scholarly journals Theoretical Studies of Nickel-Dependent Enzymes

Inorganics ◽  
2019 ◽  
Vol 7 (8) ◽  
pp. 95 ◽  
Author(s):  
Per E. M. Siegbahn ◽  
Shi-Lu Chen ◽  
Rong-Zhen Liao
Keyword(s):  
Superoxide Dismutase ◽  
Reaction Mechanisms ◽  
Quantum Chemical ◽  
Experimental Studies ◽  
Theoretical Studies ◽  
Co Dehydrogenase ◽  
Chemical Methods ◽  
Quantum Chemical Methods ◽  
Acireductone Dioxygenase ◽  
Methyl Coenzyme M Reductase

The advancements of quantum chemical methods and computer power allow detailed mechanistic investigations of metalloenzymes. In particular, both quantum chemical cluster and combined QM/MM approaches have been used, which have been proven to successfully complement experimental studies. This review starts with a brief introduction of nickel-dependent enzymes and then summarizes theoretical studies on the reaction mechanisms of these enzymes, including NiFe hydrogenase, methyl-coenzyme M reductase, nickel CO dehydrogenase, acetyl CoA synthase, acireductone dioxygenase, quercetin 2,4-dioxygenase, urease, lactate racemase, and superoxide dismutase.

Predicting Feasible Organic Reaction Pathways Using Heuristically Aided Quantum Chemistry

2018 ◽  
Author(s):  
Dmitrij Rappoport ◽  
Alan Aspuru-Guzik
Keyword(s):  
Quantum Chemistry ◽  
Reaction Mechanisms ◽  
Quantum Chemical ◽  
Organic Reactions ◽  
Reaction Pathways ◽  
Empirical Knowledge ◽  
Organic Reaction ◽  
Chemical Methods ◽  
Quantum Chemical Methods ◽  
Wide Range

Studying organic reaction mechanisms using quantum chemical methods requires from the researcher an extensive knowledge of both organic chemistry and first-principles computation. The need for empirical knowledge arises because any reasonably complete exploration of the potential energy surfaces (PES) of organic reactions is computationally prohibitive. We have previously introduced the Heuristically-Aided Quantum Chemistry (HAQC) approach to modeling complex chemical reactions, which abstracts the empirical knowledge in terms of chemical heuristics—simple rules guiding the PES exploration—and combines them with structure optimizations using quantum chemical methods. The HAQC approach makes use of heuristic kinetic criteria for selecting reaction paths that are not only plausible, that is, consistent with the empirical rules of organic reactivity, but also feasible under the reaction conditions. In this work, we develop heuristic kinetic feasilibity criteria, which correctly predict feasible reaction pathways for a wide range of simple polar (substitutions, additions, and eliminations) and pericyclic organic reactions (cyclizations, sigmatropic shifts, and cycloadditions). In contrast to knowledge-based reaction mechanism prediction methods, the same kinetic heuristics are successful in classifying reaction pathways as feasible or infeasible across this diverse set of reaction mechanisms. We discuss the energy profiles of HAQC and their potential applications in machine learning of chemical reactivity.<br>

Predicting Feasible Organic Reaction Pathways Using Heuristically Aided Quantum Chemistry

2018 ◽  
Author(s):  
Dmitrij Rappoport ◽  
Alan Aspuru-Guzik
Keyword(s):  
Quantum Chemistry ◽  
Reaction Mechanisms ◽  
Quantum Chemical ◽  
Organic Reactions ◽  
Reaction Pathways ◽  
Empirical Knowledge ◽  
Organic Reaction ◽  
Chemical Methods ◽  
Quantum Chemical Methods ◽  
Wide Range

Studying organic reaction mechanisms using quantum chemical methods requires from the researcher an extensive knowledge of both organic chemistry and first-principles computation. The need for empirical knowledge arises because any reasonably complete exploration of the potential energy surfaces (PES) of organic reactions is computationally prohibitive. We have previously introduced the Heuristically-Aided Quantum Chemistry (HAQC) approach to modeling complex chemical reactions, which abstracts the empirical knowledge in terms of chemical heuristics—simple rules guiding the PES exploration—and combines them with structure optimizations using quantum chemical methods. The HAQC approach makes use of heuristic kinetic criteria for selecting reaction paths that are not only plausible, that is, consistent with the empirical rules of organic reactivity, but also feasible under the reaction conditions. In this work, we develop heuristic kinetic feasilibity criteria, which correctly predict feasible reaction pathways for a wide range of simple polar (substitutions, additions, and eliminations) and pericyclic organic reactions (cyclizations, sigmatropic shifts, and cycloadditions). In contrast to knowledge-based reaction mechanism prediction methods, the same kinetic heuristics are successful in classifying reaction pathways as feasible or infeasible across this diverse set of reaction mechanisms. We discuss the energy profiles of HAQC and their potential applications in machine learning of chemical reactivity.<br>

scholarly journals Energetics of LOHC: Structure-Property Relationships from Network of Thermochemical Experiments and in Silico Methods

Hydrogen ◽  
2021 ◽  
Vol 2 (1) ◽  
pp. 101-121
Author(s):  
Sergey P. Verevkin ◽  
Vladimir N. Emel’yanenko ◽  
Riko Siewert ◽  
Aleksey A. Pimerzin
Keyword(s):  
In Silico ◽  
Quantum Chemical ◽  
Structure Property ◽  
Chemical Methods ◽  
Key Technology ◽  
Structure Property Relationships ◽  
Quantum Chemical Methods ◽  
Dehydrogenation Reactions ◽  
Storage Technologies ◽  
In Silico Methods

The storage of hydrogen is the key technology for a sustainable future. We developed an in silico procedure, which is based on the combination of experimental and quantum-chemical methods. This method was used to evaluate energetic parameters for hydrogenation/dehydrogenation reactions of various pyrazine derivatives as a seminal liquid organic hydrogen carriers (LOHC), that are involved in the hydrogen storage technologies. With this in silico tool, the tempo of the reliable search for suitable LOHC candidates will accelerate dramatically, leading to the design and development of efficient materials for various niche applications.

Reactions between microhydrated superoxide anions and formic acid

2017 ◽  
Vol 19 (34) ◽  
pp. 23176-23186 ◽  
Author(s):  
Mauritz Johan Ryding ◽  
Israel Fernández ◽  
Einar Uggerud
Keyword(s):  
Formic Acid ◽  
Quantum Chemical ◽  
Superoxide Anion ◽  
Water Clusters ◽  
Superoxide Anions ◽  
Chemical Methods ◽  
Quantum Chemical Methods

Reactions between water clusters containing the superoxide anion, O2˙−(H2O)n (n = 0–4), and formic acid, HCO2H, were studied experimentally in vacuo and modelled using quantum chemical methods.

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