1.3 Modelling Radicals and Their Reactivities

2021 ◽  
Author(s):  
E. Derat ◽  
B. Braïda
Keyword(s):  
Horseradish Peroxidase ◽  
Quantum Chemical ◽  
Valence Bond ◽  
Radical Reactions ◽  
Experimental Investigations ◽  
Quantum Mechanical ◽  
Enzymatic Reactions ◽  
Mechanical Methods ◽  
Electronic Configurations ◽  
Computational Quantum

AbstractIn this chapter, the application of computational quantum mechanical methods to the understanding of radical reactions is introduced. For radical reactions, access to electronic configurations through quantum chemical calculations allows rationalization of unusual reactivities. Using the valence bond approach, the nature of bonding in three-electron bonds can be characterized by large resonance interactions. Similarly, some simple reactions that are commonly believed to be radical-free, such as [3 + 2] cycloadditions, are in fact governed by a high-lying biradical intermediate that helps to stabilize the transition state. More complex radical and enzymatic reactions can also be modelled, as illustrated by the example of horseradish peroxidase. These case studies show that computational analysis can complement experimental investigations and fill in the blanks to enable a more complete understanding of radical reactions.

The acidity of β-phosphoglucomutase monofluoromethylenephosphonate ligands probed by NMR spectroscopy and quantum mechanical methods

2016 ◽  
Vol 94 (11) ◽  
pp. 902-908 ◽  
Author(s):  
Stephanie M. Forget ◽  
Eric A.C. Bushnell ◽  
Russell J. Boyd ◽  
David L. Jakeman
Keyword(s):  
Nmr Spectroscopy ◽  
Transition State ◽  
Quantum Mechanical ◽  
Phosphoryl Transfer ◽  
Quantum Mechanical Calculations ◽  
Transition State Analogues ◽  
Mechanical Methods ◽  
Insight Into ◽  
Computational Quantum

We recently described the binding of 1-β-phosphonomethylene-1-deoxy-d-glucopyranose, (S)-1-β-phosphonofluoromethylene-1-deoxy-D-glucopyranose (βG1CFSP), and (R)-1-β-phosphonofluoromethylene-1-deoxy-d-glucopyranose (βG1CFRP) to the enzyme β-phosphoglucomutase as transition state analogues of phosphoryl transfer through formation of stable MgF3− and AlF4− complexes (Proc. Natl. Acad. Sci. U.S.A. 2014, 111, 12384). Herein, we describe in detail the five-fold difference in acidity (pKa2) for the (S)- and (R)-configured diastereomeric fluorophosphonates through a series of NMR spectroscopy experiments. The differences in acidity were corroborated using computational quantum mechanical calculations to determine structures of lowest energy conformers and provide insight into why the (S) isomer is substantially more acidic.

scholarly journals Steric effects vs electron delocalization: a new look into stability of diastereomers, conformers and constitutional Isomers

2021 ◽  
Author(s):  
Sopanant Datta ◽  
Taweetham Limpanuparb
Keyword(s):  
Quantum Chemical ◽  
Electron Delocalization ◽  
Steric Effects ◽  
Quantum Mechanical ◽  
Quantum Chemical Investigation ◽  
Mechanical Methods ◽  
Qualitative Models ◽  
The Stability ◽  
Stable Forms ◽  
Meta Isomer

A quantum chemical investigation of the stability of compounds with identical formulas was carried out on 23 classes of compounds made of C, N, P, O, S atoms as core structures and halogens H, F, Cl, Br, I as substituents. All possible structures were generated and investigated by quantum mechanical methods. The prevalence of formula in which its <i>Z</i> configuration, <i>gauche</i> conformation and meta isomer are the most stable forms is calculated and discussed. Quantitative and qualitative models to explain the stability of the 23 classes of halogenated compounds were also proposed.<br>

scholarly journals Steric effects vs. electron delocalization: a new look into stability of diastereomers, conformers and constitutional Isomers

2021 ◽  
Author(s):  
Sopanant Datta ◽  
Taweetham Limpanuparb
Keyword(s):  
Quantum Chemical ◽  
Chemical Investigation ◽  
Electron Delocalization ◽  
Steric Effects ◽  
Quantum Mechanical ◽  
Stable Form ◽  
Quantum Chemical Investigation ◽  
Mechanical Methods ◽  
Qualitative Models ◽  
The Stability

<div> <p>A quantum chemical investigation of the stability of compounds with identical formulas was carried out on 23 classes of compounds made of C, N, P, O, S atoms as core structures and halogens H, F, Cl, Br, I as substituents. All possible structures were generated and investigated by quantum mechanical methods. The prevalence of a formula in which its <i>Z</i> configuration, <i>gauche</i> conformation or <i>meta</i> isomer is the most stable form is calculated and discussed. Quantitative and qualitative models to explain the stability of 23 classes of halogenated compounds were also proposed.</p></div>

scholarly journals Steric effects vs electron delocalization: a new look into stability of diastereomers, conformers and constitutional Isomers

2021 ◽  
Author(s):  
Sopanant Datta ◽  
Taweetham Limpanuparb
Keyword(s):  
Quantum Chemical ◽  
Electron Delocalization ◽  
Steric Effects ◽  
Quantum Mechanical ◽  
Quantum Chemical Investigation ◽  
Mechanical Methods ◽  
Qualitative Models ◽  
The Stability ◽  
Stable Forms ◽  
Meta Isomer

A quantum chemical investigation of the stability of compounds with identical formulas was carried out on 23 classes of compounds made of C, N, P, O, S atoms as core structures and halogens H, F, Cl, Br, I as substituents. All possible structures were generated and investigated by quantum mechanical methods. The prevalence of formula in which its <i>Z</i> configuration, <i>gauche</i> conformation and meta isomer are the most stable forms is calculated and discussed. Quantitative and qualitative models to explain the stability of the 23 classes of halogenated compounds were also proposed.<br>

scholarly journals Interactions between large molecules pose a puzzle for reference quantum mechanical methods

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Yasmine S. Al-Hamdani ◽  
Péter R. Nagy ◽  
Andrea Zen ◽  
Dennis Barton ◽  
Mihály Kállay ◽  
...  
Keyword(s):  
Experimental Information ◽  
Quantum Mechanical ◽  
Interaction Energies ◽  
Small Organic Molecules ◽  
Large Molecules ◽  
Reference Information ◽  
Mechanical Methods ◽  
Non Covalent Interactions ◽  
Semi Empirical ◽  
Covalent Interactions

AbstractQuantum-mechanical methods are used for understanding molecular interactions throughout the natural sciences. Quantum diffusion Monte Carlo (DMC) and coupled cluster with single, double, and perturbative triple excitations [CCSD(T)] are state-of-the-art trusted wavefunction methods that have been shown to yield accurate interaction energies for small organic molecules. These methods provide valuable reference information for widely-used semi-empirical and machine learning potentials, especially where experimental information is scarce. However, agreement for systems beyond small molecules is a crucial remaining milestone for cementing the benchmark accuracy of these methods. We show that CCSD(T) and DMC interaction energies are not consistent for a set of polarizable supramolecules. Whilst there is agreement for some of the complexes, in a few key systems disagreements of up to 8 kcal mol−1 remain. These findings thus indicate that more caution is required when aiming at reproducible non-covalent interactions between extended molecules.

scholarly journals A Review on Combination of Ab Initio Molecular Dynamics and NMR Parameters Calculations

2021 ◽  
Vol 22 (9) ◽  
pp. 4378
Author(s):  
Anna Helena Mazurek ◽  
Łukasz Szeleszczuk ◽  
Dariusz Maciej Pisklak
Keyword(s):  
Molecular Dynamics ◽  
Ab Initio ◽  
Small Amplitude ◽  
Ab Initio Molecular Dynamics ◽  
Quantum Mechanical ◽  
Time Step ◽  
Noticeable Effect ◽  
Nmr Parameters ◽  
Mechanical Methods ◽  
Simulation Time

This review focuses on a combination of ab initio molecular dynamics (aiMD) and NMR parameters calculations using quantum mechanical methods. The advantages of such an approach in comparison to the commonly applied computations for the structures optimized at 0 K are presented. This article was designed as a convenient overview of the applied parameters such as the aiMD type, DFT functional, time step, or total simulation time, as well as examples of previously studied systems. From the analysis of the published works describing the applications of such combinations, it was concluded that including fast, small-amplitude motions through aiMD has a noticeable effect on the accuracy of NMR parameters calculations.

scholarly journals New Approach for Correcting Noncovalent Interactions in Semiempirical Quantum Mechanical Methods: The Importance of Multiple-Orientation Sampling

2021 ◽  
Vol 17 (9) ◽  
pp. 5556-5567
Author(s):  
Sergio Pérez-Tabero ◽  
Berta Fernández ◽  
Enrique M. Cabaleiro-Lago ◽  
Emilio Martínez-Núñez ◽  
Saulo A. Vázquez
Keyword(s):  
Noncovalent Interactions ◽  
Quantum Mechanical ◽  
New Approach ◽  
Mechanical Methods
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