Reaction of thiophosphoryl fluoride with metals and metal oxides

Abstract is not available.

Redox-linked proton transfer by cytochrome c oxidase

The respiratory chain is found in the inner mitochondrial membrane of higher organisms and in the plasma membrane of many bacteria. It consists of several membrane-spanning enzymes, which conserve the energy that is liberated from the degradation of food molecules as an electrochemical proton gradient across the membrane. The proton gradient can later be utilized by the cell for different energy requiring processes, e.g. ATP production, cellular motion or active transport of ions. The difference in proton concentration between the two sides of the membrane is a result of the translocation of protons by the enzymes of the respiratory chain, from the negatively charged (N-side) to the positively charged side (P-side) of the lipid bilayer, against the proton concentration gradient. The endergonic proton transfer is driven by the flow of electrons through the enzymes of the respiratory chain, from low redox-potential electron donors to acceptors of higher potential, and ultimately to oxygen. Cytochrome c oxidase is the last enzyme in the respiratory chain and catalyzes the reduction of dioxygen to water. The redox reaction is coupled to proton transport across the membrane by a yet unresolved mechanism. Cytochrome c oxidase has two proton-conducting pathways through which protons are taken up to the interior part of the enzyme from the N-side of the membrane. The K-pathway transfers merely substrate protons, which are consumed in the process of water formation at the catalytic site. The D-pathway transfers both substrate protons and protons that are pumped to the P-side of the membrane. This thesis focuses on the role of two conserved amino acids in proton translocation by cytochrome c oxidase, glutamate 278 and tryptophan 164. Glu278 is located at the end of the D-pathway and is thought to constitute the branching point for substrate and pumped protons. In this work, it was shown that although Glu278 has an important role in the proton transfer mechanism, its presence is not an obligatory requirement. Alternative structural solutions in the area around Glu278, much like the ones present in some distantly related heme-copper oxidases, could in the absence of Glu278 support the formation of a long hydrogen-bonded water chain through which proton transfer from the D-pathway to the catalytic site is possible. The other studied amino acid, Trp164, is hydrogen bonded to the ∆-propionate of heme a3 of the catalytic site. Mutation of this amino acid showed that it may be involved in regulation of proton access to a proton acceptor, a pump site, from which the proton later is expelled to the P-side of the membrane. The ion pair that is formed by the ∆-propionate of heme a3 and arginine 473 is likely to form a gate-like structure, which regulates proton mobility to the P-side of the membrane. The same gate may also be part of an exit path through which water molecules produced at the catalytically active site are removed towards the external side of the membrane. Time-resolved optical and electrometrical experiments with the Trp164 to phenylalanine mutant revealed a so far undetected step in the proton pumping mechanism. During the A to PR transition of the catalytic cycle, a proton is transferred from Glu278 to the pump site, located somewhere in the vicinity of the ∆-propionate of heme a3. A mechanism for proton pumping by cytochrome c oxidase is proposed on the basis of the presented results and the mechanism is discussed in relation to some relevant experimental data. A common proton pumping mechanism for all members of the heme-copper oxidase family is moreover considered.

Pentoxifylline induces hyperactivation and acrosome reaction in spermatozoa of golden hamsters: changes in motility kinematics

Pentoxifylline (PF) is used to enhance motility of spermatozoa from infertile human subjects. We have previously shown that 0.45 mM PF improved capacitation of spermatozoa and fertilization of oocytes in vitro in hamsters. The present study was carried out to assess PF- induced changes in motility kinematics of hamster spermatozoa by a computer-aided sperm analyser (CASA) and determine the timing of onset of hyperactivation (HA) and acrosome reaction (AR) in PF-treated spermatozoa. Motility kinematics were analysed by CASA for 0-8 h in the absence or presence of 0.45 mM PF in Tyrode's medium supplemented with lactate, pyruvate and polyvinyl alcohol (TLP-PVA) or in TLP-PVA with bovine serum albumin (TALP-PVA). Conventional assessment was also made on the percentage of motility and quality of motility of spermatozoa; values were expressed as sperm motility index (SMI). Both in TALP-PVA and TLP-PVA, PF markedly increased SMI, especially the quality of motility (P < 0.02) by 2-3 h which was sustained up to 6 h. The motility kinematic data of PF-treated spermatozoa in TALP-PVA showed that average path velocity, curvilinear velocity and amplitude of lateral head displacement significantly (P < 0.05) increased as early as 2 h, with the expected decrease in straightness (STR) and linearity (LIN). Similar changes were also observed with PF-treated spermatozoa in TLP-PVA. Moreover, the percentage of hyperactivated spermatozoa in PF-treated samples was significantly (P < 0.001) higher than the untreated control at 2 h. To determine whether PF could induce AR, independent of bovine serum albumin, quantitative AR was assessed by observing the presence or absence of acrosomal cap on viable spermatozoa. PF significantly (P < 0.001) increased the percentage of AR as early as 2 h, reaching maximum at 4 h both in TALP-PVA (P < 0.05) and in TLP-PVA (P < 0.001). These results show that, in hamsters, PF induces early onset (by 2 h) of HA and AR and increases the proportion of spermatozoa undergoing physiological maturation.

Trifurcated (four-center) hydrogen bond in solid state crystal structure of 5'-amino-5'-deoxyadenosine p-toluenesulfonate

The crystal structure of 5'-amino-5'-deoxyadenosine (5'-Am.dA) p-toluenesulfonate has been determined by X-ray crystallographic methods. It belongs to the orthorhombic space group P2(1)2(1)2(1) with a = 7.754(3)Angstrom, b = 8.065(1)Angstrom and c = 32.481(2)Angstrom. This nucleoside side shows a syn conformation about the glycosyl bond and C2'-endo-C3'-exo puckering for the ribose sugar. The orientation of N5' atom is gauche-trans about the exocyclic C4'-C5' bond. The amino nitrogen N5' forms a trifurcated hydrogen bond with N3, O9T and O4' atoms. Adenine bases form A.A.A triplets through hydrogen bonding between N6, N7 and N1 atoms of symmetry related nucleoside molecules.

Co(II) and Cr(III) complexes of formate-formamide mixed ligands: synthesis, structures, single crystal-to-single crystal transformation and magnetic behaviour

Solvothermal treatment of an equimolar mixture of Co(NO3)(2)center dot 6H(2)O, HCONH2 and NaN3 in MeOH at 100 degrees C yielded a three-dimensional NaCl type network Co(HCOO)(2)(HCONH2)(2) center dot HCONH2 (1a) containing formamides in the pores of the structure. Solvated pink 1a undergoes single crystal-to-single crystal (SCSC) transformation at 215 degrees C to form the desolvated dark brown product Co(HCOO)(2)-( HCONH2)(2) (1b) with the retention of the original framework. Reversible single crystal-to-single crystal transformation of 1b (brown) to 1a (pink) in the presence of excess formamide was also established at room temperature. The coordination environment around Co(II) in both 1a and 1b is octahedral with a CoN2O4 coordination composition. A similar reaction replacing Co(II) by Cr(III) produced a heterometallic 3D extended network Na[Cr(HCOO)(4)(HCONH2)(2)]center dot 2H(2)O (2a) at 100 degrees C. An increase in reaction temperature to 150 degrees C produced a simple mononuclear complex Cr(HCOO)(3)(HCONH2)(3) center dot 3H(2)O (2b). Variable temperature magnetic studies revealed the presence of a canting phenomena in both 1a and 1b, and hysteresis loop in the field dependent magnetisation plot at 2 K whereas complex 2a is simply paramagnetic in nature.

Theoretical Investigation on the Effect of Different Nitrogen Donors on Intramolecular Se center dot center dot center dot N Interactions

The effect of different donor nitrogen atoms on the strength and nature of intramolecular Se center dot center dot center dot N interactions is evaluated for organoselenium compounds having N,N-dimethylaminomethyl (dime), oxazoline (oxa) and pyridyl (py) substituents. Quantum chemical calculations on three series of compounds [2-(dime)C6H4SeX (1a-g), 2-(oxa)C6H4SeX (2a-g), 2- (py)C6H4SeX (3-ag); X=Cl, Br, OH, CN, SPh, SePh, CH3] at the B3LYP/6-31G(d) level show that the stability of different conformers depends on the strength of intramolecular nonbonded Se center dot center dot center dot N interactions. Natural bond orbital (NBO), NBO deletion and atoms in molecules (AIM) analyses suggest that the nature of the Se center dot center dot center dot N interaction is predominantly covalent and involves nN ->sigma*(Se-X) orbital interaction. In the three series of compounds, the strength of the Se center dot center dot center dot N interaction decreases in the order 3>2>1 for a particular X, and it decreases in the order Cl > Br > OH>SPh approximate to CN approximate to SePh>CH3 for all the three series 1-3. However, further analyses suggest that the differences in strength of Se center dot center dot center dot N interaction in 1-3 is predominantly determined by the distance between the Se and N atoms, which in turn is an outcome of specific structures of 1, 2 and 3, and the nature of the donor nitrogen atoms involved has very little effect on the strength of Se center dot center dot center dot N interaction. It is also observed that Se center dot center dot center dot N interaction becomes stronger in polar solvents such as CHCl3, as indicated by the shorter r(Se center dot center dot center dot N) and higher E-Se center dot center dot center dot N values in CHCl3 compared to those observed in the gas phase.

[B4O9H2] Cyclic Borate Units as the Building Unit in a Family of Zinc Borate Structures

A solvothermal reaction of ZnO, boric acid (B(OH)(3)), and aliphatic airlines in a water-pyridine mixture gave four zinc borate phases of different dimensionalities: [Zn(B4O8H2)(C3H10N2)], I (one-dimensional); [Zn(B4O8H2)(C3H10N2)] H2O, II (two-dimensional); [Zn(B5O10H3)(C10H24N4)]center dot H2O, III (two-dimensional): and [Zn-2(B8O15H2)(C3H10N2)(2)], IV (three-dimensional). The structures are formed by the connectivity involving polyborate chains and layers with Zn2+ species. In all the compounds, the amine molecules act its file ligand binding either the same or different zn centers. The formation of two different structures, II and IV, from the same amine by varying the reaction time is noteworthy. Transformation studies on II indicate that the formation of IV. from II, is facile and has been investigated for the first time. Two of file compounds, I and III, exhibit activity for second-order nonlinear optical behavior. The UV exposure of the sample indicates the absorption of all the UV radiation suggesting that the zinc borate compounds could be exploited for UV-blocking applications. The compounds have been characterized by powder X-ray diffraction, infrared spectroscopy, thermogravimetric analysis, UV-vis, photoluminescence, and NMR studies.

Anomalous reaction-diffusion as a model of nonexponential DNA escape kinetics

We show that data from recent experiments carried out on the kinetics of DNA escape from alpha-hemolysin nanopores [M. Wiggin, C. Tropini, C. T. Cossa, N. N. Jetha, and A. Marziali, Biophys. J. 95, 5317 (2008)] may be rationalized by a model of chain dynamics based on the anomalous diffusion of a particle moving in a harmonic well in the presence of a delta function sink. The experiments of Wiggin found, among other things, that the occasional occurrence of unusually long escape times in the distribution of chain trapping events led to nonexponential decays in the survival probability, S(t), of the DNA molecules within the nanopore. Wiggin ascribed this nonexponentiality to the existence of a distribution of trapping potentials, which they suggested was theresult of stochastic interactions between the bases of the DNA and the amino acids located on the surface of the nanopore. Based on this idea, they showed that the experimentally determined S(t) could be well fit in both the short and long time regimes by a function of the form (1+t/tau)(-alpha) (the so called Becquerel function). In our model, S(t) is found to be given by a Mittag-Leffler function at short times and by a generalized Mittag-Leffler function at long times. By suitable choice of certain parameter values, these functions are found to fit the experimental S(t) even better than the Becquerel function. Anomalous diffusion of DNA within the trap prior to escape over a barrier of fixed height may therefore provide a second, plausible explanation of the data, and may offer fresh perspectives on similar trapping and escape problems.

Modulating the preferred O-H center dot center dot center dot O hydrogen-bonding motif in a conformationally constrained environment through hydroxy-group derivatization

The crystal structures of three conformationally locked esters, namely the centrosymmetric tetrabenzoate of all-axial per-hydronaphthalene- 2,3,4a, 6,7,8a-hexaol, viz. trans-4a, 8a-dihydroxyperhydronaphthalene-2,3,6,7-tetrayl tetrabenzoate, C38H34O10, and the diacetate and dibenzoate of all-axial perhydronaphthalene-2,3,4a, 8a-tetraol, viz. (2R*,3R*,4aS*,8aS*)-4a, 8a-dihydroxyperhydronaphthalene-2,3-diyl diacetate, C-14-H22O6, and (2R*, 3R*, 4aS*, 8aS*)-4a, 8a-dihydroxyperhydronaphthalene- 2,3-diyl dibenzoate, C24H26O6, have been analyzed in order to examine the preference of their supramolecular assemblies towards competing inter-and intramolecular O-H center dot center dot center dot O hydrogen bonds. It was anticipated that the supramolecular assembly of the esters under study would adopt two principal hydrogen-bonding modes, namely one that employs intermolecular O-H center dot center dot center dot O hydrogen bonds (mode 1) and another that sacrifices those for intramolecular O-H center dot center dot center dot O hydrogen bonds and settles for a crystal packing dictated by weak intermolecular interactions alone (mode 2). Thus, while the molecular assembly of the two crystalline diacyl derivatives conformed to a combination of hydrogen-bonding modes 1 and 2, the crystal packing in the tetrabenzoate preferred to follow mode 2 exclusively.

Effect of Bottom Bubbling Conditions on Surface Reaction Rate in Oxygen-Water System

In secondary steelmaking, the enhancement of the reaction rate in the low carbon period during the decarburization of steel is considered the most effective method to produce ultralow carbon steel. In a previous study, it was revealed that the surface reaction is dominant during the final stage of the actual refining process. In order to improve the surface reaction rate, it is necessary to enlarge the reaction region, which is usually achieved by increasing the plume eye area. In this study, water model experiments were carried out to estimate the influence of bottom stirring conditions on the gas-liquid reaction rate; for this purpose, the deoxidation rate during the bottom bubbling process was measured. Five types of nozzle configurations were used to study the effect of the plume eye area on the reaction rate at various gas flow rates. The results reveal that the surface reaction rate is influenced by the gas flow rate and the plume eye area. An empirical correlation was developed for the reaction rate and the plume eye area. This correlation was applied to estimate the gas-liquid reaction rate mat the bath surface.

Absolute quantification of human tear lactoferrin using multiple reaction monitoring technique with stable-isotopic labeling

The mass spectrometry technique of multiple reaction monitoring (MRM) was used to quantify and compare the expression level of lactoferrin in tear films among control, prostate cancer (CaP), and benign prostate hyperplasia (BPH) groups. Tear samples from 14 men with CaP, 15 men with BPH, and 14 controls were analyzed in the study. Collected tears (2 μl) of each sample were digested with trypsin overnight at 37 °C without any pretreatment, and tear lactoferrin was quantified using a lactoferrin-specific peptide, VPSHAVVAR, both using natural/light and isotopic-labeled/heavy peptides with MRM. The average tear lactoferrin concentration was 1.01 ± 0.07 μg/μl in control samples, 0.96 ± 0.07 μg/μl in the BPH group, and 0.98 ± 0.07 μg/μl in the CaP group. Our study is the first to quantify tear proteins using a total of 43 individual (non-pooled) tear samples and showed that direct digestion of tear samples is suitable for MRM studies. The calculated average lactoferrin concentration in the control group matched that in the published range of human tear lactoferrin concentration measured by enzyme-linked immunosorbent assay (ELISA). Moreover, the lactoferrin was stably expressed across all of the samples, with no significant differences being observed among the control, BPH, and CaP groups.

Anaerobic DNA cleavage activity in red light and photocytotoxicity of (pyridine-2-thiol)cobalt(III) complexes of phenanthroline bases

Cobalt(III) complexes [Co(pnt)(B)(2)](NO3)(2) (1-3) of pyridine-2-thiol (pnt) and phenanthroline bases (B), viz. 1,10-phenanthroline (phen in 1), dipyrido[3,2-d: 2',3'-f]quinoxaline (dpq in 2) and dipyrido[3,2-a:2',3'-c] phenazine (dppz in 3), have been prepared, characterized and their photo-induced anaerobic DNA cleavage activity studied. The crystal structure of 1a as mixed ClO4- and PF6- salt of 1 shows a (CoN5S)-N-III coordination geometry in which the pnt and phen showed N,S- and N,N-donor binding modes, respectively. The complexes exhibit Co(III)/Co(II) redox couple near -0.3 V (vs. SCE) in 20% DMF-Tris-HCl buffer having 0.1 M TBAP. The complexes show binding propensity to calf thymus DNA giving K-b values within 2.2 x 10(4)-7.3 x 10(5) M-1. Thermal melting and viscosity data suggest DNA surface and/or groove binding of the complexes. The complexes show significant anaerobic DNA cleavage activity in red light under argon atmosphere possibly involving sulfide anion radical or thiyl radical species. The DNA cleavage reaction under aerobic medium in red light is found to involve both singlet oxygen and hydroxyl radical pathways. The dppz complex 3 shows non-specific BSA and lysozyme protein cleavage activity in UV-A light of 365 nm via both hydroxyl and singlet oxygen pathways. The dppz complex 3 exhibits photocytotoxicity in HeLa cervical cancer cells giving IC50 values of 767 nM and 19.38 mu M in UV-A light of 365 nm and in the dark, respectively. A significant reduction of the dark toxicity of the dppz base (IC50 = 8.34 mu M in dark) is observed on binding to the cobalt(III) center.

Amine-Templated Aluminoborates Exhibiting Graphite and Diamond Nets

A solvothermal reaction of Al2O3, H3BO3, pyridine, and H2O at 180 degrees C/7 days in the presence of organic amine molecules gave rise to four new aluminoborates, [(C6H18N2)(AlB6O13H3)], I; [(C5H16N2) (AlB5O10)]center dot 2H(2)O, II; [(C5H16N2)-(AlB5O10)], III; and [(C5H17N3)(AlB5O10)] center dot H2O, IV, with two- and three-dimensional structures. All the structures have been formed by the connectivity involving Al3+ ions and [B5O10] cyclic pentaborate units. In 1, the 3-connected trigonal nodes form a layer that resembles a graphite structure has been observed. The compounds II, III, and IV, have 4-connected nodes that forms a diamond related three-dimensional structure. The formation of solvatomorphs in II and III is noteworthy and has been observed first time in a family of amine template aluminoborates. A comparison of the various aluminoborate structures reveals subtle relationships between the organic amines (length of the amines) and the final framework structures. The compounds have been characterized using a variety of techniques including IR, second-order optical behavior, and MAS NMR studies.