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 901 records · Page 50Linked to original sources
PubMed1997

A Novel Anionic Gold-Indium Cluster Compound: Synthesis and Molecular and Electronic Structure.

The insertion of InBr into the Au-Br bond of [(Ph(3)P)AuBr] in tetrahydrofuran (thf) in the presence of [(CH(2)PPh(2))(2)] (dppe) leads to the formation of an orange complex [(dppe)(2)Au](+)[(dppe)(2)Au(3)In(3)Br(7)(thf)](-), 2. Analytical, spectroscopic, and X-ray structural investigations showed that this product is an anionic analogue of a neutral chloride complex [(dppe)(2)Au(3)In(3)Cl(6)(thf)(3)], 1, prepared recently. Both complexes have an Au(3)In(3) cluster core of approximate C(2)(v)() symmetry with one extremely short Au-Au bond [Au1-Au3 2.575(1) Å] as part of a quasi-linear array P1-Au1-Au3-P4, suggesting the presence of a bis(phosphine) complex of the neutral Au(2) molecule as part of the cluster. The third gold atom (Au2) is then assigned oxidation state +1. To gain deeper insight into the structure and bonding of this novel class of gold cluster compounds, regarding mainly the peculiar cluster geometry, the charge distribution, and the oxidation states, a series of scalar relativistic all-electron density functional (DF) calculations on model systems has been performed. As a model for 1, the neutral cluster {Au(3)(PH(3))(4)[InCl(2)(H(2)O)](3)} was studied. For the examination of the geometry of complexes 1 and 2, the cluster Au(3)(PH(3))(4)I(3) has been considered as a further simplified model, where iodine replaces the InX(2)(thf) units. Experimental and calculated cluster geometries agree satisfactorily, and the formal oxidation states of the gold atoms (0 for Au1 and Au3, +1 for Au2) could be confirmed, but for the In centers no interpretable differences of the Mulliken charges were found.

Journal Article↗
PubMed2006

Probing the electronic structure of UO+ with high-resolution photoelectron spectroscopy.

The pulsed field ionization-zero kinetic energy photoelectron technique has been used to observe the low-lying energy levels of UO+. Rotationally resolved spectra were recorded for the ground state and the first nine electronically excited states. Extensive vibrational progressions were characterized. Omega+ assignments were unambiguously determined from the first rotational lines identified in each vibronic band. Term energies, vibrational frequencies, and anharmonicity constants for low-lying energy levels of UO+ are reported. In addition, accurate values for the ionization energies for UO [48,643.8(2) cm(-1)] and U [49,957.6(2) cm(-1)] were determined. The pattern of low-lying electronic states for UO+ indicates that they originate from the U3+(5f3)O2- configuration, where the uranium ion-centered interactions between the 5f electrons are significantly stronger than interactions with the intramolecular electric field. The latter lifts the degeneracy of U3+ ion-core states, but the atomic angular momentum quantum numbers remain reasonably well defined.

Journal Article↗
PubMed2006

Electronic structure and reactivity of isomeric oxo-Mn(V) porphyrins: effects of spin-state crossing and pKa modulation.

The reactivity of the isomeric oxo-Mn(V)-2-tetra-N-methylpyridyl (2-TMPyP) and oxo-Mn(V)-4-tetra-N-methylpyridyl (4-TMPyP) porphyrins has been investigated by a combined experimental and theoretical approach based on density functional theory. The unusual higher reactivity of the more electron-rich 4-TMPyP species appears to be related to both the higher basicity of its oxo ligand, compared to that of the 2-TMPyP isomer, and the smaller low-spin-high-spin promotion energy of 4-TMPyP, compared to that of 2-TMPyP, because of the stabilization of the A2u orbital in the latter isomer. Therefore, in a two-state energy profile involving crossing of the initial singlet and final quintet potential energy surfaces, the 4-TMPyP isomer should be kinetically favored. The calculated differences in the singlet-quintet gaps for the 2-TMPyP and 4-TMPyP systems compare well with the measured differences in the activation energies for two isomeric porphyrins. Both effects, proton affinity and electron-promotion energy, contribute to reduce the reactivity of the more electrophilic oxidant when electron-withdrawing groups are closer to the active site, contrary to the usual expectations based on simple chemical reactivity correlations. These theoretical results are in accord with new experimental data showing O=Mn(V)-O-H pK(a)s of 7.5 and 8.6 for the isomeric 2-TMPyP and 4-TMPyP systems, respectively.

Computer Simulation↗
PubMed2005

Evolution of the electronic structure of Be clusters.

Using a modified symbiotic genetic algorithm approach and many-body interatomic potential derived from first principles, we have calculated equilibrium geometries and binding energies of the ground-state and low-lying isomers of Be clusters containing up to 41 atoms. Molecular-dynamics study was also carried out to study the frequency of occurrence of the various geometrical isomers as these clusters are annealed during the simulation process. For a selected group of these clusters, higher-energy isomers were more often found than their ground-state structures due to large catchment areas. The accuracy of the above ground-state geometries and their corresponding binding energies were verified by carrying out separate ab initio calculations based on molecular-orbital approach and density-functional theory with generalized gradient approximation for exchange and correlation. The atomic orbitals were represented by a Gaussian 6-311G** basis, and the geometry optimization was carried out using the GAUSSIAN 98 code without any symmetry constraint. While the ground-state geometries and their corresponding binding energies obtained from ab initio calculations do not differ much from those obtained using the molecular-dynamics approach, the relative stability of the clusters and the energy gap between the highest occupied and the lowest unoccupied molecular orbitals show significant differences. The energy gaps, calculated using the density-functional theory, show distinct shell closure effects, namely, sharp drops in their values for Be clusters containing 2, 8, 20, 34, and 40 electrons. While these features may suggest that small Be clusters behave free-electron-like and, hence, are metallic, the evolution of the structure, binding energies, coordination numbers, and nearest-neighbor distances do not show any sign of convergence towards the bulk value. We also conclude that molecular-dynamics simulation based on many-body interatomic potentials may not always give the correct picture of the evolution of the structure and energetics of clusters although they may serve as a useful tool for obtaining starting geometries by efficiently searching a large part of the phase space.

Journal Article↗
PubMed2002

Metallocene-DNA: synthesis, molecular and electronic structure and DNA incorporation of C5-ferrocenylthymidine derivatives.

Ferrocenylthymidine derivatives have been prepared by Pd-catalysed cross-coupling between ethynylferrocene or vinylferrocene and 5-iodo-2'-deoxyuridine. In the latter case a mixture of trans (2a) and gem (2b) isomers was obtained. The cis-vinylferrocenyl (2c), and ethylferrocenyl (3) derivatives were obtained by catalytic hydrogenation of ethynylferrocenyl-dT (1a), and 2c respectively. Single-crystal X-ray data for 1a, the ferrocenyl-2'furano-pyrimidone 1b, and 2a show that the nucleobase is essentially co-planar with the substituted Cp ring of the metallocene. The selective reduction of the linkage between the ferrocenyl and thymidine moieties, from -C identical to C- to -CH2CH2-, causes a shift in the reduction potential of -124 mV. DFT calculations for the one-electron oxidised species indicate that the diminished conjugation reduces the spin transfer onto the bridging C2 group, but has less effect on the extent transferred to the nucleobase from the ferrocenyl group. Compound 1a was incorporated site-specifically into DNA oligonucleotides by using automated solid-phase methods. However, some interconversion of 1a-->1b occurs, even under rapid mild conditions of deprotection.

Base Pairing↗
PubMed1998

Electronic Structure of Face- and Edge-Shared Bioctahedral Systems: A Comparison of M(2)Cl(9)(3-) and M(2)Cl(10)(4-), M = Cr, Mo, W.

Potential energy curves for the broken-symmetry states of the edge-shared bimetallic systems, M(2)Cl(10)(4-) (M = Cr, Mo, W), are analyzed using approximate density functional theory. The potential energy curves are made up of distinct sections, depending on which subsets of metal-based electrons are localized or delocalized. Starting from the fully delocalized limit, the metal-based electrons localize in the order delta before pi before sigma as the metal-metal separation is progressively increased. As a result there are four distinct regions of the potential energy curve, corresponding to (a) sigma + pi + delta delocalized; (b) sigma + pi delocalized, delta localized; (c) sigma delocalized, pi + delta localized; and (d) sigma + pi + delta localized. Localization of the delta subset of electrons is particularly facile, because interactions with the bridging ligands destabilize the delta orbital relative to delta. As a result, at metal-metal separations greater than approximately 2.30 Å, delocalization of the delta electrons would result in formation of a M-M antibond rather than a bond. For Cr(2)Cl(10)(4-), the fully localized region of the curve lies much lower than the others, but for the molybdenum and tungsten congeners, all four regions lie within 1.0 eV of each other, giving rise to complex and relatively flat potential energy curves. The decahalides of the chromium triad therefore exhibit the well-established trend toward greater delocalization in complexes of the heavier transition metals. This trend is, however, found to be far less prominent than in the face-shared analogues, M(2)Cl(9)(3-), and the difference between the two structural types is traced to the inability of the edge-shared bridge to support the short metal-metal separations necessary for complete electron delocalization.

Journal Article↗
PubMed2005

Thermodynamic properties of the C5, C6, and C8 n-alkanes from ab initio electronic structure theory.

The heats of formation for the n-alkanes C(n)H(n+2) for n = 5, 6, and 8 have been calculated using ab initio molecular orbital theory. Coupled-cluster calculations with perturbative triples (CCSD(T)) were employed for the total valence electronic energies. Correlation-consistent basis sets were used, up through the augmented quadruple zeta, to extrapolate to the complete basis set limit. Geometries were optimized at the B3LYP/TZVP and MP2/aug-cc-pVTZ levels. The MP2 geometries were used in the CCSD(T) calculations. Frequencies were determined at the density functional level (B3LYP/TZVP), and scaled zero point energies were calculated from the B3LYP frequencies. Core/valence, scalar relativistic, and spin-orbit corrections were included in an additive fashion to predict the atomization energies. The core/valence corrections are not small, (approximately 1.1 kcal/mol per carbon unit) and cannot be neglected for chemical accuracy. The calculated deltaH(298)f values are -35.0, -40.2, and -50.2 kcal/mol for C5H12, C6H14, and C8H18, respectively, in excellent agreement with the respective experimental values of -35.11 +/- 0.19, -39.89 +/- 0.19, and -49.90 +/- 0.31 kcal/mol. Isodesmic reaction energies are presented for some simple reactions involving C8H18 and are shown not to be strongly method dependent.

Journal Article↗
PubMed2006

Electronic structure and excitations in oligoacenes from ab initio calculations.

Oligoacenes C(4n+2)H(2n+4) (n=2,...,6) are studied using a variety of ab initio methods. Density functional theory (DFT) optimized geometries were in good agreement with experiment. Vertical and adiabatic ionization potentials and electron affinities were computed with DFT and it was found that standard exchange-correlation (xc) functionals underestimate ionization potentials in oligoacenes. Possible reasons for this underestimation are discussed. Low lying electronic excitations were computed using time-dependent density functional theory, configuration interaction singles, and configuration interaction singles with approximate treatment of doubles. In agreement with earlier work, time-dependent DFT in conjunction with standard xc-energy functionals substantially underestimates the lowest (p) singlet-singlet electronic transition.

Journal Article↗
PubMed2005

Computational and spectroscopic characterization of the molecular and electronic structure of the Pb(II)-quercetin complex.

The interactions of lead(II) ion with a polyhydroxylated flavonoid, the quercetin molecule, were investigated in methanol solution. The quercetin/metal stoichiometries and equilibrium stability constants for metal binding to quercetin have been determined by UV-vis spectroscopy combined with chemometrics methods. The 2:1, 1:2, and predominant 1:1 species are formed in solution. Among the three potential sites of chelation present in the quercetin structure, the catechol function presents the highest complexation power toward Pb(II), in opposition with previous results found for Al(III) complexation. This result has been confirmed by the good agreement of the experimental and theoretical features for both the electronic and vibrational spectra of the 1:1 complex. DT-DFT calculations show that the bathochromic shift of the long-wavelength band of the UV-vis spectra, that occurs upon complexation, is due to a ligand-to-metal charge transfer. The molecular structure of the ligand is not much modified by the coordination of lead at the level of the catecholate.

Computer Simulation↗
PubMed2004

The first bowl-shaped stable neutral radical with a corannulene system: synthesis and characterization of the electronic structure.

[structure: see text] A bowl-shaped neutral radical with a corannulene system has been designed and synthesized for the first time as a stable solid in air. An unequivocal characterization of the electronic properties of the radical shows that an appreciable amount of spin delocalization extends onto the corannulene unit's curved surface.

Chemical Phenomena↗
PubMed2005

Spectroscopic and kinetic studies of Arabidopsis thaliana sulfite oxidase: nature of the redox-active orbital and electronic structure contributions to catalysis.

Plant sulfite oxidase from Arabidopsis thaliana has been characterized both spectroscopically and kinetically. The enzyme is unusual in lacking the heme domain that is present in the otherwise highly homologous enzyme from vertebrate sources. In steady-state assays, the enzyme exhibits a pH maximum of 8.5 and is also found to function as a selenite oxidase. Sulfite at the lowest experimentally feasible concentrations reduces the enzyme within the dead-time of a stopped-flow instrument at 5 degrees C, indicating that the A. thaliana enzyme has a limiting rate constant for reduction, k(red), at least 10 times greater than that of the chicken enzyme (190 s(-1)). The EPR parameters for the high- and low-pH forms of the A. thaliana enzyme have been determined, and the g-values are found to resemble those previously reported for the vertebrate enzymes. Finally, the A. thaliana enzyme has been probed by resonance Raman spectroscopy. A detailed analysis of the vibrational spectrum in the region where Mo=O stretching modes are anticipated to occur has been performed with the help of density functional theory calculations, evaluated in the context of the Raman data. Calculated frequencies obtained for two model systems have been compared to experimental resonance Raman spectra of oxidized A. thaliana sulfite oxidase catalytically cycled in both H2(16)O and H2(18)O. The vibrational frequency shifts observed upon (18)O-labeling of the enzyme are consistent with theoretical models in which either the equatorial oxygen or both equatorial and axial atoms of the dioxomolybdenum center are labeled. Importantly, the vibrational mode description is consistent with the active site possessing geometrically inequivalent oxo ligands and a Mo d(xy) redox-active molecular orbital oriented in the equatorial plane forming a pi-bonding interaction solely with the equatorial oxo, O(eq). Electron occupancy of this Mo=O(eq) pi* redox orbital upon interaction with substrates would effectively labilize the Mo=O(eq) bond, providing the dominant contribution to lowering the activation energy for oxygen atom transfer.

Arabidopsis↗
PubMed1981

Chloroplast ribosome structure. Electron microscopy of ribosomal subunits and localization of N6,N6-dimethyladenosine by immunoelectronmicroscopy.

Ribosomal subunits from the chloroplasts of Alaskan peas have been studied by immunoelectronmicroscopy. Electron micrographs of negatively stained small and large ribosomal subunits show particles of similar size and in the same characteristic projections described for the ribosomal subunits of Escherichia coli (Lake, J. A. (1976) J. Mol. Biol. 105, 131-159), although minor structural differences are apparent. High pressure liquid chromatographic analysis shows the modified nucleoside N6,N6-dimethyladenosine is conserved in chloroplast 16 S ribosomal RNA, presumably as two successive residues near the 3' end. Antibodies directed against N6,N6-dimethyladenosine were allowed to react with chloroplast 30S ribosomal subunits. Electron microscopy showed individual subunit-antibody complexes and pairs of ribosomal subunits cross-linked by a single antibody. In 94% of the complexes observed, antibody contact was consistent with a dimethyladenosine localization near the end of the small subunit platform, in an area of subunit contact in the 70 S ribosome. This localization is analogous to the placement of N6,N6-dimethyladenosine in the E. coli ribosome (Politz, S. M., and Glitz, D. G. (1977) Proc. Natl. Acad. Sci. U. S. A. 74, 1468-1472).

Adenosine↗
PubMed2003

Electronic structures and nonlinear optical properties of trinuclear transition metal clusters M-(mu-S)-M' (M = Mo, W; M' = Cu, Ag, Au).

A series of trinuclear metal clusters MS4(M'PPh3)2(M'PPh3) (M = Mo, W; M' = Cu, Ag, Au) have been studied using the density functional theory (DFT) method. The static polarizabilities and hyperpolarizabilities of the model clusters have been calculated using the finite-field (F-F) method. The model clusters, divided into two groups, are alike in the structure of two fragments of rhombic units M-(mu-S)2-M' (M = Mo, W; M' = Cu, Ag, Au), perpendicular to each other, which are joined by sharing the bridge metal M. It is the charge transfer from one of these moieties to the other in these characteristic sulfido-transitional metal cores that is responsible for the polarizabilities and hyperpolarizabilities. This kind of electronic delocalization, different from that of the planar pi-system, is interesting and warrants further investigation. The structural effects on properties are important. In these models, considerable third-order nonlinearities are exhibited. The element substitution effect of Mo and W is weak, while that of Cu and Ag is relatively substantial. An overall order is gamma xxxx(Mo-Ag) > gamma xxxx(W-Ag) > gamma xxxx(Mo-Au) > gamma xxxx(W-Au) > gamma xxxx (Mo-Cu) > gamma xxxx(W-Cu) and gamma av(Mo-Ag) approximately gamma av(W-Ag) > gamma av(Mo-Au) approximately gamma av(W-Au) approximately gamma av (Mo-Cu) approximately gamma av(W-Cu).

Journal Article↗
PubMed2004

On the electronic structure of molecular UO2 in the presence of Ar atoms: evidence for direct U-Ar bonding.

Calculations via scalar-relativistic density functional theory (DFT) and ab initio CCSD(T) methodologies are used to explore the possibility of direct interactions between molecular UO2 and Ar atoms. The 3Hg electronic state of UO2, which is an excited state of the isolated molecule, exhibits significant bonding to Ar in the model complexes UO2(Ar) and UO2(Ar)5. The calculated vibrational frequencies of ground-state 3Phiu UO2 and UO2(Ar)5 with an (fphi)1(fdelta)1 electron configuration agree well with the observed frequencies of UO2 in solid neon and solid argon, respectively. The results strongly suggest that the ground electron configuration of UO2 changes from 5f17s1 to 5f2 when the matrix host is changed from neon to argon.

Journal Article↗