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Advances in Molecular Modeling in Chemistry, 3rd Edition
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Advances in Molecular Modeling in Chemistry, 3rd Edition

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

Deadline for manuscript submissions: 31 January 2027 | Viewed by 2414

Editor

Dr. Heng Zhang

E-Mail Website
Guest Editor
School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, China
Interests: physical chemistry of surfactant; computer simulation about surface science; molecular simulation on self-assemble system
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Molecular modeling plays a crucial role in chemistry investigations. With the development of computing powers, large-scale simulations can be achieved. Molecular modeling has been applied successfully in many areas of chemistry, for example, to the behavior of liquid solutions, proteins, DNA, polysaccharides, lipid membranes, crystals, and amorphous solids, or any combination of them; the process of adsorption or desorption at interfaces; protein folding; self-assembly, etc.

Aside from the widespread application of molecular modeling, the simulation techniques have also developed rapidly. Many novel simulation techniques have emerged, including ab initio molecular dynamics, polarizable force field, reactive molecular dynamics, machine learning-accelerated simulation, metadynamics, etc.

This Special Issue invites original papers and reviews that report molecular simulation studies, including quantum chemistry calculation, molecular dynamic simulation, Monte Carlo simulation, combined experimental and simulation studies, etc. This Special Issue also welcomes focused review articles that examine the state of the art, identify emerging trends, and suggest future directions for the application of molecular modeling methods.

Dr. Heng Zhang
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 250 words) can be sent to the Editorial Office for assessment.

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-anonymized 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

  • molecular modeling
  • applications
  • quantum chemistry calculation
  • molecular dynamic simulation
  • Monte Carlo simulation
  • combined experimental and simulation studies

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Related Special Issues

Published Papers (3 papers)

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16 pages, 3052 KB  
Article
Molecular Dynamics Simulation of Graphene Oxide Surface-Modified ADN-Based PBX Double-Shell Structure
by Shimin Zhang, Jiaqi Wen, Hongxia Zhang, Xiaoying Cheng, Jingyu Wang, Baoyun Ye and Chongwei An
Molecules 2026, 31(5), 784; https://doi.org/10.3390/molecules31050784 - 26 Feb 2026
Cited by 1 | Viewed by 740
Abstract
Ammonium dinitramide (ADN), a new-generation green high-energy oxidizer, faces application challenges due to its strong hygroscopicity and poor compatibility with polymer binders. This study proposes a double-shell structure with ADN as the core, graphene oxide (GO) as the intermediate layer, and a binder [...] Read more.
Ammonium dinitramide (ADN), a new-generation green high-energy oxidizer, faces application challenges due to its strong hygroscopicity and poor compatibility with polymer binders. This study proposes a double-shell structure with ADN as the core, graphene oxide (GO) as the intermediate layer, and a binder as the outer shell. Molecular dynamics simulations were performed to investigate composite systems using nitrocellulose (NC), cellulose acetate butyrate (CAB), polystyrene (PS), and their blends NC/CAB and NC/PS as binders. The results demonstrate that GO acts as a “molecular double-sided adhesive”, significantly enhancing the interfacial interaction between ADN and the binders. The NC/PS blend binder exhibits the best overall performance, with the binding energy increased by 1.13 times. Analysis revealed that the NC/PS system establishes the strongest intermolecular interactions among ADN, GO, and the binder via mechanisms like π-π stacking and multiple hydrogen bonds. The glass transition temperature reaches 400.93 K, indicating excellent thermal stability and potential safety/reliability. Mechanical property analysis shows that the NC/PS composite system imparts a better comprehensive balance of stiffness, shear performance, and structural isotropy to the ADN-based polymer-bonded explosive (PBX). This research elucidates the enhancement mechanism of GO and the regulation principles of binders at the molecular scale, providing a theoretical foundation for designing high-performance energetic material. Full article
(This article belongs to the Special Issue Advances in Molecular Modeling in Chemistry, 3rd Edition)
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14 pages, 4775 KB  
Article
Combined Experimental, DFT, and MD Investigation Toward the Rational Design of Desert Planting Substrates
by Shuangnan Li, Linjie Wang, Yinghui Li, Zhenyu Zhang, Jidun Fang and Shiling Yuan
Molecules 2026, 31(3), 508; https://doi.org/10.3390/molecules31030508 - 2 Feb 2026
Viewed by 1047
Abstract
Soil moisture regulation is critical for vegetation restoration in arid ecosystems. Polymeric hydrogels, notably polyacrylic acid (PAA) and polyacrylamide (PAM), are widely employed as water-retaining agents to enhance soil water availability. However, the coupling between their distinct chemical structures and key performance metrics, [...] Read more.
Soil moisture regulation is critical for vegetation restoration in arid ecosystems. Polymeric hydrogels, notably polyacrylic acid (PAA) and polyacrylamide (PAM), are widely employed as water-retaining agents to enhance soil water availability. However, the coupling between their distinct chemical structures and key performance metrics, particularly cycling stability and water retention kinetics in desert substrates, remains unclear. In this work, we present an integrated experimental–computational study to establish a “molecular structure–interfacial behavior–macroscopic property” framework for PAA and PAM. The results show that PAA exhibits a higher equilibrium water absorption (WAC ~242 g/g) and more stable water uptake capacity under cycling, whereas PAM displays much higher zero-shear viscosity and pronounced shear thinning with a yield plateau (~30 Pa). DFT and MD simulations trace these macroscopic disparities to their distinct electronic structures and hydration dynamics. Specifically, PAA’s strong electrostatic interactions and extended chain conformations promote a more rigid and ordered hydration shell, whereas PAM adopts a compact structure with greater chain mobility, resulting in a less ordered hydration layer. Collectively, these findings provide a structure-property framework for the scientifically grounded selection of water-retaining agents. The integrated experimental–computational methodology presented herein establishes a predictive framework for the rational design of functional materials in arid land restoration. Full article
(This article belongs to the Special Issue Advances in Molecular Modeling in Chemistry, 3rd Edition)
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24 pages, 2368 KB  
Systematic Review
In Silico Approaches Targeting Quorum-Sensing Inhibition in Pseudomonas aeruginosa: A Systematic Review
by Yeimy Rojas, Cristian Sillagana-Verdezoto, Jacobus de Waard and Cristina Quiroga
Molecules 2026, 31(16), 2887; https://doi.org/10.3390/molecules31162887 - 19 Aug 2026
Viewed by 245
Abstract
Pseudomonas aeruginosa (PA) is a clinically relevant opportunistic pathogen whose persistence and antimicrobial tolerance are largely driven by biofilm formation and quorum-sensing (QS)-regulated virulence. Targeting QS has therefore emerged as an antivirulence strategy that attenuates pathogenicity without exerting strong selective pressure on bacterial [...] Read more.
Pseudomonas aeruginosa (PA) is a clinically relevant opportunistic pathogen whose persistence and antimicrobial tolerance are largely driven by biofilm formation and quorum-sensing (QS)-regulated virulence. Targeting QS has therefore emerged as an antivirulence strategy that attenuates pathogenicity without exerting strong selective pressure on bacterial growth. This systematic review (2020–2024) analyzes recent advances in the identification of QS inhibitors against PA, emphasizing studies that integrate in silico approaches. Forty-six studies met the inclusion criteria. All employed molecular docking, and 36.9% (n = 17) incorporated molecular dynamics simulations. While valuable for initial detection, these computational predictions have inherent limitations in accurately estimating binding energy and conformational dynamics, requiring empirical validation to confirm actual biological activity. Approximately one-fifth of the studies were exclusively computational, whereas the remainder combined in silico screening with in vitro and, in some cases, in vivo assays. The most frequently investigated QS regulators were LasR, PqsR, and RhlR, alongside additional virulence-associated proteins. The evaluated compounds encompassed phytochemicals, synthetic molecules, nanomaterials and natural product-derived compounds, several of which demonstrated experimental evidence of biofilm attenuation and reduction in QS-regulated virulence factors. Overall, the findings highlight the value of integrating computational and experimental strategies to rationally prioritize antivirulence candidates. However, the intrinsic complexity and redundancy of the QS network suggest that future research should increasingly focus on multitarget approaches and on the exploration of chemically diverse and previously underexplored compound libraries to improve efficacy against PA biofilms. Full article
(This article belongs to the Special Issue Advances in Molecular Modeling in Chemistry, 3rd Edition)
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