Computational and Theoretical Chemistry最新文献

{"title":"Mechanism study on quantitative adsorption of dioxin-like pollutants by pillar[6]arene and thiapillar[6]arenes","authors":"Xinmeng Zhao ,&nbsp;Yuke Zuo ,&nbsp;Wanting Wang ,&nbsp;Maoxia He ,&nbsp;Ju Xie","doi":"10.1016/j.comptc.2025.115606","DOIUrl":"10.1016/j.comptc.2025.115606","url":null,"abstract":"<div><div>Dioxins, as a class of persistent organic pollutants (POPs), pose a great danger to human health and the environment. This study proposed the use of pillar[6]arene (P6) and thiapillar[6]arene analogues (P6Ss), namely P6S, P6SO, and P6SO₂, as a kind of high-efficient adsorbent material for dioxin pollutants. P6 and P6Ss as the host molecules, polychlorinated dibenzo-p-dioxins (pCDD) as the guest molecules, and their 1:1 inclusion complexes have been studied systematically using density functional theory (DFT) calculations at the ωB97XD/6-311G(d,p) level of theory. The geometrical structures and electronic structures of P6 and P6Ss were significantly diversified by different bridging groups between two aromatic rings. Based on the spatial matching of molecular cavities and the complementarity of electronic properties, P6 and P6Ss were favorable for the formation of 1:1 inclusion complexes with dioxin molecules, mainly driven by π–π stacking, H-bonding, and van der Waals interactions. P6 and P6SO₂ exhibited strong host–guest interactions with TCDD and H₆CDD, respectively. Subsequently, molecular dynamics (MD) simulations showed that both crystalline and non-crystalline aggregates of P6 and P6Ss were able to capture pCDDs with a 1:1 stoichiometric ratio and maintain the dynamic equilibrium state. These findings indicated that pillar[<em>n</em>]arene analogues are expected to be a new solution for dioxin control.</div></div>","PeriodicalId":284,"journal":{"name":"Computational and Theoretical Chemistry","volume":"1256 ","pages":"Article 115606"},"PeriodicalIF":3.0,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145691229","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":"Mechanistic and Regioselective insights into thermal and ruthenium (II)-catalyzed (3 + 2) cycloadditions of nitrile N-oxide with internal thioalkyne: a combined on Isoxazole derivatives, molecular docking, ADMET approach, MD and PASS simulations from the MEDT perspective","authors":"Raghad Mowafak Al-Mokhtar ,&nbsp;Haydar Mohammad-Salim ,&nbsp;Muheb Algso","doi":"10.1016/j.comptc.2025.115601","DOIUrl":"10.1016/j.comptc.2025.115601","url":null,"abstract":"<div><div>This study investigates uncatalyzed and ruthenium (II)-catalyzed (3 + 2) cycloaddition (32CA) reactions between nitrile N-oxide and internal thioalkyne using the M06-2×-D3 level of theory.The def2-TZVPD basis set was employed for Ru atoms, and 6-311G(d,p) for all others. Uncatalyzed pathways toward 1,4- and 1,5-isoxazole regioisomers exhibited comparable Gibbs free energies (−65.7 and − 60.3 kcal·mol⁻¹), indicating minimal regioselectivity, consistent with experimental observations. Ru(II) catalysis significantly enhanced regioselectivity by modulating electronic structures and bonding evolution. ELF and CDFT analyses confirmed the zwitterionic character of nitrile N-oxide and electron density transfer from thioalkynes. GEDT values revealed low-polarity thermal pathways versus more polar Ru-catalyzed ones.BET supported a stepwise mechanism in uncatalyzed reactions and catalyst-dependent modulation in Ru(II)-mediated systems.Molecular docking against MCF-7 protein(PDB: <span><span>3ERT</span><svg><path></path></svg></span>)indicated moderate binding affinities (−9.3 and − 9.7 kcal·mol⁻¹) compared to the reference ligand (−13.1 kcal·mol⁻¹). ADMET, toxicity,MD simulations, and PASS predictions suggest favorable pharmacokinetic and anticancer potential for both regioisomers,underscoring their mechanistic and biological relevance.</div></div>","PeriodicalId":284,"journal":{"name":"Computational and Theoretical Chemistry","volume":"1256 ","pages":"Article 115601"},"PeriodicalIF":3.0,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145691222","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":"Comparison of the carboxylic acid and ester anchoring groups in pyrene-based sensitizers in DSSC: A computational investigation","authors":"Vandana Kumari Shukla,&nbsp;Nagaiyan Sekar","doi":"10.1016/j.comptc.2025.115648","DOIUrl":"10.1016/j.comptc.2025.115648","url":null,"abstract":"<div><div>Sixteen donor-pi-acceptor (D-π-A) type sensitizers, which consist of pyrene as the donor unit coupled to various spacers and acceptor units, are investigated using density functional theory (DFT) and time dependent DFT (TD-DFT) techniques. The effects of substituting an ester group for carboxylic acid as acceptor on the system are investigated. The addition of ester causes the destabilization of the lowest unoccupied molecular orbital (LUMO) and highest occupied molecular orbital (HOMO) of the sensitizers. In carboxylic acid acceptor-based sensitizers, the frontier molecular orbital (FMO) also illustrates an efficient intramolecular charge transfer (ICT) from the donor unit to the acceptor unit. Additionally, it is observed that ester acceptor-based sensitizers have higher computed open circuit voltage (Voc) values. According to the TD-DFT investigation, the acid acceptor-based sensitizers exhibit red-shifted vertical excitation. A positive solvatochromism is seen for all the sensitizers in TD-DFT calculations. The excited state dipole moment of acid acceptor-based sensitizer, calculated using Suppan's equation, is found to be more than the ester acceptor-based sensitizers. For the furan spacer based sensitizers with double bond between donor and spacer the following result is obtained- dipole moment moment in Debye (8.2: acid and 6.4: ester), HOMO-LUMO energy gap in eV (2.5: acid and 2.6: ester), electrophilicity index in eV (6.8: acid and 6.3: ester), hyperhardness in eV (1.7: acid and 1.8: ester) and absorption maxima in THF in nm (583: acid and 572: ester) in B3LYP functional.</div></div>","PeriodicalId":284,"journal":{"name":"Computational and Theoretical Chemistry","volume":"1256 ","pages":"Article 115648"},"PeriodicalIF":3.0,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145938347","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":"Adsorption of NH3 on TiN and Si3N4 surfaces: A theoretical study","authors":"Jae Min Jang,&nbsp;Sujin Kwon,&nbsp;Ju Hyeon Jung,&nbsp;Bonggeun Shong","doi":"10.1016/j.comptc.2025.115636","DOIUrl":"10.1016/j.comptc.2025.115636","url":null,"abstract":"<div><div>The adsorption and desorption reactions of NH₃ on two technologically important materials, TiN and Si₃N₄, are compared using a computational chemistry approach based on density functional theory (DFT) calculations. We confirm that TiN remains essentially pristine without NH₃-related adsorbates for a wide range of temperatures, whereas the Si₃N₄ surface is mostly functionalized by the NH_3-derived groups. This study provides theoretical insights for predicting surface chemical properties and NH₃ adsorption behavior across different nitride substrates.</div></div>","PeriodicalId":284,"journal":{"name":"Computational and Theoretical Chemistry","volume":"1256 ","pages":"Article 115636"},"PeriodicalIF":3.0,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145796686","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":"DFT study on hydrogen adsorption behaviour of armchair and sawtooth structure cup-stacked carbon nanotube walls with B-substituted and Pt-decorated","authors":"Zhitong Xu,&nbsp;Tingbo Liao,&nbsp;Yinquan Sui,&nbsp;Huanpeng Liu","doi":"10.1016/j.comptc.2025.115587","DOIUrl":"10.1016/j.comptc.2025.115587","url":null,"abstract":"<div><div>The hydrogen storage properties of Cup-Stacked Carbon Nanotubes (CSCNTs), which are sawtooth-shaped and armchair-shaped structures with B atom substitutions at different spacings and loaded with Pt atoms, were investigated using density functional theory. The results show that when the spacing of the B atoms is small, the Pt atoms still tend to form clusters due to the interatomic gravitational force between the Pt atoms, which is larger than the attraction between the Pt atoms and the C/B atoms. For the sawtooth-shaped structure, B-atom spacing greater than 7.3 Å, with stabilised isolated Pt atoms loading, and the maximum hydrogen adsorption capacity. In addition, electrostatic potentials, electron localisation function and Weak interaction analysis investigated the mechanism of Pt atom loading. The HOMO-LUMO orbitals and energy gap of the two structures are also compared, and it is found that the armchair-shaped structure has a larger energy gap and a more stable electronic structure.</div></div>","PeriodicalId":284,"journal":{"name":"Computational and Theoretical Chemistry","volume":"1256 ","pages":"Article 115587"},"PeriodicalIF":3.0,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145622402","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 of hydrogen adsorption energy and preferred storage site in MgNi alloys","authors":"Huan Wang ,&nbsp;Changli Shi ,&nbsp;Zihe Cao ,&nbsp;Xiaolu Chen ,&nbsp;Qiguo Zhang ,&nbsp;Gangjun Gong ,&nbsp;Qiang Lu ,&nbsp;Xinhua Yuan ,&nbsp;Bing Zhang","doi":"10.1016/j.comptc.2025.115600","DOIUrl":"10.1016/j.comptc.2025.115600","url":null,"abstract":"<div><div>Mg<img>Ni alloys are promising candidates for hydrogen storage materials due to their significant potential in sustainable energy technologies. However, accurately predicting hydrogen adsorption energies and identifying optimal storage sites remain critical challenges. This study evaluates the performance of two DFT exchange-correlation functionals (PBE and SCAN) and assesses the effects of Hubbard U correction and van der Waals interaction on Mg<img>Ni alloys. The results demonstrate that SCAN significantly outperforms PBE in predicting hydrogen adsorption energies due to its consideration of orbital kinetic energy density. Variations in the contributions of Hubbard U and vdW interactions are observed across different storage sites. Based on parameters such as volume change rate, adsorption energy, Ni<img>H bond length and ICOHP, the H2 site is identified as the preferred storage site. These findings highlight the importance of theoretical parameters in optimizing Mg<img>Ni alloy systems, providing insights for advancing efficient hydrogen storage materials and supporting sustainable energy technologies.</div></div>","PeriodicalId":284,"journal":{"name":"Computational and Theoretical Chemistry","volume":"1256 ","pages":"Article 115600"},"PeriodicalIF":3.0,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145691225","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":"Inerting mechanism of CO2 and N2 on the oxidative reaction of active groups in coal","authors":"Qihui Bai ,&nbsp;Xihua Zhou ,&nbsp;Gang Bai ,&nbsp;Fei Gao","doi":"10.1016/j.comptc.2025.115618","DOIUrl":"10.1016/j.comptc.2025.115618","url":null,"abstract":"<div><div>To investigate the influence of CO₂ and N₂ on the oxidative reaction of coal, a combined method of molecular dynamics and quantum chemical calculation was applied to infer the reaction paths of side chain and bridge bond active groups in coal with ·OH and O₂ during low-temperature oxidation. The activation stages of chemical reactions involving active groups were divided. The inerting mechanism of CO₂ and N₂ on the oxidative reaction of active groups in coal was revealed from the physical adsorption, chemical adsorption, and chemical reaction stages of coal oxidation. The results showed that before CO₂ and N₂ interacted with the active groups, CO₂ effectively hindered the physical and chemical adsorption processes of the active groups on O₂ by virtue of its strongly competitive adsorption characteristics, while having no significant effect on ·OH. In contrast, N₂ showed no substantial interference with either the physical or chemical adsorption stages of the active groups. After van der Waals interactions with the active groups, both CO₂ and N₂ could inert the chemical adsorption of the active groups with ·OH and O₂, and the inerting effect of CO₂ on the chemical adsorption of the active groups was approximately more than twice that of N₂. The chemical reactions of active groups could be subdivided into three activation stages. Stage I was the activation of cyclic chain reactions between active groups and free radicals under room-temperature conditions. Stages II and III were the activation of composite reactions between active groups and O₂ at 30–70 °C and 70–200 °C, respectively. The influence of CO₂ on the activation stages I, II, and III showed a change rule of “inhibition-promotion-inhibition,” while N₂ had a significant promotional effect on the three activation stages. The inerting effect of CO₂ on the chemical reactions of active groups consistently outperformed that of N₂ throughout the entire low-temperature oxidation process. The study results will offer an important basis for refining the fundamental theory of fire prevention and control technology using inert gases in coal mines.</div></div>","PeriodicalId":284,"journal":{"name":"Computational and Theoretical Chemistry","volume":"1256 ","pages":"Article 115618"},"PeriodicalIF":3.0,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145691179","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":"Assessment of GFN-FF and GFN2-xTB methods for binding free energy calculations: Application to cucurbit[7]uril-cationic guest complexes","authors":"Wissam Helal","doi":"10.1016/j.comptc.2025.115605","DOIUrl":"10.1016/j.comptc.2025.115605","url":null,"abstract":"<div><div>The performance of two cost-efficient computational methods, the semiempirical extended tight-binding GFN2-xTB and the GFN-FF force field, was assessed for predicting the binding free energies of cucurbit[7]uril host–guest complexes with a series of cationic ammonium guests. Binding energies were computed via the supermolecular approach and decomposed into gas-phase interaction, thermostatistical, and solvation components. Both methods reproduce the general energetic trends of experimental binding affinities, with GFN-FF yielding lower mean absolute errors and standard deviations. However, the GFN2-xTB geometries are consistently closer to high-level DFT reference structures. The results indicate that while GFN-FF offers substantial computational efficiency and acceptable accuracy for screening purposes, its apparent energetic agreement may arise partly from error cancellation rather than superior physical description. The study also highlights the limitations of the single-structure supermolecular approach, particularly for flexible host–guest systems, where conformational sampling are required for a quantitatively reliable description of binding thermodynamics.</div></div>","PeriodicalId":284,"journal":{"name":"Computational and Theoretical Chemistry","volume":"1256 ","pages":"Article 115605"},"PeriodicalIF":3.0,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145691180","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":"Structural ensemble modeling of FRET and electron transfer rates in surface-bound molecular bilayers","authors":"Jackson Nolder,&nbsp;Kenneth Hanson","doi":"10.1016/j.comptc.2025.115633","DOIUrl":"10.1016/j.comptc.2025.115633","url":null,"abstract":"<div><div>The assembly of multiple chromophores, catalysts, and redox active molecules on inorganic surfaces is of interest for applications including solar energy conversion, catalysis, and sensing. These applications typically rely on intermolecular electron and energy transfer which, in addition to energetics, are dictated by the structure of the assembly. Here we introduce a software package with a user-friendly graphical user interface (GUI) that calculates interlayer FRET and electron transfer rates for all reasonable structures of surface-bound molecular bilayers. The graphical output illustrates the energy and electron transfer rates with respect to measurable structural parameters, as well as a vector depiction of the possible bilayer structure with the fastest energy and electron transfer rates. We include a few use cases that demonstrate the effects of varying the metal linking ion and solvent on energy and electron transfer rates in metal ion linked bilayers. While our focus is primarily on metal ion linked systems, we show how, with minor input modification, this software can be applied to covalently linked dyads or other bilayer assemblies on surfaces.</div></div>","PeriodicalId":284,"journal":{"name":"Computational and Theoretical Chemistry","volume":"1256 ","pages":"Article 115633"},"PeriodicalIF":3.0,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145836693","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":"Adsorption and sensing of vildagliptin on coinage metal nanoclusters: DFT, MD and spectroscopic insights","authors":"Jamelah S. Al-Otaibi ,&nbsp;Y. Sheena Mary ,&nbsp;Vasudevan Baiju ,&nbsp;K. Jalaja ,&nbsp;Maria Cristina Gamberini","doi":"10.1016/j.comptc.2025.115640","DOIUrl":"10.1016/j.comptc.2025.115640","url":null,"abstract":"<div><div>This work presents a focused computational investigation of how the anti-diabetic drug vildagliptin (VGP) interacts with small coinage-metal clusters (Ag₃, Au₃ and Cu₃) and the implications of those interactions for sensing and nanoscale delivery. Adsorption is exothermic for all metal-drug combinations, with adsorption energies in vacuum roughly spanning −15.7 to −33.5 kcal mol⁻¹ (Ag₃ ≈ −15.7 to −21.4; Au₃ ≈ −21.3 to −33.5; Cu₃ ≈ −25.3 to −31.5), and stronger binding in water (largest for the NH-site complexes, e.g., Au₃-VGP3 ≈ −52.7 kcal mol⁻¹). The energy-gap decreases (∆Eg) and DOS changes indicate increased conductivity upon adsorption – a desirable feature for electrochemical sensing – while computed Raman/IR shifts and SERS-relevant enhancements support spectroscopic detectability. MD and docking show that VGP and Au₃-complexes tend to preserve protein structural stability, whereas Ag₃ and especially Cu₃ complexes can induce greater conformational perturbation.</div></div>","PeriodicalId":284,"journal":{"name":"Computational and Theoretical Chemistry","volume":"1256 ","pages":"Article 115640"},"PeriodicalIF":3.0,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145796687","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}