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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 (30 July 2024) | Viewed by 16846

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Prof. Dr. Małgorzata Borówko

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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
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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

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Keywords

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

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Related Special Issues

Advances in Molecular Simulation in International Journal of Molecular Sciences (16 articles)
2nd Edition: Advances in Molecular Simulation in International Journal of Molecular Sciences (16 articles)
3rd Edition: Advances in Molecular Simulation in International Journal of Molecular Sciences (7 articles)

Published Papers (12 papers)

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21 pages, 5478 KiB

Open AccessArticle

Preparation and Molecular Dynamic Simulation of Superfine CL−20/TNT Cocrystal Based on the Opposite Spray Method

by Junming Yuan, Zhenyang Liu, Tao Han, Junyi Li, Peijiang Han and Jing Wang

Int. J. Mol. Sci. 2024, 25(17), 9501; https://doi.org/10.3390/ijms25179501 - 31 Aug 2024

Viewed by 665

Abstract

In view of the current problems of slow crystallization rate, varying grain sizes, complex process conditions, and low safety in the preparation of CL−20/TNT cocrystal explosives in the laboratory, an opposite spray crystallization method is provided to quickly prepare ultrafine explosive cocrystal particles. CL−20/TNT cocrystal explosive was prepared using this method, and the obtained cocrystal samples were characterized by electron microscopy morphology, differential thermal analysis, infrared spectroscopy, and X-ray diffraction analysis. The effects of spray temperature, feed ratio, and preparation method on the formation of explosive cocrystal were studied, and the process conditions of the pneumatic atomization spray crystallization method were optimized. The crystal plane binding energy and molecular interaction forces between CL−20 and TNT were obtained through molecular dynamic simulation, and the optimal binding crystal plane and cocrystal mechanism were analyzed. The theoretical calculation temperature of the binding energy was preliminarily explored in relation to the preparation process temperature of cocrystal explosives. The mechanical sensitivity of ultrafine CL−20/TNT cocrystal samples was tested. The results showed that choosing acetone as the cosolvent, a spraying temperature of 30 °C, and a feeding ratio of 1:1 was beneficial for the formation and growth of cocrystal. The prepared CL−20/TNT cocrystal has a particle size of approximately 10 μm. The grain size is small, and the crystallization rate is fast. The impact and friction sensitivity of ultrafine CL−20/TNT cocrystal samples were significantly reduced. The experimental process conditions are simple and easy to control, and the safety of the preparation process is high, providing certain technical support for the preparation of high-quality cocrystal explosives. Full article

(This article belongs to the Special Issue Molecular Simulation and Modeling)

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14 pages, 3338 KiB

Open AccessArticle

Molecular Insights into Adhesion at Interface of Geopolymer Binder and Cement Mortar

by Anton S. Kasprzhitskii and Alexander A. Kruglikov

Int. J. Mol. Sci. 2024, 25(15), 8374; https://doi.org/10.3390/ijms25158374 - 31 Jul 2024

Viewed by 742

Abstract

The degradation of concrete and reinforced concrete structures is a significant technical and economic challenge, requiring continuous repair and rehabilitation throughout their service life. Geopolymers (GPs), known for their high mechanical strength, low shrinkage, and durability, are being increasingly considered as alternatives to traditional repair materials. However, there is currently a lack of understanding regarding the interface bond properties between new geopolymer layers and old concrete substrates. In this paper, using advanced computational techniques, including quantum mechanical calculations and stochastic modeling, we explored the adsorption behavior and interaction mechanism of aluminosilicate oligomers with different Si/Al ratios forming the geopolymer gel structure and calcium silicate hydrate as the substrate at the interface bond region. We analyzed the electron density distributions of the highest occupied and lowest unoccupied molecular orbitals, examined the reactivity indices based on electron density functional theory, performed Mulliken charge population analysis, and evaluated global reactivity descriptors for the considered oligomers. The results elucidate the mechanisms of local and global reactivity of the oligomers, the equilibrium low-energy configurations of the oligomer structures adsorbed on the surface of C-(A)-S-H(I) (100), and their adsorption energies. These findings contribute to a better understanding of the adhesion properties of geopolymers and their potential as effective repair materials. Full article

(This article belongs to the Special Issue Molecular Simulation and Modeling)

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46 pages, 8885 KiB

Open AccessArticle

A Practical Guide to All-Atom and Coarse-Grained Molecular Dynamics Simulations Using Amber and Gromacs: A Case Study of Disulfide-Bond Impact on the Intrinsically Disordered Amyloid Beta

by Pamela Smardz, Midhun Mohan Anila, Paweł Rogowski, Mai Suan Li, Bartosz Różycki and Pawel Krupa

Int. J. Mol. Sci. 2024, 25(12), 6698; https://doi.org/10.3390/ijms25126698 - 18 Jun 2024

Cited by 1 | Viewed by 2914

Abstract

Intrinsically disordered proteins (IDPs) pose challenges to conventional experimental techniques due to their large-scale conformational fluctuations and transient structural elements. This work presents computational methods for studying IDPs at various resolutions using the Amber and Gromacs packages with both all-atom (Amber ff19SB with the OPC water model) and coarse-grained (Martini 3 and SIRAH) approaches. The effectiveness of these methodologies is demonstrated by examining the monomeric form of amyloid-β (Aβ42), an IDP, with and without disulfide bonds at different resolutions. Our results clearly show that the addition of a disulfide bond decreases the β-content of Aβ42; however, it increases the tendency of the monomeric Aβ42 to form fibril-like conformations, explaining the various aggregation rates observed in experiments. Moreover, analysis of the monomeric Aβ42 compactness, secondary structure content, and comparison between calculated and experimental chemical shifts demonstrates that all three methods provide a reasonable choice to study IDPs; however, coarse-grained approaches may lack some atomistic details, such as secondary structure recognition, due to the simplifications used. In general, this study not only explains the role of disulfide bonds in Aβ42 but also provides a step-by-step protocol for setting up, conducting, and analyzing molecular dynamics (MD) simulations, which is adaptable for studying other biomacromolecules, including folded and disordered proteins and peptides. Full article

(This article belongs to the Special Issue Molecular Simulation and Modeling)

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18 pages, 6194 KiB

Open AccessArticle

The Characteristics of Structural Properties and Diffusion Pathway of Alkali in Sodium Trisilicate: Nanoarchitectonics and Molecular Dynamic Simulation

by Pham Huu Kien and Giap Thi Thuy Trang

Int. J. Mol. Sci. 2024, 25(11), 5628; https://doi.org/10.3390/ijms25115628 - 22 May 2024

Viewed by 761

Abstract

Based on nanoarchitectonics and molecular dynamics simulations, we investigate the structural properties and diffusion pathway of Na atoms in sodium trisilicate over a wide temperature range. The structural and dynamics properties are analyzed through the radial distribution function (RDF), the Voronoi Si- and O-polyhedrons, the cluster function f_CL(r), and the sets of fastest (SFA) and slowest atoms (SSA). The results indicate that Na atoms are not placed in Si-polyhedrons and bridging oxygen (BO) polyhedrons; instead, Na atoms are mainly placed in non-bridging oxygen (NBO) polyhedrons and free oxygen (FO) polyhedrons. Here BO, NBO, and FO represent O bonded with two, one, and no Si atoms, respectively. The simulation shows that O atoms in sodium trisilicate undergo numerous transformations: NBF0 ↔ NBF1, NBF1 ↔ NBF2, and BO0 ↔ BO1, where NBF is NBO or FO. The dynamics in sodium trisilicate are mainly distributed by the hopping and cooperative motion of Na atoms. We suppose that the diffusion pathway of Na atoms is realized via hopping Na atoms alone in BO-polyhedrons and the cooperative motion of a group of Na atoms in NBO- and FO-polyhedrons. Full article

(This article belongs to the Special Issue Molecular Simulation and Modeling)

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16 pages, 20385 KiB

Open AccessArticle

Molecular Dynamics Simulations of Different Nanoparticles at Substrates

by Małgorzata Borówko and Tomasz Staszewski

Int. J. Mol. Sci. 2024, 25(8), 4550; https://doi.org/10.3390/ijms25084550 - 21 Apr 2024

Viewed by 1209

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 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

Open AccessArticle

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://doi.org/10.3390/ijms25084159 - 9 Apr 2024

Cited by 1 | Viewed by 1317

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 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

Open AccessArticle

Viral Immunogenicity Prediction by Machine Learning Methods

by Nikolet Doneva and Ivan Dimitrov

Int. J. Mol. Sci. 2024, 25(5), 2949; https://doi.org/10.3390/ijms25052949 - 3 Mar 2024

Cited by 1 | Viewed by 1318

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 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

Open AccessArticle

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://doi.org/10.3390/ijms25031496 - 25 Jan 2024

Viewed by 1633

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) 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

Open AccessArticle

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://doi.org/10.3390/ijms242316644 - 23 Nov 2023

Viewed by 1345

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 pK_a 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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13 pages, 1779 KiB

Open AccessReview

Flavonoid Oxidation Potentials and Antioxidant Activities-Theoretical Models Based on Oxidation Mechanisms and Related Changes in Electronic Structure

by Ante Miličević

Int. J. Mol. Sci. 2024, 25(9), 5011; https://doi.org/10.3390/ijms25095011 - 3 May 2024

Viewed by 1132

Abstract

Herein, I will review our efforts to develop a comprehensive and robust model for the estimation of the first oxidation potential, E_p1, and antioxidant activity, AA, of flavonoids that would, besides enabling fast and cheap prediction of E_p1 and AA for a flavonoid of interest, help us explain the relationship between E_p1, AA and electronic structure. The model development went forward with enlarging the set of flavonoids and, that way, we had to learn how to deal with the structural peculiarities of some of the 35 flavonoids from the final calibration set, for which the E_p1 measurements were all made in our laboratory. The developed models were simple quadratic models based either on atomic spin densities or differences in the atomic charges of the species involved in any of the three main oxidation mechanisms. The best model takes into account all three mechanisms of oxidation, single electron transfer-proton transfer (SET-PT), sequential proton loss electron transfer (SPLET) and hydrogen atom transfer (HAT), yielding excellent statistics (R² = 0.970, S.E. = 0.043). Full article

(This article belongs to the Special Issue Molecular Simulation and Modeling)

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58 pages, 24396 KiB

Open AccessReview

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://doi.org/10.3390/ijms25021298 - 20 Jan 2024

Cited by 6 | Viewed by 2216

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 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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Other

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10 pages, 3819 KiB

Open AccessBrief Report

Ab Initio Molecular Dynamics Insight to Structural Phase Transition and Thermal Decomposition of InN

by Jacek Piechota, Stanislaw Krukowski, Bohdan Sadovyi, Petro Sadovyi, Sylwester Porowski and Izabella Grzegory

Int. J. Mol. Sci. 2024, 25(15), 8281; https://doi.org/10.3390/ijms25158281 - 29 Jul 2024

Viewed by 584

Abstract

Extensive ab initio density functional theory molecular dynamics calculations were used to evaluate stability conditions for relevant phases of InN. In particular, the p-T conditions of the thermal decomposition of InN and pressure-induced wurtzite–rocksalt solid–solid phase transition were established. The comparison of the simulation results with the available experimental data allowed for a critical evaluation of the capabilities and limitations of the proposed simulation method. It is shown that ab initio molecular dynamics can be used as an efficient tool for simulations of phase transformations of InN, including solid–solid structural transition and thermal decomposition with formation of N₂ molecules. It is of high interest, because InN is an important component of epitaxial quantum structures, but it has not been obtained as a bulk single crystal. This makes it difficult to determine its basic physical properties to develop new applications. Full article

(This article belongs to the Special Issue Molecular Simulation and Modeling)

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