G-tensors of the flavin adenine dinucleotide radicals in glucose oxidase: a comparative multifrequency electron paramagnetic resonance and electron-nuclear double resonance study

The flavin adenine dinucleotide (FAD) cofactor of Aspergillus niger glucose oxidase (GO) in its anionic (FAD*-) and neutral (FADH*) radical form was investigated by electron paramagnetic resonance (EPR) at high microwave frequencies (93.9 and 360 GHz) and correspondingly high magnetic fields and by pulsed electron-nuclear double resonance (ENDOR) spectroscopy at 9.7 GHz. Because of the high spectral resolution of the frozen-solution continuous-wave EPR spectrum recorded at 360 GHz, the anisotropy of the g-tensor of FAD*- could be fully resolved. By least-squares fittings of spectral simulations to experimental data, the principal values of g have been established with high precision: gX=2.00429(3), gY=2.00389(3), gZ=2.00216(3) (X, Y, and Z are the principal axes of g) yielding giso=2.00345(3). The gY-component of FAD*- from GO is moderately shifted upon deprotonation of FADH*, rendering the g-tensor of FAD*- slightly more axially symmetric as compared to that of FADH*. In contrast, significantly altered proton hyperfine couplings were observed by ENDOR upon transforming the neutral FADH* radical into the anionic FAD*- radical by pH titration of GO. That the g-principal values of both protonation forms remain largely identical demonstrates the robustness of g against local changes in the electron-spin density distribution of flavins. Thus, in flavins, the g-tensor reflects more global changes in the electronic structure and, therefore, appears to be ideally suited to identify chemically different flavin radicals.     

Infrared spectroscopic and density functional theory studies on the reactions of cadmium atoms with carbon monoxide in solid argon

Reactions of laser-ablated cadmium atoms with carbon monoxide molecules in solid argon have been investigated using matrix isolation infrared spectroscopy. On the basis of isotopic substitution, the absorption at 1858.2 cm(-1) is assigned to the C-O stretching of the CdCO molecule, which is formed during the sample deposition. Cadmium di- and tricarbonyls, Cd(CO)n (n = 2, 3), have not been observed under the same experimental conditions. Density functional theory calculations have been performed on the cadmium carbonyls Cd(CO)n (n = 1-3), which lend strong support to the experimental assignments of the infrared spectra. It is predicted that the CdCO molecule is a linear triplet molecule and its formation involves Cd 5s --> 5p promotion. This promotion increases the Cd-CO bonding by decreasing the sigma repulsion and increasing the Cd 5p orbital --> CO pi back-donation. The absence of cadmium di- and tricarbonyls, Cd(CO)n (n = 2, 3), has also been discussed in some detail.     

Structures and energetics of Be(n)Si(n) and Be(2n)Si(n) (n = 1-4) clusters

The structures and energies of Be(n)Si(n) and Be(2n)Si(n) (n = 1-4) clusters have been examined in ab initio theoretical electronic structure calculations. Cluster geometries have been established in B3LYP/6-31G(2df) calculations and accurate relative energies determined by the G3XMP2 method. The two atoms readily bond to each other and to other atoms of their own kind. The result is a great variety of low-energy clusters in a variety of structural types.     

Reactions of germanium atoms and small clusters with CO: experimental and theoretical characterization of Ge(n)CO (n = 1-5) and Ge2(CO)2 in solid argon

Reactions of germanium atoms and small clusters with carbon monoxide molecules in solid argon have been studied using matrix isolation infrared absorption spectroscopy. Besides the previously reported GeCO monocarbonyl, the Ge2(CO)2 and Ge(n)CO (n = 2-5) carbonyl molecules are formed spontaneously on annealing and are characterized on the basis of isotopic substitution and theoretical calculations. It is found that Ge2CO, Ge3CO, and Ge5CO are bridge-bonded carbonyl compounds, whereas Ge2(CO)2 and Ge4CO are terminal-bonded carbonyl molecules.     

Infrared photodissociation spectroscopy of Na(NH3)n clusters: probing the solvent coordination

The first mass-selective vibrational spectra have been recorded for Na(NH3)n clusters. Infrared spectra have been obtained for n = 3-8 in the N-H stretching region. The spectroscopic work has been supported by ab initio calculations carried out at both the DFT(B3LYP) and MP2 levels, using a 6-311++G(d,p) basis set. The calculations reveal that the lowest energy isomer for n or= 7 is indicative of molecules entering a second solvation shell, i.e., the inner solvation shell around the sodium atom can accommodate a maximum of six NH3 molecules.     

Reactions of silicon atoms and small clusters with CO: experimental and theoretical characterization of SinCO (n=1-5), Si2(CO)2, c-Si2(mu-O)(mu-CSi), and c-Si2(mu-O)(mu-CCO) in solid argon

Reactions of silicon atoms and small clusters with carbon monoxide molecules in solid argon have been studied using matrix isolation infrared absorption spectroscopy. In addition to the previously reported SiCO monocarbonyl, Si(2)(CO)(2) and Si(n)CO (n=2-5) carbonyl molecules were formed spontaneously on annealing and were characterized on the basis of isotopic substitution and theoretical calculations. It was found that Si(2)CO, Si(3)CO, and Si(5)CO are bridge-bonded carbonyl compounds, whereas Si(4)CO is a terminal-bonded carbonyl molecule. The Si(2)(CO)(2) and Si(3)CO molecules photochemically rearranged to the more stable c-Si(2)(mu-O)(mu-CCO) and c-Si(2)(mu-O) (mu-CSi) isomers where Si(2) is inserted into the CO triple bond.     

Infrared spectra of the (AgCO)2 and AgnCO (n=2-4) molecules in rare-gas matrices

Reactions of laser-ablated silver atoms with carbon monoxide molecules in solid argon and neon have been investigated using matrix-isolation IR spectroscopy. Small silver cluster carbonyls, (AgCO)2 and AgnCO (n=2-4), as well as mononuclear silver carbonyls, Ag(CO)2 and Ag(CO)3, are generated upon sample annealing in the argon experiments and are characterized on the basis of the isotopic substitution, the CO concentration change, and the comparison with theoretical predictions. However, these polynuclear carbonyls are absent from the neon experiments. Density functional theory calculations have been performed on these silver carbonyls and the corresponding ligand-free silver clusters, which support the identification of these silver carbonyls from the matrix IRspectrum. A terminal CO has been found in the most stable structures of (AgCO)2, Ag2CO, Ag3CO, and Ag4CO. Furthermore, a plausible reaction mechanism has been proposed to account for the formation of the (AgCO)2 and AgnCO (n=2-4) molecules.     

Theoretical study of stratospheric relevant anions: nitrate-nitric acid complexes

The ion complexes NO3-(HNO3)n, n = 1-3, have been studied by means of ab initio calculations at the B3LYP/aug-cc-pVTZ level of theory. These systems are the most abundant anionic clusters below approximately 30 km altitude in the stratosphere and also in the upper troposphere. These complexes display short strong hydrogen bonds, which should be considered to explain their abundance in the atmosphere. Equilibrium geometries, harmonic frequencies, relative energies, and thermochemical data have been calculated for these anions for the first time. The calculations indicate small differences of energy in the variation of the two nitrate groups from planarity to an almost perpendicular form for n = 1. Planar geometries are found for n = 2 and 3 to give rise to a highly symmetric C(3h) NO3-(HNO3)3. In all the cases, binding energies close to those of covalent compounds are estimated. When experimental data are available, good correlations are found with our results.     

Improper or classical hydrogen bonding? A comparative cryosolutions infrared study of the complexes of HCClF(2), HCCl(2)F,and HCCl(3) with dimethyl ether

Complexes of haloforms of the type HCCl(n)F(3-)(n) (n = 1-3) with dimethyl ether have been studied in liquid argon and liquid krypton, using infrared spectroscopy. For the haloform C[bond]H stretching mode, the complexation causes blue shifts of 10.6 and 4.8 cm(-1) for HCClF(2) and HCCl(2)F, respectively, while for HCCl(3) a red shift of 8.3 cm(-1) is observed. The ratio of the band areas of the haloform C[bond]H stretching in complex and monomer was determined to be 0.86(4) for HCClF(2), 33(3) for HCCl(2)F, and 56(3) for HCCl(3). These observations, combined with those for the HCF(3) complex with the same ether (J. Am. Chem. Soc. 2001, 123, 12290), have been analyzed using ab initio calculations at the MP2[double bond]FC/6-31G(d) level, and using some recent models for improper hydrogen bonding. Ab initio calculations on the haloforms embedded in a homogeneous electric field to model the influence of the ether suggest that the complexation shift of the haloform C[bond]H stretching is largely explained by the electric field effect induced by the electron donor in the proton donor. The model calculations also show that the electric field effect accounts for the observed intensity changes of the haloform C[bond]H stretches.     

Effects of chain length and Au spin-orbit coupling on 3(pi pi*) emission from bridging Cn2- units: theoretical characterization of spin-forbidden radiative transitions in metal-capped one-dimensional carbon chains [H3PAu(C[triple bond]C)nAuPH3

Density functional theory and CASSCF calculations have been used to optimize the geometries of binuclear gold(I) complexes [H(3)PAu(C[triple bond]C)(n)AuPH(3)] (n=1-6) in their ground states and selected lowest energy (3)(pi pi*) excited states. Vertical excitation energies obtained by time-dependent density functional calculations for the spin-forbidden singlet-triplet transitions have exponential-decay size dependence. The predicted singlet-triplet splitting limit of [H(3)PAu(C[triple bond]C)(proportional/variant)AuPH(3)] is about 8317 cm(-1). Calculated singlet-triplet transition energies are in reasonable agreement with available experimental observations. The effect of the heavy atom Au spin-orbit coupling on the (3)(pi pi*) emission of these metal-capped one-dimensional carbon allotropes has been investigated by MRCI calculations. The contribution of the spin- and dipole-allowed singlet excited state to the spin-orbit-coupling wave function of the (3)(pi pi*) excited state makes the low-lying acetylenic triplet excited states become sufficiently allowed so as to appear in both electronic absorption and emission.     

Structures and magnetic properties of CrSi(n) (-) (n = 3-12) clusters: Photoelectron spectroscopy and density functional calculations

Chromium-doped silicon clusters, CrSi(n) (-)(n = 3-12), were investigated with anion photoelectron spectroscopy and density functional theory calculations. The combination of experimental measurement and theoretical calculations reveals that the onset of endohedral structure in CrSi(n) (-) clusters occurs at n = 10 and the magnetic properties of the CrSi(n) (-) clusters are correlated to their geometric structures. The most stable isomers of CrSi(n) (-) from n = 3 to 9 have exohedral structures with magnetic moments of 3-5μ(B) while those of CrSi(10) (-), CrSi(11) (-), and CrSi(12) (-) have endohedral structures and magnetic moments of 1μ(B.).     

Determination of the distance between the two neutral flavin radicals in augmenter of liver regeneration by pulsed ELDOR

Pulsed electron-electron double resonance (ELDOR) has been used to obtain structural information from a FAD-dependent sulfhydryl oxidase, Augmenter of Liver Regeneration (ALR). ALR is a homodimer with each subunit containing a noncovalently bound FAD cofactor. Both FADs may be converted into the blue neutral radical form by aerobic treatment with DTT. From three-pulse and four-pulse ELDOR experiments, a distance of 26.1 +/- 0.8 A could be determined between the FAD cofactors in human ALR. Taking into account the electron spin density distribution in a neutral flavin radical obtained from density functional theory calculations, a distance of 26.9 A could be estimated for the separation of the spin centers in the X-ray structure of rat ALR. The good agreement confirms that rat ALR may be used as a model for mechanistic discussions of human ALR. The experiments also demonstrate that neutral flavin radicals have the appropriate properties to be used as intrinsic spin labels for distance determinations in proteins.     

Mixed uranium chloride fluorides UF6-nCln and methoxyuranium fluorides UF6-n(OCH3)n: a theoretical study of equilibrium geometries,vibrational frequencies,and the role of the f orbitals

The title compounds, the uranium (VI) fluoride chlorides (UF6-nCln, n = 0-6) and methoxyuranium (VI) fluorides [UF6-n(OCH3)n, n = 0-5], have been studied using relativistic density functional theory. Applying the B3LYP hybrid functional and an effective core potential on uranium, equilibrium geometries have been calculated for these molecules. In addition, harmonic vibrational frequencies have been computed for the chloride fluorides. Calculated frequencies have been compared to experiment where possible. All experimentally observed bands have been assigned, based on these calculations. The average deviation between theoretical and experimental frequencies is 15.6 cm-1 for 23 experimental modes. Theory always underestimates the experimental frequencies. This can be explained by the calculated bond lengths that are somewhat too long. The electronic structure of the uranium (VI) chloride fluorides has been investigated using scalar relativistic calculations and the PW91 functional. Periodic trends in the role and bonding contribution of the uranium 5f orbitals are discussed.     

Electronic spectroscopy of UO2 isolated in a solid Ar matrix

Dispersed fluorescence spectra have been recorded for UO(2) isolated in a solid Ar matrix. Near UV excitation produced groups of emission bands in the 370-420 and 465-645 nm spectral regions. These bands originated from two energetically close upper levels and terminated on a range of low-lying electronic states. Comparisons with electronic structure calculations indicate that the ground and low-lying electronic states of UO(2) are derived from the U(5f7s) configuration. The level of agreement between the observed and predicted electronic energies provides an impressive validation of the calculations. In previous studies of matrix isolated UO(2), it had been suggested that the ground state in solid Ar is U(5f(2)) (3)H. The present results do not appear to be consistent with this hypothesis.     

Theoretical study of the electronic states of Nb4, Nb5 clusters and their anions (Nb4-,Nb5-)

Geometries and energy separations of the various low-lying electronic states of Nb(n) and Nb(n) (-) (n=4,5) clusters with various structural arrangements have been investigated. The complete active space multiconfiguration self-consistent field method followed by multireference singles and doubles configuration interaction (MRSDCI) calculations that included up to 52x10(6) configuration spin functions have been used to compute several electronic states of these clusters. The ground states of both Nb(4) ((1)A('), pyramidal) and Nb(4) (-) ((2)B(3g), rhombus) are low-spin states at the MRSDCI level. The ground state of Nb(5) cluster is a doublet with a distorted trigonal bipyramid (DTB) structure. The anionic cluster of Nb(5) has two competitive ground states with singlet and triplet multiplicities (DTB). The low-lying electronic states of these clusters have been found to be distorted due to Jahn-Teller effect. On the basis of the energy separations of our computed electronic states of Nb(4) and Nb(5), we have assigned the observed photoelectron spectrum of Nb(n) (-) (n=4,5) clusters. We have also compared our MRSDCI results with density functional calculations. The electron affinity, ionization potential, dissociation and atomization energies of Nb(4) and Nb(5) have been calculated and the results have been found to be in excellent agreement with the experiment.     

Characterization of three members of the electron-transfer series [Fe(pda)2]n (n=2-, 1-, 0) by spectroscopy and density functional theoretical calculations [pda=redox non-innocent derivatives of N,N'-bis(pentafluorophenyl)-o-phenylenediamide(2-, 1.-, 0)

The four-coordinate iron complexes, [Fe(III)(pda(2-))(pda(.-))] (1) and [AsPh(4)](2)[Fe(II)(pda(2-))(2)] (2) were synthesized and fully characterized; pda(2-) is the closed-shell ligand N,N'-bis(pentafluorophenyl)-o-phenylenediamido(2-), and pda(.-) represents its one-electron-oxidized pi-radical anion. Single-crystal X-ray diffraction studies of 1 and 2 performed at 100(2) K reveal a distorted tetrahedral coordination environment at the iron centers, as a result of the intramolecular pi-pi interactions between C(6)F(5) rings. The electronic structures of 1 and 2 were unambiguously determined by a combination of (57)Fe M?ssbauer and electronic spectroscopy, magnetic susceptibility measurements, X-ray crystallography, and DFT calculations. Compound 1 contains an intermediate-spin Fe(III) ion (S(Fe)=3/2) strongly antiferromagnetically coupled to a pi-ligand radical (S(R)=1/2) yielding an S(t)=1 ground state. Complex 2 possesses a high-spin Fe(II) center (S(Fe)=2) with two closed-shell dianionic ligands. Complexes 1 and 2 are members of the redox series [Fe(pda)(2)](n) with n=0 for 1 and n=2- for 2. The anion n=1- has been reported previously in the coordination salt [Fe(dad)(3)][Fe(pda)(2)] (3; dad=N,N'-bis(phenyl)-2,3-dimethyl-1,4-diaza-1,3-butadiene). A complicated temperature-dependent electronic structure has been observed for this salt. Here, DFT calculations performed on 3 confirm the previous assignments of spin- and oxidation-states. Thus, [Fe(pda)(2)](n) (n=0, 1-, 2-) constitutes an electron-transfer series, which has also been established by cyclic voltammetry; the mono- and dications (n=1+ and 2+) are also accessible in solution, but have not been further investigated. The (57)Fe M?ssbauer spectra of [Fe(pda)(2)](n) species in 1 and 3 show extremely large quadrupole splitting constants due to addition of the valence and covalence contributions that have been confirmed by DFT calculations.     

Reactivity of atomic gold anions toward oxygen and the oxidation of CO: experiment and theory

Results for the binding of carbon monoxide and oxygen along with the oxidation of CO in the presence of atomic Au(-) have been obtained utilizing a fast-flow reactor mass spectrometer. In addition, density functional calculations have been performed to explain the experimental findings. It was observed that upon oxygen addition to the metal plasma, gold oxide species of the form AuO(n)(-), where n = 1-3, were produced. The addition of carbon monoxide to the preoxidized gold atom revealed that AuO(-) and AuO(3)(-) promote the oxidation of CO. Density functional calculations on structures and their energetics confirmed the experimental findings and allowed us to propose mechanisms for the oxidation of carbon monoxide. The reactions of CO with AuO(1,3)(-) proceed via complex formation with CO bound to the oxygen atom, followed by either cleavage of the Au-O bond or complex rearrangement to form a weakly bound CO(2) unit, leading in both cases to the emanation of CO(2).     

CH···O interaction lowers hydrogen transfer barrier to keto-enol tautomerization of β-cyclohexanedione: combined infrared spectroscopic and electronic structure calculation study

Molecular association and keto-enol tautomerization of β-cyclohexanedione (β-CHD) have been investigated in argon matrix and also in a thin solid film prepared by depositing pure β-CHD vapor on a cold (8 K) KBr window. Infrared spectra reveal that, in low-pressure vapor and argon matrix, the molecules are exclusively in diketo tautomeric form. The CH···O hydrogen bonded dimers of the diketo tautomer are produced by annealing the matrix at 28 K. No indication is found for keto-enol tautomerization of β-CHD in dimeric complexes in argon matrix within the temperature range of 8-28 K. On the other hand, in thin film of pure diketo tautomer, the conversion initiates only when the film is heated at temperatures above 165 K. The observed threshold appears to be associated with excitation of the intermolecular modes, and the IR spectra recorded at high temperatures display narrowing of vibrational bandwidths, which has been associated with reorientations of the molecules in the film. The nonoccurrence of tautomerization of the matrix isolated dimer is consistent with the barrier predicted by electronic structure calculations at B3LYP/6-311++G** and MP2/6-311++G** levels of theory. The transition state calculation predicts that CH···O interaction has a dramatic effect on lowering of the tautomerization barrier, from more than 60 kcal/mol for the bare molecule to ~35-45 kcal/mol for dimers.     

Molecular dynamics simulation study on stabilities and reactivities of NADH cytochrome B5 reductase

Binding free energies between coenzyme (FAD and NADH) and the apoenzyme of NADH-cytochrome b5 reductase (b5R) were estimated by applying the continuum Poisson-Boltzmann (PB) model to structures sampled from molecular dynamics simulations in explicit water molecules. Important residues for the enzymatic catalysis were clarified using a computational alanine scanning method. The binding free energies calculated by applying an alanine scanning method can successfully reproduce the trends of the measured steady-state enzymatic activities kcatNADH/KmNADH. Significant decreases in the binding free energy are expected when one of the four residues Arg91, Lys110, Ser127, and Thr181 is mutated into Ala. According to the results of the molecular dynamics simulation, Thr181 is considered to be one of the key residues that helps NADH to approach the isoalloxazine in FAD. Finally, we have constructed very simplified model systems and carried out density functional theory calculations using B3LYP/LANL2DZ//ROHF(or RHF)/LANL2DZ level of theory in order to elucidate a realistic and feasible mechanism of the hydride-ion transfer from NADH to FAD affected by HEME(Fe3+) as an electron acceptor. Our calculated results suggest that the electron and/or hydride-ion transfer reaction from NADH to FAD can be accelerated in the presence of HEME(Fe3+).     

Spectroscopic study of molecular associations between flavins FAD and RFN and some indole derivatives

The formation of complexes between two flavins [flavine adenine dinucleotide (FAD) and riboflavin (RFN)] and some indole derivatives has been studied in aqueous solution. The molecular associations have been examined by means of electronic absorption spectra, since in each, a new charge-transfer like band has been located, and also by observing the variation of the fluorescence emission of FAD or RFN on the solutions. The formation constants for the molecular complexes were determined from data of absorption using the Foster—Hammick—Wardley method. The quenching fluorescence phenomena observed for the FAD and RFN were related to the concentration of the indole derivatives and the corresponding quenching constants have been determined. Thermodynamic parameters have been derived from the values of association constants for the molecular complexes at several temperatures. Clear evidence is found for the influence on the stability of these complexes of the different substituent groups in the indole derivatives and the molecular structure of both flavins.