Journal of Computational Chemistry最新文献

{"title":"Beyond Born Oppenheimer (BBO)-Based Multi-Electronic State Diabatic Hamiltonians: Reactive Scattering Processes","authors":"Saikat Hazra,&nbsp;Ahitagni Roy,&nbsp;Amarendra Ghosh,&nbsp;Koushik Naskar,&nbsp;Satrajit Adhikari","doi":"10.1002/jcc.70464","DOIUrl":"10.1002/jcc.70464","url":null,"abstract":"<div>\u0000 \u0000 <p>When the electron-nuclear coupling among the electronic states of the reactive species are non-negligible, the calculated cross-sections and rate coefficients of tri-atomic chemical reactions can provide the mechanism of the reaction in conjunction with the experimental data. The construction of multi-state diabatic Hamiltonian is the inclusion of nonadiabatic coupling through Beyond Born-Oppenheimer theory, whereas the spin-orbit couplings could be incorporated as and when required. Once such diabatic Hamiltonians are derived and scattering calculations are performed, the reaction attributes generally show good agreement with the experimental data, otherwise, single surface adiabatic calculations depict deviations in many cases. The deviation and agreement with the experimental results is more pronounced over the energy range facing the conical intersection (CI) between the adiabatic potential energy surfaces. We have presented several examples of prototype reactive systems, where symmetry driven and accidental Jahn-Teller (JT)-type CI as well as Renner-Teller (RT) interaction influencing the reaction processes. Calculated cross-sections and rate coefficients are compared with experimentally measured ones to depict the necessity of inclusion of electron-nuclear coupling terms.</p>\u0000 </div>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"47 20","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148596938","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":"Fast and Accurate GPU-Accelerated Computation of Two-Electron Four-Center Coulomb Repulsion Integrals","authors":"Avleen Kaur,&nbsp;William Chen,&nbsp;Gautam Kirshan Luhana,&nbsp;Lior Silberman,&nbsp;Mark Ewert,&nbsp;Alexandra Bünger,&nbsp;Ury Segal,&nbsp;Chen Greif","doi":"10.1002/jcc.70472","DOIUrl":"10.1002/jcc.70472","url":null,"abstract":"<p>Electron repulsion integrals are fundamental in ab initio quantum chemistry calculations, as their accurate evaluation is required for predicting molecular properties. We have developed GPU software for rapidly and accurately computing two-electron, four-center Coulomb repulsion integrals using Slater-type orbitals (STOs), with a runtime of approximately 0.06 s per integral for double-precision computations. The computations involve applying a simple transformation from classical electromagnetism to eliminate the Coulomb singularity in the integrals, and using numerical quadrature techniques. We implement our algorithms in a modern GPU-based computing environment, using CUDA intrinsic functions and high-performance computational strategies. We demonstrate the efficiency and accuracy of our code with several examples.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"47 20","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.70472","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148596912","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":"WFX Molecular Fragment References for Hirshfeld Charge-Transfer Analysis in Non-Covalent Complexes","authors":"Jorge Garza,&nbsp;Rubicelia Vargas","doi":"10.1002/jcc.70476","DOIUrl":"10.1002/jcc.70476","url":null,"abstract":"<p>In this work, we introduce and assess a fragment-based Hirshfeld scheme in which molecular WFX files of isolated fragments are used to reconstruct reference densities directly. The electron density of the full complex is reconstructed from its WFX file and partitioned using either atomic WFX references or molecular WFX fragment references on the same integration grid. The method is applied to water clusters and to representative complexes from the S66 set, including hydrogen-bonded, donor–acceptor, <span></span><math>\u0000 <semantics>\u0000 <mrow>\u0000 <mi>π</mi>\u0000 </mrow>\u0000 <annotation>$$ pi $$</annotation>\u0000 </semantics></math>-stacked, symmetric, and dispersion-dominated systems. Across density-functional calculations and the available CCSD correlated-wave- function results, molecular WFX fragment references lead to substantially smaller fragment-charge magnitudes than atomic references. For hydrogen-bonded and donor–acceptor complexes, the reduction commonly reaches 75%–90% in the primary 6-311++G** calculations, whereas symmetric or dispersion-dominated systems exhibit zero or nearly zero net integrated fragment charge. The results show that atomic-reference fragment charges include contributions associated with reconstructing each molecular fragment from isolated atoms, whereas WFX fragment references measure redistribution relative to already formed isolated monomers. The proposed approach therefore provides a chemically meaningful density-based reference for analyzing intermolecular charge transfer in non-covalent complexes.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"47 20","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.70476","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148596975","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":"Exploration of Minimum Energy Paths Through Feature-Vector Force-Driven Reaction Coordinate Exploration Approach","authors":"Dudam Praveen,&nbsp;Siva Chiriki,&nbsp;K. V. Jovan Jose","doi":"10.1002/jcc.70465","DOIUrl":"10.1002/jcc.70465","url":null,"abstract":"<div>\u0000 \u0000 <p>Predicting reaction minimum-energy paths (MEPs) and locating transition states (TSs) on the potential energy surface (PES) are challenging problems. The high scaling of electronic structure methods and the computational expense of higher-energy derivative calculations limit the exploration of reaction mechanisms to smaller molecular systems. Therefore, tracing the MEPs along the intrinsic reaction coordinate is formidable. In this work, we have benchmarked a rapid method, the Feature-vector Force-driven Reaction Coordinate Exploration (FFoRCE) approach, for generating MEPs connecting the reactant to the product on the PES. This two-step approach involves a reaction-coordinate navigator that generates the initial path from reactant to product, followed by local relaxations of each structure along the sampled path. The reaction coordinate navigator transforms the coordinate space into a set of features and assigns each structure along the reaction coordinate path a unique value. The reaction coordinate navigator generates an initial path iteratively, followed by a symmetry function-constrained geometry optimization. In this process, the MEP structures are generated by minimizing the total energy along the TS. In this work, the performance of the FFoRCE approach is benchmarked on 10 elementary gas-phase organic reactions by tracing MEPs and locating TSs. Furthermore, we compared their geometries, activation energies, and vibrational frequencies with those from whole-molecule calculations. A fair agreement between them shows that the FFoRCE approach reproduces the MEP and locates the TS as accurately as DFT methods, and it is promising for future applications to complex reactions.</p>\u0000 </div>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"47 20","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-07-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148564736","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":"Reexamining Al2H2: Evidence That the Unidentified Butterfly Ground-State Isomer Was Previously Observed","authors":"Elizabeth C. Toth,&nbsp;Ethan J. Poncelet,&nbsp;Andy Jiang,&nbsp;Justin M. Turney,&nbsp;Yohannes Abate,&nbsp;Henry F. Schaefer III","doi":"10.1002/jcc.70471","DOIUrl":"10.1002/jcc.70471","url":null,"abstract":"<div>\u0000 \u0000 <p>Although popular throughout the 1990s and early 2000s, interest in Al₂H₂ suddenly diminished, leaving an unresolved chasm between theory and experiment for over 20 years. Our computations reconcile the two, unveiling evidence for the unidentified but earlier observed Al₂H₂ butterfly global minimum in matrix IR. We confirm the experimental IR assignments of the cyclic and monobridged structures. The critical ingredient in our case is the b₂ symmetry Al–H stretching frequency predicted here to be 1096 cm⁻¹. This feature was observed at 1090 cm⁻¹ by Andrews et al., but never identified. Andrews et al. also assigned a feature at 1647 cm⁻¹ to the linear structure of Al₂H₂. However, this is unlikely, as we do not find the linear structure to be an equilibrium geometry. CCSD(T) geometries and energies for four neutral Al₂H₂ isomers in this work are computed at the highest levels of theory among theoretical investigations in the literature. For final energetic predictions, basis sets as large as augmented quadruple zeta were used, as were theoretical methods as advanced as CCSDT(Q). We also report Al₂H₂ VPT2 fundamental frequencies for the first time. In addition, two anionic structures are investigated at the same levels of theory, the butterfly ground state and monobridged local minimum, which have never been characterized. We conclude that these anion structures could be identified in future mass-selected gas-phase spectroscopy experiments.</p>\u0000 </div>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"47 20","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148552316","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":"On the Role of Hydrogen Bond Strength and Charge Transfer in an On-Water Diels–Alder Reaction: Semiempirical and Free Energy Calculations","authors":"Andrés Henao,&nbsp;Yomna Gohar,&nbsp;René Wilhelm,&nbsp;Thomas D. Kühne","doi":"10.1002/jcc.70467","DOIUrl":"10.1002/jcc.70467","url":null,"abstract":"<p>On-water catalysis is widely exploited, yet the microscopic origin of rate enhancements at aqueous interfaces remains debated. In the spirit of the second-generation Car-Parrinello method, we use a modified Langevin-type scheme to accelerate density-functional based tight-binding molecular dynamics in order to investigate the free energy of two Diels-Alder reactions on-water: the cycloaddition of cyclopentadiene with ethyl cinnamate and that with ethyl thionocinnamate. The only difference between the two studied molecules is that the carbonyl oxygen of the cinnamate is a thiocarbonyl sulfur in the thionocinnamate; hence, the first is a strong and the second a weak hydrogen bond acceptor. The oxygen-containing dienophile reacts through an almost synchronous transition state with a barrier of ~13 kcal/mol, whereas the sulfur analogue follows an asynchronous pathway with a barrier of ~24 kcal/mol because a transient S<span></span>C contact competes with C<span></span>C bond formation. We find no increase in the number or strength of hydrogen bonds at the transition state. Instead, the catalytic role of the interface is to maintain an electronically productive hydrogen-bond environment that stabilizes charge reorganization along the reaction coordinate. These results indicate that, for the present on-water reactions, hydrogen-bond quality and charge-transfer capability are more decisive than the hydrogen-bond count alone.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"47 20","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-07-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.70467","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148498981","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":"How Structural Subtleties Modulate Excited-State Lifetimes in Cyclometalated Cobalt(III) Complexes: Nonadiabatic Molecular Dynamics Study","authors":"Hamada Rezk,&nbsp;Oliver Kühn,&nbsp;Olga S. Bokareva","doi":"10.1002/jcc.70453","DOIUrl":"https://doi.org/10.1002/jcc.70453","url":null,"abstract":"<p>Ultrafast excited-state dynamics of two Co(III) complexes, bearing different alkyl groups (<b>Co1</b>: Methyl, <b>Co2</b>: Ethyl) at the nitrogen of the imidazole ligand, are investigated using trajectory surface hopping based on a linear vibronic coupling model. Despite nearly identical MLCT absorption spectra, experimental singlet lifetimes differ markedly (1.45 vs. 4.3 ps). Relaxation occurs via rapid internal conversion within a strongly vibronically coupled singlet manifold, accompanied by intersystem crossing to long-lived <span></span><math>\u0000 <semantics>\u0000 <mrow>\u0000 <msup>\u0000 <mrow></mrow>\u0000 <mn>3</mn>\u0000 </msup>\u0000 <mi>MC</mi>\u0000 </mrow>\u0000 <annotation>$$ {}^3mathrm{MC} $$</annotation>\u0000 </semantics></math> states. The prolonged lifetime of <b>Co2</b> originates from enhanced vibronic coupling and larger structural distortions, which trap population in the singlet manifold rather than from spin–orbit effects. Minimum-energy crossing points reveal low barriers for nonradiative decay, rationalizing emission quenching. These results demonstrate how subtle structural differences, by modulating vibronic coupling, can substantially influence excited-state lifetimes in these complexes.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"47 20","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-07-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.70453","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148534247","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":"Solution-Phase Energy Decomposition Analysis (SP-EDA): Theory and Applications","authors":"Gábor Paragi,&nbsp;Célia Fonseca Guerra,&nbsp;F. Matthias Bickelhaupt","doi":"10.1002/jcc.70451","DOIUrl":"10.1002/jcc.70451","url":null,"abstract":"<p>We present an extension of our canonical energy decomposition analysis (EDA) from the gas phase to a Solution-Phase approach (SP-EDA), that is, to interactions between molecular fragments in the condensed phase, simulated using the Conductor-like Screening Model (COSMO). To this end, we have introduced different solvation states that serve to simulate particular physical phenomena that can be associated with the step from separate solvated fragments to the solvated complex of these fragments. In addition to the well-known deformation strain of the fragments, induced by complex formation, one can distinguish the desolvation of the contact points via which the fragments bind, the response of the solvent to the deformation of the fragments as well as the response of the solvent to the formation of the complex, and finally the complex formation between the partially desolvated fragments. We provide definitions of how to model these phenomena using a continuum model, such as COSMO. Finally, we analyze, for representative model systems, how the bonding and, in particular, the EDA terms of electrostatic attraction, Pauli repulsion, and stabilizing orbital interactions behave across the above steps associated with interactions in solution. An important practical conclusion is that neglecting the effect of the partial desolvation at the binding sites has, in most cases, only minor consequences for the values and trends in the EDA terms. This finding can be used to simplify investigations using SP-EDA.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"47 20","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.70451","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148459311","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":"Electron Affinity of Actinide (IV) Carboxylate Complexes From MN12-L Density-Functional Calculations and Explainable Machine Learning","authors":"Ali A. Khairbek,&nbsp;Mohammad Abd Al-Hakim Badawi,&nbsp;Ralph Puchta,&nbsp;Dalia I. Saleh,&nbsp;Samy F. Mahmoud,&nbsp;Renjith Thomas","doi":"10.1002/jcc.70469","DOIUrl":"10.1002/jcc.70469","url":null,"abstract":"<div>\u0000 \u0000 <p>We present a relativistic density-functional and explainable machine learning study of the vertical electron affinity (EA) of 14 homologous actinide(IV) carboxylate complexes [M(L)₃]⁺ (M = Th–Lr; L = propionate, acrylate). All values were obtained at the MN12-L level via the def2-TZVPPD basis set for H, C, and O and a Stuttgart small-core relativistic effective-core potential, together with its associated valence basis, for the actinide. For every (metal, ligand) pair, all physically accessible An(IV) multiplicities were considered (52 calculations in total), and the ground state was assigned to the multiplicity with the lowest total electronic energy. The EA, evaluated as the negative of the lower α- and β-LUMO eigenvalues (the “true LUMO”), increases monotonically across the series from 5.53 eV at Th(5f⁰) to 10.80 eV at Lr(5f¹³) for the propionates (5.95 → 10.58 eV for the acrylates), with one outlier: at Th, the LUMO is forced into the 7 s/7p–ligand manifold because no 5f acceptor is available. Squared coefficient population analysis of the corrected ground-state wavefunctions confirms that for Pa–No, the LUMO is predominantly metal-5f (59%–82% on the metal), whereas at Lr, the highest-energy 5f spin orbital mixes strongly with the carboxylate π* manifold (5f ≈20%–28%, O ≈42%–50%). A nine-feature explainable machine-learning model trained on the corrected dataset reproduces the EA series under leave–one-metal-out cross-validation with <i>R</i>² = +0.70 and MAE = 0.56 eV; permutation and SHapley additive exPlanations (SHAP) analyses identify the 5f-electron count and the atomic spin–orbit constant as the single dominant predictor cluster (Pearson r = +0.94 for the 5f count). The cross-ligand transferability is excellent (<i>R</i>² = 0.85–0.88, MAE = 0.35–0.43 eV). The combined DFT–ML analysis provides a quantitative reference for An (IV) carboxylate EAs and isolates the 5f-shell occupation as the single physical lever governing their reduction propensity.</p>\u0000 </div>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"47 20","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148459315","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":"Can Cavity Prediction Algorithms Help in Docking Experiments?","authors":"Diana A. Kondinskaia,&nbsp;Bojana Popovic","doi":"10.1002/jcc.70470","DOIUrl":"10.1002/jcc.70470","url":null,"abstract":"<div>\u0000 \u0000 <p>Blind docking is a method for predicting a binding mode of a ligand with a protein without any prior information about a binding site. Some tools allow this type of docking experiment directly, others, including some established tools<span>,</span> require binding site information being passed as an input. In this latter case, one can use cavity prediction tools and use the results of their prediction as an input in these docking calculations. However, it is still unclear if the results of these predictions can be reliably used in protein–ligand docking and what is the best technical way to pass this information to the docking algorithm. In this study we estimated the applicability of the binding pocket prediction tools in docking experiments to address this gap in knowledge. We use four different computational tools for cavity prediction and use the best predicted cavities represented in different ways to run GOLD docking calculations. Analysis of subsequent use in docking highlights that Fpocket and CAVIAR are the best performing cavity prediction tools in this context. Further analysis shows that accurate binding site input does not guarantee accurate binding pose predictions and<span>,</span> even with the predicted cavities, the more restrained the input is, the more reliable the docking results are.</p>\u0000 </div>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"47 20","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148443527","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}