Journal of molecular graphics & modelling最新文献

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Supervised machine learning and molecular docking modeling to identify potential Anti-Parkinson's agents 有监督的机器学习和分子对接模型来识别潜在的抗帕金森药物
IF 2.7 4区 生物学
Journal of molecular graphics & modelling Pub Date : 2025-05-09 DOI: 10.1016/j.jmgm.2025.109073
Adib Ghaleb , Adnane Aouidate , Mohammed Aarjane , Hafid Anane
{"title":"Supervised machine learning and molecular docking modeling to identify potential Anti-Parkinson's agents","authors":"Adib Ghaleb ,&nbsp;Adnane Aouidate ,&nbsp;Mohammed Aarjane ,&nbsp;Hafid Anane","doi":"10.1016/j.jmgm.2025.109073","DOIUrl":"10.1016/j.jmgm.2025.109073","url":null,"abstract":"<div><div>Parkinson's disease is a neurodegenerative condition that affects the brain's neurons, and causes malfunction of nerve cells and their death. A neurotransmitter called dopamine interacts with the part of the brain in charge of coordination and movement. In general, the brain produces less dopamine as Parkinson's disease worsens; therefore, it becomes harder to control the movements. In this study, a dataset collected from CHEMBL library was applied to build four machine learning models using three different descriptors functions to determine the best models with the best features and suggest the best adenosine inhibitors. Molecular docking of adenosine A2A (PDB ID: <span><span>3UZA</span><svg><path></path></svg></span>) receptor was applied to identify the potential inhibitors. The machine learning and molecular docking results indicate that XGBoost model with RDkit features is an excellent model for this dataset to explore new Anti-Parkinson's agents.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"139 ","pages":"Article 109073"},"PeriodicalIF":2.7,"publicationDate":"2025-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143931324","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}
引用次数: 0
Elucidating OASL-RNA Interactions: Structural and energetic insights into vault RNAs binding 阐明OASL-RNA相互作用:拱顶rna结合的结构和能量见解
IF 2.7 4区 生物学
Journal of molecular graphics & modelling Pub Date : 2025-05-08 DOI: 10.1016/j.jmgm.2025.109071
Erick Bahena-Culhuac , Rodolfo Daniel Avila-Avilés , José Manuel Hernández-Hernández , Rodolfo Gamaliel Avila-Bonilla
{"title":"Elucidating OASL-RNA Interactions: Structural and energetic insights into vault RNAs binding","authors":"Erick Bahena-Culhuac ,&nbsp;Rodolfo Daniel Avila-Avilés ,&nbsp;José Manuel Hernández-Hernández ,&nbsp;Rodolfo Gamaliel Avila-Bonilla","doi":"10.1016/j.jmgm.2025.109071","DOIUrl":"10.1016/j.jmgm.2025.109071","url":null,"abstract":"<div><div>Oligoadenylate synthetase-like (OASL) proteins play an essential role in the innate immune response by detecting RNA molecules and modulating antiviral signalling pathways. This study investigated the structural and functional dynamics of OASL in its interaction with endogenous vault RNAs (vtRNAs) through computational analyses, including molecular docking and molecular dynamics simulations. Predicted 3D structures of vtRNAs revealed key interactions within the positively charged RNA-binding groove of OASL, involving residues such as Arg45, Lys63, and Arg196. Among the vtRNAs analysed, vtRNA 1-1 exhibited the highest binding affinity and stability, inducing conformational changes in OASL consistent with canonical activation mechanisms. In contrast, vtRNA 1–2 and 1–3 demonstrated moderate interactions, while vtRNA 2-1 had minimal impact on OASL conformation. Our results underscore the critical role of guanine- and cytosine-enriched regions in mediating binding stability and specificity, as corroborated by MM/GBSA calculations. The study highlights the molecular determinants of OASL-vtRNA interactions, offering structural insights into the mechanisms of nucleic acid recognition.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"139 ","pages":"Article 109071"},"PeriodicalIF":2.7,"publicationDate":"2025-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143947068","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}
引用次数: 0
Investigation of the temperature effect on the properties of biological nanomembranes with different concentrations of cholesterol using molecular dynamics simulation 利用分子动力学模拟研究温度对不同浓度胆固醇生物纳米膜性能的影响
IF 2.7 4区 生物学
Journal of molecular graphics & modelling Pub Date : 2025-05-08 DOI: 10.1016/j.jmgm.2025.109074
Armin Jarahi Khameneh , Azadeh Kordzadeh , Abbas Rastgoo , Amin Hadi
{"title":"Investigation of the temperature effect on the properties of biological nanomembranes with different concentrations of cholesterol using molecular dynamics simulation","authors":"Armin Jarahi Khameneh ,&nbsp;Azadeh Kordzadeh ,&nbsp;Abbas Rastgoo ,&nbsp;Amin Hadi","doi":"10.1016/j.jmgm.2025.109074","DOIUrl":"10.1016/j.jmgm.2025.109074","url":null,"abstract":"<div><div>The cell membrane is the outermost boundary of the cell, and its role is to protect the cell. Drugs must first pass through the membrane to enter the cell; therefore, investigating the properties of the bilayer membrane is of great importance and can provide important information regarding drug delivery processes. In this study, the effect of increasing temperature on the properties of bilayer membranes with 0 %, 10 %, 30 %, and 50 % cholesterol was investigated using molecular dynamics simulation. Moreover, the phase transition temperature of the lipid bilayer was selected based on the percentages of cholesterol. The results indicated that with increasing temperature, the membrane changed from gel phase to fluid phase. Moreover, a rise in temperature led to an increase in the area per lipid and a decrease in the order parameter, the reason for which was the increase in the kinetic energy of the molecules. The fluid phase membrane, which is at a higher temperature, had a higher diffusion coefficient than the gel phase membrane. The increase in the temperature caused the membrane with 0 % cholesterol to experience a 24 % decrease in the order parameter, while the structural properties of the membrane with 50 % cholesterol are almost constant with increasing temperature, indicating the rigidity of the membrane. With the increase in cholesterol concentration from 0 % to 50 %, the time for pore formation under the electric field increased from 0.26 ns to 8.46 ns. These results will be helpful in the development of drug delivery and therapeutic processes.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"139 ","pages":"Article 109074"},"PeriodicalIF":2.7,"publicationDate":"2025-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144070523","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}
引用次数: 0
Molecular dynamics investigation of cysteine mutations: Effects on calcium ion affinity and structural stability in the RET cysteine-rich domain 半胱氨酸突变的分子动力学研究:对RET富含半胱氨酸区域钙离子亲和力和结构稳定性的影响
IF 2.7 4区 生物学
Journal of molecular graphics & modelling Pub Date : 2025-05-08 DOI: 10.1016/j.jmgm.2025.109072
Bithia. R, George Priya Doss C
{"title":"Molecular dynamics investigation of cysteine mutations: Effects on calcium ion affinity and structural stability in the RET cysteine-rich domain","authors":"Bithia. R,&nbsp;George Priya Doss C","doi":"10.1016/j.jmgm.2025.109072","DOIUrl":"10.1016/j.jmgm.2025.109072","url":null,"abstract":"<div><div>The RET receptor tyrosine kinase is essential for cell growth, differentiation, and survival. Its cysteine-rich domain (CRD) is crucial for ligand-induced dimerization, activation, and structural stability, significantly influenced by calcium ion coordination. Mutations in key cysteine residues can disrupt disulfide bonds, alter calcium binding, and destabilize the CRD, leading to oncogenic transformations. This study investigates the impact of cysteine mutations on calcium ion binding and the structural stability of the RET receptor's CRD. Using molecular dynamics simulations and free energy calculations, the research examines the structural effects of specific cysteine mutations (C565F, C581F, and C585S) in the CRD. The findings indicate that these mutations disrupt disulfide bonds, alter calcium binding, and destabilize the CRD. RMSD and RMSF analyses show that each mutant affects structural dynamics and flexibility differently. The C581F mutant exhibited the most significant effect, with average RMSD values of 0.21 nm compared to the wild-type (0.19 nm) and other mutants (C565F, 0.14 nm; C585S, 0.17 nm). Higher residue fluctuations were observed in C581F and C585S, particularly in the calcium-coordinating residues. Binding free energy analysis indicates reduced calcium-binding stability in the mutants, while weighted contact maps reveal altered residue interaction patterns and new contact formations. These results suggest that while global structural changes are minimal, cysteine mutations cause localized destabilization of calcium ion binding sites. The disruption of key disulfide bonds and reduced residue contacts likely contribute to decreased binding stability in the mutants, underscoring the importance of cysteine residues and calcium coordination in maintaining the integrity of the RET-CRD.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"140 ","pages":"Article 109072"},"PeriodicalIF":2.7,"publicationDate":"2025-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144168063","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}
引用次数: 0
A DFT study of physical properties of the new Cr2S2BrCl material 新型Cr2S2BrCl材料物理性能的DFT研究
IF 2.7 4区 生物学
Journal of molecular graphics & modelling Pub Date : 2025-05-08 DOI: 10.1016/j.jmgm.2025.109075
S. Dahri , A. Jabar , L. Bahmad , L.B. Drissi , R. Ahl Laamara
{"title":"A DFT study of physical properties of the new Cr2S2BrCl material","authors":"S. Dahri ,&nbsp;A. Jabar ,&nbsp;L. Bahmad ,&nbsp;L.B. Drissi ,&nbsp;R. Ahl Laamara","doi":"10.1016/j.jmgm.2025.109075","DOIUrl":"10.1016/j.jmgm.2025.109075","url":null,"abstract":"<div><div>Using first-principles calculations, this study comprehensively investigates the structural, magnetic, electronic, optical, and thermodynamic properties of the newly material Cr<sub>2</sub>S<sub>2</sub>BrCl compound. The crystal structure was optimized, and the exchange-correlation interactions were modeled using the GGA + SOC + U approximation to capture the material's electronic structure accurately. Our magnetic analysis reveals significant spin polarization, with Cr atoms contributing dominantly to the overall magnetic moment, further supported by computed partial and total magnetic moments. The electronic density of states (DOS) and band structure calculations show that Cr<sub>2</sub>S<sub>2</sub>BrCl possesses a spin-dependent band gap. The optical properties, including the dielectric function and absorption coefficient, were evaluated, demonstrating strong absorption in the visible range, making this compound a candidate for optoelectronic devices. Additionally, thermoelectric properties, including the Seebeck coefficient, electrical conductivity, electronic thermal conductivity, figure of merit, electronic specific heat, and Pauli magnetic susceptibility, were evaluated.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"139 ","pages":"Article 109075"},"PeriodicalIF":2.7,"publicationDate":"2025-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143937800","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}
引用次数: 0
OH-initiated degradation of 2,2′,4,4′,5,6′-hexabrominated diphenyl ether (BDE-154) in the atmosphere and wastewater: Mechanisms, kinetics, and ecotoxicity oh引发的大气和废水中2,2 ',4,4 ',5,6 ' -六溴化二苯醚(BDE-154)的降解:机制,动力学和生态毒性
IF 2.7 4区 生物学
Journal of molecular graphics & modelling Pub Date : 2025-05-01 DOI: 10.1016/j.jmgm.2025.109070
Yunju Zhang , Meilian Zhao , Cen Yao , Yuxi Sun , Huirong Li
{"title":"OH-initiated degradation of 2,2′,4,4′,5,6′-hexabrominated diphenyl ether (BDE-154) in the atmosphere and wastewater: Mechanisms, kinetics, and ecotoxicity","authors":"Yunju Zhang ,&nbsp;Meilian Zhao ,&nbsp;Cen Yao ,&nbsp;Yuxi Sun ,&nbsp;Huirong Li","doi":"10.1016/j.jmgm.2025.109070","DOIUrl":"10.1016/j.jmgm.2025.109070","url":null,"abstract":"<div><div>In the present work, the reaction mechanism and kinetics of 2,2′,4,4′,5,6′-hexabrominated diphenyl ether (BDE-154) with OH were researched by employing density functional theory (DFT) and transition state theory (TST). The gas-phase and aqueous solution reaction mechanisms and kinetic parameters were computed at the level of M06–2X/6–311++G (3df, 3pd)//M06–2X/6-311G (d,p). The OH-addition of the non-bromine replaced carbon atom of the aromatic ring in BDE-154 is superior to substitution and H-abstraction mechanisms. The secondary reaction referring to OH-addition adducts in the existence of O<sub>2</sub>/NO will generate tribromophenol and OH-addition products. The majority of conversion products are still poisonous to hydrobiont. The KiSThelP program was applied to assess the overall rate coefficient and the individual rate coefficient at 258–328 K of 760 Torr. The overall rate coefficient at 298 K and 760 Torr are 9.40 × 10<sup>−14</sup> cm<sup>3</sup> molecule<sup>−1</sup> s<sup>−1</sup> and 3.60 × 10<sup>6</sup> M<sup>−1</sup> s<sup>−1</sup> in atmosphere and wastewater. The half-lives are 123.1 days and 1.93 × 10<sup>2</sup>-1.93 × 10<sup>11</sup> s, respectively. These results elucidated the conversion mechanism, atmospheric fate and ecotoxicity of BDE-154 in advanced oxidation procedure.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"139 ","pages":"Article 109070"},"PeriodicalIF":2.7,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143929164","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}
引用次数: 0
A molecular modeling study of pristine and Li-doped B16N16 nanocages for sensing G-series nerve agents using DFT-D3 基于DFT-D3的原始和锂掺杂B16N16纳米笼传感g系列神经毒剂的分子建模研究
IF 2.7 4区 生物学
Journal of molecular graphics & modelling Pub Date : 2025-04-30 DOI: 10.1016/j.jmgm.2025.109069
Hafiz Ali Rizwan , Muhammad Usman Khan , Abida Anwar , Munazza Idrees , Nasir A. Siddiqui
{"title":"A molecular modeling study of pristine and Li-doped B16N16 nanocages for sensing G-series nerve agents using DFT-D3","authors":"Hafiz Ali Rizwan ,&nbsp;Muhammad Usman Khan ,&nbsp;Abida Anwar ,&nbsp;Munazza Idrees ,&nbsp;Nasir A. Siddiqui","doi":"10.1016/j.jmgm.2025.109069","DOIUrl":"10.1016/j.jmgm.2025.109069","url":null,"abstract":"<div><div>The detection and removal of toxic warfare agents, such as G-series nerve agents, is a critical area of research for environmental safety and public health. This research uses density functional theory (DFT) to address the gap in understanding the molecular-level interactions of G-series nerve agents with boron nitride nanocages (BNNC) and lithium-doped boron nitride nanocages (Li-BNNC). The investigated nanostructures exhibited high negative adsorption energies, allowing the G-series nerve agents to adsorb strongly onto the BNNC and Li-BNNC surfaces. The Li-BNNC complexes undergo the chemisorption process with the adsorption energy, ranging from −31.819 kcal/mol to −33.635 kcal/mol. The findings of frontier molecular orbitals (FMOs) and density of states (DOS) indicated that the electronic characteristics of GS@BNNC and GS@Li-BNNC had been significantly changed, resulting in a smaller energy gap and higher conductivity. The Li-doping results in much lower energy gaps in Li-BNNC systems, such as 2.707 eV for Tabun@Li-BNNC, that cause higher electrical conductivity. Tabun@Li-BNNC has the highest electrical conductivity of 4.60 × 10<sup>12</sup> among Li-doped systems, and Tabun@BNNC has a high conductivity of 2.84 × 10<sup>12</sup> among undoped BNNC systems. Li-BNNC systems have higher electrical conductivity, which makes them good sensors for detecting G-series nerve agents. These findings provide a molecular-level understanding of the effect of Li-doping on BNNC-based nanomaterials and their potential for advancing nanotechnology-driven gas sensors.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"139 ","pages":"Article 109069"},"PeriodicalIF":2.7,"publicationDate":"2025-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143901972","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}
引用次数: 0
Application of machine learning approaches for estimating carbon dioxide absorption capacity of a variety of blended imidazolium-based ionic liquids 应用机器学习方法估计各种混合咪唑基离子液体的二氧化碳吸收能力
IF 2.7 4区 生物学
Journal of molecular graphics & modelling Pub Date : 2025-04-26 DOI: 10.1016/j.jmgm.2025.109060
Alexei Rozhenko , Fahimeh Hadavimoghaddam , Peyvand Valeh-e-Sheyda , Mohsen Tamtaji , Jafar Abdi
{"title":"Application of machine learning approaches for estimating carbon dioxide absorption capacity of a variety of blended imidazolium-based ionic liquids","authors":"Alexei Rozhenko ,&nbsp;Fahimeh Hadavimoghaddam ,&nbsp;Peyvand Valeh-e-Sheyda ,&nbsp;Mohsen Tamtaji ,&nbsp;Jafar Abdi","doi":"10.1016/j.jmgm.2025.109060","DOIUrl":"10.1016/j.jmgm.2025.109060","url":null,"abstract":"<div><div>Ionic liquids (ILs) have gained attention in recent times as potentially effective absorbents for CO<sub>2</sub> emissions owing to the number of their notable attributes, including reduced volatility, enhanced thermal consistency etc. Due to the number of challenges of thermodynamic models in forecasting CO<sub>2</sub> solubility in ILs under a variety of operating conditions, machine learning (ML) approaches have been developed as a result of the necessity for an alternate solution. Nevertheless, there are currently quite a few of forecasting techniques available for evaluating the solubility of CO<sub>2</sub>, specifically in combinations of imidazolium-based ILs. For this reason, the present study focuses on the utilization of molecular structure-based descriptors as an alternative chemistry concept for predicting the CO<sub>2</sub> solubility in an imidazolium-based ILs mixture. This research utilized and contrasted 6 sophisticated machine learning models (AdaBoost-SVR, Extra trees, DT, CatBoost, LightGBM, XGBoost) to determine the most effective method for target parameter estimation. The study employed an exclusive and all-encompassing databank consisting of 43 imidazolium-based ILs, 26 input variables, and 4397 experimental data points in total. The remarkable 90 % overall accuracy consistently surpassed by all models serves as evidence of the ML methodologies' robustness and efficacy. The highest-performing approaches, XGBoost, exhibited a remarkable precision level of R<sup>2</sup> being equal to 0.999 and RMSE of 0.0077. A comprehensive trend analysis was performed to assess the XGBoost model's performance across different operational scenarios such as molecular weight, temperature, water content, and pressure. The developed model proved to be capable of accurately detecting patterns in various operating conditions. By employing sensitivity analysis with SHAP values, it was observed that pressure, temperature, and molecular weight were the most impactful factors influencing the XGBoost model's predictions.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"139 ","pages":"Article 109060"},"PeriodicalIF":2.7,"publicationDate":"2025-04-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143891082","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}
引用次数: 0
Unveiling charge transfer kinetics and static-dynamic nonlinear optical switching in 2-phenylthiophene push-pull chromophores: DFT-based theoretical modelling for enhanced harmonic generation and electro-optic applications 揭示2-苯基噻吩推拉发色团中的电荷转移动力学和静动态非线性光开关:基于dft的增强谐波产生和电光应用的理论建模
IF 2.7 4区 生物学
Journal of molecular graphics & modelling Pub Date : 2025-04-26 DOI: 10.1016/j.jmgm.2025.109061
Sehar Nadeem , Abida Anwar , Muhammad Usman Khan , Munazza Idrees , Mohamed A. El-Tayeb , Mahmoud A.A. Ibrahim
{"title":"Unveiling charge transfer kinetics and static-dynamic nonlinear optical switching in 2-phenylthiophene push-pull chromophores: DFT-based theoretical modelling for enhanced harmonic generation and electro-optic applications","authors":"Sehar Nadeem ,&nbsp;Abida Anwar ,&nbsp;Muhammad Usman Khan ,&nbsp;Munazza Idrees ,&nbsp;Mohamed A. El-Tayeb ,&nbsp;Mahmoud A.A. Ibrahim","doi":"10.1016/j.jmgm.2025.109061","DOIUrl":"10.1016/j.jmgm.2025.109061","url":null,"abstract":"<div><div>Addressing the growing demand for ultrafast photonic nonlinear optical (NLO) materials, ultrafast switching NLO behaviour was studied in detail in 2-phenylthiophene-based push-pull chromophores using laser pulses at 532 and 1064 nm. The EOPE β (−ω, ω, 0) and SHG β (−2ω, ω, ω) calculations for these laser pulses demonstrate an incredible NLO response with efficient energetic offsets that are approximately six times larger than BSS-1. Moreover, the correlation between experimental and theoretical dipole moments and UV absorption (λ<sub>(exp)</sub> = 397, <em>λ<sub>max</sub></em> = 394.94 nm) is analyzed, emphasizing its impact on developing NLO switching devices. Quantum chemical calculations, such as frontier molecular orbitals (FMOs), UV–Vis investigation, electron-hole overlap analysis, non-covalent interaction (NCI), molecular electrostatic potential (MEP), natural bond orbitals (NBOs), along with static and frequency-dependent NLO were performed to determine the effect of donor and acceptor modification on the enhanced harmonic generation of designed chromophores (BSSR1-BSSR8 and reference BSS-1). Notably, outstanding NLO findings were obtained for nitro and cyano-based acceptor compounds. Interestingly, among all the derivatives, BSSR4 and BSSR5 had the lowest E<sub>gap</sub> values of 1.09 and 1.246 eV, respectively, and the E<sub>gap</sub> values were found in the following decreasing order: BSS-1 (R) &gt; BSSR1 &gt; BSSR3 &gt; BSSR7 &gt; BSSR6 &gt; BSSR2 &gt; BSSR8 &gt; BSSR5 &gt; BSSR4. Surprisingly, BSSR5 and BSSR4 had maximum NLO (α and β) amplitudes of 8.62 × 10<sup>2</sup> and 8.09 × 10<sup>5</sup> a.u in the gas phase, respectively, indicating their potential towards all-optical computing and ultrahigh bandwidth information processing. These findings underscore the significance of charge transfer dynamics and ultrafast NLO switching in 2-phenylthiophene push-pull chromophores, paving the way for advanced harmonic generation and cutting-edge electro-optic applications.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"139 ","pages":"Article 109061"},"PeriodicalIF":2.7,"publicationDate":"2025-04-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143886424","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}
引用次数: 0
Fine-tuning property domain weighting factors and the objective function in force-field parameter optimization 力场参数优化中的微调特性域加权因子和目标函数
IF 2.7 4区 生物学
Journal of molecular graphics & modelling Pub Date : 2025-04-24 DOI: 10.1016/j.jmgm.2025.109035
Robin Strickstrock , Alexander Hagg , Marco Hülsmann , Karl N. Kirschner , Dirk Reith
{"title":"Fine-tuning property domain weighting factors and the objective function in force-field parameter optimization","authors":"Robin Strickstrock ,&nbsp;Alexander Hagg ,&nbsp;Marco Hülsmann ,&nbsp;Karl N. Kirschner ,&nbsp;Dirk Reith","doi":"10.1016/j.jmgm.2025.109035","DOIUrl":"10.1016/j.jmgm.2025.109035","url":null,"abstract":"<div><div>Force field (FF) based molecular modeling is an often used method to investigate and study structural and dynamic properties of (bio-)chemical substances and systems. When such a system is modeled or refined, the force-field parameters need to be adjusted. This force-field parameter optimization can be a tedious task and is always a trade-off in terms of errors regarding the targeted properties. To better control the balance of various properties’ errors, in this study we introduce weighting factors for the optimization objectives. Different weighting strategies are compared to fine-tune the balance between bulk-phase density and relative conformational energies (RCE), using <span><math><mi>n</mi></math></span>-octane as a representative system. Additionally, a non-linear projection of the individual property-specific parts of the optimized loss function is deployed to further improve the balance between them. The results show that the combined error for the reproduction of the properties targeted in this optimization is reduced. Furthermore, the transferability of the force field parameters (FFParams) to chemically similar systems is increased. One interesting outcome is a large variety in the resulting optimized FFParams and corresponding errors, suggesting that the optimization landscape is multi-modal and very dependent on the weighting factor setup. We conclude that adjusting the weighting factors can be a very important feature to lower the overall error in the FF optimization procedure, giving researchers the possibility to fine-tune their FFs.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"139 ","pages":"Article 109035"},"PeriodicalIF":2.7,"publicationDate":"2025-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143876647","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}
引用次数: 0
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