Insight into the isomerization mechanism of retinal proteins from hybrid quantum mechanics/molecular mechanics simulations

2021 ◽  
Author(s):  
Saumik Sen ◽  
Rajiv K. Kar ◽  
Veniamin A. Borin ◽  
Igor Schapiro
Keyword(s):  
Quantum Mechanics ◽  
Molecular Mechanics ◽  
Isomerization Mechanism ◽  
Retinal Proteins ◽  
Insight Into

Insight into the catalytic mechanism of meta-cleavage product hydrolase BphD: a quantum mechanics/molecular mechanics study

RSC Advances ◽  
2015 ◽  
Vol 5 (82) ◽  
pp. 66591-66597 ◽  
Author(s):  
Yanwei Li ◽  
Ruiming Zhang ◽  
Likai Du ◽  
Qingzhu Zhang ◽  
Wenxing Wang
Keyword(s):  
Quantum Mechanics ◽  
Molecular Mechanics ◽  
Catalytic Mechanism ◽  
Dienoic Acid ◽  
Cleavage Product ◽  
Natural Substrate ◽  
Catabolic Pathway ◽  
Insight Into

The catalytic mechanism of BphD (the fourth enzyme of the biphenyl catabolic pathway) toward its natural substrate 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoic acid (HOPDA) was investigated in atomistic detail by QM/MM approach.

Computational enzymology: modelling the mechanisms of biological catalysts

2008 ◽  
Vol 36 (1) ◽  
pp. 22-26 ◽  
Author(s):  
Adrian J. Mulholland
Keyword(s):  
Quantum Mechanics ◽  
Molecular Mechanics ◽  
Reaction Mechanisms ◽  
Quantitative Comparison ◽  
Atomic Level ◽  
Catalysed Reaction ◽  
Biological Catalysis ◽  
Computational Enzymology ◽  
Insight Into ◽  
Comparison With Experiments

Simulations and modelling [e.g. with combined QM/MM (quantum mechanics/molecular mechanics) methods] are increasingly important in investigations of enzyme-catalysed reaction mechanisms. Calculations offer the potential of uniquely detailed, atomic-level insight into the fundamental processes of biological catalysis. Highly accurate methods promise quantitative comparison with experiments, and reliable predictions of mechanisms, revolutionizing enzymology.

scholarly journals Azobenzene as a Photoregulator Covalently Attached to RNA: A Quantum Mechanics/Molecular Mechanics-Surface Hopping Dynamics Study

2018 ◽  
Author(s):  
Padmabati Mondal ◽  
Giovanni Granucci ◽  
Dominique Rastädter ◽  
Maurizio Persico ◽  
Irene Burghardt
Keyword(s):  
Quantum Mechanics ◽  
Quantum Yield ◽  
Molecular Mechanics ◽  
Ground State ◽  
Solution Phase ◽  
Biotechnological Applications ◽  
Surface Hopping ◽  
Left Handed ◽  
Isomerization Mechanism ◽  
Azobenzene Chromophore

The photoregulation of nucleic acids by azobenzene photoswitches has recently attracted considerable interest in the context of emerging biotechnological applications. To understand the mechanism of photoinduced isomerisation and conformational control in these complex biological environments, we employ a Quantum Mechanics/Molecular Mechanics (QM/MM) approach in conjunction with nonadiabatic Surface Hopping (SH) dynamics. Two representative RNA-azobenzene complexes are investigated, both of which contain the azobenzene chromophore covalently attached to an RNA double strand via a beta-deoxyribose linker. Due to the pronounced constraints of the local RNA environment, it is found that trans-to-cis isomerization is slowed down to a time scale of ~15 picoseconds, in contrast to 500 femtoseconds in vacuo, with a quantum yield reduced by a factor of two. By contrast, cis-to-trans isomerization remains in a sub-picosecond regime. A volume-conserving isomerization mechanism is found, similarly to the pedal-like mechanism previously identified for azobenzene in solution phase. Strikingly, the chiral RNA environment induces opposite right-handed and left-handed helicities of the ground-state cis-azobenzene chromophore in the two RNA-azobenzene complexes, along with an almost completely chirality conserving photochemical pathway for these helical enantiomers.

scholarly journals Azobenzene as a Photoregulator Covalently Attached to RNA: A Quantum Mechanics/Molecular Mechanics-Surface Hopping Dynamics Study

2018 ◽  
Author(s):  
Padmabati Mondal ◽  
Giovanni Granucci ◽  
Dominique Rastädter ◽  
Maurizio Persico ◽  
Irene Burghardt
Keyword(s):  
Quantum Mechanics ◽  
Quantum Yield ◽  
Molecular Mechanics ◽  
Ground State ◽  
Solution Phase ◽  
Biotechnological Applications ◽  
Surface Hopping ◽  
Left Handed ◽  
Isomerization Mechanism ◽  
Azobenzene Chromophore

The photoregulation of nucleic acids by azobenzene photoswitches has recently attracted considerable interest in the context of emerging biotechnological applications. To understand the mechanism of photoinduced isomerisation and conformational control in these complex biological environments, we employ a Quantum Mechanics/Molecular Mechanics (QM/MM) approach in conjunction with nonadiabatic Surface Hopping (SH) dynamics. Two representative RNA-azobenzene complexes are investigated, both of which contain the azobenzene chromophore covalently attached to an RNA double strand via a beta-deoxyribose linker. Due to the pronounced constraints of the local RNA environment, it is found that trans-to-cis isomerization is slowed down to a time scale of ~15 picoseconds, in contrast to 500 femtoseconds in vacuo, with a quantum yield reduced by a factor of two. By contrast, cis-to-trans isomerization remains in a sub-picosecond regime. A volume-conserving isomerization mechanism is found, similarly to the pedal-like mechanism previously identified for azobenzene in solution phase. Strikingly, the chiral RNA environment induces opposite right-handed and left-handed helicities of the ground-state cis-azobenzene chromophore in the two RNA-azobenzene complexes, along with an almost completely chirality conserving photochemical pathway for these helical enantiomers.

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.

scholarly journals Asset–liability modelling in the quantum era

2021 ◽  
Vol 26 ◽  
Author(s):  
T. Berry ◽  
J. Sharpe
Keyword(s):  
Quantum Mechanics ◽  
Quantum Computer ◽  
Quantum Algorithm ◽  
Capital Requirements ◽  
Quantum Computers ◽  
Investment Management ◽  
Asset Liability Management ◽  
Liability Management ◽  
Insight Into ◽  
Current Practices

Abstract This paper introduces and demonstrates the use of quantum computers for asset–liability management (ALM). A summary of historical and current practices in ALM used by actuaries is given showing how the challenges have previously been met. We give an insight into what ALM may be like in the immediate future demonstrating how quantum computers can be used for ALM. A quantum algorithm for optimising ALM calculations is presented and tested using a quantum computer. We conclude that the discovery of the strange world of quantum mechanics has the potential to create investment management efficiencies. This in turn may lead to lower capital requirements for shareholders and lower premiums and higher insured retirement incomes for policyholders.

Sign in / Sign up

Export Citation Format

Share Document