Journal of Computational Chemistry最新文献_第3页

Polarizability of 79 Monatomic Cations In Vacuo: Periodic Trends and Correlations With Other Ion-Specific Properties 真空中79个单原子阳离子的极化率：周期性趋势及其与其他离子特性的相关性

IF 2.9 3区化学

Journal of Computational Chemistry Pub Date : 2026-09-17 DOI: 10.1002/jcc.70505

Wojciech Tomaszewski, Kajetan Nocuń, Tadeusz Hofman

引用次数: 0

A Graph-Based Machine Learning Framework to Assign Empirical Interaction Parameters for Novel Molecules 为新分子分配经验相互作用参数的基于图的机器学习框架。

IF 2.9 3区化学

Journal of Computational Chemistry Pub Date : 2026-09-14 DOI: 10.1002/jcc.70508

Yao Fu, Martin Stroet, Megan L. O'Mara

{"title":"A Graph-Based Machine Learning Framework to Assign Empirical Interaction Parameters for Novel Molecules","authors":"Yao Fu, Martin Stroet, Megan L. O'Mara","doi":"10.1002/jcc.70508","DOIUrl":"10.1002/jcc.70508","url":null,"abstract":"Molecular dynamics (MD) simulations of novel molecules are essential to modern drug discovery and related fields that require large-scale sampling of chemical space. However, obtaining accurate and robust force field parameters for novel molecules remains a major challenge. One approach to this problem is to perform quantum chemical calculations on a per-molecule basis, but doing so on a large scale is prohibitively expensive. Here, we present a graph-based machine learning framework for empirical force field assignment that scales significantly more efficiently with molecule size than quantum chemical methods, giving speedups of up to seven orders of magnitude for larger (20+ atoms) molecules. We demonstrate the utility of our framework by applying it to predict harmonic bond force constants and show that the resulting model outperforms the popular Seminario method for force constant assignment when using experimental data as benchmarks. This performance gain is likely a result of the model's intrinsic homogenization effect, which counteracts the noise in the training data. Moreover, our framework overcomes several challenges in translating first-principles calculations to classical MD force field parameters, producing parameters with better transferability and interpretability compared to previous models of this class.","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"47 24","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13572964/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148962816","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}

引用次数: 0

Breaking the Ceiling of Boron-Boron Bonds: Understanding and Fine-Tuning Basicity in Diborane(4) Complexes 打破硼硼键的天花板：二硼烷(4)配合物碱度的认识和微调。

IF 2.9 3区化学

Journal of Computational Chemistry Pub Date : 2026-09-14 DOI: 10.1002/jcc.70498

Manuel Yáñez, Otilia Mó, M. Merced Montero-Campillo, Ibon Alkorta

{"title":"Breaking the Ceiling of Boron-Boron Bonds: Understanding and Fine-Tuning Basicity in Diborane(4) Complexes","authors":"Manuel Yáñez, Otilia Mó, M. Merced Montero-Campillo, Ibon Alkorta","doi":"10.1002/jcc.70498","DOIUrl":"10.1002/jcc.70498","url":null,"abstract":"Diborane(4) is a strong proton sponge when embedded in B2H4–N-base complexes, but the still available electrodeficient site may attract a second N-base, making the BB bond even more basic. High-level G4 calculations show that [BH2-(η1-N-base)]2 species can have proton affinities (PAs) larger than that of 1,8-bis(dimethylamino)naphthalene by as much as 24 orders of magnitude in the equilibrium constant, depending on the N-base selected. Trends in basicity in complexes with a pair of nitrogenous bases are different from those with only one, due to critical structural changes during protonation. The PAs in complexes joining two different N-bases are very close to the average of those of the corresponding symmetric complexes, allowing a straightforward tuning of the basicity enhancement through the appropriate selection of the N-bases. The dissociation enthalpies have been analyzed in relation to the topological features of the BB bond, finding that values can be rationalized based on the distortion of the fragments involved in bond cleavage.","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"47 24","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13575478/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148965739","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}

引用次数: 0

CO and NO Detection by MN4@SWCNT in Background Gases: Multiscale DFT, Microkinetic, Boltzmann Transport Study 背景气体中CO和NO的MN4@SWCNT检测：多尺度DFT，微动力学，玻尔兹曼输运研究

IF 2.9 3区化学

Journal of Computational Chemistry Pub Date : 2026-09-11 DOI: 10.1002/jcc.70507

Adhitya Gandaryus Saputro, Ira Puspitasari, Dicky Setianto, Farrel Dzaudan Naufal, Imran Shakir, Chin-Sung Hsiao, Febdian Rusydi

{"title":"CO and NO Detection by MN4@SWCNT in Background Gases: Multiscale DFT, Microkinetic, Boltzmann Transport Study","authors":"Adhitya Gandaryus Saputro, Ira Puspitasari, Dicky Setianto, Farrel Dzaudan Naufal, Imran Shakir, Chin-Sung Hsiao, Febdian Rusydi","doi":"10.1002/jcc.70507","DOIUrl":"https://doi.org/10.1002/jcc.70507","url":null,"abstract":"<div>\u0000 \u0000 Detecting hazardous gases like CO and NO at room temperature is vital for environmental and health monitoring. While single-walled carbon nanotubes (SWCNTs) are a potential material for a room-temperature sensor, their pristine forms exhibit very weak adsorption toward CO and NO gases. This study investigates the sensing performance of SWCNTs embedded with transition metal-nitrogen (MN4) active sites (M = Mn, Fe Co, Ni, Cu). These active sites are known for their ability to properly bind small gases in various catalytic applications. By combining density functional calculations, microkinetic simulations, and Boltzmann conductivity calculations, we account for atmospheric background gases to provide a realistic evaluation of sensor selectivity and response. Our findings indicate that relative adsorption energies govern surface coverage, while changes in conductivity correlate with the density of states near the Fermi level. Our results show that the CuN4@SWCNT system emerges as the optimal candidate for CO detection within the 1–105 ppm working range. The NiN4@SWCNT system is also viable for CO detection in this range, provided that interfering species such as NO and NO2 are absent. For NO detection, the NiN4@SWCNT system is identified as the best performer, operating effectively in the ultra-low concentration range (~0.01–100 ppb) with high selectivity. This work also elucidates the fundamental trade-off between adsorption strength and recovery time, offering a robust theoretical framework for designing highly selective and reversible gas sensors relevant to health risk monitoring and early warning applications.\u0000 </div>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"47 24","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148942964","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}

引用次数: 0

Boosting CO2 Hydrogenation to Formic Acid Through Secondary Metal Promotion in Fe3O-Based MOF Catalysts fe30基MOF催化剂中二次金属促进CO2加氢制甲酸

IF 2.9 3区化学

Journal of Computational Chemistry Pub Date : 2026-09-11 DOI: 10.1002/jcc.70509

Pavee Apilardmongkol, Manussada Ratanasak, Sirilak Kongkaew, Wilasinee Santiwarodom, Thanawit Kuamit, Tatiya Chokbunpiam, Fadjar Mulya, Thanyada Rungrotmongkol, Jun-ya Hasegawa, Yasuteru Shigeta, Vudhichai Parasuk

{"title":"Boosting CO2 Hydrogenation to Formic Acid Through Secondary Metal Promotion in Fe3O-Based MOF Catalysts","authors":"Pavee Apilardmongkol, Manussada Ratanasak, Sirilak Kongkaew, Wilasinee Santiwarodom, Thanawit Kuamit, Tatiya Chokbunpiam, Fadjar Mulya, Thanyada Rungrotmongkol, Jun-ya Hasegawa, Yasuteru Shigeta, Vudhichai Parasuk","doi":"10.1002/jcc.70509","DOIUrl":"https://doi.org/10.1002/jcc.70509","url":null,"abstract":"<div>\u0000 \u0000 Metal–organic framework (MOF) catalysts are promising platforms for hydrogen energy systems, enabling CO2 conversion to formic acid (HCOOH), a liquid organic hydrogen carrier (LOHC) for hydrogen storage and release. Density functional theory (DFT) calculations (M06-2X/6-31G(d)/LANL2DZ) are performed to investigate CO2 hydrogenation on PCN-250(Fe) clusters featuring frustrated Lewis pair (FLP) sites formed by linker removal. The full hydrogenation pathway, including H2 adsorption, activation, and HCOOH formation, is explored, with HCOOH formation identified as the rate-determining step. Activation barriers from large and small cluster models are consistent (10.0 and 9.4 kcal mol−1). Secondary metal substitution at the Fe2MO node is screened using first- and second-row transition metals (Mn–Zn and Tc–Cd). Results show electronic effects dominate first-row metals, whereas steric effects govern second-row systems. Kinetic volcano analysis identifies Cu(II) and Ru(III) as optimal catalysts for efficient CO2 hydrogenation, supporting rational design of MOF-based hydrogen storage and conversion systems for sustainable energy applications.\u0000 </div>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"47 24","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148942962","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}

引用次数: 0

Benchmark Reference Data and Computational Protocols for Predicting Excitation Energies of Thioindigoid Photoswitches 硫代靛蓝光开关激发能预测的基准参考数据和计算方案

IF 2.9 3区化学

Journal of Computational Chemistry Pub Date : 2026-09-11 DOI: 10.1002/jcc.70495

Elias Harrer, Carolin Müller, Dirk Zahn

{"title":"Benchmark Reference Data and Computational Protocols for Predicting Excitation Energies of Thioindigoid Photoswitches","authors":"Elias Harrer, Carolin Müller, Dirk Zahn","doi":"10.1002/jcc.70495","DOIUrl":"https://doi.org/10.1002/jcc.70495","url":null,"abstract":"<div>\u0000 \u0000 The accurate prediction of electronically excited states is essential for the computational design of molecular photoswitches but remains challenging for thioindigoid chromophores owing to their complex excited-state electronic structure. In this work, we establish theoretical best estimates for the two lowest singlet and three lowest triplet vertical excitation energies of a chemically diverse set of hemithiophenindigo (HTPI) derivatives using high-level coupled cluster methods (CC3 and CCSDT). The selected model systems retain the characteristic chromophoric core of thioindigo and hemithioindigo photoswitches while remaining accessible to benchmark calculations. Analysis of electron-rich and electron-poor derivatives reveals pronounced position-dependent effects on the low-lying excited states that closely resemble trends reported for larger thioindigoid chromophores. Based on this reference data, we benchmark 65 semiempirical and quantum-chemical methods, including density functional approximations across multiple rungs of Jacob's ladder as well as single- and multireference wave function approaches. To identify computationally efficient workflows for future virtual screening studies, we additionally assess 25 combinations of ground state geometry optimization and excitation-energy methods. The resulting recommendations for singlet-singlet and singlet-triplet excitation energies provide a validated methodological foundation for large-scale in silico exploration of thioindigo and hemithioindigo dyes, thus enabling the screening of tens of thousands of candidate chromophores while retaining high overall accuracy.\u0000 </div>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"47 24","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148943022","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}

引用次数: 0

Substituent Effects on the Stability of Pd–NHC Complexes: Switching From Molecular to “Cocktail-Type” Catalysis 取代基对Pd-NHC配合物稳定性的影响：从分子催化转向“鸡尾酒型”催化

IF 2.9 3区化学

Journal of Computational Chemistry Pub Date : 2026-09-11 DOI: 10.1002/jcc.70500

Vladislav O. Naumovich, Evgeniy G. Gordeev, Valentine P. Ananikov

{"title":"Substituent Effects on the Stability of Pd–NHC Complexes: Switching From Molecular to “Cocktail-Type” Catalysis","authors":"Vladislav O. Naumovich, Evgeniy G. Gordeev, Valentine P. Ananikov","doi":"10.1002/jcc.70500","DOIUrl":"https://doi.org/10.1002/jcc.70500","url":null,"abstract":"<div>\u0000 \u0000 The evolution of catalytic systems based on transition metal complexes under catalytic reaction conditions leads to the formation of a catalyst cocktail, i.e., an ensemble of species with different structures, each capable of exhibiting catalytic activity. Transformation of molecular Pd(II)–NHC complexes into a catalytically active cocktail form involves R–NHC coupling, which results in the formation of low-coordinated metal centers and [R–NHC](+)[X](−) salt (X = halogen). In this work, using DFT methods, it is demonstrated that one factor influencing the R–NHC coupling process is substituent effects within the pyridine or phosphine ligand of the Pd(II) complex (R = Me, Ph; NHC = IMe, IPr, IMes). The presence of electron-donating (–OMe) or electron-withdrawing (–CN; –F) substituents in the ligand molecule significantly influences both the activation energy and the reaction energy of the R–NHC coupling process. In particular, electron-accepting substituents reduce the potential barrier for this process and completely shift the equilibrium toward the product of the R–NHC coupling, whereas electron-donating substituents possess the opposite effect. Thus, the effect of substituents can act as a “switch” facilitating the transition from molecular catalysis to “cocktail-type” catalysis.\u0000 </div>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"47 24","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148943020","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}

引用次数: 0

Predicting the Stepwise Growth of Lithium Clusters Around Sulfur Species (S and S2) From the Topology of the Electron Localization Function 从电子局域函数的拓扑结构预测硫态（S和s2）周围锂簇的逐步生长

IF 2.9 3区化学

Journal of Computational Chemistry Pub Date : 2026-09-09 DOI: 10.1002/jcc.70503

Mohammad Esmaïl Alikhani

{"title":"Predicting the Stepwise Growth of Lithium Clusters Around Sulfur Species (S and S2) From the Topology of the Electron Localization Function","authors":"Mohammad Esmaïl Alikhani","doi":"10.1002/jcc.70503","DOIUrl":"10.1002/jcc.70503","url":null,"abstract":"In this work, we present a theoretical investigation of sulfur-doped lithium clusters, namely LinS and LinS2 (n = 1–10), with the aim of elucidating the mechanism governing the stepwise growth of lithium around sulfur centers. The equilibrium geometries of all clusters were first determined using density functional theory (DFT), and their electronic structures were subsequently analyzed through the topology of the electron localization function (ELF). The ELF analysis revealed the presence of two distinct types of topological valence domains: an inner domain fully localized on the sulfur atom and an outer domain delocalized over the lithium framework. We show that the growth of the lithium cluster is governed by the subtle interplay between these two domains. Most importantly, the combined topology of the inner and outer valence domains provides a predictive framework that not only identifies the preferred insertion site for each incoming lithium atom but also explains the progressive emergence of successive coordination shells, thereby leading systematically to the most stable structures throughout the growth process. The present findings open the way to a predictive description of lithium growth around larger sulfur species.","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"47 24","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.70503","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148915403","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}

引用次数: 0

DL_FFLUX Refactored: Accelerating Quantum Chemical Topology Simulations With Optimized Parallelization DL_FFLUX重构：加速量子化学拓扑模拟与优化并行

IF 2.9 3区化学

Journal of Computational Chemistry Pub Date : 2026-09-08 DOI: 10.1002/jcc.70501

Mohamadhosein Nosratjoo, Michael K. Bane, Paul L. A. Popelier

{"title":"DL_FFLUX Refactored: Accelerating Quantum Chemical Topology Simulations With Optimized Parallelization","authors":"Mohamadhosein Nosratjoo, Michael K. Bane, Paul L. A. Popelier","doi":"10.1002/jcc.70501","DOIUrl":"10.1002/jcc.70501","url":null,"abstract":"Molecular dynamics simulations are only as useful as they are both accurate and efficient. Here, we introduce an upgraded version of the simulation code DL_FFLUX that dramatically extends accessible time scales by combining a more efficient core algorithm with OpenMP and MPI parallelization. DL_FFLUX is a unique, state-of-the-art polarisable machine learning potential (MLP) that combines Quantum Chemical Topology (QCT) and machine learning (ML) and relies on DL_POLY as the driver for molecular dynamics simulations. This new implementation of DL_FFLUX delivers a massive performance boost, making simulations 6.8 to 49 times faster without compromising accuracy. This performance boost of DL_FFLUX is reported for condensed-phase simulations of water and ethanol and for single-molecule simulations of 6 small to medium-sized molecules. Moreover, we compared the optimized version of DL_FFLUX with other MLPs on the MD17 dataset for four molecules. DL_FFLUX is the fastest: depending on the system, it outperforms the second-fastest MLP by a factor of 1.8–9.6.","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"47 24","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.70501","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148902500","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}

引用次数: 0

Natural Atomic Orbitals at the Complete-Basis-Set Limit: A Frozen Natural-Minimal-Basis Construction 完全基集极限下的自然原子轨道：一种冻结的自然最小基构造

IF 2.9 3区化学

Journal of Computational Chemistry Pub Date : 2026-09-08 DOI: 10.1002/jcc.70491

Dariusz W. Szczepanik

{"title":"Natural Atomic Orbitals at the Complete-Basis-Set Limit: A Frozen Natural-Minimal-Basis Construction","authors":"Dariusz W. Szczepanik","doi":"10.1002/jcc.70491","DOIUrl":"10.1002/jcc.70491","url":null,"abstract":"<div>\u0000 \u0000 The standard natural atomic-orbital (NAO) construction is a mature and successful density-adaptive route to atom-centered orbitals. Here we examine it near the complete-basis-set limit, where the natural minimal basis is orthogonalized together with a large, nearly linearly dependent Rydberg space. Complete cc-pV<math>\u0000 <semantics>\u0000 <mrow>\u0000 <mi>n</mi>\u0000 </mrow>\u0000 <annotation>$$ n $$</annotation>\u0000 </semantics></math>Z (<math>\u0000 <semantics>\u0000 <mrow>\u0000 <mi>n</mi>\u0000 <mo>=</mo>\u0000 <mtext>D</mtext>\u0000 </mrow>\u0000 <annotation>$$ n=mathrm{D} $$</annotation>\u0000 </semantics></math>–7) ladders for four first-row rings, supplemented by correlated-density tests from borole to a cobaltacycle, show that valence NAOs remain localized while their AO expansions acquire large, mutually canceling contributions from neighboring centers and high-angular-momentum functions. The sensitivity appears first in the orbital coefficients and, at cc-pV7Z, in NPA charges. We introduce a frozen-NMB two-cycle construction that defines and freezes the natural minimal basis in a reduced AO subspace before restoring the full Rydberg complement. The resulting NAOs reproduce standard populations and qualitative orbital shapes in compact bases, preserve the full density, remain symmetric and smoothly convergent, and provide more compact AO coefficient expansions.\u0000 </div>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"47 24","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148902548","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}

引用次数: 0