Computational and Theoretical Chemistry最新文献

{"title":"Decoding peptide structures and structural stability via conformational ensemble searching","authors":"Zhifeng Li ,&nbsp;Xiao Ru ,&nbsp;Zijing Lin","doi":"10.1016/j.comptc.2026.115666","DOIUrl":"10.1016/j.comptc.2026.115666","url":null,"abstract":"<div><div>Computational prediction of peptide structures and conformational stability remains challenging due to their inherent structural flexibility. Existing ensemble sampling methods often lack accuracy or computational efficiency. In this study, we develop a robust computational framework for accurately predicting peptide structures and qualitatively assessing their conformational stability using kernel density estimation of the equilibrium free-energy landscape. We introduce an enhanced ensemble sampling strategy based on three-fragment splicing, replacing conventional two-fragment assembly. Validated across multiple short peptide systems, our method predicts experimental structures with accuracy comparable to AI-based techniques and surpasses pure force-field methods, and achieves superior conformational stability prediction over alternative ensemble sampling approaches. The results suggest that this work establishes a computationally efficient and accurate framework for peptide structure and structural stability prediction, offering significant promise for peptide engineering and rational drug design.</div></div>","PeriodicalId":284,"journal":{"name":"Computational and Theoretical Chemistry","volume":"1257 ","pages":"Article 115666"},"PeriodicalIF":3.0,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145923700","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Electronic and dynamic properties of N-doped LiFePO4 by first-principles calculations","authors":"DanYang Yu ,&nbsp;ZhiHua Zhang ,&nbsp;YuanZe Wei ,&nbsp;ZiYi He ,&nbsp;ShiYu Zhang ,&nbsp;JiaNan Wang","doi":"10.1016/j.comptc.2026.115687","DOIUrl":"10.1016/j.comptc.2026.115687","url":null,"abstract":"<div><div>First-principles calculations were performed to investigate the electronic structure and lithium-ion diffusion performance of nitrogen doped LiFePO₄. The configuration of the Li₈Fe₈P₈O₂₉N₃ had the smaller band gap (0.200 eV), which indicated the better electronic conductivity. The introduction of nitrogen would cause electrons to gather around iron ions, thereby attracting lithium ions and accelerating their local diffusion. On the other hand, the results of mean square displacement confirmed that lithium ion could diffuse in one-dimensional path in LiFePO₄ along the [010] direction. Doping nitrogen was able to reduce the energy barrier of diffusion to improve the diffusion of lithium ions. The diffusion coefficient and the diffusion rate of lithium ion were 2 orders of magnitude larger than the intrinsic system at most.</div></div>","PeriodicalId":284,"journal":{"name":"Computational and Theoretical Chemistry","volume":"1257 ","pages":"Article 115687"},"PeriodicalIF":3.0,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146023772","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Residual entropy of confined and interfacial monolayer water ice","authors":"Lien Le ,&nbsp;Hoan Nguyen","doi":"10.1016/j.comptc.2026.115660","DOIUrl":"10.1016/j.comptc.2026.115660","url":null,"abstract":"<div><div>Confined monolayer water exhibits a hexagonal ice phase with p6mm symmetry and intrinsic proton disorder. We derive an exact residual entropy for this phase by mapping its hydrogen-bond network to an integrable vertex model. Pairing inequivalent oxygen sites into effective four-coordinated vertices yields a five-vertex model with a dual six-vertex representation and exactly computable freeenergy density. When dangling OH bonds fluctuate among symmetry-equivalent orientations, additional degeneracies increase the residual entropy to <span><math><mfrac><mi>S</mi><msub><mi>k</mi><mi>B</mi></msub></mfrac><mo>=</mo><mn>0.820051</mn></math></span>. These results clarify how in-plane ice rules constrain the hydrogen-bond network, while out-of-plane dangling-bond fluctuations provide additional configurational degeneracy that governs disorder in interfacial and nanoconfined water.</div></div>","PeriodicalId":284,"journal":{"name":"Computational and Theoretical Chemistry","volume":"1257 ","pages":"Article 115660"},"PeriodicalIF":3.0,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145974358","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Computational investigation of curcumin–polymer interactions: a DFT–ML integrated framework for electronic structure and biodegradation analysis of PGA and PLA complexes","authors":"Mohammad Rizehbandi ,&nbsp;Hadise Nobakht ,&nbsp;Neda Jannesar ,&nbsp;Negar Yousefi","doi":"10.1016/j.comptc.2025.115641","DOIUrl":"10.1016/j.comptc.2025.115641","url":null,"abstract":"<div><div>Biodegradable polymers such as poly(glycolic acid) (PGA) and poly(lactic acid) (PLA) are widely used in biomedical applications due to their biocompatibility and tunable degradation behavior. Here, a combined Density Functional Theory (DFT) and Machine Learning (ML) framework is employed to investigate the structural and electronic properties of Curcumin–polymer complexes. Geometries were optimized at the B3LYP/6-311++G(d,p) level, and frontier-orbital descriptors were refined using ωB97X-D single-point calculations. ESP mapping shows that Curcumin–PGA exhibits a broader potential range than Curcumin–PLA, indicating stronger electrostatic polarization. FMO analysis reveals a pronounced contrast in electronic response: Curcumin–PGA displays a significantly reduced HOMO–LUMO gap (2.52 eV), whereas Curcumin–PLA retains a much larger gap (6.86 eV). AIM analysis confirms medium-strength hydrogen bonding. ML modeling, used qualitatively due to the small dataset, identifies ΔEgap and ESP range as dominant descriptors of degradation behavior. This integrated DFT–ML approach clarifies Curcumin–polymer interactions and supports rational design of biodegradable drug-delivery systems.</div></div>","PeriodicalId":284,"journal":{"name":"Computational and Theoretical Chemistry","volume":"1256 ","pages":"Article 115641"},"PeriodicalIF":3.0,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145836697","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Investigation of hydrogen storage capacity in 2D silicene polymorphs through physisorption and metal decoration – a first-principles study","authors":"S. Vijayalakshmi,&nbsp;V. Vijayapriya,&nbsp;M. Devibala,&nbsp;M. Sowmiya,&nbsp;M. Hema","doi":"10.1016/j.comptc.2025.115625","DOIUrl":"10.1016/j.comptc.2025.115625","url":null,"abstract":"<div><div>The hydrogen storage capacity analysis is done for the silicene polymorphs of low buckled silicene (LBS), trigonal dumbbell shaped silicene (TDS), honeycomb dumbbell shaped silicene (HDS) and large honeycomb dumbbell shaped silicene (LHDS). The 2 × 1 × 1 supercell of LBS, TDS, HDS, and LHDS are modelled and the hydrogen adsorption energy calculation is done. The physisorption and chemisorption analysis is made based on the adsorption energy calculation and the need of metal decoration is identified. Since none of the polymorphs exhibits physisorption Li decoration was done for the adsorption of H₂. It is found from the adsorption energy calculation that only the Li- decorated TDS alone favours the physisorption. From the electronic property analysis, it is interestingly to note that the physisorbed Li-decorated TDS exhibit the metallic behaviour whereas mon-physisorbed systems exhibit semiconducting behaviour with increased bandgaps upon hydrogenation.</div></div>","PeriodicalId":284,"journal":{"name":"Computational and Theoretical Chemistry","volume":"1256 ","pages":"Article 115625"},"PeriodicalIF":3.0,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145747791","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Acrolein detection in gaseous, aqueous, and oil phases through CaO, MgO, and BeO nanocages based on DFT","authors":"Khalid Mujasam Batoo ,&nbsp;Pawan Sharma ,&nbsp;Muhammad Farzik Ijaz ,&nbsp;Abhishek Kumar ,&nbsp;Syeda Wajida Kazmi ,&nbsp;Forat H. Alsultany ,&nbsp;Iman Samir Alalaq ,&nbsp;Ruaa Sattar ,&nbsp;Munthir Abdulwahid Abdulhussain ,&nbsp;Merwa Alhadrawi","doi":"10.1016/j.comptc.2025.115594","DOIUrl":"10.1016/j.comptc.2025.115594","url":null,"abstract":"<div><div>This paper reports a Density Functional Theory (“DFT”) assessment of “CaO”, “MgO”, and “BeO” nanocages for acrolein (“AC”) detection, analyzing various adsorption configurations and Frontier Molecular Orbital (“FMO”) variations. The calculated interaction strength follows the order “AC”@”CaO\" &gt; “AC”@”MgO\" &gt; “AC”@”BeO\". Electrical conductivity analysis reveals that the “BeO” nanocage possesses the maximum conductivity, surpassing “MgO” and “CaO”. The optimization of “AC” desorption recovery time was also performed. Crucially, the analysis of complexes in different media demonstrated that structural stability is significantly higher in aqueous media (ΔG_W analysis) compared to the oily phase (ΔG_O), confirming efficient capture across gaseous, aqueous, and oily phases. The investigation of “HOMO-LUMO\" levels and the energy gap further substantiates the viability of these oxide nanocages as high-performance sensors for toxic “AC” molecules.</div></div>","PeriodicalId":284,"journal":{"name":"Computational and Theoretical Chemistry","volume":"1256 ","pages":"Article 115594"},"PeriodicalIF":3.0,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145747792","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"First principles study on mechanical and electronic properties of high pressure phases of 2D black phosphorus and their titanium-doped systems","authors":"Jinchao Qiao ,&nbsp;Qiang Zhou ,&nbsp;Fan Bai ,&nbsp;Rufei Qiao ,&nbsp;Zhuwen Lyu ,&nbsp;Longhai Zhong ,&nbsp;Junbo Yan ,&nbsp;Peng Si","doi":"10.1016/j.comptc.2025.115628","DOIUrl":"10.1016/j.comptc.2025.115628","url":null,"abstract":"<div><div>Two-dimensional (2D) black phosphorus (BP), as a representative layered van der Waals (vdW) material, exhibits unique polymorphic transitions under high pressure, which lays the foundation for its functional regulation. This study systematically investigates the mechanical, electronic, and bonding evolution mechanisms of high pressure phases (orthorhombic, rhombohedral, cubic) of 2D BP and their titanium (Ti)-doped systems through first principles calculations, aiming to fill the gap in the property modulation of 2D layered BP under extreme conditions. Using the VASP 6.4.3 platform, Ti-doped BP models with a Ti:P atomic ratio of 1:20 were constructed based on the three high pressure phases. Geometric optimization was performed via PAW pseudopotentials and PBE-GGA functionals, incorporating DFT-D3 corrections to accurately describe interlayer vdW interactions—an essential feature of layered 2D materials. Elastic constant calculations confirm that all Ti-doped high pressure phase structures satisfy the mechanical stability criteria of their respective crystal systems, with the cubic phase showing the most significant enhancement in Young's modulus (reaching 78.62 GPa after doping). Band structure analysis reveals phase dependent electronic reconstruction characteristics of this 2D layered system: Ti doping induces bandgap narrowing (from 0.82 eV to 0.70 eV) in the orthorhombic phase, a semimetal to metal transition in the rhombohedral phase, and optimized carrier mobility via sp³-d orbital hybridization in the cubic phase. Three-dimensional charge differential density reconstructions, combined with Bader charge analysis, further decode Ti-driven bonding evolution in the 2D lattice: strong covalent Ti<img>P bonds in the orthorhombic phase, distinct ionic characteristics in the rhombohedral phase, and dominant delocalized metallic bonds in the cubic phase. The established “doping-lattice symmetry-bonding” multiscale model for 2D BP provides theoretical guidance for tailoring the performance of BP-based 2D functional materials in high temperature electronic devices and flexible sensor systems</div></div>","PeriodicalId":284,"journal":{"name":"Computational and Theoretical Chemistry","volume":"1256 ","pages":"Article 115628"},"PeriodicalIF":3.0,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145747795","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Rational molecular design of star-shaped small molecule donors based on BODIPY for high-performance organic solar cells applications","authors":"Xinhao Zhang,&nbsp;Wenmin Xiao,&nbsp;Jingfan Xin,&nbsp;Ruifa Jin","doi":"10.1016/j.comptc.2025.115629","DOIUrl":"10.1016/j.comptc.2025.115629","url":null,"abstract":"<div><div>A series of novel star-shaped small molecule donors with boron dipyrromethene (BODIPY) as core and different styryl aromatic groups as arm groups have been proposed to apply in organic solar cells (OSCs). Their optoelectronic and charge transport properties have been systematically investigated by theoretical approaches. It turns out that their optoelectronic properties can be affected by the styryl aromatic arm groups. The designed molecules exhibit suitable frontier molecular orbitals (FMOs) energy levels to match well with those of typical fullerene acceptors PC₆₁BM and PC₇₁BM. The designed molecules show strong absorption and fluorescence spectra in near-infrared region (NIR) and good photovoltaic performance, thereby improving the efficiency of OSCs. Furthermore, the studied molecules possess large hole mobility. Our results suggest that the designed molecules are expected to be the promising donors and hole transporting materials for high-performance OSCs. This work provides a rational strategy for design of multifunctional promising candidates for OSCs.</div></div>","PeriodicalId":284,"journal":{"name":"Computational and Theoretical Chemistry","volume":"1256 ","pages":"Article 115629"},"PeriodicalIF":3.0,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145748298","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Temperature-dependent decomposition mechanism of a hot DNP/DNTF liquid eutectic model: Molecular-level insights from SCC-DFTB calculations","authors":"Yahong Chen ,&nbsp;Zixuan Yang ,&nbsp;Fangfang Hou ,&nbsp;Shuangfei Zhu ,&nbsp;Ruijun Gou ,&nbsp;Shuhai Zhang","doi":"10.1016/j.comptc.2025.115650","DOIUrl":"10.1016/j.comptc.2025.115650","url":null,"abstract":"<div><div>Self-consistent charge density functional tight-binding (SCC-DFTB) molecular dynamics simulations were employed to study the initial thermal decomposition mechanisms of 3,4-dinitro-1H-pyrazole (DNP) and 3,4-dinitrofurazanfuroxan (DNTF) eutectic mixture. Different from ordered and disordered models, the eutectic system exhibits unique decomposition behaviors. N<img>O bond cleavage of DNTF predominates and increases with temperature, followed mainly by furoxan ring opening via C<img>C breakage. N<img>N bond rupture of DNP prevails, and pyrazole ring opening shifts to N<img>N bong cleavage. Notably, DNTF decomposes more readily, while DNP reactivity lies intermediately. The eutetic system also exhibited significantly distinct decomposition product characteristics compared to both ordered and disordered models. The typical cleavage products of DNP and DNTF in the eutetic model were analyzed to revealed the thermal decomposition mechanism under different molecular stacking patterns. These results elucidate the synergy between molecular packing and temperature in governing decomposition mechanisms, advancing the understanding of sensitivity and thermal behavior in energetic materials.</div></div>","PeriodicalId":284,"journal":{"name":"Computational and Theoretical Chemistry","volume":"1256 ","pages":"Article 115650"},"PeriodicalIF":3.0,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145880324","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Study on the influence of functional groups on coal surface wettability based on density functional theory, gran canonica monte caro, and moecular dynamics","authors":"Jinzhang Jia ,&nbsp;Chaoyang Li ,&nbsp;Peng Jia ,&nbsp;Fengxiao Wang","doi":"10.1016/j.comptc.2025.115622","DOIUrl":"10.1016/j.comptc.2025.115622","url":null,"abstract":"<div><div>To elucidate the wetting mechanisms of different functional groups at the molecular scale, this study systematically investigated the interaction mechanisms between 11 functional groups in coal and water using Density Functional Theory (DFT), Gran Canonica Monte Caro (GCMC), and Moecular Dynamics (MD) simulation methods. The study reveals that functional group polarity can be quantitatively distinguished by electrostatic potential maxima. As the sole bipolar functional group, the carboxyl group exhibits both strong donor and acceptor characteristics. It forms the strongest adsorption through C=O…H and O-H…O double hydrogen bonds, demonstrating superhydrophilicity. Front-line orbital analysis revealed that hydrophilic functional groups possess lower LUMO energy levels and higher electrophilic power, facilitating electron acceptance from water molecules. RDF analysis indicated that hydrophilic functional groups exhibit lower surface water molecule aggregation, promoting spreading. This study employs multiscale simulations to elucidate the mechanism by which functional groups influence coal wettability, providing precise theoretical foundations and design guidance for optimizing coal processing through surface functional group design.</div></div>","PeriodicalId":284,"journal":{"name":"Computational and Theoretical Chemistry","volume":"1256 ","pages":"Article 115622"},"PeriodicalIF":3.0,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145691223","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}