{"title":"Thermodynamics of homolytic C–H bond cleavage in proteinogenic α-amino acids: Zwitterions in aqueous solution","authors":"Dagmar Štellerová, Erik Klein, Vladimír Lukeš","doi":"10.1016/j.jmgm.2025.108974","DOIUrl":null,"url":null,"abstract":"<div><div>This work provides the systematic M06-2X theoretical study of C–H bond dissociation enthalpies (BDE) in aqueous solution for 21 proteinogenic α-amino acids present in eukaryotes. The results reveal that the formation of zwitterions in an aqueous solution significantly affects the thermodynamics of the homolytic C–H bond cleavage for alpha, beta, and gamma carbon atoms. We have found that zwitterions show significantly greater stability against a free radical attack due to considerably higher enthalpies of the hydrogen atom abstraction from the C<sub>α</sub> atom. This kind of stabilization can be beneficial during the synthesis of proteins in cells. Compared to the canonical forms, the average increase in BDE is ca. 60 kJ mol<sup>−1</sup>. For all amino acids, the BDE of the most labile C–H bond was calculated using the <em>ab initio</em> G4 and G4(MP2) composite methods, as well.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"136 ","pages":"Article 108974"},"PeriodicalIF":2.7000,"publicationDate":"2025-02-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Journal of molecular graphics & modelling","FirstCategoryId":"99","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S1093326325000348","RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"BIOCHEMICAL RESEARCH METHODS","Score":null,"Total":0}
引用次数: 0
Abstract
This work provides the systematic M06-2X theoretical study of C–H bond dissociation enthalpies (BDE) in aqueous solution for 21 proteinogenic α-amino acids present in eukaryotes. The results reveal that the formation of zwitterions in an aqueous solution significantly affects the thermodynamics of the homolytic C–H bond cleavage for alpha, beta, and gamma carbon atoms. We have found that zwitterions show significantly greater stability against a free radical attack due to considerably higher enthalpies of the hydrogen atom abstraction from the Cα atom. This kind of stabilization can be beneficial during the synthesis of proteins in cells. Compared to the canonical forms, the average increase in BDE is ca. 60 kJ mol−1. For all amino acids, the BDE of the most labile C–H bond was calculated using the ab initio G4 and G4(MP2) composite methods, as well.
期刊介绍：
The Journal of Molecular Graphics and Modelling is devoted to the publication of papers on the uses of computers in theoretical investigations of molecular structure, function, interaction, and design. The scope of the journal includes all aspects of molecular modeling and computational chemistry, including, for instance, the study of molecular shape and properties, molecular simulations, protein and polymer engineering, drug design, materials design, structure-activity and structure-property relationships, database mining, and compound library design.
As a primary research journal, JMGM seeks to bring new knowledge to the attention of our readers. As such, submissions to the journal need to not only report results, but must draw conclusions and explore implications of the work presented. Authors are strongly encouraged to bear this in mind when preparing manuscripts. Routine applications of standard modelling approaches, providing only very limited new scientific insight, will not meet our criteria for publication. Reproducibility of reported calculations is an important issue. Wherever possible, we urge authors to enhance their papers with Supplementary Data, for example, in QSAR studies machine-readable versions of molecular datasets or in the development of new force-field parameters versions of the topology and force field parameter files. Routine applications of existing methods that do not lead to genuinely new insight will not be considered.
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