Journal of Computational Chemistry最新文献

{"title":"Magnetic Exchange Interactions: Mechanistic Insights and Understanding Orbital Influences in Organic Diradicals","authors":"Chumuiria Debbarma,&nbsp;Debojit Bhattacharya,&nbsp;Suranjan Shil","doi":"10.1002/jcc.70230","DOIUrl":"10.1002/jcc.70230","url":null,"abstract":"<div>\u0000 \u0000 <p>Frontier molecular orbitals play a crucial role in determining the magnetic behavior and exchange interactions in organic radicals. In this study, we investigate the underlying mechanism influencing the need for orbital planarity and the role of frontier orbital overlap in magnetic exchange interactions. To study this, we designed a series of 12 polyacene-coupled triarylmethyl diradicals, systematically increasing in length of polyacene. We have used nine different DFT functionals for the calculation of the magnetic exchange coupling constant (<i>J</i>). The calculation of magnetic exchange coupling reveals that the GGA functionals define a more accurate spin state, hence more correct magnetic behavior than the meta-GGA and hybrid functionals. We have studied the effect of orbital orientation and their energy gap to understand the high magnetic exchange coupling in the higher polyacene-coupled diradicals. Our calculations revealed that the planarity and overlap of the frontier molecular orbitals are one of the key factors in influencing the strength and behavior of the magnetic exchange interactions in diradicals. Specifically, the overlap between SOMOs and LUMO influences the strength of the magnetic exchange interaction.</p>\u0000 </div>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 25","pages":""},"PeriodicalIF":4.8,"publicationDate":"2025-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145078274","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":"Artificial Neural Networks Fitting of Potential Energy Curves and Surfaces: The 1/R Conundrum","authors":"Siddhuram Rana,&nbsp;Uday Sankar Manoj,&nbsp;Upakarasamy Lourderaj,&nbsp;Narayanasami Sathyamurthy","doi":"10.1002/jcc.70220","DOIUrl":"10.1002/jcc.70220","url":null,"abstract":"<p>Within the Born-Oppenheimer approximation, the potential energy of a molecular system is written as a sum of electronic energy and nuclear-nuclear repulsion energy terms. The potential energy surface (PES), computed ab initio, as a function of bond distances and bond angles, has traditionally been represented using analytic functions and/or interpolation methods. We show here that the ab initio computed <i>electronic</i> energy values of a molecular system can be fitted more accurately than the corresponding potential energy values using the artificial neural network methodology. The exact Coulombic internuclear repulsion energy can be added subsequently to the fitted electronic energy to obtain an accurate PES.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 24","pages":""},"PeriodicalIF":4.8,"publicationDate":"2025-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.70220","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145059047","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Accurate Theoretical Assessment of MLCT Transitions in [M(Terpy)2]2+ (M = Fe, Ru, Os) Complexes","authors":"Aleksandr A. Chamkin,&nbsp;Elena S. Chamkina","doi":"10.1002/jcc.70227","DOIUrl":"10.1002/jcc.70227","url":null,"abstract":"<div>\u0000 \u0000 <p>The present study guides reliable and cost-effective computational approaches to metal-to-ligand charge transfer (MLCT) transitions in model [M(terpy)₂]²⁺ (M = Fe, Ru, Os) complexes relevant to electrochromic applications. We evaluated the performance of multireference perturbation theories (NEVPT2 and CASPT2), DLPNO-STEOM-CCSD, ADC(2), and 44 density functionals within TD-DFT for calculating vertical MLCT excitation energies in these systems. Multireference methods provide the most consistent agreement with experimental absorption maxima. The best theoretical estimates were obtained at the X2C NEVPT(14, 13)/x2c-QZVPPall level (2.368, 2.710, and 2.684 eV for M = Fe, Ru, and Os, respectively). DLPNO-STEOM-CCSD fails for [Fe(terpy)₂]²⁺, presumably due to its multireference character. Among DFT functionals, local meta-GGAs such as r²SCAN offer the best trade-off between accuracy and computational cost.</p>\u0000 </div>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 24","pages":""},"PeriodicalIF":4.8,"publicationDate":"2025-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145032004","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":"Geometrical Isotope Effects on Chemical Bonding in Hydrogen Bonded Systems: Combining Nuclear-Electronic Orbital DFT and Energy Decomposition Analysis","authors":"Raza Ullah Khan,&nbsp;Ralf Tonner-Zech","doi":"10.1002/jcc.70226","DOIUrl":"10.1002/jcc.70226","url":null,"abstract":"<p>We investigated primary and secondary geometric isotope effects (H, D, T) on charge-inverted hydrogen bonds (CIHB) and dihydrogen bonds (DHB) using nuclear-electronic orbital density functional theory (NEO-DFT). The dianionic but electrophilic boron cluster [B₁₂H₁₂]²⁻ served as a bonding partner, exhibiting a negatively polarized hydrogen atom in the B<span></span>H bond. CIHB systems included interactions with Lewis acids (AlH₃, BH₃, GaH₃) and carbenes (CF₂, CCl₂, CBr₂), while DHBs were analyzed with NH₃, HF, HCl, and HBr. Isotope substitution systematically decreased intermolecular and intramolecular bond lengths (H &gt; D &gt; T). Energy decomposition analysis (EDA) combined with Hirshfeld partial charge analysis confirmed the bonding interpretation but revealed significant variations in bonding contributions across different complexes. While some systems exhibited increased electrostatic attraction, others showed enhanced orbital interactions or shifts in Pauli repulsion, which could stabilize or destabilize the interaction. Natural orbital for chemical valence (NOCV) analysis highlighted charge depletion from the partially negative hydrogen towards the vacant orbital of the bonding partner in CIHB systems, further supporting the bonding model. This study demonstrates how isotope substitution influences electronic structure and lays the groundwork for extending such analyses to more strongly bound systems, where isotope effects may be more pronounced.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 24","pages":""},"PeriodicalIF":4.8,"publicationDate":"2025-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.70226","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145032351","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comprehensive DFT and SCAPS-1D Study of Structural, Electronic, Optical, Mechanical, Phonon, Thermoelectric, and Photovoltaic Properties of Lead-Free Z3BrO (Z = K, Rb, Cs, and Fr) Anti-Perovskites","authors":"Rifat Rafiu,&nbsp;Md. Sakib Hasan Saikot,&nbsp;Imtiaz Ahamed Apon,&nbsp;Imed Boukhris,&nbsp;Ali El-Rayyes,&nbsp;Mohd Taukeer Khan,&nbsp;Q. Mohsen,&nbsp;Md. Azizur Rahman","doi":"10.1002/jcc.70221","DOIUrl":"10.1002/jcc.70221","url":null,"abstract":"<div>\u0000 \u0000 <p>This study presents a comprehensive first-principles and device-performance investigation of alkali metal-based anti-perovskites Z₃BrO (Z = K, Rb, Cs, and Fr) for advanced optoelectronic and photovoltaic applications. Using density functional theory (DFT) with GGA-PBE and mGGA-rSCAN functionals, we analyzed the structural, electronic, optical, mechanical, phonon, population, and thermoelectric properties of these compounds. All Z₃BrO materials exhibit direct band gaps and strong optical absorption in the visible–UV spectrum. Mechanical and phonon analyses confirm their dynamic and elastic stability, with K₃BrO showing superior mechanical robustness and Fr₃BrO demonstrating the highest Debye temperature. SCAPS-1D simulations were conducted on heterostructures incorporating K₃BrO, Rb₃BrO, and Cs₃BrO as absorber layers. The results revealed PCEs of 23.26% for K₃BrO, 25.58% for Rb₃BrO, and 26.43% for Cs₃BrO, highlighting the tunability and performance potential of these materials. Fr₃BrO, while excluded from device simulation due to its near-metallic nature, exhibited promising optical and thermal features. These findings establish Z₃BrO anti-perovskites as promising, lead-free absorber materials for high-performance and sustainable solar energy technologies.</p>\u0000 </div>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 24","pages":""},"PeriodicalIF":4.8,"publicationDate":"2025-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145032002","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":"A New Fragment-Based Pharmacophore Virtual Screening Workflow Identifies Potent Inhibitors of SARS-CoV-2 NSP13 Helicase","authors":"Jordi Doijen,&nbsp;Jiexiong Xie,&nbsp;Simone Marsili,&nbsp;Trpta Bains,&nbsp;Mandeep Kaur Mann,&nbsp;Pravien Abeywickrema,&nbsp;Nick Van den Broeck,&nbsp;Christian Permann,&nbsp;Thierry Langer,&nbsp;Gökhan Ibis,&nbsp;Charles-Alexandre Mattelaer,&nbsp;Jeremy Harvey,&nbsp;Sebastiaan van Raalte,&nbsp;Roberto Fino,&nbsp;Vineet Pande,&nbsp;Danielle Peeters,&nbsp;Aaron Patrick,&nbsp;Ellen Van Damme,&nbsp;Herman van Vlijmen,&nbsp;Marnix Van Loock,&nbsp;Edgar Jacoby","doi":"10.1002/jcc.70201","DOIUrl":"10.1002/jcc.70201","url":null,"abstract":"<p>Herein we report the in silico discovery of 13 novel micromolar potent inhibitors of the SARS-CoV-2 NSP13 helicase validated in cellular antiviral and biophysical ThermoFluor assays. The compounds, discovered using a novel fragment-based pharmacophore virtual screening workflow named FragmentScout, enable the advancement of novel antiviral agents. FragmentScout uses publicly accessible structural data of the SARS-CoV-2 NSP13 helicase, which was previously generated at the Diamond LightSource by XChem high-throughput crystallographic fragment screening. The workflow generates a joint pharmacophore query for each binding site, thereby aggregating the pharmacophore feature information present in each experimental fragment pose. The joint pharmacophore query is then used to search 3D conformational databases using the Inte:ligand LigandScout XT software. The FragmentScout in silico workflow offers a novel tool for identifying micromolar hits from millimolar fragments in fragment-based lead discovery. It is anticipated that this workflow will enhance systematic data mining of the growing collection of XChem datasets.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 23","pages":""},"PeriodicalIF":4.8,"publicationDate":"2025-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.70201","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144995853","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Ng7Be2B5+: Binding of Noble Gas Through Both Cationic Beryllium and Anionic Boron Centers","authors":"Yahui Li,&nbsp;Yu-qian Liu,&nbsp;Chengxiang Ding,&nbsp;Ranajit Saha,&nbsp;Zhonghua Cui,&nbsp;Sudip Pan","doi":"10.1002/jcc.70219","DOIUrl":"10.1002/jcc.70219","url":null,"abstract":"<div>\u0000 \u0000 <p>Quantum chemical calculations have been performed to investigate the structure, stability, and bonding in noble gas (Ng) bound Be₂B₅⁺ complexes. The present results show that Be₂B₅⁺, a charge-separated [Be]²⁺[B₅]³⁻[Be]²⁺ cluster, can employ both its cationic Be center and anionic B center to bind Ng atoms. It can bind a total of seven Ng atoms, resulting in the formation of a highly symmetric (Ng^Be)₂Be₂(Ng^B)₅B₅⁺ complex, having <i>D</i>_5<i>h</i> point group. The thermochemical analyses reveal that the Ng-Be bonds are stronger than the Ng-B bonds. (Ng^Be)₂Be₂B₅⁺ (Ng = Ar-Rn) complexes are stable against the dissociation of Ng atoms even at room temperature. But, (Ng^Be)₂Be₂B₅⁺ (Ng = He and Ne) and (Ng^Be)₂Be₂(Ng^B)₅B₅⁺ (Ng = Ar-Rn) complexes are stable only at very low temperatures. Therefore, they can be suitable candidates for low-temperature matrix isolation. A thorough bonding analysis, through charge and energy decomposition methods, discloses that despite the Ng-B interaction being weaker than the Ng-Be interaction, the former bond is more covalent than the latter one. In fact, in the Ng-B bonds, both the orbital and electrostatic interactions are larger in magnitude than the Ng-Be bonds; however, significantly larger Pauli repulsion in the former bonds makes them weaker than the latter bonds. In both Ng-Be and Ng-B bonds, the covalent interaction originates from a strong Ng(p_<i>σ</i>) → Be₂B₅⁺ <i>σ</i> donation, complemented by two weak Ng(p_π) → Be₂B₅⁺ π donations.</p>\u0000 </div>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 23","pages":""},"PeriodicalIF":4.8,"publicationDate":"2025-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144995842","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 Most Common Drug Residues From Hospital Wastewater on Vermiculite Exchanged With Magnesium: A DFT Study","authors":"Jean Wilfried Hounfodji,&nbsp;Wilfried G. Kanhounnon,&nbsp;Gaston Kpotin,&nbsp;Juliette Lainé,&nbsp;Guy S. Atohoun,&nbsp;Yann Foucaud,&nbsp;Michael Badawi","doi":"10.1002/jcc.70204","DOIUrl":"https://doi.org/10.1002/jcc.70204","url":null,"abstract":"<div>\u0000 \u0000 <p>Significant amounts of effluents containing pharmaceuticals residues are released each year in the environment. These residues are responsible for the disruption of the metabolism of organisms. In this study, vermiculite, a low-cost and high specific area clay material, is a best and effective way to remove the micro-pollutants by adsorption. Thus, we investigate the adsorption of carbamazepine (CAR), aspirin (ASP), diazepam (DIA), diclofenac (DIC), paracetamol (PAR), and ibuprofen (IBU), the most common pharmaceutical pollutants encountered in wastewater, on the hydrated surface of vermiculite exchanged with magnesium using thermodynamic calculations and density functional theory (DFT). Our results indicate that DIC exhibits the highest affinity for the hydrated surface of vermiculite, followed by PAR, IBU, ASP, CAR, and DIA. Furthermore, it is possible to regenerate the adsorbent after use, just by heating the vermiculite to a temperature of 360 K. The adsorptions are all exothermic, with energies depending upon the structural configuration of the pollutant on the surface.</p>\u0000 </div>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 23","pages":""},"PeriodicalIF":4.8,"publicationDate":"2025-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144935084","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":"PlasmoDocking: A User-Friendly Open-Source Web Tool for Virtual Screening Targeting Plasmodium falciparum Enzymes","authors":"Fernando Loza Guariero,&nbsp;Eduardo Pantoja de Macedo,&nbsp;Elise Bittencourt de Laia,&nbsp;Joseph Albert Medeiros Evaristo,&nbsp;Geisa Paulino Caprini Evaristo,&nbsp;Fernando Berton Zanchi","doi":"10.1002/jcc.70225","DOIUrl":"https://doi.org/10.1002/jcc.70225","url":null,"abstract":"<p>Virtual screening through molecular docking represents a fundamental computational methodology extensively employed in the identification of therapeutic compounds for malaria and other parasitic diseases. Although numerous software platforms are available, including AutodockGPU, the command-line interface requirements present significant barriers to non-specialized users, while multi-target screening protocols introduce additional complexity in receptor preparation procedures. To address these limitations, we developed Plasmodocking, a comprehensive web-based platform designed to automate molecular docking simulations against predefined <i>Plasmodium falciparum</i> targets (https://plasmodocking-unir.ecotechamazonia.com.br/). The platform enables users to submit up to 10 molecular structures (.sdf format) for automated AutodockGPU screening against 38 pre-configured parasite targets, facilitating systematic comparison of binding energies with co-crystallized ligands. Developed using Python and Next.js, Plasmodocking accelerates malaria drug discovery by enabling simultaneous multi-target docking simulations within a single experimental framework. The open-source codebase is available at: https://github.com/LABIOQUIM/PlasmoDocking-Client.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 23","pages":""},"PeriodicalIF":4.8,"publicationDate":"2025-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.70225","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144935082","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Tuning Hydrogen Bond Strength in GC (WC), GC* (HG), and GC+ (HG) Base Pairs via Substituents: An Interacting Quantum Atoms Analysis","authors":"F. Pakzad,&nbsp;K. Eskandari","doi":"10.1002/jcc.70224","DOIUrl":"https://doi.org/10.1002/jcc.70224","url":null,"abstract":"<div>\u0000 \u0000 <p>Precise control over DNA stability and interactions is crucial for successful gene editing technologies. To achieve this, a detailed understanding of individual hydrogen bonds within GC (Watson-Crick) and GC*/GC⁺ (Hoogsteen) base pairs is essential, particularly regarding how strategic substitution of these base pairs modulates their strength and, ultimately, DNA stability. Leveraging the atomic-resolution capabilities of interacting quantum atoms (IQA) and interacting quantum fragments (IQF) analyses, this study investigates the impact of substituent position and electronic nature on individual hydrogen bond strengths in substituted GC (WC), GC* (HG) and GC⁺ (HG) base pairs. Our results reveal how the electronic properties of substituents and their specific location on the base pairs significantly influence the forces governing atomic interactions, ultimately impacting the strength of individual hydrogen bonds within GC (WC), GC* (HG) and GC⁺ (HG) base pairs. While IQA highlights the importance of classical interactions in stabilizing hydrogen bonds, IQF analysis, taking a more holistic perspective, reveals a more significant role for electron sharing, highlighting the intricate dance between these forces in shaping DNA stability. Furthermore, GC⁺ (HG) base pairs consistently exhibit stronger inter-fragment interactions compared to GC (WC) and GC* (HG) base pairs, consistent with their higher energy binding energies. The primary reason for the enhanced stability of the GC⁺ (HG) base pairs compared to the GC (WC) and GC* (HG) base pairs is that cytosine has added a proton to the Hoogsteen geometry, leading to strong inter-fragment interactions. By contrast, GC* (HG) geometries are substantially less favorable than GC (WC) and GC⁺ (HG) geometries. GC* (HG) base pairs consistently show weaker inter-fragment interactions compared to GC (WC) and GC⁺ (HG) bases. This reduction in stability is attributed to the substitution of the cytosine amino group with its imino tautomeric form at the electron-donating site of hydrogen bond <i>a</i>, which leads to a decrease in electron-donating ability and the polarity of the N<span></span>H bond. Our findings demonstrate the feasibility of tuning the interactions within GC (WC), GC* (HG) and GC⁺ (HG) base pairs through strategic substitution, offering a powerful tool for manipulating DNA stability, function, and interactions with other molecules.</p>\u0000 </div>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 23","pages":""},"PeriodicalIF":4.8,"publicationDate":"2025-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144935083","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}