Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “electronic structure”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,135 records · Page 63Linked to original sources
PubMed2002

(57)Fe Mössbauer isomer shifts of heme protein model systems: electronic structure calculations.

We report the results of density functional theory (DFT) calculations of the (57)Fe Mössbauer isomer shifts (delta(Fe)) for a series of 24 inorganic, organometallic, and metalloprotein/metalloporphyrin model systems in S = 0, (1)/(2), 1, (3)/(2), 2, and (5)/(2) spin states. We find an excellent correlation between calculation and experiment over the entire 2.34 mm s(-1) range of isomer shifts: a 0.07-0.08 mm s(-1) rms deviation between calculation and experiment (corresponding to 3-4% of the total delta(Fe) range, depending on the functionals used) with R(2) values of 0.973 and 0.981 (p < 0.0001). The best results are obtained by using the hybrid exchange-correlation functional B3LYP, used previously for (57)Fe Mössbauer quadrupole splittings and (57)Fe NMR chemical shifts and chemical shielding anisotropies. The relativistically corrected value of alpha, alpha(rel), converges with the large basis set used in this work, but the exact values vary somewhat with the methods used: -0.253 a(0)(3) mm s(-1) (Hartree-Fock; HF); -0.316 a(0)(3) mm s(-1) (hybrid HF-DFT; B3LYP), or -0.367 a(0)(3) mm s(-1) (pure DFT; BPW91). Both normal and intermediate spin state isomer shifts are well reproduced by the calculations, as is the broad range of delta(Fe) values: from [Fe(VI)O(4)](2-) (-0.90 mm s(-1) expt; -1.01 mm s(-1) calc) to KFe(II)F(3) (1.44 mm s(-1) expt; 1.46 mm s(-1) calc). Molecular orbital analyses of all inorganic solids as well as all organometallic and metalloporphyrin systems studied reveal that there are three major core MO contributions to rho(tot)(0), the total charge density at the iron nucleus (and hence delta(Fe)), that do not vary with changes in chemistry, while the valence MO contributions are highly correlated with delta(Fe) (R(2) = 0.915-0.938, depending on the functionals used), and the correlation between the valence MO contributions and the total MO contribution is even better (R(2) = 0.965-0.976, depending on the functionals used). These results are of general interest since they demonstrate that DFT methods now enable the accurate prediction of delta(Fe) values in inorganic, organometallic, and metalloporphyrin systems in all spin states and over a very wide range of delta(Fe) values with a very small rms error.

Electrochemistry↗
PubMed2004

Cyclic perfluorocarbon radicals and anions having high global warming potentials (GWPs): structures, electron affinities, and vibrational frequencies.

Adiabatic electron affinities, optimized molecular geometries, and IR-active vibrational frequencies have been predicted for small cyclic hydrocarbon radicals C(n)H(2)(n)(-)(1) (n = 3-6) and their perfluoro counterparts C(n)F(2)(n)(-)(1) (n = 3-6). Total energies and optimized geometries of the radicals and corresponding anions have been obtained using carefully calibrated (Chem. Rev. 2002, 102, 231) density functional methods, namely, the B3LYP, BLYP, and BP86 functionals in conjunction with the DZP++ basis set. The predicted electron affinities show that only the cyclopropyl radical tends to bind electrons among the hydrocarbon radicals studied. The trend for the perfluorocarbon (PFC) radicals is quite different. The electron affinities increase with expanding ring size until n = 5 and then slightly decrease at n = 6. Predicted electron affinities of the hydrocarbon radicals using the B3LYP hybrid functional are 0.24 eV (C(3)H(5)/C(3)H(5)(-)), -0.19 eV (C(4)H(7)/C(4)H(7)(-)), -0.15 eV (C(5)H(9)/C(5)H(9)(-)), and -0.11 eV (C(6)H(11)/C(6)H(11)(-)). Analogous electron affinities of the perflurocarbon radicals are 2.81 eV (C(3)F(5)/C(3)F(5)(-)), 3.18 eV (C(4)F(7)/C(4)F(7)(-)), 3.34 eV (C(5)F(9)/C(5)F(9)(-)), and 3.21 eV (C(6)F(11)/C(6)F(11)(-)).

Journal Article↗
PubMed2005

Role of conformation and electronic structure in the chemistry of ground and excited state o-pyrazolylphenylnitrenes.

The chemistry of 2-(1-pyrazolyl)- (2a) and 2-[1-(3,5-dimethylpyrazolyl]phenylnitrene (2b) has been studied in EtOH solution at room temperature, in EtOH glasses at 90 K, and in Ar matrices at 12 K. These nitrenes were chosen as suitable models for clarifying the mechanism of intramolecular reactions because attack at the pyrazole ring can occur according to different modes and the asymmetry of the substituent gives rise to different conformations. Detailed DFT and CASSCF/CASPT2 studies on the conformation and decay paths of both spin states of the nitrenes have been carried out. Ring expansion to dehydroazepines (via benzoazirines) is calculated to be competitive in both nitrenes, but in the dimethyl derivative, 2b, attack onto the N lone pair (which is made more nucleophilic by the methyl groups) is favored. The higher barriers (by 4-8 kcal/mol) in singlet 2a cause 60-70% of this nitrene to decay by intersystem crossing to the triplet. Thus, the seemingly straightforward formation of benzo-fused heterocycles through intramolecular attack of the pyrazoline N lone pair by the singlet phenylnitrene can only overcome ring expansion and intermolecular reactions under favorable circumstances. The comparatively persistent triplet nitrenes are characterized in matrices, and the yields of photocyclization products (mainly pyrazolo[1,5-a]benzimidazole (7) from 2a and 5,6-dihydropyrazolo[1,5-a]quinoxaline (8) from 2b) are shown to depend on the preferred conformation of the starting azide and nitrene.

Journal Article↗
PubMed2005

Ground- and excited-state electronic structure of an emissive pyrazine-bridged ruthenium(II) dinuclear complex.

The synthesis, characterization, and electrochemical, photophysical, and photochemical properties of the binuclear compounds [(Ru(H8-bpy)2)2((Metr)2Pz)](PF6)2 (1) and [(Ru(D8-bpy)2)2((Metr)2Pz)](PF6)2 (2), where bpy is 2,2'-bipyridine and H2(Metr)2Pz is the planar ligand 2,5-bis(5'-methyl-4'H-[1,2,4]triaz-3'-yl)pyrazine, are reported. Electrochemical and spectro-electrochemical investigations indicate that the ground-state interaction between each metal center is predominantly electrostatic and in the mixed-valence form only a low level of ground-state delocalization is present. Resonance Raman, transient, and time-resolved spectroscopies enable a detailed assignment to be made of the excited-state photophysical properties of the complexes. Deuteriation is employed to both facilitate spectroscopic characterization and investigate the nature of the lowest excited states.

Journal Article↗
PubMed2004

Preparation and molecular and electronic structures of iron(0) dinitrogen and silane complexes and their application to catalytic hydrogenation and hydrosilation.

Reduction of the five-coordinate iron(II) dihalide complexes (iPrPDI)FeX2 (iPrPDI = ((2,6-CHMe2)2C6H3N=CMe)2C5H3N; X = Cl, Br) with sodium amalgam under 1 atm of dinitrogen afforded the square pyramidal, high spin iron(0) bis(dinitrogen) complex (iPrPDI)Fe(N2)2. In solution, (iPrPDI)Fe(N2)2 loses 1 equiv of N2 to afford the mono(dinitrogen) adduct (iPrPDI)Fe(N2). Both dinitrogen compounds serve as effective precatalysts for the hydrogenation and hydrosilation of olefins and alkynes. Effecient catalytic reactions are observed with low catalyst loadings (< or = 0.3 mol %) at ambient temperature in nonpolar media. The catalytic hydrosilations are selective in forming the anti-Markovnikov product. Structural characterization of a high spin iron(0) alkyne and a bis(silane) sigma-complex has also been accomplished and in combination with isotopic labeling studies provides insight into the mechanism of both catalytic C-H and catalytic C-Si bond formation.

Catalysis↗
PubMed2006

1H NMR study of the magnetic properties and electronic structure of the hydroxide complex of substrate-bound heme oxygenase from Neisseria meningitidis: influence of the axial water deprotonation on the distal H-bond network.

The substrate and active site residues of the low-spin hydroxide complex of the protohemin complex of Neisseria meningitidis heme oxygenase (NmHO) have been assigned by saturation transfer between the hydroxide and previously characterized aquo complex. The available dipolar shifts allowed the quantitation of both the orientation and anisotropy of the paramagnetic susceptibility tensor. The resulting positive sign, and reduced magnitude of the axial anisotropy relative to the cyanide complex, dictate that the orbital ground state is the conventional "d(pi)" (d(2)(xy)(d(xz), d(yz))(3)); and not the unusual "d(xy)" (d(2)(xz)d(2)(yz)d(xy)) orbital ground state reported for the hydroxide complex of the homologous heme oxygenase (HO) from Pseudomonas aeruginosa (Caignan, G.; Deshmukh, R.; Zeng, Y.; Wilks, A.; Bunce, R. A.; Rivera, M. J. Am. Chem. Soc. 2003, 125, 11842-11852) and proposed as a signature of the HO distal cavity. The conservation of slow labile proton exchange with solvent from pH 7.0 to 10.8 confirms the extraordinary dynamic stability of NmHO complexes. Comparison of the diamagnetic contribution to the labile proton chemical shifts in the aquo and hydroxide complexes reveals strongly conserved bond strengths in the distal H-bond network, with the exception of the distal His53 N(epsilon)(1)H. The iron-ligated water is linked to His53 primarily by a pair of nonligated, ordered water molecules that transmit the conversion of the ligated H-bond donor (H(2)O) to a H-bond acceptor (OH(-)), thereby increasing the H-bond donor strength of the His53 side chain.

Anisotropy↗
PubMed2006

Methyaluminoxane (MAO) polymerization mechanism and kinetic model from ab initio molecular dynamics and electronic structure calculations.

MAO is the co-catalyst in metallocene catalytic systems, which are widely used in single-site olefin polymerization due to their high stereoselectivity. To date, the structures of the catalytically active compound or compounds in MAO have eluded researchers. Although many structural models have been proposed, none are generally accepted. In this study, aspects of the formation mechanism of MAO are addressed. Molecular dynamics simulations at the MP2 level of theory were carried out for presumed elementary steps in MAO formation via hydrolysis of trimethylaluminum (TMA). Methane production was observed, in agreement with experiment, as well as intermediate species that are consistent with the known structural features of MAO and similar to isolated and structurally characterized aluminoxanes. A (CH3)3Al-OH2 species, which we denote as TMA-OH2, containing a stable Al-O single bond emerged as the building block molecule. From this species, a hexameric cage was formed and activation barriers for the various reactions were calculated. Three distinct channels were identified for growth beyond the hexameric cage. It was concluded that MAO formation is a step polymerization through a bifunctional monomer, with [(CH3)Al-O] as the structural unit and a kinetic model was proposed. The structures that emerged were in agreement with the crystallographic evidence for aluminoxanes and support the experimental data regarding the MAO chemical composition.

Journal Article↗
PubMed1979

Electronic structures of cephalosporins and penicillins. 9. Departure of a leaving group in cephalosporins.

Molecular orbital calculations by the CNDO/2 method are used to study the potential energy surface for the stretching and rupturing of the CH2-OAc bond in a model cephalosporin structure, 7-amino-3-(acetoxymethyl)-3-cephem. The bond is easier to stretch and break when a nucleophilic group is in the vicinity of or attached to the beta-lactam carbonyl carbon (C8). The rate of acylation by a beta-lactam antibiotic at the receptor sites in bacterial cell-wall enzymes will be enhanced by a suitable leaving group at the 3' position. An orientational specificity is predicted for the direction of departure of the leaving group. Regardless of the direction the nucleophile approaches C8, the CH2-OAc bond is easiest to break when the acetate group departs from the alpha face of the molecule.

Cephalosporins↗