Calculating approximate quantum mechanical rates without an a priori reaction coordinate

2002 ◽  
Vol 116 (19) ◽  
pp. 8376 ◽  
Author(s):  
Yisroel Brumer ◽  
Andrei A. Golosov ◽  
Zong Da Chen ◽  
David R. Reichman
Keyword(s):  
A Priori ◽  
Reaction Coordinate ◽  
Quantum Mechanical

Inside Back Cover: The Reaction Coordinate of a Bacterial GH47 α-Mannosidase: A Combined Quantum Mechanical and Structural Approach (Angew. Chem. Int. Ed. 44/2012)

2012 ◽  
Vol 51 (44) ◽  
pp. 11171-11171
Author(s):  
Andrew J. Thompson ◽  
Jerome Dabin ◽  
Javier Iglesias-Fernández ◽  
Albert Ardèvol ◽  
Zoran Dinev ◽  
...  
Keyword(s):  
Structural Approach ◽  
Reaction Coordinate ◽  
Quantum Mechanical ◽  
Back Cover

Quantum-theoretical approaches to proteins and nucleic acids

2017 ◽  
Author(s):  
Mauro Boero ◽  
Masaru Tateno
Keyword(s):  
Nucleic Acids ◽  
Density Functional ◽  
A Priori ◽  
Alternative Methods ◽  
Parallel Tempering ◽  
Quantum Mechanical ◽  
Chemical Bonds ◽  
Functional Theory ◽  
Hartree Fock ◽  
Theoretical Approaches

This article describes quantum methods used to study proteins and nucleic acids: Hartree–Fock all-electron approaches, density-functional theory approaches, and hybrid quantum-mechanics/molecular-mechanics approaches. In addition to an analysis of the electronic structure, quantum-mechanical approaches for simulating proteins and nucleic acids can elucidate the cleavage and formation of chemical bonds in biochemical reactions. This presents a computational challenge, and a number of methods have been proposed to overcome this difficulty, including enhanced temperature methods such as high-temperature molecular dynamics, parallel tempering and replica exchange. Alternative methods not relying on the knowledge a priori of the final products make use of biasing potentials to push the initial system away from its local minimum and to enhance the sampling of the free-energy landscape. This article considers two of these biasing techniques, namely Blue Moon and metadynamics.

Theoretical prediction of vibrational spectra. The a priori scaled quantum mechanical (SQM) force field and vibrational spectra of pyrimidine

1992 ◽  
Vol 48 (1) ◽  
pp. 111-119 ◽  
Author(s):  
Gábor Pongor ◽  
Géza Fogarasi ◽  
Ildikó Magdó ◽  
James E. Boggs ◽  
Gábor Keresztury ◽  
...  
Keyword(s):  
Theoretical Prediction ◽  
Force Field ◽  
Vibrational Spectra ◽  
A Priori ◽  
Quantum Mechanical

The Reaction Coordinate of a Bacterial GH47 α-Mannosidase: A Combined Quantum Mechanical and Structural Approach

2012 ◽  
Vol 51 (44) ◽  
pp. 10997-11001 ◽  
Author(s):  
Andrew J. Thompson ◽  
Jerome Dabin ◽  
Javier Iglesias-Fernández ◽  
Albert Ardèvol ◽  
Zoran Dinev ◽  
...  
Keyword(s):  
Structural Approach ◽  
Reaction Coordinate ◽  
Quantum Mechanical

Analysis of the Reaction Coordinate of α-l-Fucosidases: A Combined Structural and Quantum Mechanical Approach

2010 ◽  
Vol 132 (6) ◽  
pp. 1804-1806 ◽  
Author(s):  
Alicia Lammerts van Bueren ◽  
Jennifer Fayers-Kerr ◽  
Bo Luo ◽  
Yongmin Zhang ◽  
Matthieu Sollogoub ◽  
...  
Keyword(s):  
Reaction Coordinate ◽  
Quantum Mechanical ◽  
Mechanical Approach ◽  
Quantum Mechanical Approach

A Priori Scaled Quantum Mechanical Vibrational Spectra of trans- and cis-Stilbene

1995 ◽  
Vol 99 (29) ◽  
pp. 11392-11398 ◽  
Author(s):  
Juan Francisco Arenas ◽  
Isabel Lopez Tocon ◽  
Juan Carlos Otero ◽  
Juan Ignacio Marcos
Keyword(s):  
Vibrational Spectra ◽  
A Priori ◽  
Quantum Mechanical

scholarly journals Innenrücktitelbild: The Reaction Coordinate of a Bacterial GH47 α-Mannosidase: A Combined Quantum Mechanical and Structural Approach (Angew. Chem. 44/2012)

2012 ◽  
Vol 124 (44) ◽  
pp. 11333-11333
Author(s):  
Andrew J. Thompson ◽  
Jerome Dabin ◽  
Javier Iglesias-Fernández ◽  
Albert Ardèvol ◽  
Zoran Dinev ◽  
...  
Keyword(s):  
Structural Approach ◽  
Reaction Coordinate ◽  
Quantum Mechanical

The Reaction Coordinate of a Bacterial GH47 α-Mannosidase: A Combined Quantum Mechanical and Structural Approach

2012 ◽  
Vol 124 (44) ◽  
pp. 11159-11163 ◽  
Author(s):  
Andrew J. Thompson ◽  
Jerome Dabin ◽  
Javier Iglesias-Fernández ◽  
Albert Ardèvol ◽  
Zoran Dinev ◽  
...  
Keyword(s):  
Structural Approach ◽  
Reaction Coordinate ◽  
Quantum Mechanical

scholarly journals Quantum Mechanical/Molecular Mechanical Analysis of the Catalytic Mechanism of Phosphoserine Phosphatase

Molecules ◽  
2018 ◽  
Vol 23 (12) ◽  
pp. 3342 ◽  
Author(s):  
Dieter Krachtus ◽  
Jeremy Smith ◽  
Petra Imhof
Keyword(s):  
Free Energy ◽  
Proton Transfer ◽  
Active Site ◽  
Catalytic Mechanism ◽  
Free Energy Calculations ◽  
Reaction Coordinate ◽  
Reaction Pathways ◽  
Quantum Mechanical ◽  
Energy Calculation ◽  
Phosphoserine Phosphatase

Phosphoserine phosphatase (PSP), a member of the haloacid dehalogenase (HAD) superfamily that comprises the vast majority of phosphotransferases, is likely a steady-state regulator of the level of d-serine in the brain. The proposed catalytic cycle of PSP consists of a two-step mechanism: formation of a phospho-enzyme intermediate by phosphate transfer to Asp11 and its subsequent hydrolysis. Our combined quantum mechanical/molecular mechanical (QM/MM) calculations of the reaction pathways favour a dissociative mechanism of nucleophilic substitution via a trigonal-planar metaphosphate-like configuration for both steps, associated with proton transfer to the leaving group or from the nucleophile. This proton transfer is facilitated by active site residue Asp13 that acts as both a general base and a general acid. Free energy calculation on the reaction pathways further support the structural role of the enzymatic environment and the active site architecture. The choice of a proper reaction coordinate along which to bias the free energy calculations can be guided by a projection of the canonical reaction coordinate obtained from a chain-of-state optimisation onto important internal coordinates.

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