Journal of Chemical Theory and Computation最新文献

{"title":"Python Library for Monte Carlo Simulations with Ab Initio and Machine-Learned Interatomic Potentials.","authors":"Woodrow N Wilson,Vivek S Bharadwaj,Neeraj Rai","doi":"10.1021/acs.jctc.5c01148","DOIUrl":"https://doi.org/10.1021/acs.jctc.5c01148","url":null,"abstract":"There is a growing need in the simulation community for software that provides a transparent, reproducible, usable, and extensible (TRUE) Monte Carlo (MC) simulation framework employing energies from ab initio methods and machine-learning interatomic potentials (MLIPs). We introduce a Python library (ASE-MC) that adds Monte Carlo functionality to the Atomic Simulation Environment (ASE) package. Now, we can combine the powerful tools used to build systems and perform ab initio and MLIP in ASE with MC simulation algorithms to sample the configurational space with a concise Python script. After presenting the design philosophy, we demonstrate the flexibility of our approach using selected examples. These example simulations include liquid water described with a message-passing MLIP in the canonical and isothermal-isobaric ensembles, sampling the characteristic dihedral angle of biphenyl and comparing an MLIP to first-principles calculations, and a grand canonical Monte Carlo simulation of ammonia adsorption on Pt(111). These examples showcase the main features of the software, which include flexibility in the choice of ab initio or MLIP engine, ab initio or MLIP grand canonical MC with cavity bias insertions and deletions, the ability to add custom MC moves to the move set, and how users can condense complex MC workflows into a single Python script. This library serves as a framework for reproducible Monte Carlo simulations, facilitating easy reproduction of the work and application to new systems.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"80 1","pages":""},"PeriodicalIF":5.5,"publicationDate":"2025-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145235870","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":"All-Atom Reactive Monte Carlo Molecular Dynamics for Molecular Doping in Organic Semiconductors.","authors":"Vishnu Raghuraman, Archana Verma, Nicholas E Jackson","doi":"10.1021/acs.jctc.5c01206","DOIUrl":"https://doi.org/10.1021/acs.jctc.5c01206","url":null,"abstract":"<p><p>The computational study of molecular doping in organic semiconductors (OSCs) is challenged by multiple competing length and time scales. We present an all-atom Reactive Monte Carlo Molecular Dynamics (RMCMD) method for quantitatively determining molecular doping efficiency in OSCs. A Metropolis criterion is employed for the doping reaction, which is parametrized from density functional theory (DFT) calculations of energetics and atomic partial charges of the doped and neutral molecular species. Polaronic effects are included in the RMCMD method to enable geometric reorganization upon doping, including the flattening of the inter-ring dihedrals. Extensions to partial charge transfer states are also developed to allow for the inclusion of charge transfer complexes. To demonstrate the validity of the approach, the doping efficiency and radial distribution function of a poly(3-hexylthiophene) system doped with 2,3,5,6-tetrafluoro-7,7,8,8-tetracyanoquinodimethane are calculated in an amorphous morphology. The method is implemented as a fix in LAMMPS, with the code made publicly available on GitHub.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":""},"PeriodicalIF":5.5,"publicationDate":"2025-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145243338","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":"Energy Decomposition Analysis of Excited States Based on Time-Dependent Density Functional Theory Calculations Employing a Dielectric-Screened Range-Separated Hybrid Functional.","authors":"Roshan Khatri,Barry D Dunietz","doi":"10.1021/acs.jctc.5c01234","DOIUrl":"https://doi.org/10.1021/acs.jctc.5c01234","url":null,"abstract":"Controlling the alignment of low-lying excited states is central to molecular design efforts aimed at improving the performance in targeted optoelectronic applications. Typically, the energies of these states are governed by the gap between the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO), with exchange repulsion destabilizing the lowest singlet state (S1) relative to the triplet (T1). However, through rational molecular design, the S1-T1 energy gap can be minimized─or even inverted. Such excited-state scenarios can enable mechanisms like thermally activated delayed fluorescence (TADF), which enhance the light-emission efficiency. In this work, we apply energy component analysis to time-dependent DFT (TDDFT) calculated excited states to better understand the role of the dielectric environment on S1 and T1 state energies. The analysis is performed using the SRSH-PCM approach, which provides a consistent treatment of environmental effects by combining a dielectric-screened range-separated hybrid (SRSH) functional with a polarizable continuum model (PCM). We demonstrate the utility of this approach by analyzing the excited-state properties of three representative molecular systems relevant to optoelectronics. Our results offer valuable insight into energy trends governing the alignment and coupling of excited states, which are key to optimizing efficiency in relevant applications.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"80 1","pages":""},"PeriodicalIF":5.5,"publicationDate":"2025-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145240943","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":"Equation-of-Motion Coupled-Cluster Variants in Combination with Perturbative Triples Corrections in Strong Magnetic Fields.","authors":"Marios-Petros Kitsaras, Florian Hampe, Lena Reimund, Stella Stopkowicz","doi":"10.1021/acs.jctc.5c00779","DOIUrl":"https://doi.org/10.1021/acs.jctc.5c00779","url":null,"abstract":"<p><p>In this paper, we report on the implementation of the EOM spin-flip (SF), ionization-potential (IP), and electron-affinity (EA) coupled cluster singles doubles (CCSD) methods for atoms and molecules in strong magnetic fields for energies as well as one-electron properties. Moreover, non-perturbative triples corrections using the EOM-CCSD(T)(a)* scheme were implemented in the finite-field framework for the EE, SF, IP, and EA variants. These developments allow access to a large variety of electronic states as well as the investigation of IPs and EAs in a strong magnetic field. The last two indicate the relative stability of the different oxidation states of elements. The increased flexibility to target challenging electronic states and access to the electronic states of the anion and cation are important for the assignment of spectra from strongly magnetic white dwarf (WD) stars. Here, we investigate the development of IPs and EAs in the presence of a magnetic field for the elements of the first and second rows of the periodic table. In addition, we study the development of the electronic structure of Na, Mg, and Ca in an increasingly strong magnetic field that aided in the assignment of metal lines in a magnetic WD. Lastly, we investigate the electronic excitations of CH in different magnetic-field orientations and strengths, a molecule that has been found in the atmospheres of WD stars.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":""},"PeriodicalIF":5.5,"publicationDate":"2025-10-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145237498","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":"Electron Affinities from Equation-of-Motion Frozen Pair-Type Coupled Cluster Methods and Their Dependence on Single Excitations, Molecular Orbitals, and Basis Set Sizes.","authors":"Saman Behjou,Paweł Tecmer,Katharina Boguslawski","doi":"10.1021/acs.jctc.5c01258","DOIUrl":"https://doi.org/10.1021/acs.jctc.5c01258","url":null,"abstract":"We introduce a series of alternative electron affinity equation-of-motion frozen-pair coupled cluster (EA-EOM-fpCC) methods for computing electron affinities and open-shell electronic structures. These methods are systematically benchmarked against the reference Δ-CCSD(T) approach and experimental data for a representative molecular data set using natural pair coupled cluster doubles (pCCD) orbitals and various basis set sizes. A comparison to canonical CC methods is also discussed. Additionally, EA-EOM-fpCC results are compared with those derived from the difference between double and single ionization potentials (DIP-EOM-CC and IP-EOM-CC) of dicationic species within the same ground-state fpCC reference framework. Our results demonstrate that frozen-pair approaches significantly reduce computational costs while maintaining high accuracy, offering an efficient strategy for studying electron affinities and open-shell systems in large molecules. The IP/DIP-EOM-fp(L)CCSD model stood out as the best post-pCCD flavor to predict EAs, achieving a mean error of 0.09 eV compared to experimental results, while EA-EOM-fpCCD is closest to Δ-CCSD(T) reference data. Finally, diffuse functions are not recommended for EA calculations using the IP/DIP-EOM-fpCC recipe and are not required for the EA-EOM-fpCC variants if sufficiently large basis sets are employed.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"71 1","pages":""},"PeriodicalIF":5.5,"publicationDate":"2025-10-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145229269","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":"Calculating Nonbonded Potentials for Classical Simulations of Atoms in Molecules and Metal Surfaces.","authors":"Scott T Milner","doi":"10.1021/acs.jctc.5c01017","DOIUrl":"https://doi.org/10.1021/acs.jctc.5c01017","url":null,"abstract":"Classical simulations of real molecules require realistic nonbonded interactions between constituent atoms, which have traditionally been adjusted for good agreement with liquid properties and copied extensively among similar atom types. In this work, we propose ab initio methods to compute both the C12 short-range repulsion and the C6 dispersive attraction between atoms. We relate the repulsion to the distance at which the electron density near an atom falls below a certain threshold, chosen to match radii for atoms in the OPLS force field. We compute the dispersive attraction by applying the McLachlan integral formula to the polarizability contributions of each atom in a molecule as a function of imaginary frequency. These polarizability contributions can be computed by time-dependent Hartree-Fock methods in GAMESS, which conveniently partitions the total polarizability among bonds and lone pairs. Our method produces values for both C12 and C6 parameters in good agreement with existing OPLS values when applied to nearly 200 atom types in over 100 organic molecules from the virtualchemistry.org archive. We verify that different instances of OPLS atom types have nearly identical polarizabilities, lending credence both to our method and to atom types based on local chemical environments. We extend our frequency-integral method for computing dispersive interactions to atoms in molecules near metal surfaces, which screen nearby fluctuating fields, with a frequency response limited by the plasma frequency. The screening is equivalent to a fluctuating image dipole with which the atom interacts, giving rise to a 1/z3 interaction with a metal half-space. This interaction can be conveniently represented as a conventional 1/r6 interaction with each metal atom, summed over the half-space.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"128 1","pages":""},"PeriodicalIF":5.5,"publicationDate":"2025-10-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145235841","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":"End-to-End Modeling of Reaction Field Energy Using Data-Driven Geometric Graph Neural Networks","authors":"Yongxian Wu,&nbsp;, ,&nbsp;Qiang Zhu,&nbsp;, and ,&nbsp;Ray Luo*,&nbsp;","doi":"10.1021/acs.jctc.5c01193","DOIUrl":"10.1021/acs.jctc.5c01193","url":null,"abstract":"<p >Electrostatic interactions are fundamental to the structure, dynamics, and function of biomolecules, with broad applications in protein–ligand binding, enzymatic catalysis, and nucleic acid regulation. The Poisson–Boltzmann (PB) equation provides a physically grounded framework for modeling these interactions. However, solving the PB equation for large and complex biomolecular systems remains computationally expensive as traditional numerical solvers scale poorly with system size. While the Generalized Born (GB) model offers a more computationally efficient approximation, it does so at the cost of reduced accuracy relative to full PB solutions. To overcome these limitations, we propose PBGNN, a novel end-to-end framework that uses data-driven geometric graph neural networks to directly approximate PB electrostatic energies without relying on the GB approximation. PBGNN incorporates sinusoidal embeddings of atomic charges and a message-passing architecture to efficiently capture long-range interactions in large biomolecules. To address training instability caused by high variance in atomic electrostatic potentials, we introduce a charge-weighted mean squared error (CMSE) optimization objective that improves convergence. We benchmark PBGNN on the AMBER PBSA suite and PBSMALL, a new dataset designed for rapid evaluation of small-molecule electrostatics in drug discovery contexts. The results demonstrate that PBGNN consistently achieves high accuracy in predicting the PB energy with linear computational complexity. Furthermore, it provides reliable and precise PB free energy predictions for both large biomolecular complexes and small-molecule datasets, showcasing its strong generalizability, scalability, and potential utility in drug discovery tasks requiring accurate electrostatic modeling of small molecules. Comprehensive ablation studies further reveal the impact of architectural components, such as geometric representation, objective design, and cutoff strategy, informing future research directions. Finally, we release PBGNN as an open-source, self-contained codebase, along with preprocessed datasets and a complete training and evaluation pipeline, to support scalable and accurate electrostatic analysis that facilitates future research in associated areas.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"21 19","pages":"9710–9725"},"PeriodicalIF":5.5,"publicationDate":"2025-10-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145229267","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":"Can Semilocal Approximations to the Embedding Potential Tackle Charge-Transfer-to-Solvent Excitations? An Aqueous Thiocyanate Example.","authors":"Pierre-Olivier Roy,Mingxue Fu,Ronit Sarangi,Anna I Krylov,Tomasz A Wesolowski","doi":"10.1021/acs.jctc.5c00991","DOIUrl":"https://doi.org/10.1021/acs.jctc.5c00991","url":null,"abstract":"Frozen-density embedding theory (FDET) provides a formal basis for methods employing density-dependent embedding potentials. FDET-based methods involve approximations concerning: (i) the choice of the approximant for the bifunctional vxctnad[ρA,ρB], (ii) the localization of the embedded wave function, and (iii) the approach used to generate the electron density of the environment. The set of approximations that has been shown to yield highly accurate complexation-induced shifts in vertical excitation energies for valence excitations localized on the chromophore─referred to as the \"standard FDET protocol\"─is expected to fail if applied to charge-transfer-to-solvent excitations. This work illustrates that such excitations can also be treated using an FDET-based method; however, they require refinement of the approximations used in the standard protocol.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"21 1","pages":""},"PeriodicalIF":5.5,"publicationDate":"2025-10-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145229265","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 Particle-Based Implicit Solvent Model for Short-Range Oscillatory Solvation Forces.","authors":"Chuncheng Li,Yao Lu,Lei Liu,Meng Deng,Zhaochuan Fan","doi":"10.1021/acs.jctc.5c01267","DOIUrl":"https://doi.org/10.1021/acs.jctc.5c01267","url":null,"abstract":"Experimental and theoretical studies have demonstrated that when two parallel surfaces approach within nanometer separations, ordered layering of solvent molecules in the confined region gives rise to pronounced short-range, periodic oscillatory forces. However, the high computational expense of explicit solvent simulations has hindered detailed exploration of how these oscillatory forces regulate colloidal assembly dynamics. We develop an implicit solvent model for surfaces grafted with nonpolar ligands in nonpolar solvents, which resolves angle-dependent oscillatory solvation forces with molecular-level fidelity and computational efficiency, parametrized using explicit-solvent potential of mean force profiles. Microsecond-scale implicit solvent simulations of colloidal systems containing hundreds of nanoparticles further uncover that assembly pathways and phase behavior critically depend on particle shape and size. This efficient modeling framework offers a robust theoretical and numerical tool for elucidating solvent-mediated self-assembly mechanisms and for precision control of colloidal architectures.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"28 1","pages":""},"PeriodicalIF":5.5,"publicationDate":"2025-10-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145229266","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":"Structure and Dynamics of the Misfolding Intermediate in the Pathogenic T183A Prion Protein Mutant","authors":"Carmen Biancaniello,&nbsp;, ,&nbsp;Alessandro Emendato,&nbsp;, and ,&nbsp;Alfonso De Simone*,&nbsp;","doi":"10.1021/acs.jctc.5c00742","DOIUrl":"10.1021/acs.jctc.5c00742","url":null,"abstract":"<p >Characterizing high-energy conformations in protein molecules is crucial to delineate the nature of dynamic processes that underlie biological activity, as these elusive species often play critical roles in fundamental mechanisms of the cell, such as enzyme catalysis or protein folding and aggregation, among many others. In this context, the integration of molecular simulations with experimental biophysics represents a powerful strategy to delineate complex conformational landscapes, enabling the study of transient conformations at atomic resolution. Here, we characterized intermediate states along the misfolding pathway of the human prion protein (PrP) variant T183A, which is associated with familial Creutzfeldt–Jakob disease. Using replica-averaged molecular dynamics simulations, restrained with nuclear magnetic resonance chemical shifts, we obtained structural ensembles showing enhanced conformational heterogeneity for the T183A variant compared with the WT protein. The mutant ensemble was found to populate partially misfolded states characterized by disruption of the β-sheet and local unfolding of key helical regions of the protein. Additionally, dynamic cross-correlation analyses evidenced significant loss of cooperative fluctuations across secondary structure elements, delineating how structural destabilization in the T183A variant leads to the insurgence of misfolding intermediates. Collectively, these findings provide critical insights into the underlying mechanisms of T183A-induced PrP misfolding and its consequent aggregation into amyloid fibrils.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"21 19","pages":"9909–9918"},"PeriodicalIF":5.5,"publicationDate":"2025-10-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/pdf/10.1021/acs.jctc.5c00742","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145215853","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}