Journal of Theoretical & Computational Chemistry最新文献_第7页

Regulating the NLO response of anthraquinone-supported thiourea-linked crown ether macrocycle by introducing metal cations: A DFT study 引入金属阳离子调节蒽醌负载硫脲连接冠醚大环的非线性光学响应：DFT研究

IF 2.4

Journal of Theoretical & Computational Chemistry Pub Date : 2020-07-04 DOI: 10.1142/s0219633620500170

Yao Yao, Jin-Ting Ye, Xiang Li, Y. Zhang, Sinan Zhu, Y. Qiu

引用次数: 2

Quantum chemical, experimental exploration of biological activity and inhibitory potential of new cytotoxic kochiosides fromKochia prostrata(L.) Schrad 鳖甲新细胞毒总苷的量子化学、生物活性及抑制潜力的实验研究Schrad

IF 2.4

Journal of Theoretical & Computational Chemistry Pub Date : 2020-07-01 DOI: 10.1142/s0219633620500121

A. Irfan, Muhammad Imran, A. Al‐Sehemi, M. Assiri, A. Hussain, Noreen Khalid, S. Ullah, G. Abbas

引用次数: 6

In-silico analysis to identify the role of MEN1 missense mutations in breast cancer 通过计算机分析确定MEN1错义突变在乳腺癌中的作用

IF 2.4

Journal of Theoretical & Computational Chemistry Pub Date : 2020-06-30 DOI: 10.1142/s0219633620410023

S. R. Ganakammal, Mahesh Koirala, Bohua Wu, E. Alexov

引用次数: 3

Theoretical study of new push–pull molecules based on transition metals for NLO applications and determination of ICT mechanisms by DFT calculations NLO应用中基于过渡金属的新型推挽分子的理论研究和用DFT计算确定ICT机制

IF 2.4

Journal of Theoretical & Computational Chemistry Pub Date : 2020-06-23 DOI: 10.1142/s0219633620500261

A. M. Elhorri

{"title":"Theoretical study of new push–pull molecules based on transition metals for NLO applications and determination of ICT mechanisms by DFT calculations","authors":"A. M. Elhorri","doi":"10.1142/s0219633620500261","DOIUrl":"https://doi.org/10.1142/s0219633620500261","url":null,"abstract":"This study is based on the valuation of a few model molecules. The objective of this research is focussed on the nonlinear optical (NLO) improvement of four organometallic molecules and one organic molecule. These molecules have been subjected to several calculations by different functionals: CAM–B3LYP, LC–BLYP, LC–wPBE, wB97X, M11, M06–2X, M08–HX and M08–SO. These functionals gave three orders of classification of the [Formula: see text] parameters. The CAM–B3LYP functional recorded very good agreement between [Formula: see text] parameters and gaps ([Formula: see text]. Significant first hyperpolarizabilities ([Formula: see text] have been obtained around 880 * 10[Formula: see text][Formula: see text]esu. The mechanisms of intramolecular charge transfer (ICT) have shown energetic passages from donor groups to acceptors and vice versa. The substitution of metals influences the location of [Formula: see text] electrons at the level of the chromophores. Finally, the lengthening of the aromatic chains between the acceptor and donor groups shows significant NLO improvements. The first and second hyperpolarizabilities ([Formula: see text] and ([Formula: see text] for a chain of several benzene rings are of the order of 21,663.16 * 10[Formula: see text][Formula: see text]esu and 16,464.65 * 10[Formula: see text][Formula: see text]esu, respectively.","PeriodicalId":49976,"journal":{"name":"Journal of Theoretical & Computational Chemistry","volume":"19 1","pages":"2050026"},"PeriodicalIF":2.4,"publicationDate":"2020-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1142/s0219633620500261","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44302752","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}

引用次数: 4

Thermal behavior of complex model with the cellulose II and amorphous chain 纤维素Ⅱ和无定形链复合模型的热行为

IF 2.4

Journal of Theoretical & Computational Chemistry Pub Date : 2020-06-15 DOI: 10.1142/s0219633620400040

Yu Chen, Xuewei Jiang, Huhe Wu, Lu Zheng

{"title":"Thermal behavior of complex model with the cellulose II and amorphous chain","authors":"Yu Chen, Xuewei Jiang, Huhe Wu, Lu Zheng","doi":"10.1142/s0219633620400040","DOIUrl":"https://doi.org/10.1142/s0219633620400040","url":null,"abstract":"to investigate the thermal behavior of complex model with amorphous region and crystallization region of cellulose ii, the structures and properties of cellulose ii, amorphous chain and their combined models were studied by molecular dynamics simulation . the results showed that the amorphous chain is more susceptible to temperature than the cellulose ii. it can form anti- parallel structure similar to cellulose ii at high temperature . in the complex model , one end of the amorphous chain is fixed to form hydrogen bonds with the cellulose ii, and the other end is not. at 300[formula: see text]k, the free part of amorphous chain is approximately perpendicular to the axial direction of the cellulose ii. when the temperature increases, the free part of amorphous chain adheres to the surface of cellulose ii. the free part of amorphous chain did not form hydrogen bond with the cellulose ii. the formation of amorphous chain and surface of the cellulose ii is a zipper process at 450[formula: see text]k. furthermore, water molecules penetrate into the inter-space of the amorphous and crystalline regions. the probability of hydrogen bonds between water molecules and the complex model was less than 8.21% which explains why cellulose is insoluble in water. these conclusions provide a guiding significance for the dissolution mechanism of cellulose.","PeriodicalId":49976,"journal":{"name":"Journal of Theoretical & Computational Chemistry","volume":"19 1","pages":"2040004"},"PeriodicalIF":2.4,"publicationDate":"2020-06-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1142/s0219633620400040","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48933571","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}

引用次数: 4

Changes in structure and flexibility of p53 TAD2 upon binding to p300 Taz2 p53 TAD2与p300 Taz2结合后结构和灵活性的变化

IF 2.4

Journal of Theoretical & Computational Chemistry Pub Date : 2020-06-15 DOI: 10.1142/s0219633620400076

Tongtong Li, Amy O. Stevens, Laura I. Gil Pineda, Shenghan Song, Christabel A. Ameyaw Baah, Yi He

引用次数: 4

The accuracy of force fields on the simulation of intrinsically disordered proteins: A benchmark test on the human p53 tumor suppressor 模拟内在无序蛋白的力场的准确性:对人类p53肿瘤抑制因子的基准测试

IF 2.4

Journal of Theoretical & Computational Chemistry Pub Date : 2020-06-01 DOI: 10.1142/s021963362050011x

Shangbo Ning, Jun Liu, Na Liu, Da-zhong Yan

{"title":"The accuracy of force fields on the simulation of intrinsically disordered proteins: A benchmark test on the human p53 tumor suppressor","authors":"Shangbo Ning, Jun Liu, Na Liu, Da-zhong Yan","doi":"10.1142/s021963362050011x","DOIUrl":"https://doi.org/10.1142/s021963362050011x","url":null,"abstract":"Intrinsically disordered proteins (IDPs) are a class of proteins without stable three-dimensional structures under physiological conditions. IDPs exhibit high dynamic nature and could be described by structural ensembles. As one of the most widely used tools, molecular dynamics (MD) simulation could provide the atomic descriptions of the structural ensemble of IDPs. However, the accuracy of the MD simulation largely depends on the accuracy of the force field. In this paper, we compared the structural ensembles of the activation domain 1 (AD1) in p53 tumor suppressor obtained from the widely used force fields, AMBER99SB-ILDN, CHARMM27, CHARMM36m with different water models. The results show that CHARMM36m generates more extended conformations than other force fields, while CHARMM27 prefers to sample the [Formula: see text]-helical structure. Moreover, the chemical shifts obtained by CHARMM36m are the closest to the experimental measurements. These results indicate that the CHARMM36m force field performs best in characterizing the structure properties of p53 AD1. Water models are also critical to describe the structural ensemble of IDPs. TIP4P water model can obtain more extended conformations and produce more local helical conformations than the TIP3P model in our simulation. In addition, we also compare the chemical shifts predicted by different chemical shift predicting programs with experimental measurements, the results show that SHIFTX2 obtains the best performance in the chemical shifts prediction.","PeriodicalId":49976,"journal":{"name":"Journal of Theoretical & Computational Chemistry","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2020-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1142/s021963362050011x","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47680489","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}

引用次数: 2

Xanthine oxidoreductase inhibition – A review of computational aspect 黄嘌呤氧化还原酶抑制——计算方面的综述

IF 2.4

Journal of Theoretical & Computational Chemistry Pub Date : 2020-06-01 DOI: 10.1142/s0219633620400088

Chaonan Dong, M. Montes, W. Al-Sawai

引用次数: 4

A new way to recognize downhill folding based on generalized path length 基于广义路径长度的下坡折叠识别新方法

IF 2.4

Journal of Theoretical & Computational Chemistry Pub Date : 2020-06-01 DOI: 10.1142/s0219633620400052

Xuewei Jiang, Zhengwu Wu, Z. Fan, Junhua Yin, Lu Zheng

引用次数: 1

Adaptive lasso with weights based on normalized filtering scores in molecular big data 分子大数据中基于归一化滤波分数的权重自适应套索

IF 2.4

Journal of Theoretical & Computational Chemistry Pub Date : 2020-06-01 DOI: 10.1142/s0219633620400106

Abhijeet R. Patil, Byung-Kwon Park, Sangjin Kim

{"title":"Adaptive lasso with weights based on normalized filtering scores in molecular big data","authors":"Abhijeet R. Patil, Byung-Kwon Park, Sangjin Kim","doi":"10.1142/s0219633620400106","DOIUrl":"https://doi.org/10.1142/s0219633620400106","url":null,"abstract":"The molecular big data are highly correlated, and numerous genes are not related. The various classification methods performance mainly rely on the selection of significant genes. Sparse regularized regression (SRR) models using the least absolute shrinkage and selection operator (lasso) and adaptive lasso (alasso) are popularly used for gene selection and classification. Nevertheless, it becomes challenging when the genes are highly correlated. Here, we propose a modified adaptive lasso with weights using the ranking-based feature selection (RFS) methods capable of dealing with the highly correlated gene expression data. Firstly, an RFS methods such as Fisher’s score (FS), Chi-square (CS), and information gain (IG) are employed to ignore the unimportant genes and the top significant genes are chosen through sure independence screening (SIS) criteria. The scores of the ranked genes are normalized and assigned as proposed weights to the alasso method to obtain the most significant genes that were proven to be biologically related to the cancer type and helped in attaining higher classification performance. With the synthetic data and real application of microarray data, we demonstrated that the proposed alasso method with RFS methods is a better approach than the other known methods such as alasso with filtering such as ridge and marginal maximum likelihood estimation (MMLE), lasso and alasso without filtering. The metrics of accuracy, area under the receiver operating characteristics curve (AUROC), and geometric mean (GM-mean) are used for evaluating the performance of the models.","PeriodicalId":49976,"journal":{"name":"Journal of Theoretical & Computational Chemistry","volume":"1 1","pages":""},"PeriodicalIF":2.4,"publicationDate":"2020-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1142/s0219633620400106","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41397785","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}

引用次数: 2