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At least 91 records · Page 5Linked to original sources
PubMed2003

Molecular crystals: the crystal field effect on molecular electronic structure.

The effect of crystal packing on the electronic structure of organic molecules was modeled by incorporation of the external electrostatic potential into the semiempirical Hamiltonian of the molecule. An empirical correction procedure was devised in order to compensate for systematic errors in the charge distribution typical of semiempirical methods. The model was applied to 79 crystal structures belonging to various syngonies and space groups. The effect of the crystal field is subject to wide variations depending on the crystal packing motif. The difference between the effect of the crystal field on the molecular electronic structure and the solvent effect modeled with COSMO is highlighted. The effect of intermolecular hydrogen bonds on the molecular electronic structure and electronic spectra was modeled with this approach, and it does not predominate over the effect of long-range electrostatic interactions. INDO/S calculations employing the crystal electrostatic potential give an insight into the origin of crystallochromy, in particular, they properly predict color difference for several groups of polymorphs.

Algorithms↗
PubMed2004

Spectral differences in real-space electronic structure calculations.

Real-space grids for electronic structure calculations are efficient because the potential is diagonal while the second derivative in the kinetic energy may be sparsely evaluated with finite differences or finite elements. In applications to vibrational problems in chemical physics a family of methods known as spectral differences has improved finite differences by several orders of magnitude. In this paper the use of spectral differences for electronic structure is studied. Spectral differences are implemented in two electronic structure programs PARSEC and HARES which currently employ finite differences. Applications to silicon clusters and lattices indicate that spectral differences achieve the same accuracy as finite differences with less computational work.

Biopolymers↗
PubMed2002

DFT investigation of structural, electronic, and catalytic properties of diiron complexes related to the [2Fe](H) subcluster of Fe-only hydrogenases.

Hydrogenases catalyze the reversible oxidation of dihydrogen to protons and electrons. The structures of two Fe-only hydrogenases have been recently reported [Peters, J. W.; Lanzilotta, W. N.; Lemon, B. J.; Seefeldt, L. C. Science 1998, 282, 1853-1858. Nicolet, Y.; Piras, C.; Legrand, P.; Hatchikian, E. C.; Fontecilla-Camps, J. C. Structure 1999, 7, 13-23], showing that the likely site of dihydrogen activation is the so-called [2Fe](H) cluster, where each Fe ion is coordinated by CO and CN(-) ligands and the two metals are bridged by a chelating S-X(3)-S ligand. Moreover, the presence of a water molecule coordinated to the distal Fe2 center suggested that the Fe2 atom could be a suitable site for binding and activation of H(2). In this contribution, we report a density functional theory investigation of the structural and electronic properties of complexes derived from the [(CO)(CH(3)S)(CN)Fe(II)(mu-PDT)Fe(II)(CO)(2)(CN)](-1) species, which is related to the [2Fe](H) cluster observed in Fe-only hydrogenases. Our results show that the structure of the [2Fe](H) cluster observed in the enzyme does not correspond to a stable form of the isolated cluster, in the absence of the protein. As a consequence, the reactivity of [(CO)(CH(3)S)(CN)Fe(II)(mu-PDT)Fe(II)(CO)(2)(CN)](-1) derivatives in solution may be expected to be quite different from that of the active site of Fe-only hydrogenases. In fact, the most favorable path for H(2) activation involves the two metal atoms and one of the bridging S atoms and is associated with a very low activation energy (5.3 kcal mol(-1)). The relevance of these observations for the catalytic properties of Fe-only hydrogenases is discussed in light of available experimental and theoretical data.

Binding Sites↗
PubMed1999

Spin-Spin Interactions in the Oxides A(3)M'MO(6) (M = Rh, Ir; A = Ca, Sr; M' = Alkaline Earth, Zn, Cd, Na) of the K(4)CdCl(6) Structure Type Examined by Electronic Structure Calculations.

The oxides A(3)M'MO(6) (M = Rh, Ir; A = Ca, Sr; M' = alkaline earth, Zn, Cd) of the K(4)CdCl(6) structure type consist of isolated (MO(6))(8)(-) octahedral anions and exhibit an antiferromagnetic ordering at low temperatures. The spin-spin interactions in these oxides, Ca(3)NaMO(6) (M = Ir, Ru), and Sr(3)NaRuO(6) were examined by calculating how strongly the t(2g)-block levels of adjacent (MO(6))((6+)(n)()())(-) (n = 1, 2) anions interact in the presence and absence of the intervening cations A(2+) and M' (n)()(+) (n = 1, 2). Our calculations show that the spin-spin interactions in these oxides are three-dimensional, and the superexchange interactions occur mainly through the short intrachain and interchain M-O.O-M linkages. When the M(n)()(+) cation is very small compared with the A(2+) cation, the intrachain interaction is substantially stronger than the interchain interaction. The opposite is found when the sizes of the M(n)()(+) and A(2+) cations become similar.

Journal Article↗
PubMed2005

Probing the ground state electronic structure of a correlated electron system by quantum well states: Ag/Ni(111).

The ground state electronic properties of the strongly correlated transition metal Ni are usually not accessible from the excitation spectra measured in photoelectron spectroscopy. We show that the bottom of the Ni d band along [111] can be probed through the energy dependence of the phase of quantum-well states in Ag/Ni(111). Our model description of the quantum-well energies measured by angle-resolved photoemission determines the bottom of the empty set 1 d band of Ni as 2.6 eV, in full agreement with standard local density theory and at variance with the values of 1.7-1.8 eV from direct angle-resolved photoemission experiments of Ni.

Journal Article↗
PubMed2003

Structural trends and the electronic structure of the rare-earth oxomolybdates RMo(5)O(8) (R = La, Ce, Pr, Nd, Sm, Eu and Gd) containing chains of bioctahedral Mo(10) clusters.

The crystal structures of the rare-earth members of the series RMo(5)O(8) (R = Ce to Eu) have been investigated and compared with those of the La and Gd members previously published in order to understand the influences of the size and the charge of the cation on the different Mo-Mo bonds. The RMo(5)O(8) compounds crystallize in the monoclinic space group P2(1)/c. Their crystal structure is characterized by bioctahedral Mo(10) clusters forming extended chains. The results of our single-crystal studies show that the modification of charge predominantly affects the Mo-Mo bonds between the Mo(10) clusters and, to a lesser extent, the intra-cluster distances, while the cationic size induces only small variations. Theoretical investigations confirm this statement and allow the understanding of the bonding mode in these compounds.

Journal Article↗
PubMed1996

Spectroscopic investigations of dehydroepiandrosterone. Part II: Photoelectron spectrum and electronic structure.

The gas phase electronic structure of dehydroepiandrosterone (3 beta-hydroxy-5 alpha-androstene-17-one, DHEA) is elucidated from its Het photoelectron spectrum, quantum chemical calculations, and correlation with spectra of the related molecules 5 alpha-androstene-17-one (I) and epiandrosterone (3 beta-hydroxy-5 alpha-androstane-17-one) (2). The lowest ionization energy event in DHEA is shown to correspond to a pi-ionization energy of approximately 8.5 eV, followed closely and overlapped in part by the carbonyl lone pair ionization at 8.7 eV.

Androsterone↗
PubMed2005

On the electronic structure of ethidium.

The electronic structure of the common intercalating agent ethidium bromide (3,8-diamino-5-ethyl-6-phenylphenanthridinium bromide) is dominated by an interplay of electron donating and withdrawing effects mediated by its nitrogen atoms. X-ray crystallography, UV/Vis and IR absorption, fluorescence emission, and NMR spectroscopy are used to probe the electronic properties of the phenanthridinium "core" of ethidium as well as its exocyclic amines and 6-phenyl groups. Interestingly, despite its positive charge, most of ethidium's aromatic carbon and hydrogen atoms have high electron densities (compared to both 6-phenylphenanthridine and benzene). The data suggest that electron donation by ethidium's exocyclic amines dominates over the electron withdrawing effects of its endocyclic iminium in their combined influence on the electron densities of these atoms. Ethidium's nitrogen atoms are, conversely, electron deficient where the 5-position is the most electropositive, followed by the 3-amino, and lastly the 8-amino group. These results have been used to generate an empirically-based pi-electron density map of ethidium that may prove useful to understanding its nucleic acid binding specificity.

Crystallography, X-Ray↗
PubMed2000

EPR and ligand field studies of iron superoxide dismutases and iron-substituted manganese superoxide dismutases: relationships between electronic structure of the active site and activity.

The problem of metal selectivity of iron/manganese superoxide dismutases (SODs) is addressed through the electronic structures of active sites using electron paramagnetic resonance and ligand field calculations. Studies of wild-type iron(III) SOD (FeSOD) from Escherichia coli and from Methanobacterium thermoautotrophicum and iron-substituted manganese(III) SOD (Fe(sub)MnSOD) from E. coli and from Serratia marcescens are reported. EPR spectroscopy of wild-type enzymes shows transitions within all three Kramers doublets identified by their g values. From the temperature dependence of the observed transitions, the zero-field splitting is found to be negative, D = -2 +/- 0.2 cm-1. The electronic structure is typical of a distorted trigonal bipyramid, all the EPR features being reproduced by ligand field analysis. This unique and necessary electronic structure characterizes wild-type enzymes whatever their classification from the amino acid sequence into iron or manganese types, as E. coli FeSOD or M. thermoautotrophicum FeSOD. In iron-substituted manganese SODs, reduced catalytic activity is found. We describe how inhomogeneity of all reported substituted MnSODs might explain the activity decrease. EPR spectra of substituted enzymes show several overlapping components. From simulation of these spectra, one component is identified which shares the same electronic structure of the wild-type FeSODs, with the proportion depending on pH. Ligand field calculations were performed to investigate distortions of the active site geometry which induce variation of the excitation energy of the lowest quartet state. The corresponding coupling between the ground state and the excited state is found to be maximum in the geometry of the native SODs. We conjecture that such coupling should be considered in the electron-transfer process and in the contribution of the typical electronic structure of FeSOD to the activity.

Binding Sites↗
PubMed2004

Electronic structure of persistent radicals: nitroxides.

The molecular and electronic structures of 10 free nitroxide radicals have been investigated by HeI/HeII photoelectron spectroscopy (UPS), DFT calculations, and comparison with the spectra of related compounds. We observe that the electronic structure of the nitroxide group is unaffected by substitution except in a carbonyl derivative where nitroxide group orbitals are noticeably stabilized. Also, we have detected small variations in the photoionization cross-sections for singlet and triplet states of cation, the states belonging to the same electron configuration. The relationship between electronic structure and radical reactivity is discussed, and an experimentally based estimate of delocalization energy of the unpaired electron is given. Some conflicting kinetic data on radical reactivity have been analyzed in view of the UPS results.

Journal Article↗
PubMed2002

Electronic structure of coumarins.

The electronic structure of coumarin derivatives has been investigated by a combination of UV photoelectron spectra (UPS), semi-empirical MO calculations and comparison with the spectra of related coumarins. The influence of substituents on the S0 and S1 electronic states energies is discussed.

Coumarins↗
PubMed2000

Controlled modification of individual adsorbate electronic structure

Modification of the electronic structure of a single Mn adsorbate placed within a geometrical array of adatoms on Ag(111) is observed using local spectroscopy with the scanning tunneling microscope. The changes result from coupling between the adsorbate level and surface electronic states of the substrate. These surface states are scattered coherently within the adatom array, mediating the presence and shape of the array to the adsorbate within. The dimension and geometry of the adatom array thus provide a degree of control over the induced changes.

Journal Article↗