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At least 235 records · Page 13Linked to original sources
PubMed2005

The electronic structure of human erythropoietin as an aid in the design of oxidation-resistant therapeutic proteins.

The electronic structure of human erythropoietin (HuEPO) has been investigated with the aid of quantum mechanical calculations. The results indicate that the protein is highly polarized and its permanent dipole moment has a magnitude of 471 D. The HOMO of HuEPO is localized on Trp51, which stays in close proximity to Met54. Three oxidation-resistant mutants of HuEPO (W51F, M54V, and W51F-M54V) have been modeled and their electronic structures are compared to that of the native protein. Among them, the W51F mutation is predicted to be the most effective in increasing the oxidation potential of the protein.

Drug Design↗
PubMed2005

Zori 1.0: a parallel quantum Monte Carlo electronic structure package.

The Zori 1.0 package for electronic structure computations is described. Zori performs variational and diffusion Monte Carlo computations as well as correlated wave function optimization. This article presents an overview of the implemented methods and code capabilities.

Journal Article↗
PubMed2005

Electronic structure of the K3Bi2 metallic phase.

The electronic structure of K3Bi2 is discussed on the basis of first-principles DFT calculations. It is shown that the dimers are formally (Bi2)3-, even though this might seem to be in contradiction with the metallic character of the salt. The apparent puzzle is explained by the sizable participation of the K levels in the bonding.

Journal Article↗
PubMed1999

Electronic Structure of Metallacyclophosphazene and Metallacyclothiazene Complexes.

The electronic structure of metallacyclotriphosphazene complexes with several substituents at the phosphorus atoms and metallacyclothiazene complexes is explored for a variety of transition metal elements using density functional theory methods. Accordingly the metallacyclophosphazenes possess a large HOMO-LUMO energy separation while the metallacyclothiazenes bear stronger open-shell character. In addition our calculations predict the existence of experimentally so far unknown dimetallacyclophosphazenes. All structures show to be highly dynamical. The double bond character of the transition metal nitrogen bond is much less pronounced than in nitrido or imido complexes. For the ring compounds vibrational spectra are reported and compared with experimental data.

Journal Article↗
PubMed2006

Geometric and electronic structures of metal-substitutional fullerene C59Sm and metal-exohedral fullerenes C60Sm.

The geometric and electronic structures of metal-substituted fullerene C59Sm and exohedral fullerenes C60Sm are studied using the density-functional theory. The geometric optimization shows that the replacement of a C atom with a Sm in C60 yields a stable substitutionally doped fullerene C59Sm, and among the five possible optimized geometries for C60Sm, the most favorable exohedral sites are above the center of a hexagon and a pentagon ring. The calculations for electronic structures show that the magnetic moment of Sm is preserved for all the stable structures as tiny hybridization takes place between the orbitals of the Sm atom and those of their neighboring carbons. Because of the small energy gaps and the half occupation of the highest occupied molecular orbitals, all the stable C60Sm isomers are inferred to be conductors.

Journal Article↗
PubMed2000

Photochemically induced nuclear spin polarization in reaction centers of photosystem II observed by 13C-solid-state NMR reveals a strongly asymmetric electronic structure of the P680(.+) primary donor chlorophyll.

We report (13)C magic angle spinning NMR observation of photochemically induced dynamic nuclear spin polarization (photo-CIDNP) in the reaction center (RC) of photosystem II (PS2). The light-enhanced NMR signals of the natural abundance (13)C provide information on the electronic structure of the primary electron donor P(680) (chlorophyll a molecules absorbing around 680 nm) and on the p(z) spin density pattern in its oxidized form, P(680)(.+). Most centerband signals can be attributed to a single chlorophyll a (Chl a) cofactor that has little interaction with other pigments. The chemical shift anisotropy of the most intense signals is characteristic for aromatic carbon atoms. The data reveal a pronounced asymmetry of the electronic spin density distribution within the P(680)(.+). PS2 shows only a single broad and intense emissive signal, which is assigned to both the C-10 and C-15 methine carbon atoms. The spin density appears shifted toward ring III. This shift is remarkable, because, for monomeric Chl a radical cations in solution, the region of highest spin density is around ring II. It leads to a first hypothesis as to how the planet can provide itself with the chemical potential to split water and generate an oxygen atmosphere using the Chl a macroaromatic cycle. A local electrostatic field close to ring III can polarize the electronic charge and associated spin density and increase the redox potential of P(680) by stabilizing the highest occupied molecular orbital, without a major change of color. This field could be produced, e.g., by protonation of the keto group of ring V. Finally, the radical cation electronic structure in PS2 is different from that in the bacterial RC, which shows at least four emissive centerbands, indicating a symmetric spin density distribution over the entire bacteriochlorophyll macrocycle.

Carbon Isotopes↗
PubMed2005

Elucidating the vibrational spectra of hydrogen-bonded aggregates in solution: electronic structure calculations with implicit solvent and first-principles molecular dynamics simulations with explicit solvent for 1-hexanol in n-hexane.

Fourier transform infrared spectroscopy is a popular method for the experimental investigation of hydrogen-bonded aggregates, but linking spectral information to microscopic information on aggregate size distribution and aggregate architecture is an arduous task. Static electronic structure calculations with an implicit solvent model, Car-Parrinello molecular dynamics (CPMD) using the Becke-Lee-Yang-Parr (BLYP) exchange and correlation energy functionals and classical molecular dynamics simulations for the all-atom version of the optimized parameters for liquid simulations (OPLS-AA) force field were carried out for an ensemble of 1-hexanol aggregates solvated in n-hexane. The initial configurations for these calculations were size-selected from a distribution of aggregates obtained from a large-scale Monte Carlo simulation. The vibrational spectra computed from the static electronic structure calculations for monomers and dimers and from the CPMD simulations for aggregates up to pentamers demonstrate the extent of the contribution of dangling or nondonating hydroxyl groups found in linear and branched aggregates to the "monomeric" peak. Furthermore, the computed spectra show that there is no simple relationship between peak shift and aggregate size nor architecture, but the effect of hydrogen-bond cooperativity is shown to differentiate polymer-like (cooperative) and dimer-like (noncooperative) hydrogen bonds in the vibrational spectrum. In contrast to the static electronic structure calculations and the CPMD simulations, the classical molecular dynamics simulations greatly underestimate the vibrational peak shift due to hydrogen bonding.

Journal Article↗
PubMed2005

Metal-metal interactions in mixed-valence [M2Cl9]2- species: electronic structure of d1d2 (V, Nb, Ta) and d4d5 (Fe, Ru, Os) face-shared systems.

The molecular and electronic structures of mixed-valence d1d2 (V, Nb, Ta) and d4d5 (Fe, Ru, Os) face-shared [M2Cl(9)]2- dimers have been calculated by density functional methods in order to investigate metal-metal bonding in this series. General similarities are observed between d1d2 and d4d5 systems and can be considered to reflect the electron-hole equivalence of the individual d1-d5 and d2-d4 configurations. The electronic structures of the dimers have been analyzed using potential energy curves for the broken-symmetry and other spin states resulting from the d1d2 and d4d5 coupling modes. In general, a spin-doublet (S = 1/2) state, characterized by delocalization of the metal-based electrons in a metal-metal bond with a formal order of 1.5, is favored in the systems containing 4d and 5d metals, namely, the Nb, Ta, Ru, and Os dimers. In contrast, the calculated ground structures for [V2Cl9]2- and [Fe2Cl9]2- correspond to a spin-quartet (S = 3/2) state involving weaker coupling between the metal centers and electron localization. In the case of [Ru2Cl9]2-, both the spin-doublet and spin-quartet states are predicted to be energetically favored suggesting that this species may exhibit double-minima behavior. A comparison of computational results across the (d1d1, d1d2, d2d2) [Nb2Cl9]z- and [Ta2Cl9]z- and (d4d4, d4d5, d5d5) [Ru2Cl9]z- and [Os2Cl9]z- series has revealed that, in all four cases, the shortening of the metal-metal distances correlates with an increase in formal metal-metal bond order.

Journal Article↗
PubMed2005

Electronic structure of the hydroxo and methoxo oxometalate anions MO3(OH)- and MO3(OCH3)- (M = Cr, Mo, and W).

The electronic structure of the mononuclear hydroxo MO3(OH)- and methoxo MO3(OCH3)- Group 6 oxometalate anions (M = Cr, Mo, and W) were examined by photodetachment photoelectron spectroscopy and electronic structure calculations at the density functional and CCSD(T) levels of theory. All of the anions exhibited high electron binding energies (>4.9 eV), with the lowest-energy detachment features arising from oxygen 2p-based orbitals. The combined experimental and theoretical results allowed the change in molecular orbital energy levels to be investigated as a function of metal (Cr, Mo, or W) and ligand (-OH, -OCH3). A number of fundamental thermodynamic properties of the anions and corresponding neutrals were predicted on the basis of the theoretical calculations. The calculations indicate high O-H bond dissociation energies for MO2(OR)(O-H) (R = H, CH3) and MO3(O-H), consistent with their high Brønsted acidities (just below that of H2SO4 in the gas phase) and the high ionization energies of their conjugate base anions. This suggests that the corresponding radicals should readily abstract H atoms from organic molecules.

Journal Article↗
PubMed2005

QM/MM studies of the electronic structure of the compound I intermediate in cytochrome c peroxidase and ascorbate peroxidase.

Cytochrome c peroxidase (CcP) and ascorbate peroxidase (APX) both involve reactive haem oxoferryl intermediates known as 'compound I' species. These two enzymes also have a very similar structure, especially in the vicinity of the haem group. Despite this similarity, the electronic structure of compound I in the two enzymes is known to be very different. Compound I intermediates have three unpaired electrons, two of which are always situated on the Fe-O core, whilst the third is located in a porphyrin orbital in APX and many other compound I species. In CcP, however, this third unpaired electron is positioned on a tryptophan residue lying close to the haem ring. The same residue is present in the same position in APX, yet it is not oxidized in that case. We report QM/MM calculations, using accurate B3LYP density functional theory for the QM region, on the active intermediate for both enzymes. We reproduce the observed difference in electronic structure, and show that it arises as a result of subtle electrostatic effects which affect the ionization potential of both the tryptophan and porphyrin groups. The computed structures of both enzymes do not involve deprotonation of the tryptophan group, or protonation of the oxoferryl oxygen.

Ascorbate Peroxidases↗
PubMed2002

Ab initio electronic structure of the progestogen norethisterone and its 5 alpha-derivatives.

The steroid 17 alpha-ethynyl-19-nor-4-androsten-17 beta-ol, 3-one (Norethisterone; NET) and its 5 alpha-dihydro (5 alpha-NET), 3 alpha- and 3 beta-tetrahydro derivatives (3 alpha,5 alpha- and 3 beta,5 alpha-NET), were comparatively studied by the ab initio quantum mechanics theory. Additionally, 5 alpha-androstan-3 beta,17 beta-diol (ADIOL) was also studied. The Hartree-Fock method and the 6-31G(*) basis set were used to obtain the lowest energy conformation, geometries, electronic structure and physicochemical properties of the steroids. The results showed bond distances and valence angles similar among all steroids, but some differences in dihedral angles in the A-B-ring system were observed. The electronic structure analysis showed that NET has both frontier orbitals that is, the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) located at the C4-C5 pi-bond. In A-ring reduced derivatives, the HOMO was found at the 17 beta-OH and ethynyl groups. In the case of 5 alpha-NET, the LUMO was confined to the A-ring and its C3 carbonyl group while the two NET tetrahydro-reduced derivatives showed the LUMO at the 17 beta-OH and ethynyl groups. The energy changes of the rotational barrier of the 17 beta-OH group suggest that its movement is somewhat restricted by the 17 alpha-ethynyl group. Interestingly both groups at C17 form a single electrostatic potential with high electronic density. On the other side, the 19-nor condition increases the A-ring mobility. However, the 3 beta-OH group of 3 beta,5 alpha-NET may rotate without significant energy differences as compared to the same group in ADIOL. The electronic structure of NET and its A-ring reduced derivatives explains in some extent their interaction with androgen and progesterone receptors as well as their selectivity for the estrogen alpha-receptor.

Binding Sites↗
PubMed2005

Electronic structure effects of amide group: Vince lactam.

HeI photoelectron spectrum of 2-azabicyclo[2.2.1]hept-5-en-3-one (Vince lactam) has been measured. The assignment of the spectrum was made by comparison with photoelectron spectra of related compounds and by taking into account the lactam's molecular structure. The analysis of the electronic structure of amide group, in terms of inductive and conjugative effects, is presented on the basis of photoelectron spectroscopic data.

Amides↗
PubMed2001

Changes in electronic structure by Li ion deintercalation in LiCoO2 from cobalt L-edge and oxygen K-edge XANES.

Cobalt L-edge and oxygen K-edge X-ray Absorption Near Edge Structure (XANES) investigated change in electronic structure by electrochemical lithium ion de-intercalation in LiCoO2. The Co L-edge XANES of Li(1-x)CoO2 did not show any chemical shift even at high x value. The oxygen K-edge XANES of Li(1-x)CoO2 indicated that the holes compensating the lithium ion deintercalation are located primarily in the oxygen 2p states rather than in the Co 3d states.

Journal Article↗
PubMed2004

Resonant states in the electronic structure of the high performance thermoelectrics AgPbmSbTe2+m: the role of Ag-Sb microstructures.

Ab initio electronic structure calculations based on gradient corrected density-functional theory were performed on a class of novel quaternary compounds AgPb(m)SbTe(2+m), which were found to be excellent high temperature thermoelctrics with a large figure of merit ZT approximately 2.2 at 800 K. We find that resonant states appear near the top of the valence and bottom of the conduction bands of bulk PbTe when Ag and Sb replace Pb. These states can be understood in terms of modified Te-Ag(Sb) bonds. The electronic structure near the gap depends sensitively on the microstructural arrangements of Ag-Sb atoms, suggesting that large ZT values may originate from the nature of these ordering arrangements.

Journal Article↗
PubMed1994

Cytochrome c electronic structure characterization toward the analysis of electron transfer mechanism.

Seventy-four kinds of cytochrome c sequences have been compared in order to determine the conserved residues and residues of which the characters are conserved. Twenty-three residues are invariant throughout all the aligned sequences, while the residues at 17 other positions share common characters. The prosthetic group as well as these conserved and character-conserved residues are considered to constitute a model molecule to elucidate the electron transfer process in cytochrome c. Their coordinates in the structure of tuna cytochrome c are extracted, and an extended Hückel molecular orbital calculation has been executed on this molecule. The examination of the shapes and the energy levels of the resulting MOs has suggested that three nearly degenerate HOMOs might play an important role in the electron transfer. These HOMOs are exposed to the protein surface around the heme, Cys-17, and Phe-82. A delocalized electron system developing in these regions is proposed to be the electron transfer pathway of cytochrome c.

Amino Acid Sequence↗
PubMed1993

Electronic structure contributions to function in bioinorganic chemistry.

Many metalloenzymes exhibit distinctive spectral features that are now becoming well understood. These reflect active site electronic structures that can make significant contributions to catalysis. Copper proteins provide well-characterized examples in which the unusual electronic structures of their active sites contribute to rapid, long-range electron transfer reactivity, oxygen binding and activation, and the multielectron reduction of dioxygen to water.

Amino Acid Sequence↗
PubMed2001

Electronic structure of high-spin iron(III)-alkylperoxo complexes and its relation to low-spin analogues: reaction coordinate of O-O bond homolysis.

The spectroscopic properties of the high-spin Fe(III)-alkylperoxo model complex [Fe(6-Me(3)TPA)(OH(x))(OO(t)Bu)](x)(+) (1; TPA = tris(2-pyridylmethyl)amine, (t)Bu = tert-butyl, x = 1 or 2) are defined and related to density functional calculations of corresponding models in order to determine the electronic structure and reactivity of this system. The Raman spectra of 1 show four peaks at 876, 842, 637, and 469 cm(-1) that are assigned with the help of normal coordinate analysis, and corresponding force constants have been determined to be 3.55 mdyn/A for the O-O and 2.87 mdyn/A for the Fe-O bond. Complex 1 has a broad absorption feature around 560 nm that is assigned to a charge-transfer (CT) transition from the alkylperoxo to a t(2g) d orbital of Fe(III) with the help of resonance Raman profiles and MCD spectroscopy. An additional contribution to the Fe-O bond arises from a sigma interaction between and an e(g) d orbital of iron. The electronic structure of 1 is compared to the related low-spin model complex [Fe(TPA)(OH(x))(OO(t)Bu)](x)(+) and the reaction coordinate for O-O homolysis is explored for both the low-spin and the high-spin Fe(III)-alkylperoxo systems. Importantly, there is a barrier for homolytic cleavage of the O-O bond on the high-spin potential energy surface that is not present for the low-spin complex, which is therefore nicely set up for O-O homolysis. This is reflected by the electronic structure of the low-spin complex having a strong Fe-O and a weak O-O bond due to a strong Fe-O sigma interaction. In addition, the reaction coordinate of the Fe-O homolysis has been investigated, which is a possible decay pathway for the high-spin system, but which is thermodynamically unfavorable for the low-spin complex.

Ferric Compounds↗
PubMed1987

Effect of pH and ions on the electronic structure of saccharin.

The sodium salt of saccharin is biologically more active as a urothelial cell mitogen in vivo, when fed to male rats, than are the potassium or calcium salts or the acid form, despite similar concentrations of saccharin excreted in the urine. The differences in bladder-mitogenic activity between sodium saccharin and the other salts of saccharin may be the result of known differences in the ionic composition of the urine of rats receiving these various forms of saccharin. These changes in the rat urine following administration of the different salts of saccharin could be responsible for the observed mitogenic responses to oral saccharin; alternatively the differences in the ionic composition of the urine could result in changes in the electronic structure of the saccharin molecule itself, allowing it to be more active in certain ionic environments. Since the pKa of saccharin is 1.8, essentially all of the saccharin in urine (pH greater than 5) will exist in the ionized form. We have used 17O, 15N, 13C and two-dimensional nuclear magnetic resonance (NMR) spectroscopy to explore the electronic structure of the saccharin molecule in aqueous solution. By observing the NMR spectra of the saccharinate ion in the presence of varying concentrations of hydrogen, potassium, sodium, calcium, magnesium, bicarbonate and urate, we have demonstrated that at physiological levels none of these ions significantly alters the electronic structure of the saccharin molecule. Hence the differences in the mitogenic response to the different saccharin salts cannot be explained by alterations in the structure of the saccharin molecule.

Carbon Isotopes↗