Georges Stéphane Dembélé, M. Koné, Fandia Konate, Doh Soro, N. Ziao
This work was carried out on a series of twenty-two (22) benzimidazole derivatives with inhibitory activities against Mycobacterium tuberculosis H37Rv by applying the Quantitative Structure-Activity Relationship (QSAR) method. The molecules were optimized at the level DFT/B3LYP/6−31 + G (d, p), to obtain the molecular descriptors. We used three statistical learning tools namely, the linear multiple regression (LMR) method, the nonlinear regression (NLMR) and the artificial neural network (ANN) method. These methods allowed us to obtain three (3) quantitative models from the quantum descriptors that are, chemical potential (μ), polarizability (α), bond length l (C = N), and lipophilicity. These models showed good statistical performance. Among these, the ANN has a significantly better predictive ability R 2 = 0.9995; RMSE = 0.0149; F = 31879.0548. The external validation tests verify all the criteria of Tropsha et al. and Roy et al. Also, the internal validation tests show that the model has a very satisfactory internal predictive character and can be considered as robust. Moreover, the applicability range of this model determined from the levers shows that a prediction of the pMIC of the new benzimidazole derivatives is acceptable when its lever value is lower than 1.
采用定量构效关系(Quantitative Structure-Activity Relationship, QSAR)方法对22个具有抑制结核分枝杆菌H37Rv活性的苯并咪唑衍生物进行了研究。在DFT/B3LYP/6−31 + G (d, p)水平对分子进行优化，得到分子描述符。我们使用了三种统计学习工具，即线性多元回归(LMR)方法、非线性回归(NLMR)方法和人工神经网络(ANN)方法。这些方法使我们能够从化学势(μ)、极化率(α)、键长l (C = N)和亲脂性这三个量子描述符中获得3个定量模型。这些模型具有良好的统计性能。其中，人工神经网络的预测能力显著优于人工神经网络(r2 = 0.9995);Rmse = 0.0149;F = 31879.0548。外部验证试验验证了Tropsha et al.和Roy et al.的所有标准。内部验证试验表明，该模型具有良好的内部预测特性，具有较强的鲁棒性。此外，该模型由杠杆确定的适用范围表明，当杠杆值小于1时，可以对新苯并咪唑衍生物的pMIC进行预测。
{"title":"Quantitative Structure-Activity Relationship Study of a Benzimidazole-Derived Series Inhibiting <i>Mycobacterium tuberculosis H37Rv</i>","authors":"Georges Stéphane Dembélé, M. Koné, Fandia Konate, Doh Soro, N. Ziao","doi":"10.4236/cc.2022.102004","DOIUrl":"https://doi.org/10.4236/cc.2022.102004","url":null,"abstract":"This work was carried out on a series of twenty-two (22) benzimidazole derivatives with inhibitory activities against Mycobacterium tuberculosis H37Rv by applying the Quantitative Structure-Activity Relationship (QSAR) method. The molecules were optimized at the level DFT/B3LYP/6−31 + G (d, p), to obtain the molecular descriptors. We used three statistical learning tools namely, the linear multiple regression (LMR) method, the nonlinear regression (NLMR) and the artificial neural network (ANN) method. These methods allowed us to obtain three (3) quantitative models from the quantum descriptors that are, chemical potential (μ), polarizability (α), bond length l (C = N), and lipophilicity. These models showed good statistical performance. Among these, the ANN has a significantly better predictive ability R 2 = 0.9995; RMSE = 0.0149; F = 31879.0548. The external validation tests verify all the criteria of Tropsha et al. and Roy et al. Also, the internal validation tests show that the model has a very satisfactory internal predictive character and can be considered as robust. Moreover, the applicability range of this model determined from the levers shows that a prediction of the pMIC of the new benzimidazole derivatives is acceptable when its lever value is lower than 1.","PeriodicalId":49976,"journal":{"name":"Journal of Theoretical & Computational Chemistry","volume":"37 1","pages":""},"PeriodicalIF":2.4,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"84299476","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Essoh Akpa Eugène, N’guessan Boka Robert, Adenidji Ganiyou, Yapo Kicho Denis, A. Ané, Bamba El Hadji Sawaliho
Catechin and epicatechin are two isomeric flavonoids. Despite the vital properties highlighted by numerous scientific studies, very little data is available on the intrinsic reactivity of these compounds. To provide more details on the stability and reactivity of catechin and epicatechin, this study is performed by means of theoretical calculation methods. For this purpose, geometry optimizations and frequency calculations at the B3LYP/6-31 + G (d, p) level of theory has been carried out and Natural Bond Orbital (NBO) analysis and VEDA (Vibrational Energy Distribution Analysis). The geometric and energy parameters and NBO analysis show that catechin appears more stable than epicatechin. The hydroxyl group position on the ring C of the catechol structure represents a factor that influences this relative stability. The global and local reactivity parameters reveal that epicatechin becomes more reactive than catechin. They indicate that their hydroxyl groups correspond to their most receptive sites. Fukui indices, VEDA and acidity study establish that O28–H29 remains the most reactive.
儿茶素和表儿茶素是两种异构体黄酮类化合物。尽管许多科学研究强调了这些重要的性质，但关于这些化合物的内在反应性的数据很少。为了更详细地了解儿茶素和表儿茶素的稳定性和反应性，本研究采用理论计算方法进行。为此，在B3LYP/6-31 + G (d, p)理论水平上进行了几何优化和频率计算，并进行了自然键轨道(NBO)分析和VEDA(振动能量分布分析)。几何参数和能量参数以及NBO分析表明，儿茶素比表儿茶素更稳定。儿茶酚结构C环上羟基的位置是影响这种相对稳定性的一个因素。整体和局部反应性参数显示表儿茶素比儿茶素更具反应性。它们表示它们的羟基对应于它们最容易接受的位置。Fukui指数、VEDA和酸度研究表明，O28-H29仍然是最具活性的。
{"title":"Catechin and Epicatechin. What’s the More Reactive?","authors":"Essoh Akpa Eugène, N’guessan Boka Robert, Adenidji Ganiyou, Yapo Kicho Denis, A. Ané, Bamba El Hadji Sawaliho","doi":"10.4236/cc.2022.102003","DOIUrl":"https://doi.org/10.4236/cc.2022.102003","url":null,"abstract":"Catechin and epicatechin are two isomeric flavonoids. Despite the vital properties highlighted by numerous scientific studies, very little data is available on the intrinsic reactivity of these compounds. To provide more details on the stability and reactivity of catechin and epicatechin, this study is performed by means of theoretical calculation methods. For this purpose, geometry optimizations and frequency calculations at the B3LYP/6-31 + G (d, p) level of theory has been carried out and Natural Bond Orbital (NBO) analysis and VEDA (Vibrational Energy Distribution Analysis). The geometric and energy parameters and NBO analysis show that catechin appears more stable than epicatechin. The hydroxyl group position on the ring C of the catechol structure represents a factor that influences this relative stability. The global and local reactivity parameters reveal that epicatechin becomes more reactive than catechin. They indicate that their hydroxyl groups correspond to their most receptive sites. Fukui indices, VEDA and acidity study establish that O28–H29 remains the most reactive.","PeriodicalId":49976,"journal":{"name":"Journal of Theoretical & Computational Chemistry","volume":"18 1","pages":""},"PeriodicalIF":2.4,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85932791","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2021-06-07DOI: 10.1515/9783110682045-012
T. Yusuf, E. Akintemi, S. Olagboye, G. Tolufashe
{"title":"12 Investigating the biological actions of some Schiff bases using density functional theory study","authors":"T. Yusuf, E. Akintemi, S. Olagboye, G. Tolufashe","doi":"10.1515/9783110682045-012","DOIUrl":"https://doi.org/10.1515/9783110682045-012","url":null,"abstract":"","PeriodicalId":49976,"journal":{"name":"Journal of Theoretical & Computational Chemistry","volume":"20 1","pages":""},"PeriodicalIF":2.4,"publicationDate":"2021-06-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"80399408","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2021-06-07DOI: 10.1515/9783110682045-002
F. Opoku, P. P. Govender
{"title":"2 Atomistic insight into the significantly enhanced photovoltaic cells of monolayer GaTe2 via two-dimensional van der Waals heterostructures engineering","authors":"F. Opoku, P. P. Govender","doi":"10.1515/9783110682045-002","DOIUrl":"https://doi.org/10.1515/9783110682045-002","url":null,"abstract":"","PeriodicalId":49976,"journal":{"name":"Journal of Theoretical & Computational Chemistry","volume":"15 1","pages":""},"PeriodicalIF":2.4,"publicationDate":"2021-06-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89591325","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2021-06-07DOI: 10.1515/9783110682045-202
P. Ramasami
A virtual conference on computational science (VCCS-2019) was organized online from 1 to 31 August 2019. This was the seventh virtual conference which was started in 2013. The month of August was chosen to commemorate the birth anniversary of Erwin Schrödinger, the father of quantum mechanics, on 12 August. There were 40 presentations for the virtual conference with 110 participants from 25 countries. A secured platform was used for virtual interactions of the participants. After the virtual conference, there was a call for full papers to be considered for publication in the conference proceedings. Manuscripts were received and they were processed and reviewed as per the policy of De Gruyter. This book is a collection of the thirteen accepted manuscripts based on the use of computational chemistry methods. These manuscripts cover a range of topics from fundamental to applied science. Parlak et al investigated the structural and spectroscopic properties of 3-halogenobenzaldehydes using DFT and TDDFT simulations. Francis and Govender studied photovoltaic cells of monolayer GaTe2 via two-dimensional van der Waals heterostructures engineering. Sekar et al explored fluorescent styryl chromophores with rigid (pyrazole) donor and rigid (benzothiophenedioxide) acceptor using DFT, TDDFT and nonlinear optical methods. Sekar and Shinde did comparative studies of the ESIPT and azo-hydrazone tautomerism in naphthalene based fluorescent acid azo dyes by DFT computations. Olasegun et al examined the efficiency of anthocyanidins as sensitizers in dye-sensitized solar cells. Oluwasegun et al analysed the inhibitory potential of the oxypeucedanin, which has anti-tumour activity against human prostate carcinoma DU145 cells, by computation docking studies. Ambrose et al provides a mechanistic insight into interactions between thiazolidinedones derivatives and PTP-1B through combination of three dimensional quantity structural-activity relationship and molecular docking. Kuznetsov reviewed research of nanocomposites based on graphene quantum dots. Oloba-Whenu et al studied the reaction of 3,5-dinitroethoxypyridine and 3,5-dinitromethoxypyridine with piperidine using DFT method. Alabi et al synthesised, characterized and 1,3-bis [(E)-furan-2-yl) methylene] urea and 1,3-bis [(E)-furan-2-yl) methylene] thiourea and they complemented the experimental research using DFT method. Bilonda and Mammino reports on the computational studies of biologically active alkaloids of plant origin. Yusuf et al investigated the biological actions of some Schiff bases using DFT method. Ntie-Kang reviewed molecular mechanics approaches for rational drug design with a special emphasis on the role of force fields and solvation models. I hope that these chapters will add to literature and they will be useful references for researchers.
{"title":"Preface of the Book of Proceedings of the Virtual Conference on Computational Science (VCCS-2019)","authors":"P. Ramasami","doi":"10.1515/9783110682045-202","DOIUrl":"https://doi.org/10.1515/9783110682045-202","url":null,"abstract":"A virtual conference on computational science (VCCS-2019) was organized online from 1 to 31 August 2019. This was the seventh virtual conference which was started in 2013. The month of August was chosen to commemorate the birth anniversary of Erwin Schrödinger, the father of quantum mechanics, on 12 August. There were 40 presentations for the virtual conference with 110 participants from 25 countries. A secured platform was used for virtual interactions of the participants. After the virtual conference, there was a call for full papers to be considered for publication in the conference proceedings. Manuscripts were received and they were processed and reviewed as per the policy of De Gruyter. This book is a collection of the thirteen accepted manuscripts based on the use of computational chemistry methods. These manuscripts cover a range of topics from fundamental to applied science. Parlak et al investigated the structural and spectroscopic properties of 3-halogenobenzaldehydes using DFT and TDDFT simulations. Francis and Govender studied photovoltaic cells of monolayer GaTe2 via two-dimensional van der Waals heterostructures engineering. Sekar et al explored fluorescent styryl chromophores with rigid (pyrazole) donor and rigid (benzothiophenedioxide) acceptor using DFT, TDDFT and nonlinear optical methods. Sekar and Shinde did comparative studies of the ESIPT and azo-hydrazone tautomerism in naphthalene based fluorescent acid azo dyes by DFT computations. Olasegun et al examined the efficiency of anthocyanidins as sensitizers in dye-sensitized solar cells. Oluwasegun et al analysed the inhibitory potential of the oxypeucedanin, which has anti-tumour activity against human prostate carcinoma DU145 cells, by computation docking studies. Ambrose et al provides a mechanistic insight into interactions between thiazolidinedones derivatives and PTP-1B through combination of three dimensional quantity structural-activity relationship and molecular docking. Kuznetsov reviewed research of nanocomposites based on graphene quantum dots. Oloba-Whenu et al studied the reaction of 3,5-dinitroethoxypyridine and 3,5-dinitromethoxypyridine with piperidine using DFT method. Alabi et al synthesised, characterized and 1,3-bis [(E)-furan-2-yl) methylene] urea and 1,3-bis [(E)-furan-2-yl) methylene] thiourea and they complemented the experimental research using DFT method. Bilonda and Mammino reports on the computational studies of biologically active alkaloids of plant origin. Yusuf et al investigated the biological actions of some Schiff bases using DFT method. Ntie-Kang reviewed molecular mechanics approaches for rational drug design with a special emphasis on the role of force fields and solvation models. I hope that these chapters will add to literature and they will be useful references for researchers.","PeriodicalId":49976,"journal":{"name":"Journal of Theoretical & Computational Chemistry","volume":"418 1","pages":""},"PeriodicalIF":2.4,"publicationDate":"2021-06-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"79497717","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2021-06-07DOI: 10.1515/9783110682045-008
A. Kuznetsov
{"title":"8 Review of research of nanocomposites based on graphene quantum dots","authors":"A. Kuznetsov","doi":"10.1515/9783110682045-008","DOIUrl":"https://doi.org/10.1515/9783110682045-008","url":null,"abstract":"","PeriodicalId":49976,"journal":{"name":"Journal of Theoretical & Computational Chemistry","volume":"22 1","pages":""},"PeriodicalIF":2.4,"publicationDate":"2021-06-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"91152306","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2021-06-07DOI: 10.1515/9783110682045-007
A. Igunnu, G. Ambrose, T. Adigun
{"title":"7 Mechanistic insight into the interactions between thiazolidinedione derivatives and PTP-1B combining 3D QSAR andmolecular docking in the treatment of type 2 diabetes","authors":"A. Igunnu, G. Ambrose, T. Adigun","doi":"10.1515/9783110682045-007","DOIUrl":"https://doi.org/10.1515/9783110682045-007","url":null,"abstract":"","PeriodicalId":49976,"journal":{"name":"Journal of Theoretical & Computational Chemistry","volume":"35 1","pages":""},"PeriodicalIF":2.4,"publicationDate":"2021-06-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"78026522","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2021-06-07DOI: 10.1515/9783110682045-001
C. Parlak, Berna Sümeyra Atan, L. Rhyman, P. Ramasami
{"title":"1 Structural and spectroscopic properties of 3-halogenobenzaldehydes: DFT and TDDFT simulations","authors":"C. Parlak, Berna Sümeyra Atan, L. Rhyman, P. Ramasami","doi":"10.1515/9783110682045-001","DOIUrl":"https://doi.org/10.1515/9783110682045-001","url":null,"abstract":"","PeriodicalId":49976,"journal":{"name":"Journal of Theoretical & Computational Chemistry","volume":"116 1","pages":""},"PeriodicalIF":2.4,"publicationDate":"2021-06-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85078308","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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