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 145 records · Page 8Linked to original sources
PubMed2001

Calculation of the electronic structure and spectra of model cytochrome P450 compound I.

The electronic structure and spectra of the oxyferryl (Fe=O) compound I P450 heme species, the transient putative active intermediate of cytochrome P450s, have been calculated employing a full protoporphyrin IX heme model representation. The principal aim of this work was to compare the computed spectra of this species with the observed transient spectra attributed to it. Computations were made using both nonlocal density functional theory (DFT) and semiempirical INDO/CI methods to characterize the electronic structure of the compound I P450 species. Both methods resulted in a similar antiferromagnetic doublet as the ground state with a ferromagnetic quartet excited state partner, slightly higher in energy. The INDO/ROHF/CI semiempirical method was used to calculate the spectrum of the protoporphyrin IX P450 compound I heme species in its lowest energy antiferromagnetic doublet state at the DFT optimized geometry. As a reference, the spectrum of the ferric resting form of the protoporphyrin IX P450 heme species was also calculated. The computed shifts in the Soret and Q bands of compound I relative to the resting state were both in good agreement with the corresponding experimentally observed shifts in the transient spectra of cytochrome P450cam (Biochem. Biophys. Res. Commun. 201 (1994) 1464) and chloroperoxidase (Biochem. Biophys. Res. Commun. 94 (1980) 1123) both ascribed to their common compound I heme site. This consistency provides additional, independent support for the assignment of compound I as the origin of the reported observed transient spectra.

Cytochrome P-450 Enzyme System↗
PubMed2006

The electronic structures of Co and Ni tetraazaannulenes.

We compare the electronic structure of two metal-centered tetramethyldibenzo-tetraazaannulene (TMTAA) macrocyclic complex molecules: 5,7,12,14- tetramethyl-2,3:9,10-dibenzo[b,i]-1,4,8,11-tetraazacyclotetradecine nickel (II) and 5,7,12,14-tetramethyl-2,3:9,10-dibenzo[b,i]-1,4,8,11-tetraazacyclotetradecine cobalt (II). The experimental gap between the highest occupied molecular orbital to the lowest unoccupied molecular orbital for both molecules, obtained from combined ultraviolet photoemission and inverse photoemission studies, is close to the value of 6.6 eV expected from simple model calculations, but with the Fermi level placed closer to the lowest unoccupied molecular orbital. While both the Co(II) (s = 1/2) and Ni(II) (s = 0) TMTAA molecular electronic structures are very similar, the Ni(II) adopts a high-symmetry molecular configuration upon adsorption, with a strong preferential orientation.

Journal Article↗
PubMed2003

Bonding and electronic structure in consanguineous and conjugal iron and rhenium sp carbon chain complexes [MC4M'](n)+: computational analyses of the effect of the metal.

Density functional theory has been used to probe the bonding and electronic properties of the homo- and heterobimetallic sp carbon chain complexes (ML(m), = (eta(5)-C(5)R(5))(eta(2)-R(2)PCH(2)CH(2)PR(2))Fe, (eta(5)-C(5)R(5))(NO)(PR(3))Re; z = 0-4). All neutral complexes are best described by MCtbd1;CCtbd1;CM electronic structures, in accord with much experimental data. The singlet dications are best described by cumulenic (+)M=C=C=C=C=M(+) valence formulations. However, the diiron and rhenium/iron dications are found to possess triplet states of nearly identical energy, clarifying experimental magnetic data. Their electronic structures have dominant *(+)MCtbd1;CCtbd1;CM(+)* character, with some spin delocalization onto the carbon chain. The mixed valence monocation radicals exhibit delocalized unpaired electrons, in accord with class III (strongly coupled) and II (weakly coupled) assignments made from experimental data earlier, with some spin density on the carbon chain. An isolable diiron trication has a doublet ground state, but some computational data suggest a close-lying quartet. For the unknown diiron tetracation, a bis(carbyne) or (2+)Fetbd1;CCtbd1;CCtbd1;Fe(2+) electronic structure is predicted. Calculated adiabatic ionization potentials show the iron endgroup to be more electron-releasing than rhenium, in accord with electrochemical data. This polarizes the electronic structures of the rhenium/iron complexes. To help validate the computed model structures, crystal structures of ((eta(5)-C(5)Me(5))Fe(eta(2)-dppe))(2)(mu-C(4)) and [((eta(5)-C(5)Me(5))Fe(eta(2)-dippe))(2)(mu-C(4))](3+) 3PF(6)(-) are determined. Data are analyzed with respect to related diruthenium and dimanganese complexes.

Journal Article↗
PubMed2006

The electronic structure and spectra of spin-triplet ground state bis(biuretato)cobalt(III) coordination compounds.

The planar coordination compounds of cobalt(III) with bis(biuretato) ligands are highly unusual due to their intermediate spin triplet ground state. Density functional theory (DFT) and time-dependent DFT have been applied in a study of the structure and electronic spectroscopy of this type of coordination compounds. The investigations included prediction and spectroscopic measurements of the absorption and circular dichroism (CD), as well as an experimental study of the magnetic CD. The results obtained by TD-DFT were in excellent agreement with the observed spectral features, both regarding the d-d and the charge transfer regions. There was noted a systematic blue-shift of the TD-DFT results compared to experiment, corresponding to an offset of ca. 0.5 microm(-1) and a scaling factor of 1.25 for the transition energies. The DFT results are rationalized in terms of a qualitative MO analysis.

Biuret↗
PubMedDate not supplied

[Interrelation of the electronic structure of nucleic acid components and their ability and specificity in template synthesis].

A hypotesis suggesting that the specificity of polynucleotide template synthesis is based not on complementarity but on the correspondence of the electronic structure of the precursor and the enzyme active site (EAS), the latter being formed by the template, enzyme, and, possibly, by the polynucleotide synthesized is described. Comparison of the electronic structure of natural nucleic bases and their analogs allows to suppose that the EAS discriminates between adenine and cytosine, and uracil (thymine) and guanine, by electrostatic features: sign of the potential in the region of exocyclic substituents at C(4) of pyrimidines and C(5) of purines. For adenine and cytosine this sign is positive while for uracil (thymine) and guanine it is negative. The second feature allowing to discriminate between purines and pyrimidines is connected with general difference of their electronic structure. The total charge of N-glycoside center, more negative for pyrimidines, can serve as an index of this difference. According to the hypothesis the compounds unable to form complementary pairs can be functionally active in the polynucleotide template synthesis and can show ambiguous functional specificity due not only to the presence of different ionic and/or tautomeric species but also to the potential in the aforementioned region being close to zero or the charge of N-glycoside center being intermediate. It can be assumed that for the formation of EAS the same features of the electronic structure of the nucleotide residues of the template are used, which are important for the interaction of the precursor with the EAS (recognition of the precursor).

Adenine↗
PubMed2005

An evolved explanation for the molecular geometry and electronic structure of diphenyl-substituted cyclic trimethylenemethane in the ground state: a nearly planar conformation with a considerably localized electronic state.

[structures: see text] We reinvestigated the molecular geometry and electronic structure of the diphenyl-substituted, five-membered cyclic trimethylenemethane (TMM) diradical (Berson's TMM, 3**) using UV/VIS absorption and emission spectroscopy combined with density functional theory (DFT) and time-dependent (TD)-DFT calculations. Two intense absorption bands, A and B, with lambda(ab) at 298 and 328 nm, respectively, a weak absorption band C, with lambda(ab) at 472 nm, and an intense emission band D, with lambda(em) at 491 nm, were observed for 3**. By comparing the spectrum of 3** with those of the 1,1-diphenylethyl (7*) and cyclopent-2-en-1-yl (9*) radicals, it was found that bands B, C, and D originated from the diphenylmethyl radical moiety (subunit I), while band A should most likely be assigned to an electronic transition related to an interaction between subunit I and residual subunit II, the cyclopentenyl radical moiety. An UB3LYP/cc-pVDZ calculation indicated that, in the ground state, the two unpaired electrons of 3** are mainly localized in subunits I and II, respectively, and the interaction between them is inefficient, despite the nearly planar conformation (theta = +23.5 degrees). Furthermore, a TD-UB3LYP/cc-pVDZ calculation suggested that absorption band A is assigned to an electronic transition involved with enhancement of the electron density of the C-2-C-3 bond. Substituent effects on the absorption and emission spectra of 3** using 11** and 13** support the conclusion based on the experiments and calculations. Therefore, we propose an evolved explanation for the molecular geometry and electronic structure of the ground state of 3** in a low-temperature matrix, a nearly planar conformation with a considerably localized electronic state, which alone accounts for the spectroscopic characteristics.

Journal Article↗
PubMed2002

Solution structure of cyanoferricytochrome c: ligand-controlled conformational flexibility and electronic structure of the heme moiety.

The solution structure of cyanoferricytochrome c has been determined using NMR spectroscopy. As a result of including additional constraints derived from pseudocontact shifts, a high-resolution NMR structure was obtained with high accuracy. In order to study the conformational transition between the native protein and its ligand adducts, the present structure was compared with the solution structures of the wild-type cytochrome c and the imidazole-cytochrome c complex. Like the solution structure of imidazole-cytochrome c, the heme crevice is widened by the swinging out of residues 77-85 and a noticeable shift of the 50s helix. However, unlike imidazole, cyanide exerts less significant perturbation on the conformation of the heme cavity, which is revealed by a more compact residue package in the distal pocket. Furthermore, comparison of the solution structure of CN-iso-1Met80Ala cytochrome c with the structure of cyanoferricytochrome c indicated that the binding of cyanide has a different impact on the distal cavity conformation in the two proteins. In addition, the magnetic properties of the present system are discussed and a comprehensive study of the electronic structure of ligand-cytochrome c complexes and the native protein is also described. Electronic supplementary material to this paper can be obtained by using the Springer Link server located at http://dx.doi.org/10.1007/s00775-001-0334-y.

Amino Acid Sequence↗
PubMed2004

First principles study of the stability and electronic structure of the icosahedral La13, La(-1) (13), and La(+1) (13) clusters.

The structural stability and electronic-structure of icosahedral La(13), La(-1) (13), and La(+1) (13) clusters have been studied by DMOL cluster method based on density-functional theory. The ground state of all-electron with relativity results is shown to be a distorted D(2h) icosahedron by the Jahn-Teller effect. However, the binding energies of D(3d) and D(5d) are very close to that of the D(2h) structure for La(13), La(-1) (13), and La(+1) (13) clusters. The effective core potential results show that the true ground state is D(5d) structure. The clusters have small magnetic moments and the symmetry of cluster is an important factor in determining the magnetic moments of the clusters. The effects of interatomic spacing and coordination on atomic magnetic moment are discussed. Further, 5d electrons dominate the hybrid orbitals below the Fermi level in the neutral cluster and contribute the main spin of clusters.

Journal Article↗
PubMed2006

Role of spin-orbit coupling and hybridization effects in the electronic structure of ultrathin Bi films.

The electronic structure of Bi(001) ultrathin films (thickness > or =7 bilayers) on Si(111)-7x7 was studied by angle-resolved photoemission spectroscopy and first-principles calculations. In contrast with the semimetallic nature of bulk Bi, both the experiment and theory demonstrate the metallic character of the films with the Fermi surface formed by spin-orbit-split surface states (SSs) showing little thickness dependence. Below the Fermi level, we clearly detected quantum well states (QWSs) at the M point, which were surprisingly found to be non-spin-orbit split; the films are "electronically symmetric" despite the obvious structural nonequivalence of the top and bottom interfaces. We found that the SSs hybridize with the QWSs near M and lose their spin-orbit-split character.

Journal Article↗
PubMed2006

Ab initio quantum chemistry calculations on the electronic structure of heavier alkyne congeners: diradical character and reactivity.

The electronic structure of the heavier congeners of alkynes has been studied with emphasis on characterizing their extent of diradical character. Four orbitals play a crucial role in determining the electronic structure in planar trans-bent geometries. Two are associated with an out-of-plane pi interaction, pi and pi, and two are associated with in-plane interactions and/or in-plane lone pairs, LP(n-) and LP(n+). The ordering of these orbitals can change depending upon geometry. One extreme, corresponding to the local minimum for Si-Si and Ge-Ge, is a diradicaloid multiple-bonding configuration where LP and pi are nominally occupied. Another extreme, corresponding to a local minimum for Sn-Sn, is a relatively closed-shell single-bond configuration where LP and LP are nominally occupied. This ordering leads to predicted bond shortening upon excitation from singlet to triplet state. For the heavier elements, there appears to be very little energy penalty for large geometric distortions that convert from one ordering to the other on the singlet surface. The implications of these results with respect to experimental observations are discussed.

Journal Article↗
PubMedDate not supplied

[Difference in the Mössbauer spectrum parameters and electron structure of active sites of non-equivalent subunits of tetrameric deoxyhemoglobin and deoxymyoglobin].

The calculations of the electronic structure of fifth-coordinated ferroporphyrin-imidazole complexes modeling alpha- and beta-subunits in desoxyhemoglobin and desoxymyoglobin are made using the interative extended Hückel method. The features of the electronic structure of the model complexes resulting from the stereochemical differences of the active site are studied and compared. Theoretical calculations of the Mössbauer parameters of model complexes are made and compared with experimental data. The results show that basic features of the Mössbauer parameters are qualitatively confirmed by the theoretical analysis. The necessity of the accounting of the stereochemical and electronic structure nonequivalence of nonidentical subunits in tetrameric desoxyhemoglobins during the Mössbauer spectra approximation is also confirmed.

Binding Sites↗
PubMed2003

Comparative theoretical investigation of the vertical excitation energies and the electronic structure of [MoVOCl4]-: influence of basis set and geometry.

The electronic structures, geometries, and vibration frequencies of the open-shell molybdenum(V) ion, [MoOCl(4)](-), have been calculated at the extended Hückel, semiempirical ZINDO/1, ZINDO/S, and PM3(tm), as well as ab initio and DFT theoretical levels. Electronic structure calculations suggest that the expected metal-fold orbital order can be satisfied only at the DFT level. The time-dependent density functional theory (TDDFT) approach has been used for the calculation of the vertical excitation energies in the UV-vis region with different basis sets, starting geometries, and exchange-correlation functionals. A good agreement between the predicted and the experimental electronic absorption and MCD spectra of the complex, [MoOCl(4)](-), was observed when the B3LYP and B3P86 exchange-correlation functionals were used with a full electron valence double-zeta with polarization basis set for the molybdenum and 6-311G(d) for all other atoms. Similar results were obtained when the LANL2DZ effective core potential for molybdenum atom and 6-31G(d) for all other atoms were used. The best absolute deviation of 0.13 and mean deviation of 0.01 eV were calculated for the bands in the UV-vis region by B3P86, while the results for the B3LYP exchange-correlation functional were less satisfactory. Compared to polarization functions, the inclusion of diffuse functions resulted in little improvement. The calculated excitations energies and charge-transfer band intensities are found to be sensitive to the Mo=O distance and O-Mo-Cl angle.

Crystallography, X-Ray↗
PubMed2004

Chiral morphologies and interfacial electronic structure of naphtho[2,3-a]pyrene on Au(111).

The adsorption of the two-dimensionally chiral naphtho[2,3-a]pyrene molecule has been studied on Au(111). Both structural and electronic properties of the naphtho[2,3-a]pyrene (NP)/Au(111) interface have been measured. Ultraviolet and X-ray photoelectron spectroscopy have been employed to measure the energies of the molecular orbitals of the NP film with respect to the gold Fermi level. A Schottky junction with a large interface dipole (0.99 eV) is formed between Au(111) and NP. Temperature-programmed desorption was used to determine that adsorbed NP has a binding energy of 102.2 kJ/mol. Chiral domains have been observed with scanning tunneling microscopy due to the spontaneous phase separation of the 2-D enantiomers. Two distinct structural polymorphs have been observed, one of which has homochiral paired molecular rows. Models of the 2D structure are proposed that are in excellent agreement with experimental measurements.

Electrons↗
PubMed2005

Electronic structures and molecular properties of chalcogen nitrides Se2N2 and SeSN2.

The electronic structures and molecular properties of S2N2 as well as the currently unknown chalcogen nitrides Se2N2 and SeSN2 have been studied using various ab initio and density functional methods. All molecules share a qualitatively similar electronic structure and can be primarily described as 2pi-electron aromatics having minor singlet diradical character of 6-8% that can be attributed solely to the nitrogen atoms. This diradical character is manifested in the prediction of their molecular properties, in which coupled cluster and multiconfigurational approaches, as well as density functional methods, show the best performance. The conventional ab initio methods RHF and MP2 completely fail to describe these systems. Predictions for the vibrational frequencies, IR intensities, Raman activities, and 14N, 15N, and 77Se chemical shifts, as well as singlet excitation energies of Se2N2 and SeSN2, have been made. The computed high-level spectroscopic data will be of considerable value in future efforts aimed at the preparation of the conducting polymers (SeN)x and (SeNSN)x.

Journal Article↗
PubMed2003

Characterization of electronic structure and properties of a Bis(histidine) heme model complex.

Ferric and ferrous hemes, such as those present in electron transfer proteins, often have low-lying spin states that are very close in energy. To explore the relationship between spin state, geometry, and cytochrome electron transfer, we investigate, using density functional theory, the relative energies, electronic structure, and optimized geometries for a high- and low-spin ferric and ferrous heme model complex. Our model consists of an iron-porphyrin axially ligated by two imidazoles, which model the interaction of a heme with histidine residues. Using the B3LYP hybrid functional, we found that, in the ferric model heme complex, the doublet is lower in energy than the sextet by 8.4 kcal/mol and the singlet ferrous heme is 6.7 kcal/mol more stable than the quintet. The difference between the high-spin ferric and ferrous model heme energies yields an adiabatic electron affinity (AEA) of 5.24 eV, and the low-spin AEA is 5.17 eV. Both values are large enough to ensure electron trapping, and electronic structure analysis indicates that the iron d(pi) orbital is involved in the electron transfer between hemes. Mössbauer parameters calculated to verify the B3LYP electronic structure correlate very well with experimental values. Isotropic hyperfine coupling constants for the ligand nitrogen atoms were also evaluated. The optimized geometries of the ferric and ferrous hemes are consistent with structures from X-ray crystallography and reveal that the iron-imidazole distances are significantly longer in the high-spin hemes, which suggests that the protein environment, modeled here by the imidazoles, plays an important role in regulating the spin state. Iron-imidazole dissociation energies, force constants, and harmonic frequencies were calculated for the ferric and ferrous low-spin and high-spin hemes. In both the ferric and the ferrous cases, a single imidazole ligand is more easily dissociated from the high-spin hemes.

Hemeproteins↗
PubMed2005

Photoelectron spectra and electronic structures of some chlorosulfonyl pseudohalides.

The electronic structures of chlorosulfonyl pseudohalide ClSO2X (X = Cl, NCO, N3) are studied by photoelectron spectroscopy (PES) combined with the OVGF calculation at 6-311++G(3df) basis sets. The first ionization potentials for ClSO2NCO and ClSO2N3 are determined to be 12.02 and 11.43 eV, respectively, for the first time, and their features in the PE spectra were assigned based on comparison with related compounds and with high level quantum calculations. Photoelectron spectra of ClSO2NCO and ClSO2N3 suggest that the interactions between chlorine "lone-pair" electrons and two pseudohalogen groups have significant effect on the HOMOs of two compounds, besides the influence of their electronegativity on the first ionization energies.

Azides↗
PubMed2006

Changes in electronic structure upon Li insertion reaction of monoclinic Li3Fe2(PO4)3.

The electrochemical lithium insertion reaction of monoclinic Li(3)Fe(2)(PO(4))(3) as cathode materials of lithium-ion batteries was investigated from the viewpoint of the electronic structure around Fe and the polyanion unit (PO(4)). Fe K-edge and L(III,II)-edge XAS measurements revealed that Fe(3+) was reduced to Fe(2+) upon Li insertion. In addition, O K-edge and P K-edge XAS also showed spectral changes upon Li insertion, which corresponded to changes in the electronic structure of the PO(4) polyanion unit. The ab initio density functional calculation was performed within the GGA and LDA+U methods. The LDA+U method reproduced well the cell potential upon lithium intercalation into Li(3)Fe(2)(PO(4))(3), whereas the GGA method underestimated the intercalation. The calculated electronic structure of Li(3)Fe(2)(PO(4))(3) described strong P 3p-O 2p covalent bonding, while weak hybridization was indicated in Fe 3d-O 2p. Moreover, the difference in electronic density between Li(3)Fe(2)(PO(4))(3) and the lithiated model indicated that the polarization effect between inserted Li and oxygen induced the changes in the electronic structure around the polyanion unit.

Journal Article↗
PubMed2006

Spectroscopy and electronic structures of mono- and binuclear high-valent non-heme iron-oxo systems.

High-valent iron-oxo intermediates are known or believed to be key oxidizing species in the catalytic mechanisms of many mononuclear and binuclear non-heme iron enzymes. So far only limited experimental data on their electronic structures are available. In this study we extend knowledge from the experimentally well characterized mononuclear Fe(IV)=O (S=1) biomimetic model system to computational insight into the spectroscopy and electronic structures of mono-and binuclear high-valent iron-oxo enzyme intermediates. In the mononuclear Fe(IV)=O complexes, we predict the spectroscopy and energies of the electronic transitions to be very different for the S=1 and S=2 spin states, but the iron-oxo bonding for both spin states to be very similar. A comparison of the S=2 mono- and binuclear high-valent iron-sites predicts similar electronic transitions. However, the bent iron-oxo bridge and interactions with the second iron-center in the dimer shift the transitions to higher energies and splits the d(xz/yz) orbital set. These electronic structure and TD-DFT results provide a basis for understanding the spectroscopy and electronic structures of high-valent intermediates in mono- and binuclear non-heme iron enzymes.

Biomimetic Materials↗