Mechanism of C–P bond formation via Pd-catalyzed decarbonylative phosphorylation of amides: insight into the chemistry of the second coordination sphere

2020 ◽  
Vol 56 (1) ◽  
pp. 113-116
Author(s):  
Wen-Yan Tong ◽  
Thu D. Ly ◽  
Tao-Tao Zhao ◽  
Yan-Bo Wu ◽  
Xiaotai Wang
Keyword(s):  
Reaction Mechanism ◽  
Proton Transfer ◽  
Coordination Sphere ◽  
Bond Formation ◽  
Dft Computations ◽  
Detailed Reaction Mechanism ◽  
Non Covalent Interactions ◽  
Second Coordination Sphere ◽  
Covalent Interactions ◽  
Insight Into

DFT computations establish a detailed reaction mechanism for the first Pd-catalyzed decarbonylative phosphorylation of amides forming C–P bonds, which includes non-covalent interactions as well as proton transfer in the second coordination sphere.

Computational insight into the cooperative role of non-covalent interactions in the aza-Henry reaction catalyzed by quinine derivatives: mechanism and enantioselectivity

2016 ◽  
Vol 14 (40) ◽  
pp. 9588-9597 ◽  
Author(s):  
Yunsheng Xue ◽  
Yuhui Wang ◽  
Zhongyan Cao ◽  
Jian Zhou ◽  
Zhao-Xu Chen
Keyword(s):  
Hydrogen Bonding ◽  
Dft Calculations ◽  
Ion Pair ◽  
Henry Reaction ◽  
Brönsted Acid ◽  
Non Covalent Interactions ◽  
Dual Activation ◽  
Covalent Interactions ◽  
Insight Into

DFT calculations reveal the viability of the two possible ion pair-hydrogen bonding and Brønsted acid-hydrogen bonding dual activation modes.

scholarly journals Molecular determinants and bottlenecks in the unbinding dynamics of biotin-streptavidin

2017 ◽  
Author(s):  
Pratyush Tiwary
Keyword(s):  
Atomistic Simulations ◽  
Enhanced Sampling ◽  
Protein Ligand Interactions ◽  
Direct Benefits ◽  
Molecular Determinants ◽  
Bond Stretching ◽  
Ligand Interactions ◽  
Non Covalent Interactions ◽  
Covalent Interactions ◽  
Insight Into

Biotin-streptavidin is a very popular system used to gain insight into protein-ligand interactions. In its tetrameric form, it is well-known for its extremely long residence times, being one of the strongest known non-covalent interactions in nature, and is heavily used across the biotechnological industry. In this work we gain understanding into the molecular determinants and bottlenecks in the unbinding of the dimeric biotinstreptavidin system in its wild type and with N23A mutation. Using new enhanced sampling methods with full atomistic resolution, we reproduce the variation caused by N23A mutation in experimentally reported residence time. We also answer a longstanding question regarding cause/effect in the coupled events of bond stretching and bond hydration during unbinding and establish that in this system, it is the bond stretching and not hydration which forms the bottleneck in the early parts of the unbinding. We believe these calculations represent a step forward in the use of atomistic simulations to study pharmacodynamics. An improved understanding of biotin-streptavidin unbinding dynamics should also have direct benefits in biotechnological and nanobiotechnological applications.

scholarly journals Catalytic Enantioselective Synthesis of Heterocyclic Vicinal Fluoroamines Using Asymmetric Protonation: A Method Development and Mechanistic Study

2020 ◽  
Author(s):  
Matthew Ashford ◽  
Chao Xu ◽  
john molloy ◽  
Cameron Carpenter-Warren ◽  
Alexandra Slawin ◽  
...  
Keyword(s):  
Method Development ◽  
Data Bank ◽  
Enantioselective Synthesis ◽  
Mechanistic Study ◽  
Type Analysis ◽  
Conformational Landscape ◽  
Non Covalent Interactions ◽  
Chiral Bronsted Acid ◽  
Covalent Interactions ◽  
Insight Into

<div> <div> <div> <p>A catalytic enantioselective synthesis of heterocyclic vicinal fluoroamines is reported. A chiral Brønsted acid promotes aza-Michael addition to fluoroalkenyl heterocycles to give a prochiral enamine intermediate, which undergoes asymmetric protonation upon rearomatization. The reaction accommodates a range of azaheterocycles and nucleophiles, generating the C–F stereocenter in high enantioselectivity, and is also amenable to stereogenic C–CF3 bonds. Extensive DFT calculations have provided insight into the reaction mechanism and the origin of catalyst selectivity. Crystal structure data shows the dominance of non-covalent interactions in the core structure conformation, enabling modulation of the conformational landscape. Ramachandran-type analysis of conformer distribution and protein data bank mining has indicated benzylic fluorination using this approach has potential for improved potency in several marketed drugs. </p> </div> </div> </div>

Insight on the Factors Controlling the Equilibrium of Allylic Azides

2019 ◽  
Author(s):  
Margarita Vallejos ◽  
Guillermo Labadie
Keyword(s):  
Weak Interaction ◽  
Density Functional ◽  
Equilibrium Mixture ◽  
Hydroxyl Group ◽  
Functional Theory ◽  
Non Covalent Interactions ◽  
Allylic Azides ◽  
Covalent Interactions ◽  
Insight Into ◽  
Good Linear Correlation

<p>Several allylic azides with different double bond substitution were studied to understand the factors governing their equilibrium using density functional theory along with quantum theory of atoms in molecules, Non-covalent Interactions and Natural Bond Orbitals approaches. The results showed the hydroxyl group or heteroatoms in allylic azides interact with the molecule through an electrostatic weak interaction in each pair of regioisomers. The equilibrium shifts of substituted allylic azides, compared to non-substituted allylic azides, are not attributed to the presence of specific interactions, such as hydrogen bond. The observed equilibrium shifts stem mainly from the strengthening and weakening of negative hyperconjugative interactions, which is affected by the weak interaction involving the proximal substituent in each regioisomer. A good linear correlation was obtained between the hyperconjugative energies of pC=C→s*<i>Z</i><sub>b</sub> interactions and the calculated percentages of secondary azide and tertiary azides in the equilibrium mixture. Also, the effect of aromatic ring substituent was analysed using such approaches. This study not only provides insight into the factor controlling the stabilities of the substituted allylic azides, but also settle the basis to predict the regioisomer predominance in the equilibrium mixture.</p>

The mechanism and structure–activity relationship of amide bond formation by silane derivatives: a computational study

2019 ◽  
Vol 17 (41) ◽  
pp. 9232-9242 ◽  
Author(s):  
Ben Hu ◽  
Yuan-Ye Jiang ◽  
Peng Liu ◽  
Rui-Xue Zhang ◽  
Qi Zhang ◽  
...  
Keyword(s):  
Reaction Mechanism ◽  
Computational Study ◽  
Bond Formation ◽  
Structure Activity Relationship ◽  
Amide Bond ◽  
Activity Relationship ◽  
Amide Bond Formation ◽  
Structure Activity ◽  
Detailed Reaction Mechanism ◽  
Relationship Of

The detailed reaction mechanism and structure–activity relationship of substrates in silane reagent-mediated amide bond formation reactions are clarified.

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