Journal of molecular graphics & modelling最新文献_第2页

Theoretical insights into adsorption behaviors and 17O nuclear magnetic resonance investigations of water clusters over xylitol-decorated hexagonal boron nitride 木糖醇修饰六方氮化硼表面水团簇吸附行为的理论见解及17O核磁共振研究。

IF 3 4区生物学 Q2 BIOCHEMICAL RESEARCH METHODS

Journal of molecular graphics & modelling

Pub Date : 2026-02-05 DOI: 10.1016/j.jmgm.2026.109318

Songjin Zheng , Wei Shen , Di Kang , Haitao Wang , Yifan Bu , Ningyang Mao , Yihan Zhang , Tao Wang , Li Xu , Henan Li , Hongping Li

The precise modulation of water cluster behavior on material surfaces is critical for numerous technological applications but remains challenging due to the complexity of hydrogen-bonding interactions. This study presents a comprehensive theoretical investigation into the adsorption structures, interaction energetics, and ¹⁷O nuclear magnetic resonance (NMR) spectroscopic signatures of water clusters on both pristine and xylitol-decorated hexagonal boron nitride (h-BN-xyl) surfaces, using density functional theory (DFT) calculations. Results demonstrate that xylitol functionalization drastically enhances the adsorption capacity of h-BN, with interaction energies increasing up to threefold compared to pristine h-BN, which is attributed to the formation of multiple bidirectional hydrogen bonds between the hydroxyl groups of xylitol and the water clusters. Topological and electrostatic potential analyses confirm the introduction of strong, electron-rich adsorption sites on h-BN-xyl. Crucially, ¹⁷O NMR chemical shifts exhibit systematic downfield displacements upon adsorption on h-BN-xyl, indicating a deshielding effect due to reduced electron density on oxygen atoms and a more complex hydrogen-bonding network. This work establishes a robust structure-spectroscopy relationship, highlighting the dual utility of DFT and NMR simulations in deciphering interfacial water dynamics and providing predictive design principles for advanced functional materials in fields such as catalysis, sensing, and environmental technology.

材料表面水团簇行为的精确调节对于许多技术应用至关重要，但由于氢键相互作用的复杂性，仍然具有挑战性。本研究利用密度泛函理论（DFT）计算，对原始表面和木糖醇修饰的六方氮化硼（h-BN-xyl）表面的水团簇的吸附结构、相互作用能量学和17O核磁共振（NMR）光谱特征进行了全面的理论研究。结果表明，木糖醇功能化后，h-BN的吸附能力显著增强，其相互作用能比原始的h-BN增加了三倍，这是由于木糖醇羟基与水团簇之间形成了多个双向氢键。拓扑和静电势分析证实在h- bn -羟基上引入了强的、富电子的吸附位点。关键是，在h- bn -羟基上吸附时，17O NMR化学位移表现出系统的下场位移，表明由于氧原子上的电子密度降低和更复杂的氢键网络而产生的去屏蔽效应。这项工作建立了一个强大的结构-光谱关系，突出了DFT和NMR模拟在破译界面水动力学方面的双重效用，并为催化、传感和环境技术等领域的先进功能材料提供了预测设计原则。

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引用次数: 0

A theoretical study on the mechanism of photoinduced ring-opening reaction of spiropyran derivatives 螺吡喃衍生物光诱导开环反应机理的理论研究。

IF 3 4区生物学 Q2 BIOCHEMICAL RESEARCH METHODS

Journal of molecular graphics & modelling

Pub Date : 2026-02-05 DOI: 10.1016/j.jmgm.2026.109314

Sha Ding, Yong Xia

Spiropyran (SP) derivatives, as stimuli-responsive fluorescent materials, undergo reversible isomerization between closed-ring (SP) and open-ring (merocyanine, MC) forms upon light irradiation, holding promise for applications in optical switches and sensing. However, their excited-state dynamics and the roles of substituents/solvents in photoinduced ring-opening remain elusive. Herein, we use TD-CAM-B3LYP/6-31G(d) to clarify the photoinduced ring-opening mechanism of carboxyl-functionalized SP derivatives (SP-R, R = NO₂, H, OCH₃). Ground-state (S₀) SP-R is stable with high C2-O1 cleavage barriers (15.5–31.4 kcal/mol), impeding spontaneous ring-opening; the electron-withdrawing NO₂ reduces barriers, while the electron-donating OCH₃ increases them. In the excited state (S₁), these barriers are drastically lowered or even eliminated, facilitating SP→MC conversion, with “bright states" identified as S₂ for SP-NO₂ and S₁ for SP-H/SP-OCH₃. Structural changes promote ring-opening, with SP-OCH₃ exhibiting the most pronounced effects. AIM analysis reveals weakened C2-O1 bond covalency in S₁, particularly for SP-H and SP-OCH₃. Solvent polarity modulates stability, dipole moments, and emission properties: polar solvents enhance trans-MC stability, and Trans-MC-OCH₃ emits the longest wavelengths (602.2–639.3 nm) due to extended π-conjugation. This study clarifies SP→MC mechanisms, highlights the regulatory roles of substituents and solvents, and provides guidance for designing photoresponsive materials.

Spiropyran （SP）衍生物作为一种刺激响应型荧光材料，在光照射下闭合环（SP）和开环（merocyanine， MC）之间发生可逆异构化，在光学开关和传感领域具有广阔的应用前景。然而，它们的激发态动力学和取代基/溶剂在光致开环中的作用仍然是难以捉摸的。本文利用TD-CAM-B3LYP/6-31G(d)研究了羧基功能化SP衍生物（SP-R, R = NO2， H, OCH3）的光致开环机理。基态SP-R稳定，具有较高的C2-O1解理势垒（15.5 ~ 31.4 kcal/mol），阻碍自发开环；吸电子的NO2降低了势垒，而给电子的OCH3则增加了势垒。在激发态（S1）中，这些势垒急剧降低甚至消除，有利于SP→MC的转化，SP- no2的“亮态”为S2， SP- h /SP- och3的“亮态”为S1。结构变化促进了环的开环，其中SP-OCH3的作用最为明显。AIM分析显示S1中C2-O1键共价减弱，特别是SP-H和SP-OCH3。溶剂极性调节稳定性、偶极矩和发射特性：极性溶剂增强了反式mc的稳定性，由于扩展π共轭作用，反式mc - och3发射波长最长（602.2 ~ 639.3 nm）。本研究阐明了SP→MC的机理，强调了取代基和溶剂的调控作用，为光响应材料的设计提供了指导。

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引用次数: 0

Drug repurposing strategy to identify the putative leads against the Epidermal growth factor receptor (EGFR) from the USFDA-approved drug pool: Investigating the utility as an anticancer agent 从美国fda批准的药物库中确定针对表皮生长因子受体（EGFR）的推定线索的药物再利用策略：研究其作为抗癌剂的效用。

IF 3 4区生物学 Q2 BIOCHEMICAL RESEARCH METHODS

Journal of molecular graphics & modelling

Pub Date : 2026-01-31 DOI: 10.1016/j.jmgm.2026.109310

Nemat Ali , Ali M. Alaseem , M. Arockia Babu , Thakur Gurjeet Singh , Glowi Alasiri , Mohammad Fareed , Yogita Tyagi , Nisha Bansal

EGFR is a validated drug target in anticancer drug discovery. However, the existing issues of drug resistance, toxicities, and evolving mutations in EGFR have led to the global decline in the putative and potent anti-EGFR therapeutics. To address this gap, drug repurposing or repositioning is a valid technique for drug identification in a quick time and in an economical way. We herein employed the drug repurposing techniques from the library of 3500 approved USFDA small molecules. The initial HTVS (high-throughput virtual screening), followed by XP analysis and molecular mechanics (MMGBSA) and ADME profiling, led to the identification of Cycloguanil (antimalarial) and Metformin (antidiabetic) as the putative lead molecules with the potential to inhibit the EGFR. The top-scoring ligand was subjected to a molecular dynamics simulation study that stabilized the stability of cycloguanil within the ATP pocket of EGFR. The biological investigations further corroborated the in-silico studies. Cycloguanil inhibited the EGFR with a half maximal inhibitory concentration (IC50) of IC₅₀ of 490 nM compared to erlotinib with an IC₅₀ of 222 nM. Besides this, cycloguanil was able to halt the cell cycle progression at the G1 phase (46.54%), a peculiar feature of the kinase inhibitors that affect the CDKs and cyclins required for the passage of cancer cells through G1. Annexin V assay revealed that cycloguanil induced profound apoptosis in A549 cells. The lead molecules were also found to possess cytotoxicity profiles in MCF-7, A549, and HCT-116, which were reported to harbor the expression of EGFR. From the analysis, it was deduced that cycloguanil exhibited the most potent cytotoxicity towards the A549 cell with an IC50 of 6.83 μM, followed by HCT-116 with an IC50 of 9.32 μM, while in MCF-7, it exhibited an IC₅₀ of 14.82 μM. The lead molecule, cycloguanil, may plausibly serve as an important template that may be optimized by performing bioisosteric replacements, leading to a putative kinase inhibitor with a potent anticancer profile.

表皮生长因子受体（EGFR）是抗癌药物发现中一个经过验证的药物靶点。然而，EGFR中存在的耐药性、毒性和进化突变等问题导致了公认有效的抗EGFR治疗方法在全球范围内的下降。为了解决这一差距，药物再利用或重新定位是一种快速、经济的药物鉴定技术。本文采用了美国fda批准的3500个小分子库中的药物再利用技术。最初的HTVS（高通量虚拟筛选），随后的XP分析和分子力学（MMGBSA）以及ADME分析，导致环胍（抗疟疾）和二甲双胍（抗糖尿病）被认定为可能抑制EGFR的先导分子。对得分最高的配体进行了分子动力学模拟研究，以稳定环胍在EGFR ATP袋内的稳定性。生物学研究进一步证实了计算机研究。环胍尼抑制EGFR的IC50是厄洛替尼的一半，IC50为490 nM，而厄洛替尼的IC50为222 nM。除此之外，环胍能够在G1期停止细胞周期进程（46.54%），这是激酶抑制剂的一个特殊特征，它影响癌细胞通过G1所需的CDKs和细胞周期蛋白。膜联蛋白V检测显示环胍可诱导A549细胞深度凋亡。铅分子也被发现在MCF-7、A549和HCT-116中具有细胞毒性，据报道这些细胞含有EGFR的表达。结果表明，环胍对A549细胞的IC50为6.83 μM，对MCF-7细胞的IC50为14.82 μM，对HCT-116细胞的IC50为9.32 μM，对MCF-7细胞的IC50为14.82 μM。先导分子环胍可能是一种重要的模板，可以通过进行生物等构替代来优化，从而产生一种具有有效抗癌特性的激酶抑制剂。

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引用次数: 0

Computational assessment of clerodane-type furano-diterpenoids from Tinospora crispa: A potential source for anticancer lead compounds crispa Tinospora中氯罗丹型呋喃二萜的计算评估：抗癌先导化合物的潜在来源。

IF 3 4区生物学 Q2 BIOCHEMICAL RESEARCH METHODS

Journal of molecular graphics & modelling

Pub Date : 2026-01-31 DOI: 10.1016/j.jmgm.2026.109312

Juhaer Anjum , Sabiha Enam Spriha , Mir Sabit Hossain , S.M. Abdur Rahman

Tinospora crispa, a plant with widespread use in ethnomedicine, has several extracts as well as phytoconstituents that have been reported to possess anticancer properties. Clerodane-type furano-diterpenoids from this genus of plants show promise as anticancer agents, although only a few of these have been assayed in vitro. 38 clerodane-type furano-diterpenoids from T. crispa were assayed computationally against 13 common anticancer macromolecular targets. The assayed ligand library displayed higher binding affinities than the respective controls in six of the thirteen anticancer macromolecular targets. Binding affinity values that were higher than the respective controls were obtained for two ligands against BRCA1, for four against CDK9/Cyclin T1, for two against C-ROS1, for thirty-seven against EGFR, for three against MEK 1-kinase, and for one against STAT3. Many of these ligands displayed greater binding affinity values than the respective controls against multiple macromolecules. Notable among these are tinocrispide (against BRCA1, C-ROS1, EGFR and MEK1), tinosporol C (against CDK9/Cyclin T1 and MEK1-kinase), crispene E (against BRCA1 and CDK9/Cyclin T1) and (5R,6R,8S,9R,10R,12S)-15,16-Epoxy-2-oxo-6-O-(β-D-glucopyranosyl)-cleroda-3,13(16),14-trien-17,12-olid-18-oic acid methyl ester (against BRCA1 and EGFR). The top scoring compounds of each macromolecule were subjected to molecular dynamics simulations, and the obtained protein-ligand complexes were observed to be stable for all macromolecules except EGFR. The ligand library was mostly predicted to be soluble, but GI absorption was predicted to vary. A few were predicted to be carcinogenic, immunotoxic, and/or cytotoxic. Overall, the clerodane-type furano-diterpenoids from T. crispa show encouraging results in in-silico studies and may be considered for further modification and lead development.

crispa是一种在民族医学中广泛使用的植物，它有几种提取物和植物成分，据报道具有抗癌特性。从该属植物中提取的克罗丹型呋喃二萜显示出抗癌剂的前景，尽管只有少数已经在体外进行了试验。对38种氯罗丹型呋喃二萜对13种常见抗癌大分子靶点的作用进行了计算分析。在所分析的13个抗癌大分子靶点中，6个配体文库显示出比相应对照更高的结合亲和力。两种配体对BRCA1、四种对CDK9/Cyclin T1、两种对C-ROS1、37种对EGFR、三种对MEK 1-激酶和一种对STAT3的结合亲和力值均高于各自的对照。这些配体中的许多对多个大分子表现出比各自对照更大的结合亲和力值。其中值得注意的是tinocrispide（针对BRCA1， C- ros1， EGFR和MEK1）， tinosporol C（针对CDK9/Cyclin T1和MEK1激酶），crispenene E（针对BRCA1和CDK9/Cyclin T1）和(5R,6R,8S,9R,10R,12S)-15,16-环氧-2-氧-6- o- （β- d-葡萄糖吡喃基）-cleroda-3,13(16)，14-三烯-17,12-脂-18-酸甲酯（针对BRCA1和EGFR）。对每个大分子中得分最高的化合物进行分子动力学模拟，观察到所得的蛋白质配体复合物对除EGFR外的所有大分子都是稳定的。大多数的配体库预测是可溶的，但胃肠道吸收预测是不同的。一些被预测为致癌、免疫毒性和/或细胞毒性。总的来说，从crispa中提取的氯罗丹型呋喃二萜在计算机研究中显示出令人鼓舞的结果，可以考虑进一步的修饰和先导开发。

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引用次数: 0

In silico engineering of transaminase variants for enhanced biocatalytic conversion of an ACE inhibitor precursor 转氨酶变异体的硅工程以增强ACE抑制剂前体的生物催化转化

IF 3 4区生物学 Q2 BIOCHEMICAL RESEARCH METHODS

Journal of molecular graphics & modelling

Pub Date : 2026-01-27 DOI: 10.1016/j.jmgm.2026.109308

Mohammad Asad , Mohamed Usman , Anisha Ashokan, Naveen Kulkarni

Angiotensin-converting enzyme (ACE) inhibitors are widely prescribed for cardiovascular disorders, yet their conventional chemical synthesis involves multiple steps, high energy consumption, and poor stereoselectivity. In this work, we present a fully in silico framework for the computational design and prediction of transaminase (TA) variants capable of catalyzing the asymmetric amination of ethyl 2-oxo-4-phenylbutanoate (OPBE) to yield L-homophenylalanine ethyl ester (L-HPE), a key chiral intermediate in ACE inhibitor synthesis. A homology model of the Silicibacter transaminase (62.7 % identity to 5KR6) was constructed in its dimeric form. Eleven active-site variants were designed and screened through molecular docking, followed by 100 ns molecular dynamics simulations. The top variants SbTA10, SbTA01, and SbTA11 exhibited reactive distances below 6 Å, binding energies between −17.7 and −20.8 kcal/mol, and substrate RMSD values under 2.0 Å, indicating stable enzyme–substrate complexes. A composite QZ-score integrating productive conformations, binding energy, pocket contacts, and structural stability ranked SbTA10 highest (0.89), followed by SbTA01 (0.88) and SbTA11 (0.85). Free-energy profiles derived from umbrella sampling revealed binding minima of −10.2 kcal/mol (SbTA10) and −8.1 kcal/mol (SbTA11), suggesting distinct substrate retention characteristics that may influence catalytic turnover. Collectively, these results identify plausible transaminase variants with favorable structural and energetic features for the proposed OPBE to L-HPE transformation. This study presents a computational framework for predicting transaminase variants, providing a basis for rational biocatalyst design that warrants future experimental validation to confirm catalytic efficiency and stereoselectivity.

血管紧张素转换酶（ACE）抑制剂被广泛用于心血管疾病，但其传统的化学合成涉及多个步骤，高能量消耗，立体选择性差。在这项工作中，我们提出了一个全硅框架，用于计算设计和预测能够催化2-氧-4-苯基丁酸乙酯（OPBE）不对称胺化生成l -同苯丙氨酸乙酯（L-HPE）的转氨酶（TA）变体。l -同苯丙氨酸乙酯是ACE抑制剂合成中的关键手性中间体。以二聚体形式构建了硅酸菌转氨酶的同源性模型（与5KR6的同源性为62.7%）。通过分子对接设计筛选了11个活性位点变异，并进行了100ns分子动力学模拟。结果表明，SbTA10、SbTA01和SbTA11的反应距离小于6 Å，结合能在- 17.7和- 20.8 kcal/mol之间，底物RMSD值小于2.0 Å，表明酶-底物复合物稳定。综合生产构象、结合能、口袋接触和结构稳定性的综合qz得分，SbTA10最高（0.89），其次是SbTA01（0.88）和SbTA11（0.85）。伞式采样的自由能谱显示，结合最小值为- 10.2 kcal/mol （SbTA10）和- 8.1 kcal/mol (SbTA11)，表明不同的底物保留特性可能影响催化周转。总的来说，这些结果确定了具有有利的结构和能量特征的转氨酶变体，用于建议的OPBE到L-HPE的转化。本研究提出了一个预测转氨酶变异的计算框架，为合理的生物催化剂设计提供了基础，保证了未来的实验验证，以确认催化效率和立体选择性。

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引用次数: 0

Structure-based computational assessment of Bacopa monnieri-derived compounds as potential dual target anti-seizure medications: An integrated docking and molecular dynamics simulation approach 假马齿苋衍生化合物作为潜在双靶点抗癫痫药物的结构计算评估：一种集成对接和分子动力学模拟方法

IF 3 4区生物学 Q2 BIOCHEMICAL RESEARCH METHODS

Journal of molecular graphics & modelling

Pub Date : 2026-01-27 DOI: 10.1016/j.jmgm.2026.109309

Uttara Bakshi, Ashis Datta

Epilepsy remains a debilitating neurological disorder affecting approximately 50 million individuals worldwide. Current Anti-seizure medications (ASM) targeting Synaptic Vesicle Protein 2A (SV2A), such as levetiracetam, exhibit variable efficacy and adverse effect profiles, necessitating exploration of novel therapeutic approaches. This study investigates Bacopa monnieri-derived compounds as potential dual inhibitors of SV2A and Carbonic Anhydrase II (CA-II), two mechanistically distinct targets implicated in seizure pathophysiology. An integrated computational workflow comprising ADMET profiling, molecular docking, molecular dynamics (MD) simulations, and MM-GBSA binding free energy calculations was implemented to evaluate selected phytoconstituents. ADMET analysis revealed favourable pharmacokinetic parameters for several compounds, particularly Ebelin Lactone and Jujubogenin, with superior blood-brain barrier permeability (BBB >0.9) and human intestinal absorption (>95 %) compared to reference drugs. Molecular docking identified compelling binding affinities, with Ebelin Lactone (−11.2 kcal/mol) and Jujubogenin (−10.9 kcal/mol) exhibiting stronger interactions with SV2A than brivaracetam (−6.8 kcal/mol). Similarly, these compounds demonstrated robust binding to CA-II (−8.4 and −8.7 kcal/mol, respectively). Protein-ligand interaction profiler analysis elucidated key stabilizing interactions, including hydrogen bonds with Thr199 and His64 in CA-II and hydrophobic contacts within the SV2A binding pocket. MD simulations confirmed structural stability of the protein-ligand complexes, evidenced by equilibrated RMSD trajectories (0.2–0.3 nm). MM-GBSA calculations substantiated the thermodynamic favourability of these interactions, with binding free energies for top candidates significantly exceeding reference compounds. These findings establish an in silico framework for prioritizing Bacopa monnieri phytoconstituents as computationally predicted dual-target candidates, highlighting their potential relevance for seizure management, with the possibility of improved efficacy through simultaneous modulation of distinct pathophysiological mechanisms. All findings are based solely on in silico analyses and require experimental validation.

癫痫仍然是一种使人衰弱的神经系统疾病，影响全世界约5000万人。目前针对突触囊泡蛋白2A （SV2A）的抗癫痫药物（ASM），如左乙拉西坦，表现出不同的疗效和不良反应，需要探索新的治疗方法。本研究探讨假马齿苋衍生化合物作为SV2A和碳酸酐酶II （CA-II）的潜在双重抑制剂，这两个机制不同的靶点涉及癫痫病理生理。通过ADMET分析、分子对接、分子动力学（MD）模拟和MM-GBSA结合自由能计算等综合计算流程，对选定的植物成分进行评估。ADMET分析显示，与参比药物相比，几种化合物具有良好的药代动力学参数，特别是Ebelin内酯和Jujubogenin，具有优越的血脑屏障通透性（BBB >0.9）和人体肠道吸收（> 95%）。分子对接发现了令人信服的结合亲和性，Ebelin内酯（- 11.2 kcal/mol）和Jujubogenin （- 10.9 kcal/mol）与SV2A的相互作用强于布瓦西坦（- 6.8 kcal/mol）。同样，这些化合物与CA-II的结合能力很强（分别为- 8.4和- 8.7 kcal/mol）。蛋白质-配体相互作用分析阐明了关键的稳定相互作用，包括CA-II中与Thr199和His64的氢键以及SV2A结合袋内的疏水接触。通过平衡的RMSD轨迹（0.2-0.3 nm）， MD模拟证实了蛋白质-配体复合物的结构稳定性。MM-GBSA计算证实了这些相互作用的热力学优势，顶级候选化合物的结合自由能显著超过参考化合物。这些发现建立了一个计算机框架，优先考虑假马齿苋植物成分作为计算预测的双靶点候选物，突出了它们与癫痫发作管理的潜在相关性，并有可能通过同时调节不同的病理生理机制来提高疗效。所有发现仅基于计算机分析，需要实验验证。

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引用次数: 0

Significantly improved optoelectronic properties of WWC-103 engineered for efficient perovskite solar cells: A DFT approach 用于高效钙钛矿太阳能电池的WWC-103光电性能显著改善：DFT方法

IF 3 4区生物学 Q2 BIOCHEMICAL RESEARCH METHODS

Journal of molecular graphics & modelling

Pub Date : 2026-01-22 DOI: 10.1016/j.jmgm.2026.109300

Umer Yaqoob , Sidra Rafiq , Muhammad Zohaib Sabir , Ali Raza Ayub , Salba , Makhvela Anwer , Asma Parveen

Incorporating hole-transporting materials (HTMs) with optimal hole mobility and solution-processability is crucial for modifying effective materials of solar cells. In this investigation, we designed eight molecules with a D-A-type arrangement. The modified hole-transporting materials were studied using a quantum computation approach using density functional theory to found structural properties related to the electrochemical, charge transfer, quantum physical, solubility, and photovoltaic properties. The outcomes reveal that accepting fragments manifested hole-transport materials appropriate band alignment with deeper

E_{H O M O}

levels (ranging from −6.50 to −6.76 eV), higher absorption coefficients, remarkable solution processibility, and hole mobility with low exciton binding energy. These features revealed a higher photocurrent-generating ability, as estimated from transition density calculations across the molecular frameworks, a low charge-coupling estimated by the lower reorganization energy, and robust exciton dissociation. These notable outcomes unveiled that modified molecules are comparatively better than WWC-103 as HTMs for fabricating efficient material in the photovoltaic industry.

引入具有最佳空穴迁移率和溶液可加工性的空穴传输材料是改进太阳能电池有效材料的关键。在这项研究中，我们设计了8个d - a型排列的分子。利用量子计算方法，利用密度泛函理论对改性空穴输运材料进行了研究，发现了与电化学、电荷转移、量子物理、溶解度和光伏性能相关的结构特性。结果表明，接受碎片的空穴输运材料具有较高的EHOMO能级（−6.50 ~−6.76 eV）、较高的吸收系数、显著的溶液可加工性和低激子结合能的空穴迁移率。这些特征揭示了更高的光电流产生能力，正如通过分子框架的跃迁密度计算估计的那样，通过较低的重组能量估计的低电荷耦合，以及强大的激子解离。这些显著的结果表明，改性分子相对于WWC-103更适合作为光伏工业中制造高效材料的HTMs。

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引用次数: 0

ClathPLM: Deep multi-view feature extraction with CNN and attention enhances clathrin protein identification ClathPLM：基于CNN和注意力的深度多视图特征提取增强了网格蛋白的识别。

IF 3 4区生物学 Q2 BIOCHEMICAL RESEARCH METHODS

Journal of molecular graphics & modelling

Pub Date : 2026-01-21 DOI: 10.1016/j.jmgm.2026.109307

Shuxin Song, Yusen Su, Qingyang Guo, Taigang Liu

Clathrin is a key structural protein in intracellular vesicle transport, mainly mediating clathrin-mediated endocytosis (CME) through trimeric assembly. Its functional abnormalities are closely associated with various diseases, including neurodegenerative disorders, tumor metastasis, and immune system dysregulation. Traditional experimental methods for identifying the presence of Clathrin have limitations such as high cost and time consumption. Therefore, it is particularly urgent to develop efficient and reliable computational methods to assist in Clathrin recognition. In this study, we propose a model named ClathPLM, which integrates sequence embeddings from three pre-trained protein language models (PPLMs), i.e., ProtT5, ProtBert, and ESM-3, and performs deep representation learning on each feature through an independent branch composed of a convolutional neural network (CNN) and a multi-head Attention (MHA) mechanism, finally fusing the representations of the three views to accomplish the classification task. To validate the effectiveness of this design, we further examined variants of the fusion strategy and attention mechanism. Evaluation results show that ClathPLM demonstrates excellent overall classification performance and robustness, surpassing current state-of-the-art methods. Moreover, the model performs strongly on an additional case-study dataset and shows good scalability on an extra vesicular transport proteins (VTPs) dataset. We anticipate that ClathPLM may contribute to a deeper understanding of the role of Clathrin in cellular regulation and disease mechanisms, and facilitate future biological studies as well as potential clinical applications.

网格蛋白是细胞内囊泡运输的关键结构蛋白，主要通过三聚体组装介导网格蛋白介导的内吞作用（CME）。其功能异常与多种疾病密切相关，包括神经退行性疾病、肿瘤转移、免疫系统失调等。传统的检测网格蛋白存在的实验方法存在成本高、耗时长等局限性。因此，开发高效可靠的计算方法来辅助网格蛋白识别显得尤为迫切。在本研究中，我们提出了一个名为ClathPLM的模型，该模型整合了ProtT5、ProtBert和ESM-3三个预训练蛋白语言模型（pplm）的序列嵌入，并通过由卷积神经网络（CNN）和头部注意（MHA）机制组成的独立分支对每个特征进行深度表征学习，最终融合三种视图的表征来完成分类任务。为了验证这一设计的有效性，我们进一步研究了融合策略和注意机制的变体。评估结果表明，ClathPLM具有出色的整体分类性能和鲁棒性，超过了目前最先进的方法。此外，该模型在额外的案例研究数据集上表现良好，并在额外的囊泡转运蛋白（vtp）数据集上显示出良好的可扩展性。我们期待ClathPLM可以为更深入地了解Clathrin在细胞调节和疾病机制中的作用做出贡献，并促进未来的生物学研究和潜在的临床应用。

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引用次数: 0

Integrated experimental and DFT study of dielectric relaxation and optical properties in the chlorobenzene–n-butyl alcohol 氯苯正丁醇介电弛豫和光学性质的综合实验和DFT研究

IF 3 4区生物学 Q2 BIOCHEMICAL RESEARCH METHODS

Journal of molecular graphics & modelling

Pub Date : 2026-01-21 DOI: 10.1016/j.jmgm.2026.109305

Samir Azizov , Vusala Nabi Jafarova , Khayala Ajdar Hasanova

An integrated experimental and first-principles investigation was carried out to elucidate the dielectric relaxation and optical properties of the chlorobenzene–n-butyl alcohol binary system containing 0.25 vol fraction of alcohol. The real (ε′) and imaginary (ε″) parts of the complex dielectric permittivity were measured over microwave wavelengths λ = 2.14–37.9 cm and radio frequencies of 0.047–15 MHz in a wide temperature range from −40 °C to 100 °C. The dielectric spectra in the liquid phase reveal two well-defined Debye-type relaxation regions, which are assigned to the independent reorientation of chlorobenzene and n-butyl alcohol molecules, as well as an asymmetric dispersion near the liquidus–solidus interval that is satisfactorily described by the Davidson–Cole model and attributed to hydrogen-bonded alcohol clusters. These features indicate pronounced microheterogeneity and cluster formation governed by hydrogen bonding. Complementary density functional theory (DFT) calculations were performed to provide atomistic insight into the polarization mechanisms and electronic structure of the chlorobenzene–n-butyl alcohol complex. Optical properties were systematically investigated using both the GGA-PBE approach and the more advanced LDA-RPA framework, allowing assessment of polarization screening and collective excitation effects. The calculations predict a wide band gap of about 4–4.5 eV and reveal strong optical anisotropy in the dielectric function, refractive index, optical conductivity, reflectivity, and absorption spectra, with the dominant response along the hydrogen-bonded molecular axis. The onset of intense π→π∗ and n→σ∗ electronic transitions above 4 eV in both GGA-PBE and LDA-RPA spectra is consistent with the experimentally observed dielectric relaxation and absorption behavior. The close agreement between experimental dielectric measurements and DFT-based optical responses confirms that hydrogen-bond-assisted dipole alignment governs both dielectric relaxation and optical polarization. As a result, the chlorobenzene–n-butyl alcohol system can be classified as a low-loss, wide-band-gap dielectric material, making it a promising candidate for microwave resonators, optoelectronic coatings, and polarization-sensitive sensing applications.

采用实验和第一性原理相结合的方法，研究了含0.25 vol分数醇的氯苯-正丁醇二元体系的介电弛豫和光学性质。复介电常数的实部（ε′）和虚部（ε″）在微波波长λ = 2.14-37.9 cm和射频0.047-15 MHz范围内测量，温度范围为- 40°C至100°C。液相中的介电光谱显示了两个定义明确的debye型弛豫区，这两个弛豫区被分配给氯苯和正丁醇分子的独立重定向，以及在液相-固相区间附近的不对称弥散，这是由戴维森-科尔模型满意地描述的，归因于氢键醇簇。这些特征表明明显的微观非均质性和由氢键控制的团簇形成。利用互补密度泛函理论（DFT）计算了氯苯-正丁醇配合物的极化机制和电子结构。使用GGA-PBE方法和更先进的LDA-RPA框架系统地研究了光学性质，从而评估了偏振筛选和集体激发效应。计算结果表明，该材料具有约4-4.5 eV的宽带隙，在介电函数、折射率、光导率、反射率和吸收光谱等方面具有较强的光学各向异性，且主要沿氢键分子轴方向响应。在GGA-PBE和LDA-RPA光谱中，在4 eV以上发生π→π∗和n→σ∗的强烈电子跃迁与实验观察到的介电弛豫和吸收行为一致。实验电介质测量与基于dft的光学响应之间的密切一致证实了氢键辅助偶极子排列控制着介电弛豫和光偏振。因此，氯苯-正丁醇体系可以被归类为一种低损耗、宽带隙的介电材料，使其成为微波谐振器、光电涂层和偏振敏感传感应用的有前途的候选者。

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引用次数: 0

Green chemistry strategies for CO2 valorization: Impact of substituents, solvents and catalysts on the cycloaddition of CO2 with epoxides forming cyclic carbonates 二氧化碳增值的绿色化学策略：取代基、溶剂和催化剂对二氧化碳与环氧化物形成环状碳酸盐的环加成的影响。

IF 3 4区生物学 Q2 BIOCHEMICAL RESEARCH METHODS

Journal of molecular graphics & modelling

Pub Date : 2026-01-21 DOI: 10.1016/j.jmgm.2026.109306

Imen Ferchichi , Frédéric Guégan , Muneerah Mogren Al-Mogren , Majdi Hochlaf , Youssef Arfaoui

A theoretical study of the reaction forming a cyclic carbonate from the cycloaddition of CO₂ with a typical substituted epoxide, was carried out using first principles methodologies. As epoxide, we considered trans 1-(4-methoxyphenyl)-2-methoxy epoxyethane, exhibiting an optimal reactivity for cycloaddition with CO₂. We found that this reaction exhibits a high energy barrier in the gas phase, thus requiring an activation method. We also investigated the role of various substituted epoxides (mono- and disubstituted) and solvent types, including nonpolar, polar protic, and polar aprotic solvents. Our findings revealed a preference for polar protic solvents, particularly water. Besides, we used catalysts, including Lewis bases and Lewis acids, to selectively favor one reaction pathway over the other. In sum, this study provides deep insights into the factors influencing the reactivity of this cycloaddition and identifies the most suitable solvents and catalysts to promote the reaction, with potential implications for the development of more efficient CO₂ valorization processes.

采用第一性原理方法，对CO2与典型取代环氧化物环加成生成环状碳酸盐的反应进行了理论研究。作为环氧化物，我们考虑了反式1-（4-甲氧基苯基）-2-甲氧基环氧乙烷，它与CO2的环加成反应活性最佳。我们发现该反应在气相中表现出高能量势垒，因此需要激活方法。我们还研究了各种取代环氧化物（单取代和双取代）和溶剂类型的作用，包括非极性，极性质子和极性非质子溶剂。我们的发现揭示了极性质子溶剂的偏好，特别是水。此外，我们还使用了催化剂，包括路易斯碱和路易斯酸，来选择性地促进一种反应途径。综上所述，本研究深入了解了影响该环加成反应活性的因素，并确定了最适合促进该反应的溶剂和催化剂，对开发更高效的CO2增值工艺具有潜在的指导意义。

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引用次数: 0