Computational and Theoretical Chemistry最新文献

{"title":"Predicting inclusion free energy for clomiphene in HPβCD cyclodextrin using QC/MD approach","authors":"Hélio F. Dos Santos ,&nbsp;Cleber P.A. Anconi","doi":"10.1016/j.comptc.2025.115484","DOIUrl":"10.1016/j.comptc.2025.115484","url":null,"abstract":"<div><div>Low aqueous solubility has motivated the development of new formulations through complexation with β-cyclodextrins (βCD). In this study, the inclusion of clomiphene isomers (ECL and ZCL) into 2-hydroxypropyl-βCD (HPβCD) was investigated using a sequential approach combining molecular dynamics (MD) simulations for structural sampling with quantum computational (QC) calculations for free energy estimation. The experimental association constant and inclusion free energy (3838 M⁻¹; −4.836 kcal mol⁻¹) were satisfactorily reproduced by a weighted average over 2000 configurations (4267 M⁻¹; −4.90 kcal mol⁻¹). Beyond providing mechanistic insights into the inclusion process, this work extends the applicability of the QC/MD methodology to flexible systems with high association constants and examines the effect of two force fields (GAFF2 and GLYCAM06) on configurational sampling. The results highlight the importance of MD sampling prior to QC calculations, as docking followed by QC alone fails to yield reliable association constants.</div></div>","PeriodicalId":284,"journal":{"name":"Computational and Theoretical Chemistry","volume":"1254 ","pages":"Article 115484"},"PeriodicalIF":3.0,"publicationDate":"2025-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145044845","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":"Revealing the functional importance of tyrosine and tryptophan of human hemoglobin for development of structural templates representing protein microenvironment","authors":"Madhurima Chakraborty ,&nbsp;Nineesha Sen Banerjee ,&nbsp;Deborin Ghosh ,&nbsp;Prabuddha Bhattacharya ,&nbsp;Tapan Ganguly","doi":"10.1016/j.comptc.2025.115483","DOIUrl":"10.1016/j.comptc.2025.115483","url":null,"abstract":"<div><div>Microenvironment surrounding Tyrosine (Tyr) / Tryptophan (Trp) and heme appear to characterize the UV–vis absorption spectra of human hemoglobin (HHb). Structural elucidation of HHb using multiple tools, that may contribute to its spectral properties, then indicate greater structural stability of subunit A and the significance of its heme, Tyr42 and Trp14. Mutagenesis of Tyr42 and Trp14 of subunit A to Glycine (Gly) further validate their contribution in determining the structural stability, physicochemical properties, functional properties, and secondary structure of HHb. Accordingly, the use of structural coordinates of Tyr42 and heme as the first cluster and Trp14, Tyr42 and heme as the second cluster to represent the microenvironment of HHb is assessed for the first time. The calculated (DFT) absorption and FTIR properties of both the clusters are in well agreement with experimental absorption and FTIR characteristics of whole HHb suggesting prospective biomedical applications of these clusters.</div></div>","PeriodicalId":284,"journal":{"name":"Computational and Theoretical Chemistry","volume":"1254 ","pages":"Article 115483"},"PeriodicalIF":3.0,"publicationDate":"2025-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145044841","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":"Thermodynamic and structural insights into full-length amyloid-β42 dimerization using enhanced sampling and MD-based techniques","authors":"J. Kavitha ,&nbsp;K.S. Sindhu ,&nbsp;T.G. Abi","doi":"10.1016/j.comptc.2025.115486","DOIUrl":"10.1016/j.comptc.2025.115486","url":null,"abstract":"<div><div>Amyloid-β (Aβ) peptide aggregation into oligomers is a key pathological feature of Alzheimer's disease (AD). Of early aggregates, the Aβ dimer is the most basic neurotoxic species. Despite numerous computational studies that offer helpful information about the structural and energetic properties of Aβ dimers, comprehensive studies that integrate binding energetics with conformational dynamics of the full-length Aβ42 dimer under near-physiological conditions remain scarce. In the present work, we used molecular docking, molecular dynamics (MD), steered MD (SMD), and umbrella sampling (US) approaches to examine the different stages of full-length Aβ42 dimerization. The free energy of dimerization, predicted as −37.57 kcal/mol by the SMD-US method from crystallographic aggregate (PDB ID: <span><span>5OQV</span><svg><path></path></svg></span>), reflects thermodynamically favorable binding of monomer peptides. We also identified certain particular non-covalent interactions that stabilize the dimer structure and oligomerization process. These findings offer mechanistic insights into Aβ42 oligomerization and deepen our understanding of amyloid aggregation in AD.</div></div>","PeriodicalId":284,"journal":{"name":"Computational and Theoretical Chemistry","volume":"1254 ","pages":"Article 115486"},"PeriodicalIF":3.0,"publicationDate":"2025-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145044838","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 prediction of two-dimensional metal-hexahydroxybenzene frameworks as promising CO gas sensors","authors":"Shulei Wang ,&nbsp;Qian Wang ,&nbsp;Li Lv ,&nbsp;Yinfang Xu ,&nbsp;Yuanyuan Sun ,&nbsp;Changmin Shi ,&nbsp;Xiaolong Li ,&nbsp;Jianwei Zhao ,&nbsp;Hongmei Liu","doi":"10.1016/j.comptc.2025.115480","DOIUrl":"10.1016/j.comptc.2025.115480","url":null,"abstract":"<div><div>Two-dimensional (2D) metal-organic frameworks (MOFs) have been adopted in gas sensing due to their large surface area and abundant active sites. In this study, we performed density functional theory calculations to systematically investigate the gas sensing properties of 2D metal-hexahydroxybenzene frameworks (M₃(HHB)₂, where M represents V, Cr, Mn, Fe, Co, Ni, Cu, and Zn). Our results reveal that the eight M₃(HHB)₂ monolayers exhibit distinct responses to CO molecules. Specifically, the adsorption of CO on one surface of the films significantly increases the conductance of V₃(HHB)₂, Fe₃(HHB)₂, and Co₃(HHB)₂, with a conductance response exceeding 68 %. This is attributed to the reduction of the band gap in V₃(HHB)₂ and the transition of Fe₃(HHB)₂ and Co₃(HHB)₂ from half-metallic to metallic properties upon CO adsorption. In contrast, CO adsorption leads to a noticeable reduction in the conductance of Cr₃(HHB)₂, Mn₃(HHB)₂, Ni₃(HHB)₂, and Zn₃(HHB)₂ with a conductance response of more than −88 %. Cr₃(HHB)₂ and Ni₃(HHB)₂ monolayers change from metallic to half-metallic properties, while Mn₃(HHB)₂ and Zn₃(HHB)₂ transition from half-metallic to semiconducting properties upon CO adsorption. The current-voltage curves further confirm the high sensitivity of M₃(HHB)₂ to CO gas. Additionally, the desorption time of CO on Mn₃(HHB)₂, Ni₃(HHB)₂, and Zn₃(HHB)₂ is less than 1 × 10⁻⁵ s at room temperature, indicating their potential as reusable CO sensors. Our findings suggest that M₃(HHB)₂ films exhibit higher sensitivity when one surface of the nanosheet is exposed to CO gas, making them promising candidates for resistive CO gas sensors.</div></div>","PeriodicalId":284,"journal":{"name":"Computational and Theoretical Chemistry","volume":"1254 ","pages":"Article 115480"},"PeriodicalIF":3.0,"publicationDate":"2025-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145044839","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":"Charge-transfer cocrystal engineering of anthracene chalcone compound containing cyano group: DFT-guided modulation of solid-state optical properties","authors":"Wenhao Su ,&nbsp;Zhouyu Jiang ,&nbsp;Arshad Khan ,&nbsp;Rabia Usman ,&nbsp;Mingliang Wang","doi":"10.1016/j.comptc.2025.115465","DOIUrl":"10.1016/j.comptc.2025.115465","url":null,"abstract":"<div><div>The charge transfer (CT) cocrystal A4BTC of anthracene chalcone compound (α<em>Z</em>)-α-(9-Anthracenylmethylene)-4-pyridineacetonitrile (A4BCN) with 1,2,4,5-Benzenetetracarbonitrile (TCNB) was successfully constructed by supramolecular self-assembly technology. The cocrystal was formed based on π^…π interactions in the D^…A^…D mode was stacked in the solid state. The A4BCN acted as a donor (D) and the electron-deficient TCNB acted as an acceptor (A). The pure phase formation of the cocrystal was confirmed by PXRD and FT-IR analysis. Solid-state optical properties revealed that, in comparison with the donor, A4BTC exhibited a red-shifted UV absorption band of 75 nm and a 73 nm red-shifted fluorescence emission peak. Moreover, the emission quantum yield and fluorescence lifetime showed a remarkable increase. Specifically, the quantum yield was enhanced by a factor of 4.47, and the fluorescence lifetime was extended by 6.9 ns, significantly improving the fluorescence performance. Using Density Functional Theory, the weak intermolecular and π^…π interactions in A4BTC were analyzed based on the obtained SXRD crystal data, confirming the CT effect. It could also be inferred that the narrowing of the cocrystal's bandgap due to the CT effect induced a change in the transition dipole moment of the excited state. The change in the excited state dipole moment was directly correlated with the optical properties, thereby achieving the modulation of the optical properties. This study integrated theoretical calculations and experimental investigations, not only clarifying the mechanism by which π^…π stacking-mediated CT effect modulates optical properties, but also establishing a theoretical model for the development of high-performance tunable organic fluorescent materials.</div></div>","PeriodicalId":284,"journal":{"name":"Computational and Theoretical Chemistry","volume":"1254 ","pages":"Article 115465"},"PeriodicalIF":3.0,"publicationDate":"2025-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144997031","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":"Theoretical study of excited-state dynamics and pH detection of 2,2’-binaphthol chiral probes","authors":"Mingyue Xu ,&nbsp;Ruiqi Wu ,&nbsp;Yanliang Zhao ,&nbsp;Quanjiang Li ,&nbsp;Shenghui Chen ,&nbsp;Haiwen Wei ,&nbsp;Meishan Wang","doi":"10.1016/j.comptc.2025.115467","DOIUrl":"10.1016/j.comptc.2025.115467","url":null,"abstract":"<div><div>Chiral probes with excited state intramolecular proton transfer (ESIPT) show significant potential in bioimaging, environmental detection, etc. The chiral 2,2′-binaphthol derivative (<em>R</em>-BTOBD) probe demonstrates pH-dependent luminescence characteristics. In this paper, hydrogen bond dynamics, ESIPT process, and spectral attribution of <em>R</em>-BTOBD are investigated by the time-dependent density functional theory. Results show that the thermodynamically favored enol configuration undergoes charge transfer excitation, with photoinduced strengthening of the O<img>H⋯N hydrogen bond facilitating a near-barrierless ESIPT process. The protonation/deprotonation configurations of <em>R</em>-BTOBD and its spectra studies reveal its remarkable pH-response mechanism. This study provides theoretical guidance for the design of chiral probes.</div></div>","PeriodicalId":284,"journal":{"name":"Computational and Theoretical Chemistry","volume":"1254 ","pages":"Article 115467"},"PeriodicalIF":3.0,"publicationDate":"2025-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145020187","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":"Theoretical investigations on electronic structures and spectroscopic properties of the diatomic lithium bismuthide cation","authors":"Xin-Tong Wang ,&nbsp;Shi-Ying Yang ,&nbsp;Mei-Lin Xiong,&nbsp;Fei Xue,&nbsp;Yan Chen,&nbsp;Shan-Jun Chen,&nbsp;Song Li","doi":"10.1016/j.comptc.2025.115471","DOIUrl":"10.1016/j.comptc.2025.115471","url":null,"abstract":"<div><div>We report a systematic theoretical investigation of the diatomic cation LiBi⁺, which is a previously not studied computationally species. High-level ab initio calculations characterize its structural, electronic and spectroscopic properties, focusing on low-lying Λ-S states correlated with the five lowest dissociation limits. Using the icMRCI+Q method with extended basis sets, we have obtained potential energy curves, spectroscopic constants and vibrational energy levels of the cation. The spin-orbit coupling effect demonstrates significant influence on the cation's electronic structure. We further quantify transition properties such as Einstein coefficients and radiative lifetimes. Benchmark computations for neutral LiBi validate our theoretical approach for the cationic system. Simulated single photo-ionization process of LiBi→LiBi⁺+e offers direct guidance for spectroscopic detections. The information obtained from this work could shed some light on future experimental designs and theoretical investigations of diatomic LiBi⁺.</div></div>","PeriodicalId":284,"journal":{"name":"Computational and Theoretical Chemistry","volume":"1254 ","pages":"Article 115471"},"PeriodicalIF":3.0,"publicationDate":"2025-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145044842","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":"Covalent triazine framework (CTF-0) as a drug delivery system for anti-cancer drugs mercaptopurine and thiotepa: A DFT and MD simulation study on drug adsorption","authors":"Mubeen Naz ,&nbsp;Muhammad Yar ,&nbsp;Yasair S.S. Al-Faiyz ,&nbsp;Mohammed A. Alkhalifah","doi":"10.1016/j.comptc.2025.115468","DOIUrl":"10.1016/j.comptc.2025.115468","url":null,"abstract":"<div><div>This study explores the potential of CTF-0 as a nanocarrier for the anticancer drugs Mercaptopurine (MP) and Thiotepa (TEP) using density functional theory (DFT) and molecular dynamics (MD) simulations. Adsorption energies of −21.26 kcal/mol for MP and -22.28 kcal/mol for TEP indicate non-covalent stabilization, primarily through van der Waals interactions as confirmed by QTAIM and IGM based NCI analyses. EDA results reveal that electrostatic interactions are the major stabilizing contributors to binding. FMO analysis shows a reduced HOMO–LUMO gap in MP@CTF-0, supported by greater charge transfer and dipole moment, suggesting enhanced polarity and interaction in solvent. A 100 ns MD simulation further confirms the structural stability of MP@CTF-0. These findings highlight CTF-0's potential as an efficient carrier for Mercaptopurine in targeted drug delivery applications.</div></div>","PeriodicalId":284,"journal":{"name":"Computational and Theoretical Chemistry","volume":"1254 ","pages":"Article 115468"},"PeriodicalIF":3.0,"publicationDate":"2025-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145044844","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":"Theoretical investigation on enhancing quantum efficiency of TADF molecules through modulating substituent effects","authors":"Yanying Zhang ,&nbsp;Ziye Ning ,&nbsp;Yizi Meng ,&nbsp;Bowen Tang ,&nbsp;Lingling Lv","doi":"10.1016/j.comptc.2025.115466","DOIUrl":"10.1016/j.comptc.2025.115466","url":null,"abstract":"<div><div>Thermally activated delayed fluorescence (TADF) molecules with a Donor-Acceptor-Donor (D-A-D) architecture have attracted extensive attention by virtue of their widespread applications in organic light-emitting diodes (OLEDs). In this work, The time-dependent density functional theory (TD-DFT), combined with the path integral approach to dynamics considering the Herzberg-Teller effect, was employed to theoretically calculate the decay rates of the designed five molecules. Molecule II with meta-substituted has a high internal conversion rate, resulting in a significantly lower delayed fluorescence quantum efficiency compared to molecule I with para-substitute. Additionally, the introduction of weak electron-donating substituents on the acceptor unit effectively reduce the energy gap of the excited states and increase the spin-orbit coupling (SOC) constant, thereby enhancing the rates of intersystem crossing (ISC) and reverse intersystem crossing (RISC), which significantly improves the delayed fluorescence quantum efficiency. This research will contribute to the design of novel and highly efficient TADF materials.</div></div>","PeriodicalId":284,"journal":{"name":"Computational and Theoretical Chemistry","volume":"1254 ","pages":"Article 115466"},"PeriodicalIF":3.0,"publicationDate":"2025-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144988717","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":"The sensing mechanism of Rh3 doped GaSe monolayer toward SF6 decomposition products: A first-principle study","authors":"Guan Yongxin ,&nbsp;Wen Lei ,&nbsp;Chen Yao ,&nbsp;Wang Hong ,&nbsp;Huizhan Li","doi":"10.1016/j.comptc.2025.115464","DOIUrl":"10.1016/j.comptc.2025.115464","url":null,"abstract":"<div><div>In this work, By analyzing parameters such as adsorption energy, charge density, density of states, sensing response and recovery time, the adsorption performance and gas-sensing mechanism of each adsorption system were investigated. The results show that: the Rh₃-GaSe monolayer exhibited strong chemisorption behavior toward H₂S, SO₂ and SOF₂ gases because of the higher adsorption energies of −1.84, −2.85 and − 1.45 eV, respectively. Furthermore, significant changes occur in the electronic and optical characteristics of the Rh₃-GaSe monolayer following the adsorption of these gases, resulting in remarkable sensitivity of the Rh₃-GaSe monolayer in relation to electrical conductivity and optical absorption. Meanwhile, all of these gas adsorption systems exhibited extremely long recovery times. The aforementioned theoretical findings suggest that the Rh₃-GaSe monolayer has the potential to be an effective gas scavenger for the storage or removal of the SF₆ decomposition components.</div></div>","PeriodicalId":284,"journal":{"name":"Computational and Theoretical Chemistry","volume":"1254 ","pages":"Article 115464"},"PeriodicalIF":3.0,"publicationDate":"2025-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144988768","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}