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

Deadline for manuscript submissions: 31 December 2024 | Viewed by 9343

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Dr. Chao Dong

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Department of Chemistry and Physics, The University of Texas of the Permian Basin, Odessa, TX 79762, USA
Interests: organometallic synthesis; theoretical and computational chemistry; medicinal chemistry; environmental chemistry
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Dear Colleagues,

The fields of computational and theoretical chemistry are growing fast and facilitate complementary methods to prediction, experimental design, and data interpretation in the disciplines of chemistry, biology, and drug design. Widely used tools in computational and theoretical chemistry, such as quantum mechanics (QM), molecular dynamics (MD), and quantum mechanics/molecular mechanics (QM/MM), allow for the study of interactions and chemical processes in various circumstances (gases, solutions, and proteins) from the electronic to molecular levels. This Special Issue welcomes researchers to submit their unpublished manuscripts (research articles and review papers) on all topics of computational and theoretical chemistry, including theoretical studies of reaction mechanisms, structural and spectral properties of new compounds in inorganic/organic chemistry, medicinal chemistry, drug design, and covalent/noncovalent interactions between (metallo)proteins and proteins/ligands. Studies on the development of new computational approaches and algorithms are also welcomed.

Dr. Chao Dong
Guest Editor

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Keywords

quantum mechanical calculations
molecular dynamic modeling
QM/MM
reaction mechanism
structure and reactivity
spectral properties
protein–protein interaction
protein–ligand interaction
covalent bonding and noncovalent interaction
drug design

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Related Special Issue

Advances in Computational and Theoretical Chemistry in Molecules (11 articles)

Published Papers (11 papers)

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Research

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10 pages, 2796 KiB

Open AccessArticle

The Thermodynamic and Kinetic Properties of the dA-rU DNA-RNA Hybrid Base Pair Investigated via Molecular Dynamics Simulations

by Taigang Liu, Lei Bao and Yujie Wang

Molecules 2024, 29(20), 4920; https://doi.org/10.3390/molecules29204920 - 17 Oct 2024

Viewed by 605

Abstract

DNA-RNA hybrid duplexes play essential roles during the reverse transcription of RNA viruses and DNA replication. The opening and conformation changes of individual base pairs are critical to their biological functions. However, the microscopic mechanisms governing base pair closing and opening at the atomic level remain poorly understood. In this study, we investigated the thermodynamic and kinetic parameters of the dA-rU base pair in a DNA-RNA hybrid duplex using 4 μs all-atom molecular dynamics (MD) simulations at different temperatures. Our results showed that the thermodynamic parameters of the dA-rU base pair aligned with the predictions of the nearest-neighbor model and were close to those of the AU base pair in RNA. The temperature dependence of the average lifetimes of both the open and the closed states, as well as the transition path times, were obtained. The free-energy barrier for a single base pair opening and closing arises from an increase in enthalpy due to the disruption of the base-stacking interactions and hydrogen bonding, along with an entropy loss attributed to the accompanying restrictions, such as torsional angle constraints and solvent viscosity. Full article

(This article belongs to the Special Issue Advances in Computational and Theoretical Chemistry—2nd Edition)

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13 pages, 1503 KiB

Open AccessArticle

Molecular Interactions Governing the Rat Aryl Hydrocarbon Receptor Activities of Polycyclic Aromatic Compounds and Predictive Model Development

by Lingmin Jin, Bangyu Chen, Guangcai Ma, Xiaoxuan Wei and Haiying Yu

Molecules 2024, 29(19), 4619; https://doi.org/10.3390/molecules29194619 - 29 Sep 2024

Viewed by 526

Abstract

Polycyclic aromatic compounds (PACs) exhibit rat aryl hydrocarbon receptor (rAhR) activities, leading to diverse biological or toxic effects. In this study, the key amino residues and molecular interactions that govern the rAhR activity of PACs were investigated using in silico strategies. The homology model of rAhR was first docked with 90 PACs to yield complexes, and the results of the molecular dynamics simulations of 16 typical complexes showed that the binding energies of the complexes range from −7.37 to −26.39 kcal/mol. The major contribution to the molecular interaction comes from van der Waals forces, and Pro295 and Arg316 become the key residues involved in most complexes. Two QSAR models were further developed to predict the rAhR activity of PACs (in terms of log IEQ for PACs without halogen substitutions and log%-TCDD-max for halogenated PACs). Both models have good predictive ability, robustness, and extrapolation ability. Molecular polarizability, electronegativity, size, and nucleophilicity are identified as the important factors affecting the rAhR activity of PACs. The developed models could be employed to predict the rAhR activity of other reactive PACs. This work provides insight into the mechanisms and interactions of the rAhR activity of PACs and assists in the assessment of their fate and risk in organisms. Full article

(This article belongs to the Special Issue Advances in Computational and Theoretical Chemistry—2nd Edition)

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14 pages, 1801 KiB

Open AccessArticle

Strength of London Dispersion Forces in Organic Structure Directing Agent—Zeolite Assemblies

by Karima Ata, Tzonka Mineva and Bruno Alonso

Molecules 2024, 29(18), 4489; https://doi.org/10.3390/molecules29184489 - 21 Sep 2024

Viewed by 624

Abstract

Herein, we study the London dispersion forces between organic structure directing agents (OSDAs)—here tetraalkyl-ammonium or -phosphonium molecules—and silica zeolite frameworks (FWs). We demonstrate that the interaction energy for these dispersion forces is correlated to the number of H atoms in OSDAs, irrespective of the structures of OSDAs or FWs, and of variations in charges and thermal motions. All calculations considered—DFT-D3 and BOMD undertaken by us, and molecular mechanics from an accessible database—led to the same trend. The mean energy of these dispersion forces is ca. −2 kcal.mol⁻¹ per H for efficient H-O contacts. Full article

(This article belongs to the Special Issue Advances in Computational and Theoretical Chemistry—2nd Edition)

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14 pages, 2728 KiB

Open AccessArticle

Force Fields, Quantum-Mechanical- and Molecular-Dynamics-Based Descriptors of Radiometal–Chelator Complexes

by Işılay Öztürk, Silvia Gervasoni, Camilla Guccione, Andrea Bosin, Attilio Vittorio Vargiu, Paolo Ruggerone and Giuliano Malloci

Molecules 2024, 29(18), 4416; https://doi.org/10.3390/molecules29184416 - 17 Sep 2024

Viewed by 933

Abstract

Radiopharmaceuticals are currently a key tool in cancer diagnosis and therapy. Metal-based radiopharmaceuticals are characterized by a radiometal–chelator moiety linked to a bio-vector that binds the biological target (e.g., a protein overexpressed in a particular tumor). The right match between radiometal and chelator influences the stability of the complex and the drug’s efficacy. Therefore, the coupling of the radioactive element to the correct chelator requires consideration of several features of the radiometal, such as its oxidation state, ionic radius, and coordination geometry. In this work, we systematically investigated about 120 radiometal–chelator complexes taken from the Cambridge Structural Database. We considered 25 radiometals and about 30 chelators, featuring both cyclic and acyclic geometries. We used quantum mechanics methods at the density functional theoretical level to generate the general AMBER force field parameters and to perform 1 µs-long all-atom molecular dynamics simulations in explicit water solution. From these calculations, we extracted several key molecular descriptors accounting for both electronic- and dynamical-based properties. The whole workflow was carefully validated, and selected test-cases were investigated in detail. Molecular descriptors and force field parameters for the complexes considered in this study are made freely available, thus enabling their use in predictive models, molecular modelling, and molecular dynamics investigations of the interaction of compounds with macromolecular targets. Our work provides new insights in understanding the properties of radiometal–chelator complexes, with a direct impact for rational drug design of this important class of drugs. Full article

(This article belongs to the Special Issue Advances in Computational and Theoretical Chemistry—2nd Edition)

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15 pages, 1575 KiB

Open AccessArticle

Microsolvation of a Proton by Ar Atoms: Structures and Energetics of Ar_nH⁺ Clusters

by María Judit Montes de Oca-Estévez and Rita Prosmiti

Molecules 2024, 29(17), 4084; https://doi.org/10.3390/molecules29174084 - 28 Aug 2024

Viewed by 625

Abstract

We present a computational investigation on the structural arrangements and energetic stabilities of small-size protonated argon clusters, Ar

_{n}

^{+}

. Using high-level ab initio electronic structure computations, we determined that the linear symmetric triatomic ArH

^{+}

Ar ion [...] Read more.

We present a computational investigation on the structural arrangements and energetic stabilities of small-size protonated argon clusters, Ar

_{n}

^{+}

. Using high-level ab initio electronic structure computations, we determined that the linear symmetric triatomic ArH

^{+}

Ar ion serves as the molecular core for all larger clusters studied. Through harmonic normal-mode analysis for clusters containing up to seven argon atoms, we observed that the proton-shared vibration shifts to lower frequencies, consistent with measurements in gas-phase IRPD and solid Ar-matrix isolation experiments. We explored the sum-of-potentials approach by employing kernel-based machine-learning potential models trained on CCSD(T)-F12 data. These models included expansions of up to two-body, three-body, and four-body terms to represent the underlying interactions as the number of Ar atoms increases. Our results indicate that the four-body contributions are crucial for accurately describing the potential surfaces in clusters with

n >

3. Using these potential models and an evolutionary programming method, we analyzed the structural stability of clusters with up to 24 Ar atoms. The most energetically favored Ar

_{n}

^{+}

structures were identified for magic size clusters at n = 7, 13, and 19, corresponding to the formation of Ar-pentagon rings perpendicular to the ArH

^{+}

Ar core ion axis. The sequential formation of such regular shell structures is compared to ion yield data from high-resolution mass spectrometry measurements. Our results demonstrate the effectiveness of the developed sum-of-potentials model in describing trends in the nature of bonding during the single proton microsolvation by Ar atoms, encouraging further quantum nuclear studies. Full article

(This article belongs to the Special Issue Advances in Computational and Theoretical Chemistry—2nd Edition)

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19 pages, 13292 KiB

Open AccessArticle

Study on the Hydrophobic Modification Mechanism of Stearic Acid on the Surface of Coal Gasification Fly Ash

by Jian Yang, Longjiang Li and Wenyuan Wang

Molecules 2024, 29(17), 4071; https://doi.org/10.3390/molecules29174071 - 28 Aug 2024

Viewed by 641

Abstract

In this study, the hydrophobic modification of coal gasification fly ash (FA) was investigated given the adverse effects of surface hydrophilic structures on the material field. The surface of FA was modified using stearic acid (SA), which successfully altered its hydrophilic structure. When the contact angle of S-FA increased from 23.4° to 127.2°, the activation index increased from 0 to 0.98, the oil absorption decreased from 0.564 g/g to 0.510 g/g, and the BET-specific surface area decreased from 13.973 m²/g to 3.218 m²/g. The failure temperature of SA on the surface of S-FA was 210 °C. The adsorption mechanism of FA was analyzed using density functional theory (DFT) and molecular dynamics (MD). The adsorption of water molecules by FA involved both chemical and physical adsorption, with active adsorption sites for Al, Fe, and Si. The adsorbed water molecules on the surface of FA formed hydrogen bonds with a bond length of 1.5–2.5 Å, leading to agglomeration. In addition, the long alkyl chain in SA mainly relied on the central carbon atom in the (-CH₃) structure to obtain electrons in different directions from the H atoms in space, increasing the Coulomb repulsion with the O atoms in the water molecule and thereby achieving the hydrophobic effect. In the temperature range of 298 K to 358 K, the combination of FA and SA became stronger as the temperature increased. Full article

(This article belongs to the Special Issue Advances in Computational and Theoretical Chemistry—2nd Edition)

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26 pages, 23787 KiB

Open AccessArticle

Hierarchical Modeling of the Nonlinear Optical Response of Composite Materials Based on Tetrathiafulvalene Derivatives

by Lucia Mydlova, Bouchta Sahraoui, Abdelkrim El-Ghayoury, Janusz Berdowski, Anna Migalska-Zalas and Malgorzata Makowska-Janusik

Molecules 2024, 29(16), 3720; https://doi.org/10.3390/molecules29163720 - 6 Aug 2024

Viewed by 867

Abstract

The presented work concerns computational investigations of the physical properties of composite materials based on polymer matrix and nonlinear optical (NLO) active chromophores. The structural, electronic, and optical properties of selected tetrathiafulvalene (TTF)-based chromophores have been calculated using quantum chemical methods. The polymer matrix changes the physical properties of the inserted chromophores influencing their optical parameters. To explain the mechanism of the NLO signal occurrence from the composites based on poly(methyl methacrylate) (PMMA) matrix and TTF chromophores, their structures are modeled using the classical molecular dynamics. In consequence, the structural properties of the composites are discussed according to the NLO requirements. By developing the theoretical model based on a discrete multipole local field approach, the impact of polymer matrix on the optical properties of chromophores is explained. Full article

(This article belongs to the Special Issue Advances in Computational and Theoretical Chemistry—2nd Edition)

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16 pages, 4177 KiB

Open AccessArticle

Deciphering the Role of Trehalose in Chroococcidiopsis sp. 029’s High-Desiccation Resistance: Sequence Determination, Structural Modelling and Simulative Analysis of the 30S Ribosomal Subunit

by Davide Pietrafesa, Alessandro Napoli, Federico Iacovelli, Alice Romeo, Fabio Giovanni Tucci, Daniela Billi and Mattia Falconi

Molecules 2024, 29(15), 3486; https://doi.org/10.3390/molecules29153486 - 25 Jul 2024

Viewed by 778

Abstract

Desert strains of the genus Chroococcidiopsis are among the most desiccation-resistant cyanobacteria capable of anhydrobiosis. The accumulation of two sugars, sucrose and trehalose, facilitates the entrance of anhydrobiotes into a reversible state of dormancy by stabilizing cellular components upon water removal. This study aimed to evaluate, at the atomistic level, the role of trehalose in desiccation resistance by using as a model system the 30S ribosomal subunit of the desert cyanobacterium Chroococcidiopsis sp. 029. Molecular dynamic simulations provided atomistic evidence regarding its protective role on the 30S molecular structure. Trehalose forms an enveloping shell around the ribosomal subunit and stabilizes the structures through a network of direct interactions. The simulation confirmed that trehalose actively interacts with the 30S ribosomal subunit and that, by replacing water molecules, it ensures ribosomal structural integrity during desiccation, thus enabling protein synthesis to be carried out upon rehydration. Full article

(This article belongs to the Special Issue Advances in Computational and Theoretical Chemistry—2nd Edition)

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20 pages, 53035 KiB

Open AccessArticle

Effect of Diffusion on the Ultimate Axial Load of Complex-Shaped Al-SiC Samples: A Molecular Dynamics Study

by Mostafa Fathalian, Eligiusz Postek, Masoud Tahani and Tomasz Sadowski

Molecules 2024, 29(14), 3343; https://doi.org/10.3390/molecules29143343 - 16 Jul 2024

Viewed by 883

Abstract

Metal matrix composites (MMCs) combine metal with ceramic reinforcement, offering high strength, stiffness, corrosion resistance, and low weight for diverse applications. Al-SiC, a common MMC, consists of an aluminum matrix reinforced with silicon carbide, making it ideal for the aerospace and automotive industries. In this work, molecular dynamics simulations are performed to investigate the mechanical properties of the complex-shaped models of Al-SiC. Three different volume fractions of SiC particles, precisely 10%, 15%, and 25%, are investigated in a composite under uniaxial tensile loading. The tensile behavior of Al-SiC composites is evaluated under two loading directions, considering both cases with and without diffusion effects. The results show that diffusion increases the ultimate tensile strength of the Al-SiC composite, particularly for the 15% SiC volume fraction. Regarding the shape of the SiC particles considered in this research, the strength of the composite varies in different directions. Specifically, the ultimate strength of the Al-SiC composite with 25% SiC reached 11.29 GPa in one direction, and 6.63 GPa in another, demonstrating the material’s anisotropic mechanical behavior when diffusion effects are considered. Young’s modulus shows negligible change in the presence of diffusion. Furthermore, diffusion improves toughness in Al-SiC composites, resulting in higher values compared to those without diffusion, as evidenced by the 25% SiC volume fraction composite (2.086 GPa) versus 15% (0.863 GPa) and 10% (1.296 GPa) SiC volume fractions. Full article

(This article belongs to the Special Issue Advances in Computational and Theoretical Chemistry—2nd Edition)

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24 pages, 15824 KiB

Open AccessArticle

Insights into Transfer of Supramolecular Doxorubicin/Congo Red Aggregates through Phospholipid Membranes

by Anna Stachowicz-Kuśnierz, Paulina Rychlik, Jacek Korchowiec and Beata Korchowiec

Molecules 2024, 29(11), 2567; https://doi.org/10.3390/molecules29112567 - 30 May 2024

Cited by 1 | Viewed by 775

Abstract

Doxorubicin (DOX) is a commonly used chemotherapeutic drug, from the anthracycline class, which is genotoxic to neoplastic cells via a DNA intercalation mechanism. It is effective and universal; however, it also causes numerous side effects. The most serious of them are cardiotoxicity and a decrease in the number of myeloid cells. For this reason, targeted DOX delivery systems are desirable, since they would allow lowering the drug dose and therefore limiting systemic side effects. Recently, synthetic dyes, in particular Congo red (CR), have been proposed as possible DOX carriers. CR is a planar molecule, built of a central biphenyl moiety and two substituted naphthalene rings, connected with diazo bonds. In water, it forms elongated ribbon-shaped supramolecular structures, which are able to selectively interact with immune complexes. In our previous studies, we have shown that CR aggregates can intercalate DOX molecules. In this way, they preclude DOX precipitation in water solutions and increase its uptake by MCF7 breast cancer cells. In the present work, we further explore the interactions between DOX, CR, and their aggregates (CR/DOX) with phospholipid membranes. In addition to neutral molecules, the protonated doxorubicin form, DXP, is also studied. Molecular dynamics simulations are employed to study the transfer of CR, DOX, DXP, and their aggregates through POPC bilayers. Interactions of CR, DOX, and CR/DOX with model monolayers are studied with Langmuir trough measurements. This study shows that CR may support the transfer of doxorubicin molecules into the bilayer. Both electrostatic and van der Waals interactions with lipids are important in this respect. The former promote the initial stages of the insertion process, the latter keep guest molecules inside the bilayer. Full article

(This article belongs to the Special Issue Advances in Computational and Theoretical Chemistry—2nd Edition)

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27 pages, 7833 KiB

Open AccessReview

Time-Resolved Circular Dichroism in Molecules: Experimental and Theoretical Advances

by Marta Monti, Leonardo Biancorosso and Emanuele Coccia

Molecules 2024, 29(17), 4049; https://doi.org/10.3390/molecules29174049 - 27 Aug 2024

Viewed by 1447

Abstract

Following changes in chirality can give access to relevant information on the function or reactivity of molecular systems. Time-resolved circular dichroism (TRCD) spectroscopy proves to be a valid tool to achieve this goal. Depending on the class of molecules, different temporal ranges, spanning from seconds to femtoseconds, need to be investigated to observe such chiroptical changes. Therefore, over the years, several approaches have been adopted to cover the timescale of interest, especially based on pump–probe schemes. Moreover, various theoretical approaches have been proposed to simulate and explain TRCD spectra, including linear and non-linear response methods as well as non-adiabatic molecular dynamics. In this review, an overview on both experimental and theoretical advances in the TRCD field is provided, together with selected applications. A discussion on future theoretical developments for TRCD is also given. Full article

(This article belongs to the Special Issue Advances in Computational and Theoretical Chemistry—2nd Edition)

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