{"title":"耦合反应体系动力学要求的计算分析。","authors":"Sara Incarbone, Luca De Gioia","doi":"10.3390/molecules30040911","DOIUrl":null,"url":null,"abstract":"<p><p>The art of designing coupling systems to drive reactions for endergonic synthesis is a subject of great interest in the scientific community, but it still presents major challenges. The aim of this kinetic study was to run simulations in COPASI 4.39 to test the behavior of hypothetical models for a system that couples two independent reactions, one exergonic and the other endergonic. In our computational study, we unraveled the qualitative and quantitative conditions that allow and benefit coupling, considering all possible reaction pathways within the network. Optimal conditions were reached by assigning favorable directionalities and low activation energies to six reaction steps within a network that featured twenty reaction steps. Moreover, different models were designed and tested in order to investigate the availability of coupling with different reaction steps.</p>","PeriodicalId":19041,"journal":{"name":"Molecules","volume":"30 4","pages":""},"PeriodicalIF":5.1000,"publicationDate":"2025-02-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11858731/pdf/","citationCount":"0","resultStr":"{\"title\":\"Computational Analysis of the Kinetic Requirements for Coupled Reaction Systems.\",\"authors\":\"Sara Incarbone, Luca De Gioia\",\"doi\":\"10.3390/molecules30040911\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><p>The art of designing coupling systems to drive reactions for endergonic synthesis is a subject of great interest in the scientific community, but it still presents major challenges. The aim of this kinetic study was to run simulations in COPASI 4.39 to test the behavior of hypothetical models for a system that couples two independent reactions, one exergonic and the other endergonic. In our computational study, we unraveled the qualitative and quantitative conditions that allow and benefit coupling, considering all possible reaction pathways within the network. Optimal conditions were reached by assigning favorable directionalities and low activation energies to six reaction steps within a network that featured twenty reaction steps. Moreover, different models were designed and tested in order to investigate the availability of coupling with different reaction steps.</p>\",\"PeriodicalId\":19041,\"journal\":{\"name\":\"Molecules\",\"volume\":\"30 4\",\"pages\":\"\"},\"PeriodicalIF\":5.1000,\"publicationDate\":\"2025-02-15\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11858731/pdf/\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Molecules\",\"FirstCategoryId\":\"92\",\"ListUrlMain\":\"https://doi.org/10.3390/molecules30040911\",\"RegionNum\":2,\"RegionCategory\":\"化学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q2\",\"JCRName\":\"BIOCHEMISTRY & MOLECULAR BIOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Molecules","FirstCategoryId":"92","ListUrlMain":"https://doi.org/10.3390/molecules30040911","RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"BIOCHEMISTRY & MOLECULAR BIOLOGY","Score":null,"Total":0}
Computational Analysis of the Kinetic Requirements for Coupled Reaction Systems.
The art of designing coupling systems to drive reactions for endergonic synthesis is a subject of great interest in the scientific community, but it still presents major challenges. The aim of this kinetic study was to run simulations in COPASI 4.39 to test the behavior of hypothetical models for a system that couples two independent reactions, one exergonic and the other endergonic. In our computational study, we unraveled the qualitative and quantitative conditions that allow and benefit coupling, considering all possible reaction pathways within the network. Optimal conditions were reached by assigning favorable directionalities and low activation energies to six reaction steps within a network that featured twenty reaction steps. Moreover, different models were designed and tested in order to investigate the availability of coupling with different reaction steps.
期刊介绍：
Molecules (ISSN 1420-3049, CODEN: MOLEFW) is an open access journal of synthetic organic chemistry and natural product chemistry. All articles are peer-reviewed and published continously upon acceptance. Molecules is published by MDPI, Basel, Switzerland. Our aim is to encourage chemists to publish as much as possible their experimental detail, particularly synthetic procedures and characterization information. There is no restriction on the length of the experimental section. In addition, availability of compound samples is published and considered as important information. Authors are encouraged to register or deposit their chemical samples through the non-profit international organization Molecular Diversity Preservation International (MDPI). Molecules has been launched in 1996 to preserve and exploit molecular diversity of both, chemical information and chemical substances.
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