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PubMed1980

The electronic structure of Fe2+ in reaction centers from Rhodopseudomonas sphaeroides. I. Static magnetization measurements.

We have measured the static magnetization of unreduced and reduced reaction centers that vary in their quinone content. Measurements were performed in the temperature range 0.7 degrees K less than T less than 200 degrees K and magnetic fields of up to 10 kG. The electronic g-value, crystal field parameters D, E, and the exchange interaction, J, between the quinone spin and Fe2+ were determined using the spin Hamiltonian formalism. The effective moment mu eff/Fe2+ of both reduced and unreduced samples were determined to be 5.35 +/- 0.15 Bohr magnetons. This shows, in agreement with previous findings, that Fe2+ does not change its valence state when the reaction centers are reduced. Typical values of D congruent to +5 cm-1 and E/D congruent to 0.27 are consistent with Fe being in an octahedral environment with rhombic distortion. The values of D and E were approximately the same for reaction centers having one and two quinones. These findings imply that quinone is most likely not a ligand of Fe. The Fe2+ and the spin on the quinone in reduced reaction centers were found to be coupled with an exchange interaction 0 less than /J/ less than 1 cm-1. The validity of the spin Hamiltonian was checked by using an orbital Hamiltonian to calculate energy levels of the 25 states of the S = 2, L = 2 manifold and comparing the magnetization of the lowest five states with those obtained from the spin Hamiltonian. Using the orbital Hamiltonian, we calculated the position of the first excited quintet state to be 340 cm-1 above the ground state quintet. This is in good agreement with the temperature dependence of the quadrupole splitting as determined by Mossbauer spectroscopy.

Bacterial Proteins↗
PubMed2006

Electronic structures of size-selected single-layered platinum clusters on silicon(111)-7x7 surface at a single cluster level by tunneling spectroscopy.

Tunneling spectra of size-selected single-layered platinum clusters (size range of 5-40) deposited on a silicon(111)-7x7 surface were measured individually at a temperature of 77 K by means of a scanning tunneling microscope (STM), and the local electronic densities of states of individual clusters were derived from their tunneling spectra measured by placing an STM tip on the clusters. In a bias-voltage (V(s)) range from -3 to 3 V, each tunneling spectrum exhibits several peaks assignable to electronic states associated with 5d states of a constituent platinum atom and an energy gap of 0.1-0.6 eV in the vicinity of V(s)=0. Even when platinum cluster ions having the same size were deposited on the silicon(111)-7x7 surface, the tunneling spectra and the energy gaps of the deposited clusters are not all the same but can be classified in shape into several different groups; this finding is consistent with the observation of the geometrical structures of platinum clusters on the silicon(111)-7x7 surface. The mean energy gap of approximately 0.4 eV drops to approximately 0.25 eV at the size of 20 and then decreases gradually as the size increases, consistent with our previous finding that the cluster diameter remains unchanged, but the number density of Pt atoms increases below the size of 20 while the diameter increases, but the density does not change above it. It is concluded that the mean energy gap tends to decrease gradually with the mean cluster diameter. The dependence of the mean energy gap on the mean Pt-Pt distance shows that the mean energy gap decreases sharply when the mean Pt-Pt distance exceeds that of a platinum metal (0.28 nm).

Journal Article↗
PubMed2005

Synthesis and reaction of [[HC(CMeNAr)2]Mn]2 (Ar = 2,6-iPr2C6H3): the complex containing three-coordinate manganese(I) with a Mn-Mn bond exhibiting unusual magnetic properties and electronic structure.

This paper reports on the synthesis, X-ray structure, magnetic properties, and DFT calculations of [[HC(CMeNAr)2]Mn]2 (Ar = 2,6-iPr2C6H3) (2), the first complex with three-coordinate manganese(I). Reduction of the iodide [[HC(CMeNAr)2]Mn(mu-I)]2 (1) with Na/K in toluene afforded 2 as dark-red crystals. The molecule of 2 contains a Mn2(2+) core with a Mn-Mn bond. The magnetic investigations show a rare example of a high-spin manganese(I) complex with an antiferromagnetic interaction between the two Mn(I) centers. The DFT calculations indicate a strong s-s interaction of the two Mn(I) ions with the open shell configuration (3d54s1). This suggests that the magnetic behavior of 2 could be correctly described as the coupling between two S1 = S2 = 5/2 spin centers. The Mn-Mn bond energy is estimated at 44 kcal mol(-1) by first principle calculations with the B3LYP functional. The further oxidative reaction of 2 with KMnO4 or O2 resulted in the formation of manganese(III) oxide [[HC(CMeNAr)2]Mn(mu-O)]2 (3). Compound 3 shows an antiferromagnetic coupling between the two oxo-bridged manganese(III) centers by magnetic measurements.

Crystallography, X-Ray↗
PubMed2001

The symmetry-broken formalism applied to the electronic structure of an iminosemiquinone copper(II) catalyst: a key to the qualitative understanding of its reactivity.

A concise outline of the known derivation of the singlet-triplet energy-gap equations within the symmetry-broken wavefunction framework is given. They allow a computation of the singlet-triplet energy gap for molecules that exhibit a weak antiferromagnetic coupling of electrons. The accuracy of the equations is assessed by computation of the singlet-triplet gaps in model Na2 molecules. Various antiferromagnetic coupling strengths are simulated by the use of different Na-Na bond lengths in the computations. The singlet-triplet energy gaps obtained with the different equations are compared with the gaps computed with the more accurate coupled-cluster methods. Subsequently, the equations are applied to an iminosemiquinone copper(II) complex found previously to have remarkable catalytic properties. The application is performed by employing wave-function equations but with quantities computed within the density functional framework. The electronic ground state of this complex is computed to be a singlet state, which is also the experimental finding. Moreover, the experimental geometry and the singlet-triplet gap are reasonably reproduced by the computation. A straightforward method to determine the magnetic orbitals is suggested and applied. We illustrate that the form of the magnetic orbitals indicates in a qualitative manner that hydrogen-atom abstraction should be a major reaction pathway of the iminosemiquinone copper(II) complex. Hydrogen-atom abstraction has been suggested previously to be the rate-determining step in a catalytic process initiated by the iminosemiquinone copper(II) complex. The results support the notion that the form of the magnetic orbitals might be a qualitative indicator for the reactivity of molecules that exhibit weak antiferromagnetic coupling.

Journal Article↗
PubMed2006

Electronic structure studies of tetrazolium-based ionic liquids.

New energetic ionic liquids are investigated as potential high energy density materials. Ionic liquids are composed of large, charge-diffuse cations, coupled with various (usually oxygen containing) anions. In this work, calculations have been performed on the tetrazolium cation with a variety of substituents. Density functional theory (DFT) with the B3LYP functional, using the 6-311G(d,p) basis set was used to optimize geometries. Improved treatment of dynamic electron correlation was obtained using second-order perturbation theory (MP2). Heats of formation of the cation with different substituent groups were calculated using isodesmic reactions and Gaussian-2 calculations on the reactants. The cation was paired with oxygen rich anions ClO4-, NO3-, or N(NO2)2- and those structures were optimized using both DFT and MP2. The reaction pathway for proton transfer from the cation to the anion was investigated.

Journal Article↗
PubMed2006

Spectroscopic and electronic structure studies of the role of active site interactions in the decarboxylation reaction of alpha-keto acid-dependent dioxygenases.

The alpha-ketoglutate (alpha-KG)-dependent dioxygenases are a large class of mononuclear non-heme iron enzymes that require Fe(II), alpha-KG and dioxygen for catalysis, with the alpha-KG cosubstrate supplying the two additional electrons required for dioxygen activation. A sub-class of these enzymes exists in which the alpha-keto acid is covalently attached to the substrate, including (4-hydroxy)mandelate synthase (HmaS) and (4-hydroxyphenyl)pyruvate dioxygenase (HPPD) which utilize the same substrate but exhibit two different general reactivities (H-atom abstraction and electrophilic attack). Previous kinetic studies of Streptomyces avermitilis HPPD have shown that the substrate analog phenylpyruvate (PPA), which only differs from the normal substrate (4-hydroxyphenyl)pyruvate (HPP) by the absence of a para-hydroxyl group on the aromatic ring, does not induce a reaction with dioxygen. While an Fe(IV)O intermediate is proposed to be the reactive species in converting substrate to product, the key step utilizing O(2) to generate this species is the decarboxylation of the alpha-keto acid. It has been generally proposed that the two requirements for decarboxylation are bidentate coordination of the alpha-keto acid to Fe(II) and the presence of a 5C Fe(II) site for the O(2) reaction. Circular dichroism and magnetic circular dichroism studies have been performed and indicate that both enzyme complexes with PPA are similar with bidentate alpha-KG coordination and a 5C Fe(II) site. However, kinetic studies indicate that while HmaS reacts with PPA in a coupled reaction similar to the reaction with HPP, HPPD reacts with PPA in an uncoupled reaction at an approximately 10(5)-fold decreased rate compared to the reaction with HPP. A key difference is spectroscopically observed in the n-->pi( *) transition of the HPPD/Fe(II)/PPA complex which, based upon correlation to density functional theory calculations, is suggested to result from H-bonding between a nearby residue and the carboxylate group of the alpha-keto acid. Such an interaction would disfavor the decarboxylation reaction by stabilizing electron density on the carboxylate group such that the oxidative cleavage to yield CO(2) is disfavored.

3-Methyl-2-Oxobutanoate Dehydrogenase (Lipoamide)↗
PubMed1996

Synthetic, X-ray Structure, Electron Paramagnetic Resonance, and Magnetic Studies of the Manganese(II) Complex of 1-Thia-4,7-diazacyclononane ([9]aneN(2)S).

Reaction of manganese(II) perchlorate hexahydrate with a methanol solution of 1-thia-4,7-diazacyclononane ([9]aneN(2)S) resulted in the isolation of the manganese(II) complex [Mn([9]aneN(2)S)(2)](ClO(4))(2). The X-ray structure of this complex is reported: crystal system orthorhombic, space group Pbam, No. 55, a = 7.937(2) Å,b = 8.811(2) Å, c = 15.531(3) Å, Z = 2, R = 0.0579. The complex is high spin (S = (5)/(2)) with an effective magnetic moment (&mgr;(eff)) 5.82 &mgr;(B) at 298 K and 5.65 &mgr;(B) at 4.2 K. Computer simulation of the Q-band EPR spectrum of [Mn([9]aneN(2)S)(2)](ClO(4))(2) yields g = 1.99 +/- 0.01, |D| = 0.19 +/- 0.005 cm(-)(1), and E/D = 0.04 +/- 0.02. For the analogous hexaamine complex [Mn([9]aneN(3))(2)](ClO(4))(2) ([9]aneN(3) = 1,4,7-triazacyclononane) analysis of the EPR spectra produced the following values: g = 1.98 +/- 0.01, |D| = 0.09 +/- 0.003 cm(-)(1), and E/D = 0.1 +/- 0.01. The spin Hamiltonian parameters for [Mn([9]aneN(2)S)(2)](ClO(4))(2) derived from the EPR spectra produced a good fit to the magnetic susceptibility data.

Journal Article↗
PubMed2002

Electronic structure of high-valent transition metal corrolazine complexes. The young and innocent?

This is a first quantum chemical study of corrolazine complexes. DFT calculations suggest that despite their extremely contracted central cavities, compared with porphyrins, a variety of corrolazine complexes may be expected to exist as stable compounds. The calculations also indicate that corrolazine complexes may be regarded as strongly electron-deficient analogues of corrole complexes. Thus, the calculated valence ionization potentials of P(V) and Cu(III) corrolazine derivatives are dramatically higher than those of analogous corrole derivatives. In addition, DFT calculations on Fe(IV) and Mn(IV) corrole and corrolazine derivatives suggest that compared with the often noninnocent corrole ligands, corrolazines are electronically more innocent and stabilize "purer" high-valent states of transition metal ions.

Journal Article↗
PubMed2003

Comparison of the electronic structures of imine and hydrazone side-chain functionalities with the aid of 13C and 15N NMR chemical shifts and PM3 calculations. The influence of C=N-substitution on the sensitivity to aromatic substitution.

Benzaldehyde derivatives possessing a C=N double bond in the side-chain of the aromatic ring exhibit a reverse dependence of the (13)C NMR chemical shifts of the C=N carbon on the benzylidenic substituents X. Thus, electron-withdrawing substituents cause shielding (shift is reduced), while electron-donating ones cause deshielding. The origin of this phenomenon, which is in contrast with the idea of the generalized electronic effect, is extensively studied here by comparing the behavior of sets of benzaldehyde derivatives bearing various substitutents Y on the C=N nitrogen (Y-N=CH-C(6)H(4)-X). The effects of substituents X on the C=N unit change when Y is varied. Combination of the influences of the substituents X and Y gives a sensitive balance between the different resonance structures of the compounds. Our graphical treatment, where the rho(I) and rho(R) values observed for substituent X are plotted against the sigma(p)(+) value of substituent Y, is a novel use of Hammett-type substituent parameters. The justification of this method and our conclusions could be verified, for instance, by the fair correlation between the rho(I) or rho(R) values and the atomic charges of the imine carbon of the unsubstitued phenyl derivatives as well as by the correlations of the relevant bond orders and/or bond lengths both with the substituent parameters and with the atomic charges.

Journal Article↗
PubMed2004

Electronic structure of the water-oxidation catalyst [(bpy)2(OHx)RuORu(OHy)(bpy)2]z+: weak coupling between the metal centers is preferred over strong coupling.

High-level DFT calculations indicate that the singlet ground state of the water-oxidizing blue Ru dimer [(bpy)2(OH2)RuIIIORuIII(OH2)(bpy)2]4+ is not due to a strong coupling of the excess electrons from each of the low-spin d5 RuIII centers across the Ru-O-Ru moiety, as has been assumed to date. Instead, broken symmetry orbital calculations suggest that a weak antiferromagnetically (AF) coupled singlet state is energetically more favorable by 10-35 kcal/mol. Experimentally observed redox potentials can only be reproduced if antiferromagnetic coupling is invoked.

Journal Article↗
PubMed2003

Iron nitrosyls of a pentadentate ligand containing a single carboxamide group: syntheses, structures, electronic properties, and photolability of NO.

Three iron complexes of a pentadentate ligand N,N-bis(2-pyridylmethyl)amine-N-ethyl-2-pyridine-2-carboxamide (PaPy(3)H, H is the dissociable amide proton) have been synthesized. All three species, namely, two nitrosyls [(PaPy(3))Fe(NO)](ClO(4))(2) (2) and [(PaPy(3))Fe(NO)](ClO(4)) (3) and one nitro complex [(PaPy(3))Fe(NO(2))](ClO(4)) (4), have been structurally characterized. These complexes provide the opportunity to compare the structural and spectral properties of a set of isostructural [Fe-NO](6,7) complexes (2 and 3, respectively) and an analogous genuine Fe(III) complex with an "innocent" sixth ligand ([(PaPy(3))Fe(NO(2))](ClO(4)), 4). The most striking difference in the structural features of 2 and 3 is the Fe-N-O angle (Fe-N-O = 173.1(2) degrees in the case of 2 and 141.29(15) degrees in the case of 3). The clean (1)H NMR spectrum of 2 in CD(3)CN reveals its S = 0 ground state and confirms its [Fe-NO](6) configuration. The binding of NO at the non-heme iron center in 2 is completely reversible and the bound NO is photolabile. Mössbauer data, electron paramagnetic resonance signal at g approximately 2.00, and variable temperature magnetic susceptibility measurements indicate the S = (1)/(2) spin state of the [Fe-NO](7) complex 3. Analysis of the spectroscopic data suggests Fe(II)-NO(+) and Fe(II)-NO(*) formulations for 2 and 3, respectively. The bound NO in 3 does not show any photolability. However, in MeCN solution, it reacts rapidly with dioxygen to afford the nitro complex 4, which has also been synthesized independently from [(PaPy(3))Fe(MeCN)](2+) and NO(2)(-). Nucleophilic attack of hydroxide ion to the N atom of the NO ligand in 2 in MeCN in the dark gives rise to 4 in high yield.

Amides↗
PubMed2004

Accurate redetermination of the X-ray structure and electronic bonding in adenosylcobalamin.

The electronic structure of adenosylcobalamin (B12 coenzyme, AdoCbl) has been calculated by a density functional method, using the orthogonalized linear combination of the atomic orbital method (OLCAO). Since a fixed accurately determined geometry was needed in such calculations, the crystal structure of adenosylcobalamin has been redone and refined to R = 0.065, using synchrotron diffraction data. Comparison with the recently reported electronic structures of cyano- (CNCbl) and methylcobalamin (MeCbl) shows that the net charges and bond orders vary only on the axial donors. The values in the three cobalamins suggest that the Co-C bond in MeCbl has a strength similar to that in AdoCbl, but it is significantly weaker that that in CNCbl. Present results are compared with those previously reported for the analogous corrin derivatives; i.e., simplified cobalamins with the side chains a-f replaced by H atoms. Despite a qualitative agreement, a discrepancy in the calculated HOMO-LUMO gap is found.

Cobamides↗
PubMed2005

Importance of cations in the properties of Zintl phases: the electronic structure of and bonding in metallic Na6TlSb41.

The novel metallic compound Na(6)TlSb(4) consists of four-membered TlSb(3) rings joined by pairs of Sb atoms into Tl(2)Sb(8) units, the last of which is further interconnected into 1D anionic chains via Tl-Tl bonds. The contrast of its metallic conductivity with that of the 2 - e(-) poorer, electron precise, and semiconducting Zintl phase K(6)Tl(2)Sb(3), which has virtually the same anionic network, has been investigated by ab initio LMTO-DFT methods. Sodium ion participation is found to be appreciable in the (largely) Sb p valence band and especially significant in an additional low-lying conduction band generated by antimony ppi and sodium orbitals. The one pyramidal 3-bonded Sb atom appears to be largely responsible for the interchain conduction process. The substitution of one Tl by Sb, which occurs when the countercation is changed from potassium in K(6)Tl(2)Sb(3) to sodium, yielding only Na(6)TlSb(4), is driven by a distinctly tighter packing, a corresponding increase in the Madelung energy, and binding of the excess pair of electrons in the new conduction band.

Journal Article↗
PubMed2006

Photodissociation of HBr. 1. Electronic structure, photodissociation dynamics, and vector correlation coefficients.

Ab initio potential energy curves, transition dipole moments, and spin-orbit coupling matrix elements are computed for HBr. These are then used, within the framework of time-dependent quantum-mechanical wave-packet calculations, to study the photodissociation dynamics of the molecule. Total and partial integral cross sections, the branching fraction for the formation of excited-state bromine atoms Br(2P(1/2)), and the lowest order anisotropy parameters, beta, for both ground and excited-state bromine are calculated as a function of photolysis energy and compared to experimental and theoretical data determined previously. Higher order anisotropy parameters are computed for the first time for HBr and compared to recent experimental measurements. A new expression for the Re[a1(3) (parallel, perpendicular)] parameter describing coherent parallel and perpendicular production of ground-state bromine in terms of the dynamical functions is given. Although good agreement is obtained between the theoretical predictions and the experimental measurements, the discrepancies are analyzed to establish how improvements might be achieved. Insight is obtained into the nonadiabatic dynamics by comparing the results of diabatic and fully adiabatic calculations.

Anisotropy↗
PubMed2003

Gold nanoparticles deposited on SiO2/Si100: correlation between size, electron structure, and activity in CO oxidation.

Nanosize gold particles were prepared by Ar(+) ion implantation of 10-nm thick gold film deposited onto a SiO(2)/Si(100) wafer possessing no catalytic activity in the CO oxidation. Along with size reduction the valence band of the gold particles and the actual size were determined by ultraviolet- and X-ray photoelectron spectroscopy (UPS, XPS) and by transmission electron microscopy (TEM) as well as atomic force microscopy (AFM), respectively. The catalytic activity was determined in the CO oxidation. Energy distribution of the photoelectrons excited from 5d valence band of gold was strongly affected by Ar(+) implantation. This variation was interpreted by the redistribution of the valence band density of states (DOS). The intrinsic catalytic activity of the gold particles increased with decreasing size. When an Au/FeO(x) interface was created by FeO(x) deposition on large gold nanoparticles, a significant increase in the rate of the CO oxidation was observed. These data can be regarded as an experimental verification of the correlation between the catalytic activity and valence band density of states of gold.

Journal Article↗