophie Kelly ◽  
Thao Kim ◽  
...  
Keyword(s):  
Active Catalyst ◽  
Minimum Energy ◽  
Mechanistic Study ◽  
Hydrogen Activation ◽  
First Order ◽  
Catalytic Intermediates ◽  
Global Fit ◽  
Ruthenium Dihydride ◽  
Energy Pathways

<p>We previously demonstrated that Milstein’s seminal diethylamino-substituted PNN-pincer-ruthenium catalyst for ester hydrogenation is activated by dehydroalkylation of the pincer ligand, releasing ethane and eventually forming an NHEt-substituted derivative that we proposed is the active catalyst. In this paper, we present a computational and experimental mechanistic study supporting this hypothesis. Our DFT analysis shows that the minimum-energy pathways for hydrogen activation, ester hydrogenolysis, and aldehyde hydrogenation rely on the key involvement of the nascent N-H group. We have isolated and crystallographically characterized two catalytic intermediates, a ruthenium dihydride and a ruthenium hydridoalkoxide, the latter of which is the catalyst resting state. A detailed kinetic study shows that catalytic ester hydrogenation is first-order in ruthenium and hydrogen, shows saturation behavior in ester, and is inhibited by the product alcohol. A global fit of the kinetic data to a simplified model incorporating the hydridoalkoxide and dihydride intermediates and three kinetically relevant transition states showed excellent agreement with the results from DFT. <b></b></p><br>

scholarly journals The Key Role of the Latent N-H Group in Milstein's Catalyst for Ester Hydrogenation

2021 ◽  
Author(s):  
John Pham ◽  
Cole Jarczyk ◽  
Eamon Reynolds ◽  
Sophie Kelly ◽  
Thao Kim ◽  
...  
Keyword(s):  
Active Catalyst ◽  
Minimum Energy ◽  
Mechanistic Study ◽  
Hydrogen Activation ◽  
First Order ◽  
Catalytic Intermediates ◽  
Global Fit ◽  
Ruthenium Dihydride ◽  
Energy Pathways

<p>We previously demonstrated that Milstein’s seminal diethylamino-substituted PNN-pincer-ruthenium catalyst for ester hydrogenation is activated by dehydroalkylation of the pincer ligand, releasing ethane and eventually forming an NHEt-substituted derivative that we proposed is the active catalyst. In this paper, we present a computational and experimental mechanistic study supporting this hypothesis. Our DFT analysis shows that the minimum-energy pathways for hydrogen activation, ester hydrogenolysis, and aldehyde hydrogenation rely on the key involvement of the nascent N-H group. We have isolated and crystallographically characterized two catalytic intermediates, a ruthenium dihydride and a ruthenium hydridoalkoxide, the latter of which is the catalyst resting state. A detailed kinetic study shows that catalytic ester hydrogenation is first-order in ruthenium and hydrogen, shows saturation behavior in ester, and is inhibited by the product alcohol. A global fit of the kinetic data to a simplified model incorporating the hydridoalkoxide and dihydride intermediates and three kinetically relevant transition states showed excellent agreement with the results from DFT. <b></b></p><br>

scholarly journals Experimental and Computational Evidence of non-MEP Pathways in the Fragmentation and Rearrangement of Bicyclo[3.3.1] heptane Diazonium Ions

2021 ◽  
Author(s):  
Bastian Wulff ◽  
Patrick Sakrausky ◽  
Katrin Adamczyk ◽  
Nils Huse ◽  
Julia Rehbein
Keyword(s):  
Computational Chemistry ◽  
Stationary Point ◽  
Minimum Energy ◽  
Md Simulations ◽  
Point Analysis ◽  
Diazonium Ions ◽  
Energy Pathways

The non-minimum energy pathways on the fragmentation of bicyclic diazoniumions and subsequent carbocationic rearrangements has been studied by a combination of computational chemistry (MD simulations, IRC, stationary point analysis) and experiments (TR-IR and UV from ps to µs, NMR kinetics).<div><br></div>

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