AB INITIO QUANTUM CHEMICAL AND MIXED QUANTUM MECHANICS/MOLECULAR MECHANICS (QM/MM) METHODS FOR STUDYING ENZYMATIC CATALYSIS

In this paper we review the results of a group of computational studies of the spectroscopy and photochemistry of light-responsive proteins. We focus on the use of quantum mechanics/molecular mechanics protocols based on a multiconfigurational quantum chemical treatment. More specifically, we discuss the use, limitations, and application of the ab initio CASPT2//CASSCF protocol that, presently, constitutes the method of choice for the investigation of excited state organic molecules, most notably, biological chromophores and fluorophores. At the end of this Review we will also see how the computational investigation of the visual photoreceptor rhodopsin is providing the basis for the design of light-driven artificial molecular devices.

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Hybrid ab Initio Quantum Mechanics/Molecular Mechanics Calculations of Free Energy Surfaces for Enzymatic Reactions: The Nucleophilic Attack in Subtilisin

The Journal of Physical Chemistry B ◽

10.1021/jp973480y ◽

1998 ◽

Vol 102 (12) ◽

pp. 2293-2301 ◽

Cited By ~ 115

Author(s):

J. Bentzien ◽

R. P. Muller ◽

J. Florián ◽

A. Warshel

Keyword(s):

Free Energy ◽

Quantum Mechanics ◽

Ab Initio ◽

Molecular Mechanics ◽

Nucleophilic Attack ◽

Enzymatic Reactions ◽

Molecular Mechanics Calculations ◽

Energy Surfaces

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Free Energies of Chemical Reactions in Solution and in Enzymes with Ab Initio Quantum Mechanics/Molecular Mechanics Methods

Annual Review of Physical Chemistry ◽

10.1146/annurev.physchem.59.032607.093618 ◽

2008 ◽

Vol 59 (1) ◽

pp. 573-601 ◽

Cited By ~ 327

Author(s):

Hao Hu ◽

Weitao Yang

Keyword(s):

Quantum Mechanics ◽

Ab Initio ◽

Molecular Mechanics ◽

Chemical Reactions ◽

Free Energies

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Ab initio quantum mechanics/molecular mechanics method with periodic boundaries employing Ewald summation technique to electron-charge interaction: Treatment of the surface-dipole term

The Journal of Chemical Physics ◽

10.1063/1.5048451 ◽

2019 ◽

Vol 150 (12) ◽

pp. 124103 ◽

Cited By ~ 1

Author(s):

Y. Kawashima ◽

K. Ishimura ◽

M. Shiga

Keyword(s):

Quantum Mechanics ◽

Ab Initio ◽

Molecular Mechanics ◽

Electron Charge ◽

Ewald Summation ◽

Molecular Mechanics Method ◽

Interaction Treatment ◽

Charge Interaction ◽

Dipole Term ◽

Surface Dipole

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Color Tuning in Short Wavelength-Sensitive Human and Mouse Visual Pigments: Ab initio Quantum Mechanics/Molecular Mechanics Studies

The Journal of Physical Chemistry A ◽

10.1021/jp902754p ◽

2009 ◽

Vol 113 (43) ◽

pp. 11685-11692 ◽

Cited By ~ 36

Author(s):

Ahmet Altun ◽

Shozo Yokoyama ◽

Keiji Morokuma

Keyword(s):

Quantum Mechanics ◽

Ab Initio ◽

Molecular Mechanics ◽

Short Wavelength ◽

Visual Pigments ◽

Color Tuning ◽

Human And Mouse

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Developing ab initio quality force fields from condensed phase quantum-mechanics/molecular-mechanics calculations through the adaptive force matching method

The Journal of Chemical Physics ◽

10.1063/1.2965882 ◽

2008 ◽

Vol 129 (6) ◽

pp. 064108 ◽

Cited By ~ 86

Author(s):

Omololu Akin-Ojo ◽

Yang Song ◽

Feng Wang

Keyword(s):

Quantum Mechanics ◽

Ab Initio ◽

Molecular Mechanics ◽

Condensed Phase ◽

Force Fields ◽

Matching Method ◽

Molecular Mechanics Calculations ◽

Force Matching

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Mechanism of Spectral Tuning Going from Retinal in Vacuo to Bovine Rhodopsin and its Mutants: Multireference ab Initio Quantum Mechanics/Molecular Mechanics Studies

The Journal of Physical Chemistry B ◽

10.1021/jp807172h ◽

2008 ◽

Vol 112 (51) ◽

pp. 16883-16890 ◽

Cited By ~ 69

Author(s):

Ahmet Altun ◽

Shozo Yokoyama ◽

Keiji Morokuma

Keyword(s):

Quantum Mechanics ◽

Ab Initio ◽

Molecular Mechanics ◽

Spectral Tuning ◽

Bovine Rhodopsin

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Cation solvation with quantum chemical effects modeled by a size-consistent multi-partitioning quantum mechanics/molecular mechanics method

Physical Chemistry Chemical Physics ◽

10.1039/c7cp01708a ◽

2017 ◽

Vol 19 (27) ◽

pp. 17985-17997 ◽

Cited By ~ 8

Author(s):

Hiroshi C. Watanabe ◽

Maximilian Kubillus ◽

Tomáš Kubař ◽

Robert Stach ◽

Boris Mizaikoff ◽

...

Keyword(s):

Quantum Mechanics ◽

Molecular Mechanics ◽

Condensed Phase ◽

Quantum Chemical ◽

Chemical Properties ◽

Many Body ◽

Charge Fluctuations ◽

Structure And Dynamics ◽

Chemical Effects ◽

Solvation Structure

In the condensed phase, quantum chemical properties such as many-body effects and intermolecular charge fluctuations are critical determinants of the solvation structure and dynamics.

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