Jorge Alberto Sanchez Alvarez, Luis López-Sosa, Andreas M Köster, Patrizia Calaminici
{"title":"Constrained Structure Minimizations on Hyperspheres for Minimum Energy Path Following.","authors":"Jorge Alberto Sanchez Alvarez, Luis López-Sosa, Andreas M Köster, Patrizia Calaminici","doi":"10.1021/acs.jcim.4c02351","DOIUrl":null,"url":null,"abstract":"<p><p>In this work, a reliable and robust trust region method for restricted minimizations on hyperspheres is developed. The working equations of this new methodology are presented, together with their validation. The performance and characteristics of this new algorithm are discussed by a constrained minimization on a sphere using a two-dimensional Quapp model surface. The obtained results show that the proposed method for minimizations on hyperspheres guarantees convergence to constrained minima. Its enhanced numerical stability permits tight convergence criteria for constrained minimizations. The application of the new restricted minimizer in the framework of the hierarchical transition state finder and for the calculation of intrinsic reaction coordinates for 38 chemical reactions demonstrates its robustness and efficiency.</p>","PeriodicalId":44,"journal":{"name":"Journal of Chemical Information and Modeling ","volume":" ","pages":"3488-3501"},"PeriodicalIF":5.3000,"publicationDate":"2025-04-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12004539/pdf/","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Journal of Chemical Information and Modeling ","FirstCategoryId":"92","ListUrlMain":"https://doi.org/10.1021/acs.jcim.4c02351","RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2025/4/1 0:00:00","PubModel":"Epub","JCR":"Q1","JCRName":"CHEMISTRY, MEDICINAL","Score":null,"Total":0}
引用次数: 0
Abstract
In this work, a reliable and robust trust region method for restricted minimizations on hyperspheres is developed. The working equations of this new methodology are presented, together with their validation. The performance and characteristics of this new algorithm are discussed by a constrained minimization on a sphere using a two-dimensional Quapp model surface. The obtained results show that the proposed method for minimizations on hyperspheres guarantees convergence to constrained minima. Its enhanced numerical stability permits tight convergence criteria for constrained minimizations. The application of the new restricted minimizer in the framework of the hierarchical transition state finder and for the calculation of intrinsic reaction coordinates for 38 chemical reactions demonstrates its robustness and efficiency.
期刊介绍：
The Journal of Chemical Information and Modeling publishes papers reporting new methodology and/or important applications in the fields of chemical informatics and molecular modeling. Specific topics include the representation and computer-based searching of chemical databases, molecular modeling, computer-aided molecular design of new materials, catalysts, or ligands, development of new computational methods or efficient algorithms for chemical software, and biopharmaceutical chemistry including analyses of biological activity and other issues related to drug discovery.
Astute chemists, computer scientists, and information specialists look to this monthly’s insightful research studies, programming innovations, and software reviews to keep current with advances in this integral, multidisciplinary field.
As a subscriber you’ll stay abreast of database search systems, use of graph theory in chemical problems, substructure search systems, pattern recognition and clustering, analysis of chemical and physical data, molecular modeling, graphics and natural language interfaces, bibliometric and citation analysis, and synthesis design and reactions databases.
京公网安备 11010802042870号
京ICP备2023020795号-1
分享
求助内容：
应助结果提醒方式：
扫码关注我们
