Tungsten and Molybdenum Heteropolyanions with Different Central Ions-Correlation between Theory and Experiment.

Density functional theory calculations were carried out to investigate the electronic structures of Keggin-typed [XMo12O40]n- and [XW12O40]n- anions with different heteroatoms (X = Zn2+, B3+, Al3+, Ga3+, Si4+, Ge4+, P5+, As5+, and S6+). The influence of solvent on redox properties of heteropolyanions was discussed. For [XW12O40]n- systems two linear correlation: first, between the experimental redox potential and energies of LUMO orbital; and second, between the experimental redox potential and total energy interaction (calculated between internal tetrahedron (XO4n-), and rest of Kegging anion skeleton, (W12O36)) were designated. Taking into account the similarity of XW12O40n- and XMo12O40n- systems (in geometry and electronic structure), the estimated redox potential of molybdenum heteropolyanions (with X being p block elements) in different solvent were proposed.

Physicochemical and Biological Characterisation of Diclofenac Oligomeric Poly(3-hydroxyoctanoate) Hybrids as ß-TCP Ceramics Modifiers for Bone Tissue Regeneration.

Nowadays, regenerative medicine faces a major challenge in providing new, functional materials that will meet the characteristics desired to replenish and grow new tissue. Therefore, this study presents new ceramic-polymer composites in which the matrix consists of tricalcium phosphates covered with blends containing a chemically bounded diclofenac with the biocompatible polymer-poly(3-hydroxyoctanoate), P(3HO). Modification of P(3HO) oligomers was confirmed by NMR, IR and XPS. Moreover, obtained oligomers and their blends were subjected to an in-depth characterisation using GPC, TGA, DSC and AFM. Furthermore, we demonstrate that the hydrophobicity and surface free energy values of blends decreased with the amount of diclofenac modified oligomers. Subsequently, the designed composites were used as a substrate for growth of the pre-osteoblast cell line (MC3T3-E1). An in vitro biocompatibility study showed that the composite with the lowest concentration of the proposed drug is within the range assumed to be non-toxic (viability above 70%). Cell proliferation was visualised using the SEM method, whereas the observation of cell penetration into the scaffold was carried out by confocal microscopy. Thus, it can be an ideal new functional bone tissue substitute, allowing not only the regeneration and restoration of the defect but also inhibiting the development of chronic inflammation.

Novel bioresorbable tricalcium phosphate/polyhydroxyoctanoate (TCP/PHO) composites as scaffolds for bone tissue engineering applications.

Development of new composite materials for bone tissue engineering is a constantly growing field of medicine. Therefore there is a continuous need in creating novel materials that can not only regenerate the defected tissue but also nourish it while the healing process progresses. Here we present a novel type of composite material that fulfils these requirements. The study describes creation of a composite with macroporous bioceramic core that is infiltrated with a thin biopolymer layer. The ceramic component, namely tricalcium phosphate (TCP), due to its mechanistic and bioactive properties may promote new bone creation as shown through the in vitro studies. To the best of our knowledge the coating layer was created for the first time from a representative of bacterially derived medium chain length polyhydroxyalkanoate polymers (mcl-PHA), namely polyhydroxyoctanoate (PHO). This polymer layer not only profoundly changed the stress-strain characteristics of the bioceramic foam but also released (R)-3-hydroxyacids and their dimers/trimers to the investigated environment. In the manuscript we have in depth characterised these materials employing a set of basic procedures, through 3D structure reconstruction and finishing with prolonged in vitro experiments.

Mechanistic basis for the enantioselectivity of the anaerobic hydroxylation of alkylaromatic compounds by ethylbenzene dehydrogenase.

The enantioselectivity of reactions catalyzed by ethylbenzene dehydrogenase, a molybdenum enzyme that catalyzes the oxygen-independent hydroxylation of many alkylaromatic and alkylheterocyclic compounds to secondary alcohols, was studied by chiral chromatography and theoretical modeling. Chromatographic analyses of 22 substrates revealed that this enzyme exhibits remarkably high reaction enantioselectivity toward (S)-secondary alcohols (18 substrates converted with >99% ee). Theoretical QM:MM modeling was used to elucidate the structure of the catalytically active form of the enzyme and to study the reaction mechanism and factors determining its high degree of enantioselectivity. This analysis showed that the enzyme imposes strong stereoselectivity on the reaction by discriminating the hydrogen atom abstracted from the substrate. Activation of the pro(S) hydrogen atom was calculated to be 500 times faster than of the pro(R) hydrogen atom. The actual hydroxylation step (i.e., hydroxyl group rebound reaction to a carbocation intermediate) does not appear to be enantioselective enough to explain the experimental data (the calculated rate ratios were in the range of only 2-50 for pro(S): pro(R)-oriented OH rebound).

Mechanistic insight into peroxo-shunt formation of biomimetic models for compound†II, their reactivity toward organic substrates, and the influence of N-methylimidazole axial ligation.

High-valent iron-oxo species have been invoked as reactive intermediates in catalytic cycles of heme and nonheme enzymes. The studies presented herein are devoted to the formation of compound II model complexes, with the application of a water soluble (TMPS)Fe(III)(OH) porphyrin ([meso-tetrakis(2,4,6-trimethyl-3-sulfonatophenyl)porphinato]iron(III) hydroxide) and hydrogen peroxide as oxidant, and their reactivity toward selected organic substrates. The kinetics of the reaction of H2O2 with (TMPS)Fe(III)(OH) was studied as a function of temperature and pressure. The negative values of the activation entropy and activation volume for the formation of (TMPS)Fe(IV)=O(OH) point to the overall associative nature of the process. A pH-dependence study on the formation of (TMPS)Fe(IV)=O(OH) revealed a very high reactivity of OOH(-) toward (TMPS)Fe(III)(OH) in comparison to H2O2. The influence of N-methylimidazole (N-MeIm) ligation on both the formation of iron(IV)-oxo species and their oxidising properties in the reactions with 4-methoxybenzyl alcohol or 4-methoxybenzaldehyde, was investigated in detail. Combined experimental and theoretical studies revealed that among the studied complexes, (TMPS)Fe(III)(H2O)(N-MeIm) is highly reactive toward H2O2 to form the iron(IV)-oxo species, (TMPS)Fe(IV)=O(N-MeIm). The latter species can also be formed in the reaction of (TMPS)Fe(III)(N-MeIm)2 with H2O2 or in the direct reaction of (TMPS)Fe(IV)=O(OH) with N-MeIm. Interestingly, the kinetic studies involving substrate oxidation by (TMPS)Fe(IV)=O(OH) and (TMPS)Fe(IV)=O(N-MeIm) do not display a pronounced effect of the N-MeIm axial ligand on the reactivity of the compound II mimic in comparison to the OH(-) substituted analogue. Similarly, DFT computations revealed that the presence of an axial ligand (OH(-) or N-MeIm) in the trans position to the oxo group in the iron(IV)-oxo species does not significantly affect the activation barriers calculated for C-H dehydrogenation of the selected organic substrates.

Ammonium adsorption on Brønsted acidic centers on low-index vanadium pentoxide surfaces.

Vanadium-based catalysts are used in many technological processes, among which the removal of nitrogen oxides (NOx) from waste gases is one of the most important. The chemical reaction responsible for this selective catalytic reaction (SCR) is based on the reduction of NOx molecules to N2, and a possible reductant in this case is pre-adsorbed NH3. In this paper, NH3 adsorption on Brønsted OH acid centers on low-index surfaces of V2O5 (010, 100, 001) is studied using a theoretical DFT method with a gradient-corrected functional (RPBE) in the embedded cluster approximation model. The results of the calculations show that ammonia molecules are spontaneously stabilized on all low-index surfaces of the investigated catalyst, with adsorption energies ranging from -0.34 to -2 eV. Two different mechanisms of ammonia adsorption occur: the predominant mechanism involves the transfer of a proton from a surface OH group and the stabilization of ammonia as an NH4 (+) cation bonded to surface O atom(s), while an alternative mechanism involves the hydrogen bonding of NH3 to a surface OH moiety. The latter binding mode is present only in cases of stabilization over a doubly coordinated O(2) center at a (100) surface. The results of the calculations indicate that a nondirectional local electrostatic interaction with ammonia approaching a surface predetermines the mode of stabilization, whereas hydrogen-bonding interactions are the main force stabilizing the adsorbed ammonia. Utilizing the geometric features of the hydrogen bonds, the overall strength of these interactions was quantified and qualitatively correlated (R = 0.93) with the magnitude of the stabilization effect (i.e., the adsorption energy).

Metallobacteriochlorophylls as potential dual agents for photodynamic therapy and chemotherapy.

A theoretical analysis of bacteriochlorophyll a containing its non-native divalent metal ions: Co, Ni, Cu, Zn, Ru, Rh, Pd, and Pt, has been carried out by means of density functional theory (DFT) calculations. The main stress was put on the derivatives with metals, which already found applications as coordination compounds in anti-tumor therapy (Ru, Pt, Pd, and Rh). The idea was to combine their cytotoxic properties with the known suitability of bacteriochlorophylls macrocycle for photodynamic therapy. The geometries of the studied systems are compared and reveal a number of similarities. The cores of the modified bacteriochlorophylls are flat, and the introduced metal ions lie in plane of the macrocycle, showing its large ability to accommodate metal ions of different sizes. However, four metal-nitrogen bonds, linking the central ions with the macrocycle ligand, are not equivalent. Metals are the strongest attached to nitrogens, which come from the pyrrole, which is fused with isocyclic ring. Based on the known spectroscopic data, the absorption properties of the proposed systems are predicted. Finally, it is found that all studied metal-macrocycle adducts are stable in aqueous media. The only exceptions are Mg-BChla (the finding is reflected by experimental facts) and Zn-BChla. The predicted high stability of Ru-, Rh-, Pt- and Pd-bacteriochlorophylls might turn out beneficial for therapeutic purposes.

Ligation of water to magnesium chelates of biological importance.

Water binding to several Mg(2+) chelates, ethylenediamine, ethylenediamine-N,N'-diacetate, porphyrin, chlorophyll a and bacteriochlorophyll a, to form five- and six-coordinate complexes is studied by means of density functional theory. The results obtained for magnesium chelates are compared with the properties of the respective aqua complexes and the influence of the permittivity of environment on the ligand binding energies is discussed. Although the most common coordination number of Mg(2+) is six, in the tetrapyrrolic chelates it is reduced to five because the accommodation of the sixth water ligand results in no gain in energy. This is in line with the experimental observations made for coordination of chlorophylls in vivo. The binding between Mg(2+) and water is mostly of electrostatic nature, which is supported by the finding that its energy is correlated both with the electron density of the chelator and with electrostatic potential determined at the ligand binding site.

Ab initio modeling of ethylbenzene dehydrogenase reaction mechanism.

Density functional theory calculations were performed to study the mechanism of ethylbenzene oxidation by ethylbenzene dehydrogenase (EBDH). EBDH is a bacterial molybdopterin enzyme capable of stereospecific anaerobic hydroxylation of alkylaromatic compounds to secondary alcohols. It is a key biocatalyst in the metabolism of ethylbenzene-degrading bacteria such as Aromatoleum aromaticum , which converts ethylbenzene to (S)-1-phenylethanol. The recently determined EBDH structure enabled the theoretical description of the ethylbenzene oxidation mechanism. In this work, theoretical calculations and kinetic isotopic experiments were conducted and combined in order to elucidate the reaction mechanism. We considered three aspects: (i) Does the reaction concur with one two-electron or two one-electron transfers? (ii) Is the active site His192 important for the reaction and what is its protonation state? (iii) What catalytic consequences have different possible arrangements of the molybdopterin ligand? The most important outcome of the calculations is that mechanisms involving two one-electron transfers and a radical-type intermediate have lower energy barriers than the corresponding two-electron transfer mechanisms and are, therefore, more plausible. The mechanism involves two transition states: radical-type TS1 associated with the C-H bond cleavage, and carbocation-type TS2 associated with the transfer of the second electron and OH rebound. Using models with protonated and nonprotonated His 192, we conclude that this amino acid takes part in the mechanism. However, as both models yielded plausible reaction pathways, its protonation state cannot be easily predicted. Qualitative agreement was reached between the calculated kinetic isotope effects (KIE) obtained for radical TS1 and the KIE measured experimentally at optimum pH, but we observed a very strong pH dependence of KIE throughout the investigated pH range (3.1 for pH 6, 5.9 for pH 7, up to 10.5 at pH 8.). This may be explained by assuming a gradual shift of the rate-determining step from TS1 associated with high KIE to TS2 associated with low KIE with lowered pH and an increasing contribution of proton/deuteron tunneling associated with high pH. Finally, models were calculated with different signs of the conformational twist of the pterin ligands, yielding only slightly different energy profiles of the reaction pathways.

Relative stability of low-index V(2)O(5) surfaces: a density functional investigation.

Ab initio density functional calculations of the structural and electronic properties of V(2)O(5) bulk and its low-index surfaces are presented. For the bulk oxide and the (010) surface (the natural cleavage plane) a good agreement with experiment and with earlier ab initio calculations is found. For the first time, the investigations are extended to other low-index surfaces: (001) and (100). On both surfaces, termination conserving a bulk-like stoichiometry is preferred, but-in contrast to the (010) surface-a strong structural relaxation takes place. Relaxation reduces the surface energy from 1.16 to 0.48 J m(-2) for the (001) and from 0.61 to 0.55 J m(-2) for the (100) surface. Although the relaxed surface energies are still one order of magnitude higher than calculated for the (010) surface (0.047 J m(-2)), the Wulff construction demonstrates that (001) and (100) surfaces contribute about 15% of the total surface area of a V(2)O(5) crystallite, indicating a non-negligible role in the catalytic activity of V(2)O(5).

Kinetics and mechanism of oxygen-independent hydrocarbon hydroxylation by ethylbenzene dehydrogenase.

Ethylbenzene dehydrogenase (EBDH) from the denitrifying bacterium Azoarcus sp. strain EbN1 (to be renamed Aromatoleum aromaticum) catalyzes the oxygen-independent, stereospecific hydroxylation of ethylbenzene to (S)-1-phenylethanol, the first known example of direct anaerobic oxidation of a nonactivated hydrocarbon. The enzyme is a trimeric molybdenum/iron-sulfur/heme protein of 155 kDa that is quickly inactivated in air in its reduced state. Enzyme activity can be coupled to ferricenium tetrafluoroborate, providing a convenient way for kinetic measurements. EBDH exhibits activity with a wide range of ethylbenzene analogues, which were analyzed for their kinetic parameters, stoichiometry, and formed products. The reactivity was correlated to the chemical structures by a quantitative structure-activity relationship (QSAR) model. On the basis of these results, quantum chemical calculations of DeltaG298 for formation of carbocations of the respective substrates were performed and used in reactivity analysis. A putative reaction mechanism is proposed on the basis of the experimental results and theoretical considerations. Finally, the enzyme reaction has been established in an electrochemical reactor, allowing sustained enzymatic reaction and potential technical applications of the enzyme.

Theoretical density functional theory studies on interactions of small biologically active molecules with isolated heme group.

We present ab-initio density functional theory studies on the interactions of small biologically active molecules, namely NO, CO, O(2), H(2)O, and NO(2) (-) with the full-size heme group. Our results show that the small molecule-iron bond is the strongest in carbonyl and the weakest in nitrite system. Trans influence induced by NO binding to the five-coordinate heme complex is shown. Nitric oxide in the resulting complex might be described as NO(-). The differences among the small ligands of XO type (CO, NO, O(2)), and their distant chemical behavior from H(2)O and NO(2) (-) ligands in binding to the Fe(II) ion, are shown. Moreover, the role of the heme ring as a reservoir of electrons in the studied complexes is invoked. The analysis of the parameters defining the iron-histidine bond indicates that this bond is longer and weaker in nitrosyl and carbonyl complexes than in the other systems. Our findings support the proposed mechanism of soluble guanylate cyclase (sGC) activation and suggest that the first step of sGC activation by CO may be the same as during the activation by NO. Obtained results are then compared with the data concerning smaller model of the heme, the porphyrin complexes, available in the literature.

Application of artificial neural networks and DFT-based parameters for prediction of reaction kinetics of ethylbenzene dehydrogenase.

Artificial neural networks (ANNs) are used for classification and prediction of enzymatic activity of ethylbenzene dehydrogenase from EbN1 Azoarcus sp. bacterium. Ethylbenzene dehydrogenase (EBDH) catalyzes stereo-specific oxidation of ethylbenzene and its derivates to alcohols, which find its application as building blocks in pharmaceutical industry. ANN systems are trained based on theoretical variables derived from Density Functional Theory (DFT) modeling, topological descriptors, and kinetic parameters measured with developed spectrophotometric assay. Obtained models exhibit high degree of accuracy (100% of correct classifications, correlation between predicted and experimental values of reaction rates on the 0.97 level). The applicability of ANNs is demonstrated as useful tool for the prediction of biochemical enzyme activity of new substrates basing only on quantum chemical calculations and simple structural characteristics. Multi Linear Regression and Molecular Field Analysis (MFA) are used in order to compare robustness of ANN and both classical and 3D-quantitative structure-activity relationship (QSAR) approaches.

Nitrite binding to metmyoglobin and methemoglobin in comparison to nitric oxide binding.

Nitrite binds reversibly to the ferriheme proteins metmyoglobin and methemoglobin in aqueous buffer solution at a physiological pH of 7.4. The spectral changes recorded for the formation of metMb(NO2-) differ significantly from those observed for the nitrosylation of metMb, which can be accounted for in terms of the different reaction products. Nitric oxide binding to metMb produces a nitrosyl product with Fe(II)-NO+ character, whereas the reaction with nitrite produces an Fe(III)-NO2- complex. The kinetics of the binding and release of nitrite by metMb and metHb were investigated by stopped-flow techniques at ambient and high pressure. The kinetic traces recorded for the reaction of nitrite with metMb exhibit excellent single-exponential fits, whereas nitrite binding to metHb is characterized by double-exponential kinetics which were assigned to the reactions of the alpha- and beta-chains of metHb with NO2-. The rate constants for the binding of nitrite to metMb and metHb were found to be much smaller than those reported for the binding of NO, such that nitrite impurities will not affect the latter reaction. The activation parameters (deltaH++,deltaS(ne),deltaV++) obtained from the temperature and pressure dependence of the reactions support the operation of a dissociative mechanism for the binding and release of nitrite, similar to that found for the binding and release of NO in metMb.