Exploration of the Global Minimum and Conical Intersection with Bayesian Optimization.

IF 2.8 4区 医学 Q3 CHEMISTRY, MEDICINAL Molecular Informatics Pub Date : 2025-02-01 DOI:10.1002/minf.202400041
Riho Somaki, Taichi Inagaki, Miho Hatanaka
{"title":"Exploration of the Global Minimum and Conical Intersection with Bayesian Optimization.","authors":"Riho Somaki, Taichi Inagaki, Miho Hatanaka","doi":"10.1002/minf.202400041","DOIUrl":null,"url":null,"abstract":"<p><p>Conventional molecular geometry searches on a potential energy surface (PES) utilize energy gradients from quantum chemical calculations. However, replacing energy calculations with noisy quantum computer measurements generates errors in the energies, which makes geometry optimization using the energy gradient difficult. One gradient-free optimization method that can potentially solve this problem is Bayesian optimization (BO). To use BO in geometry search, an acquisition function (AF), which involves an objective variable, must be defined suitably. In this study, we propose a strategy for geometry searches using BO and examine the appropriate AFs to explore two critical structures: the global minimum (GM) on the singlet ground state (S<sub>0</sub>) and the most stable conical intersection (CI) point between S<sub>0</sub> and the singlet excited state. We applied our strategy to two molecules and located the GM and the most stable CI geometries with high accuracy for both molecules. We also succeeded in the geometry searches even when artificial random noises were added to the energies to simulate geometry optimization using noisy quantum computer measurements.</p>","PeriodicalId":18853,"journal":{"name":"Molecular Informatics","volume":"44 2","pages":"e202400041"},"PeriodicalIF":2.8000,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11781018/pdf/","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Molecular Informatics","FirstCategoryId":"3","ListUrlMain":"https://doi.org/10.1002/minf.202400041","RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q3","JCRName":"CHEMISTRY, MEDICINAL","Score":null,"Total":0}
引用次数: 0

Abstract

Conventional molecular geometry searches on a potential energy surface (PES) utilize energy gradients from quantum chemical calculations. However, replacing energy calculations with noisy quantum computer measurements generates errors in the energies, which makes geometry optimization using the energy gradient difficult. One gradient-free optimization method that can potentially solve this problem is Bayesian optimization (BO). To use BO in geometry search, an acquisition function (AF), which involves an objective variable, must be defined suitably. In this study, we propose a strategy for geometry searches using BO and examine the appropriate AFs to explore two critical structures: the global minimum (GM) on the singlet ground state (S0) and the most stable conical intersection (CI) point between S0 and the singlet excited state. We applied our strategy to two molecules and located the GM and the most stable CI geometries with high accuracy for both molecules. We also succeeded in the geometry searches even when artificial random noises were added to the energies to simulate geometry optimization using noisy quantum computer measurements.

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
求助全文
约1分钟内获得全文 去求助
来源期刊
Molecular Informatics
Molecular Informatics CHEMISTRY, MEDICINAL-MATHEMATICAL & COMPUTATIONAL BIOLOGY
CiteScore
7.30
自引率
2.80%
发文量
70
审稿时长
3 months
期刊介绍: Molecular Informatics is a peer-reviewed, international forum for publication of high-quality, interdisciplinary research on all molecular aspects of bio/cheminformatics and computer-assisted molecular design. Molecular Informatics succeeded QSAR & Combinatorial Science in 2010. Molecular Informatics presents methodological innovations that will lead to a deeper understanding of ligand-receptor interactions, macromolecular complexes, molecular networks, design concepts and processes that demonstrate how ideas and design concepts lead to molecules with a desired structure or function, preferably including experimental validation. The journal''s scope includes but is not limited to the fields of drug discovery and chemical biology, protein and nucleic acid engineering and design, the design of nanomolecular structures, strategies for modeling of macromolecular assemblies, molecular networks and systems, pharmaco- and chemogenomics, computer-assisted screening strategies, as well as novel technologies for the de novo design of biologically active molecules. As a unique feature Molecular Informatics publishes so-called "Methods Corner" review-type articles which feature important technological concepts and advances within the scope of the journal.
期刊最新文献
Exploration of the Global Minimum and Conical Intersection with Bayesian Optimization. Predicting the Price of Molecules Using Their Predicted Synthetic Pathways. KNIME Workflows for Chemoinformatic Characterization of Chemical Databases. Active learning approaches in molecule pKi prediction. Chemography-guided analysis of a reaction path network for ethylene hydrogenation with a model Wilkinson's catalyst.
×
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