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Molecules
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Multiscale Chemical Modeling and Simulations Using Quantum Mechanics/Molecular Mechanics (QM/MM)
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Multiscale Chemical Modeling and Simulations Using Quantum Mechanics/Molecular Mechanics (QM/MM)

A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Physical Chemistry".

Deadline for manuscript submissions: closed (31 January 2019) | Viewed by 15099

Special Issue Editors

Dr. Antonio Monari

E-Mail Website
Guest Editor
Theoretical Physics and Theoretical Chemistry Laboratory (LPCT), University of Lorraine and CNRS, Nancy, France
Interests: molecular modeling and simulation; theoretical photophysics and photochemistry; time resolved spectroscopy; non-adiabatic phenomena; structural biophysics; DNA photosensitization; DNA lesions and repair mechanism; epigenetic regulations
Special Issues, Collections and Topics in MDPI journals
Dr. Elise Dumont

E-Mail Website
Guest Editor
Laboratoire de Chimie, UMR 5182 CNRS-Ecole Nationale Supérieure de Lyon, Université Claude Bernard Lyon 1-CEA, 46 Allée d’Italie, Lyon Cedex 07 69364, France
Interests: computational biochemistry; molecular dynamics; structural biology; QM/MM; DNA damage and repair; photochemistry; supramolecular systems
Dr. Marco Marazzi

E-Mail Website1 Website2
Guest Editor
Department of Analytical Chemistry, Physical Chemistry and Chemical Engineering, Physical Chemistry Unit, University of Alcalá, Ctra. Madrid-Barcelona Km. 33,600 E-28871 Alcalá de Henares (Madrid), Spain
Interests: computational chemistry; photochemistry and photophysics; ultrafast spectroscopy; quantum mechanics/ molecular mechanics methods; photoswitches and motors; DNA damage; mechanochemistry

Special Issue Information

Dear Colleagues,

This Special Issue of Molecules is dedicated to the developments and applications of theoretical and computational methods in the description of environmental effects. Especially, it aims at covering the different flavors of hybrid quantum mechanics/molecular mechanics (QM/MM) methods, as a tool to explicitly include the effects of the surroundings on the molecular system. Indeed, QM/MM multiscaling approach constitutes an emerging field across the last decade, as a key to describe–and in some cases predict–both chemical reactivity and spectroscopic properties.

All researchers working in the field are cordially invited to contribute with original research papers or reviews to this Special Issue, reporting on ground-state, as well as excited-state, QM/MM simulations, hence including thermal processes and also photophysical and photochemical phenomena. Specific solvent effects, along with biological mechanisms and materials inspired systems will be welcome.

Dr. Antonio Monari
Dr. Elise Dumont
Dr. Marco Marazzi
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Molecules is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Quantum mechanics/molecular mechanics
  • Environmental effects
  • Chemical reactivity
  • Photochemistry
  • Photophysics
  • Spectroscopy
  • Simulations

Published Papers (3 papers)

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Research

21 pages, 1886 KiB  
Article
QM/MM Benchmarking of Cyanobacteriochrome Slr1393g3 Absorption Spectra
by Christian Wiebeler and Igor Schapiro
Molecules 2019, 24(9), 1720; https://doi.org/10.3390/molecules24091720 - 03 May 2019
Cited by 24 | Viewed by 4566
Abstract
Cyanobacteriochromes are compact and spectrally diverse photoreceptor proteins that are promising candidates for biotechnological applications. Computational studies can contribute to an understanding at a molecular level of their wide spectral tuning and diversity. In this contribution, we benchmark methods to model a 110 [...] Read more.
Cyanobacteriochromes are compact and spectrally diverse photoreceptor proteins that are promising candidates for biotechnological applications. Computational studies can contribute to an understanding at a molecular level of their wide spectral tuning and diversity. In this contribution, we benchmark methods to model a 110 nm shift in the UV/Vis absorption spectrum from a red- to a green-absorbing form of the cyanobacteriochrome Slr1393g3. Based on an assessment of semiempirical methods to describe the chromophore geometries of both forms in vacuo, we find that DFTB2+D leads to structures that are the closest to the reference method. The benchmark of the excited state calculations is based on snapshots from quantum mechanics/molecular mechanics molecular dynamics simulations. In our case, the methods RI-ADC(2) and sTD-DFT based on CAM-B3LYP ground state calculations perform the best, whereas no functional can be recommended to simulate the absorption spectra of both forms with time-dependent density functional theory. Furthermore, the difference in absorption for the lowest energy absorption maxima of both forms can already be modelled with optimized structures, but sampling is required to improve the shape of the absorption bands of both forms, in particular for the second band. This benchmark study can guide further computational studies, as it assesses essential components of a protocol to model the spectral tuning of both cyanobacteriochromes and the related phytochromes. Full article
(This article belongs to the Special Issue Multiscale Chemical Modeling and Simulations Using Quantum Mechanics/Molecular Mechanics (QM/MM))
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31 pages, 6626 KiB  
Article
Molecular Simulations with in-deMon2k QM/MM, a Tutorial-Review
by Aurélien de la Lande, Aurelio Alvarez-Ibarra, Karim Hasnaoui, Fabien Cailliez, Xiaojing Wu, Tzonka Mineva, Jérôme Cuny, Patrizia Calaminici, Luis López-Sosa, Gerald Geudtner, Isabelle Navizet, Cristina Garcia Iriepa, Dennis R. Salahub and Andreas M. Köster
Molecules 2019, 24(9), 1653; https://doi.org/10.3390/molecules24091653 - 26 Apr 2019
Cited by 31 | Viewed by 6529
Abstract
deMon2k is a readily available program specialized in Density Functional Theory (DFT) simulations within the framework of Auxiliary DFT. This article is intended as a tutorial-review of the capabilities of the program for molecular simulations involving ground and excited electronic states. The program [...] Read more.
deMon2k is a readily available program specialized in Density Functional Theory (DFT) simulations within the framework of Auxiliary DFT. This article is intended as a tutorial-review of the capabilities of the program for molecular simulations involving ground and excited electronic states. The program implements an additive QM/MM (quantum mechanics/molecular mechanics) module relying either on non-polarizable or polarizable force fields. QM/MM methodologies available in deMon2k include ground-state geometry optimizations, ground-state Born–Oppenheimer molecular dynamics simulations, Ehrenfest non-adiabatic molecular dynamics simulations, and attosecond electron dynamics. In addition several electric and magnetic properties can be computed with QM/MM. We review the framework implemented in the program, including the most recently implemented options (link atoms, implicit continuum for remote environments, metadynamics, etc.), together with six applicative examples. The applications involve (i) a reactivity study of a cyclic organic molecule in water; (ii) the establishment of free-energy profiles for nucleophilic-substitution reactions by the umbrella sampling method; (iii) the construction of two-dimensional free energy maps by metadynamics simulations; (iv) the simulation of UV-visible absorption spectra of a solvated chromophore molecule; (v) the simulation of a free energy profile for an electron transfer reaction within Marcus theory; and (vi) the simulation of fragmentation of a peptide after collision with a high-energy proton. Full article
(This article belongs to the Special Issue Multiscale Chemical Modeling and Simulations Using Quantum Mechanics/Molecular Mechanics (QM/MM))
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14 pages, 2989 KiB  
Article
Effect of Protein Conformation and AMP Protonation State on Fireflies’ Bioluminescent Emission
by Cristina Garcia-Iriepa and Isabelle Navizet
Molecules 2019, 24(8), 1565; https://doi.org/10.3390/molecules24081565 - 20 Apr 2019
Cited by 11 | Viewed by 3566
Abstract
The emitted color in fireflies’ bioluminescent systems depends on the beetle species the system is extracted from and on different external factors (pH, temperature…) among others. Controlling the energy of the emitted light (i.e., color) is of crucial interest for the use of [...] Read more.
The emitted color in fireflies’ bioluminescent systems depends on the beetle species the system is extracted from and on different external factors (pH, temperature…) among others. Controlling the energy of the emitted light (i.e., color) is of crucial interest for the use of such bioluminescent systems. For instance, in the biomedical field, red emitted light is desirable because of its larger tissue penetration and lower energies. In order to investigate the influence of the protein environment and the AMP protonation state on the emitted color, the emission spectra of the phenolate-keto and phenolate-enol oxyluciferin forms have been simulated by means of MD simulations and QM/MM calculations, considering: two different protein conformations (with an open or closed C-terminal domain with respect to the N-terminal) and two protonation states of AMP. The results show that the emission spectra when considering the protein characterized by a closed conformation are blue-shifted compared to the open conformation. Moreover, the complete deprotonation of AMP phosphate group (AMP2−) can also lead to a blue-shift of the emission spectra but only when considering the closed protein conformation (open form is not sensitive to changes of AMP protonation state). These findings can be reasoned by the different interactions (hydrogen-bonds) found between oxyluciferin and the surrounding (protein, AMP and water molecules). This study gets partial insight into the possible origin of the emitted color modulation by changes of the pH or luciferase conformations. Full article
(This article belongs to the Special Issue Multiscale Chemical Modeling and Simulations Using Quantum Mechanics/Molecular Mechanics (QM/MM))
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