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PubMed2005

Multireference calculations of the electronic structure of VF2 and VCl2.

We investigated the electronic structure of two members of the transition-metal dihalide family, VF(2) and VCl(2). Using the configuration-interaction method in large basis sets we calculated the lowest 17 states of these molecules in the vicinity of their ground-state geometry. We compute the ground-state bond lengths, vibrational frequencies, and dissociation energies. In contrast to predictions of ligand-field theory, we find (4)Sigma(g) (-) ground states for both molecules.

Journal Article↗
PubMed2000

Electronic structure of Sr2FeMoO6

We have analyzed the unusual electronic structure of Sr2FeMoO6 combining ab initio and model Hamiltonian approaches. Our results indicate that there are strong enhancements of the intra-atomic exchange strength at the Mo site as well as the antiferromagnetic coupling strength between Fe and Mo sites. We discuss the possibility of a negative effective Coulomb correlation strength ( U(eff)) at the Mo site due to these renormalized interaction strengths.

Journal Article↗
PubMed2001

Effects of extrinsic imidazole ligation on the molecular and electronic structure of cytochrome c.

Although imidazole ligand binding to cytochrome c is not directly related to its physiological function, it has the potential to provide valuable information on the molecular and electronic structure of the protein. The solution structure of the imidazole adduct of oxidized horse heart cytochrome c (Im-cyt c) has been determined through 2D NMR spectroscopy. The Im-cyt c, 8 mM in 1.2 M imidazole solution at pH 5.7 and 313 K, provided altogether 2,542 NOEs (1,901 meaningful NOEs) and 194 pseudocontact shifts. The 35 conformers of the family show the RMSD values to the average structure of 0.063+/-0.007 nm for the backbone and 0.107+/-0.007 nm for all heavy atoms, respectively. The characterization of Im-cyt c is discussed in detail both in terms of structure and electronic properties. The replacement of the axial ligand Met80 with the exogenous imidazole ligand induces significant conformation changes in both backbone and side chains of the residues located in the distal axial ligand regions. The imidazole ligand binds essentially parallel to the imidazole of the proximal histidine, the two planes forming an angle of 8+/-7 degrees. The electron delocalization on the heme moiety and the magnetic susceptibility tensor are consistent with these structural features.

Amino Acid Sequence↗
PubMed2001

Simulation of geometrical and electronic structure of quasi-two-dimensional layer consisting of fullerenes D6h-C36.

This article describes a computer simulation of the geometrical and electronic structure of a quasi-two-dimensional carbon layer with a trigonal lattice consisting of fullerenes C36 (1) with topological symmetry D6h. Every polyhedral cluster 1 of this polymeric layer (2) is surrounded by six similar fullerenes and connected with every such a fullerene by two covalent bonds. Atomic coordinates of the repeating unit are estimated on the basis of MNDO/PM3 calculations of hydrocarbon molecule (D6h)-C132H48 (3). The carbon skeleton of 3 coincides with a sufficiently large fragment of the polymeric layer 2. The electronic spectrum of the quasi-two-dimensional layer 2 is calculated by the crystalline orbital method in the EHT approximation. The band gap in the electronic spectrum of 2 was found to be equal to 1.5 eV. The geometric and electronic structure of some oligomers of cluster C36, quasi-linear macromolecule [C36]n, and "hypergraphite" layer is also discussed.

Carbon↗
PubMed2005

Potentiometric, electronic structural, and ground- and excited-state optical properties of conjugated bis[(porphinato)zinc(II)] compounds featuring proquinoidal spacer units.

We report the synthesis, optical, electrochemical, electronic structural, and transient optical properties of conjugated (porphinato)zinc(II)-spacer-(porphinato)zinc(II) (PZn-Sp-PZn) complexes that possess intervening conjugated Sp structures having varying degrees of proquinoidal character. These supermolecular PZn-Sp-PZn compounds feature Sp moieties {(4,7-diethynylbenzo[c][1,2,5]thiadiazole (E-BTD-E), 6,13-diethynylpentacene (E-PC-E), 4,9-diethynyl-6,7-dimethyl[1,2,5]thiadiazolo[3,4-g]quinoxaline (E-TDQ-E), and 4,8-diethynylbenzo[1,2-c:4,5-c']bis([1,2,5]thiadiazole) (E-BBTD-E)} that regulate frontier orbital energy levels and progressively increase the extent of the quinoidal resonance contribution to the ground and electronically excited states, augmenting the magnitude of electronic communication between terminal (5,-10,20-di(aryl)porphinato)zinc(II) units, relative to that evinced for a bis[(5,5',-10,20-di(aryl)porphinato)zinc(II)]butadiyne benchmark (PZnE-EPZn). Electronic absorption spectra show significant red-shifts of the respective PZn-Sp-PZn x-polarized Q state (S0 --> S1) transition manifold maxima (240-4810 cm(-1)) relative to that observed for PZnE-EPZn. Likewise, the potentiometrically determined PZn-Sp-PZn HOMO-LUMO gaps (E1/2(0/+) - E1/2(-/0)) display correspondingly diminished energy separations that range from 1.88 to 1.11 eV relative to that determined for PZnE-EPZn (2.01 eV). Electronic structure calculations provide insight into the origin of the observed PZn-Sp-PZn electronic and optical properties. Pump-probe transient spectral data for these PZn-Sp-PZn supermolecules demonstrate that the S1 --> S(n) transition manifolds of these species span an unusually broad spectral domain of the NIR. Notably, the absorption maxima of these S1 --> S(n) manifolds can be tuned over a 1000-1600 nm spectral region, giving rise to intense excited-state transitions approximately 4000 cm(-1) lower in energy than that observed for the analogous excited-state absorption maximum of the PZnE-EPZn benchmark; these data highlight the unusually large quinoidal resonance contribution to the low-lying electronically excited singlet states of these PZn-Sp-PZn species. The fact that the length scales of the PZn-Sp-PZn species (approximately 25 angstrom) are small with respect to those of classic conducting polymers, yet possess NIR S1 --> S(n) manifold absorptions lower in energy, underscore the unusual electrooptic properties of these conjugated structures.

Electrochemistry↗
PubMed1991

Electronic structure of DNA by DV-X alpha cluster calculations. I. d(GG).d(CC), d(CG)2, d(GC)2 A and B conformations.

The electronic structure of d(GG).d(CC), d(CG)2, d(GC)2 which are stacked base pairs in the DNA double helix, are elucidated for both A and B conformations in detail by DV-X alpha cluster calculations. These three DNA double helix fragments are constructed from the same bases, G and C, but the electronic structure of the fragments for A and B conformations differs from each other characteristically. In particular, the electronic states of the O2 and O3 in phosphates differ drastically from each other, and might play a crucial role as recognition sites in various reaction processes concerning DNA. These differences are caused by the delicate differences in the admixture of the orbital components and the intra- and inter-bases interactions. Contour maps of the wavefunction of the HOMO and LUMO are compared among the stacking isomers.

Animals↗
PubMed2004

Spectroscopic properties and electronic structure of pentammineruthenium(II) dinitrogen oxide and corresponding nitrosyl complexes: binding mode of N(2)O and reactivity.

The spectroscopic properties and the electronic structure of the only nitrous oxide complex existing in isolated form, [Ru(NH(3))(5)(N(2)O)]X(2) (1, X = Br(-), BF(4)(-)), are investigated in detail in comparison to the nitric oxide precursor, [Ru(NH(3))(5)(NO)]X(3) (2). IR and Raman spectra of 1 and of the corresponding (15)NNO labeled complex are presented and assigned with the help of normal coordinate analysis (NCA) and density functional (DFT) calculations. This allows for the identification of the Ru-N(2)O stretch at approximately 300 cm(-)(1) and for the unambiguous definition of the binding mode of the N(2)O ligand as N-terminal. Obtained force constants are 17.3, 9.6, and 1.4 mdyn/A for N-N, N-O, and Ru-N(2)O, respectively. The Ru(II)-N(2)O bond is dominated by pi back-donation, which, however, is weak compared to the NO complex. This bond is further weakened by Coulomb repulsion between the fully occupied t(2g) shell of Ru(II) and the HOMO of N(2)O. Hence, nitrous oxide is an extremely weak ligand to Ru(II). Calculated free energies and formation constants for [Ru(NH(3))(5)(L)](2+) (L = NNO, N(2), OH(2)) are in good agreement with experiment. The observed intense absorption at 238 nm of 1 is assigned to the t(2g) --> pi(*) charge transfer transition. These data are compared in detail to the spectroscopic and electronic structural properties of NO complex 2. Finally, the transition metal centered reaction of nitrous oxide to N(2) and H(2)O is investigated. Nitrous oxide is activated by back-donation. Initial protonation leads to a weakening of the N-O bond and triggers electron transfer from the metal to the NN-OH ligand through the pi system. The implications of this mechanism for biological nitrous oxide reduction are discussed.

Journal Article↗
PubMed2003

Change of electronic structure in Ca2RuO4 induced by orbital ordering.

Optical conductivity spectra sigma(omega) were used to investigate the effect of orbital ordering on the electronic structure of Ca2RuO4. Our LDA+U calculation predicts Ru 4d(xy) ferro-orbital ordering at the ground state, and well explains the present sigma(omega) as well as the reported O 1s x-ray absorption spectra. Variation of temperature (T) causes a large change of spectral weight over several eV as well as collapse of a charge gap accompanied by elongation of the c-axis Ru-O bond length. These results clearly indicate that the d(xy) orbital ordering plays a crucial role in the metal-insulator transition and the T-dependent electronic structure on a large energy scale.

Journal Article↗
PubMed2005

Influence of multi-atom bridging ligands on the electronic structure and magnetic properties of homodinuclear titanium molecules.

The electronic structure and magnetic properties of homodinuclear titanium(III) molecules with bridging ligands from groups 14, 15, and 16 are examined. Single- and multireference methods with triple-zeta plus polarization basis sets are employed. Dynamic electron correlation effects are included via second-order multireference perturbation theory. Isotropic interaction parameters are calculated, and two of the complexes studied are predicted to be ferromagnetic based on multireference second-order perturbation (MRMP2) theory, using the TZVP(fg) basis set. Zero-field splitting parameters are determined using spin-orbit coupling obtained from complete active space (CAS) self-consistent field (SCF) and multiconfigurational quasi-degenerate perturbation theory (MCQDPT) wave functions. Three Breit-Pauli-based spin coupling methods were employed: full Breit-Pauli (HSO2), the partial two-electron method (P2E), and the semiempirical one-electron method (HSO1).

Computer Simulation↗
PubMedDate not supplied

[Electronic structure of hemoglobin's heme complexes with nitric oxide and dynamics of atomic base under physiological temperature].

The comparative study of atomic and electronic structure of hem complexes of hemoglobin with molecular oxygen and nitric oxide has been performed by semiempirical quantum chemical PM3 method. It has been shown that the length of chemical bonding in oxygen molecule coordinated with hem increases by 0.046 A and the length of chemical bonding in nitrogen oxide coordinated with hem increases by 0.064 A in comparison with pure substances. This fact indicates that chemical bonding between nitric oxide and Fe atom of hem is stronger that one with oxygen molecule. Analysis of charge of the molecules indicates that NO bounded with Fe by covalent chemical bonding and oxygen molecule bounded with Fe by weak dipole interaction. Atomic orbitals of ligand atoms in oxygen complex play small part in high occupied (HOMO) and low vacant (LVMO) molecular orbitals in comparison with HOMO and LVMO of complex with NO. In the last one unpaired electron of NO molecule moves from ligand to d-orbitals of Fe atom and creates d7-configuration. Molecular dynamics simulation under physiological temperature (310 K) indicates visible difference in atomic and electronic structure of the complexes in comparison with ones under low (from 77 up to 0 K) temperatures.

Heme↗
PubMed2000

Exploring the electronic structure of elemental lithium: from small molecules to nanoclusters, bulk metal, and surfaces

Clusters of lithium atoms ranging in size from Li4 to Li40 and bulk metallic solids, including surfaces, are investigated through first principles electronic structure calculations, which are based upon density functional theory and the electron localization function (ELF). It is found that large lithium ppi-type contributions in the electronic wavefunction cause the electrons to localize in interstitial regions, which leads to multicenter bonding for both the clusters and the solids, including their surfaces. For the smaller clusters these stabilizing ppi interactions also lead to short Li-Li interatomic distances, which in conjunction with the longer bonds induces "distance alternation" in the range from 2.45 A to 3.15 A. This consequence of the additional ppi interactions is absent in simple solids due to symmetry. The electronic structure of the clusters is topologically insensitive to deformations that do not affect their general shape, but changes significantly upon isomerization. The ramifications upon dynamic properties is that the clusters are quasi-rigid at low temperatures and retain their shape though the distance alternation pattern is suppressed. The picture which emerges for bonding in the bulk solid is that the metallic state arises from the presence of a large number of partially occupied multicenter bonds. For nanoscale clusters only the surface of these clusters exhibits strong localization, whereas their interiors display localization properties similar to the bulk metallic solid. On the other hand, localized states similar to those of the clusters ("dangling bonds") are found on the (001) surface of body-centered cubic (bcc) and face-centered cubic (fcc) lithium solids.

Journal Article↗
PubMedDate not supplied

[Electron spectroscopy and the electron structure of molecules].

The experimental-theoretical approach to the study of physico-chemical, in particular, spectroscopic and photochemical properties of groups of related molecules is considered. The problem of physically correct spectral decompositions of complex electronic spectra into bands corresponding to separate electronic transitions and of the information obtained therefrom is discussed. Concrete examples of revealing photo- and enzymatic reaction mechanisms by combined spectroscopic and theoretical studies of molecular electronic structure and spectra are given. Special attention is paid to the connection of electronic structure of molecules with their physico-chemical, in particular, spectroscopic properties.

Electrons↗
PubMed2004

Theoretical study of the electronic structure of CnS (n=1-6) thiocumulenes.

Linear sulfur-carbon chains C(n)S (n=1-6) of astronomical interest were examined by means of several theoretical methods. The three smallest compounds of the series were chosen to evaluate the performance of several computational models, including Hartree-Fock theory, density functional theory with the Becke's three parameter exchange functional and the correlation functional of Lee, Yang, and Parr (B3LYP), and electron-correlated methods (second-order Moller-Plesset perturbation method (MP2), configuration interaction method including single and double excitations (CISD), and quadratic configuration interaction method including single and double excitations (QCISD) in combination with a large variety of basis sets. The systematic comparison between the experiment and theory indicates that the B3LYP/6-311G** method can be considered suitable for the study of the electronic structures of the C(n)S compounds. The electronic ground states of the C(n)S molecules alternate between 1Sigma and 3Sigma for odd and even values of n, respectively. The B3LYP/6-311G** wave functions for these electronic ground states were analyzed by means of the atoms in molecules (AIM) and natural bond orbital (NBO) methods. Both approaches suggest that the electronic structures for the singlet and triplet compounds must be considered separately. According to the NBO method, singlet compounds can be properly represented by acetylenic structures with alternating single and triple bonds (S[triple bond]C-C[triple bond]C...). However, triplet compounds are better described by means of double bond-double bond cumulenic structures (S=C=C=C=C...) as a consequence of the average between different alpha and beta electronic densities. AIM delocalization indexes and NBO interactions between localized orbitals also indicate that these structures are strongly pi delocalized. Finally, the different singlet and triplet structures proposed provide a consistent explanation for the geometries, dipole moments, and spin-density values of the C(n)S compounds studied.

Journal Article↗
PubMed2005

A density-functional study of the structural, electronic, magnetic, and vibrational properties of Ti8C12 metallocarbohedrynes.

Calculations are presented for the structural, electronic, and vibrational properties of the different Ti8C12 metallocarbohedrynes. (Please note that we adopt the name "metallocarbohedrynes" instead of "metallocarbohedrenes" to denote the acetylenic nature of C2 units in this class of clusters demonstrated by several contributions in literature.) The density-functional theory (DFT) calculations are performed with the all-electron projector augmented-wave method and generalized gradient approximation for the exchange-correlation functional. We study the seven low-energy isomers of the Ti8C12 metallocarbohedrynes using spin-polarized DFT, where we find a correlation between the number of rotated carbon dimers and the cohesive energy of the structure. The electronic density of states (eDOS) show that C3nu, D*3d, and D3d isomers are spin polarized. The partial eDOS shows that, depending on the dimer orientation, carbon atoms and a subgroup of the metal atoms form a covalent framework while other metal atoms are bonded to this framework more ionically. This picture is further supported by the charge density of the different structures, where we see that the Ti atoms with higher charge density show less contribution to the covalent bonding of the Ti-C framework. The vibrational spectra of the different structures are calculated using the frozen-vibration method. Also, we calculate the vibrational spectra of the C3nu and C2nu structures using molecular-dynamics simulations at two different temperatures. The results of the simulations demonstrate the local stability of the structures beyond the harmonic limit explored by the frozen-vibration method.

Journal Article↗
PubMed2006

Structural consequences of the one-electron reduction of d4 [Mo(CO)2(eta-PhC[triple bond]CPh)Tp']+ and the electronic structure of the d5 radicals [M(CO)L(eta-MeC[triple bond]CMe)Tp'] {L = CO and P(OCH2)3CEt}.

Reduction of [M(CO)2(eta-RC[triple bond]CR')Tp']X {Tp' = hydrotris(3,5-dimethylpyrazolyl)borate, M = Mo, X = [PF6]-, R = R' = Ph, C6H4OMe-4 or Me; R = Ph, R' = H; M = W, X = [BF4]-, R = R' = Ph or Me; R = Ph, R' = H} with [Co(eta-C5H5)2] gave paramagnetic [M(CO)2(eta-RC[triple bond]CR')Tp'], characterised by IR and ESR spectroscopy. X-Ray structural studies on the redox pair [Mo(CO)2(eta-PhC[triple bond]CPh)Tp'] and [Mo(CO)2(eta-PhC[triple bond]CPh)Tp'][PF6] showed that oxidation is accompanied by a lengthening of the C[triple bond]C bond and shortening of the Mo-C(alkyne) bonds, consistent with removal of an electron from an orbital antibonding with respect to the Mo-alkyne bond, and with conversion of the alkyne from a three- to a four-electron donor. Reduction of [Mo(CO)(NCMe)(eta-MeC[triple bond]CMe)Tp'][PF6] with [Co(eta-C5H5)2] in CH2Cl2 gives [MoCl(CO)(eta-MeC[triple bond]CMe)Tp'], via nitrile substitution in [Mo(CO)(NCMe)(eta-MeC[triple bond]CMe)Tp'], whereas a similar reaction with [M(CO){P(OCH2)3CEt}(eta-MeC[triple bond]CMe)Tp']+ (M = Mo or W) gives the phosphite-containing radicals [M(CO){P(OCH2)3CEt}(eta-MeC[triple bond]CMe)Tp']. ESR spectroscopic studies and DFT calculations on [M(CO)L(eta-MeC[triple bond]CMe)Tp'] {M = Mo or W, L = CO or P(OCH2)3CEt} show the SOMO of the neutral d5 species (the LUMO of the d4 cations) to be largely d(yz) in character although much more delocalised in the W complexes. Non-coincidence effects between the g and metal hyperfine matrices in the Mo spectra indicate hybridisation of the metal d-orbitals in the SOMO, consistent with a rotation of the coordinated alkyne about the M-C2 axis.

Journal Article↗
PubMed1983

A new spatial structure for the axial methionine observed in cytochrome c5 from Pseudomonas mendocina. Correlations with the electronic structure of heme c.

Cytochrome c5 from Pseudomonas mendocina has been isolated and the coordination geometry at the heme iron was investigated by 1H nuclear magnetic resonance and circular dichroism spectroscopy. Individual assignments were obtained for heme c and the axial ligands. From studies of nuclear Overhauser enhancements the axial histidine imidazole ring orientation relative to the heme group was found to coincide with that of other c-type cytochromes. In contrast, a new structure was observed for the axial methionine. This includes S chirality at the iron-bound sulfur atom, but compared to cytochromes c-551 from Pseudomonads and Rhodopseudomonas gelatinosa, which also contain S-chiral methionine, the spatial arrangement of the gamma- and beta-methylene groups and the alpha carbon of methionine is markedly different. Analysis of the electron spin density distribution in ferricytochrome c5 in the light of this new coordination geometry provides additional support for the hypothesis that the electronic structure of heme c is primarily governed by the orientation of the sp3 lone-pair orbital of the axial sulfur atom with respect to the heme plane.

Circular Dichroism↗
PubMed2003

First-principles approach to the electronic structure of strongly correlated systems: combining the GW approximation and dynamical mean-field theory.

We propose a dynamical mean-field approach for calculating the electronic structure of strongly correlated materials from first principles. The scheme combines the GW method with dynamical mean-field theory, which enables one to treat strong interaction effects. It avoids the conceptual problems inherent to conventional "LDA+DMFT," such as Hubbard interaction parameters and double-counting terms. We apply a simplified version of the approach to the electronic structure of nickel and find encouraging results.

Journal Article↗
PubMed2003

Electronic structure control of single-walled carbon nanotube functionalization.

Diazonium reagents functionalize single-walled carbon nanotubes suspended in aqueous solution with high selectivity and enable manipulation according to electronic structure. For example, metallic species are shown to react to the near exclusion of semiconducting nanotubes under controlled conditions. Selectivity is dictated by the availability of electrons near the Fermi level to stabilize a charge-transfer transition state preceding bond formation. The chemistry can be reversed by using a thermal treatment that restores the pristine electronic structure of the nanotube.

Journal Article↗