Large-Scale Parameter Estimation for Crystal Structure Prediction. Part 1: Dataset, Methodology, and Implementation.

IF 5.7 1区 化学 Q2 CHEMISTRY, PHYSICAL Journal of Chemical Theory and Computation Pub Date : 2024-11-12 DOI:10.1021/acs.jctc.4c01091
D H Bowskill, B I Tan, A Keates, I J Sugden, C S Adjiman, C C Pantelides
{"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":null,"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":""},"PeriodicalIF":5.7000,"publicationDate":"2024-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Journal of Chemical Theory and Computation","FirstCategoryId":"92","ListUrlMain":"https://doi.org/10.1021/acs.jctc.4c01091","RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"CHEMISTRY, PHYSICAL","Score":null,"Total":0}
引用次数: 0

Abstract

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 ab initio/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.

查看原文
分享 分享
微信好友 朋友圈 QQ好友 复制链接
本刊更多论文
晶体结构预测的大规模参数估计。第 1 部分:数据集、方法和实施。
晶体结构预测(CSP)旨在确定特定化合物在热力学上可获得的所有固态形式,更重要的是,确定不同多晶体之间的相对热力学稳定性。传统的分层 CSP 工作流程表明,没有任何一种能量模型可以满足工作流程中所有阶段的需求,因此需要不同保真度和计算成本的能量模型。ab initio/经验力场混合模型(HAIEFF)已证明能很好地平衡这两个因素,但力场部分是影响模型准确性的主要瓶颈。现有的用于拟合这一经验成分的参数估计工具效率低下,而且对可管理的问题规模有严重限制。再加上缺乏用于参数拟合的可靠参考数据,导致 HAIEFF 模型力场部分的发展大多停滞不前。在这项工作中,我们将解决这些进展障碍。首先,我们引入了一个包含 755 个有机晶体结构的数据库,这些晶体结构是通过高质量的固态 DFT-D 计算获得的,提供了一套完整的几何和能量数据。与各种理论和实验数据源的比较表明,该数据库为参数拟合提供了适当的多样性。与此同时,我们还提出了一种作为 CrystalEstimator 程序实现的新参数估计算法。我们的测试表明,CrystalEstimator 能够有效地处理大规模参数估计问题,根据 445 个结构的数据同时拟合多达 62 个模型参数。这个问题的规模远远超过了之前报道的任何与 CSP 力场参数化相关的工作。这些进展为今后所有涉及 HAIEFF 模型可转移或定制力场参数估计的工作奠定了坚实的基础。这最终为大幅提高 HAIEFF 模型的精度开辟了道路。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
求助全文
约1分钟内获得全文 去求助
来源期刊
Journal of Chemical Theory and Computation
Journal of Chemical Theory and Computation 化学-物理:原子、分子和化学物理
CiteScore
9.90
自引率
16.40%
发文量
568
审稿时长
1 months
期刊介绍: The Journal of Chemical Theory and Computation invites new and original contributions with the understanding that, if accepted, they will not be published elsewhere. Papers reporting new theories, methodology, and/or important applications in quantum electronic structure, molecular dynamics, and statistical mechanics are appropriate for submission to this Journal. Specific topics include advances in or applications of ab initio quantum mechanics, density functional theory, design and properties of new materials, surface science, Monte Carlo simulations, solvation models, QM/MM calculations, biomolecular structure prediction, and molecular dynamics in the broadest sense including gas-phase dynamics, ab initio dynamics, biomolecular dynamics, and protein folding. The Journal does not consider papers that are straightforward applications of known methods including DFT and molecular dynamics. The Journal favors submissions that include advances in theory or methodology with applications to compelling problems.
期刊最新文献
Bayesian Approach for Computing Free Energy on Perturbation Graphs with Cycles. Deterministic and Faster GW Calculations with a Reduced Number of Valence States: O(N2 ln N) Scaling in the Plane-Waves Formalism. The Dynamic Diversity and Invariance of Ab Initio Water. Automatic Feature Selection for Atom-Centered Neural Network Potentials Using a Gradient Boosting Decision Algorithm. Data Quality in the Fitting of Approximate Models: A Computational Chemistry Perspective.
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
现在去查看 取消
×
提示
确定
0
微信
客服QQ
Book学术公众号 扫码关注我们
反馈
×
意见反馈
请填写您的意见或建议
请填写您的手机或邮箱
已复制链接
已复制链接
快去分享给好友吧!
我知道了
×
扫码分享
扫码分享
Book学术官方微信
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术
文献互助 智能选刊 最新文献 互助须知 联系我们:info@booksci.cn
Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。
Copyright © 2023 Book学术 All rights reserved.
ghs 京公网安备 11010802042870号 京ICP备2023020795号-1