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ABSTRACT: A study of the molecular, electronic, and vibrational characteristics of the molybdenum-containing enzyme complex xanthine oxidase with violapterin has been carried out using density functional theory calculations and resonance Raman spectroscopy. The electronic structure calculations were carried out on a model consisting of the enzyme molybdopterin cofactor [in the four-valent, reduced state; Mo(IV)O(SH)] covalently linked to violapterin (1H,3H,8H-pteridine-2,4,7-trione in the neutral form) via an oxygen bridge, Mo-O-C7. Full geometry optimizations were performed for all models using the SDD basis set and the three-parameter exchange functional of Becke combined with the Lee, Yang, and Parr correlational functional. Harmonic vibrational frequencies were determined for a variety of isotopes in an attempt to correlate experimentally observed shifts upon 18O-labeling of the Mo-OR bridge to bound product as well as shifts seen upon substitution of solvent-exchangeable protons in samples prepared in D2O. The theoretical vibrational frequencies compared favorably with experimentally observed vibrational modes in the resonance Raman spectra of the reduced xanthine oxidase-violapterin complex prepared in H2O and D2O and with 18O-labeled product. Correlating the isotopic shifts from the calculations with those from the resonance Raman experiments resulted in complete normal mode assignments for all modes observed in the 350-1750 cm(-1) range. The present work demonstrates that a model in which the violapterin is coordinated to the molybdenum of the active site in a simple end-on manner via the hydroxyl group introduced by an enzyme accurately predicts the observed resonance Raman spectrum of the complex. Given the numerous modes involving the bridging oxygen, a side-on binding mode can be eliminated.
The Journal of Physical Chemistry B 03/2005; 109(7):3023-31. · 3.70 Impact Factor
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ChemPhysChem 01/2004; 4(12):1358-60. · 3.41 Impact Factor
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ABSTRACT: Harmonic vibrational frequencies and transition intensities of lumazine (2,4-(1H,3H)pteridinedione in the neutral state) have been calculated in a self-consistent reaction field of high dielectric medium (ε = 78.54) using ab initio Hartree−Fock (HF) and hybrid HF/density functional theory (DFT) methods. For the DFT method, the 4-31G basis set and the three parameter exchange functional of Becke combined with the Lee, Yang, and Parr correlational functional are used. The 6-31+G* basis set is used in the HF calculations. Both the spherical cavity model (SCM) and the self-consistent isodensity polarizable continuum model (SCIPCM) are used to simulate an aqueous environment for the N-protonated lumazines. For the N-deuterated lumazines, only the SCM is used. Simple scaling of the vibrational frequencies resulting from the DFT calculations incorporating the reaction field models of neutral lumazine, lumazine A1/N3-H monoanion, and lumazine A1,A3-dianion compare closely with Raman and Fourier transform infrared spectra of lumazine taken in aqueous media (both H2O and D2O) over a wide pH/pD range. The mean deviation between calculated and experimental vibrational frequencies is 9.10 cm-1 for neutral lumazine (9.37 cm-1 in D2O), 9.18 cm-1 for the monoanion (10.77 cm-1 in D2O), and 16.06 cm-1 for the dianion (16.00 cm-1 when prepared in D2O). Calculated vibrational energy shifts with changes in ionization exhibit many trends that are evident in the experimental data although the absolute magnitudes of many of the individual shifts do not agree exactly. The calculated H/D isotopic shifts for the neutral and monoanionic species of lumazine agree well with those seen experimentally. Correlating shifts with ionization and the H/D isotopic shifts of the vibrational modes of each species of lumazine investigated have resulted in normal mode assignments of all in-plane vibrational modes observed in the 300−1750 cm-1 range in aqueous solution.
02/2003;
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ABSTRACT: The active site of the mononuclear molybdenum enzyme xanthine oxidase has an LMoOS(OH) center that catalyzes the hydroxylation of substrate (L representing an enedithiolate ligand contributed by a pterin cofactor in the enzyme). Reaction of the enzyme with cyanide results in the replacement of the Mo=S group with a second Mo=O group, which results in loss of enzyme activity. To understand the basis for this loss of activity, we have computationally examined the interaction of a model for the LMoO2(OH) as well the LMoOTe(OH) congener of the enzyme with formamide (a substrate for the enzyme). Our electronic structure calculations for the oxo congener indicate a reduced electron density on the hydrogen being transferred from substrate in the course of the reaction, a shorter O-H bond in the transition state, and a longer nascent O-C bond of product, factors which combine to account for the loss of reactivity in the LMoO2(OH) species. Interestingly, our calculations indicate that the Te congener is characterized by an increased electron density on the hydrogen species being transferred, a longer Te-H bond in the transition state, and a shorter O-C nascent bond in the product and suggest that a Te congener of xanthine oxidase, were it to be prepared experimentally, should exhibit catalytic activity.
Journal of the American Chemical Society 07/2002; 124(24):6796-7. · 9.91 Impact Factor
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ABSTRACT: The intrinsic reactivity of the molybdenum center in xanthine oxidase has been studied by electronic structure calculations of a molybdenum−dithiolene model, based on the crystal structure of the closely related aldehyde oxidoreductase from Desulfovibrio gigas. Using first-principles electronic structure calculations (the HF/DF B3LYP method at the LanL2DZ level), we find that the reoxidation of the substrate-reduced molybdenum center proceeds through hydration, followed by subsequent loss of two electrons. The oxidation is likely to be coupled with loss of protons first from water coordinated to Mo(IV) species to give MoV−OH and second from the Mo−SH ligand of the Mo(V) species to give a MoVIS species. Starting with the structure of the oxidized center and formamide as a substrate, and using (U)MP2/LanL2DZ formalism, we identify the reaction transition state as a planar SMo−O···C complex formed upon nucleophilic attack of metal-bound hydroxide on the substrate carbon atom that is to be hydroxylated. Following sp2 → sp3 rehybridization of this carbon atom to create an R-chiral tetrahedral center, the transition state breaks down via hydride transfer from the substrate carbonyl carbon to the MoS as the dominant reaction coordinate. The reaction is completed by product dissociation and replacement by water in the metal coordination sphere. Alternative transition states, involving molybdenum−carbon bond formation, are found to be energetically and stereochemically prohibitive.
06/1999;
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ABSTRACT: Fourier transform infrared (FTIR) spectra have been obtained from solution samples of the heterocycles uracil, lumazine, and violapterin and reveal interpretable carbonyl stretching frequencies. Spectra of conjugate bases of lumazine and violapterin demonstrate decreases in these carbonyl stretching frequencies upon ionization. Based on isotopic shifts from amide deuterated analogs, semiempirical QCFF/PI calculations were used to assign the vibrational frequencies in the region 1100–1800 cm−1 observed from samples in dimethylsulfoxide (DMSO) and aqueous solutions to specific normal modes. The observed deuterium shifts and the calculations suggest that, in some cases, N—H bending motions are coupled to the C=O stretching motions of the pyrimidine ring. These data suggest that for lumazine anions a change in solvent can significantly change the mixing of the N—H bending and C=O stretching vibrational motions. This implies that vibrational analysis for lumazine species in relatively noninteracting media like nonpolar solvents, mulls or pellets cannot necessarily be transferred to the system when it is dissolved in a polar, hydrogen-bonding solvent such as water. Although other explanations can be offered, our vibrational analysis suggests that the changes in normal mode composition of the predominantly C=O stretching vibrations of lumazine anion on going from dimethylsulfoxide to water solution are consistent with a change in the predominant tautomer of the heterocycle. This change appears to correspond to a shifting of the location of the remaining acidic proton to a different ring nitrogen atom. This interpretation is of interest in view of recent ab initio calculations which suggest that proton shifts may occur during the hydroxylation of lumazine as mediated by the enzyme xanthine oxidase. © 1998 John Wiley & Sons, Inc. Biospectroscopy 4: 235–256, 1998
Biospectroscopy 12/1998; 4(4):235 - 256.
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ABSTRACT: Harmonic vibrational frequencies and transition strengths in uracil have been calculated in self-consistent reaction fields of low (ε = 1.53) and high (ε = 78.54) dielectric constant using ab initio Hartree−Fock and density functional theory methods at the 6-31+G* level of theory. Uniformly scaled frequencies calculated in low dielectric medium agree well with infrared spectra of uracil in argon matrix, Δν(avg) = 2.2 cm-1, although only partial agreement is obtained for individual matrix-induced frequency shifts and intensity changes. Reaction field calculations with a tighter spherical cavity or solute cavity determined by the isodensity polarizable continuum method yield better match with experiment for certain vibrations. In a polar protic medium, the vibrational analysis is extended beyond neutral uracil to its (de)protonation derivatives selected by reaction field calculations. Unscaled vibrational frequencies, as well as infrared and Raman intensities of the uracil-4-ol cation, neutral uracil, uracil N1-anion, and uracil N1,3-dianion calculated in continuous high dielectric medium are found to agree fairly well with vibrational spectra of uracil in aqueous media recorded over a wide pH range. The deficiencies of the reaction field model, like hydrogen bonding and ion−solvent interactions, are highlighted and their contributions quantitatively estimated.
12/1997;
