Density functional study of the roles of chemical composition of di-transition-metal-substituted gamma-Keggin polyoxometalate anions

The roles of chemical composition (X, M and M(FW)) of di-transition-metal-substituted gamma-Keggin polytungstates and polymolybdates, [(X(n)(+)O(4))M(2)(OH)(2)(M(FW))(10)O(32)]((8-n)-), on the geometry, electronic structure, and magnetic properties of these species have been investigated at the density functional level. It was shown that the change of the heteroatom X via Al(III)-Si(IV)-P(V)-S(VI) slightly stabilizes the broken-symmetry (BS) state over the high-spin (HS) state, increases the antiferromagnetic coupling constant, J, of these species, and lowers the energies of their highest-occupied molecular orbitals (HOMOs) and lowest-unoccupied molecular orbitals (LUMOs). The change of the redox-active center M from Mn to Fe slightly increases the M-(XO(4)) interaction, J-coupling constant, and energy gap between the HS and BS states. Meanwhile, the LUMOs are stabilized, indicating the stronger oxidant character of [(X(n)(+)O(4))M(2)(OH)(2)W(10)O(32)]((8-n)-) for M = Fe than Mn. It was shown that the change of addenda atom M(FW) from W to Mo makes (a) the geometry of Keggin "cage" slightly smaller, (b) the interaction of redox-active centers (Fe) with the central XO(4)-unit slightly stronger, and (c) the J-coupling constant, as well as the energy gap DeltaE(BS-HS), slightly larger.     

Is the protein surrounding the active site critical for hydrogen peroxide reduction by selenoprotein glutathione peroxidase? An ONIOM study

In this ONIOM(QM:MM) study, we evaluate the role of the protein surroundings in the mechanism of H2O2 reduction catalyzed by the glutathione peroxidase enzyme, using the whole monomer (3113 atoms in 196 amino acid residues) as a model. A new optimization scheme that allows the full optimization of transition states for large systems has been utilized. It was found that in the presence of the surrounding protein the optimized active site structure bears a closer resemblance to the one in the X-ray structure than that without the surrounding protein. H2O2 reduction occurs through a two-step mechanism. In the first step, the selenolate anion (E-Se(-)) formation occurs with a barrier of 16.4 kcal/mol and is endothermic by 12.0 kcal/mol. The Gln83 residue plays the key role of the proton abstractor, which is in line with the experimental suggestion. In the second step, the O-O bond is cleaved, and selenenic acid (R-Se-OH) and a water molecule are formed. The calculated barrier for this process is 6.0 kcal/mol, and it is exothermic by 80.9 kcal/mol. The overall barrier of 18.0 kcal/mol for H2O2 reduction is in reasonable agreement with the experimentally measured barrier of 14.9 kcal/mol. The protein surroundings has been calculated to exert a net effect of only 0.70 kcal/mol (in comparison to the "active site only" model including solvent effects) on the overall barrier, which is most likely due to the active site being located at the enzyme surface.     

Quantum chemical prediction of reaction pathways and rate constants for dissociative adsorption of CO(x) and NO(x) on the graphite (0001) surface

We present predictions of reaction rate constants for dissociative adsorption reactions of CO(x) (x = 1, 2) and NO(x) (x = 1, 2) molecules on the basal graphite (0001) surface based on potential energy surfaces (PES) obtained by the integrated ONIOM(B3LYP:DFTB-D) quantum chemical hybrid approach with dispersion-augmented density functional tight binding (DFTB-D) as low level method. Following an a priori methodology developed in a previous investigation of water dissociative adsorption reactions on graphite, we used a C(94)H(24) dicircumcoronene graphene slab as model system for the graphite surface in finite-size molecular structure investigations, and single adsorbate molecules reacting with the pristine graphene sheet. By employing the ONIOM PES information in RRKM theory we predict reaction rate constants in the temperature range between 1,000 and 5,000 K. We find that among CO(x) and NO(x) adsorbate species, the dissociative adsorption reactions of CO(2) and both radical species NO and NO(2) are likely candidates as a cause for high temperature oxidation and erosion of graphite (0001) surfaces, whereas reaction with CO is not likely to lead to long-lived surface defects. High temperature quantum chemical molecular dynamics simulations (QM/MD) at T = 5,000 K using on-the-fly DFTB-D energies and gradients confirm the results of our PES study.     

Proteins responsible for seed pubescence of cotton genetic lines

The activities of fiber-forming enzymes (glucansynthetase, peroxidase, cellulase) from smooth- and pubescent-seeded cotton were compared. Protein inhibitor from the smooth-seeded line was isolated and studied. One of the aspects of the mechanism regulating growth and differentiating epidermal cotton ovule cells into fiber was investigated. Translated from Khimiya Prirodnykh Soedinenii, No. 4, pp. 394–396, July–August, 2008.     

Internal degrees of freedom,structural motifs,and conformational energetics of the 5'-deoxyadenosyl radical: implications for function in adenosylcobalamin-dependent enzymes. A computational study

The potential energy surface of the free 5'-deoxyadenosyl radical in the gas phase is explored using density functional and second-order M?ller-Plesset perturbation theories with 6-31G(d) and 6-31++G(d,p) basis sets and interpreted in terms of attractive and repulsive interactions. The 5',8-cyclization is found to be exothermic by approximately 20 kcal/mol but kinetically unfavorable; the lowest cyclization transition state (TS) lies about 7 kcal/mol higher than the highest TS for conversion between most of the open isomers. In open isomers, the two energetically most important attractive interactions are the hydrogen bonds (a) between the 2'-OH group and the N3 adenine center and (b) between the 2'-OH and 3'-OH groups. The relative ribose-adenine rotation about the C1'-N9 glycosyl bond in a certain range changes the energy by as much as 10-15 kcal/mol, the origin being (i) the repulsive 2'-H.H-C8 and O1'.N3 and (ii) the attractive 2'-OH.N3 ribose-adenine interactions. The hypothetical synergy between the glycosyl rotation and the Co-C bond scission may contribute to the experimentally established labilization of the Co-C bond in enzyme-bound adenosylcobalamin. The computational results are not inconsistent with the rotation about the C1'-N9 glycosyl bond being the principal coordinate for long-range radical migration in coenzyme B(12)-dependent enzymes. The effect of the protein environment on the model system results reported here remains an open question.     

Theoretical study of the mechanism of alkane hydroxylation and ethylene epoxidation reactions catalyzed by diiron bis-oxo complexes. The effect of substrate molecules

The hybrid density functional method B3LYP was used to study the mechanism of the hydrocarbon (methane, ethane, methyl fluoride, and ethylene) oxidation reaction catalyzed by the complexes cis-(H(2)O)(NH(2))Fe(mu-O)(2)(eta(2)-HCOO)(2)Fe(NH(2))(H(2)O), I, and cis-(HCOO)(Imd)Fe(mu-O)(2)(eta(2)-HCOO)(2)Fe(Imd)(HCOO) (Imd = Imidazole), I_m, the "small" and "medium" model of compound Q of the methane monooxygenase (MMO). The improvement of the model from "small" to "medium" did not change the qualitative conclusions but significantly changed the calculated energetics. As in the case of methane oxidation reported by the authors previously, the reaction of all the substrates studied here is shown to start by coordination of the substrate molecule to the bridging oxygen atom, O(1) of I, an Fe(IV)-Fe(IV) complex, followed by the H-atom abstraction at the transition state III leading to the bound hydroxy alkyl intermediate IV of Fe(III)-Fe(IV) core. IV undergoes a very exothermic coupling of alkyl and hydroxy groups to give the alcohol complex VI of Fe(III)-Fe(III) core, from which alcohol dissociates. The H(b)-atom abstraction (or C-H bond activation) barrier at transition state III is found to be a few kcal/mol lower for C(2)H(6) and CH(3)F than for CH(4). The calculated trend in the H(b)-abstraction barrier, CH(4) (21.8 kcal/mol) > CH(3)F (18.8 kcal/mol) > or = C(2)H(6) (18.5 kcal/mol), is consistent with the C-H(b) bond strength in these substrates. Thus, the weaker the C-H(b) bond, the lower is the H(b)-abstraction barrier. It was shown that the replacement of a H-atom in a methane molecule with a more electronegative group tends to make the H(b)-abstraction transition state less "reactant-like". In contrast, the replacement of the H-atom in CH(4) with a less electronegative group makes the H(b)-abstraction transition state more "reactant-like". The epoxidation of ethylene by complex I is found to proceed without barrier and is a highly exothermic process. Thus, in the reaction of ethylene with complex I the only product is expected to be ethylene oxide, which is consistent with the experiment.     

Mechanism of polymerization of colchicidyl-L-lysine N-carboxyanhydride

It has been shown that the polymerization of colchicidyl-L-lysine N-carboxyhydride under the action of amines obeys the general laws of the occurrence of anionic polymerization and is described, when primary amines are used, by a mechanism of “normal” amine addition and, when tertiary amines are used by the “activated monomer” mechanism.     

Synthetic magnetic opals

We present studies of novel nanocomposites of BiNi impregnated into the structure of opals as well as inverse opals. Atomic force microscopy and high resolution elemental analyses show a highly ordered structure and uniform distribution of the BiNi filler in the matrix. These BiNi-based nanocomposites are found to exhibit distinct ferromagnetic-like ordering with transition temperature of about 675 K. As far as we know there exists no report in literature on any BiNi compound which is magnetic.     

Determination of the surface area of supported metallic catalysts by a kinetic method

The possibility of using a kinetic method to determine the surface area of supported platinum and nickel catalysts with a low active-phase surface area is considered. The advantages and drawbacks of the method are discussed.Translated from Teoreticheskaya i Éksperimental'naya Khimiya, Vol. 26, No. 1, pp. 125–127, January–February, 1990.