Importance of Polarization in Quantum Mechanics/Molecular Mechanics Descriptions of Electronic Excited States:  NaI(H2O)nPhotodissociation Dynamics as a Case Study†

2008 ◽  
Vol 112 (2) ◽  
pp. 636-649 ◽  
Author(s):  
Denise M. Koch ◽  
Gilles H. Peslherbe
Keyword(s):  
Quantum Mechanics ◽  
Molecular Mechanics ◽  
Excited States ◽  
Electronic Excited States

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

scholarly journals Assessing Configurational Sampling in the Quantum Mechanics/Molecular Mechanics Calculation of Temoporfin Absorption Spectrum and Triplet Density of States

Molecules ◽  
2018 ◽  
Vol 23 (11) ◽  
pp. 2932 ◽  
Author(s):  
Martina De Vetta ◽  
Omar Baig ◽  
Dorika Steen ◽  
Juan Nogueira ◽  
Leticia González
Keyword(s):  
Quantum Mechanics ◽  
Molecular Mechanics ◽  
Excited States ◽  
Experimental Spectrum ◽  
Triplet States ◽  
Absorption Properties ◽  
Exchange Correlation ◽  
Molecular Mechanics Calculation ◽  
Electrostatic Embedding ◽  
Good Agreement

The absorption properties of Temoporfin, a second-generation photosensitizer employed in photodynamic therapy, are calculated with an electrostatic-embedding quantum mechanics/molecular mechanics (QM/MM) scheme in methanol. The suitability of several ensembles of geometries generated by different sampling techniques, namely classical-molecular-dynamics (MD) and QM/MM-MD thermal sampling, Wigner quantum sampling and a hybrid protocol, which combines the thermal and quantum approaches, is assessed. It is found that a QM description of the chromophore during the sampling is needed in order to achieve a good agreement with respect to the experimental spectrum. Such a good agreement is obtained with both QM/MM-MD and Wigner samplings, demonstrating that a proper description of the anharmonic motions of the chromophore is not relevant in the computation of the absorption properties. In addition, it is also found that solvent organization is a rather fast process and a long sampling is not required. Finally, it is also demonstrated that the same exchange-correlation functional should be employed in the sampling and in the computation of the excited states properties to avoid unphysical triplet states with relative energies close or below 0 eV.

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.

Excited State Tracking During the Relaxation of Coordination Compounds

2018 ◽  
Author(s):  
Juan Sanz García ◽  
Martial Boggio-Pasqua ◽  
Ilaria Ciofini ◽  
Marco Campetella
Keyword(s):  
Excited State ◽  
Excited States ◽  
Potential Energy Surfaces ◽  
Photochemical Reactions ◽  
Complex Nature ◽  
Electronic Excited States ◽  
Ruthenium Nitrosyl ◽  
State Tracking ◽  
Energy Surfaces ◽  
Electronic Wavefunction

<div>The ability to locate minima on electronic excited states (ESs) potential energy surfaces (PESs) both in the case of bright and dark states is crucial for a full understanding of photochemical reactions. This task has become a standard practice for small- to medium-sized organic chromophores thanks to the constant developments in the field of computational photochemistry. However, this remains a very challenging effort when it comes to the optimization of ESs of transition metal complexes (TMCs), not only due to the presence of several electronic excited states close in energy, but also due to the complex nature of the excited states involved. In this article, we present a simple yet powerful method to follow an excited state of interest during a structural optimization in the case of TMC, based on the use of a compact hole-particle representation of the electronic transition, namely the natural transition orbitals (NTOs). State tracking using NTOs is unambiguously accomplished by computing the mono-electronic wavefunction overlap between consecutive steps of the optimization. Here, we demonstrate that this simple but robust procedure works not only in the case of the cytosine but also in the case of the ES optimization of a ruthenium-nitrosyl complex which is very problematic with standard approaches.</div>

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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