Journal of Molecular Structure-theochem最新文献

{"title":"A theoretical study on the substituent effect of DNA-photocleavage by [Ru(phen)2(6-R-dppz)]2+ (R = H, OH, and NO2)","authors":"Lian-cai Xu ,&nbsp;Qian-shu Li ,&nbsp;Zhi-qiang Zhang ,&nbsp;Ti-fang Miao ,&nbsp;Kang-cheng Zheng ,&nbsp;Liang-nian Ji","doi":"10.1016/j.theochem.2010.08.030","DOIUrl":"10.1016/j.theochem.2010.08.030","url":null,"abstract":"<div><p>A theoretical study was conducted on the effects of three substituents in the Ru(II) polypyridyl complex, [Ru(phen)₂(6-R-dppz)]²⁺, (R<!--> <!-->=<!--> <!-->H for complex <strong>1</strong>, OH for complex <strong>2</strong>, and NO₂ for complex <strong>3</strong>), on the photocleavage of DNA. The geometric and electronic structures of these complexes in the ground (S₀), first singlet (S₁), and triplet (T₁) excited states, were calculated using the density functional theory (DFT), Hartree–Fock (HF), and configuration interaction singles (CIS) methods. The excited reduction potentials of the Ru(II) complexes in aqueous solution, which appear to be primarily responsible for the DNA-photocleavage behavior, were calculated by thermodynamic cycle, and determined to be higher than the oxidation potentials of some DNA-bases. The order of the reduction potentials changes from <strong>3</strong> <!-->&gt;<!--> <strong>2</strong> <!-->&gt;<!--> <strong>1</strong> in the ground state to <strong>2</strong> <!-->&gt;<!--> <strong>1</strong> <!-->&gt;<!--> <strong>3</strong> in the excited state, suggesting that the substituent on the main ligand has a significant effect on the electrochemical properties of the excited Ru(II) polypyridyl complexes. In addition, these theoretical results can explain two experimentally-observed phenomena: (a) the cleavage of DNA by complex <strong>3</strong> in the absence of light irradiation; (b) the inability of complex <strong>3</strong> to emit luminescence in its excited triplet state in aqueous solution.</p></div>","PeriodicalId":16419,"journal":{"name":"Journal of Molecular Structure-theochem","volume":"961 1","pages":"Pages 35-41"},"PeriodicalIF":0.0,"publicationDate":"2010-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.theochem.2010.08.030","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"90546917","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":"On the role of halogen bond in the halophilic reaction: A theoretical study","authors":"Yu Zhang","doi":"10.1016/j.theochem.2010.08.039","DOIUrl":"10.1016/j.theochem.2010.08.039","url":null,"abstract":"<div><p>Halophilic reactions have been modeled theoretically by employing CBr₄, Cl₃CCN, Cl₃CCOCl, CCl₄ and Cl₃CF as substrates and Cl⁻ as a nucleophile. It was found that the formation of the strong halogen bond is a necessary but not sufficient condition for the occurring of the halophilic reaction: the strong red-shifting halogen bond facilitates the reaction whereas the strong blue-shifting halogen bond retards it. The theoretical results are in good agreement with the experimental results.</p></div>","PeriodicalId":16419,"journal":{"name":"Journal of Molecular Structure-theochem","volume":"961 1","pages":"Pages 6-8"},"PeriodicalIF":0.0,"publicationDate":"2010-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.theochem.2010.08.039","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87106464","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":"Theoretical studies on the structures and properties of As-doped Sin (n = 1–8) clusters","authors":"Aimei Gao,&nbsp;Guoliang Li,&nbsp;Yu Chang,&nbsp;Hongyu Chen,&nbsp;Qian-shu Li","doi":"10.1016/j.theochem.2010.09.003","DOIUrl":"10.1016/j.theochem.2010.09.003","url":null,"abstract":"<div><p>The As-doped small silicon clusters AsSi<em>_n</em>/<span><math><mrow><msubsup><mrow><mtext>AsSi</mtext></mrow><mrow><mi>n</mi></mrow><mrow><mo>+</mo></mrow></msubsup><mo>/</mo><msubsup><mrow><mtext>AsSi</mtext></mrow><mrow><mi>n</mi></mrow><mrow><mo>-</mo></mrow></msubsup></mrow></math></span> (<em>n</em> <!-->=<!--> <!-->1–8) have been systematically investigated at the B3LYP/6–311+G^* level of theory. The most stable isomer of the neutral AsSi₂ cluster has an isosceles triangle structure (<strong>2n</strong> <!-->−<!--> <strong>1</strong>). Edge-capping with a silicon atom to <strong>2n</strong> <!-->−<!--> <strong>1</strong>, yields the lowest energy structure of the neutral AsSi₃ cluster, a deformed planar rhombus structure (<strong>3n</strong> <!-->−<!--> <strong>1</strong>). The ground state structure of the neutral AsSi₄ cluster is predicted to have a trigonal bipyramid form (<strong>4n</strong> <!-->−<!--> <strong>1</strong>). Adding one, two, or three Si atoms to different positions in this <strong>4n</strong> <!-->−<!--> <strong>1</strong> structure gives the lowest energy structures of the neutral AsSi₅, AsSi₆, and AsSi₇ clusters (<strong>5n</strong> <!-->−<!--> <strong>1</strong>, <strong>6n</strong> <!-->−<!--> <strong>1</strong>, and <strong>7n</strong> <!-->−<!--> <strong>1</strong>), respectively. The global minimum of neutral AsSi₈ (<strong>8n</strong> <!-->−<!--> <strong>1</strong>) can be gained by capping the most stable AsSi₇ structure with a silicon atom. The ground states of the neutral AsSi<em>_n</em> clusters are all doublet. The three low-energy states of ionic <span><math><mrow><msubsup><mrow><mtext>AsSi</mtext></mrow><mrow><mi>n</mi></mrow><mrow><mo>+</mo></mrow></msubsup><mo>/</mo><msubsup><mrow><mtext>AsSi</mtext></mrow><mrow><mi>n</mi></mrow><mrow><mo>-</mo></mrow></msubsup></mrow></math></span> have very similar structures to those of their neutral AsSi<em>_n</em> counterparts, but their orders of stability are somewhat changed. Except for the smaller AsSi⁺, the most stable <span><math><mrow><msubsup><mrow><mtext>AsSi</mtext></mrow><mrow><mi>n</mi></mrow><mrow><mo>+</mo></mrow></msubsup><mo>/</mo><msubsup><mrow><mtext>AsSi</mtext></mrow><mrow><mi>n</mi></mrow><mrow><mo>-</mo></mrow></msubsup></mrow></math></span> isomers all have singlet electronic states. Based on the optimized geometries, various energetic properties, including the incremental binding energies, the gaps between the highest occupied molecular orbital and lowest unoccupied molecular orbital, the adiabatic ionization potentials, and electron affinities, are calculated for the most stable isomers of AsSi<em>_n</em>/<span><math><mrow><msubsup><mrow><mtext>AsSi</mtext></mrow><mrow><mi>n</mi></mrow><mrow><mo>+</mo></mrow></msubsup><mo>/</mo><msubsup><mrow><mtext>AsSi</mtext></mrow><mrow><mi>n</mi><","PeriodicalId":16419,"journal":{"name":"Journal of Molecular Structure-theochem","volume":"961 1","pages":"Pages 88-96"},"PeriodicalIF":0.0,"publicationDate":"2010-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.theochem.2010.09.003","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87848898","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":"Density functional modelling studies on N-2-Methoxyphenyl-2-oxo-5-nitro-1-benzylidenemethylamine","authors":"Metin Yavuz ,&nbsp;Hasan Tanak","doi":"10.1016/j.theochem.2010.08.035","DOIUrl":"10.1016/j.theochem.2010.08.035","url":null,"abstract":"<div><p>Density functional calculations of the structure, molecular electrostatic potential and thermodynamic functions have been performed at B3LYP/6-31G(d) level of theory for the title compound of <em>N</em>-2-Methoxyphenyl-2-oxo-5-nitro-1-benzylidenemethylamine. To investigate the tautomeric stability, optimization calculations at B3LYP/6-31G(d) level were performed for the enol and keto forms of the title compound. Calculated results reveal that the enol form of the title compound is more stable than its keto form. The predicted non-linear optical properties of the title compound are much greater than ones of p-Nitroaniline. The changes of thermodynamic properties from the monomers to title compound with the temperature ranging from 200<!--> <!-->K to 450<!--> <!-->K have been obtained using the statistical thermodynamic method. At 298.15<!--> <!-->K the change of Gibbs free energy for the formation reaction of the title compound is 30.654<!--> <!-->kJ/mol. The title compound cannot be spontaneously produced from the isolated monomers at room temperature. The tautomeric equilibrium constant is computed as 0.0192 at 298.15<!--> <!-->K for enol-imine<!--> <!-->↔<!--> <!-->keto-amine tautomerization of the title compound. In addition, natural bond orbital analysis of the title compound were performed using the B3LYP/6-31G(d) method.</p></div>","PeriodicalId":16419,"journal":{"name":"Journal of Molecular Structure-theochem","volume":"961 1","pages":"Pages 9-16"},"PeriodicalIF":0.0,"publicationDate":"2010-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.theochem.2010.08.035","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"77572245","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":"Structures, stabilities and electronic properties of C50 dimers","authors":"Hongcun Bai,&nbsp;Ruiying Du,&nbsp;Weiye Qiao,&nbsp;Yuanhe Huang","doi":"10.1016/j.theochem.2010.08.033","DOIUrl":"10.1016/j.theochem.2010.08.033","url":null,"abstract":"<div><p>The dumbbell-shaped dimers constructed from C₅₀ cages are investigated using self-consistent field molecular orbital method based on density functional theory. Our study focuses on the structures, stabilities, electronic and vibrational properties of the C₅₀ dumbbell-shaped dimers. It is found that the stability of these C₅₀ dimers is related to bonding positions and linking patterns. For the dimers by [2<!--> <!-->+<!--> <!-->2] cycloaddition, a simple rule is proposed to predict the stabilities of these additive products of fullerenes according to the environment around the C–C bonds on the addition position. Moreover, higher thermodynamic stability is accompanied with larger HOMO–LUMO gaps for these dimers. The vibrational properties of the C₅₀ dimers are also discussed in this paper.</p></div>","PeriodicalId":16419,"journal":{"name":"Journal of Molecular Structure-theochem","volume":"961 1","pages":"Pages 42-47"},"PeriodicalIF":0.0,"publicationDate":"2010-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.theochem.2010.08.033","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74696434","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":"On tautomerism and substituent effect in 8-hydroxyquinoline-derived medicine molecules","authors":"Grażyna Karpińska ,&nbsp;Aleksander P. Mazurek ,&nbsp;Jan Cz. Dobrowolski","doi":"10.1016/j.theochem.2010.09.006","DOIUrl":"10.1016/j.theochem.2010.09.006","url":null,"abstract":"<div><p>The 8-hydroxyquinoline (8HQ) molecule and its four derivatives used as medicines: <em>chloroxine</em>, <em>clioquinol</em>, <em>iodoquinol</em>, and <em>nitroxoline</em> (8HQ substituted in the benzene ring by 5,7-dichloro-, 5-chloro-7-iodo-, 5,7-diiodo-, and 7-nitro-, respectively), were studied using the DFT/B3LYP/6-311G∗∗ method. Three forms of each molecule were considered: (OH⋯N) with the intramolecular OH⋯N hydrogen bond, (OH;N) with the broken intramolecular hydrogen bond, and (NH), the tautomer with the H-atom attached to the pyridine N-atom. Regardless of the substitution, the (OH⋯N) form, with the intramolecular OH⋯N hydrogen bond, was the most stable form. Breaking the intramolecular bond led to the formation of (OH;N), which was less stable by at least 25<!--> <!-->kJ/mol. The NH tautomer was higher in energy than the (OH⋯N) tautomer by at least 40<!--> <!-->kJ/mol. Based on AIM analysis, it was found that the intramolecular OH⋯N bond was the weakest in 8HQ, stronger in <em>chloroxine</em>, <em>clioquinol</em> and <em>iodoquinol</em>, and it was the strongest in <em>nitroxolin.</em> The benzene ring aromaticity decreased from 8HQ, through halogenosubstituted 8HQ, to <em>nitroxoline</em>, which was in line with the decrease of the π-electron population in the benzene ring. The sum of aromaticities of the two rings was largest for the (OH⋯N) tautomers, significantly lower for the (OH;N) tautomers, and the smallest for (NH) tautomers. From the electron population in σ and π valence orbitals of the two quinoline rings it appears that, for the benzene ring, the halogens acted as σ-electron withdrawing and π-electron donating substituents, whereas NO₂ was a σ- and π-electron withdrawing substituent. The σ substituent effect almost solely influenced the substitution site, i.e., the benzene ring, whereas the π substituent effect was extended to the pyridine ring. Here, we also present changes in the σ and π-electron populations resulting from tautomerization and breaking of the intramolecular OH⋯N hydrogen bonds.</p></div>","PeriodicalId":16419,"journal":{"name":"Journal of Molecular Structure-theochem","volume":"961 1","pages":"Pages 101-106"},"PeriodicalIF":0.0,"publicationDate":"2010-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.theochem.2010.09.006","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74898008","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":"Theoretical studies and topological analysis of the electron density of clusters of O3 with HNCO and HCNO","authors":"Abedien Zabardasti ,&nbsp;Ali Kakanejadifard ,&nbsp;Mozhgan Kikhaei ,&nbsp;Mohammad Solimannejad","doi":"10.1016/j.theochem.2010.08.015","DOIUrl":"10.1016/j.theochem.2010.08.015","url":null,"abstract":"<div><p>Ab initio and density functional calculations were used to analyze the O₃–HNCO and O₃–HCNO clusters in the gas phase. Interaction of O₃ with HNCO and HCNO have been investigated at the B3LYP/6-311++G(d,p) and MP2/6-311++G(d,p) computational levels. Three isomers were found for each system in both methods. The NH⋯O, CH⋯O, O⋯O, N⋯O and C⋯O interactions are predicted in the optimized structures. The atoms in molecules (AIM) theory were also applied to explain the nature of the interaction in predicted clusters.</p></div>","PeriodicalId":16419,"journal":{"name":"Journal of Molecular Structure-theochem","volume":"961 1","pages":"Pages 1-5"},"PeriodicalIF":0.0,"publicationDate":"2010-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.theochem.2010.08.015","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"77423491","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":"C–N bond dissociation energies: An assessment of contemporary DFT methodologies","authors":"Cai Qi ,&nbsp;Qiu-Han Lin ,&nbsp;Ya-Yu Li ,&nbsp;Si-Ping Pang ,&nbsp;Ru-Bo Zhang","doi":"10.1016/j.theochem.2010.09.005","DOIUrl":"10.1016/j.theochem.2010.09.005","url":null,"abstract":"<div><p>The assessment of the C–N bond dissociation energies is performed by using the various density functionals at 6-31+g(d,p) level. CBS-QB3 method was used to provide the theoretical benchmark values. The present results show that the three hybrid meta GGA functionals, BB1K, MPWB1K and M06 reproduce the experimental values well. M06-2X could normally overestimate the homolytic C–N bond dissociation energies. For the hybrid functionals, B3P86 and PBE1PBE can also behave almost as well as the above meta GGA functionals. Thus, they should be recommended as the most reliable method to estimate the energetic C–N bond dissociation energies.</p></div>","PeriodicalId":16419,"journal":{"name":"Journal of Molecular Structure-theochem","volume":"961 1","pages":"Pages 97-100"},"PeriodicalIF":0.0,"publicationDate":"2010-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.theochem.2010.09.005","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"79121237","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":"Density functional theory calculations of the gas-phase elimination kinetics of 2-(dimethylamino)ethyl chloride and ethyl chloride","authors":"Alexis Maldonado ,&nbsp;José R. Mora ,&nbsp;Tania Cordova ,&nbsp;Gabriel Chuchani","doi":"10.1016/j.theochem.2010.08.037","DOIUrl":"10.1016/j.theochem.2010.08.037","url":null,"abstract":"<div><p>The kinetic and mechanism of the unimolecular gas-phase elimination of 2-(dimethylamino)ethyl chloride were examined by using density functional theory methods to explain the enhanced reactivity in gas-phase elimination compared to the parent compound ethyl chloride. The plausible anchimeric assistance of the dimethylamino proposed in the literature was investigated. The theoretical calculations were carried out at B3LYP/6-31G(d,p), B3LYP/6-31++G(d,p), MPW1PW91/6-31G(d,p), MPW1PW91/6-31++G(d,p), PBEPBE/6-31G(d,p), and PBEPBE/6-31++G(d,p) levels of theory. The previous proposed reaction path of anchimeric assistance has an energy of activation 60<!--> <!-->kJ/mol higher than the experimental value. The located transition state in the minimum energy path is a four-centered cyclic configuration comprising chlorine, hydrogen and two carbon atoms. Calculation results give a lower energy of activation of 2-(dimethylamino)ethyl chloride when compared to the parent compound ethyl chloride. This result is due to the stabilization of the transition state because of electron delocalization involving the dimethylamino substituent.</p></div>","PeriodicalId":16419,"journal":{"name":"Journal of Molecular Structure-theochem","volume":"961 1","pages":"Pages 55-61"},"PeriodicalIF":0.0,"publicationDate":"2010-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.theochem.2010.08.037","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"77770308","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":"High second-order NLO responses of dehydrogenated hydrogen cyanide borane(1) oligomers","authors":"Miroslav Medveď ,&nbsp;Šimon Budzák ,&nbsp;Ivan Černušák","doi":"10.1016/j.theochem.2010.09.001","DOIUrl":"10.1016/j.theochem.2010.09.001","url":null,"abstract":"<div><p>Second-order non-linear optical (NLO) properties of dehydrogenated hydrogen cyanide borane(1) oligomers (up to dodecamers) are investigated by the Hartree–Fock, hybrid DFT (including long-range corrected functionals) and MP2 approaches. Due to one-dimensional extension of the systems the longitudinal component of the properties is addressed with focus on the electronic contributions. Direct and indirect electron correlation effects are evaluated at the MP2 level paying particular attention to the basis set effects. Unit-cell asymmetry and delocalization effects in the NLO responses are discussed in terms of the evolution of the bond-length alternation parameter, dipole moment and polarizability (reduced per unit cell) with the increasing chain length. It was found that suitable combination of the unit-cell asymmetry and electron delocalization leads to extremely large NLO response (MP2/6-311++G(d,p) value for the dodecamer is 43.7<!--> <!-->×<!--> <!-->10³ <!-->a.u.<!--> <!-->per unit cell) what makes the conjugated BCN oligomers (if one takes into account their thermodynamic stability) a promising material for NLO applications.</p></div>","PeriodicalId":16419,"journal":{"name":"Journal of Molecular Structure-theochem","volume":"961 1","pages":"Pages 66-72"},"PeriodicalIF":0.0,"publicationDate":"2010-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.theochem.2010.09.001","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"72793185","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}