scholarly journals autodE: Automated Calculation of Reaction Energy Profiles – Application to Organic and Organometallic Reactions

2020 ◽  
Author(s):  
Tom Young ◽  
Joseph Silcock ◽  
Alistair Sterling ◽  
Fernanda Duarte
Keyword(s):  
Claisen Rearrangement ◽  
Reductive Elimination ◽  
Conformational Sampling ◽  
Reaction Energy ◽  
General Applicability ◽  
Organometallic Reactions ◽  
Energy Profiles ◽  
Migratory Insertion ◽  
Human Effort ◽  
Metal Catalyzed

Calculating reaction profiles to aid in mechanistic elucidation has long been the domain of the expert computational chemist. We introduce autodE, an open-source tool capable of locating transition states and minima and delivering a full reaction energy profile with minimal human effort (https://github.com/duartegroup/autodE). autodE is broadly applicable to study organic and organometallic reaction classes, including addition, substitution, elimination, migratory insertion, oxidative addition and reductive elimination; it accounts for conformational sampling of both minima and TSs, and is compatible with many electronic structure packages. The general applicability of autodE is demonstrated in complex multi-step reactions, including metal-catalyzed cobalt- and rhodium-catalyzed hydroformylation, and an Ireland-Claisen rearrangement.

scholarly journals autodE: Automated Calculation of Reaction Energy Profiles – Application to Organic and Organometallic Reactions

2020 ◽  
Author(s):  
Tom Young ◽  
Joseph Silcock ◽  
Alistair Sterling ◽  
Fernanda Duarte
Keyword(s):  
Claisen Rearrangement ◽  
Reductive Elimination ◽  
Conformational Sampling ◽  
Reaction Energy ◽  
General Applicability ◽  
Organometallic Reactions ◽  
Energy Profiles ◽  
Migratory Insertion ◽  
Human Effort ◽  
Metal Catalyzed

Calculating reaction profiles to aid in mechanistic elucidation has long been the domain of the expert computational chemist. We introduce autodE, an open-source tool capable of locating transition states and minima and delivering a full reaction energy profile with minimal human effort (https://github.com/duartegroup/autodE). autodE is broadly applicable to study organic and organometallic reaction classes, including addition, substitution, elimination, migratory insertion, oxidative addition and reductive elimination; it accounts for conformational sampling of both minima and TSs, and is compatible with many electronic structure packages. The general applicability of autodE is demonstrated in complex multi-step reactions, including metal-catalyzed cobalt- and rhodium-catalyzed hydroformylation, and an Ireland-Claisen rearrangement.

scholarly journals Computational Design of Radical Recognition Assay with the Possible Application of Cyclopropyl Vinyl Sulfides as Tunable Sensors

2021 ◽  
Vol 22 (14) ◽  
pp. 7637
Author(s):  
Liliya T. Sahharova ◽  
Evgeniy G. Gordeev ◽  
Dmitry B. Eremin ◽  
Valentine P. Ananikov
Keyword(s):  
Uv Light ◽  
Computational Design ◽  
Energy Profiles ◽  
Vinyl Sulfides ◽  
Tunable Sensors ◽  
Radical Generation ◽  
Metal Catalyzed ◽  
Dynamics Simulations ◽  
Simulations And Modeling ◽  
Insight Into

The processes involving the capture of free radicals were explored by performing DFT molecular dynamics simulations and modeling of reaction energy profiles. We describe the idea of a radical recognition assay, where not only the presence of a radical but also the nature/reactivity of a radical may be assessed. The idea is to utilize a set of radical-sensitive molecules as tunable sensors, followed by insight into the studied radical species based on the observed reactivity/selectivity. We utilize this approach for selective recognition of common radicals—alkyl, phenyl, and iodine. By matching quantum chemical calculations with experimental data, we show that components of a system react differently with the studied radicals. Possible radical generation processes were studied involving model reactions under UV light and metal-catalyzed conditions.

Factors Promoting Alkene Migratory Insertion into Metal-Nitrogen Bond during Hydroamination in Recent Studies

2021 ◽  
Vol 18 ◽  
Author(s):  
Wenlai Han
Keyword(s):  
Transition Metal ◽  
Late Transition Metal ◽  
Electronic Effects ◽  
Metal Centers ◽  
Unsaturated Bond ◽  
Factors Influencing ◽  
Migratory Insertion ◽  
Late Transition ◽  
Metal Catalyzed ◽  
Nitrogen Bond

: Migratory insertion is a fundamental organometallic transformation that enables the functionalization of an unsaturated bond. Recent reports on catalytic hydroamination provide evidence that supports an intermolecular migratory insertion pathway featuring alkene insertion into metal-nitrogen (M-N) bonds. This article presents factors influencing the rate of migratory insertion in late-transition metal-catalyzed hydroamination, including steric and electronic effects from ligands, alkenes, and metal centers, along with stabilization from coordinated amine intermediates and ordered transition states.

scholarly journals Recent Advances in Palladium-Catalyzed Bridging C–H Activation by Using Alkenes, Alkynes or Diazo Compounds as Bridging Reagents

Synthesis ◽  
2020 ◽  
Vol 53 (02) ◽  
pp. 238-254
Author(s):  
Fulin Zhang ◽  
Luoting Xin ◽  
Saihu Liao ◽  
Xueliang Huang ◽  
Yinghua Yu
Keyword(s):  
Bond Distance ◽  
Short Review ◽  
Diazo Compounds ◽  
Bond Functionalization ◽  
Migratory Insertion ◽  
Intramolecular Reactions ◽  
Palladium Catalyzed ◽  
Direct Functionalization ◽  
Intermolecular Reactions ◽  
Metal Catalyzed

AbstractTransition-metal-catalyzed direct inert C–H bond functionalization has attracted much attention over the past decades. However, because of the high strain energy of the suspected palladacycle generated via C–H bond palladation, direct functionalization of a C–H bond less than a three-bond distance from a catalyst center is highly challenging. In this short review, we summarize the advances on palladium-catalyzed bridging C–H activation, in which an inert proximal C–H bond palladation is promoted by the elementary step of migratory insertion of an alkene, an alkyne or a metal carbene intermediate.1 Introduction2 Palladium-Catalyzed Alkene Bridging C–H Activation2.1 Intramolecular Reactions2.2 Intermolecular Reactions3 Palladium-Catalyzed Alkyne Bridging C–H Activation3.1 Intermolecular Reactions3.2 Intramolecular Reactions4 Palladium-Catalyzed Carbene Bridging C–H Activation5 Conclusion and Outlook

QM and QM/MM umbrella sampling MD study of the formation of Hg(II)–thymine bond: Model for evaluation of the reaction energy profiles in solutions with constant pH

2020 ◽  
Vol 41 (16) ◽  
pp. 1509-1520
Author(s):  
Filip Šebesta ◽  
Jakub Šebera ◽  
Vladimír Sychrovský ◽  
Yoshiyuki Tanaka ◽  
Jaroslav V. Burda
Keyword(s):  
Umbrella Sampling ◽  
Reaction Energy ◽  
Bond Model ◽  
Energy Profiles ◽  
Constant Ph
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