Ab initio quantum mechanical gas phase and reaction field solvation study on the proton abstraction from hydroxyacetaldehyde by formate: implications for enzyme catalysis

1997 ◽  
pp. 2185-2190 ◽  
Author(s):  
Mikael Peräkylä
Keyword(s):  
Ab Initio ◽  
Gas Phase ◽  
Enzyme Catalysis ◽  
Quantum Mechanical ◽  
Proton Abstraction ◽  
Reaction Field

Ab initio self-consistent reaction field calculations on amino acids: asparagine zwitterions in polar medium and gas phase

1997 ◽  
Vol 98 (1) ◽  
pp. 5-15 ◽  
Author(s):  
J. T. López Navarrete ◽  
J. Casado ◽  
V. Hernández ◽  
F. J. Ramírez
Keyword(s):  
Amino Acids ◽  
Ab Initio ◽  
Gas Phase ◽  
Polar Medium ◽  
Reaction Field ◽  
Self Consistent

The hydration mechanism of ketene: 15 years later

1999 ◽  
Vol 77 (5-6) ◽  
pp. 817-829 ◽  
Author(s):  
Minh Tho Nguyen ◽  
Greet Raspoet
Keyword(s):  
Ab Initio ◽  
Gas Phase ◽  
Water Clusters ◽  
Field Method ◽  
Polarizable Continuum Model ◽  
Water Molecules ◽  
Orbital Theory ◽  
Acid Product ◽  
Reaction Field ◽  
Hydration Mechanism

New insights into the detailed mechanism of the hydration of ketene yielding acetic acid (H2C=C=O + H2O →> CH3COOH) were obtained by theoretical methods in both gas phase and solution. While gas phase calculations were performed using ab initio molecular orbital theory, bulk solvent effects were included using the self-consistent reaction field method (SCRF) and the polarizable continuum model (PCM). The hydration modeled by attack of water clusters containing two, three, and four water molecules confirms that a two-step addition of water to the ketene C=O bond, yielding a 1,1-enediol intermediate as initially demonstrated in 1984, is energetically, slightly but consistently, preferred over a concerted addition across the C=C bond leading directly to the acid product. Attempts to locate a zwitterion intermediate in solution were not successful. At least a cluster of three hydrogen-bonded water molecules is present in the gas phase supersystem to facilitate the proton transfer. Further incorporation of active water molecules in the catalytic water chain induces rather minor energetic improvements on the proton relay, which indicates a certain saturation of the cluster when reaching 3-4 water molecules. Effects of the surrounding solvent bulk do not change qualitatively the facts found in gas phase. The C=O addition mechanism is in better agreement with recent experimental developments in identifying enols of carboxylic acids than other mechanisms involving either a zwitterion or a direct C=C addition, as proposed for years in the literature.Key words: ketene, ketene hydration, hydration mechanism, solvent effect, ab initio calculations.

Quantum Mechanical Interpretation of the Ultra-Low Energy Methyl-Rotation Dynamics in Porous Metal-Organic Frameworks Probed by Low-Frequency Vibrational Spectroscopy and ab initio Simulations

2018 ◽  
Author(s):  
Qi Li ◽  
Adam J. Zaczek ◽  
Timothy M. Korter ◽  
J. Axel Zeitler ◽  
Michael T. Ruggiero
Keyword(s):  
Ab Initio ◽  
Metal Organic Frameworks ◽  
Low Frequency ◽  
Rotor Dynamics ◽  
Quantum Mechanical ◽  
Valuable Insight ◽  
Void Space ◽  
Ab Initio Simulations ◽  
Metal Organic ◽  
Insight Into

<div>Understanding the nature of the interatomic interactions present within the pores of metal-organic frameworks</div><div>is critical in order to design and utilize advanced materials</div><div>with desirable applications. In ZIF-8 and its cobalt analogue</div><div>ZIF-67, the imidazolate methyl-groups, which point directly</div><div>into the void space, have been shown to freely rotate - even</div><div>down to cryogenic temperatures. Using a combination of ex-</div><div>perimental terahertz time-domain spectroscopy, low-frequency</div><div>Raman spectroscopy, and state-of-the-art ab initio simulations,</div><div>the methyl-rotor dynamics in ZIF-8 and ZIF-67 are fully charac-</div><div>terized within the context of a quantum-mechanical hindered-</div><div>rotor model. The results lend insight into the fundamental</div><div>origins of the experimentally observed methyl-rotor dynamics,</div><div>and provide valuable insight into the nature of the weak inter-</div><div>actions present within this important class of materials.</div>

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.

Solvent and temperature effects on the tautomerization of a carbonitrile molecule: A conductor-like polarizable continuum model (CPCM) study

2021 ◽  
Vol 20 (1) ◽  
pp. 59-68
Author(s):  
Zohreh Khanjari ◽  
Bita Mohtat ◽  
Reza Ghiasi ◽  
Hoorieh Djahaniani ◽  
Farahnaz Kargar Behbahani
Keyword(s):  
Gas Phase ◽  
Solvent Effects ◽  
Continuum Model ◽  
Solvent Polarity ◽  
Polarizable Continuum Model ◽  
Dielectric Constants ◽  
Frontier Orbitals ◽  
Reaction Field ◽  
Polarizable Continuum ◽  
Homo Lumo

This research examined the effects of solvent polarity and temperature on the tautomerization of a carbonitrile molecule at CAM-B3LYP/6-311G (d,p) level of theory. The selected solvents were n-hexane, diethyl ether, pyridine, ethanol, methanol, and water. The solvent effects were examined by the self-consistent reaction field theory (SCRF) based on conductor-like polarizable continuum model (CPCM). The solvent effects were explored on the energy barrier, frontier orbitals energies, and HOMO-LUMO gap. Dependencies of thermodynamic parameters (ΔG and ΔH) on the dielectric constants of solvents were also tested. Specifically, the temperature dependencies of the thermodynamics parameters were studied within 100–1000 K range. The rate constant of the tautomerism reaction was computed from 300 to 1200 K, in the gas phase.

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