Bharti Dehariya, Mini Bharati Ahirwar, Ayush Shivhare, Milind M. Deshmukh
{"title":"分子晶体中单个氢键能量学的Fragments - In - Fragments方法评价","authors":"Bharti Dehariya, Mini Bharati Ahirwar, Ayush Shivhare, Milind M. Deshmukh","doi":"10.1002/jcc.70008","DOIUrl":null,"url":null,"abstract":"<div>\n \n <p>We report a direct application of the molecular tailoring approach-based (MTA-based) method to calculate the individual hydrogen bond (HB) energy in molecular crystal. For this purpose, molecular crystals of nitromalonamide (NMA) and salicylic acid (SA) were taken as test cases. Notably, doing a correlated computation using a large molecular crystal structure is difficult. Among 15 density functional theory functionals, the B3LYP provides accurate estimates of HB energies closed to the CCSD(T) ones using the 6–311 + G(d,p) basis set for all atoms. The direct application of the MTA-based method to these crystal structures is although straightforward. For instance, the calculated energy suggests that three intramolecular HBs in NMA crystal are of stronger strength (7.3–17.0 kcal/mol) than the intermolecular ones (2.7–4.0 kcal/mol). On the other hand, intermolecular HB in SA crystal is moderately stronger (9.9 kcal/mol) than intramolecular one (8.1 kcal/mol). However, these energy calculations by the MTA-based method are very expensive. For instance, the time needed to evaluate the energy of all seven HBs in NMA crystal (having molecules within maximum of 15 unit cells) is 122,681 min (~2.7 months). In view of this, we assessed our recently proposed linear-scaling Fragments-in-Fragments (<i>Frags-in-Frags</i>) method for estimating the single-point energies of parent molecular crystal and fragments of the MTA-based method. It has been found that the estimated HB energies by the <i>Frags-in-Frags</i> method are in excellent linear agreement with their MTA-based counterparts (R<sup>2</sup> = 0.9993). Furthermore, root mean square deviation is 0.12 kcal/mol. Mean and maximum absolute errors are 0.10 and 0.5 kcal/mol, respectively, and the standard deviation is 0.14 kcal/mol. Importantly, the <i>Frags-in-Frags</i> method is computationally efficient; it needs only 18,289 min (~12.7 days) for the estimation of energy of all HBs in NMA crystal and 3499 min (~2.4 days) for all HBs in SA crystal.</p>\n </div>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 1","pages":""},"PeriodicalIF":3.4000,"publicationDate":"2025-01-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Appraisal of the Fragments-In-Fragments Method for the Energetics of Individual Hydrogen Bonds in Molecular Crystals\",\"authors\":\"Bharti Dehariya, Mini Bharati Ahirwar, Ayush Shivhare, Milind M. Deshmukh\",\"doi\":\"10.1002/jcc.70008\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<div>\\n \\n <p>We report a direct application of the molecular tailoring approach-based (MTA-based) method to calculate the individual hydrogen bond (HB) energy in molecular crystal. For this purpose, molecular crystals of nitromalonamide (NMA) and salicylic acid (SA) were taken as test cases. Notably, doing a correlated computation using a large molecular crystal structure is difficult. Among 15 density functional theory functionals, the B3LYP provides accurate estimates of HB energies closed to the CCSD(T) ones using the 6–311 + G(d,p) basis set for all atoms. The direct application of the MTA-based method to these crystal structures is although straightforward. For instance, the calculated energy suggests that three intramolecular HBs in NMA crystal are of stronger strength (7.3–17.0 kcal/mol) than the intermolecular ones (2.7–4.0 kcal/mol). On the other hand, intermolecular HB in SA crystal is moderately stronger (9.9 kcal/mol) than intramolecular one (8.1 kcal/mol). However, these energy calculations by the MTA-based method are very expensive. For instance, the time needed to evaluate the energy of all seven HBs in NMA crystal (having molecules within maximum of 15 unit cells) is 122,681 min (~2.7 months). In view of this, we assessed our recently proposed linear-scaling Fragments-in-Fragments (<i>Frags-in-Frags</i>) method for estimating the single-point energies of parent molecular crystal and fragments of the MTA-based method. It has been found that the estimated HB energies by the <i>Frags-in-Frags</i> method are in excellent linear agreement with their MTA-based counterparts (R<sup>2</sup> = 0.9993). Furthermore, root mean square deviation is 0.12 kcal/mol. Mean and maximum absolute errors are 0.10 and 0.5 kcal/mol, respectively, and the standard deviation is 0.14 kcal/mol. Importantly, the <i>Frags-in-Frags</i> method is computationally efficient; it needs only 18,289 min (~12.7 days) for the estimation of energy of all HBs in NMA crystal and 3499 min (~2.4 days) for all HBs in SA crystal.</p>\\n </div>\",\"PeriodicalId\":188,\"journal\":{\"name\":\"Journal of Computational Chemistry\",\"volume\":\"46 1\",\"pages\":\"\"},\"PeriodicalIF\":3.4000,\"publicationDate\":\"2025-01-04\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Journal of Computational Chemistry\",\"FirstCategoryId\":\"92\",\"ListUrlMain\":\"https://onlinelibrary.wiley.com/doi/10.1002/jcc.70008\",\"RegionNum\":3,\"RegionCategory\":\"化学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q2\",\"JCRName\":\"CHEMISTRY, MULTIDISCIPLINARY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Journal of Computational Chemistry","FirstCategoryId":"92","ListUrlMain":"https://onlinelibrary.wiley.com/doi/10.1002/jcc.70008","RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"CHEMISTRY, MULTIDISCIPLINARY","Score":null,"Total":0}
引用次数: 0
摘要
我们报告了基于分子裁剪方法(MTA - based)的方法在分子晶体中计算单个氢键(HB)能量的直接应用。为此,以硝基丙二胺(NMA)和水杨酸(SA)的分子晶体为实验用例。值得注意的是,使用大分子晶体结构进行相关计算是困难的。在15个密度泛函理论泛函中,B3LYP使用6-311 + G(d,p)基集对所有原子提供了接近CCSD(T)的HB能量的准确估计。基于MTA的方法直接应用于这些晶体结构是很简单的。例如,计算能量表明,NMA晶体中3个分子内HBs的强度(7.3 ~ 17.0 kcal/mol)高于分子间HBs的强度(2.7 ~ 4.0 kcal/mol)。另一方面,SA晶体中分子间HB的强度为9.9 kcal/mol,略高于分子内HB的8.1 kcal/mol。然而,这些基于MTA方法的能量计算是非常昂贵的。例如,评估NMA晶体中所有7个HBs(分子最多在15个单位胞内)的能量所需的时间为122,681分钟(约2.7个月)。鉴于此,我们评估了我们最近提出的用于估计母分子晶体单点能量的线性缩放fragment - In - Fragments (Frags - In - Frags)方法和基于MTA的片段方法。通过Frags - in - Frags方法估计的HB能量与基于MTA的对应值具有良好的线性一致性(R2 = 0.9993)。均方根偏差为0.12 kcal/mol。平均和最大绝对误差分别为0.10和0.5 kcal/mol,标准差为0.14 kcal/mol。重要的是,Frags - in - Frags方法具有计算效率;NMA晶体中所有HBs的能量估算仅需18289 min (~12.7 d), SA晶体中所有HBs的能量估算仅需3499 min (~2.4 d)。
Appraisal of the Fragments-In-Fragments Method for the Energetics of Individual Hydrogen Bonds in Molecular Crystals
We report a direct application of the molecular tailoring approach-based (MTA-based) method to calculate the individual hydrogen bond (HB) energy in molecular crystal. For this purpose, molecular crystals of nitromalonamide (NMA) and salicylic acid (SA) were taken as test cases. Notably, doing a correlated computation using a large molecular crystal structure is difficult. Among 15 density functional theory functionals, the B3LYP provides accurate estimates of HB energies closed to the CCSD(T) ones using the 6–311 + G(d,p) basis set for all atoms. The direct application of the MTA-based method to these crystal structures is although straightforward. For instance, the calculated energy suggests that three intramolecular HBs in NMA crystal are of stronger strength (7.3–17.0 kcal/mol) than the intermolecular ones (2.7–4.0 kcal/mol). On the other hand, intermolecular HB in SA crystal is moderately stronger (9.9 kcal/mol) than intramolecular one (8.1 kcal/mol). However, these energy calculations by the MTA-based method are very expensive. For instance, the time needed to evaluate the energy of all seven HBs in NMA crystal (having molecules within maximum of 15 unit cells) is 122,681 min (~2.7 months). In view of this, we assessed our recently proposed linear-scaling Fragments-in-Fragments (Frags-in-Frags) method for estimating the single-point energies of parent molecular crystal and fragments of the MTA-based method. It has been found that the estimated HB energies by the Frags-in-Frags method are in excellent linear agreement with their MTA-based counterparts (R2 = 0.9993). Furthermore, root mean square deviation is 0.12 kcal/mol. Mean and maximum absolute errors are 0.10 and 0.5 kcal/mol, respectively, and the standard deviation is 0.14 kcal/mol. Importantly, the Frags-in-Frags method is computationally efficient; it needs only 18,289 min (~12.7 days) for the estimation of energy of all HBs in NMA crystal and 3499 min (~2.4 days) for all HBs in SA crystal.
期刊介绍:
This distinguished journal publishes articles concerned with all aspects of computational chemistry: analytical, biological, inorganic, organic, physical, and materials. The Journal of Computational Chemistry presents original research, contemporary developments in theory and methodology, and state-of-the-art applications. Computational areas that are featured in the journal include ab initio and semiempirical quantum mechanics, density functional theory, molecular mechanics, molecular dynamics, statistical mechanics, cheminformatics, biomolecular structure prediction, molecular design, and bioinformatics.