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

2017 ◽  
Vol 19 (27) ◽  
pp. 17985-17997 ◽  
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.

Many-Body Perturbation Theory Extended to the Quantum Mechanics/Molecular Mechanics Approach: Application to Indole in Water Solution

2009 ◽  
Vol 5 (7) ◽  
pp. 1822-1828 ◽  
Author(s):  
Adriano Mosca Conte ◽  
Emiliano Ippoliti ◽  
Rodolfo Del Sole ◽  
Paolo Carloni ◽  
Olivia Pulci
Keyword(s):  
Perturbation Theory ◽  
Quantum Mechanics ◽  
Molecular Mechanics ◽  
Water Solution ◽  
Many Body ◽  
Many Body Perturbation Theory

Computational Photobiology and Beyond

2010 ◽  
Vol 63 (3) ◽  
pp. 413 ◽  
Author(s):  
Igor Schapiro ◽  
Mikhail N. Ryazantsev ◽  
Wan Jian Ding ◽  
Mark M. Huntress ◽  
Federico Melaccio ◽  
...  
Keyword(s):  
Quantum Mechanics ◽  
Excited State ◽  
Ab Initio ◽  
Molecular Mechanics ◽  
Chemical Treatment ◽  
Quantum Chemical ◽  
Organic Molecules ◽  
Molecular Devices ◽  
Computational Studies ◽  
Computational Investigation

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.

Quantitative Analysis and Correction of Quantum Mechanics/Molecular Mechanics Boundary Artifacts in Adaptive QM/MM Methods

2019 ◽  
Author(s):  
Hiroshi Watanabe ◽  
Qiang Cui
Keyword(s):  
Quantum Mechanics ◽  
Quantitative Analysis ◽  
Molecular Mechanics ◽  
Bulk Water ◽  
Dynamics Simulation ◽  
Chemical Effects ◽  
Temporal Continuity ◽  
Temporal And Spatial ◽  
Dynamics Simulations ◽  
Spatial Discontinuity

The incorporation of quantum chemical effects of solvation into molecular dynamics simulation has been a challenging issue due to solvent diffusion. To this end, various adaptive quantum mechanics/molecular mechanics (QM/MM) methods have been proposed, in which free solvent exchanges are allowed via a flexible switching of their identities between QM and MM models according to their distances from the QM solute. However, temporal and spatial discontinuities that remain in the standard implementations continue to hamper stable and accurate dynamics simulations using adaptive QM/MM approaches. We previously demonstrated that the size-consistent multi-partitioning (SCMP) method achieved temporal continuity while avoiding spatial discontinuities to some extent. In the present study, however, we demonstrate that the residual spatial discontinuity may lead to severe problems under certain conditions; via quantitative analysis, we show that not only adaptive QM/MM but also all multiscale approaches might share these problems implicitly, which have not been investigated in depth so far. To alleviate these artifacts, we propose a correction based on the SCMP approach and conduct benchmark simulations using bulk water systems.

Quantitative Analysis of Quantum Mechanics/Molecular Mechanics Boundary Artifacts and the correction in Adaptive QM/MM Methods

2019 ◽  
Author(s):  
Hiroshi Watanabe ◽  
Qiang Cui
Keyword(s):  
Quantum Mechanics ◽  
Quantitative Analysis ◽  
Molecular Mechanics ◽  
Bulk Water ◽  
Dynamics Simulation ◽  
Chemical Effects ◽  
Temporal Continuity ◽  
Temporal And Spatial ◽  
Dynamics Simulations ◽  
Spatial Discontinuity

The incorporation of quantum chemical effects of solvation into molecular dynamics simulation has been a challenging issue due to solvent diffusion. To this end, various adaptive quantum mechanics/molecular mechanics (QM/MM) methods have been proposed, in which free solvent exchanges are allowed via a flexible switching of their identities between QM and MM models according to their distances from the QM solute. However, temporal and spatial discontinuities that remain in the standard implementations continue to hamper stable and accurate dynamics simulations using adaptive QM/MM approaches. We previously demonstrated that the size-consistent multi-partitioning (SCMP) method achieved temporal continuity while avoiding spatial discontinuities to some extent. In the present study, however, we demonstrate that the residual spatial discontinuity may lead to severe problems under certain conditions; via quantitative analysis, we show that not only adaptive QM/MM but also all multiscale approaches might share these problems implicitly, which have not been investigated in depth so far. To alleviate these artifacts, we propose a correction based on the SCMP approach and conduct benchmark simulations using bulk water systems.

Quantitative Analysis of Quantum Mechanics/Molecular Mechanics Boundary Artifacts and the correction in Adaptive QM/MM Methods

2019 ◽  
Author(s):  
Hiroshi Watanabe ◽  
Qiang Cui
Keyword(s):  
Quantum Mechanics ◽  
Quantitative Analysis ◽  
Molecular Mechanics ◽  
Bulk Water ◽  
Dynamics Simulation ◽  
Chemical Effects ◽  
Temporal Continuity ◽  
Temporal And Spatial ◽  
Dynamics Simulations ◽  
Spatial Discontinuity

The incorporation of quantum chemical effects of solvation into molecular dynamics simulation has been a challenging issue due to solvent diffusion. To this end, various adaptive quantum mechanics/molecular mechanics (QM/MM) methods have been proposed, in which free solvent exchanges are allowed via a flexible switching of their identities between QM and MM models according to their distances from the QM solute. However, temporal and spatial discontinuities that remain in the standard implementations continue to hamper stable and accurate dynamics simulations using adaptive QM/MM approaches. We previously demonstrated that the size-consistent multi-partitioning (SCMP) method achieved temporal continuity while avoiding spatial discontinuities to some extent. In the present study, however, we demonstrate that the residual spatial discontinuity may lead to severe problems under certain conditions; via quantitative analysis, we show that not only adaptive QM/MM but also all multiscale approaches might share these problems implicitly, which have not been investigated in depth so far. To alleviate these artifacts, we propose a correction based on the SCMP approach and conduct benchmark simulations using bulk water systems.

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