A Density Functional Theory Study on the Active Center of Fe-Only Hydrogenase: Characterization and Electronic Structure of the Redox States

We have carried out extensive density functional theory (DFT) calculations for possible redox states of the active center in Fe-only hydrogenases. The active center is modeled by [(H(CH(3))S)(CO)(CN(-))Fe(p)(mu-DTN)(mu-CO)Fe(d)(CO)(CN(-))(L)](z) (z is the net charge in the complex; Fe(p)= the proximal Fe, Fe(d) = the distal Fe, DTN = (-SCH(2)NHCH(2)S-), L is the ligand that bonds with the Fed at the trans position to the bridging CO). Structures of possible redox states are optimized, and CO stretching frequencies are calculated. By a detailed comparison of all the calculated structures and the vibrational frequencies with the available experimental data, we find that (i) the fully oxidized, inactive state is an Fe(II)-Fe(II) state with a hydroxyl (OH(-)) group bonded at the Fe(d), (ii) the oxidized, active state is an Fe(II)-Fe(l) complex which is consistent with the assignment of Cao and Hall (J. Am. Chem. Soc. 2001, 123, 3734), and (iii) the fully reduced state is a mixture with the major component being a protonated Fe(l)-Fe(l) complex and the other component being its self-arranged form, Fe(II)-Fe(II) hydride, Our calculations also show that the exogenous CO can strongly bond with the Fe(II)-Fe(l) species, but cannot bond with the Fe(l)-Fe(l) complex. This result is consistent with experiments that CO tends to inhibit the oxidized, active state, but not the fully reduced state. The electronic structures of all the redox states have been analyzed. It is found that a frontier orbital which is a mixing state between the e(g) of Fe and the 2pi of the bridging CO plays a key role concerning the reactivity of Fe-only hydrogenases: (1) it is unoccupied in the fully oxidized, inactive state, half-occupied in the oxidized, active state, and fully occupied in the fully reduced state; (ii) the e(g)-2pi orbital is a bonding state, and this is the key reason for stability of the low oxidation states, such as Fe(l)-Fe(l) complexes; and (iii) in the e(g)-2pi orbital more charge accumulates between the bridging CO and the Fe(d) than between the bridging CO and the Fe(p), and the occupation increase in this orbital will enhance the bonding between the bridging CO and the Fe(d), leading to the bridging-CO shift toward the Fe(d).

High-resolution crystal structure of the intramolecular d(TpA) thymine-adenine photoadduct and its mechanistic implications.

A high-resolution crystal structure is reported for d(TpA)*, the intramolecular thymine–adenine photoadduct that is produced by direct ultraviolet excitation of the dinucleoside monophosphate d(TpA). It confirms the presence of a central 1,3-diazacyclooctatriene ring linking the remnants of the T and A bases, as previously deduced from heteronuclear NMR measurements by Zhao et al. (The structure of d(TpA)*, the major photoproduct of thymidylyl-(3'-5')-deoxyadenosine. Nucleic Acids Res., 1996, 24, 1554–1560). Within the crystal, the d(TpA)* molecules exist as zwitterions with a protonated amidine fragment of the eight-membered ring neutralizing the charge of the internucleotide phosphate monoanion. The absolute configuration at the original thymine C5 and C6 atoms is determined as 5S,6R. This is consistent with d(TpA)* arising by valence isomerization of a precursor cyclobutane photoproduct with cis–syn stereochemistry that is generated by [2 + 2] photoaddition of the thymine 5,6-double bond across the C6 and C5 positions of adenine. This mode of photoaddition should be favoured by the stacked conformation of adjacent T and A bases in B-form DNA. It is probable that the primary photoreaction is mechanistically analogous to pyrimidine dimerization despite having a much lower quantum yield.

Identification and functional analysis of a novel bradykinin inhibitory peptide in the venoms of New World Crotalinae pit vipers.

A novel undecapeptide has been isolated and structurally characterized from the venoms of three species of New World pit vipers from the subfamily, Crotalinae. These include the Mexican moccasin (Agkistrodon bilineatus), the prairie rattlesnake (Crotalus viridis viridis), and the South American bushmaster (Lachesis muta). The peptide was purified from all three venoms using a combination of gel permeation chromatography and reverse-phase HPLC. Automated Edman degradation sequencing and MALDI-TOF mass spectrometry established its peptide primary structure as: Thr-Pro-Pro-Ala-Gly-Pro-Asp-Val-Gly-Pro-Arg-OH, with a non-protonated molecular mass of 1063.18 Da. A synthetic replicate of the peptide was found to be an antagonist of bradykinin action at the rat vascular B2 receptor. This is the first bradykinin inhibitory peptide isolated from snake venom. Database searching revealed the peptide to be highly structurally related (10/11 residues) with a domain residing between the bradykinin-potentiating peptide and C-type natriuretic peptide domains of a recently cloned precursor from tropical rattlesnake (Crotalus durissus terrificus) venom gland. BIP thus represents a novel biological entity from snake venom.

Electrochemical ammonia gas sensing in nonaqueous systems: A comparison of propylene carbonate with room temperature ffonc liquids

First, the direct and indirect electrochemical oxidation of ammonia has been studied by cyclic voltammetry at glassy carbon electrodes in propylene carbonate. In the case of the indirect oxidation of ammonia, its analytical utility of indirect for ammonia sensing was examined in the range from 10 and 100 ppm by measuring the peak current of new wave resulting from reaction between ammonia and hydroquinone, as function of ammonia concentration, giving a sensitivity 1.29 x 10(-7) A ppm(-1) (r(2)=0.999) and limit-of-detection 5 ppm ammonia. Further, the direct oxidation of ammonia has been investigated in several room temperature ionic liquids (RTILs), namely 1-butyl-3-methylimidazolium tetrafluoroborate ([C(4)mim] [BF4]), 1-butyl-3-methylimiclazolium trifluoromethylsulfonate ([C4mim] [OTf]), 1-Ethyl -3-methylimidazolium bis(trifluoromethylsulfonyl)imide ([C(2)mim] [NTf2]), 1-butyl-3-methylimidazolium bis(tritluoromethylsulfonyl)imide ([C4mim] [NTf2]) and 1-butyl-3-methylimidazolium hexafluorophosphate ([C4mim] [PF6]) on a 10 put diameter Pt microdisk electrode. In four of the RTILs studied, the cyclic voltammetric analysis suggests that ammonia is initially oxidized to nitrogen, N-2, and protons, which are transferred to an ammonia molecule, forming NH4+ via the protonation of the anion(s) (A(-)). However, in [C4mim] [PF6], the protonated anion was formed first, followed by NH4+. In all five RTILs, both HA and NH4+ are reduced at the electrode surface, forming hydrogen gas, which is then oxidized. The analytical ability of this work has also been explored further, giving a limit-of-detection close to 50 ppm in [C(2)mim] [NTf2], [C(4)mim] [OTf], [C(4)mim] [BF4], with a sensitivity of ca. 6 x 10(-7) A ppm(-1) (r(2) = 0.999) for all three ionic liquids, showing that the limit of detection was ca. ten times larger than that in propylene carbonate since ammonia in propylene carbonate might be more soluble in comparison with RTILs when considering the higher viscosity of RTILs.

Mechanistic studies of the electro-oxidation pathway of ammonia in several room-temperature ionic liquids

A mechanistic study of the direct oxidation of ammonia has been reported in several room-temperature ionic liquids (RTILs), namely, [C(4)mim][BF4], [C(4)mim][OTf], [C(2)mim][NTf2], [C(4)mim][NTf2], and [C(4)mim][PF6], on a 10 mu m diameter Pt microdisk electrode. In four of the RTILs studied, the cyclic voltammetric analysis suggests that ammonia is initially oxidized to nitrogen, N-2, and protons, which are transferred to an ammonia molecule, forming NH4+ via the protonation of the anion(s) (A(-)). In contrast, NH4+ is formed first in [C(4)mim][PF6], followed by the protonated anion(s), HA. In all five RTILs, both HA and NH4+ are reduced at the electrode surface, forming hydrogen gas, which is then oxidized. The effect of changing the RTIL anion is discussed, and this may have implications in the defining of pK(a) in RTIL media. This work also has implications in the possible amperometric sensing of ammonia gas.

Characterization of silica-supported dodecatungstic heteropolyacids as a function of their dehydroxylation temperature

Dodecatungsto-silicic H4SiW12O40 and -phosphoric acids H3PW12O40 were deposited on silica by a classical impregnation technique. The resulting materials were studied by in situ Raman and infrared spectroscopy, XPS and by solid-state H-1 MAS NMR as a function of their dehydroxylation temperature. The data show that in the case of H3PW12O40 three silanol groups are protonated while in the case of H4SiW12O40 at least one acidic proton remains. Upon heating this proton reacts leading to a disordered structure and a broadening of the W-O Raman bands.

The structure of [Co(H-tptz)Cl-3] center dot H2O (tptz=2,4,6-tri(2-pyridyl)-1,3,5-triazine) prepared by crystallization from the ionic liquid, N-butyl-N-methyl-pyrrolidinium bis(trifluoromethanesulfonyl)imide

The structure of tris-chloro[2,6-bis(2'-pyridyl)-4-(2'-pyridinium)-1,3,5-triazine]cobalt(II) monohydrate, [Co(C18H13N6)Cl-3]center dot H2O (C2/c (No. 15), a = 7.783(11), b = 22.42(3), c = 11.001(15) angstrom, beta = 90.05(2)degrees), crystallized from the open air reaction of CoCl2 and 2,4,6-tri(2-pyridyl)-1,3,5-triazine in the ionic liquid, N-butyl-N-methyl-pyrrolidinium bis(trifluoromethanesulfonyl)imide is reported. The structure consists of six coordinate cobalt in an octahedral geometry bonded to the tridentate tptz ligand and three chlorines. The non-coordinating pyridyl group in the tptz ligand is protonated (with the protonated nitrogen crystallographically disordered over two possible sites), providing overall charge neutrality for the complex.

Task-specific ionic liquid for solubilizing metal oxides

Protonated betaine bis(trifluoromethylsulfonyl) imide is an ionic liquid with the ability to dissolve large quantities of metal oxides. This metal-solubilizing power is selective. Soluble are oxides of the trivalent rare earths, uranium(VI) oxide, zinc(II) oxide, cadmium( II) oxide, mercury( II) oxide, nickel( II) oxide, copper(II) oxide, palladium(II) oxide, lead(II) oxide, manganese( II) oxide, and silver( I) oxide. Insoluble or very poorly soluble are iron(III), manganese(IV), and cobalt oxides, as well as aluminum oxide and silicon dioxide. The metals can be stripped from the ionic liquid by treatment of the ionic liquid with an acidic aqueous solution. After transfer of the metal ions to the aqueous phase, the ionic liquid can be recycled for reuse. Betainium bis( trifluoromethylsulfonyl) imide forms one phase with water at high temperatures, whereas phase separation occurs below 55.5 degrees C ( temperature switch behavior). The mixtures of the ionic liquid with water also show a pH-dependent phase behavior: two phases occur at low pH, whereas one phase is present under neutral or alkaline conditions. The structures, the energetics, and the charge distribution of the betaine cation and the bis( trifluoromethylsulfonyl) imide anion, as well as the cation-anion pairs, were studied by density functional theory calculations.

Binding of serum albumin to the anthelmintic drugs albendazole, triclabendazole and their sulphoxides

The binding of drugs to plasma proteins – especially serum albumin – is an important factor in controlling the availability and distribution of these drugs. In this study we have investigated the binding of two drugs commonly used to treat liver fluke infections, albendazole (ABZ) and triclabendazole (TCBZ), and their sulphoxide metabolites to bovine serum albumin (BSA). Both ABZ and TCBZ caused shifts in the mobility of BSA in native gel electrophoresis. No such changes were observed with the sulphoxides under identical conditions. The drugs, and their sulphoxides, caused quenching of the intrinsic tryptophan fluorescence of BSA, indicating association between the drugs and this protein. Quantification of this quenching suggested a 5–10-fold reduction in affinity of the sulphoxides compared to the parent compounds. These results are discussed in respect to previous work on the pharmacodynamics of these fasciolicides and will inform the design of novel anthelmintics.

The electrochemical oxidation of catechol and dopamine on platinum in 1-Ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide ([C(2)mim][NTf2]) and 1-Butyl-3-methylimidazolium tetrafluoroborate ([C(4)mim][BF4]): Adsorption effects in ionic liquid voltammetry

The electrochemical oxidation of catechol and dopamine has been studied at a platinum micro-electrode (10 pm diameter) in two room temperature ionic liquids (RTILs): 1-Ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide ([C(2)mim][NTf2]) and 1-Butyl-3-methylimidazolium tetrafluoroborate ([C(4)mim][BE4]). For catechol in [C(2)mim][NTf2], an electrochemically quasi-reversible oxidation peak was observed at 1.1 V vs. Pt with a back peak at 0.4 V vs. Pt. This is assigned to the two-electron oxidation of catechol to doubly protonated o-benzoquinone. Double-step chronoamperometry gave a diffusion coefficient for the catechol and the oxidised species which is 3.8 x 10(-11) m(2) s(-1) for both. For catechol in [C(4)mim][BF4], a two-electron oxidation wave was observed at 1.0 V vs. Pt with no back peak. Another peak at less positive potential was also observed at 0.6 V vs. Pt in [C(4)mim][BF4] but not in [C(2)mim][NTf2] which is assigned to the adsorption of electrochemically formed neutral o-benzoquinone on the platinum electrode. The oxidised protonated o-benzoquinone is suggested to be deprotonated by the [BF4](-) anion, but not by the [NTf2](-) anion: hence adsorption of the neutral species at the platinum electrode, not the charged species. For dopamine in both RTILs, two chemically irreversible oxidation peaks were observed at 0.75 V and 1.1 V vs. Pt, and assigned to the oxidation of dopamine to the corresponding semi-quinone and the quinone. Potential-step chronoamperometry was carried out on the oxidation waves of dopamine in [C(2)mim][NTf2] and the diffusion coefficient of species in solution was calculated to be 6.85 x 10(-12) m(2) s(-1) and confirmed that the waves corresponded to one and two electron processes. A third wave was observed at 1.8 V vs. Pt which is attributed to the oxidation of the amine group to a radical cation with likely subsequent follow up chemistry. In [C(4)mim][BF4] a peak at less positive potential was observed for dopamine, similar to catechol which is assigned to the adsorption of the neutral quinone species on the platinum electrode formed by the reaction of the removal of protons from the oxidised dopamine with the [BF4](-) anion. (C) 2009 Elsevier B.V. All rights reserved.

Comprehensive Inhibitor Profiling Of The Proteus Mirabilis Metalloprotease Virulence Factor Zapa (Mirabilysin)

In this study we report for the first time the comprehensive inhibitor profiling of the Proteus mirabilis metalloprotease virulence factor, ZapA (mirabilysin) using a 160 compound focused library of N-alpha mercaptoamide dipeptides, in order to map the S1´ and S2´ binding site preferences of this important enzyme. This study has revealed a preference for the aromatic residues tyrosine and tryptophan in P1´ and aliphatic residues in P2´. From this library, six compounds were identified which exhibited sub- to low micromolar Ki values. The most potent inactivator, SH-CO2-Y-V-NH2 was capable of preventing ZapA-mediated hydrolysis of heat denatured IgA, indicating these inhibitors may be capable of protecting host proteins against ZapA during colonisation and infection.

The role of the active site residues in human galactokinase: implications for the mechanisms of GHMP kinases.

Galactokinase catalyses the phosphorylation of galactose at the expense of ATP. Like other members of the GHMP family of kinases it is postulated to function through an active site base mechanism in which Asp-186 abstracts a proton from galactose. This asparate residue was altered to alanine and to asparagine by site-directed mutagenesis of the corresponding gene. This resulted in variant enzyme with no detectable galactokinase activity. Alteration of Arg-37, which lies adjacent to Asp-186 and is postulated to assist the catalytic base, to lysine resulted in an active enzyme. However, alteration of this residue to glutamate abolished activity. All the variant enzymes, except the arginine to lysine substitution, were structurally unstable (as judged by native gel electrophoresis in the presence of urea) compared to the wild type. This suggests that the lack of activity results from this structural instability, in addition to any direct effects on the catalytic mechanism. Computational estimations of the pK(a) values of the arginine and aspartate residues, suggest that Arg-37 remains protonated throughout the catalytic cycle whereas Asp-186 has an abnormally high pK(a) value (7.18). Quantum mechanics/molecular mechanics (QM/MM) calculations suggest that Asp-186 moves closer to the galactose molecule during catalysis. The experimental and theoretical studies presented here argue for a mechanism in which the C-1-OH bond in the sugar is weakened by the presence of Asp-186 thus facilitating nucleophilic attack by the oxygen atom on the gamma-phosphorus of ATP.