Journal of molecular graphics & modelling最新文献

{"title":"Novel flucytosine salt: Structure, Hirshfild surface analysis, morphology, FIMs, and computational studies","authors":"Hela Ferjani","doi":"10.1016/j.jmgm.2025.109012","DOIUrl":"10.1016/j.jmgm.2025.109012","url":null,"abstract":"<div><div>5-Flucytosine (FC) exhibits an advanced solid-state structure, which presents challenges for its pharmaceutical development. This paper presents experimental, and theoretical studies of a novel pharmaceutical salt, fluorocytosinium chloride, HFC⁺.Cl⁻. Single crystal X-ray diffraction (SCXRD) investigation indicates that HFC⁺.Cl⁻ forms crystals in the monoclinic system and <em>P</em>2₁/<em>c</em> space group. The structure is maintained by a series of hydrogen bonding interactions, comprising N-H···Cl, N-H···O, and C-H···F. In addition, noncovalent anion···π interactions between chloride anions and HFC⁺ cations play a role in establishing a three-dimensional network. Hirshfeld surface analysis (HS) and two-dimensional fingerprinting were used to enumerate the intermolecular interactions within the crystal. The results demonstrate that the H···Cl/Cl···H, O···H/H···O, and F···H/H···F interactions are the most significant. Full Interaction Maps (FIMs) analysis predicts the positions of hydrogen bond acceptors and donors, confirming the supramolecular arrangement observed in HFC⁺.Cl⁻. Computational modeling studies using the Bravais-Friedel, Donnay-Harker (BFDH), and Growth Morphology (GM) methods predict the morphology of the HFC⁺.Cl⁻ crystal. Both approaches estimate a comparable crystal shape characterized by six principal facets. Density functional theory (DFT) calculations were conducted utilizing the DMol³ software to investigate the electronic structure and comprehensive reactivity features of HFC⁺.Cl⁻. The low HOMO energy suggests significant stability against electrophilic attacks, while the high HOMO-LUMO band gap indicates high chemical hardness. Fukui functions were also calculated to identify atomic sites susceptible to nucleophilic and electrophilic attacks. This study offers a comprehensive insight into the structural and electronic properties of HFC⁺.Cl⁻, offering valuable information for the development of new pharmaceutical compositions.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"137 ","pages":"Article 109012"},"PeriodicalIF":2.7,"publicationDate":"2025-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143663369","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Thiazole modified covalent triazine framework as carcinogenic metabolites adsorbent: A DFT insight","authors":"Hasher Irshad ,&nbsp;Muhammad Abdullah Azhar ,&nbsp;Katrine Qvortrup","doi":"10.1016/j.jmgm.2025.109009","DOIUrl":"10.1016/j.jmgm.2025.109009","url":null,"abstract":"<div><div>The potential of a novel thiazole-modified covalent triazine framework (<strong>S-CTF</strong>) as surface for the adsorption and sensing of the carcinogenic metabolites acrylamide (AM), 2-amino-3,8-dimethylimidazo-[4,5-f]quinoxaline (MEIQX), 2-amino-1-methyl-6-phenylimidazole[4,5-f]pyridine (PhlP) and 3-amino-1,4-dimethyl-5H-pyrido[4,3-b]indole (Trp-P-1) is explored. The selectivity, sensitivity, and adsorption properties of the <strong>S-CTF</strong> surface are investigated through noncovalent interaction (NCI), quantum theory of atoms in molecules (QTAIM) and symmetry adapted perturbation theory (SAPT0) analyses. All the analytes were found to be physiosorbed on the surface of the sensor with the following strength of interaction: MEIQX@<strong>S-CTF</strong> = PhlP@<strong>S-CTF</strong> &gt; Trp-P-1@<strong>S-CTF</strong> &gt; AM@<strong>S-CTF</strong>. Evaluation of the electronic properties was done by natural bond orbital (NBO), electron density difference (EDD), frontier molecular orbital (FMO) and density of states (DOS) analyses. Through SAPT0 analysis, MEIQX@<strong>S-CTF</strong> has shown to have the highest E_SAPT0 energy data (−24.58 kcal/mol) whereas FMO analysis reveals that the <strong>S-CTF</strong> surface shows the highest sensing power for Trp-P-1 among all analytes.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"137 ","pages":"Article 109009"},"PeriodicalIF":2.7,"publicationDate":"2025-03-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143601727","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Mechanism of cyclization-degradation of silazanes: A DFT study","authors":"Yun-qiao Ding ,&nbsp;Qiu-hong Mou ,&nbsp;Tao wang ,&nbsp;Jun zhang","doi":"10.1016/j.jmgm.2025.109008","DOIUrl":"10.1016/j.jmgm.2025.109008","url":null,"abstract":"<div><div>The present calculations at the B3LYP/6-31G (d) level confirm that the cyclization-degradation of silazanes proceeds via two mechanisms: Si-N bond interchange and hydrogen abstraction. The energy barrier for hydrogen abstraction is approximately 20 kcal/mol lower than that of the Si-N bond interchange pathway. Substituent effects critically influence the thermal stability of silazanes. For the Si-N bond interchange mechanism, factors that enhance nucleophilic attack or reduce Si-N bond strength destabilize silazanes. This implies that substituents with the electron-donating inductive effects, electron-donating conjugation effects, or bulky steric profiles should be avoided to improve thermal stability. In contrast, hydrogen abstraction predominantly occurs at chain termini. To suppress this pathway, substituents with low basicity and weak reducing capacity are recommended as terminal blocking groups. Based on these findings, using phenyl groups as terminal substituents represents an economically viable and thermodynamically favorable strategy for enhancing silazane stability.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"137 ","pages":"Article 109008"},"PeriodicalIF":2.7,"publicationDate":"2025-03-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143636283","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Mangiferin as a potential inhibitor of transthyretin fibrillogenesis","authors":"Grudinina N.A ,&nbsp;Petukhov M.G ,&nbsp;Sokolov A.V ,&nbsp;Shaldzhyan A.A ,&nbsp;Zabrodskaya Y.A ,&nbsp;Gavrilova N.V ,&nbsp;Morozkina S.N ,&nbsp;Egorov V.V","doi":"10.1016/j.jmgm.2025.109007","DOIUrl":"10.1016/j.jmgm.2025.109007","url":null,"abstract":"<div><div>By using <em>in silico</em> molecular docking, we predicted a high potential of mangiferin to inhibit transthyretin amyloidogenesis. Subsequently, we tested this prediction in an <em>in vitro</em> system. The study involved testing effect of mangiferrin in a system that included isolated and purified recombinant transthyretin under fibrillogenesis conditions and a detection assay based on the fluorescent dye thioflavin T, characteristic of amyloid fibrils. The conditions for fibrillogenesis of this protein at neutral pH values were established. Using the developed test system, it was shown that mangiferin is able to inhibit abnormal transthyretin fibrillogenesis.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"137 ","pages":"Article 109007"},"PeriodicalIF":2.7,"publicationDate":"2025-03-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143620890","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The impact of increasing Zr dopant concentration in Ruddlesden Popper perovskite to enhance Resistive Random-Access Memory performance: Using the DFT method","authors":"Fayyaz Hussain ,&nbsp;Aqsa Arooj ,&nbsp;Muhammad Imran ,&nbsp;Ammar Mohamed Tighezza ,&nbsp;Umbreen Rasheed ,&nbsp;R.M.Arif Khalil ,&nbsp;Muhammad Fahad Ehsan","doi":"10.1016/j.jmgm.2025.109000","DOIUrl":"10.1016/j.jmgm.2025.109000","url":null,"abstract":"<div><div>As Resistive Random- Access memory (RRAM) emerges as a promising solution for high-performance memory application, this study applies density functional theory (DFT) to analyze the structural, electronic, and optical properties of pure and Zr-doped Mg₃Hf₂O₇ at various doping concentrations (0, 0.25, 0.50, 0.75, and 1.0). The electronic analysis reveals that increasing Zr doping reduces the bandgap, thereby enhancing the conductivity of the composites. These findings highlight their potential for resistive switching memory applications. Iso-surface charge density plots revealed that the substitutional replacement of all Hf atoms by Zr atoms significantly increased the number of conducting channels, which enhanced the material's overall conductivity and increased the efficiency of non-volatile memory. Optical analysis showed that Mg₃Zr₂O₇ composite has significant conductivity and absorption over a wide range of photon energies and low reflectivity. In particular, Mg₃Zr₂O₇ exhibited the least formation energy and highest conductivity, suggesting it is the most stable composite. Mechanical properties confirm all studied materials' stability, anisotropic nature, and ductility. The analysis indicates that Mg₃Zr₂O₇ holds strong potential for Resistive Random- Access memory applications.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"137 ","pages":"Article 109000"},"PeriodicalIF":2.7,"publicationDate":"2025-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143611361","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Unveiling the impact of the fluorophore pyrrole, indole, furan, benzofuran, thiophene, benzothiophene, and pyrene attachments on the C7 atom of the isomorphic fluorescent thieno-guanine: A theoretical investigation","authors":"Laibin Zhang,&nbsp;Yaping Zhang","doi":"10.1016/j.jmgm.2025.108999","DOIUrl":"10.1016/j.jmgm.2025.108999","url":null,"abstract":"<div><div>Thieno-guanine (thG) is a prominent emissive surrogate of natural guanine (G), which almost perfectly mimics G in nucleic duplexes. In this paper, to widen the utility of thG, the C7 attachment effects by aromatic pyrrole, indole, furan, benzofuran, thiophene, benzothiophene, and pyrene on the structural, electronic, and photophysical properties of thG were theoretically examined by using the density functional theory (DFT) and the time-dependent DFT (TD-DFT). Calculations were performed employing the hybrid B3LYP and the long-range corrected CAM-B3LYP density functionals in combination with the 6–311++G(d, p) basis set. Rigid scan calculations and optimizations were performed to obtain the most stable rotamers, and totally 14 bases (including thG) were studied. The hole-electron theory and the interfragment charge transfer (IFCT) method were applied to reveal the intrinsic characteristics of the low-lying electron excitation processes. In water solution, all the S₁ states of the thG-derivatives are highly allowed ππ∗ states dominated by HOMO (L)→LUMO (L) with some charges (0.028–0.193 e) been transferred from the introduced groups to the thG-moiety. The introduced groups can tune the photophysics of thG resulting in improved fluorescent properties, including visible excitation and emission wavelengths, greater absorption and emission intensities (oscillator strengths), and larger Stokes shifts. In water solution, all substituents display fluorescence wavelength longer than 500 nm and the Stokes shifts are larger than 100 nm. Also examined are the effects of base pairing with cytosine (C), and it was revealed that the S₁ states of all the studied base pairs (totally 14) are local excitations of the thG-derivatives. Both the S₁ state excitation energies and the fluorescence wavelengths are red-shifted to some extent after base pair with C, with a concomitantly decrease of the corresponding oscillator strength.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"137 ","pages":"Article 108999"},"PeriodicalIF":2.7,"publicationDate":"2025-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143580007","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Assessment of dynamic removal mechanism of non-steroidal anti-inflammatory biomolecules in the aqueous environments by a novel covalent organic framework","authors":"Saeed Pourmand ,&nbsp;Sara Zareei ,&nbsp;Mohammad Pourmand ,&nbsp;Sima Majidi ,&nbsp;Hamid Erfan-Niya","doi":"10.1016/j.jmgm.2025.109006","DOIUrl":"10.1016/j.jmgm.2025.109006","url":null,"abstract":"<div><div>Covalent Organic Frameworks (COFs) are a new class of highly porous crystalline substances which have demonstrated excellent potential as novel adsorbents for efficient depollution of pharmaceutical compounds from wastewater. Herein, the molecular mechanism involved in the removal process of non-steroidal anti-inflammatory drug residues, Ibuprofen (IBP) and Naproxen (NPX), from polluted water by an emerging novel COF functionalized with vinyl groups (COF-V), is evaluated through molecular dynamics (MD) simulations under various external electric fields (EFs). MD analyses show that COF-V is efficient in drug loading capacity of % 100 with total interaction energy value of −519.66 and −415.21 kJ/mol for NPX and IBP in single-component systems. In addition, both drug molecules can be simultaneously and efficiently removed in NPX/IBP/COF-V binary system. The van der Waals (vdW) potential is the primary force during the removal mechanism of drug residues. The efficacy of removing biomolecules from wastewater using COF-V substrate is reduced as the strength of EF is intensified in such a way an enhancement of solvent-accessible surface area (SASA) value of the adsorbent and the decreasing of Drug/COF-V contact area are found. The changes in the interaction energy and the RDF patterns are well in agreement with the adsorption mechanism observed in the presence of EFs. This work highlights using of COF as an effective adsorbent for removing pollutant from aqueous solution.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"137 ","pages":"Article 109006"},"PeriodicalIF":2.7,"publicationDate":"2025-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143580165","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Las Vegas algorithm in the prediction of intrinsic solubility of drug-like compounds","authors":"Aleksandar M. Veselinović ,&nbsp;Alla P. Toropova ,&nbsp;Andrey A. Toropov ,&nbsp;Alessandra Roncaglioni ,&nbsp;Emilio Benfenati","doi":"10.1016/j.jmgm.2025.109004","DOIUrl":"10.1016/j.jmgm.2025.109004","url":null,"abstract":"<div><div>A randomized algorithm that always succeeds in producing a correct output, but whose running time depends on random events is known as a Las Vegas algorithm. In this study, the Las Vegas algorithm aimed to improve QSPR models of intrinsic solubility of drug-like compounds obtained by the Monte Carlo method. Corresponding computational experiments were carried out with the CORAL software. The developed QSPR models were rigorously validated using a battery of statistical parameters, demonstrating excellent predictive ability and robustness. It has been shown, that the Las Vegas algorithm is a suitable way to improve the predictive potential of models obtained with the Monte Carlo technique. Additionally, the study identified key molecular fragments derived from the SMILES notation descriptors that influence the intrinsic solubility (increase or decrease). Overall, this work underscores the efficacy of the Monte Carlo method optimization with applied Las Vegas algorithm in constructing conformation-independent QSPR models with strong predictive power for prediction of intrinsic solubility of drug-like compounds.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"137 ","pages":"Article 109004"},"PeriodicalIF":2.7,"publicationDate":"2025-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143551519","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The ability of ZnO and MgO nanocages for adsorption and sensing performance of anticancer drug detection","authors":"Mohamed J. Saadh ,&nbsp;Ali B.M. Ali ,&nbsp;Z. Hanoon ,&nbsp;Vicky Jain ,&nbsp;Piyus Kumar Pathak ,&nbsp;Anjan Kumar ,&nbsp;Abdulrahman A. Almehizia ,&nbsp;Devendra Pratap Rao","doi":"10.1016/j.jmgm.2025.109003","DOIUrl":"10.1016/j.jmgm.2025.109003","url":null,"abstract":"<div><div>In recent years, researchers have carried out numerous research studies on the application of nanomaterials as tools for detecting various types of drugs within the field of pharmaceuticals, particularly for treating various cancer types such as Nitrosourea (NURS). Based on DFT calculations, the present study aims at examining the capability of the ZnO nanocage (ZnONC) and the MgO nanocage (MgONC) in detecting NURS. Different parameters such as the sensor mechanism, non-covalent interactions (NCIs), natural bond orbitals (NBOs), frontier molecular orbitals (FMOs) and adhesion energies were analyzed. The adhesion of NURS onto ZnO was accompanied by an energy of −45.01 kcal/mol. However, the adhesion energy of the complexes of MgONC was less. The bandgap of the complexes of ZnO and MgO decreased from 5.98 eV to 6.76 eV respectively for the pristine nanocage, which showed that these nanocages could be used for detecting NURS. Based on the analysis of FMOs, the complex of 6m-ZnONC@Nur had the lowest bandgap of 2.81 eV. Moreover, the recovery time of NURS from the MgONC was substantially shorter than its recovery time from the ZnONC. According to the topological analyses, the interactions between the ZnONC and MgONC were non-covalent. Following the adhesion process, there was an increase in the electrical conductance values. The complex of ZnO had the highest electrical conductance value. The analysis of the sensor mechanism revealed that the complexes of the ZnONC had the highest sensitivity since the bandgaps were narrow. Hence, the ZnONC can be used for detecting NURS and delivering NURS for treating cancers.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"137 ","pages":"Article 109003"},"PeriodicalIF":2.7,"publicationDate":"2025-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143562107","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Effect of the mixture composition of Acetonitrile/Benzene on excited state intramolecular proton transfer in 3-hydroxyflavone, theoretical insights: QTAIM, NBO, NLO behavior, thermodynamic and kinetic aspects","authors":"Fatma Zohra Imene Yeddou ,&nbsp;Mohamed Ali Benmensour ,&nbsp;Anissa Amar","doi":"10.1016/j.jmgm.2025.109001","DOIUrl":"10.1016/j.jmgm.2025.109001","url":null,"abstract":"<div><div>The effect of the Acetonitrile/Benzene mixture composition on excited state intramolecular proton transfer in 3-hydroxyflavone (3HF) was studied by means of density functional theory (DFT) and time-dependent DFT (TDDFT). The static dielectric constant ε_m is considered as a polarity parameter to characterize the composition of the two mixed solvents. We used the B3LYP/6-31G(d) level of theory for all the calculations of various properties (structural, electronic, spectroscopic, photophysical) in both ground and excited states. Our initial findings show that the mixture composition has a negligible effect on the geometry parameters. The computation of the maximum absorption and fluorescence wavelengths for 3HF and its tautomer correlates well with their corresponding experimental counterparts. The QTAIM and NBO tools were employed to estimate the strength of intramolecular hydrogen bond IHB. It reveals that E_HB is weakened with the increase of ε_m, due to the existence of electrostatic interactions. The title molecule is prone to exhibit remarkable NLO response. Secondly, the kinetic and thermodynamic outcomes, together with all former results, strongly support the occurrence of ESIPT phenomenon. Meanwhile, they also highlight the limits of PCM model in accurately describing solute-solvent interactions. Finally, the estimated ESIPT time is very close to the experimental values, which validates our level of theory.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"137 ","pages":"Article 109001"},"PeriodicalIF":2.7,"publicationDate":"2025-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143551517","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}