Journal of Computational Chemistry最新文献

{"title":"Heterogeneous Autoxidation of VOCs Promotes Light-Scattering of Atmospheric Mineral Particle: A DFT Study","authors":"Weina Zhang,&nbsp;Zhichao Fan,&nbsp;Yao Zhou,&nbsp;Kaixin Zhang","doi":"10.1002/jcc.70195","DOIUrl":"https://doi.org/10.1002/jcc.70195","url":null,"abstract":"<div>\u0000 \u0000 <p>Recently, the heterogeneous autoxidation of volatile organic compounds (VOCs) has been shown to alter the light-scattering property of atmospheric mineral particles. Here, we investigate how VOCs with different central atoms dictate autoxidation pathways and subsequent highly oxygenated molecules (HOMs) properties, ultimately influencing the complex refractive index of VOC-mineral particles via density functional theory (DFT) and quantitative structure–property relationship (QSPR) analysis. Using dimethylsulfide (DMS)/dimethylether (DME) as ether-type proxies and triethylamine (TEA)/trimethylphosphine (TMP) as alkane-type proxies, we reveal two distinct autoxidation paths: alkane-type VOCs undergo more O₂-addition steps due to their structural capacity for H-shift reactions, generating HOMs with higher oxidation states (OS), molar mass, and polarizability. These properties drive stepwise increases in the refractive index (<i>n</i>) for alkane-VOC-mineral particles, leading to stronger light-scattering ability compared to ether-type counterparts. Our results establish a direct link between VOCs' autoxidation mechanisms and optical properties, providing new insights into climate-relevant aerosol interactions.</p>\u0000 </div>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 20","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-07-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144712128","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":"Population Analysis From Variational Chemical Partition of Molecular Position Space","authors":"Bernard Silvi,&nbsp;M. Esmaïl Alikhani","doi":"10.1002/jcc.70184","DOIUrl":"https://doi.org/10.1002/jcc.70184","url":null,"abstract":"<p>Two years ago, a partition was proposed in the position space of the charge distribution of atoms and molecules, relying on the optimization of the boundaries of space-filling non-overlapping localization regions. This is achieved with the help of global objective functions providing either a measure of the dispersion of numbers of electrons in each localization region or of the dependence of these numbers between them. The output of the method reproduces very well the expected chemical structures in terms of atomic shells, bonds, and lone pairs domains. This method, inspired by the data processing of experimental results, is by construction free of any approximation since it only requires as input the one and two-particle densities of probability. It is based on a strict definition of the concepts of chemical entity, i, e, a set of nuclei and of a given number of localized electrons, for which an electron count followed by a multivariate analysis is carried out. In its first version, the software was extremely inefficient, and its use was therefore limited to atoms and small molecular systems to keep the computational effort within reasonable limits. A significant improvement has been recently achieved, enabling calculations of molecules as large as polyaromatic hydrocarbons. In the present paper, we first discuss the philosophy of previous population schemes, then we describe the features of our new family of population analysis, and then report the results obtained on a rather large sample of molecules and complexes, including polyaromatic hydrocarbons, propellanes, transition metal carbonyl 1:1 complexes and hydrogen-bonded systems as well as reaction mechanisms.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 20","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-07-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.70184","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144705626","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":"Large-Scale Calculations by Integrating the Fragmentation Approach With Neural Network Potentials","authors":"Rei Oshima,&nbsp;Mikito Fujinami,&nbsp;Yuya Nakajima,&nbsp;Hiromi Nakai","doi":"10.1002/jcc.70193","DOIUrl":"https://doi.org/10.1002/jcc.70193","url":null,"abstract":"<div>\u0000 \u0000 <p>A fragmentation method is introduced to enable large-scale molecular simulations using neural network potentials (NNPs). The method partitions a system into cube-shaped fragments and reconstructs the total energy using a many-body expansion formalism with a distance-based cut-off approximation. Validation with Au, NaCl, diamond, H₂O, and graphite crystals demonstrated that including three-body interactions with 26 neighboring fragments reduces per-atom energy error to within 0.04 eV. This approach enables simulations of systems with up to 1 million atoms, surpassing conventional NNP limits. The scaling exponent for three-body calculations remains below 1.64, suggesting feasibility for even larger-scale applications.</p>\u0000 </div>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 20","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-07-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144687879","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":"Reduction-Induced Structural and Motional Changes of Plant-Type Ferredoxin Using Molecular Dynamics and Umbrella Sampling Simulations","authors":"Tomoki Nakayoshi,&nbsp;Yusuke Ohnishi,&nbsp;Hideaki Tanaka,&nbsp;Genji Kurisu,&nbsp;Yu Takano","doi":"10.1002/jcc.70180","DOIUrl":"https://doi.org/10.1002/jcc.70180","url":null,"abstract":"<div>\u0000 \u0000 <p>Plant-type ferredoxin (Fd) is a metalloprotein that contains a [2Fe–2S] cluster as its active center and plays an important role in electron transfer in photosynthesis. In this study, to investigate the effects of the redox-state conversions of Fd on its structures and motions, 5-μs long-time molecular dynamics (MD) simulations were performed on both the oxidized and reduced forms of <i>Anabaena</i> PCC7119 Fds. Although the overall geometrical properties of the oxidized and reduced forms were virtually identical, there were differences in local structure and motion. In particular, the <i>C</i>-terminal region of the reduced form was allowed to have more conformations than that of the oxidized form. Furthermore, the free-energy profile of the flip of the peptide bond linking Cys46 and Ser47 (conversion from “CO-in” to “CO-out” conformations) with the Fd reduction was obtained using 14.6-μs umbrella sampling simulation. It was estimated that the “CO-out” conformation was substantially more stable than “CO-in” conformation and that the activation free energy of the peptide-bond flip was very low. The dynamical structural information obtained in this study on plant-type Fds is expected to contribute to the elucidations of Fd functions.</p>\u0000 </div>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 20","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144688144","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":"Ring Size Dependent Lactam-Lactim Tautomeric Equilibrium in Imidazolin-2-Chalcogenones and Pyrimidin-2-Chalcogenones: A Role of Aromaticity","authors":"Linta Mary Jose,&nbsp;Susmita De","doi":"10.1002/jcc.70177","DOIUrl":"https://doi.org/10.1002/jcc.70177","url":null,"abstract":"<div>\u0000 \u0000 <p>The dynamic nature of tautomerism has profound implications for structure, function, and reactivity of biologically important molecules. This study investigates the effect of ring size and aromaticity on tautomeric stability of Imidazolin-2-chalcogenones and Pyrimidin-2-chalcogenones using quantum mechanical methods. Analysis of the tautomerisation energies reveals that five-membered unsaturated analogues favor lactams, whereas six-membered ones prefer lactims, a reversal in tautomeric preference not observed in saturated lactams or acyclic amides. Charge and population analyses reveal that the nature of C<span></span>N(C<i>N</i>)/CX(C<span></span>X) bonds contribute to tautomeric stability. EDA-NOCV analysis indicates that the primary difference in C<span></span>N(C<i>N</i>) bonds between the five- and six-membered analogues lies in the low <span></span><math>\u0000 <semantics>\u0000 <mrow>\u0000 <mo>∆</mo>\u0000 </mrow>\u0000 <annotation>$$ Delta $$</annotation>\u0000 </semantics></math><i>E</i>_π in six-membered lactams, supported by low NICSzz (1) values. The tautomerisation of six-membered lactams to lactims results in gain in aromatic stabilization, which plays a crucial role in reversal of tautomeric stability in Pyrimidin-2-chalcogenones, overcoming the intrinsic stability of C<span></span>N(C<i>N</i>) bonds in Imidazolin-2-chalcogenones.</p>\u0000 </div>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 20","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144681532","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":"Exact Rovibronic Equivalence of the Adiabatic and Diabatic Representations of \u0000 \u0000 \u0000 N\u0000 \u0000 $$ N $$\u0000 -Coupled State Diatomic Systems","authors":"Ryan P. Brady,&nbsp;S. N. Yurchenko","doi":"10.1002/jcc.70181","DOIUrl":"https://doi.org/10.1002/jcc.70181","url":null,"abstract":"<p>The Born–Oppenheimer approximation assumes nuclear motion evolves on single, uncoupled potential energy surfaces, widely used to solve the time-independent Schrödinger equation for atomistic systems. However, for near-degenerate same-symmetry electronic states, avoided crossings in the potential energy curves occur and non-adiabatic couplings (NACs) become significant. In such cases, the adiabatic approximation is unsuitable for high-resolution spectroscopy. A unitary transformation to the diabatic representation can eliminate NACs, resulting in smooth molecular property curves that may cross. Computing this adiabatic-to-diabatic transformation (AtDT) is desirable but non-analytic for multi-state coupled systems, necessitating numerical solutions. It remains unclear if current methods yield numerically exact AtDTs ensuring rovibronic energy level equivalence between adiabatic and diabatic pictures. We demonstrate (for the first time) numerically exact equivalence of adiabatic and diabatic representations for <span></span><math>\u0000 <semantics>\u0000 <mrow>\u0000 <mi>N</mi>\u0000 </mrow>\u0000 <annotation>$$ N $$</annotation>\u0000 </semantics></math>-state diatomic molecules using ab initio data for <span></span><math>\u0000 <semantics>\u0000 <mrow>\u0000 <msub>\u0000 <mrow>\u0000 <mi>N</mi>\u0000 </mrow>\u0000 <mrow>\u0000 <mn>2</mn>\u0000 </mrow>\u0000 </msub>\u0000 </mrow>\u0000 <annotation>$$ {N}_2 $$</annotation>\u0000 </semantics></math>, CH, and a model 10-state system. We show how the equivalence can be efficiently used to assess the importance of non-adiabatic effects and the impact of omitting them when computing rovibronic energies of diatomic molecules. The adiabatic and diabatic representations of the spectroscopic model, including all coupling terms, have been implemented in the diatomic code <span>Duo</span>.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 20","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.70181","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144672983","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":"Atomization Energy Calculations in 13-Atom Alkali Metal Clusters: Is There an Appropriate Exchange-Correlation Functional?","authors":"Wagner F. D. Angelotti,&nbsp;Lucila C. Z. Angelotti,&nbsp;Roberto L. A. Haiduke","doi":"10.1002/jcc.70187","DOIUrl":"https://doi.org/10.1002/jcc.70187","url":null,"abstract":"<p>Density functional theory (DFT) is a treatment widely employed for exploring the electronic structure of atoms, molecules, solids, and complex systems. Despite its efficiency and popularity, the accuracy of DFT results is highly dependent on the choice of exchange–correlation (XC) functionals. This study evaluates several XC functionals for calculating atomization energies in 13-atom homo- and heteronuclear alkali metal clusters (X₁₃ and YX₁₂, with X, Y = Li, Na, K, Rb, and Cs), comparing these results with reference data obtained from fixed-node Diffusion Monte Carlo (DMC) simulations. Our findings emphasize the critical role of the correlation functional in achieving more accurate results. Moreover, empirical dispersion corrections are shown to be quite important for these systems. Notably, PBE and PBE0 functionals with D3-BJ dispersion seem particularly reliable for atomization energy calculations in these clusters.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 20","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.70187","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144666468","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":"Correction to “Three-Dimensional Metallic Boron Carbide: Stability and Properties”","authors":"","doi":"10.1002/jcc.70185","DOIUrl":"https://doi.org/10.1002/jcc.70185","url":null,"abstract":"<p>K. Hussain, Q. Liu, B. Chen, et al., “Three-Dimensional Metallic Boron Carbide: Stability and Properties,” <i>Journal of Computational Chemistry</i> 46, no. 17 (2025): e70168, https://doi.org/10.1002/jcc.70168.</p><p>In the above referenced article, the city name was mistakenly removed in each of the noted author affiliations. The online version of this article has been corrected accordingly.</p><p>We apologize for this error.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 20","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.70185","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144647157","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":"DFT Study of Structural, Chemical, and Optical Properties in Cun and PdCun−1 Clusters (n = 3–20)","authors":"José Aminadat Morato-Márquez,&nbsp;José Gilberto Torres-Torres,&nbsp;Filiberto Ortíz-Chi","doi":"10.1002/jcc.70183","DOIUrl":"https://doi.org/10.1002/jcc.70183","url":null,"abstract":"<div>\u0000 \u0000 <p>Bimetallic nanoclusters exhibit catalytic activity and electronic properties susceptible to single-atom changes. Previous theoretical studies on Pd-doped copper clusters have focused on narrow size ranges or <i>magic numbers</i> of atoms (e.g., 13, 38, 43, and 55), limiting comprehensive understanding and experimental comparison. We employ a growth-pattern algorithm to explore the potential energy surface of the Cu_<i>n</i> and PdCu_<i>n</i>−1 clusters (<i>n</i> = 3–20), identifying new putative global minima for PdCu₇ and PdCu_9–11. For both systems, we analyze their structural, electronic, chemical, and optical properties as a function of size. Structural analysis shows that progressive Cu addition stabilizes Pd in apical positions, reducing electron acceptance barriers and enhancing nucleophilicity compared to its pure copper counterpart. Concurrently, Cu addition induces a blueshift in UV–Vis absorption spectra, indicating increased electronic transition energies. These findings suggest promising applications for these bimetallic clusters in catalysis and electronic sensing.</p>\u0000 </div>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 20","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144647719","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":"Topology-Induced Modifications in the Critical Behavior of the Yaldram–Khan Catalytic Reaction Model","authors":"Paulo F. Gomes,&nbsp;Henrique A. Fernandes,&nbsp;Roberto da Silva","doi":"10.1002/jcc.70182","DOIUrl":"https://doi.org/10.1002/jcc.70182","url":null,"abstract":"<div>\u0000 \u0000 <p>In this work, we investigated how the use of complex networks as catalytic surfaces can affect the phase diagram of the Yaldram–Khan model, as well as how the order of the phase transitions present in the seminal work behaves when randomness is added to the model. The study was conducted by taking into consideration two well-known random networks, the Erdős-Rényi network (ERN), with its long-range randomness, and the random geometric graph (RGG), with its spatially constrained randomness. We perform extensive steady-state Monte Carlo simulations for <span></span><math>\u0000 <semantics>\u0000 <mrow>\u0000 <msub>\u0000 <mrow>\u0000 <mi>r</mi>\u0000 </mrow>\u0000 <mrow>\u0000 <mtext>NO</mtext>\u0000 </mrow>\u0000 </msub>\u0000 <mo>=</mo>\u0000 <mn>1</mn>\u0000 </mrow>\u0000 <annotation>$$ {r}_{mathrm{NO}}=1 $$</annotation>\u0000 </semantics></math>, the NO dissociation rate, and show the behavior of the reactive window as a function of the average degree of the networks. Our results also show that, different from the ERN, which preserves the nature of the phase transitions of the original model for all considered average degrees, the RGG seems to have two second-order phase transitions for small values of average degree.</p>\u0000 </div>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 20","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144647720","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}