Journal of Chemical Theory and Computation最新文献

{"title":"A Case Study of an Energy Barrier in Li-Ion Battery Cathode Material Using DFT and Post-HF Approaches.","authors":"Laura Bonometti, Denis Usvyat, Lorenzo Maschio","doi":"10.1021/acs.jctc.4c01020","DOIUrl":"10.1021/acs.jctc.4c01020","url":null,"abstract":"<p><p>With the ever-increasing interest toward energy storage materials, an accurate understanding of the underlying physicochemical processes becomes mandatory for enabling accurate and predictive simulations. In this study, we apply multilevel quantum chemical calculations on a benchmark material commonly adopted as a cathode in Lithium batteries, Li_0.5Co_0.5⁺³Ni_0.5⁺⁴O₂. We estimate the Lithium hopping barrier, a key quantity for the estimate of Li diffusion coefficient, at different levels: Hartree-Fock (HF), density functional theory (DFT), periodic local Møller-Plesset perturbation theory of second order, complemented with a coupled cluster correction evaluated using an embedded-fragment approach. The post-HF methods were used here not only for benchmarking the key quantities themselves but also for assessing the accuracy of different functionals and probing the influence of the long-range and static correlation. For the given system and quantity in question, we observe that obtained results do not significantly vary across different DFT functionals or post-HF methods, which is rather uncommon. Such an agreement between the employed methods suggests that static correlation, even if prominent in this system, cancels out in the studied energy differences. In fact, the values of the T1 diagnostics, which test the reliability of the single-reference description, do vary from one fragment to another. But for certain fragments they are fairly small and of similar magnitude, indicating the applicability of such fragments for the correction. Our best estimate of the reaction barrier is about 0.85 eV.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":"10114-10119"},"PeriodicalIF":5.7,"publicationDate":"2024-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142589482","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":"Generalized Path Integral Energy and Heat Capacity Estimators of Quantum Oscillators and Crystals Using Harmonic Mapping.","authors":"Sabry G Moustafa, Andrew J Schultz","doi":"10.1021/acs.jctc.4c01088","DOIUrl":"10.1021/acs.jctc.4c01088","url":null,"abstract":"<p><p>Imaginary-time path integral (PI) is a rigorous tool to treat nuclear quantum effects in static properties. However, with its high computational demand, it is crucial to devise precise estimators. We introduce generalized PI estimators for the energy and heat capacity that utilize coordinate mapping. While it can reduce to the standard thermodynamic and centroid virial (CVir) estimators, the formulation can also take advantage of harmonic character of quantum oscillators and crystals to construct a coordinate mapping. The method is not applicable to fluids or systems with imaginary modes such as double-well potentials. This yields harmonically mapped averaging (HMA) estimators, with mappings that decouple (HMAc) or couple (HMAq) the centroid and internal modes. The HMAq is constructed with normal mode coordinates (HMAq-NM) with quadratic scaling of cost or harmonic oscillator staging (HMAq-SG) coordinates with linear scaling. The estimator performance is examined for a 1D anharmonic oscillator and a 3D Lennard-Jones crystal using path integral molecular dynamics (PIMD) simulation. The HMA estimators consistently provide more precise estimates compared to CVir, with the best performance obtained by HMAq-NM, followed by HMAq-SG, and then HMAc. We also examine the effect of anharmonicity (for AO), intrinsic quantumness, and Trotter number. The HMA formulation introduced assumes the availability of forces and Hessian matrix; however, an equally efficient finite difference alternative is possible when these derivatives are inaccessible. The remarkable improvement in precision offered by HMAq estimators provides a framework for efficient PI simulation of more challenging systems, such as those based on <i>ab initio</i> calculations.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":"10132-10146"},"PeriodicalIF":5.7,"publicationDate":"2024-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142612537","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":"Synergistic Modeling of Liquid Properties: Integrating Neural Network-Derived Molecular Features with Modified Kernel Models.","authors":"Hyuntae Lim, YounJoon Jung","doi":"10.1021/acs.jctc.4c00961","DOIUrl":"10.1021/acs.jctc.4c00961","url":null,"abstract":"<p><p>A significant challenge in applying machine learning to computational chemistry, particularly considering the growing complexity of contemporary machine learning models, is the scarcity of available experimental data. To address this issue, we introduce an approach that derives molecular features from an intricate neural network-based model and applies them to a simpler conventional machine learning model that is robust to overfitting. This method can be applied to predict various properties of a liquid system, including viscosity or surface tension, based on molecular features drawn from the <i>ab initio</i> calculated free energy of solvation. Furthermore, we propose a modified kernel model that includes Arrhenius temperature dependence to incorporate theoretical principles and diminish extreme nonlinearity in the model. The modified kernel model demonstrated significant improvements in certain scenarios and possible extensions to various theoretical concepts of molecular systems.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":"9849-9856"},"PeriodicalIF":5.7,"publicationDate":"2024-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142612682","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":"Does the Traditional Band Picture Correctly Describe the Electronic Structure of n-Doped Conjugated Polymers? A TD-DFT and Natural Transition Orbital Study.","authors":"Eric C Wu, Benjamin J Schwartz","doi":"10.1021/acs.jctc.4c00817","DOIUrl":"10.1021/acs.jctc.4c00817","url":null,"abstract":"<p><p>Doped conjugated polymers have a variety of potential applications in thermoelectric and other electronic devices, but the nature of their electronic structure is still not well understood. In this work, we use time-dependent density functional theory (TD-DFT) calculations along with natural transition orbital (NTO) analysis to understand electronic structures of both p-type (e.g., poly(3-hexylthiophene-2,5-diyl), P3HT) and n-type (e.g., poly{[<i>N</i>,<i>N</i>'-bis(2-octyldodecyl)-naphthalene-1,4,5,8-bis(dicarboximide)-2,6-diyl]-<i>alt</i>-5,5'-(2,2'-bithiophene)}, N2200) conjugated polymers that are both p-doped and n-doped. Of course, the electronic transitions of doped conjugated polymers are multiconfigurational in nature, but it is still useful to have a one-electron energy level diagram with which to interpret their spectroscopy and other electronic behaviors. Based on the NTOs associated with the TD-DFT transitions, we find that the \"best\" one-electron orbital-based energy level diagram for doped conjugated polymers such as P3HT is the so-called traditional band picture. We also find that the situation is more complicated for donor-acceptor-type polymers like N2200, where the use of different exchange-correlation functionals leads to different predicted optical transitions that have significantly less one-electron character. For some functionals, we still find that the \"best\" one-electron energy level diagram agrees with the traditional picture, but for others, there is no obvious route to reducing the multiconfigurational transitions to a one-electron energy level diagram. We also see that the presence of both electron-rich and electron-poor subunits on N2200 breaks the symmetry between n- and p-doping, because different types of polarons reside on different subunits leading to different degrees of charge delocalization. This effect is exaggerated by the presence of dopant counterions, which interact differently with n- and p-polarons. Despite these complications, we argue that the traditional band picture suffices if one wishes to employ a simple one-electron picture to explain the spectroscopy of n- and p-doped conjugated polymers.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":"10059-10070"},"PeriodicalIF":5.7,"publicationDate":"2024-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11603617/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142612491","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}

{"title":"Large-Scale Parameter Estimation for Crystal Structure Prediction. Part 1: Dataset, Methodology, and Implementation.","authors":"D H Bowskill, B I Tan, A Keates, I J Sugden, C S Adjiman, C C Pantelides","doi":"10.1021/acs.jctc.4c01091","DOIUrl":"10.1021/acs.jctc.4c01091","url":null,"abstract":"<p><p>Crystal structure prediction (CSP) seeks to identify all thermodynamically accessible solid forms of a given compound and, crucially, to establish the relative thermodynamic stability between different polymorphs. The conventional hierarchical CSP workflow suggests that no single energy model can fulfill the needs of all stages in the workflow, and energy models across a spectrum of fidelities and computational costs are required. Hybrid <i>ab initio</i>/empirical force-field (HAIEFF) models have demonstrated a good balance of these two factors, but the force-field component presents a major bottleneck for model accuracy. Existing parameter estimation tools for fitting this empirical component are inefficient and have severe limitations on the manageable problem size. This, combined with a lack of reliable reference data for parameter fitting, has resulted in development in the force-field component of HAIEFF models having mostly stagnated. In this work, we address these barriers to progress. First, we introduce a curated database of 755 organic crystal structures, obtained using high quality, solid-state DFT-D calculations, which provide a complete set of geometry and energy data. Comparisons to various theoretical and experimental data sources indicate that this database provides suitable diversity for parameter fitting. In tandem, we also put forward a new parameter estimation algorithm implemented as the CrystalEstimator program. Our tests demonstrate that CrystalEstimator is capable of efficiently handling large-scale parameter estimation problems, simultaneously fitting as many as 62 model parameters based on data from 445 structures. This problem size far exceeds any previously reported works related to CSP force-field parametrization. These developments form a strong foundation for all future work involving parameter estimation of transferable or tailor-made force-fields for HAIEFF models. This ultimately opens the way for significant improvements in the accuracy achieved by the HAIEFF models.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":"10288-10315"},"PeriodicalIF":5.7,"publicationDate":"2024-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11603618/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142612571","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}

{"title":"Hyperparameter Optimization for Atomic Cluster Expansion Potentials.","authors":"Daniel F Thomas du Toit, Yuxing Zhou, Volker L Deringer","doi":"10.1021/acs.jctc.4c01012","DOIUrl":"10.1021/acs.jctc.4c01012","url":null,"abstract":"<p><p>Machine learning-based interatomic potentials enable accurate materials simulations on extended time- and length scales. ML potentials based on the atomic cluster expansion (ACE) framework have recently shown promising performance for this purpose. Here, we describe a largely automated computational approach to optimizing hyperparameters for ACE potential models. We extend our openly available Python package, XPOT, to include an interface for ACE fitting, and discuss the optimization of the functional form and complexity of these models based on systematic sweeps across relevant hyperparameters. We showcase the usefulness of the approach for two example systems: the covalent network of silicon and the phase-change material Sb₂Te₃. More generally, our work emphasizes the importance of hyperparameter selection in the development of advanced ML potential models.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":"10103-10113"},"PeriodicalIF":5.7,"publicationDate":"2024-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11603601/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142580830","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}

{"title":"Development of Multiscale Force Field for Actinide (An³⁺) Solutions.","authors":"Junjie Song, Xiang Li, Xiaocheng Xu, Junbo Lu, Hanshi Hu, Jun Li","doi":"10.1021/acs.jctc.4c01048","DOIUrl":"10.1021/acs.jctc.4c01048","url":null,"abstract":"<p><p>A multiscale force field (FF) is developed for an aqueous solution of trivalent actinide cations An³⁺ (An = U, Np, Pu, Am, Cm, Bk, and Cf) by using a 12-6-4 Lennard-Jones type potential considering ion-induced dipole interaction. Potential parameters are rigorously and automatically optimized by the meta-multilinear interpolation parametrization (meta-MIP) algorithm via matching the experimental properties, including ion-oxygen distance (IOD) and coordination number (CN) in the first solvation shell and hydration free energy (HFE). The water solvent models incorporate an especially developed polar coarse-grained (CG) water scheme named PW32 and three widely used all-atom (AA) level SPC/E, TIP3P, and TIP4P water schemes. Each PW32 is modeled as two bonded beads to represent three neighboring water molecules, the simulation efficiency of which is 1 to 2 orders of magnitude higher than that of AA waters. The newly developed FF shows high accuracy and transferability in reproducing the IOD, CN, and HFE of An³⁺. The molecular structure and water exchange dynamics of the first An³⁺ hydration shell and the ionic (van der Waals) radii are reinvestigated in this work. Moreover, the new FF can readily be transferred to other popular FFs, as it has practicably predicted the permeability of An³⁺ in a graphene oxide filter within the framework of optimized potentials for liquid simulations (OPLS)-AA FF. It holds promise for applications in exploring actinide aqueous solutions with multiscale computational overhead.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":"9799-9813"},"PeriodicalIF":5.7,"publicationDate":"2024-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142612487","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":"Fully Polarizable Multiconfigurational Self-Consistent Field/Fluctuating Charges Approach.","authors":"Chiara Sepali, Linda Goletto, Piero Lafiosca, Matteo Rinaldi, Tommaso Giovannini, Chiara Cappelli","doi":"10.1021/acs.jctc.4c01125","DOIUrl":"10.1021/acs.jctc.4c01125","url":null,"abstract":"<p><p>A multiscale model based on the coupling of the multiconfigurational self-consistent field (MCSCF) method and the classical atomistic polarizable fluctuating charges (FQ) force field is presented. The resulting MCSCF/FQ approach is validated by exploiting the CASSCF scheme through application to compute vertical excitation energies of formaldehyde and <i>para</i>-nitroaniline in aqueous solution. The procedure is integrated with molecular dynamics simulations to capture the solute's conformational changes and the dynamic aspects of solvation. Comparative analysis with alternative solvent models, gas-phase calculations, and experimental data provides insights into the model's accuracy in reproducing solute-solvent molecular interactions and spectral signals.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":"9954-9967"},"PeriodicalIF":5.7,"publicationDate":"2024-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142612519","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":"Enhancing the Assembly Properties of Bottom-Up Coarse-Grained Phospholipids.","authors":"Patrick G Sahrmann, Gregory A Voth","doi":"10.1021/acs.jctc.4c00905","DOIUrl":"10.1021/acs.jctc.4c00905","url":null,"abstract":"<p><p>A plethora of key biological events occur at the cellular membrane where the large spatiotemporal scales necessitate dimensionality reduction or coarse-graining approaches over conventional all-atom molecular dynamics simulation. Constructing coarse-grained descriptions of membranes systematically from statistical mechanical principles has largely remained challenging due to the necessity of capturing amphipathic self-assembling behavior in coarse-grained models. We show that bottom-up coarse-grained lipid models can possess metastable morphological behavior and that this potential metastability has ramifications for accurate development and training. We in turn develop a training algorithm which evades metastability issues by linking model training to self-assembling behavior, and demonstrate its robustness via construction of solvent-free coarse-grained models of various phospholipid membranes, including lipid species such as phosphatidylcholines, phosphatidylserines, sphingolipids, and cholesterol. The resulting coarse-grained lipid models are orders of magnitude faster than their atomistic counterparts while retaining structural fidelity and constitute a promising direction for the development of coarse-grained models of realistic cell membranes.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":"10235-10246"},"PeriodicalIF":5.7,"publicationDate":"2024-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11604101/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142612494","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}

{"title":"Nonspecific Yet Selective Interactions Contribute to Small Molecule Condensate Binding.","authors":"Cong Wang, Henry R Kilgore, Andrew P Latham, Bin Zhang","doi":"10.1021/acs.jctc.4c01024","DOIUrl":"10.1021/acs.jctc.4c01024","url":null,"abstract":"<p><p>Biomolecular condensates are essential in various cellular processes, and their misregulation has been demonstrated to underlie disease. Small molecules that modulate condensate stability and material properties offer promising therapeutic approaches, but mechanistic insights into their interactions with condensates remain largely lacking. We employ a multiscale approach to enable long-time, equilibrated all-atom simulations of various condensate-ligand systems. Systematic characterization of the ligand binding poses reveals that condensates can form diverse and heterogeneous chemical environments with one or multiple chains to bind small molecules. Unlike traditional protein-ligand interactions, these chemical environments are dominated by nonspecific hydrophobic interactions. Nevertheless, the chemical environments feature unique amino acid compositions and physicochemical properties that favor certain small molecules over others, resulting in varied ligand partitioning coefficients within condensates. Notably, different condensates share similar sets of chemical environments but at different populations. This population shift drives ligand selectivity toward specific condensates. Our approach can enhance the interpretation of experimental screening data and may assist in the rational design of small molecules targeting specific condensates.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":"10247-10258"},"PeriodicalIF":5.7,"publicationDate":"2024-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142612674","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}