Electronic structure of the interstitial lithium-associated electron trap in crystalline quartz.
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Structure of Si(001) surfaces. II. The electronic structure of the symmetric dimer in the ground state.
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Journal Article↗
Electronic structures of CuFeS2 and CuAl0.9Fe0.1S2 studied by electron and optical spectroscopies.
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Journal Article↗
X-ray crystal structures of [XF(6)][Sb(2)F(11)] (X = Cl, Br, I); (35,37)Cl, (79,81)Br, and (127)I NMR studies and electronic structure calculations of the XF(6)(+) cations.
The single-crystal X-ray structures of [XF(6)][Sb(2)F(11)] (X = Cl, Br, I) have been determined and represent the first detailed crystallographic study of salts containing the XF(6)(+) cations. The three salts are isomorphous and crystallize in the monoclinic space group P2(1)/n with Z = 4: [ClF(6)][Sb(2)F(11)], a = 11.824(2) A, b = 8.434(2) A, c = 12.088(2) A, beta = 97.783(6) degrees , V = 1194.3(4) A(3), R(1) = 0.0488 at -130 degrees C; [BrF(6)][Sb(2)F(11)], a = 11.931(2) A, b = 8.492(2) A, c = 12.103(2) A, beta = 97.558(4) degrees , V = 1215.5(4) A(3), R(1) = 0.0707 at -130 degrees C; [IF(6)][Sb(2)F(11)], a = 11.844(1) A, b = 8.617(1) A, c = 11.979(2) A, beta = 98.915(2) degrees , V = 1207.8(3) A(3), R(1) = 0.0219 at -173 degrees C. The crystal structure of [IF(6)][Sb(2)F(11)] was also determined at -100 degrees C and was found to crystallize in the monoclinic space group P2(1)/m with Z = 4, a = 11.885(1) A, b = 8.626(1) A, c = 12.000(1) A, beta = 98.44(1), V = 1216.9(2) A(3), R(1) = 0.0635. The XF(6)(+) cations have octahedral geometries with average Cl-F, Br-F, and I-F bond lengths of 1.550(4), 1.666(11) and 1.779(6) [-173 degrees C]/1.774(8) [-100 degrees C] A, respectively. The chemical shifts of the central quadrupolar nuclei, (35,37)Cl, (79,81)Br, and (127)I, were determined for [ClF(6)][AsF(6)] (814 ppm), [BrF(6)][AsF(6)] (2080 ppm), and [IF(6)][Sb(3)F(16)] (3381 ppm) in anhydrous HF solution at 27 degrees C, and spin-inversion-recovery experiments were used to determine the T(1)-relaxation times of (35)Cl (1.32(3) s), (37)Cl (2.58(6) s), (79)Br (24.6(4) ms), (81)Br (35.4(5) ms), and (127)I (6.53(1) ms). Trends among the central halogen chemical shifts and T(1)-relaxation times of XF(6)(+), XO(4)(-), and X(-) are discussed. The isotropic (1)J-coupling constants and reduced coupling constants for the XF(6)(+) cations and isoelectronic hexafluoro species of rows 3-6 are empirically assessed in terms of the relative contributions of the Fermi-contact, spin-dipolar, and spin-orbit mechanisms. Electronic structure calculations using Hartree-Fock, MP2, and local density functional methods were used to determine the energy-minimized gas-phase geometries, atomic charges, and Mayer bond orders of the XF(6)(+) cations. The calculated vibrational frequencies are in accord with the previously published assignments and experimental vibrational frequencies of the XF(6)(+) cations. Bonding trends within the XF(6)(+) cation series have been discussed in terms of natural bond orbital (NBO) analyses, the ligand close-packed (LCP) model, and the electron localization function (ELF).
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Synthesis and structural, electronic, and optical properties of oligo(thienylfuran)s in comparison with oligothiophenes and oligofurans.
[structure: see text] Alternate thiophene/furan oligomers having four and six heterocycles, i.e., oligo(thienylfuran) dimer and trimer 2 (n = 4 and 6), were newly synthesized by repetitive Stille coupling reactions. The structural, electronic, and optical properties of these oligomers were investigated by X-ray crystallography (for n = 4), cyclic voltammetry (CV), UV-vis and fluorescence spectroscopy, and DFT calculations, and the results were compared with those of corresponding oligothiophenes (1) and oligofurans (3). The inter-ring torsional energy profiles calculated for bithiophene 1 (n = 2), thienylfuran 2 (n = 2), and bifuran 3 (n = 2) at the B3LYP/6-31G(d) level indicated that the most stable conformers of 2 (n = 2) and 3 (n = 2) are fully coplanar with transoid structure while that of 1 (n = 2) is twisted with a dihedral angle of 158 degrees . In accord with this, X-ray crystallographic analysis of 2 (n = 4) revealed that the pi-conjugated system is nearly planar with the inter-ring C=C-C=C dihedral angles between the thiophene and furan rings of 173.6(7) degrees , -177.0(7) degrees , and 172.6(6) degrees . In the packing structure, these nearly planar molecules are arranged in a herringbone pattern. The CV on a series of oligo(thienylfuran)s 2 showed irreversible oxidation peaks at +0.90, +0.42, and +0.29 V vs Fc/Fc(+) for n = 2, 4, and 6, which were 0.15-0.18 V lower than those for corresponding oligothiophenes 1 and were closer to those for oligofurans 3. On the other hand, the UV-vis spectra of 2 showed the longest wavelength absorption to be almost identical with those of the corresponding 1, and more bathochromically shifted than those of the corresponding 3. The results of CV and UV-vis measurements were supported by DFT calculations (B3LYP/ 6-311+G(2d,p)//B3LYP/6-31G(d)). Thus, oligo(thienylfuran)s 2 have HOMOs which are higher than those of oligothiophenes 1 and close to those of 3, and HOMO-LUMO gaps which are close to those of 1 and smaller than those of 3. In fluorescence spectra, the quantum yield of 2 increased with elongation of the pi-system (n = 2 (3.5%), 4 (19%), 6 (24%)).
Journal Article↗
Effects of peripheral substituents and axial ligands on the electronic structure and properties of iron phthalocyanine.
The effects of peripheral substituents and axial ligands on the electronic structure and properties of iron phthalocyanine, H(16)PcFe, have been investigated using a DFT method. Substitution by electron-withdrawing fluorinated groups alters the ground state of H(16)PcFe and gives rise to large changes in the ionization potentials and electron affinity. For the six-coordinate adducts with acetone, H(2)O, and pyridine, the axial coordination of two weak-field ligands leads to an intermediate-spin ground state, while the strong-field ligands make the system diamagnetic. The electronic configuration of a ligated iron phthalocyanine is determined mainly by the axial ligand-field strength but can also be affected by peripheral substituents. Axial ligands also exert an effect on ionization potentials and electron affinity and can, as observed experimentally, even change the site of oxidation/reduction.
Algorithms↗
Theoretical study of the electronic structure of the lower states of the [Cr2Cl9]3- and [Mo2Cl9]3- ions.
The electronic structure of the lower states of a trigonal Cr3+ pair and Mo3+ pair, which occur in the Cs3M2Cl9 crystal (M=Cr,Mo), were studied by theoretical calculations carried out according to several methods: multireference singly and doubly excited configuration interaction, second-order configuration interaction, and multireference coupled-pair approximation. We employed a model of a [M2Cl9]3- anion embedded in a cage of point charges, which were arranged so as to simulate the anion in the crystal. The model core potential was utilized, where the relativistic effect was included for Mo. Results of the Cr complex showed that there were no direct bonds between the Cr metals. The lower electronic spectra of the [Cr2Cl9]3- ion were interpreted in terms of the electronic spectra of [CrCl6]3-. The lowest state of simultaneous excitation in both metals was considered. The [Mo2Cl9]3- ion exhibited a single direct bond between the metals. Reflecting this single bond, the observed singlet-triplet splitting was much larger than that in the case of Cr and the calculated splitting was in good agreement with the observed one. We account for the electronic spectra of the [Mo2Cl9]3- complex, which exhibited quite different features in the electronic excitation spectra in comparison with those of the Cr complex.
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Electronic structure of compound I in human isoforms of cytochrome P450 from QM/MM modeling.
Human cytochromes P450 play a vital role in drug metabolism. The key step in substrate oxidation involves hydrogen atom abstraction or C=C bond addition by the oxygen atom of the Compound I intermediate. The latter has three unpaired electrons, two on the Fe-O center and one shared between the porphyrin ring and the proximal cysteinyl sulfur atom. Changes in its electronic structure have been suggested to affect reactivity. The electronic and geometric structure of Compound I in three important human subfamilies of cytochrome P450 (P450, 2C, 2B, and 3A) that are major contributors to drug metabolism is characterized here using combined quantum mechanical/molecular mechanical (QM/MM) calculations at the B3LYP:CHARMM27 level. Compound I is remarkably similar in all isoforms, with the third unpaired electron located mainly on the porphyrin ring, and this prediction is not very sensitive to details of the QM/MM methodology, such as the DFT functional, the basis set, or the size of the QM region. The presence of substrate also has no effect. The main source of variability in spin density on the cysteinyl sulfur (from 26 to 50%) is the details of the system setup, such as the starting protein geometry used for QM/MM minimization. This conformational effect is larger than the differences between human isoforms, which are therefore not distinguishable on electronic grounds, so it is unlikely that observed large differences in substrate selectivity can be explained to a large extent in these terms.
Crystallography, X-Ray↗
Molecular conformations and relative stabilities can be as demanding of the electronic structure method as intermolecular calculations.
We have performed a variety of high-level electronic structure calculations on two moderately sized organic molecules and found considerable sensitivity of the intramolecular potential energy surface to the method employed. The gas-phase structure of tyrosine-glycine varies qualitatively between B3LYP and MP2 optimizations, producing different close contacts between the tyrosine ring and the glycine moiety. The relative energies of the 2-(acetylamino)benzamide conformations found in its two polymorphs can vary by over 20 kJ mol-1 between MP2 and B3LYP calculations, using the same basis set. It is shown by a novel analysis that the intramolecular equivalent of basis set superposition error competes with the errors in the intramolecular dispersion in causing this sensitivity.
Benzamides↗
Effects of peripheral substituents and axial ligands on the electronic structure and properties of cobalt porphyrins.
The effects of peripheral substituents and axial ligands (L) on the electronic structure and properties of cobalt tetraphenylporphyrin (CoTPP) have been studied using DFT methods. Various density functionals were tested, and the ground state of each system was determined by considering several possible low-lying states. The ground states of the fully fluorinated CoTPPF28(L)2 complexes with L = THF, Py, and Im were identified to be high-spin (4E(g)) by the meta-GGA functional tau-HCTH, which contains the kinetic energy density tau, in agreement with experimental measurements. All the pure GGA functionals, including the recently developed mPBE, OPBE, and HCTH/407, show more or less overestimation of the relative energies of the high-spin states. The energy gap between the 2A(1g) and 4E(g) states is insignificant (approximately 0.1 eV) and varies in the order L = Py < L = THF < L = Im. The results and their trend are consistent with 19F NMR studies which show partial population of the 4E(g) state in CoTPPF28(THF)2 and CoTPPF28(Py)2 and a complete conversion to the high-spin state in CoTPPF28(1-MeIm)2. Upon coordination by two very strong field axial CO ligands, CoTPPF28(CO)2 becomes low-spin, as in unligated CoTPPF(x). The influence of the peripheral substituents and axial ligands on the ionization potentials, electron affinities, and CoTPPF(x)-(L)2 binding strength was also investigated in detail.
Algorithms↗
Synthesis, characterization, and electronic structure of Ba5In4Bi5: an acentric and one-electron deficient phase.
The new ternary phase Ba(5)In(4)Bi(5) was synthesized by direct reaction of the corresponding elements at high temperature. It crystallizes in a noncentrosymmetric space group and represents a new structure type (tetragonal, P4nc with a=10.620(2) and c=9.009(2) A, Z=2). The structure is built of interconnected heteroatomic clusters of In(4)Bi(5), square pyramids with In(4)-bases and four exo-bonded bismuth atoms (bond to the In atoms). According to Wade's rule the compound is electron-deficient with one electron per cluster, that is, [In(4)Bi(5)](10-) instead of the expected [In(4)Bi(5)](11-) for a closed-shell species. The clusters are discussed also in light of the known heteroatomic deltahedral clusters with the same composition but different charge, [In(4)Bi(5)](3-). Band structure calculations on the new compound suggest substantial participation of barium in the overall bonding of the structure that "accounts" for the electron shortage
Journal Article↗
NMR study of the molecular and electronic structure of the heme cavity in Dolabella met-cyano myoglobin.
The molecular and electronic structure of the active site of the cyanide-ligated ferric complex of the myoglobin from the mollusc Dolabella auricularia has been investigated using NMR. Analysis of nuclear Overhauser effects has revealed that the correlation times for the internal motion of the heme propionate alpha-CH2 and beta-CH2 groups at ambient temperature are about 5 and 4 ns, respectively. These correlation times indicate that the terminal carboxylate groups of both the heme propionates are not bound to the protein via salt bridges. Although the absence of the propionate-protein interaction does not influence the equilibrium population of the two heme orientational isomers involving rotation about the alpha,gamma-meso axis, it allows the heme to rotate about the iron-His bond in the active site of the myoglobin. Such rotational motion of the heme resulted in an anomalous temperature-dependence of the heme methyl-proton hyperfine shift. Thus the present myoglobin studies provide the first example demonstrating the rotation of the heme about the iron-His bond in native myoglobin.
Animals↗
First-principles study of the electronic structures of icosahedral TiN (N=13,19,43,55) clusters.
We have studied the electronic structures of icosahedral Ti(N) clusters (N=13, 19, 43, and 55) by using a real-space first-principles cluster method with generalized gradient approximation for exchange-correlation potential. The hexagonal close-packed and fcc close-packed clusters have been studied additionally for comparisons. It is found that the icosahedral structures are the most stable ones except for Ti(43), where fcc close-packed structure is favorable in energy. We present and discuss the variation of bond length, the features of the highest occupied molecular orbitals and the lowest unoccupied molecular orbital, the evolution of density of states, and the magnetic moment in detail. The results are in good agreement with the predictions from the collision-induced dissociation and size-selected anion photoelectron spectroscopy experiments.
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Bilayer splitting in the electronic structure of heavily overdoped Bi(2)Sr(2)CaCu(2)O(8+delta).
The electronic structure of heavily overdoped Bi(2)Sr(2)CaCu(2)O(8+delta) is investigated by angle-resolved photoemission spectroscopy. The long-sought bilayer band splitting in this two-plane system is observed in both normal and superconducting states, which qualitatively agrees with the bilayer Hubbard model calculations. The maximum bilayer energy splitting is about 88 meV for the normal state feature, while it is only about 20 meV for the superconducting peak.
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Electronic structure and chemical bonding in MO(n)- and MO(n) clusters (M = Mo, W; n = 3-5): a photoelectron spectroscopy and ab initio study.
Photoelectron spectroscopy (PES) and ab initio calculations are combined to investigate the electronic structure of MO(n)- clusters (M = W, Mo; n = 3-5). Similar PES spectra were observed between the W and Mo species. A large energy gap between the first and second PES bands was observed for MO3- and correlated with a stable closed-shell MO3 neutral cluster. The electron binding energies of MO4- increase significantly relative to those of MO3-, and there is also an abrupt spectral pattern change between MO3- and MO4-. Both MO4- and MO5- give PES features with extremely high electron binding energies (>5.0 eV) due to oxygen-2p-based orbitals. The experimental results are compared with extensive density functional and ab initio [CCSD(T)] calculations, which were performed to elucidate the electronic and structural evolution for the tungsten oxide clusters. WO3 is found to be a closed-shell, nonplanar molecule with C3v symmetry. WO4 is shown to have a triplet ground state (3A2) with D2d symmetry, whereas WO5 is found to be an unusual charge-transfer complex, (O2-)WO3+. WO4 and WO5 are shown to possess W-O* and O2-* radical characters, respectively.
Journal Article↗
Electronic structure of glassy chalcogenides As4Se4 and As2Se3: a joint theoretical and experimental study.
We present an interpretation of the x-ray absorption spectra of arsenic chalcogenide glasses, As4Se4 and As2Se3, from a first-principles calculation. Our calculation identifies the atomistic origins of the observed photoemission data. The importance of structural "building blocks" present in a particular glass to the electron states is emphasized. The effects of disorder on the electronic spectra are clearly demonstrated by a significant change in the electronic density of states, originating in the breakdown of long-range order coherence in the bonding states of the building blocks. We discuss the relation between observed in situ light-induced changes and the electronic structure.
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[The connection of the electronic structure and biological activity of various derivatives of 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine].
Electron structure of 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) and some of its analogs--the substrates of monoaminooxidase--substituted by phenyl cycles was studied by semiempiric quantum-chemical CNDOR, MINDOB methods. The relationship between the obtained electron and conformation parameters (orientation of the phenyl ring in particular) and biological activity of the compounds under consideration is discussed. A comparative analysis of the distribution pattern of the electron density for the MPTP molecule calculated by the above methods showed a good agreement between the results obtained.
Electrons↗
The fulvenediyls and related biradicals: Molecular and electronic structure.
The structures, stabilities, and electronic properties of the nine fulvenediyls have been investigated and compared to the isomeric benzynes using density functional theory (DFT) and ab initio multireference configuration interaction methods (MRCI). Given the significant biradical character of several singlet fulvenediyls, the BLYP method reproduces the relative energies of these systems rather accurately. In contrast, some triplet states (3A'-12, 3A'-13, and 3B2-14) suffer from artifactual symmetry breaking towards a nonplanar geometry at the DFT level. The structures and properties of the title biradicals are readily rationalized within the framework of through-space and through-bond molecular orbital interactions. The degree of coupling between the formally unpaired electrons strongly depends on the number and arrangement of intervening sigma-bonds, and often parallels the trends observed for annellated arynes of similar topology. In some cases, novel structural patterns can be identified that are characteristic of five-membered-ring systems. These similarities and differences between five- and six-membered-ring arynes are discussed on the basis of molecular orbital arguments.
Journal Article↗