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Quantum and Classical Molecular Dynamics
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Quantum and Classical Molecular Dynamics

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Physical Chemistry and Chemical Physics".

Deadline for manuscript submissions: closed (25 April 2024) | Viewed by 2328

Special Issue Editor

Dr. Cristina Sanz-Sanz

E-Mail Website
Guest Editor
Departamento de Química Física Aplicada, Universidad Autónoma de Madrid, 28049 Madrid, Spain
Interests: electronic structure; quantum/classical dynamics; non-adiabatic dynamics; photoinitiated processes; control of reactivity; spectroscopy

Special Issue Information

Dear Colleagues,

It is our pleasure to introduce a Special Issue on quantum and classical molecular dynamics. We are interested in collecting new works to present the current status of dynamics simulations, from methods to applications, in small and large systems.

The last decade has been crucial in the field of quantum and classical molecular dynamics, from simulations of new, small and intermediate size molecules experimentally observed in the interstellar medium, to larger systems for medical applications in cancer research and drug design, as well as simulations in materials to design new devices for optoelectronics.

In addition, thanks to machine learning approaches and more advanced computer capabilities, we are able to accurately simulate very large systems, including solvents, biological environments and molecular aggregates. Such improvements have also made it possible to simulate small systems in the gas phase with more precise quantum chemistry and/or molecular dynamics methods, pushing towards the limit of formally exact solutions of the time-dependent Schrödinger equation.

This collection aims to gather highly relevant manuscripts from the areas of quantum dynamics and classical dynamics, in order to share the state of the art of the field in a concise and well-presented manner. We look forward to your contributions!

This Special Issue is supervised by Dr. Cristina Sanz-Sanz (UAM) and assisted by our Topical Advisory Panel Member Dr. Sandra Gómez (University of Salamanca).

Dr. Cristina Sanz-Sanz
Guest Editor

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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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/classical dynamics
  • astrochemistry
  • photoinduced
  • non-adiabatic
  • ultrafast
  • ground/excited states chemistry
  • surface-hopping
  • QM/MM
  • photochemistry
  • direct dynamics

Published Papers (2 papers)

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Research

14 pages, 2055 KiB  
Article
Ionization Cross Sections of Hydrogen Molecule by Electron and Positron Impact
by Károly Tőkési and Robert D. DuBois
Int. J. Mol. Sci. 2024, 25(6), 3410; https://doi.org/10.3390/ijms25063410 - 18 Mar 2024
Viewed by 606
Abstract
We present ionization cross sections of hydrogen molecules by electron and positron impact for impact energies between 20 and 1000 eV. A three-body Classical Trajectory Monte Carlo approximation is applied to mimic the collision system. In this approach, the H2 molecule is [...] Read more.
We present ionization cross sections of hydrogen molecules by electron and positron impact for impact energies between 20 and 1000 eV. A three-body Classical Trajectory Monte Carlo approximation is applied to mimic the collision system. In this approach, the H2 molecule is modeled by a hydrogen-type atom with one active electron bound to a central core of effective charge with an effective binding energy. Although this model is crude for describing a hydrogen molecule, we found that the total cross sections for positron impact agree reasonably well with the experimental data. For the electron impact, our calculated cross sections are in good agreement with the experimental data in impact energies between 80 eV and 400 eV but are smaller at higher impact energies and larger at lower impact energies. Our calculated cross sections are compared with the scaled cross sections obtained experimentally for an atomic hydrogen target. We also present single differential cross sections as a function of the energy and angle of the ejected electron and scattered projectiles for a 250 eV impact. These are shown to agree well with available data. Impact parameter distributions are also compared for several impact energies. Full article
(This article belongs to the Special Issue Quantum and Classical Molecular Dynamics)
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33 pages, 12501 KiB  
Article
In Silico Exploration of the Trypanothione Reductase (TryR) of L. mexicana
by Francisco J. Barrera-Téllez, Fernando D. Prieto-Martínez, Alicia Hernández-Campos, Karina Martínez-Mayorga and Rafael Castillo-Bocanegra
Int. J. Mol. Sci. 2023, 24(22), 16046; https://doi.org/10.3390/ijms242216046 - 07 Nov 2023
Viewed by 1237
Abstract
Human leishmaniasis is a neglected tropical disease which affects nearly 1.5 million people every year, with Mexico being an important endemic region. One of the major defense mechanisms of these parasites is based in the polyamine metabolic pathway, as it provides the necessary [...] Read more.
Human leishmaniasis is a neglected tropical disease which affects nearly 1.5 million people every year, with Mexico being an important endemic region. One of the major defense mechanisms of these parasites is based in the polyamine metabolic pathway, as it provides the necessary compounds for its survival. Among the enzymes in this route, trypanothione reductase (TryR), an oxidoreductase enzyme, is crucial for the Leishmania genus’ survival against oxidative stress. Thus, it poses as an attractive drug target, yet due to the size and features of its catalytic pocket, modeling techniques such as molecular docking focusing on that region is not convenient. Herein, we present a computational study using several structure-based approaches to assess the druggability of TryR from L. mexicana, the predominant Leishmania species in Mexico, beyond its catalytic site. Using this consensus methodology, three relevant pockets were found, of which the one we call σ-site promises to be the most favorable one. These findings may help the design of new drugs of trypanothione-related diseases. Full article
(This article belongs to the Special Issue Quantum and Classical Molecular Dynamics)
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