Abel S. Maldonado , Susana B. Ramos , Gabriela F. Cabeza
{"title":"Shape-dependent CO chemisorption on Pt13 nanocluster deposited on reduced TiO2(110)","authors":"Abel S. Maldonado , Susana B. Ramos , Gabriela F. Cabeza","doi":"10.1016/j.jmgm.2024.108902","DOIUrl":"10.1016/j.jmgm.2024.108902","url":null,"abstract":"<div><div>This article delves into the impact of nanoparticle shape on CO chemisorption and the reactivity of Pt<sub>13</sub> nanocatalysts supported on reduced TiO<sub>2</sub>(110). Distinct reactivity in carbon monoxide adsorption is observed among nanoparticles, all composed of 13 platinum atoms but varying in shape. The calculated formation and CO adsorption energies are correlated to the electronic properties of the system and the oxidation states of the Pt atoms involved. Through an analysis of band shifting during the deposition of Pt clusters onto the oxide, and a comparison of the valence band maximum with the measured oxidation potential for the CO to CO<sub>2</sub> reaction, we make predictions about the system's oxidation capability in this reaction. Our findings suggest that Pt<sub>13</sub> clusters with cuboid, double triangle DT2 and octahedral Oh shapes, supported on the surface, are particularly advantageous for catalyzing the conversion of CO to CO<sub>2</sub>. Within these geometries, several configurations for CO adsorption are evaluated, focusing on the ratio between anionic and cationic Pt sites. This ratio appears to govern the activity for CO oxidation, aligning with recent experimental reports.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"134 ","pages":"Article 108902"},"PeriodicalIF":2.7,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142603823","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}
Elena Ermakova , Rauf Kurbanov , Igor Sedov , Yuriy Zuev
{"title":"Thermal unfolding of alpha-lactalbumin at acidic pH: Insights from molecular dynamics simulations","authors":"Elena Ermakova , Rauf Kurbanov , Igor Sedov , Yuriy Zuev","doi":"10.1016/j.jmgm.2024.108900","DOIUrl":"10.1016/j.jmgm.2024.108900","url":null,"abstract":"<div><div>The transformation of globular proteins into fibrils passes through several stages, including the formation of partially expanded conformational states different from the native or fully unfolded forms. Here we used molecular dynamics simulations to characterize the thermal unfolding of alpha-lactalbumin on the microsecond timescale in the range of temperatures of 300–440 K. Comparative analysis of structural changes, mobility of different parts of protein, and pathways through the free energy landscape during the unfolding of alpha-lactalbumin at different temperatures reveals the existence of several intermediate states separated by small energy barriers. The lifetime of these intermediates depends on temperature and varies from nanoseconds to microseconds.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"134 ","pages":"Article 108900"},"PeriodicalIF":2.7,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142568950","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":"Comparative study of various molecular feature representations for solvation free energy predictions of neutral species","authors":"Valerii V. Isaev , Yury Minenkov","doi":"10.1016/j.jmgm.2024.108901","DOIUrl":"10.1016/j.jmgm.2024.108901","url":null,"abstract":"<div><div>Predicting molecular properties with the help of Neural Networks is a common way to substitute or enhance comprehensive quantum-chemical calculations. One of the problems facing researchers is the choice of vectorization approach to representing the solvent and the solute for the estimator model. In this work, 10 different approaches have been investigated for both organic solute and solvent including vectorizers that relied on macroscopic parameters, functional groups classification, molecular graphs, or atomic coordinates. A variation of the Bag of Bonds approach called JustBonds, trained on the MNSol database, showed the best overall performance resulting in RMSD <2 kcal/mol for the blind dataset that contains the solutes not presented in the training subset and <1 kcal/mol on records from Solv@TUM database, which is close to contemporary continuum models. We have also demonstrated that the most important bags usually contain heteroatom and play a key role in the solvation process. Furthermore, the small role of solvent vectorization was demonstrated and revealed that approaches based on functional groups or macroscopic solvent parameters are often enough to efficiently represent solvent media.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"134 ","pages":"Article 108901"},"PeriodicalIF":2.7,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142603822","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}
Yabing Li , Ali B.M. Ali , Nelly Esther Flores Tapia , Nargiza Kamolova , Soheil Salahshour , Rozbeh Sabetvand
{"title":"Effect of channel roughness on the particle diffusion and permeability of carbon nanotubes in reverse electrodialysis process applying molecular dynamics simulation","authors":"Yabing Li , Ali B.M. Ali , Nelly Esther Flores Tapia , Nargiza Kamolova , Soheil Salahshour , Rozbeh Sabetvand","doi":"10.1016/j.jmgm.2024.108899","DOIUrl":"10.1016/j.jmgm.2024.108899","url":null,"abstract":"<div><div>Innovative technology and methods are crucial for making pure and refreshing water. Two main methods are present to delete soluble salts from water: membrane processes and thermal processes. A beneficial membrane technique is reverse electrodialysis. This research used molecular dynamics (MD) simulation to investigate how channel roughness affected particle diffusion and permeability in carbon nanotubes (CNTs) via the reverse electrodialysis process. The results indicate that adding roughness in the CNT duct increased the force between the primary fluid and the duct. Using an armchair-edged CNT structure maximized the electric current in the sample. Furthermore, the roughness increased the intensity of force in the channel, which was due to gravity, leading to a decrease in the mobility of fluid particles. Additionally, several broken hydrogen bonds inside the simulation box increased from 116 to 128 in the duct sample with roughness.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"134 ","pages":"Article 108899"},"PeriodicalIF":2.7,"publicationDate":"2024-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142568948","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":"Molecular dynamics simulations, essential dynamics and MMPBSA to evaluate natural compounds as potential inhibitors for AccD6, a key drug target in the fatty acid biosynthesis pathway in Mycobacterium tuberculosis","authors":"Chandra Jyoti Singha, Ramadas Krishna","doi":"10.1016/j.jmgm.2024.108898","DOIUrl":"10.1016/j.jmgm.2024.108898","url":null,"abstract":"<div><div>Antibiotic resistance in <em>Mycobacterium tuberculosis</em>, the primary causative agent of the tuberculosis disease is an ever growing threat especially in developing and underdeveloped countries. Isoniazid is a commonly used first line anti-tuberculosis drug used during the first phase of tuberculosis treatment. However, due to its improper use, many strains of <em>Mycobacterium tuberculosis</em> have acquired resistance to the drug. Advancements in next generation sequencing technologies, such as transcriptomics have paved way for identifying alternative drug targets based on the differential expression pattern of genes. Therefore, this study makes use of RNA-Seq data of <em>Mycobacterium tuberculosis</em> isolates treated with different concentrations of isoniazid to identify genes that can be proposed as drug targets. From the differential expression analysis, it was observed that four genes were significantly upregulated under all the conditions. Among the four genes, <em>accD6</em> was selected as the drug target for virtual screening and molecular dynamics studies, because of its role in fatty acid elongation and contribution to the synthesis of mycolic acids. The protein-protein interaction network and gene ontology based functional enrichment studies show an enrichment in fatty acid biosynthesis related pathways. Furthermore, virtual screening studies successfully screened the top three natural inhibitor molecules with satisfactory ADME properties and a better glide score than the reference compound, NCI-172033. The trajectory analysis, essential dynamics studies and MMPBSA analysis, concluded that among the hit molecules, NPC41982, a thiazole derivative showed the most promising results and can be considered as a potential drug candidate.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"134 ","pages":"Article 108898"},"PeriodicalIF":2.7,"publicationDate":"2024-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142561017","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}
Cihat Güleryüz , Duha M. Hasan , Masar A. Awad , Azal S. Waheeb , Abrar U. Hassan , Ayesha Mohyuddin , Hussein A.K. Kyhoiesh , Mohammed T. Alotaibi
{"title":"Molecular engineering on tyrian puprle natural dye as TiO2 based fined tuned photovoltaic dye material: DFT molecular analysis","authors":"Cihat Güleryüz , Duha M. Hasan , Masar A. Awad , Azal S. Waheeb , Abrar U. Hassan , Ayesha Mohyuddin , Hussein A.K. Kyhoiesh , Mohammed T. Alotaibi","doi":"10.1016/j.jmgm.2024.108894","DOIUrl":"10.1016/j.jmgm.2024.108894","url":null,"abstract":"<div><div>In this research, molecular modification is employed to see the enhancement in the efficiency of Tyrian Purple (TP), a natural dye, for organic photovoltaic materials. By using Density Functional Theory (DFT) based molecular modeling, seven new structures are designed with pi spacer to extend electron donor moieties. Teheir Frontier Molecular Orbital (FMO) analysis demonstartes their charges with a similar pattern of distributions over their Highest Occupied and Lowed Unocuupied Molecular Orbitals (HOMO/lUMO). This analysls also show their energy gaps (E<sub>gaps</sub>) to range around 2.97–3.02 eV. Their maximum absorption wavelength (<em>λ<sub>max</sub></em>) demosntartes 486–490 nm range to indicate their tendency of absorbing light efficiently. Their Transition Density Matrix (TDM) analysis also reveals their facile electronic transitions without a significant charges over spacers. From calculating their photovoltaic paramters, their Light Harvesting Efficiency (LHE) reaches to 72.4–95.5 %. Also their Open Circuit Voltage (V<sub>oc</sub>) varies across 1.16–1.34 V. It is found that dyes actively adsorb onto TiO<sub>2</sub> clusters to demonstrate their promise for tuning their Conduction Band (CB). This research is an effort for to evaluate the structural correlations to the develop photovoltaic materials through molecular-level design and optimization.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"134 ","pages":"Article 108894"},"PeriodicalIF":2.7,"publicationDate":"2024-10-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142561018","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":"Unraveling the adsorption dynamics of asphaltene molecules on silica surfaces","authors":"Fengfeng Gao","doi":"10.1016/j.jmgm.2024.108897","DOIUrl":"10.1016/j.jmgm.2024.108897","url":null,"abstract":"<div><div>Understanding the adsorption behavior of heavy oil components on reservoir solids is crucial for improving oil recovery, yet the molecular mechanism remains unclear. This study used molecular dynamics simulations to explore the adsorption kinetics and thermodynamics of asphaltene molecules on silica surfaces. The adsorption process was divided into three stages: free, adsorption, and equilibrium. In the adsorption stage, asphaltenes must pass through two dense hydration layers and adhere to the silica surface in a flat configuration. Carboxyl groups increase asphaltene hydrophilicity, raising interaction energy with water molecules and hindering adsorption. In addition, two distinct hydration layers of water molecules on the silica surface. The first hydration layer, with a peak density of 2000 kg m<sup>−3</sup>, was located around 0.6 nm from the surface, driven by hydrogen bonding between Si-OH groups and water molecules. The second layer, found at 1.44–1.80 nm, had a lower density of 1200 kg m<sup>−3</sup>, formed through hydrogen bonding between water molecules. This study aims to enhance the understanding of the physicochemical mechanisms governing oil droplet adsorption on silica surfaces, potentially informing the design of improved oil recovery strategies.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"134 ","pages":"Article 108897"},"PeriodicalIF":2.7,"publicationDate":"2024-10-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142522153","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":"QSPR modeling to predict surface tension of psychoanaleptic drugs using the hybrid DA-SVR algorithm","authors":"Meriem Ouaissa , Maamar Laidi , Othmane Benkortbi , Hasmerya Maarof","doi":"10.1016/j.jmgm.2024.108896","DOIUrl":"10.1016/j.jmgm.2024.108896","url":null,"abstract":"<div><div>A robust Quantitative Structure-Property Relationship (QSPR) model was presented to predict the surface tension property of psychoanaleptic (psychostimulant and antidepressant) drugs. A dataset of 112 molecules was utilized, and three feature selection methods were applied: genetic algorithm combined with Ordinary Least Squares (GA-OLS), Partial Least Squares (GA-PLS), and Support Vector Machines (GA-SVM), each identifying ten pertinent AlvaDesc descriptors. The models were constructed using the Dragonfly Algorithm combined with the Support Vector Regressor (DA-SVR), with the GA-SVM-based model emerging as the top performer. Rigorous statistical metrics validate its superior predictive accuracy (<em>R</em><sup><em>2</em></sup> = 0.98142, <em>Q</em><sup><em>2</em></sup><sub><em>LOO</em></sub> = 0.98142, <em>RMSE</em> = 1.12836, <em>AARD</em> = 0.78746). Furthermore, an external test set of ten compounds was employed for model validation and extrapolation, along with assessing the applicability domain, further underscoring the model’s reliability. The selected descriptors (X0Av, VE1sign_B(e), ATSC1e, MATS6v, P_VSA_ppp_A, TDB01u, E1s, R2m+, N-067, SssO) collectively elucidate the key structural factors influencing surface tension in the studied drugs. The model provides excellent predictions and can be used to determine the surface tension of new psychoanaleptic drugs. Its outcomes will guide the design of novel medications with targeted surface tension properties.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"134 ","pages":"Article 108896"},"PeriodicalIF":2.7,"publicationDate":"2024-10-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142545963","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}
Murillo H. Queiroz , Suelen A. Santos , Joel L. Nascimento , Bruno S. Sampaio , Tiago V. Alves , Roberto Rivelino
{"title":"Evaluating interaction energy versus electron density relationships to estimate inter and intramolecular H-bonding","authors":"Murillo H. Queiroz , Suelen A. Santos , Joel L. Nascimento , Bruno S. Sampaio , Tiago V. Alves , Roberto Rivelino","doi":"10.1016/j.jmgm.2024.108895","DOIUrl":"10.1016/j.jmgm.2024.108895","url":null,"abstract":"<div><div>We investigate the computational effects on the relationships between interaction energy (ΔE) and electron density (ρ), at the critical point obtained from 19 intermolecular H-bonded dimers, to estimate inter and intramolecular interactions of larger H-bonded systems. Our analysis examines basis set superposition error (BSSE) effects, dispersion energy corrections, and the exchange-correlation energy model on the ΔE vs. ρ linear regressions. The calculations were carried out within density functional theory (DFT) combined with the 6-31+G(d,p) and def2-TZVPP basis sets. This procedure quantifies the average effects of BSSE for different levels of approximation, and underscore the sensitivity of the ΔE estimation together with dispersion corrections. This is valuable for the development of DFT-based estimators of multiple interaction energies of large H-bonded systems with low computational cost. We have applied this procedure by analyzing H-bonded biological molecules, such as DNA base pairs, an asparagine side chain, and an AZT molecule. Our estimated H-bond interaction energies are in agreement with previous studies, and emphasize the importance of methodological considerations for accurately predicting interaction energies using DFT combined with topological parameters.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"134 ","pages":"Article 108895"},"PeriodicalIF":2.7,"publicationDate":"2024-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142502240","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":"Molecular dynamics simulations of hydrogen-bonded network structures of polybenzoxazines in the gas phase and aqueous solution","authors":"Pakuna Panbo , Uthen Thubsuang , Apirak Payaka","doi":"10.1016/j.jmgm.2024.108893","DOIUrl":"10.1016/j.jmgm.2024.108893","url":null,"abstract":"<div><div>The crucial role of the amine functional group at the Mannich bridge of polybenzoxazines (PBZs) has been reported to be responsible for their hydrogen-bonded network structures. However, they have not been thoroughly studied in an aqueous solution and at the atomistic level. In this study, molecular dynamics simulations were applied to investigate the formation of hydrogen bond interactions of PBZs prepared from bisphenol A/methylamine (m-PBZ), bisphenol A/aniline-based (a-PBZ), and bisphenol A/2-(methylamino)ethylamine (e-PBZ). Based on the simulation results, the hydrogen-bonded network structures of the PBZs interfered with water molecules, leading to less compaction of the PBZ structure in the aqueous solution. The hydrogen bonding species of the m-PBZ and a-PBZ structures consisted of the –OH<sup>…</sup>N (Mannich) and –OH<sup>…</sup>O intramolecular interactions. However, for e-PBZ, the –OH<sup>…</sup>O species was not present, but the 2-(ethylamino)ethylamine substituent formed more hydrogen bonding species than those of m-PBZ and a-PBZ. Additionally, the intermolecular hydrogen bond interactions of the PBZs and water molecules were not detected in any of the aqueous solution simulations.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"134 ","pages":"Article 108893"},"PeriodicalIF":2.7,"publicationDate":"2024-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142502241","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}