Dual Photochemical Reaction Pathway in Flavin-Based Photoreceptor LOV Domain: A Combined Quantum-Mechanics/Molecular-Mechanics Investigation

2017 ◽  
Vol 121 (41) ◽  
pp. 9583-9596 ◽  
Author(s):  
Setsuko Nakagawa ◽  
Oliver Weingart ◽  
Christel M. Marian
Keyword(s):  
Quantum Mechanics ◽  
Molecular Mechanics ◽  
Photochemical Reaction ◽  
Reaction Pathway ◽  
Lov Domain

Quantum Mechanics/Molecular Mechanics Free Energy Maps and Nonadiabatic Simulations for a Photochemical Reaction in DNA: Cyclobutane Thymine Dimer

2016 ◽  
Vol 7 (21) ◽  
pp. 4391-4397 ◽  
Author(s):  
Jesús I. Mendieta-Moreno ◽  
Daniel G. Trabada ◽  
Jesús Mendieta ◽  
James P. Lewis ◽  
Paulino Gómez-Puertas ◽  
...  
Keyword(s):  
Free Energy ◽  
Quantum Mechanics ◽  
Molecular Mechanics ◽  
Photochemical Reaction ◽  
Thymine Dimer ◽  
Energy Maps ◽  
Cyclobutane Thymine Dimer

Influence of the LOV Domain on Low-Lying Excited States of Flavin: A Combined Quantum-Mechanics/Molecular-Mechanics Investigation

2009 ◽  
Vol 113 (47) ◽  
pp. 15610-15618 ◽  
Author(s):  
Susanne Salzmann ◽  
Mario R. Silva-Junior ◽  
Walter Thiel ◽  
Christel M. Marian
Keyword(s):  
Quantum Mechanics ◽  
Molecular Mechanics ◽  
Excited States ◽  
Lov Domain

A multi-level quantum mechanics and molecular mechanics study of SN2 reaction at nitrogen: NH2Cl + OH−in aqueous solution

2016 ◽  
Vol 18 (8) ◽  
pp. 6146-6152 ◽  
Author(s):  
Jing Lv ◽  
Jingxue Zhang ◽  
Dunyou Wang
Keyword(s):  
Aqueous Solution ◽  
Quantum Mechanics ◽  
Molecular Mechanics ◽  
Reaction Pathway ◽  
Potential Of Mean Force ◽  
Stationary Points ◽  
Sn2 Reaction ◽  
Multi Level

The potential of mean force, solvation contribution and the stationary points along the reaction pathway for the SN2 reaction at nitrogen: NH2Cl + OH−→ NH2OH + Cl−, in aqueous solution.

On-the-Fly Determination of Active Region Centers in Adaptive-Partitioning QM/MM

2020 ◽  
Author(s):  
Zenghui Yang
Keyword(s):  
Quantum Mechanics ◽  
Active Region ◽  
Molecular Mechanics ◽  
Active Regions ◽  
Available Energy ◽  
Adaptive Partitioning ◽  
Different Levels

Quantum mechanics/molecular mechanics (QM/MM) methods partition the system into active and environmental regions and treat them with different levels of theory, achieving accuracy and efficiency at the same time. Adaptive-partitioning (AP) QM/MM methods allow on-the-fly changes to the QM/MM partitioning of the system. Many of the available energy-based AP-QM/MM methods partition the system according to distances to pre-chosen centers of active regions. For such AP-QM/MM methods, I develop an adaptive-center (AC) method that allows on-the-fly determination of the centers of active regions according to general geometrical or potential-related criteria, extending the range of application of energy-based AP-QM/MM methods to systems where active regions may occur or vanish during the simulation.

A Conserved Asparagine in a Ubiquitin Conjugating Enzyme Positions the Substrate for Nucleophilic Attack

2018 ◽  
Author(s):  
Walker M. Jones ◽  
Aaron G. Davis ◽  
R. Hunter Wilson ◽  
Katherine L. Elliott ◽  
Isaiah Sumner
Keyword(s):  
Molecular Dynamics ◽  
Quantum Mechanics ◽  
Molecular Mechanics ◽  
Reaction Rates ◽  
Nucleophilic Attack ◽  
Classical Molecular Dynamics ◽  
Ubiquitin Conjugating Enzyme ◽  
Conjugating Enzyme

We present classical molecular dynamics (MD), Born-Oppenheimer molecular dynamics (BOMD), and hybrid quantum mechanics/molecular mechanics (QM/MM) data. MD was performed using the GPU accelerated pmemd module of the AMBER14MD package. BOMD was performed using CP2K version 2.6. The reaction rates in BOMD were accelerated using the Metadynamics method. QM/MM was performed using ONIOM in the Gaussian09 suite of programs. Relevant input files for BOMD and QM/MM are available.

Automated Parametrization of Biomolecular Force Fields from Quantum Mechanics/Molecular Mechanics (QM/MM) Simulations through Force Matching

2007 ◽  
Vol 3 (2) ◽  
pp. 628-639 ◽  
Author(s):  
Patrick Maurer ◽  
Alessandro Laio ◽  
Håkan W. Hugosson ◽  
Maria Carola Colombo ◽  
Ursula Rothlisberger
Keyword(s):  
Quantum Mechanics ◽  
Molecular Mechanics ◽  
Force Fields ◽  
Force Matching
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