Structural-Chemical Transformations of Two-Dimensional Iron-Oxygen Nanostructures in the Course of Transport Reduction

Transport reduction was shown to allow finely controlling the Fe^{+ 3}/Fe^{+ 2} ratio in iron-oxygen two-dimensional nanostructures (nanolayers, thickness 3-15 Å) on silica. It was found by Müossbauer spectroscopy that isolated surface iron-oxygen groups >-Si-O-Fe(OH)₂ and (>-Si-O-)₂FeOH are not reduced at 400-600°C, which is explained by their covalent bonding with silica. The transport reduction of samples with applied nanolayers (one and four) at T 600°C was shown to form bulk phases [iron(II) silicate and metallic iron] on the silica surface. The features of structural-chemical transformations on transport reduction of iron-oxygen nanolayers on supports are primarily associated with the specifics of phase formation in nanostructures.     

Synthesis of Iron-Oxygen Nanostructures on Silicon and Analysis of Their Structure by NEXAFS Spectroscopy

The near-edge fine structure of the Fe2p and Si2p X-ray absorption spectra (NEXAFS) of iron-oxygen nanolayers on the surface of single-crystal silicon (100) was studied for the first time. The structure of the quasi-2D iron-oxygen nanosystems synthesized by molecular layering was considered on this basis.     

The effect of temperature on the development of nanosized nucleus iron-oxygen structures in Fe<Superscript>0</Superscript>-H<Superscript>2</Superscript>O-O<Superscript>2</Superscript> Systems

The formation of nucleus iron-oxygen structures in Fe⁰-H₂O-O₂ systems has been investigated. It has been shown that temperature affects the rate of iron(II) oxidation and, accordingly, the composition of components involved in phase formation. At 10°C, only nucleus structures of protolepidocrocites are formed on the surface; at 20–40°C, structures of protolepidocrocites and ferrihydrite; and at 50–70°C, structures of magnetite and FeO. The analysis of thermodynamic functions has revealed the most probable formation reactions of nucleus iron-oxygen structures and the optimal conditions for the structure formation in morphological series.     

Collision-induced dissociation of three groups of hydroxamate siderophores: ferrioxamines, ferrichromes and coprogens/fusigens

The behaviour of a series of hydroxamate siderophores--microbially produced iron complexes - was investigated using electrospray ionisation mass spectrometry (ESI-MS). Three groups of iron hydroxamate siderophores, namely the ferrioxamines, ferrichromes and coprogens/fusigens, were separated by high-performance liquid chromatography (HPLC) prior to ESI and MS(2) fragmentation. For the majority of the siderophores, both protonated molecules and sodium adducts were observed. The most abundant ion was selected for collision-induced fragmentation. Potential fragmentation mechanisms are postulated and discussed. Fragmentation patterns differed between siderophore groups; however, common fragmentation patterns were observed for siderophore ions within the groups examined. Cleavage frequently occurred at carbon-nitrogen or carbon-oxygen bonds. Fragmentation of the ions also involved cleavage of iron-oxygen bonds and transfer of the charge to iron.     

Phase formation in Fe0-H2O-O2 system in the presence of iron cations: 1. Fe0-H2O-O2-FeSO4 system

Formation mechanisms of ultradispersed (nanosized) iron-oxygen particles in a Fe⁰-H₂O-O₂ system in the presence of bivalent iron cations are investigated. It is shown that, depending on the solution concentration and pH and the presence or absence of an oxidant, nanosized nucleation structures, mainly protolepidocrocites, are formed on the surface of an iron sample, in a surface layer of the sample, and in the solution. Subsequent development of these structures proceeds through several mechanisms to yield ultradispersed phases of iron oxides and monohydrates with different crystalline structures.     

Fe3O4(001)-B表面水煤气变换反应机理第一性原理研究

采用自旋极化的密度泛函理论方法系统地研究了Fe_3O_4(001)-B表面水煤气变换的反应机理,计算了整个反应历程。结果表明,对于Fe_3O_4(001)-B表面上的水煤气变换反应,氧化还原、联合和再生三种反应路径共存,但氧化还原和联合机理的有效能垒较低,因而更占优势。对于生成H_2的基元反应,其活性受表面H浓度和催化剂表面O缺陷浓度影响;较高的表面H浓度和O缺陷浓度均有利于H_2生成。这些结果有助于进一步认识铁氧催化剂上的水煤气变换反应机理。     

Phase formation in Fe0-H2O-O2 system in the presence of iron cations: 2. Fe0-H2O-O2-Fe2(SO4)3 system

Formation mechanisms of ultradispersed (nanosized) iron-oxygen particles in a Fe⁰-H₂O-O₂ system in the presence of trivalent iron cations are investigated. It is shown that, depending on the solution concentration and pH and the presence or absence of an oxidant on the surface of iron, nanosized nuclei, mainly ferrihydrite, are formed in the surface layer and in the solution. Further growth of these nuclei occurs via several mechanisms to yield ultradispersed phases of iron oxides and monohydrates with different crystalline modifications. Original Russian Text ? V.A. Prokopenko, E.N. Lavrinenko, S.V. Mamunya, 2007, published in Kolloidnyi Zhurnal, 2007, Vol. 69, No. 1, pp. 88–95.     

The structures and electronic configuration of compound I intermediates of Helicobacter pylori and Penicillium vitale catalases determined by X-ray crystallography and QM/MM density functional theory calculations

The structures of Helicobacter pylori (HPC) and Penicillium vitale (PVC) catalases, each with two subunits in the crystal asymmetric unit, oxidized with peroxoacetic acid are reported at 1.8 and 1.7 A resolution, respectively. Despite the similar oxidation conditions employed, the iron-oxygen coordination length is 1.72 A for PVC, close to what is expected for a Fe=O double bond, and 1.80 and 1.85 A for HPC, suggestive of a Fe-O single bond. The structure and electronic configuration of the oxoferryl heme and immediate protein environment is investigated further by QM/MM density functional theory calculations. Four different active site electronic configurations are considered, Por*+-FeIV=O, Por*+-FeIV=O...HisH+, Por*+-FeIV-OH+ and Por-FeIV-OH (a protein radical is assumed in the latter configuration). The electronic structure of the primary oxidized species, Por*+-FeIV=O, differs qualitatively between HPC and PVC with an A2u-like porphyrin radical delocalized on the porphyrin in HPC and a mixed A1u-like "fluctuating" radical partially delocalized over the essential distal histidine, the porphyrin, and, to a lesser extent, the proximal tyrosine residue. This difference is rationalized in terms of HPC containing heme b and PVC containing heme d. It is concluded that compound I of PVC contains an oxoferryl Por*+-FeIV=O species with partial protonation of the distal histidine and compound I of HPC contains a hydroxoferryl Por-FeIV-OH with the second oxidation equivalent delocalized as a protein radical. The findings support the idea that there is a relation between radical migration to the protein and protonation of the oxoferryl bond in catalase.     

Application of a ligand-based theoretical approach to derive conversion paths and ligand conformations in CYP11B2-mediated aldosterone formation

The biosynthesis of the mineralocorticoid hormone aldosterone involves a multistep hydroxylation of 11-deoxycorticosterone at the 11- and 18-positions, resulting in the formation of corticosterone and 18-hydroxycorticosterone, the final precursor of aldosterone. Two members of the cytochrome P450 11B family, CYP11B1 and CYP11B2, are known to catalyze these 11- and 18-hydroxylations, however, only CYP11B2 can oxidize 18-hydroxycorticosterone to aldosterone. It is unknown what sequence of hydroxylations leads to the formation of 18-hydroxycorticosterone. In this study we have investigated which of the possible conversion paths towards formation of 18-hydroxycorticosterone and aldosterone are most likely from the ligand perspective. Therefore, we combined quantum mechanical investigations on the steroid conformations of 11-deoxycorticosterone and its ensuing reaction intermediates with Fukui indices calculations to predict the reactivity of their carbon atoms for an attack by the iron-oxygen species. Both F(-) and F(0) were calculated to account for different mechanisms of substrate conversion. We show which particular initial conformations of 11-deoxycorticosterone and which conversion paths are likely to result in the successful synthesis of aldosterone, and thereby may be representative for the mechanism of aldosterone biosynthesis by CYP11B2. Moreover, we found that the most likely path for aldosterone synthesis coincides with the substrate conformation proposed in an earlier publication. To summarize, we show that on a theoretical and strictly ligand-directed basis only a limited number of reaction paths in the conversion of 11-deoxycorticosterone to aldosterone is possible. Despite its theoretical nature, this knowledge may help to understand the catalytic function of CYP11B1 and CYP11B2.     

A three-phase method for identifying functionally related protein groups in weighted PPI networks

Identifying significant protein groups is of great importance for further understanding protein functions. This paper introduces a novel three-phase heuristic method for identifying such groups in weighted PPI networks. In the first phase a variable neighborhood search (VNS) algorithm is applied on a weighted PPI network, in order to support protein complexes by adding a minimum number of new PPIs. In the second phase proteins from different complexes are merged into larger protein groups. In the third phase these groups are expanded by a number of 2-level neighbor proteins, favoring proteins that have higher average gene co-expression with the base group proteins. Experimental results show that: (i) the proposed VNS algorithm outperforms the existing approach described in literature and (ii) the above-mentioned three-phase method identifies protein groups with very high statistical significance.     

Application of Badger's rule to heme and non-heme iron-oxygen bonds: an examination of ferryl protonation states

To gain insight into the protonation state of enzymatic ferryl species we have examined the applicability of Badger's rule to heme and non-heme iron-oxygen bonds. Using density functional theory we have calculated r(e) and nu(e) for the Fe-O bonds of complexes with different axial ligands, iron-oxidation, oxygen-protonation, and spin states. Our results indicate that Badger's rule holds for heme and non-heme oxo and hydroxo complexes. We find that the long Fe-O bonds that have been reported in the crystal structures of the ferryl forms of myoglobin, horseradish peroxidase, cytochrome c peroxidase, and catalase deviate substantially from the values predicted by Badger's rule, while the short Fe-O bonds obtained from X-ray absorption measurements are in good agreement with Badger's rule. In light of our analysis we conclude that the ferryl forms of myoglobin, horseradish peroxidase, and cytochrome c peroxidase are authentic iron(IV)oxos with Fe-O bonds on the order of 1.66 A and pKa's < 4.     

Application of esca to semi-quantitative surface and state analysis of iron oxides

In order to study oxidation states in the surface analysis of solids, a semi-quantitative ESCA (X-ray photoelectron spectroscopy-XPS and X-ray-excited Auger-electron spectroscopy-XAES) method was proposed. Taking iron-oxygen compounds as examples, the summation or subtraction technique was utilized in the analysis of ESCA spectra to identify the co-ordination type and crystal structure. The "XAES intensity factors" for the lines Cr L(3)M(2,3)M(4,5), Ti L(3)M(2,3)M(4,5) and from Fe L(3)M(4,5)M(4,5) to Zn L(3)M(4,5)M(4,5) were estimated and their occurrence discussed.     

Use of insoluble yeast beta-glucan as a support for immobilization of Candida rugosa lipase

In the present study, insoluble yeast beta-glucan (IYG) has been explored as a support matrix for enzyme immobilization. IYG contains mainly beta-(1-3) linkages along with some intra- or inter-molecular branches of beta-(1-6) linkages with large number of free hydroxyl groups. Epichlorohydrin was used to convert these free hydroxyl groups into activated epoxy groups that are capable of forming covalent linkages with various groups of enzyme molecule. The epoxy-activated IYG was evaluated for immobilization of Candida rugosa lipase (CRL). Post-immobilization treatment of 5% glutaraldehyde was given in order to achieve stable and irreversible binding of enzyme on the support. The resultant biocatalytic IYG support expressed lipase activity of 8136.7 U/g and 59.6% activity yield. There was 51.05% retention of synthetic activity after six repeated esterification cycles, indicating its stability and reusability in non-aqueous medium. Moreover, the immobilized lipase gave the storage half-life of about 285 days (at 4 degrees C).     

Molecular Dynamics of Hexamethylbenzene at Low Temperatures: Evidence of Unconventional Magnetism Based on Rotational Motion of Protons

The types of magnetism known to date are all mainly based on contributions from electron motion. We show how rotational motion of protons (H⁺) within the methyl groups in hexamethylbenzene (C₆(CH₃)₆) also contribute significantly to the magnetic susceptibility. Starting from below 118 K, as the rotational motion of the methyl groups set in, an associated magnetic moment positive in nature due to charge of the protons renders the susceptibility to become anomalously dependent on temperature. Starting from 20 K, the susceptibility diverges with decreasing temperature indicative of spin–spin interactions between methyl groups aligned in a previously unclassified type of anti‐ferromagnetic configuration. Complementary dielectric constant measurements also show the existence of magneto‐dielectric coupling. Our findings allow for the study of strongly correlated systems that are based on a species that possesses much slower dynamics.     

处理方法对多壁碳纳米管结构及负载Ru催化剂氨分解反应活性的影响

分别用H2O2、强碱（NaOH、KOH）和HNO3处理CNTs。以处理后的CNTs为载体、通过浸渍RuCl3水溶液结合高温H2还原制备Ru/CNTs催化剂,并将其应用在氨分解催化反应中。利用XRD、TPR、TPD-MS表征手段研究了Ru在CNTs表面的分散、还原性能及CNTs表面化学基团,探究催化剂结构-性能间构效关系。结果表明,强碱及双氧水处理CNTs,为其表面引入了数量适宜的羧基、酸酐、酚等官能团,而传统硝酸处理则引入了大量的羧基、酸酐、酯、内酯、酚、醌和羰基等官能团,对CNTs本征结构性质影响很大。经强碱及双氧水处理CNTs上负载Ru后所得催化剂的效果明显优于传统硝酸处理CNTs上负载Ru催化剂。本研究为CNTs的新型处理方法、表面化学官能团分析、提高Ru/CNTs催化分解氨活性提供了新的思路。     

Structure-function correlations in oxygen activating non-heme iron enzymes

A large group of mononuclear non-heme iron enzymes exist which activate dioxygen to catalyze key biochemical transformations, including many of medical, pharmaceutical and environmental significance. These enzymes utilize high-spin Fe(II) active sites and additional reducing equivalents from cofactors or substrates to react with O2 to yield iron-oxygen intermediates competent to transform substrate to product. While Fe(II) sites have been difficult to study due to the lack of dominant spectroscopic features, a spectroscopic methodology has been developed which allows the elucidation of the geometric and electronic structures of these active sites and provides molecular level insight into the mechanisms of catalysis. This review provides a summary of this methodology with emphasis on its application to the determination of important active site structure-function correlations in mononuclear non-heme iron enzymes. These studies provide key insight into the mechanisms of oxygen activation, active site features that contribute to differences in reactivity and, combined with theoretical calculations and model studies, the nature of oxygen intermediates active in catalysis.     

EPR, 1H and 2H NMR, and reactivity studies of the iron-oxygen intermediates in bioinspired catalyst systems

Complexes [(BPMEN)Fe(II)(CH(3)CN)(2)](ClO(4))(2) (1, BPMEN = N,N'-dimethyl-N,N'-bis(2-pyridylmethyl)-1,2-diaminoethane) and [(TPA)Fe(II)(CH(3)CN)(2)](ClO(4))(2) (2, TPA = tris(2-pyridylmethyl)amine) are among the best nonheme iron-based catalysts for bioinspired oxidation of hydrocarbons. Using EPR and (1)H and (2)H NMR spectroscopy, the iron-oxygen intermediates formed in the catalyst systems 1,2/H(2)O(2); 1,2/H(2)O(2)/CH(3)COOH; 1,2/CH(3)CO(3)H; 1,2/m-CPBA; 1,2/PhIO; 1,2/(t)BuOOH; and 1,2/(t)BuOOH/CH(3)COOH have been studied (m-CPBA is m-chloroperbenzoic acid). The following intermediates have been observed: [(L)Fe(III)(OOR)(S)](2+), [(L)Fe(IV)═O(S)](2+) (L = BPMEN or TPA, R = H or (t)Bu, S = CH(3)CN or H(2)O), and the iron-oxygen species 1c (L = BPMEN) and 2c (L = TPA). It has been shown that 1c and 2c directly react with cyclohexene to yield cyclohexene oxide, whereas [(L)Fe(IV)═O(S)](2+) react with cyclohexene to yield mainly products of allylic oxidation. [(L)Fe(III)(OOR)(S)](2+) are inert in this reaction. The analysis of EPR and reactivity data shows that only those catalyst systems which display EPR spectra of 1c and 2c are able to selectively epoxidize cyclohexene, thus bearing strong evidence in favor of the key role of 1c and 2c in selective epoxidation. 1c and 2c were tentatively assigned to the oxoiron(V) intermediates.     

处理方法对多壁碳纳米管结构及负载Ru催化剂氨分解反应活性的影响

分别用H_2O_2、强碱(NaOH、 KOH)和强酸HNO_3处理CNTs.以处理后的CNTs为载体、通过浸渍RuCl_3水溶液结合高温H_2还原制备Ru/CNTs催化剂,并将其应用在氨分解催化反应中.利用XRD、 TPR、 TPD-MS表征手段研究了Ru在CNTs表面的分散、还原性能及CNTs表面化学基团,探究催化剂结构-性能间构效关系.结果表明,强碱及双氧水处理CNTs,为其表面引入了数量适宜的羧基、酸酐、酚等官能团,而传统硝酸处理则引入了大量的羧基、酸酐、酯、内酯、酚、醌和羰基等官能团,对CNTs本征结构性质影响很大.经强碱及双氧水处理CNTs上负载Ru后所得催化剂的效果明显优于传统硝酸处理CNTs上负载Ru催化剂.我们发展的CNTs的新型处理方法为研制高活性Ru/CNTs催化分解氨催化剂提供了新的思路.     

Refined calculation of the magnetic susceptibility and polarizability of the BH molecule in different vibrational levels of the ground electronic state

Refined calculations of the dependence of the components of the magnetic susceptibility and polarizability of the BH molecule in the electronic ground state on the vibrational quantum number have been carried out. It has been found that, as the vibrational quantum number increases from v=0 to v=17, the transverse magnetic susceptibility averaged over the molecular vibrations increases by a factor of 7.1, while the longitudinal polarizability increases by a factor of 2.2. The results obtained confirm the sharp increase in the anomalous paramagnetic susceptibility of the BH molecule upon excitation of the vibrational levels of its ground electronic state predicted in the preceding work of the authors.Translated from Teoreticheskaya i Éksperimental'naya Khimiya, Vol. 23, No. 1, pp. 83–86, January–February, 1987.     

N-取代吩噻嗪衍生物分子的结构和二阶非线性光学性质的理论研究

在ZINDO方法基础上, 按完全态求和(SOS)公式, 编制了计算分子二阶非线性光学系数βijk的程序。研究了各种取代基在吩噻嗪的氮上取代后衍生物的结构和二阶非线性光学系数。结论是N上取代推电子基对增大二阶光学非线性有利, N上取代吸电子基对增大二阶光学非线性不利。扩大共轭范围对增大二阶光学非线性有利。对上述结果在微观上给予了解释。