Journal of Chemical Theory and Computation最新文献

{"title":"A Near-FCI Framework for Vibrationally Resolved X-ray Absorption Spectra","authors":"Yang Guo,&nbsp;Ning Zhang,&nbsp;Minrui Wei,&nbsp;Lu Zhang,&nbsp;Weijie Hua","doi":"10.1021/acs.jctc.6c01279","DOIUrl":"10.1021/acs.jctc.6c01279","url":null,"abstract":"<p>Wepresent a near-full configuration interaction frameworkbasedon iterative configuration interaction with selection and second-orderperturbation theory (iCIPT2) for simulating vibrationally resolvedX-ray absorption spectra. By combining high-fidelity potential energycurves with quantum wavepacket dynamics, our approach captures strongcorrelation and nuclear dynamics. Benchmarking on six diatomic systemsyields sub-0.1 eV accuracy and quantitative agreement with high-resolutionexperiments. This work demonstrates a promising approach for interpretingvibrationally resolved core-level spectroscopy, established here fordiatomic systems as an initial step, and lays a theoretical foundationfor applications in more-complex ultrafast experiments at large-scaleX-ray facilities.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"22 19","pages":"9881–9887"},"PeriodicalIF":5.8,"publicationDate":"2026-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149049663","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":"Benchmarking Hierarchical Double-Ended Transition-State Search Methods for Metal-Catalyzed Reactions","authors":"Shoubhik R. Maiti,&nbsp;David Buttar,&nbsp;Fernanda Duarte","doi":"10.1021/acs.jctc.6c00992","DOIUrl":"10.1021/acs.jctc.6c00992","url":null,"abstract":"<p>Efficient and reliable identification of transition states(TS)is critical for reaction modeling. Among the available approaches,the combination of double-ended TS search with eigenvector-following,referred to as hierarchical TS search, is an effective tool for locatingTSs starting from reactant and product geometries. However, systematicbenchmarking of these methods on transition metal-catalyzed reactionsremains limited. Here, we benchmark eight pipelined hierarchical methodsusing out-of-the-box settings on a diverse set of 30 single-step,closed-shell metal-catalyzed reactions, evaluating their success rateand computational efficiency. Most workflows achieve high successrates across the data set, indicating that modern double-ended methodsare generally robust for locating TSs in elementary organometallicreactions, and the main differences between methods lie in their computationalefficiency. The benchmark also reveals several key trends: (i) thefinal eigenvector-following step requires an accurate Hessian matrixor explicitly calculated <em>min-mode</em> for a high successrate, (ii) TS searches from interpolation-only paths (e.g., image-dependentpair potential, IDPP) and bracket methods (e.g., Dewar-Healy-Stewart,DHS) are often more efficient than popular methods, such as climbingimage nudged elastic band (CI-NEB), (iii) different hierarchical workflowscan converge to different TSs even when starting from the same twominima, (iv) larger structural changes between reactants and productsare associated with lower success rates and higher computational costs.We also show that further parameter tuning can reduce computationalexpense without reducing the success rate on our data set. These conclusionsare further supported by two case studies involving industrially relevantorganometallic reactions.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"22 19","pages":"10227–10243"},"PeriodicalIF":5.8,"publicationDate":"2026-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149049666","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":"Efficient Nonadiabatic Molecular Dynamics for Exploring Excitation Energy Transfer in Thermally Fluctuating Molecular Aggregates","authors":"Shunsuke Yabu,&nbsp;Hirofumi Sato,&nbsp;Masahiro Higashi","doi":"10.1021/acs.jctc.6c00422","DOIUrl":"10.1021/acs.jctc.6c00422","url":null,"abstract":"<p>Excitationenergy transfer (EET) in molecular aggregates is a fundamentalprocess in a wide range of condensed-phase systems, including photosyntheticcomplexes and organic semiconductors. Among the key factors influencingEET efficiency, thermal fluctuations play a critical role; however,accurately capturing their impact at the atomistic level remains computationallychallenging. To address this, we developed an efficient simulationframework that combines the Frenkel exciton model, the nonadiabaticmolecular dynamics (NAMD) simulation, and the molecular mechanicswith Shepard interpolation correction (MMSIC) method. The MMSIC significantlyaccelerates the evaluation of excitation energies during the NAMDsimulation, enabling atomistic treatment of thermal fluctuations.We applied this framework to two representative systems: exciton diffusionin crystalline anthracene and EET in the Fenna–Matthews–Olsonlight-harvesting complex. In both cases, the calculated results arein good agreement with previous studies, demonstrating the capabilityof the proposed approach to explore the interplay between thermalfluctuations and EET dynamics in complex molecular systems.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"22 19","pages":"9911–9926"},"PeriodicalIF":5.8,"publicationDate":"2026-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148255701","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":"Designing Coulombic Contact Interactions between Polarizable Particles through Asymmetry","authors":"Yanyu Duan,&nbsp;Zecheng Gan","doi":"10.1021/acs.jctc.6c00946","DOIUrl":"10.1021/acs.jctc.6c00946","url":null,"abstract":"<p>Polarizable particle systems, including charged colloids,polarizableions, biomolecular assemblies, and soft nanomaterials, can exhibitcontact electrostatic interactions that depart strongly from Coulombbehavior when the dielectric mismatch and geometric singularitiesamplify polarization effects. Here, we use charged dielectric spheresas a model system and show that these polarization contributions canbe canceled by jointly tuning size, charge, and dielectric asymmetries.By extending a recently developed image-charge formula to contactingdielectric spheres, at the two-body level, we derive analytical conditionsunder which the two-body contact interaction reduces to the bare Coulombform. At the selected design points, accurate two-sphere calculationsgive root-mean-square (RMS) contact force deviations below 3% fromthe Coulomb target. Separately, many-body molecular dynamics simulationsthat retain nonadditive polarization show that under the tested assemblyconditions, the structural correlations of six systems satisfyingthese two-body rules closely match those of their pure Coulomb references.These results establish asymmetry as a route for turning electrostaticcomplexity into Coulombic simplicity at contact, with implicationsfor predictable and controlled self-assembly and material design.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"22 19","pages":"9954–9962"},"PeriodicalIF":5.8,"publicationDate":"2026-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148805997","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":"Dissipative Quantum Algorithms for Excited-State Quantum Chemistry","authors":"Hao-En Li,&nbsp;Lin Lin","doi":"10.1021/acs.jctc.6c01298","DOIUrl":"10.1021/acs.jctc.6c01298","url":null,"abstract":"<p>Electronic excited states are central to a vast arrayof physicaland chemical phenomena, yet accurate and efficient methods for preparingthem on quantum devices remain challenging and are comparatively underexplored.We introduce a general dissipative algorithm for selectively preparing <em>ab initio</em> electronic excited states. The key idea is torecast excited-state preparation as an effective ground-state problemby suitably modifying the underlying Lindblad dynamics so that thetarget excited state becomes the unique steady state of a designedquantum channel. We develop three complementary strategies tailoredto different types of prior information about the excited state, suchas symmetry and approximate energy. We demonstrate the effectivenessand versatility of these schemes through numerical simulations ofatomic and molecular spectra, including valence excitations in prototypicalplanar-conjugated molecules and transition-metal complexes. Takentogether, these results provide a new pathway for advancing quantumsimulation methods for realistic, strongly correlated electronic systems.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"22 19","pages":"10137–10149"},"PeriodicalIF":5.8,"publicationDate":"2026-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149003488","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":"Dielectric-Screened Functionals for Cis–Trans Excitation Energies of Solvated Azobenzene Derivatives: Screening Trends in Comparison with Experiment and Published GW/BSE Calculations","authors":"Aswathy Jayachandran,&nbsp;Barry D. Dunietz","doi":"10.1021/acs.jctc.6c01302","DOIUrl":"10.1021/acs.jctc.6c01302","url":null,"abstract":"<p>Accurate modeling of electronically excited states insolutionis essential for the rational design of photoactive molecular systems,but requires a reliable treatment of environmental effects. We presenta mean-field approach that combines density functional theory witha polarizable continuum model (PCM) to account for environmental dielectricscreening, providing an efficient mean-field alternative to higher-costwavefunction- or many-body-based approaches. The framework employsdielectric-screened range-separated hybrid (SRSH) functionals withinPCM to obtain excited states of solvated azobenzene derivatives, aprototypical molecular photoswitch. SRSH–PCM excitation energiesbetter reproduce experiment when the larger static dielectric constant,which also accounts for nuclear polarization, is used to define long-rangescreening. Using the smaller optical dielectric constant, which representspurely electronic polarization, SRSH–PCM energies align betterwith previously reported high-quality GW–Bethe–Salpeterequation (GW/BSE) energies [Kshirsagar et al., JCTC 2020]. Our findingsdemonstrate that mean-field SRSH–PCM provides an effectivedescription of excited-state properties while offering insights intothe role of environmental screening and, in particular, the importanceof accounting for nuclear contributions to dielectric screening inmany-body calculations of solution-phase excitation energies.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"22 19","pages":"10341–10351"},"PeriodicalIF":5.8,"publicationDate":"2026-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149010288","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":"Achieving Near-Chemical Accuracy with Atom-Centered Potential-Augmented M06-2X","authors":"Zhehan Jia,&nbsp;Mahsa Nazemi-Ashani,&nbsp;Alberto Otero-de-la-Roza,&nbsp;Gino A. DiLabio","doi":"10.1021/acs.jctc.6c01050","DOIUrl":"10.1021/acs.jctc.6c01050","url":null,"abstract":"<p>The calculation of accurate thermodynamic properties,such as activationand reaction free energies, is an essential tool for elucidating reactionmechanisms. The method most commonly employed, density functionaltheory (DFT), generally falls short of chemical accuracy (1 kcal/molerror), resulting in order-of-magnitude errors in the calculationof equilibrium constants and rate constants. The inaccuracy of commonexchange-correlation functionals is compounded by the use of smalland medium-sized basis sets, which are mandatory for molecular systemswith realistic sizes. The basis set incompleteness error incurredby the use of these basis sets further diminishes the accuracy ofthermochemical calculations. In previous works, we proposed energycorrections based on the use of atom-centered potentials (ACP) asa way of mitigating functional and basis set incompleteness error.ACPs are one-electron potentials that, when applied in combinationwith a functional and basis set, yield results comparable to a higherlevel of theory with little additional cost. In this work, and basedon previous studies, we develop ACPs for thermochemical calculationsbased on the M06-2X density functional and the 6-31+G(d,p) basis.The resulting M06-2X/6-31+G(d,p)-ACP method is tested on a varietyof cases, demonstrating excellent performance for thermochemistryand kinetics calculations well outside the parametrization set, particularlyfor reaction energies and barrier heights of moderately large systems.At the same time, M06-2X/6-31+G(d,p)-ACP retains the low cost of theuncorrected functional and basis set combination.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"22 19","pages":"10052–10063"},"PeriodicalIF":5.8,"publicationDate":"2026-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149021791","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":"Nonadiabatic Excited-State Dynamics with Quantum Monte Carlo-Trained Machine Learning: Azomethane as a Stringent Test","authors":"Alfonso Annarelli,&nbsp;Emiel Slootman,&nbsp;Claudia Filippi","doi":"10.1021/acs.jctc.6c01442","DOIUrl":"10.1021/acs.jctc.6c01442","url":null,"abstract":"<p>We introduce quantumMonte Carlo (QMC)-trained multistate machine-learned(ML) force fields for nonadiabatic excited-state dynamics, targetingphotochemical processes in which the electronic character changesalong the reaction path and a consistent correlated description isrequired. In this framework, variational Monte Carlo (VMC) wave functionscombine compact selected configuration-interaction (CIPSI) expansionswith a Jastrow factor that explicitly accounts for dynamical correlation,while neural networks convert the stochastic VMC/CIPSI data into smoothpotential energy surfaces for large surface-hopping ensembles. Weapply this approach to azomethane, a demanding test case involvingtorsional relaxation through conical-intersection regions and C–Nbond dissociation on the hot ground state. Benchmark calculationssupport the accuracy of the QMC reference data and show robust forceconvergence across isomerization and dissociation geometries. TheQMC-trained dynamics preserves the expected photoisomerization mechanism,strongly reduces the excessive C–N breaking obtained with completeactive space self-consistent field, and predicts a small but non-negligibleprompt dissociation component after internal conversion, with a timescale consistent with femtosecond-resolved mass-spectrometry experiments.These results establish ML-QMC as a practical route to nonadiabaticphotochemical dynamics with accurate wave function reference data.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"22 19","pages":"10180–10191"},"PeriodicalIF":5.8,"publicationDate":"2026-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149022247","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":"Accelerating Chemical Potential Calculations with Minimal Normalizing Flows","authors":"Philippe B. Baron,&nbsp;Athanassios Z. Panagiotopoulos","doi":"10.1021/acs.jctc.6c01266","DOIUrl":"10.1021/acs.jctc.6c01266","url":null,"abstract":"<p>Chemical potentials are among the most important propertiesthatcan be obtained from a molecular simulation since they define manytechnologically relevant collective properties such as solubilitiesand activity coefficients. The chemical potential of a species insolution is typically obtained by computing the free energy changeof adding that species into a bulk system, a calculation typicallyvery expensive for systems of technological interest such as electrolytes,due to the lack of phase space overlap between “not-inserted″and “inserted″ states. Recently, normalizing flows havebeen introduced as a way to accelerate free energy computations bylearning a bijective function to map the configuration space of oneBoltzmann distribution onto another. Currently, these trainable mappingsare constructed to be as expressive as possible, theoretically havingthe ability to create a perfect mapping between states. This expressivitymakes them difficult to train, limiting their ability to be generated“on-the-fly″ for any new free energy estimation challenge,and in practice these mappings have shown only modest performanceimprovements for liquid systems. We address these issues by introducingthe concept of a “minimal″ normalizing flow (MNF). Thisis a trainable bijective mapping that is intentionally limited inexpressivity and instead applies low-dimensional, physically informedtransformations. Useful MNFs can be trained in approximately 1 minof GPU time due to their simplicity and our introduction of a novelloss function based on the Bhattacharyya distance as an alternativeto the Kullback–Leibler divergence. We show how calculationsof chemical potentials of pure and binary Lennard-Jones particle systemscan be accelerated by at least an order of magnitude with a simpleradial mapping. For a more complex illustration of the approach, weapply a two-dimensional (radial and orientational) mapping to thesolvation of sodium and chloride ions in water, showing that MNFscan increase the effective sample size by as much as 3 times for chargingfree energy calculations and as much as 8 times for calculating freeenergy changes due to force field perturbations. This provides thefoundation for the development of physically informed normalizingflows that can accelerate complex free energy calculations while retaininglow training costs.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"22 19","pages":"9976–9991"},"PeriodicalIF":5.8,"publicationDate":"2026-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149049670","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":"Mechanistic Dissection of Conformational Transitions in a Bicyclic Peptide via Molecular Modeling and Deep Learning","authors":"Ta I Hung,&nbsp;Raghu Venkatesan,&nbsp;Chia-en A. Chang","doi":"10.1021/acs.jctc.6c01233","DOIUrl":"10.1021/acs.jctc.6c01233","url":null,"abstract":"<p>Molecular conformations play a critical role in determiningmolecularproperties, such as membrane permeability, binding affinity, and ultimatelytherapeutic efficacy. Experimental and computational approaches cancharacterize conformations and provide insight into why certain conformationsare thermodynamically preferred over others. However, examining staticconformations alone may not fully explain why subtle differences,such as a single LEU-to-ILE mutation in a bicyclic peptide, can producemarkedly distinct conformational ensembles. Furthermore, analyzingtransition pathways between conformations reveals the mechanisms thatshape these ensembles. Here, we introduce a deep learning model, termedICoN-v1, trained on molecular dynamics (MD) simulation data to learnthe underlying physics that governs cyclic peptide conformationaldynamics. We examined cyclic hexapeptides with Nuclear Magnetic Resonance(NMR)-determined structures, and MYC-targeting bicyclic peptides thatare stereo-diversified or have a single LEU-to-ILE mutation. By followingminimum-energy pathways in the latent space constructed by ICoN-v1,we efficiently generated smooth conformational transition paths. Thesepathways reveal sequential sets of concerted backbone and side-chaintorsional rotations moving between energy minima. Notably, smoothtransition pathways that are absent from MD output were observed usingICoN-v1. Our results identify various sets of concerted torsionalmotions that are nonlinearly combined during conformational transitionsand reveal the key residues governing each stage of the transition,thereby elucidating how the observed conformations are generated andinforming molecular design.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"22 19","pages":"10281–10294"},"PeriodicalIF":5.8,"publicationDate":"2026-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148973888","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}