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Molecular Simulation and Modeling

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: 30 July 2024 | Viewed by 4877

Special Issue Editor

Prof. Dr. Małgorzata Borówko

E-Mail Website
Guest Editor
Department of Theoretical Chemistry, Institute of Chemical Sciences, Faculty of Chemistry, Maria Curie-Skłodowska University in Lublin, 20-031 Lublin, Poland
Interests: molecular simulations; theory of fluids; interfacial phenomena; phase transitions; Janus particles; hairy nanoparticles; chromatography
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Molecular simulations play an increasingly significant role in science today. The rapid progress in computer technology has given a strong impetus to the development of many statistical–mechanical methods for modeling physical, chemical, and biological processes. Among the simulation techniques, molecular dynamics and the Monte Carlo method are the most popular. The simulations provide a tool which allows for interpolation between laboratory experiments and theory, and for a deeper insight into the processes being studied when direct measurements are not possible.

We are currently observing the explosive development of simulation methods and their applications in fundamental and technological research. The latter include the design of new smart materials, active materials, the development of drugs and drug delivery, the fabrication of novel biomaterials for DNA sequencing, and many others.

This Special Issue collects papers devoted to the extension of novel simulation techniques and new methods for the analysis of the results. The other aim is to present applications of computer simulations to explore different phenomena with a focus on the explanation of their molecular mechanism and on the description of potential practical applications in nanotechnology, biotechnology, and medicine.

Prof. Dr. Małgorzata Borówko
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

  • molecular simulation
  • molecular dynamics
  • Monte Carlo method
  • molecular modeling
  • self-assembly
  • phase transitions
  • nanoparticles
  • supramolecular structures
  • biotechnology
  • nanotechnology

Related Special Issues

Published Papers (6 papers)

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Research

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16 pages, 20385 KiB  
Article
Molecular Dynamics Simulations of Different Nanoparticles at Substrates
by Małgorzata Borówko and Tomasz Staszewski
Int. J. Mol. Sci. 2024, 25(8), 4550; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms25084550 - 21 Apr 2024
Viewed by 338
Abstract
We report the results of large-scale molecular dynamics simulations of adsorption nanoparticles on solid surfaces. The particles were modeled as stiff aggregates of spherical segments. Three types of particles were studied: rods, rectangles, and triangles built of the same number of segments. We [...] Read more.
We report the results of large-scale molecular dynamics simulations of adsorption nanoparticles on solid surfaces. The particles were modeled as stiff aggregates of spherical segments. Three types of particles were studied: rods, rectangles, and triangles built of the same number of segments. We show how the particle shape affects the adsorption, the structure of the surface layer, and the degree of the removal of particles from the solvent. The systems with different segment–segment and segment–surface interactions and different concentrations of particles were investigated. The ordered structures formed in adsorption monolayers were also analyzed. The results are consistent with experimental observations. Full article
(This article belongs to the Special Issue Molecular Simulation and Modeling)
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14 pages, 3179 KiB  
Article
Design of New Schiff Bases and Their Heavy Metal Ion Complexes for Environmental Applications: A Molecular Dynamics and Density Function Theory Study
by Maria Assunta Chiacchio, Agata Campisi, Daniela Iannazzo, Salvatore V. Giofrè and Laura Legnani
Int. J. Mol. Sci. 2024, 25(8), 4159; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms25084159 - 09 Apr 2024
Viewed by 326
Abstract
Schiff bases (SBs) are important ligands in coordination chemistry due to their unique structural properties. Their ability to form complexes with metal ions has been exploited for the environmental detection of emerging water contaminants. In this work, we evaluated the complexation ability of [...] Read more.
Schiff bases (SBs) are important ligands in coordination chemistry due to their unique structural properties. Their ability to form complexes with metal ions has been exploited for the environmental detection of emerging water contaminants. In this work, we evaluated the complexation ability of three newly proposed SBs, 1–3, by complete conformational analysis, using a combination of Molecular Dynamics and Density Functional Theory studies, to understand their ability to coordinate toxic heavy metal (HMs) ions. From this study, it emerges that all the ligands present geometries that make them suitable to complex HMs through the N-imino moieties or, in the case of 3, with the support of the oxygen atoms of the ethylene diether chain. In particular, this ligand shows the most promising coordination behavior, particularly with Pb2+. Full article
(This article belongs to the Special Issue Molecular Simulation and Modeling)
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13 pages, 950 KiB  
Article
Viral Immunogenicity Prediction by Machine Learning Methods
by Nikolet Doneva and Ivan Dimitrov
Int. J. Mol. Sci. 2024, 25(5), 2949; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms25052949 - 03 Mar 2024
Viewed by 596
Abstract
Since viruses are one of the main causes of infectious illnesses, prophylaxis is essential for efficient disease control. Vaccines play a pivotal role in mitigating the transmission of various viral infections and fortifying our defenses against them. The initial step in modern vaccine [...] Read more.
Since viruses are one of the main causes of infectious illnesses, prophylaxis is essential for efficient disease control. Vaccines play a pivotal role in mitigating the transmission of various viral infections and fortifying our defenses against them. The initial step in modern vaccine design and development involves the identification of potential vaccine targets through computational techniques. Here, using datasets of 1588 known viral immunogens and 468 viral non-immunogens, we apply machine learning algorithms to develop models for the prediction of protective immunogens of viral origin. The datasets are split into training and test sets in a 4:1 ratio. The protein structures are encoded by E-descriptors and transformed into uniform vectors by the auto- and cross-covariance methods. The most relevant descriptors are selected by the gain/ratio technique. The models generated by Random Forest, Multilayer Perceptron, and XGBoost algorithms demonstrate superior predictive performance on the test sets, surpassing predictions made by VaxiJen 2.0—an established gold standard in viral immunogenicity prediction. The key attributes determining immunogenicity in viral proteins are specific fingerprints in hydrophobicity and steric properties. Full article
(This article belongs to the Special Issue Molecular Simulation and Modeling)
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18 pages, 13040 KiB  
Article
Homology Modeling, Molecular Dynamics Simulation, and Prediction of Bovine TLR2 Heterodimerization
by Alireza Mansouri, Mohamed Samy Yousef, Rasoul Kowsar and Akio Miyamoto
Int. J. Mol. Sci. 2024, 25(3), 1496; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms25031496 - 25 Jan 2024
Viewed by 737
Abstract
Toll-like receptor 2 (TLR2) is a major membrane-bound receptor with ligand and species specificity that activates the host immune response. Heterodimerization of TLR2 with TLR1 (TLR2/1) or TLR6 (TLR2/6), triggered by ligand binding, is essential to initiating the signaling pathway. Bovine TLR2 (bTLR2) [...] Read more.
Toll-like receptor 2 (TLR2) is a major membrane-bound receptor with ligand and species specificity that activates the host immune response. Heterodimerization of TLR2 with TLR1 (TLR2/1) or TLR6 (TLR2/6), triggered by ligand binding, is essential to initiating the signaling pathway. Bovine TLR2 (bTLR2) heterodimerization has not been defined yet compared with human and mouse TLR2s (hTLR2 and mTLR2). The aim of the present study was to model bovine TLRs (TLRs 1, 2 and 6) and create the heterodimeric forms of the bovine TLR2 using molecular dynamics (MD) simulations. We compared the intermolecular interactions in bTLR2/1-PAM3 and bTLR2/6-PAM2 with the hTLR2 and mTLR2 complexes through docking simulations and subsequent MD analyses. The present computational findings showed that bTLR2 dimerization could have a biological function and activate the immune response, similar to hTLR2 and mTLR2. Agonists and antagonists that are designed for hTLR2 and mTLR2 can target bTLR2. However, the experimental approaches to comparing the functional immune response of TLR2 across species were missing in the present study. This computational study provides a structural analysis of the bTLR2 interaction with bTLR1 and bTLR6 in the presence of an agonist/antagonist and reveals the three-dimensional structure of bTLR2 dimerization. The present findings could guide future experimental studies targeting bTLR2 with different ligands and lipopeptides. Full article
(This article belongs to the Special Issue Molecular Simulation and Modeling)
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22 pages, 2990 KiB  
Article
Investigation of the Affinity of Ceftobiprole for Selected Cyclodextrins Using Molecular Dynamics Simulations and HPLC
by Dariusz Boczar and Katarzyna Michalska
Int. J. Mol. Sci. 2023, 24(23), 16644; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms242316644 - 23 Nov 2023
Viewed by 997
Abstract
This paper presents the theoretical calculations of the inclusion complex formation between native ceftobiprole, a promising antibiotic from the cephalosporin group, and selected cyclodextrins (CDs) approved by the European Medicines Agency. Ceftobiprole was studied in three protonation states predicted from pKa calculations, [...] Read more.
This paper presents the theoretical calculations of the inclusion complex formation between native ceftobiprole, a promising antibiotic from the cephalosporin group, and selected cyclodextrins (CDs) approved by the European Medicines Agency. Ceftobiprole was studied in three protonation states predicted from pKa calculations, along with three selected CDs in a stoichiometric ratio of 1:1. It was introduced into the CD cavity in two opposite directions, resulting in 18 possible combinations. Docking studies determined the initial structures of the complexes, which then served as starting structures for molecular dynamics simulations. The analysis of the obtained trajectories included the spatial arrangement of ceftobiprole and CD, the hydrogen bonds forming between them, and the Gibbs free energy (ΔG) of the complex formation, which was calculated using the Generalised Born Surface Area (GBSA) equation. Among them, a complex of sulfobutyl ether- (SBE-) β-CD with protonated ceftobiprole turned out to be the most stable (ΔG = −12.62 kcal/mol = −52.80 kJ/mol). Then, experimental studies showed changes in the physiochemical properties of the ceftobiprole in the presence of the CDs, thus confirming the validity of the theoretical results. High-performance liquid chromatography analysis showed that the addition of 10 mM SBE-β-CD to a 1 mg/mL solution of ceftobiprole in 0.1 M of HCl increased the solubility 1.5-fold and decreased the degradation rate constant 2.5-fold. Full article
(This article belongs to the Special Issue Molecular Simulation and Modeling)
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Review

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58 pages, 24396 KiB  
Review
Density Functional Theory Calculations: A Useful Tool to Investigate Mechanisms of 1,3-Dipolar Cycloaddition Reactions
by Maria Assunta Chiacchio and Laura Legnani
Int. J. Mol. Sci. 2024, 25(2), 1298; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms25021298 - 20 Jan 2024
Cited by 1 | Viewed by 1334
Abstract
The present review contains a representative sampling of mechanistic studies, which have appeared in the literature in the last 5 years, on 1,3-dipolar cycloaddition reactions, using DFT calculations. Attention is focused on the mechanistic insights into 1,3-dipoles of propargyl/allenyl type and allyl type [...] Read more.
The present review contains a representative sampling of mechanistic studies, which have appeared in the literature in the last 5 years, on 1,3-dipolar cycloaddition reactions, using DFT calculations. Attention is focused on the mechanistic insights into 1,3-dipoles of propargyl/allenyl type and allyl type such as aza-ylides, nitrile oxides and azomethyne ylides and nitrones, respectively. The important role played by various metal–chiral–ligand complexes and the use of chiral eductors in promoting the site-, regio-, diastereo- and enatioselectivity of the reaction are also outlined. Full article
(This article belongs to the Special Issue Molecular Simulation and Modeling)
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