Journal of Chemical Theory and Computation最新文献

{"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":"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}

{"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":"A Multipole-Based Reactive Force Field for Hydrocarbons.","authors":"Junben Weng, Hongqiang Cui, Da Zheng, Zhenhao Zhou, Dinglin Zhang, Huiying Chu, Anhui Wang, Guohui Li","doi":"10.1021/acs.jctc.4c01285","DOIUrl":"10.1021/acs.jctc.4c01285","url":null,"abstract":"<p><p>The computational complexity of quantum chemistry methods has prompted the development of reactive force fields, facilitating practical applications of molecular dynamics simulations for large-scale reactive systems. Current reactive force fields typically employ intricate corrections based on prior chemical knowledge, which severely impedes their further advancement. This study presents a new atomic multipole-based reactive model with bond free (OPERATOR). The force field is constructed on a simple, physically motivated model within the AMOEBA framework that closely resembles the physical representation of the chemical reaction processes. In the force field, the atomic multipoles are generated dynamically according to the atomic environments, aiming to effectively capture significant changes in the electrostatic environments during chemical reactions. Subsequently, atomic multipole-based charge penetration, polarization, and charge transfer effects are incorporated into the force field to describe the complex electrostatic interactions in the system. The force field also includes van der Waals interactions and three-body potentials. In addition, to extend these nonreactive interactions to chemical reactions, the atom distribution multipole moments are used to characterize different chemical environments. The force field has been optimized using the dataset of potential energy surfaces (PESs) of hydrocarbons derived from DFT results of millions of conformations with six degrees of freedom (DOFs). The results demonstrate that the new force field effectively replicates both the monopoles and the energies. In comparison to ReaxFF, the new force field exhibits comparable or superior performance. Furthermore, molecular dynamics simulations of <i>n</i>-heptane decomposition effectively reproduce the primary products and reactions observed in the experiments. Given the simplicity and physically motivated nature of the model, it is expected that the new force field will be utilized in future studies to investigate chemical reaction mechanisms involving more elements.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":"10045-10058"},"PeriodicalIF":5.7,"publicationDate":"2024-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142574944","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":"Nonequilibrium Molecular Dynamics Method to Generate Poiseuille-Like Flow between Lipid Bilayers.","authors":"Masaki Otawa, Satoru G Itoh, Hisashi Okumura","doi":"10.1021/acs.jctc.4c00750","DOIUrl":"10.1021/acs.jctc.4c00750","url":null,"abstract":"<p><p>There are various flows inside and outside cells in vivo. Nonequilibrium molecular dynamics (NEMD) simulation is a useful tool for understanding the effects of these flows on the dynamics of biomolecules. We propose an NEMD method to generate a Poiseuille-like flow between lipid bilayers. We extended the conventional equilibrium MD method to produce a flow by adding constant external force terms to the water molecules. Using the Lagrange multiplier method, the center of mass of the lipid bilayer is constrained so that the flow does not sweep away the lipid bilayer, but the individual lipid molecules fluctuate. The temperature of the system is controlled properly in the solution and membrane by using the Nosé-Hoover thermostat. We found that the flow velocity increases linearly as the applied external force term increases. It is possible to estimate the appropriate value of acceleration to generate a flow with an arbitrary velocity using this proportional relation once a single short MD simulation is performed. We also found that the flow between two lipid bilayers is slower than the analytical solution of the Navier-Stokes equations between rigid parallel plates due to the interactions between water molecules and the membrane. This method can be applied not only to a flow on lipid membranes but also to a flow on soft surfaces generally.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":"10199-10208"},"PeriodicalIF":5.7,"publicationDate":"2024-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142612672","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":"Integrating Self-Initialized Local Thermalizing Lindblad Operators for Variational Quantum Algorithm with Quantum Jump: Implementation and Performance.","authors":"Zhihao Lan, WanZhen Liang","doi":"10.1021/acs.jctc.4c00490","DOIUrl":"https://doi.org/10.1021/acs.jctc.4c00490","url":null,"abstract":"<p><p>Quantum computing holds great potential for simulating quantum systems, such as molecular systems, due to its inherent ability to represent and manipulate quantum states. However, simulating nonunitary dynamics of open quantum systems on a quantum computer is still challenging. Here, we present a scheme denoted as VQS-QJ-LTLME, which adopts the trajectory average of quantum jump Monte Carlo wave function variational evolution to evolve the system's density matrix and local thermalizing Lindblad operators to describe the system-environment interactions. This combination allows the quantum circuit to be initialized after a period of evolution, thereby eliminating the accumulation of errors. The VQS-QJ-LTLME algorithm requires only log₂(<i>n</i>) qubits for system size <i>n</i> and holds a time complexity of <math><mi>O</mi><mrow><mo>(</mo><mi>T</mi><msup><mi>n</mi><mn>3</mn></msup><mo>)</mo></mrow></math>, making it particularly suitable for operation on noisy intermediate-scale quantum devices. To accelerate the Monte Carlo sampling process in VQS-QJ-LTLME, we introduce an efficient sampling method, named No-evolution sampling (NES). The VQS-QJ-LTLME aided by NES requires simulating only <i>n</i>³ + 1 trajectories on quantum computers, and then makes 10⁶ to 10⁷ samplings on classical computers in a few seconds. To demonstrate the performance of the VQS-QJ-LTLME algorithm, we simulate the dynamics of a two-level spin-boson model and a four-level reduced Fenna-Matthews-Olson system with real superconducting quantum computers and classical simulators. It is shown that the simulations produced by VQS-QJ-LTLME algorithm align closely with those obtained from the purely classical methods.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142724532","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}