Journal of Theoretical & Computational Chemistry最新文献

{"title":"Basis set convergence of binding energy with and without CP-correction utilizing PBE0 method: A benchmark study of X2 (X=Ge, As, Se, Sc, Ti, V, Cr, Mn, Co, Cu, Zn)","authors":"S. Akbudak, G. Uğur, Ş. Uğur, H. Y. Ocak","doi":"10.1142/s0219633619500342","DOIUrl":"https://doi.org/10.1142/s0219633619500342","url":null,"abstract":"A DFT study of homonuclear X2 (X=Ge, As, Se, Sc, Ti, V, Cr, Mn, Fe, Co, Cu, Zn) is presented using PBEO exchange (xc) functional which is a mixing of Perdew–Burke–Ernzerhof (PBE) and Hartree Fock (...","PeriodicalId":49976,"journal":{"name":"Journal of Theoretical & Computational Chemistry","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2019-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1142/s0219633619500342","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44441902","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}

{"title":"Insights into the inhibitory mechanism and molecular interaction of novel alkaloids from Beilschmiedia glabra with lipoxygenase and acetylcholinesterase","authors":"Wan Mohd Nuzul Hakimi Wan Salleh, T. H. Ogunwa","doi":"10.1142/s021963361950038x","DOIUrl":"https://doi.org/10.1142/s021963361950038x","url":null,"abstract":"In this study, the mechanism underlying acetylcholinesterase (AChE) and 5-lipoxygenase (LOX) inhibition by two novel alkaloids, beilschglabrine A and beilschglabrine B, as well as their interaction...","PeriodicalId":49976,"journal":{"name":"Journal of Theoretical & Computational Chemistry","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2019-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1142/s021963361950038x","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44357746","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}

{"title":"Comparing statistical predictions of quantum particle transit times in molecular systems to experimental measurements","authors":"Gloria Bazargan, Evan M. Curtin, K. Sohlberg","doi":"10.1142/s0219633619500391","DOIUrl":"https://doi.org/10.1142/s0219633619500391","url":null,"abstract":"The movement of quantum particles between distinct spatial regions is an essential feature of nanoscale devices. Consequently, theoretical methods for characterizing the transit time associated wit...","PeriodicalId":49976,"journal":{"name":"Journal of Theoretical & Computational Chemistry","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2019-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1142/s0219633619500391","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47427738","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}

{"title":"Geometrical, vibrational and physical properties of polyvinyl chloride nanocomposites: Molecular modeling approach","authors":"A. Refaat, M. Ibrahim, H. Elhaes, R. Badry, H. Ezzat, I. Yahia, H. Zahran, M. Shkir","doi":"10.1142/s0219633619500378","DOIUrl":"https://doi.org/10.1142/s0219633619500378","url":null,"abstract":"B3LYP/6-31G(d, p) quantum mechanical calculations were conducted to study polyvinyl chloride (PVC) and PVC with metal oxides (ZnO and CuO). Accordingly, model molecules for PVC; PVC/xZnO; PVC/yCuO ...","PeriodicalId":49976,"journal":{"name":"Journal of Theoretical & Computational Chemistry","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2019-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1142/s0219633619500378","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44376532","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}

{"title":"Structure–Activity relationship studies of two dietary flavonoids and their Nitric Oxide Synthase inhibition activity by spectroscopic and quantum/classical computational techniques","authors":"A. S. Ben Geoffrey, J. Prasana, S. Muthu, C. S. Abraham, H. David","doi":"10.1142/s0219633619500317","DOIUrl":"https://doi.org/10.1142/s0219633619500317","url":null,"abstract":"The Nitric Oxide Synthase inhibitory activity of two dietary phytocompounds naringenin and quercetin that belong to the family of flavonoids was studied by spectroscopic and computational methods. The determining role played by the global reactivity parameters that were calculated using spectroscopic and computational methods were correlated with the Nitric Oxide Synthase inhibitory activity by a Quantitative Structure–Activity Relationship (QSAR) study. The inter and intramolecular charge–transfer interactions responsible for the biological activity of naringenin and quercetin were studied using Natural Bond Orbital Analysis. The reactive sites of the title compounds were studied using their molecular electrostatic map. The likelihood of naringenin and quercetin to be a small drug molecule was determined by Lipinski’s rule. The molecular dynamics and docking studies were carried out to test the energetic and structural favorability of the inhibition of Nitric Oxide Synthase by small drug molecules naringenin and quercetin. Experimental cell culture-based in vitro assays were done to test theoretical predictions. A QSAR study revealed that for Nitric Oxide Synthase inhibitory activity to be better, the compounds belonging to the family of flavonoids ought to have a more negative ionization energy and chemical softness while bandgap and electrophilicity index ought to be more positive.","PeriodicalId":49976,"journal":{"name":"Journal of Theoretical & Computational Chemistry","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2019-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1142/s0219633619500317","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41471632","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}

{"title":"Benchmark study of the linear and nonlinear optical polarizabilities in proto-type NLO molecule of para-nitroaniline","authors":"S. Muhammad, R. A. Shehzad, J. Iqbal, A. Al‐Sehemi, M. Saravanabhavan, M. Khalid","doi":"10.1142/s0219633619500305","DOIUrl":"https://doi.org/10.1142/s0219633619500305","url":null,"abstract":"In the present investigation, for the first time, we have performed a thorough study about different functionals and basis sets for linear and nonlinear optical (NLO) properties of para-nitroaniline ([Formula: see text]-NA), which is considered as proto-type NLO molecule, among organic NLO materials. There is a dire need of such data base for [Formula: see text]-NA because many investigators are using such values of [Formula: see text]-NA for comparative analysis. A range of different functionals including HF, BLYP, PW91, PBE, B3LYP, M06, M06-2X, PBE0, BHandHLYP, CAM-B3LYP, LC-BLYP, and B3LYP-D3 are applied in conjugation with several commonly basis sets such as 6-31G*, 6-311G*, 6-311G**, 6-311+G**, cc-pVDZ, and cc-pVTZ. A variety of functional and basis sets combinations are calculated and graphically compared with each other. The calculated total dipole moment for the [Formula: see text]-NA is found to be 6.79[Formula: see text]D which is quite closer to experimentally determined value. The lowest calculated value for linear isotropic polarizability at HF/6-31G* level of theory is [Formula: see text] esu while higher values observed with remaining all methods especially 14% polarizability increases in presence of basis set with diffuse functions and similar trend of variation is also observed in linear anisotropic polarizability. Similarly, the calculated value of frequency dependent second-order polarizability is found to be [Formula: see text] esu at PBE0/6-311+G** level of theory which is quite closer to experimental value of [Formula: see text] esu. A comparison between the calculated and experimental results shows good agreement among geometries, dipole moments and NLO polarizabilities for [Formula: see text]-NA. Moreover, the frontier molecular orbital (FMO) and electron density difference map (EDDM) analysis along with density of state (DOS) plots are also presented to get more physical intuitions into the structure–property relationship and electronic communications between terminal accepter and donor groups through [Formula: see text]-conjugation. The present investigation provides benchmark data including various commonly used functionals and basis sets for the calculation of NLO properties of [Formula: see text]-NA. Thus, the present investigation will put straight several future studies when it comes to comparative NLO study of organic materials.","PeriodicalId":49976,"journal":{"name":"Journal of Theoretical & Computational Chemistry","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2019-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1142/s0219633619500305","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41354762","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}

{"title":"Spectral and quantum chemical analysis of ethyl 4-[3-(adamantan-1-yl)-4-phenyl-5-sulfanylidene-4,5-dihydro-1H-1,2,4-triazole-1-yl]methylpiperazine-1-carboxylate","authors":"H. Al-Ghulikah, Darya Meniailava, Ulada Vysotskaya, A. S. Matsukovich, A. El-Emam, M. Shundalau","doi":"10.1142/s0219633619500299","DOIUrl":"https://doi.org/10.1142/s0219633619500299","url":null,"abstract":"The Fourier transform infrared and Raman spectra of the adamantane-based compound ethyl 4-[3-(adamantan-1-yl)-4-phenyl-5-sulfanylidene-4,5-dihydro-1H-1,2,4-triazol-1-yl]methylpiperazine-1-carboxylate were recorded in the ranges of 3200–650[Formula: see text]cm[Formula: see text] and 3200–150[Formula: see text]cm[Formula: see text], respectively. The UV/Vis spectrum of solution of the title compound in ethanol was measured in the range of 450–200[Formula: see text]nm. The DFT calculations at the B3LYP/cc-pVDZ and B3LYP/cc-pVTZ levels of the theory were performed to obtain the equilibrium geometric structure and to predict vibrational IR and Raman spectra of the title molecule. The TDDFT calculations at the CAM-B3LYP/cc-pVTZ level of the theory, as well as MRPT calculations at the CASSCF(4,5)/XMCQDPT2 level of the theory were carried out to reproduce the electronic absorption spectrum. The experimental IR, Raman and UV/Vis spectra were interpreted on the basis of results of quantum chemical modeling. Based on Mulliken and Löwdin atomic population analysis, it was established that the compound under study exhibits features of an intramolecular charge transfer.","PeriodicalId":49976,"journal":{"name":"Journal of Theoretical & Computational Chemistry","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2019-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1142/s0219633619500299","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48805607","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}

{"title":"The mutual noncovalent interactions based on metallophilic cluster and anions: A theoretical investigation of the molecular structure and spectroscopic properties of Host–Guest complexes","authors":"Xiao-ping Yang, Huixue Li, K. Yuan, Guofang Zuo, Zhi-feng Li","doi":"10.1142/s0219633619500287","DOIUrl":"https://doi.org/10.1142/s0219633619500287","url":null,"abstract":"The d[Formula: see text] metallophilic host clusters [Au(NHC)2][Formula: see text] [M(CN)2][Formula: see text] [Au(NHC)2][Formula: see text](NHC [Formula: see text] N-heterocyclic carbene, [Formula: see text], Ag) with high phosphorescence are synthesized recently and their phosphorescent modulation by solvents is investigated in theory. In this paper, the guest anions (F−, Cl−, Br−, NO[Formula: see text], and BF[Formula: see text] are used to elucidate their effects on metallophilic interactions and phosphorescence of hosts, and also they served as the probes to study the recognition characters of metallophilic hosts. The calculation shows that the guest anions can mutually interact with the host clusters and further, which can modulate the metallophilic Au[Formula: see text]M distances and the phosphorescence spectra of the hosts.","PeriodicalId":49976,"journal":{"name":"Journal of Theoretical & Computational Chemistry","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2019-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1142/s0219633619500287","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42945226","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}

{"title":"In silico modeling and in vitro activity of vitexin and isovitexin against SGLT2","authors":"Yongheng Shi, Fancui Meng, Ji-ping Liu, Bin Wang","doi":"10.1142/s0219633619500354","DOIUrl":"https://doi.org/10.1142/s0219633619500354","url":null,"abstract":"The homology model of hSGLT2 (human sodium dependent glucose co-transporter 2) was used as a target for diabetes mellitus. Molecular docking and dynamics simulations were carried out on vitexin- and isovitexin-SGLT2 complexes with dapagliflozin as positive control. The results show that both vitexin and isovitexin have weaker binding energies compared to dapagliflozin, indicating that both ligands may exhibit weak anti-diabetic effects through inhibiting SGLT2. The poor binding mode of vitexin and isovitexin may be responsible for their weak anti-diabetic effect. These results are in accordance with the inhibitory activity against hSGLT2 in vitro test with the inhibitory rate 26.3% of vitexin and 11.2% of isovitexin at the dose of 10[Formula: see text][Formula: see text]mol[Formula: see text][Formula: see text][Formula: see text]L[Formula: see text]. The results of calculation and in vitro test may explain the possible inhibiting mechanism of vitexin and isovitexin against SGLT2, and therefore enhance our understanding of the structure-activity relationships of SGLT2 inhibitors.","PeriodicalId":49976,"journal":{"name":"Journal of Theoretical & Computational Chemistry","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2019-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1142/s0219633619500354","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42939798","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}

{"title":"Author Index Volume 18 (2019)","authors":"","doi":"10.1142/s0219498819990019","DOIUrl":"https://doi.org/10.1142/s0219498819990019","url":null,"abstract":"","PeriodicalId":49976,"journal":{"name":"Journal of Theoretical & Computational Chemistry","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2019-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1142/s0219498819990019","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44035906","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}