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B3LYP Calculations (b3lyp + calculation)
Selected AbstractsTheory of chemical bonds in metalloenzymes XIII: Singlet and triplet diradical mechanisms of hydroxylations with iron-oxo species and P450 are revisitedINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 15 2009Kizashi Yamaguchi Abstract Electronic structures of the Compound I (CpdI) in P450 are investigated on the basis of spin coupling forms of iron-oxo (Fe(IV)O) cores and radical ligand (,L) groups to generalize previous singlet and triplet diradical (TD) mechanisms for oxygenations of alkanes with Fe( IV)O. Orbital interaction schemes for four lower-lying spin configurations of CpdI with HC bond of substrate are examined to elucidate how magnetic coupling modes correlate with radical reaction pathways for hydroxylation reactions on the basis of the broken symmetry (BS) molecular orbital (MO) model. The configuration correlation diagrams for the four configurations model are depicted on the basis of the isoelectronic analogy among O, O2, and Fe( IV)O, in addition to Coulomb exchange energy on the iron site, which determines its local spin configuration. Important role of ligand spin (,L) of CpdI for regulation of hydroxylation mechanisms is clarified with the aid of the spin coupling forms. Transition states for one quartet and three doublet configurations under the BS MO approximation are examined on the basis of potential curve crossings along reaction pathways. The four transition structures and corresponding radical intermediates for methane and trimethyl methane with CpI are located by the BS hybrid Kohn,Sham density functional theory (DFT) (B3LYP) method to confirm the orbital interaction schemes. Spin density populations obtained by the BS B3LYP calculations are found to be consistent with the theoretical predictions based on the four configurations model. The configuration and state correlation diagrams by BS B3LYP before and after spin projection are also consistent with the BS MO interaction schemes, which provide local SD and TD mechanisms of hydroxylation with CpdI. The present BS MO-theoretical framework is useful for systematic understanding of a lot of recent BS hybrid DFT computational results for hydroxylation reactions with CpdI and configuration correlation diagrams reported by several groups. Implications of the present theoretical and computational results are discussed in relation to several experimental characteristics of hydroxylation reactions with iron-oxo species and P450. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009 [source] Competitive coordination between lead and oligoelements with respect to some therapeutic heavy-metal chelatorsINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 11 2008C. Gourlaouen Abstract The competitive complexation of Ca2+, Fe2+, Cu2+, Zn2+, and Pb2+ toward ethylene diamine tetraacetate (EDTA), dimercaprol and D -penicillamine, three liganding agents commonly used in chelation therapy against heavy metal, especially lead, poisonings is examined by means of B3LYP calculations, natural population analyses, and the topological analysis of the electron localization function. It is shown that Pb2+ can displace any of Ca2+, Fe2+, Cu2+, or Zn2+ chelated by any of dimercaprol or D -penicillamine, but can only displace Ca2+ if EDTA is concerned. The first two chelators thus appear as better entities than EDTA to be used in chelation therapy, where in vivo selective complexation is essential. Moreover, the comparison of the bonding characteristics of Pb2+ with those of the other cations allows deriving three features to be taken into account in designing new chelators expecting to have an increased selectivity toward this cation. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008 [source] Six-coordinate Co2+ with imidazole, NH3, and H2O ligands: Approaching spin crossoverINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 6 2007Ann M. Schmiedekamp Abstract Octahedral, six-coordinate Co2+ can exist in two spin states: S = 3/2 and S = 1/2. The difference in energy between high spin (S = 3/2) and low spin (S = 1/2) is dependent on both the ligand mix and coordination stereochemistry. B3LYP calculations on combinations of neutral imidazole, NH3, and H2O ligands show that low-spin isomers are stabilized by axial H2O ligands and in structures that also include trans pairs of equatorial NH3 and protonated imidazole ligands, spin crossover structures are predicted from spin state energy differences. Occupied Co d orbitals from the DFT calculations provide a means of estimating effective ligand strength for homoleptic and mixed ligand combinations. These calculations suggest that in a labile biological system, a spin crossover environment can be created. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007 [source] B3LYP calculations on bishomoaromaticity in substituted semibullvalenes*JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 13 2001David A. Hrovat Abstract B3LYP/6-31G* calculations on the degenerate rearrangements of substituted semibullvalenes spuriously predict the relative enthalpies of the bishomoaromatic TSs to be lower than the experimental values. However, the calculations do make the useful and experimentally testable prediction that the two cyano and two phenyl substituents in 2,6-dicyano-4,8-diphenylsemibullvalene (9d) are more likely than four cyano substituents in 2,4,6,8-tetracyanosemibullvalene (9f) or the four phenyl substituents in 2,4,6,8-tetraphenylsemibullvalene (9g) to produce a semibullvalene that has a bishomoaromatic equilibrium geometry in the gas phase. The major reason for the surprising finding that 9d is more likely to be bishomoaromatic than 9g is shown to be steric interactions between the phenyl groups at C-2 and C-8 and at C-4 and C-6 in bishomoaromatic structure 10g. These interactions inhibit the conjugative stabilization of 10g; but they are absent in bishomoaromatic structure 10d, where cyano groups replace the phenyl groups at C-2 and C-6 in 10g. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1565,1573, 2001 [source] Photoionization studies on various quinones by an infrared laser desorption/tunable VUV photoionization TOF mass spectrometryJOURNAL OF MASS SPECTROMETRY (INCORP BIOLOGICAL MASS SPECTROMETRY), Issue 12 2008Yang Pan Abstract Photoionization and dissociative photoionization characters of six quinones, including 1,2-naphthoquinone (1,2-NQ), 1,4-naphthoquinone (1,4-NQ), 9,10-phenanthroquinone (PQ), 9,10-anthraquinone (AQ), benz[a]- anthracene-7,12-dione (BAD) and 1,2-acenaphthylenedione (AND) have been studied with an infrared laser desorption/tunable synchrotron vacuum ultraviolet (VUV) photoionization mass spectrometry (IR LD/VUV PIMS) technique. Mass spectra of these compounds are obtained at different VUV photon energies. Consecutive losses of two carbon monoxide (CO) groups are found to be the main fragmentation pathways for all the quinones. Detailed dissociation processes are discussed with the help of ab initio B3LYP calculations. Ionization energies (IEs) of these quinones and appearance energies (AEs) of major fragments are obtained by measuring the photoionization efficiency (PIE) spectra. The experimental results are in good agreement with the theoretical data. Copyright © 2008 John Wiley & Sons, Ltd. [source] Conformational analysis, Part 41.JOURNAL OF PHYSICAL ORGANIC CHEMISTRY, Issue 6 2006-unsaturated carbonyl compounds, A modelling, LIS/NMR investigation of the conformations of Abstract A novel Lanthanide Induced Shift Analysis (LISA) is presented. In this analysis both the paramagnetic and the diamagnetic lanthanide induced chemical shifts are normalised separately in contrast to previous techniques in which only the paramagnetic shifts were normalised. This procedure is used together with molecular mechanics (MMFF94) and ab initio (RHF/6-31G, RHF/6-311G** and B3LYP/6-311G**) calculations to investigate s - cis/s - trans isomerism in some ,,, -unsaturated aldehydes, ketones and esters. In tiglic aldehyde 1 and trans -cinnamaldehyde 4 the s - trans conformer predominates with energy differences ,E (s - cis,s - trans) of 1.64 and 1.76,kcal/mol. In methyl vinyl ketone 2 and trans -cinnamyl methyl ketone 5 the populations of the s - cis and s - trans isomers are almost equal (,E 0.24 and 0.0,kcal/mol) and in methyl crotonate 3 and methyl trans -cinnamate 6 the s - cis conformer is more stable (,E ,0.72 and ,0.41,kcal/mol). These results are in agreement with both the MMFF94 and ab initio calculated energies for the compounds except tiglic aldehyde 1 in which all the calculated values are too large and cinnamyl ketone 5. In this compound the ab initio calculations predict the s - cis form to be more stable than the s - trans in contrast to both the MM calculations and the observed result which give both forms of equal energy. Also in both the MM and ab initio calculations phenyl substitution in the ketone (2 vs. 5) considerably stabilises the s - cis form. This is not observed in practise. In phenyl acetate 7 the B3LYP calculations give two equally stable structures, one planar one non-planar. The MMFF94 and MP2 calculations and the LIS analysis support the existence of only the non -planar conformer in solution, which is also the conformation of phenyl acetate in the crystal. Copyright © 2006 John Wiley & Sons, Ltd. [source] | ||||||||||