Journal of Chemical Theory and Computation最新文献

{"title":"The Potential Energy Landscape Formalism for Quantum Liquids in the Continuous Ring-Polymer Limit","authors":"Yang Zhou,&nbsp;Gustavo E. Lopez,&nbsp;Nicolas Giovambattista","doi":"10.1021/acs.jctc.6c01077","DOIUrl":"10.1021/acs.jctc.6c01077","url":null,"abstract":"<p>The potential energy landscape (PEL) formalism is a powerfultoolwithin statistical mechanics to study the thermodynamic behavior ofclassical and quantum liquids as well as non-annealing glasses. Inthe quantum case, this theoretical framework is based on the path-integralformulation of statistical mechanics where the liquid/non-annealingglass is mapped onto a classical system of ring-polymers. In previousstudies, and motivated by path-integral (PI) computer simulations,the PEL formalism was developed assuming that the ring-polymers werediscrete, i.e., each ring-polymer was composed of a finite numberof beads, <em>n</em>_<em>b</em>. In thiswork, we revisit the PEL formalism for the case where the ring-polymersof the system are continuous, i.e., <em>n</em>_<em>b</em> → ∞ (as required in the PI formulationof statistical mechanics). We find that in this limit, the PEL ofthe quantum liquid is unique and well-defined. The main PEL propertiesof the system, including the average inherent structure energy <em>E</em>_<em>IS</em>, configurational entropy <em>S</em>_<em>IS</em>, and vibrational Helmholtzfree energy <em>F</em>_<em>vib</em>, arealso well-defined (i.e., they converge). Notably, in the harmonicapproximation of the PEL, <em>F</em>_<em>vib</em> can be expressed analytically; it is identical to the freeenergy of a multidimensional quantum harmonic oscillator with thecorresponding frequencies given by the normal mode frequencies ofthe classical liquid counterpart (accessible from classical computersimulations). When applied to non-annealing glasses and crystals,this new version of the PEL formalism reduces to the so-called <em>quasi-harmonic approximation</em>, commonly used in the studyof solids. Overall, the PEL formalism for <em>n</em>_<em>b</em> → ∞ provides an alternative approachto its previous version (finite <em>n</em>_<em>b</em>); it is also more elegant and intuitive, and simpler to apply.For a Gaussian and harmonic PEL, this formalism (<em>n</em>_<em>b</em> → ∞) allows one to obtainthe Helmholtz free energy of the quantum liquid using classical computersimulations, avoiding the more expensive PI computer simulations.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"22 19","pages":"9963–9975"},"PeriodicalIF":5.8,"publicationDate":"2026-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148985068","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Correction to “Measuring Differences in Protein Allosteric Graphs Constructed via Molecular Dynamics Simulations”","authors":"Jiale Shi,&nbsp;Zhongyi Wan,&nbsp;Renjie Zhu,&nbsp;Qiang Cui","doi":"10.1021/acs.jctc.6c01745","DOIUrl":"10.1021/acs.jctc.6c01745","url":null,"abstract":"","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"22 19","pages":"10507–10509"},"PeriodicalIF":5.8,"publicationDate":"2026-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148985069","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"ML26: New Ingredients for an Integral-Features Density Functional with Broad Chemical Accuracy","authors":"Dayou Zhang,&nbsp;Yinan Shu,&nbsp;Benjamin G. Janesko,&nbsp;Donald G. Truhlar","doi":"10.1021/acs.jctc.6c01681","DOIUrl":"10.1021/acs.jctc.6c01681","url":null,"abstract":"<p>Integral-features density functional theory (IF-DFT)replaces theconventional integration over local ingredients with a nonlinear mappingfrom global integral descriptors, enabling machine-learned densityfunctionals with broad transferability. Here we report ML26@MN15,a new IF functional that extends the earlier ML25@MN15 model by incorporating12 additional correlation features─including overlap-projectedrung-3.5 terms, CS1 dynamic-correlation ingredients, and VV10 nonlocalcorrelation─and by treating Hartree–Fock exchange asan integral feature rather than as a fixed hybrid percentage. ML26@MN15employs 79 integral features evaluated on MN15 ingredients and a single-hidden-layerneural network with 5000 nodes to produce a size-extensive exchange–correlationenergy. Trained on 185 databases comprising 7242 reference data, ML26@MN15achieves a data-averaged energetic mean unsigned error of 0.89 kcal/mol,improving upon ML25@MN15 by 15% and outperforming a group of previousleading functionals across all eight chemical partitions examined.For the widely used MDB2019S, MGCDB84, and GMTKN55 data sets, ML26@MN15yields the lowest averaged errors among all tested functionals, includingthe results for GMTKN55 by ML-based Skala-1.1 and DM21 density functionalapproximations. The new functional also maintains strong performancefor systems containing heavy elements and exhibits improved behavioron a challenging self-interaction benchmark. These results show thatexpanding the integral-feature space with physically motivated nonlocalingredients yields a density functional with unprecedented accuracyacross diverse chemical benchmarks. The broad and consistent accuracyof ML26@MN15 highlights the promise of integral-features density functionalapproximations as a scalable framework for incorporating additionalnonlocal physics into future functional development.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"22 19","pages":"9901–9910"},"PeriodicalIF":5.8,"publicationDate":"2026-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149022248","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Spin-Consistency Constraints in Noncollinear Tensor TDA","authors":"Wenxian Qin,&nbsp;Tai Wang,&nbsp;Yue Yu,&nbsp;Yuanyang Liu,&nbsp;Yi Qin Gao,&nbsp;Yunlong Xiao","doi":"10.1021/acs.jctc.6c01470","DOIUrl":"10.1021/acs.jctc.6c01470","url":null,"abstract":"<p>TDDFT for open-shell systems, whether spin-conservingor spin-flip,has long suffered from spin contamination. This problem arises becausethe single-excitation space built upon a single Kohn–Sham determinantis not spin-complete. Adopting spin tensor reference states thereforeoffers an elegant and promising route to resolving this issue. Inthis work, we revisit the tensor TDDFT equations within the Tamm–Dancoffapproximation (TDA) from a noncollinear perspective. We show that,for <em>S</em> = 1/2 reference states, the internal consistencyof the spin tensor formulation can, with the aid of the zero-excitation-energytheorem, be recast as a set of constraints that the exchange–correlationkernel must satisfy. Standard noncollinear functionals, however, generallyfail to meet these constraints. To address this, we propose a kernelreconstruction scheme that is independent of the specific functionalform and free of empirical parameters. This scheme enforces the requiredconstraints, restoring internal consistency in the full spin tensorstructure, with spin adaptation following as a natural consequence.Furthermore, when extended to tensor reference states with other valuesof S, such as S = 1 for the oxygen molecule, the scheme eliminatesthe so-called artifact states, namely solutions with severely underestimatedexcitation energies. In addition, the scheme allows the target statesthat ROKS reference states aim to describe to be expressed and computed,at the TDA level, within the same unified framework as other states,a capability that spin-adapted spin-conserving TDDFT has so far lacked.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"22 19","pages":"10192–10202"},"PeriodicalIF":5.8,"publicationDate":"2026-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149049669","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Machine Learning Meets Spin–Orbit Coupling: Reconstruction of Spin–Orbit-Mixed Potential Energy Curves in MgCa","authors":"Giovanna C. Rizkallah,&nbsp;Samir N. Tohme","doi":"10.1021/acs.jctc.6c01257","DOIUrl":"10.1021/acs.jctc.6c01257","url":null,"abstract":"<p>Spin–orbit coupling (SOC) induces state mixingand distortionsin potential energy curves (PECs), complicating their constructionand interpretation for diatomic molecules. We introduce a fully automatedmachine-learning framework for reconstructing physically consistentSOC-resolved PECs across independent electronic-structure calculationswith different basis-set representations. The approach combines generativedata augmentation using a conditional Wasserstein Generative AdversarialNetwork with gradient penalty (cWGAN-GP) with supervised regressionmodels (Ridge Regression, Gradient Boosting, and Extremely RandomizedTrees) to learn the relationship between raw SOC-affected PECs, spin–orbitcomposition tables, and their physically corrected counterparts. UsingMgCa as a demonstration system, SOC-resolved PECs and spectroscopicconstants were computed at the MRCI level for the ground and 26 low-lyingexcited states. Models trained on a single manually corrected referencebasis accurately predict physically corrected PEC energies for independentbasis sets, achieving sub-percent deviations in dissociation energieswhile preserving asymptotic limits, equilibrium geometries, and fine-structuresplittings without explicit constraints. This framework eliminatesmanual postprocessing of SOC-mixed PECs and provides a scalable strategyfor consistent spin–orbit treatment in high-level electronic-structureworkflows.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"22 19","pages":"10366–10380"},"PeriodicalIF":5.8,"publicationDate":"2026-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148973886","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Developing the Atom-Bond Electronegativity Equalization Method Polarizable Force Field for Zinc Metalloproteins and Their Simulations","authors":"Zhan-Qing Yu,&nbsp;Zuo-Peng Liang,&nbsp;Wan-Qing Wang,&nbsp;Qing-Yan Sun,&nbsp;Hong Huang,&nbsp;Cui Liu,&nbsp;Dong-Xia Zhao,&nbsp;Zhong-Zhi Yang","doi":"10.1021/acs.jctc.6c01082","DOIUrl":"10.1021/acs.jctc.6c01082","url":null,"abstract":"<p>Zinc(Zn), the second most abundant transition metalin biologicalsystems, plays essential roles in numerous metalloproteins presentin diverse organisms including humans, plants, and bacteria. Currently,Zn-based proteins have attracted research interest owing to theirinvolvement in a series of vital physiological processes, such asenzymatic reactions, deoxyribonucleic acid and ribonucleic acid binding,and the stability of biological structures. Although experimentalmethods can reveal macroscopic processes, they cannot efficientlycapture the detailed behavior of these compounds. Therefore, theoreticalexploration of Zn-binding conformations is significant. Herein, afluctuating charge force field for Zn-containing metalloproteins isreported based on the atom-bond electronegativity equalization method(ABEEM). We designed our model molecules based on the Protein DataBank (PDB) database, focusing primarily on tetracoordinated Zn proteins.The ABEEM polarizable force field parameters were determined and optimizedusing the quantum mechanical method, which were in good agreementwith computed charge distributions, potential energy surfaces, andgeometric structures. Molecular dynamics simulations were subsequentlyperformed on 10 different protein segments. The developed ABEEM modelreproduces the first Zn–O_w peak position and maintainsthe structural stability of the systems throughout the simulations.Compared with the crystal structures from the PDB database, the ABEEMmodel shows lower root mean square deviation values for heavy atomsin these domains. All protein domains can dynamically capture thechange in charge distributions. This process can be further appliedto simulate the detailed behavior of the molecules and investigatetheir properties. The identified force field for Zn metalloproteinsby the ABEEM provides a promising approach for simulating Zn-relatedbiological systems while simplifying several complex and time-consumingprocesses.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"22 19","pages":"10244–10262"},"PeriodicalIF":5.8,"publicationDate":"2026-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148973887","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Implementation of the Multigrid Gaussian-Plane-Wave Algorithm with GPU Acceleration in PySCF","authors":"Rui Li,&nbsp;Xing Zhang,&nbsp;Qiming Sun,&nbsp;Yuanheng Wang,&nbsp;Junjie Yang,&nbsp;Garnet Kin-Lic Chan","doi":"10.1021/acs.jctc.6c00947","DOIUrl":"10.1021/acs.jctc.6c00947","url":null,"abstract":"<p>We introduce a GPU-accelerated multigrid Gaussian-Plane-Wavedensityfitting (FFTDF) approach for efficient Fock builds and nuclear gradientevaluations within Kohn–Sham density functional theory, asimplemented in the G<span>PU4PySCF</span> module of P<span>ySCF</span>. OurCUDA kernels employ a grid-based parallelization strategy for contractingGaussian basis function pairs and achieve 50% to 80% of the FP64 peakperformance on NVIDIA GPUs, with no loss of efficiency for high angularmomentum (up to <em>f</em>-shell) functions. Benchmark calculationson molecules and solids with up to 1536 atoms and 20480 basis functionsshow up to 25 × speedup on an H100 GPU relative to the CPU implementationon a 28-core shared-memory node. For a 256-water cluster, the ground-stateenergy and nuclear gradients can be computed in ∼30 secondson a single H100 GPU. This implementation serves as an open-sourcefoundation for many applications, such as <em>ab initio</em> molecular dynamics and high-throughput calculations.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"22 19","pages":"10101–10112"},"PeriodicalIF":5.8,"publicationDate":"2026-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148985067","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A Physics-Constrained Synergetic Active- and Transfer-Learning Framework for Constructing a Spectroscopically Accurate Full-Dimensional Potential Energy Surface of H2O–N2 Complex","authors":"Jia Nie,&nbsp;You Li,&nbsp;Zhixia Wang,&nbsp;Xiaolong Zhang,&nbsp;Hui Li","doi":"10.1021/acs.jctc.6c01295","DOIUrl":"10.1021/acs.jctc.6c01295","url":null,"abstract":"<p>High-resolution spectroscopy of weaklybound molecularcomplexesrequires theoretical predictions with uncertainties below 0.1 cm^–1. Achieving this level of accuracy places stringentdemands on the underlying full-dimensional potential energy surfaces(PESs). However, constructing such PESs remains challenging becauseflexible configuration space requires dense sampling and the <em>ab initio</em> energies used for fitting must meet spectroscopicaccuracy requirements. Here, we develop a physics-constrained synergeticactive- and transfer-learning framework (SynATL) that combines uncertainty-drivenactive learning, high-level refinement via transfer learning, andan explicit long-range representation to construct spectroscopicallyaccurate full-dimensional PESs. SynATL was used to construct a full-dimensionalPES of the H₂O–N₂ complex at the post-CCSD(T)level, achieving a weighted root-mean-square error (RMSE) of 0.815cm^–1 on the test set and sub-cm^–1 RMSEs in the spectroscopically relevant low-energy and attractiveregions. Applied to rovibrational calculations of H₂O–N₂ and D₂O–N₂, the resulting PESreproduces microwave transitions with a root-mean-square deviation(RMSD) of 1.6 × 10^–4 cm^–1, about 80% lower than previous theoretical values, and gives 10^–3 cm^–1 level band-specific RMSDsfor 235 assigned infrared lines across the H₂O–N₂ bending/overtone and D₂O–N₂ stretching/bendingbands. SynATL therefore provides an efficient and transferable frameworkfor full-dimensional PESs for quantitative spectroscopy of weaklybound complexes.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"22 19","pages":"10352–10365"},"PeriodicalIF":5.8,"publicationDate":"2026-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149003487","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Primary Role of Semi-Local and Exact-Exchange Difference in the Description of Correlation Effects in Hybrid Functionals","authors":"Vignesh Balaji Kumar,&nbsp;Szymon Śmiga,&nbsp;Rodrigo Araújo Mendes,&nbsp;Bogumiła Jezierska,&nbsp;Rodney Bartlett,&nbsp;Ireneusz Grabowski","doi":"10.1021/acs.jctc.6c00843","DOIUrl":"10.1021/acs.jctc.6c00843","url":null,"abstract":"<p>Hybrid density functionalapproximations are among themost widelyused electronic-structure methods, yet the physical origin of theirrepresentation of correlation effects remains incompletely understood.In this work, we analyze correlation in hybrid functionals from theperspectives of Kohn–Sham exchange–correlation potentials,correlated densities, and energy-related observables. We show thatthe dominant qualitative features of correlation in hybrid DFAs donot arise primarily from the semilocal correlation functional itself,but instead from the difference between the semilocal exchange andexact-exchange contributions. This exchange-difference term is essentialfor restoring the physically correct structure of the correlationcomponent of the exchange–correlation potential and the correspondingcorrelated density, whereas the semilocal correlation part acts mainlyas a compensating contribution in the core and valence regions. Basedon this analysis, we propose an interpretable construction principlefor hybrid functionals in which the semilocal/exact-exchange differenceis scaled in a controlled way. As a proof of concept, this methodologyyields the simple global hybrid UMK26 functional. Despite its uncomplicatedglobal-hybrid form, the functional produces correlation potentialsand correlated densities in good agreement with CCSD(T) references,delivers accurate ionization potentials from orbital energies, andyields very good charge-transfer excitation energies, performing ona comparable footing with several recently proposed range-separatedhybrids. Although UMK26 is not uniformly optimal across all thermochemicalbenchmarks, it performs particularly well for self-interaction-sensitivesystems and provides a physically transparent route for the rationaldesign of future hybrid density functionals.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"22 19","pages":"10036–10051"},"PeriodicalIF":5.8,"publicationDate":"2026-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149010289","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Many-Body Expansion of the MP2 Correlation Contribution to the Binding Energies of Water Clusters: A Localized Excitation Analysis","authors":"Long H. Nguyen,&nbsp;Sotiris S. Xantheas","doi":"10.1021/acs.jctc.6c01287","DOIUrl":"10.1021/acs.jctc.6c01287","url":null,"abstract":"<p>Themany-body expansions of Hartree–Fock (HF)and correlationcontributions to water cluster MP2 binding energies converge differently:the HF contribution (one-body (1B) repulsive, two-body (2B) and three-body(3B) attractive) converges at the 3B term, whereas the MP2 correlationcontribution (1B and 2B attractive) converges at the 2B term, with99.7% arising from localized double excitations spanning one and twomonomers. Two orbital excitation truncation approximations, MP2-1B2B(geometry based) and localized LMP2-1M2M (excitation space based),recover ≥99.2% of the canonical MP2 binding energies.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"22 19","pages":"9888–9900"},"PeriodicalIF":5.8,"publicationDate":"2026-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149022246","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}