Insights into the mechanism of the reaction between ttrachloro-p-bnzoquinone and hydrogen peroxide and their implications in the catalytic role of water molecules in producing the hydroxyl radial

Detailed mechanisms for the formation of hydroxyl or alkoxyl radicals in the reactions between tetrachloro-p-benzoquinone (TCBQ) and organic hydroperoxides are crucial for better understanding the potential carcinogenicity of polyhalogenated quinones. Herein, the mechanism of the reaction between TCBQ and H2O2 has been systematically investigated at the B3LYP/6-311++G** level of theory in the presence of different numbers of water molecules. We report that the whole reaction can easily take place with the assistance of explicit water molecules. Namely, an initial intermediate is formed first. After that, a nucleophilic attack of H2O2 onto TCBQ occurs, which results in the formation of a second intermediate that contains an OOH group. Subsequently, this second intermediate decomposes homolytically through cleavage of the O-O bond to produce a hydroxyl radical. Energy analyses suggest that the nucleophilic attack is the rate-determining step in the whole reaction. The participation of explicit water molecules promotes the reaction significantly, which can be used to explain the experimental phenomena. In addition, the effects of F, Br, and CH3 substituents on this reaction have also been studied.

Anisotropy of spin relaxation of water protons in cartilage and tendon

Transverse spin relaxation rates of water protons in articular cartilage and tendon depend on the orientation of the tissue relative to the applied static magnetic field. This complicates the interpretation of magnetic resonance images of these tissues. At the same time, relaxation data can provide information about their organisation and microstructure. We present a theoretical analysis of the anisotropy of spin relaxation of water protons observed in fully hydrated cartilage. We demonstrate that the anisotropy of transverse relaxation is due almost entirely to intramolecular dipolar coupling modulated by a specific mode of slow molecular motion: the diffusion of water molecules in the hydration shell of a collagen fibre around the fibre, such that the molecular director remains perpendicular to the fibre. The theoretical anisotropy arising from this mechanism follows the “magic-angle” dependence observed in magnetic-resonance measurements of cartilage and tendon and is in good agreement with the available experimental results. We discuss the implications of the theoretical findings for MRI of ordered collagenous tissues.

Hydrogen bonding in the water stabilized structure of the modified unsymmetrically substituted viologen chromophore, N-ethyl-N'-(2-phosphonomethyl)-4,4'-bipyridylium dichloride

The crystal structure of the modified unsymmetrically N, N'-substituted viologen chromophore, N-ethyl- N'-(2-phosphonoethyl)-4, 4'-bipyridinium dichloride 0.75 hydrate. (1) has been determined. Crystals are triclinic, space group P-1 with Z = 2 in a cell with a = 7.2550(1), b = 13.2038(5), c = 18.5752(7) Å, α = 86.495(3), β = 83.527(2), γ = 88.921(2)o. The two independent but pseudo-symmetrically related cations in the asymmetric unit form one-dimensional hydrogen-bonded chains through short homomeric phosphonic acid O-H...O links [2.455(4), 2.464(4)A] while two of the chloride anions are similarly strongly linked to phosphonic acid groups [O-H…Cl, 2.889(4), 2.896(4)Å]. The other two chloride anions together with the two water molecules of solvation (one with partial occupancy) form unusual cyclic hydrogen-bonded bis(Cl...water) dianion units which lie between the layers of bipyridylium rings of the cation chain structures with which they are weakly associated.

Guanidinium phenylarsonate-guanidine-water (1/1/2)

In the structure of CH6N3+ C6H6AsO3- . CH5N3 . 2H2O, the phenylarsonate anion gives two R2/2(8) cyclic hydrogen-bonding interactions, one with a guanidinium cation, the other with a guanidine molecule. The anions are also bridged by the water molecules, one of which completes a cyclic R3/5(9) hydrogen-bonding association with the guanidinum cation, conjoint with one of the three R^2^~2~(8) associations about that ion, as well as forming an R1/2(6) cyclic association with the guanidine molecule. The result is a three-dimensional framework structure.

Langevin dynamics modeling of the water diffusion tensor in partially aligned collagen networks

In this work, a Langevin dynamics model of the diffusion of water in articular cartilage was developed. Numerical simulations of the translational dynamics of water molecules and their interaction with collagen fibers were used to study the quantitative relationship between the organization of the collagen fiber network and the diffusion tensor of water in model cartilage. Langevin dynamics was used to simulate water diffusion in both ordered and partially disordered cartilage models. In addition, an analytical approach was developed to estimate the diffusion tensor for a network comprising a given distribution of fiber orientations. The key findings are that (1) an approximately linear relationship was observed between collagen volume fraction and the fractional anisotropy of the diffusion tensor in fiber networks of a given degree of alignment, (2) for any given fiber volume fraction, fractional anisotropy follows a fiber alignment dependency similar to the square of the second Legendre polynomial of cos(θ), with the minimum anisotropy occurring at approximately the magic angle (θMA), and (3) a decrease in the principal eigenvalue and an increase in the transverse eigenvalues is observed as the fiber orientation angle θ progresses from 0◦ to 90◦. The corresponding diffusion ellipsoids are prolate for θ < θMA, spherical for θ ≈ θMA, and oblate for θ > θMA. Expansion of the model to include discrimination between the combined effects of alignment disorder and collagen fiber volume fraction on the diffusion tensor is discussed.

Interaction of water with the fluorine-covered anatase TiO2(001) surface

The interaction of water with the fluorine-covered (001) surface of anatase titanium dioxide (TiO2) has been studied within the framework of density functional theory (DFT). Our results show that water dissociation is unfavorable due to repulsive interactions between surface fluorine and oxygen. We also found that the reaction of hydrofluoric acid with a surface hydroxyl group to form a surface Ti–F bond is exothermic, while the removal of fluorine from the surface needs additional energy of about half an eV. Therefore, water molecules are predicted to remain intact at the interface with the F-terminated anatase (001).

Raman microscopy of formamide-intercalated kaolinites treated by controlled-rate thermal analysis technology

Raman spectroscopy of formamide-intercalated kaolinites treated using controlled-rate thermal analysis technology (CRTA), allowing the separation of adsorbed formamide from intercalated formamide in formamide-intercalated kaolinites, is reported. The Raman spectra of the CRTA-treated formamide-intercalated kaolinites are significantly different from those of the intercalated kaolinites, which display a combination of both intercalated and adsorbed formamide. An intense band is observed at 3629 cm-1, attributed to the inner surface hydroxyls hydrogen bonded to the formamide. Broad bands are observed at 3600 and 3639 cm-1, assigned to the inner surface hydroxyls, which are hydrogen bonded to the adsorbed water molecules. The hydroxyl-stretching band of the inner hydroxyl is observed at 3621 cm-1 in the Raman spectra of the CRTA-treated formamide-intercalated kaolinites. The results of thermal analysis show that the amount of intercalated formamide between the kaolinite layers is independent of the presence of water. Significant differences are observed in the CO stretching region between the adsorbed and intercalated formamide.

Near-infrared spectroscopic study of basic aluminum sulfate and nitrate

The tridecameric Al-polymer [AlO4Al12(OH)24(H2O)12]7+ was prepared by forced hydrolysis of Al3+ up to an OH/Al molar ratio of 2.2. Under slow evaporation crystals were formed of Al13-nitrate. Upon addition of sulfate the tridecamer crystallised as the monoclinic Al13-sulfate. These crystals have been studied using near-infrared spectroscopy and compared to Al2(SO4)3.16H2O. Although the near-infrared spectra of the Al13-sulfate and nitrate are very similar indicating similar crystal structures, there are minor differences related to the strength with which the crystal water molecules are bonded to the salt groups. The interaction between crystal water and nitrate is stronger than with the sulfate as reflected by the shift of the crystal water band positions from 6213, 4874 and 4553 cm–1 for the Al13 sulfate towards 5925, 4848 and 4532 cm–1 for the nitrate. A reversed shift from 5079 and 5037 cm–1 for the sulfate towards 5238 and 5040 cm–1 for the nitrate for the water molecules in the Al13 indicate that the nitrate-Al13 bond is weakened due to the influence of the crystal water on the nitrate. The Al-OH bond in the Al13 complex is not influenced by changing the salt group due to the shielding by the water molecules of the Al13 complex.

Raman spectroscopic study of the mixed anion mineral Yecoraite Bi5Fe3O9(Te4+O3)(Te6+O4)2•9H2O

Tellurates are rare minerals as the tellurate anion is readily reduced to the tellurite ion. Often minerals with both tellurate and tellurite anions in the mineral are found. An example of such a mineral containing tellurate and tellurite is yecoraite. Raman spectroscopy has been used to study this mineral, the exact structure of which is unknown. Two Raman bands at 796 and 808 cm-1 are assigned to the ν1 (TeO4)2- symmetric and ν3 (TeO3)2- antisymmetric stretching modes and Raman bands at 699 cm-1 are attributed to the the ν3 (TeO4)2- antisymmetric stretching mode and the band at 690 cm-1 to the ν1 (TeO3)2- symmetric stretching mode. The intense band at 465 cm-1 with a shoulder at 470 cm-1 is assigned the (TeO4)2- and (TeO3)2- bending modes. Prominent Raman bands are observed at 2878, 2936, 3180 and 3400 cm-1. The band at 3936 cm-1 appears quite distinct and the observation of multiple bands indicates the water molecules in the yecoraite structure are not equivalent. The values for the OH stretching vibrations listed provide hydrogen bond distances of 2.625 Å (2878 cm-1), 2.636 Å (2936 cm-1), 2.697 Å (3180 cm-1) and 2.798 Å (3400 cm-1). This range of hydrogen bonding contributes to the stability of the mineral. A comparison of the Raman spectra of yecoraite with that of tellurate containing minerals kuranakhite, tlapallite and xocomecatlite is made.

Sodium 2-nitrocinnamate dihydrate: a one-dimensional hydrogen-bonded coordination polymer

The title compound catena-poly[aqua-mu3-2-nitrocinnamato], [Na(C9H6NO4)(H2O)2]n, the sodium salt of trans-2-nitrocinnamic acid, is a one-dimensional coordination polymer based on six-coordinate octahedral NaO6 centres comprising three facially-related monodentate carboxylate O-atom donors from separate ligands (all bridging)[Na-O, 2.4370(13)-2.5046(13)A] and three water molecules (two bridging, one monodentate) [Na-O, 2.3782(13)-2.4404(17)A]. The structure is also stabilized by intra-chain water-O-H...O(carboxylate) and O-H...O(nitro) hydrogen bonds.

Unusual hydrate stabilization in the two-dimensional layered structure of quinacrinium bis(2-carboxy-4,5-dichlorobenzoate) tetrahydrate, a proton-transfer compound of the drug quinacrine

The crystal structure of the hydrated proton-transfer compound of the drug quinacrine [rac-N'-(6-chloro-2-methoxyacridin-9-yl)-N,N-diethylpentane-1,4-diamine] with 4,5-dichlorophthalic acid, C23H32ClN3O2+ . 2(C8H3Cl2O4-).4H2O (I), has been determined at 200 K. The four labile water molecules of solvation form discrete ...O--H...O--H... hydrogen-bonded chains parallel to the quinacrine side chain, the two N--H groups of which act as hydrogen-bond donors for two of the water acceptor molecules. The other water molecules, as well as the acridinium H atom, also form hydrogen bonds with the two anion species and extend the structure into two-dimensional sheets. Between these sheets there are also weak cation--anion and anion--anion pi-pi aromatic ring interactions. This structure represents only the third example of a simple quinacrine derivative for which structural data are available but differs from the other two in that it is unstable in the X-ray beam due to efflorescence, probably associated with the destruction of the unusual four-membered water chain structures.

Raman spectroscopic study of the uranyl mineral natrouranospinite (Na2,Ca)[(UO2)(AsO4)]2•5H2O

Raman spectra of natrouranospinite complemented with infrared spectra were studied and related to the structure of the mineral. Observed bands were assigned to the stretching and bending vibrations of (UO2)2+ and (AsO4)3- units and of water molecules. U-O bond lengths in uranyl and O-H…O hydrogen bond lengths were calculated from the Raman and infrared spectra.

Raman spectroscopic study of the uranyl sulphate mineral jáchymovite (UO2)8(SO4)(OH)14•13H2O

Raman spectra of jáchymovite, (UO2)8(SO4)(OH)14•13H2O, were studied, complemented with infrared spectra, and compared with published Raman and infrared spectra of uranopilite, [(UO2)6(SO4)O2(OH)6(H2O)6] •6H2O. Bands related to the stretching and bending vibrations of (UO2)2+, (SO4)2-, (OH)- and water molecules were assigned. U-O bond lengths in uranyl and O-H…O hydrogen bond lengths were calculated from the Raman and infrared spectra.

EPR, UV-visible and near infrared spectroscopic characterization of dolomite

Dolomite mineral samples having white and light green colours of Indian origin have been characterized by EPR, optical and NIR spectroscopy. The optical spectrum exhibits a number of electronic bands due to presence of Fe(III) ions in the mineral. From EPR studies, the parameters of g for Fe(III) and g, A and D for Mn(II) are evaluated and the data confirm that the ions are in distorted octahedron. Optical absorption studies reveal that Fe(III) is in distorted octahedron. The bands in NIR spectra are due to the overtones and combinations of water molecules. Thus EPR and optical absorption spectral studies have proven useful for the study of the chemistry of dolomite.

Raman spectroscopic study of the uranyl mineral pseudojohannite Cu6.5[(UO2)4O4(SO4)2]2(OH)5.25H2O

Raman spectra of pseudojohannite were studied and related to the structure of the mineral. Observed bands were assigned to the stretching and bending vibrations of (UO2)2+ and (SO4)2- units and of water molecules. The published formula of pseudojohannite is Cu6.5(UO2)8\[O8](OH)5\[(SO4)4].25H2O; however Raman spectroscopy does not detect any hydroxyl units. Raman bands at 805 and 810 cm-1 are assigned to (UO2)2+ stretching modes. The Raman bands at 1017 and 1100 cm-1 are assigned to the (SO4)2- symmetric and antisymmetric stretching vibrations. The three Raman bands at 423, 465 and 496 cm-1 are assigned to the (SO4)2- ν2 bending modes. The bands at 210 and 279 cm-1 are assigned to the doubly degenerate ν2 bending vibration of the (UO2)2+ units. U-O bond lengths in uranyl and O-H…O hydrogen bond lengths were calculated from the Raman and infrared spectra.