Artem V. Chaikin , Timofey P. Rozov , Alexander S. Ryzhako , Andrey D. Moshchenkov , Arseniy A. Otlyotov , Yury Minenkov
{"title":"越简单越好?用从头算、DFT、基团可加性和半经验近似计算短链氯化石蜡的生成焓和熵","authors":"Artem V. Chaikin , Timofey P. Rozov , Alexander S. Ryzhako , Andrey D. Moshchenkov , Arseniy A. Otlyotov , Yury Minenkov","doi":"10.1016/j.jmgm.2025.109106","DOIUrl":null,"url":null,"abstract":"<div><div>An automated reaction-based approach coupled with DLPNO-CCSD(T)/CBS calculations was used to derive enthalpies of formation (Δ<sub>f</sub><em>H</em><sup>0</sup>) of 32 short-chain chlorinated paraffins (SCCPs) containing 10–13 C atoms and 3–11 Cl atoms. Absolute entropies (<em>S</em>) were obtained using B3LYP-D3(BJ)/def2-TZVP optimized geometries and vibrational frequencies in the framework of the modified and scaled rigid rotor – harmonic oscillator (msRRHO) approximation. Conformational corrections to entropies were estimated using the CREST program and GFN<em>n</em>-xTB/FF methods. Examination of the performance of fast semiempirical methods reveals them to be suitable for the express evaluation of molecular entropies (mean unsigned deviation MUD<sub>RM1</sub> = 2.3 cal mol<sup>−1</sup> K<sup>−1</sup>), while only PM6 method reproduces reference Δ<sub>f</sub><em>H</em><sup>0</sup> with MUD<sub>PM6</sub> = 2.4 kcal mol<sup>−1</sup>, approximately within the estimated average error limits (2.8 kcal mol<sup>−1</sup>). In contrast, simple Benson's group additivity method (GA) yields Δ<sub>f</sub><em>H</em><sup>0</sup> values with MUD<sub>GA</sub> = 0.8 kcal mol<sup>−1</sup> but turns out to significantly overestimate entropies with MUD<sub>GA</sub> = 20.4 cal mol<sup>−1</sup> K<sup>−1</sup>. The obtained datasets of reliable Δ<sub>f</sub><em>H</em><sup>0</sup> and <em>S</em> values can be used for the further development of fast and efficient methods for the gas-phase thermochemistry evaluations of medium-sized molecules with rich conformational landscapes.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"140 ","pages":"Article 109106"},"PeriodicalIF":3.0000,"publicationDate":"2025-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"The simpler the better? Enthalpies of formation and entropies of short-chain chlorinated paraffins by ab initio, DFT, group additivity and semiempirical approximations\",\"authors\":\"Artem V. Chaikin , Timofey P. Rozov , Alexander S. Ryzhako , Andrey D. Moshchenkov , Arseniy A. Otlyotov , Yury Minenkov\",\"doi\":\"10.1016/j.jmgm.2025.109106\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<div><div>An automated reaction-based approach coupled with DLPNO-CCSD(T)/CBS calculations was used to derive enthalpies of formation (Δ<sub>f</sub><em>H</em><sup>0</sup>) of 32 short-chain chlorinated paraffins (SCCPs) containing 10–13 C atoms and 3–11 Cl atoms. Absolute entropies (<em>S</em>) were obtained using B3LYP-D3(BJ)/def2-TZVP optimized geometries and vibrational frequencies in the framework of the modified and scaled rigid rotor – harmonic oscillator (msRRHO) approximation. Conformational corrections to entropies were estimated using the CREST program and GFN<em>n</em>-xTB/FF methods. Examination of the performance of fast semiempirical methods reveals them to be suitable for the express evaluation of molecular entropies (mean unsigned deviation MUD<sub>RM1</sub> = 2.3 cal mol<sup>−1</sup> K<sup>−1</sup>), while only PM6 method reproduces reference Δ<sub>f</sub><em>H</em><sup>0</sup> with MUD<sub>PM6</sub> = 2.4 kcal mol<sup>−1</sup>, approximately within the estimated average error limits (2.8 kcal mol<sup>−1</sup>). In contrast, simple Benson's group additivity method (GA) yields Δ<sub>f</sub><em>H</em><sup>0</sup> values with MUD<sub>GA</sub> = 0.8 kcal mol<sup>−1</sup> but turns out to significantly overestimate entropies with MUD<sub>GA</sub> = 20.4 cal mol<sup>−1</sup> K<sup>−1</sup>. The obtained datasets of reliable Δ<sub>f</sub><em>H</em><sup>0</sup> and <em>S</em> values can be used for the further development of fast and efficient methods for the gas-phase thermochemistry evaluations of medium-sized molecules with rich conformational landscapes.</div></div>\",\"PeriodicalId\":16361,\"journal\":{\"name\":\"Journal of molecular graphics & modelling\",\"volume\":\"140 \",\"pages\":\"Article 109106\"},\"PeriodicalIF\":3.0000,\"publicationDate\":\"2025-06-04\",\"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/S1093326325001664\",\"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}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Journal of molecular graphics & modelling","FirstCategoryId":"99","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S1093326325001664","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}
The simpler the better? Enthalpies of formation and entropies of short-chain chlorinated paraffins by ab initio, DFT, group additivity and semiempirical approximations
An automated reaction-based approach coupled with DLPNO-CCSD(T)/CBS calculations was used to derive enthalpies of formation (ΔfH0) of 32 short-chain chlorinated paraffins (SCCPs) containing 10–13 C atoms and 3–11 Cl atoms. Absolute entropies (S) were obtained using B3LYP-D3(BJ)/def2-TZVP optimized geometries and vibrational frequencies in the framework of the modified and scaled rigid rotor – harmonic oscillator (msRRHO) approximation. Conformational corrections to entropies were estimated using the CREST program and GFNn-xTB/FF methods. Examination of the performance of fast semiempirical methods reveals them to be suitable for the express evaluation of molecular entropies (mean unsigned deviation MUDRM1 = 2.3 cal mol−1 K−1), while only PM6 method reproduces reference ΔfH0 with MUDPM6 = 2.4 kcal mol−1, approximately within the estimated average error limits (2.8 kcal mol−1). In contrast, simple Benson's group additivity method (GA) yields ΔfH0 values with MUDGA = 0.8 kcal mol−1 but turns out to significantly overestimate entropies with MUDGA = 20.4 cal mol−1 K−1. The obtained datasets of reliable ΔfH0 and S values can be used for the further development of fast and efficient methods for the gas-phase thermochemistry evaluations of medium-sized molecules with rich conformational landscapes.
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.