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Advances in Molecular Dynamics and Molecular Modeling

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

Deadline for manuscript submissions: 30 June 2024 | Viewed by 1245

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Theory Department, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
Interests: molecular biology; chemical thermodynamics; physical chemistry; theoretical chemistry
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Special Issue Information

Dear Colleagues,

Molecular dynamics simulations have proven to be a powerful computational tool for studying the properties of molecular systems, as they can provide accurate insight into a wide range of time and length scales of molecular processes. Molecular simulations have also become indispensable for complementing and advancing structural and dynamic experimental studies. All of this is possible thanks to a fascinating and continuing development of new ideas underlying computational approaches, as well as dramatically improved computational power. Advances in materials science and physical chemistry further require an atomistic understanding of molecular interactions and their role in linking biomolecular structure and function, in the development of new materials, new drugs, and their delivery, to name just a few examples.

In this Special Issue, we present a selection of papers on advanced simulation approaches that use extended free energy and kinetic sampling techniques, such as metadynamics and generalized Langevin formalism, multiscale modeling, principal component analysis, machine learning, and tools for deriving experimental observables from simulations, that aim to integrate and elucidate the relationship between molecular structure, dynamics, and function.

Dr. Franci Merzel
Guest Editor

Manuscript Submission Information

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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.


  • MD simulations
  • advanced sampling techniques
  • multiscale modeling
  • principal component analysis

Published Papers (1 paper)

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20 pages, 28048 KiB  
The Effect of Solvents on the Crystal Morphology of Isosorbide Mononitrate and Its Molecular Mechanisms
by Penghui Li, Guimin Zhang, Zongyi Zhou, Ying Sun, Yan Wang, Yu Yang and Xiaolai Zhang
Molecules 2024, 29(2), 367; - 11 Jan 2024
Viewed by 791
In this work, the modified attachment energy model was used to predict the crystal morphology of isosorbide mononitrate (ISMN) in the dichloromethane (CH2Cl2) solvent system and dichloromethane-n-hexane (CH2Cl2-C6H14) mixed solvent system. [...] Read more.
In this work, the modified attachment energy model was used to predict the crystal morphology of isosorbide mononitrate (ISMN) in the dichloromethane (CH2Cl2) solvent system and dichloromethane-n-hexane (CH2Cl2-C6H14) mixed solvent system. The solvent effect can significantly affect the crystal morphology, which can profoundly impact both the drug’s physicochemical properties and the subsequent technological treatment process. In addition, the interactions between solvent molecules and crystal faces were investigated using molecular dynamics simulation, and radial distribution function (RDF) analysis was performed to determine the types of interactions. The structural parameter S was introduced to characterize the roughness of each crystal surface; the change in the CH2Cl2 diffusion coefficient before and after the addition of C6H14 was analyzed using mean square displacement (MSD). The calculation results of the modified attachment energy from the two solvent systems revealed that C6H14 could accelerate crystal growth, while the crystal morphology was not greatly affected, which is of some significance as a guide for the industrial crystallization process. Full article
(This article belongs to the Special Issue Advances in Molecular Dynamics and Molecular Modeling)
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