Implicit and Explicit Solvent Effects on the Global Reactivity and the Density Topological Parameters of the Preferred Conformers of Caespitate

IF 1.9 Q2 MATHEMATICS, INTERDISCIPLINARY APPLICATIONS Computation Pub Date : 2024-01-03 DOI:10.3390/computation12010005
Andrea Moreno-Ceballos, Maria Eugenia Castro, Norma A Caballero, Liliana Mammino, Francisco J. Melendez
{"title":"Implicit and Explicit Solvent Effects on the Global Reactivity and the Density Topological Parameters of the Preferred Conformers of Caespitate","authors":"Andrea Moreno-Ceballos, Maria Eugenia Castro, Norma A Caballero, Liliana Mammino, Francisco J. Melendez","doi":"10.3390/computation12010005","DOIUrl":null,"url":null,"abstract":"In the search to cover the urgent need to combat infectious diseases, natural products have gained attention in recent years. The caespitate molecule, isolated from the plant Helichrysum caespititium of the Asteraceae family, is used in traditional African medicine. Caespitate is an acylphloroglucinol with biological activity. Acylphloroglucinols have attracted attention for treating tuberculosis due to their structural characteristics, highlighting the stabilizing effect of their intramolecular hydrogen bonds (IHBs). In this work, a conformational search for the caespitate was performed using the MM method. Posteriorly, DFT calculations with the APFD functional were used for full optimization and vibrational frequencies, obtaining stable structures. A population analysis was performed to predict the distribution of the most probable conformers. The calculations were performed in the gas phase and solution using the implicit SMD model for water, chloroform, acetonitrile, and DMSO solvents. Additionally, the multiscale ONIOM QM1/QM2 model was used to simulate the explicit solvent. The implicit and explicit solvent effects were evaluated on the global reactivity indexes using the conceptual-DFT approach. In addition, the QTAIM approach was applied to analyze the properties of the IHBs of the most energetically and populated conformers. The obtained results indicated that the most stable and populated conformer is in the gas phase, and chloroform has an extended conformation. However, water, acetonitrile, and DMSO have a hairpin shape. The optimized structures are well preserved in explicit solvent and the interaction energies for the IHBs were lower in explicit than implicit solvents due to non-covalent interactions formed between the solvent molecules. Finally, both methodologies, with implicit and explicit solvents, were validated with 1H and 13C NMR experimental data. In both cases, the results agreed with the experimental data reported in the CDCl3 solvent.","PeriodicalId":52148,"journal":{"name":"Computation","volume":"19 2","pages":""},"PeriodicalIF":1.9000,"publicationDate":"2024-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Computation","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.3390/computation12010005","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"MATHEMATICS, INTERDISCIPLINARY APPLICATIONS","Score":null,"Total":0}
引用次数: 0

Abstract

In the search to cover the urgent need to combat infectious diseases, natural products have gained attention in recent years. The caespitate molecule, isolated from the plant Helichrysum caespititium of the Asteraceae family, is used in traditional African medicine. Caespitate is an acylphloroglucinol with biological activity. Acylphloroglucinols have attracted attention for treating tuberculosis due to their structural characteristics, highlighting the stabilizing effect of their intramolecular hydrogen bonds (IHBs). In this work, a conformational search for the caespitate was performed using the MM method. Posteriorly, DFT calculations with the APFD functional were used for full optimization and vibrational frequencies, obtaining stable structures. A population analysis was performed to predict the distribution of the most probable conformers. The calculations were performed in the gas phase and solution using the implicit SMD model for water, chloroform, acetonitrile, and DMSO solvents. Additionally, the multiscale ONIOM QM1/QM2 model was used to simulate the explicit solvent. The implicit and explicit solvent effects were evaluated on the global reactivity indexes using the conceptual-DFT approach. In addition, the QTAIM approach was applied to analyze the properties of the IHBs of the most energetically and populated conformers. The obtained results indicated that the most stable and populated conformer is in the gas phase, and chloroform has an extended conformation. However, water, acetonitrile, and DMSO have a hairpin shape. The optimized structures are well preserved in explicit solvent and the interaction energies for the IHBs were lower in explicit than implicit solvents due to non-covalent interactions formed between the solvent molecules. Finally, both methodologies, with implicit and explicit solvents, were validated with 1H and 13C NMR experimental data. In both cases, the results agreed with the experimental data reported in the CDCl3 solvent.
查看原文
分享 分享
微信好友 朋友圈 QQ好友 复制链接
本刊更多论文
溶剂对开司培的全局反应活性和首选构象的密度拓扑参数的隐性和显性影响
近年来,为满足防治传染病的迫切需要,天然产品备受关注。从菊科植物 Helichrysum caespititium 中分离出来的开司培特分子被用于非洲传统医药中。开司培特是一种具有生物活性的酰基氯葡萄糖醇。酰基氯葡萄糖苷因其结构特征而在治疗结核病方面备受关注,其中突出的是其分子内氢键(IHB)的稳定作用。在这项工作中,采用 MM 方法对头孢烷酸进行了构象搜索。随后,利用 APFD 函数进行了 DFT 计算,以全面优化和振动频率,从而获得了稳定的结构。为了预测最可能构象的分布,还进行了群体分析。计算是在气相和溶液中进行的,使用的是针对水、氯仿、乙腈和 DMSO 溶剂的隐式 SMD 模型。此外,还使用多尺度 ONIOM QM1/QM2 模型模拟显式溶剂。使用概念-DFT 方法评估了隐式和显式溶剂对全局反应性指数的影响。此外,还采用 QTAIM 方法分析了能量最高、最多的构象的 IHB 特性。结果表明,气相中的构象最稳定、最多,氯仿具有扩展构象。然而,水、乙腈和二甲基亚砜具有发夹形。优化后的结构在显式溶剂中得到了很好的保留,由于溶剂分子之间形成的非共价相互作用,IHB 在显式溶剂中的相互作用能低于隐式溶剂。最后,用 1H 和 13C NMR 实验数据验证了隐式溶剂和显式溶剂的两种方法。在这两种情况下,结果都与在 CDCl3 溶剂中报告的实验数据一致。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
求助全文
约1分钟内获得全文 去求助
来源期刊
Computation
Computation Mathematics-Applied Mathematics
CiteScore
3.50
自引率
4.50%
发文量
201
审稿时长
8 weeks
期刊介绍: Computation a journal of computational science and engineering. Topics: computational biology, including, but not limited to: bioinformatics mathematical modeling, simulation and prediction of nucleic acid (DNA/RNA) and protein sequences, structure and functions mathematical modeling of pathways and genetic interactions neuroscience computation including neural modeling, brain theory and neural networks computational chemistry, including, but not limited to: new theories and methodology including their applications in molecular dynamics computation of electronic structure density functional theory designing and characterization of materials with computation method computation in engineering, including, but not limited to: new theories, methodology and the application of computational fluid dynamics (CFD) optimisation techniques and/or application of optimisation to multidisciplinary systems system identification and reduced order modelling of engineering systems parallel algorithms and high performance computing in engineering.
期刊最新文献
Analytical and Numerical Investigation of Two-Dimensional Heat Transfer with Periodic Boundary Conditions Enhancement of Machine-Learning-Based Flash Calculations near Criticality Using a Resampling Approach Corporate Bankruptcy Prediction Models: A Comparative Study for the Construction Sector in Greece Analysis of Effectiveness of Combined Surface Treatment Methods for Structural Parts with Holes to Enhance Their Fatigue Life A New Mixed Fractional Derivative with Applications in Computational Biology
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
现在去查看 取消
×
提示
确定
0
微信
客服QQ
Book学术公众号 扫码关注我们
反馈
×
意见反馈
请填写您的意见或建议
请填写您的手机或邮箱
已复制链接
已复制链接
快去分享给好友吧!
我知道了
×
扫码分享
扫码分享
Book学术官方微信
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术
文献互助 智能选刊 最新文献 互助须知 联系我们:info@booksci.cn
Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。
Copyright © 2023 Book学术 All rights reserved.
ghs 京公网安备 11010802042870号 京ICP备2023020795号-1