Journal of Computational Chemistry最新文献

{"title":"Molecular Tailoring Approach (MTA) Assisted Density Functional Theory Study for Large Core and Core-Shell Nanocluster Quantum Dots","authors":"Anant D. Kulkarni","doi":"10.1002/jcc.70189","DOIUrl":"https://doi.org/10.1002/jcc.70189","url":null,"abstract":"<div>\u0000 \u0000 <p>Molecular fragmentation-based method, viz. molecular tailoring approach (MTA) was employed with density functional framework to investigate prototype medium and large sized semiconductor quantum dots (QDs) of (CdSe)_n, <i>n</i> = 33, 66, 99, 146, and 185 typically of size 1.5–2.7 nm. The trends computed for structural parameters and the band gap energies of prototype structures show a good agreement with those reported earlier for <i>n</i> ≤ 99. In order to study the effect of surface passivation, we use a representative model where 2-coordinated surface atoms of (CdSe)_n QDs were saturated by hydrogen atoms. The prototype for passivated nanoclusters shows enhancement of band gap energy over their bare (CdSe)_n counterparts. We further highlight the strength of our approach by extending the study for the modeled nanoclusters larger than 2.2 nm size, viz. (CdSe)₁₄₆ (diameter d = 2.5 nm), (CdSe)₁₈₅ (d = 2.7 nm), and a prototype core-shell (CS) QD, viz. (CdSe)₆₆/(ZnS)₁₁₉, (d = 2.8 nm), which is otherwise an arduous task on off-the-shelf contemporary hardware. MTA-assisted density functional method offers a reliable and rapid approach for initial steps of geometry optimization of medium and large nanoclusters. The geometrical features viz. surface reorganization through self-healing, selective localization of molecular orbitals, and size dependency of band gap are also retained by MTA. The present approach coupled with a dedicated high performance computer cluster thus has the potential of extending the limits of density functional framework to handle the nanoclusters larger than 3.5 nm (~few hundred atoms).</p>\u0000 </div>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 20","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144716666","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":"Two-Step Hybrid Method for the Energetics of Individual Noncovalent Interactions in Molecular Crystals","authors":"Bharti Dehariya,&nbsp;Ayush Shivhare,&nbsp;Mini Bharati Ahirwar,&nbsp;Milind M. Deshmukh","doi":"10.1002/jcc.70190","DOIUrl":"https://doi.org/10.1002/jcc.70190","url":null,"abstract":"<div>\u0000 \u0000 <p>We present a two-step method for the direct estimation of the energy of individual non-covalent interactions (NCIs) such as hydrogen bond (HB), CH…π or π…π interactions in any given molecular crystal. The first step of this method is to calculate the energy of a NCI by a molecular tailoring approach based (MTA-based) method utilizing a sufficiently large molecular crystal structure. This calculation is performed at the low Hartree–Fock (HF) level. In the next step, the energy of the same referenced NCI is evaluated by the MTA-based method employing a suitable monomeric or dimeric species. This calculation is usually performed at both the high (B3LYP, MP2 or CCSD(T)) and low (HF) levels. Note that the NCI energies in monomeric or dimeric species are significantly different from those in the actual crystal. The difference in the energy calculated in the second step at high and low levels is added to the energy of this NCI calculated (at HF level) in the first step employing a large molecular crystal. The energies of NCIs calculated by this two-step method are compared with their actual crystal counterparts. For this purpose, molecular crystals of L-Histidine (LH), nitromalonamide (NMA) and salicylic acid (SA) are chosen as test cases. It is found that the proposed two-step method provides very accurate energy of individual NCIs in these molecular crystals. For instance, the estimated energies of NCIs by the proposed two-step method are in excellent linear agreement with their actual crystal counterparts (<i>R</i>² = 0.9983). Furthermore, RMSD and standard deviation are 0.22 and 0.24 kcal/mol, respectively, with a mean and maximum absolute error being 0.15 and 0.51 kcal/mol, respectively. Importantly, the two-step method is computationally efficient and saves nearly 50% of computational time <i>vis-à-vis</i> its full calculation counterpart employing the actual molecular crystal.</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":"144712127","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":"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}