Photolysis of gamma-(alpha-carboxy-2-nitrobenzyl)-L-glutamic acid investigated in the mcrosecond time scale by time-resolved FTIR

The photolytic release of substrates from caged substrates has proven to be an excellent method to generate concentration jumps for kinetic measurements in the microsecond time scale. In this report we use time-resolved FTIR in the step-scan mode to probe the photolysis mechanism of one such caged compound, namely gamma-(alpha-carboxy-2-nitrobenzyl)glutamate, and to obtain a direct measure of the rate of photorelease of the substrate glutamate. The time-resolved difference FTIR spectra exhibit specific signals that can be assigned to the reactant caged glutamate, photolytically released product glutamate, as well as to the aci-nitro intermediate, the key intermediate of the photolysis reaction. Therefore these signals allow the characterization of the kinetics of formation and decay of the intermediate and products. This is the first such report that provides a direct determination of the rate of formation of the photolysis product from a caged compound in the microsecond time scale. Furthermore, the results presented provide a good basis for further time-resolved FTIR studies of molecular reaction mechanisms, such as ligand protein interactions, in the microsecond time scale through the photolytic release of substrates from caged compounds.     

Dinuclear peroxo complexes of molybdenum(VI) containing Mannich base ligands

Dinuclear molybdenum(VI) peroxo complexes containing Mannich base ligands having formulae [Mo₂O₄(O₂)₂L-L(H₂O)₂] · H₂O [where L-L = N-[1-morpholinobenzyl] acetamide (MBA), N-[1-piperidinobenzyl] acetamide (PBA), N-[1-morpholino(-4-nitrobenzyl)] benzamide (MPNBB), N-[1-piperidino(-3-nitrobenzyl)] benzamide (PMNBB), N-[1-morpholino(-2-nitrobenzyl)] acetamide (MONBA), and N-[1-morpholino(-3-nitrobenzyl)] acetamide (MMNBA)] have been synthesized by stirring ammonium heptamolybdate with excess 30% aqueous hydrogen peroxide followed by treatment with ethanolic solution of corresponding ligands. The complexes have been characterized by elemental analysis, molar conductance, magnetic measurements, infrared (IR), electronic, TGA/DTA, mass spectral, and ¹H NMR studies. The complexes are non-electrolytes and diamagnetic. The IR spectral studies suggest that the ligands are bidentate to metal through carbonyl oxygen and ring nitrogen. Thermal analyses provide conclusive evidence for the presence of coordinated, as well as lattice water in the complexes. Dinuclear complexes preserve the individuality of the molybdenum oxo peroxo core. The complexes exhibit higher antibacterial activity against bacterium Ralastonia solanacearum (Pseudomonas solanacearum) than the free ligands.     

Sydnones IV. Synthesis of Sydnones Analogous to the Photochromic Compounds

N-(6-methoxy-3-pyridyl)-sydnone (I), N-(4-nitrobenzyl)sydnone (II-1), and N-(2-nitrobenzyl)sydnone (II-2) have been prepared. Condensation of 2, 4-dinitrochlorohenzene with N-(carbethoxymethyl)sydnone (II-4) produced N-[(2, 4-dinitrophenyl) carbethoxymethyl]-sydnone (II-5). Under normal conditions none of them are photochromic.     

Amperometric determination of urea using an NADH-dependent coupled enzyme

Enzyme electrodes for the amperometric measurement of urea were prepared by co-immobilizing l-glutamate dehydrogenase and urease onto an Immobilon-AV affinity membrane with attachment to a glassy carbon electrode. Reduced nicotinamide adenine dinucleotide (NADH) was used as the electroactive species. The electrochemical oxidation of NADH was monitored at +1.0 V vs. Ag/AgCl. The enzyme immobilized electrode was linear over the range of 2.0 x 10(-5) to 2 x 10(-4)M. The response time of the electrode was 3 min and the optimum pH of enzyme immobilized membrane was pH 7.4-7.6 (Dulbecco's buffer solution). It was stable for at least two weeks and 50 assays. There were no interferences from other physiological material, except for high levels of ascorbic acid.     

Studies on urea biosensors based on immobilized corynebacterium glutamicum and their kinetic response processes

Two novel biosensors for urea based on immobilized corynebacterium glutamicum 617 and corynebacterium glutamicum ATCC13032 in calcium alginate gel coupled with an ammonia gas-sensing electrode, were designed and constructed. Calibration plots of measured potential difference (mV) vs. log of urea concentration were linear in the range of 5.6 x 10(-5)-1.4 x 10(-2) and 5.6 x 10(-5)-1.1 x 10(-2) mol l(-1), with slopes of 59.2 and 61.3 mV per decade respectively, in pH 8.0, 0.1 mol l(-1) phosphate buffer solution at 30 degrees C. The relationship between the initial response velocity and the substrate concentration was also discussed. The results indicate that the kinetic response process of the reaction catalyzed by bacteria is similar to that by isolated enzyme. Using an Eadie-Hofstee plot, the apparent Michaelis constant K(m) and the maximum initial response velocity V(m) for urease in the immobilized bacterial membrane were determined. The two urea biosensors were successfully applied for the actual measurement of urea in urine and were relatively stable for 20 and 40 days respectively.     

New caged coumarin fluorophores with extraordinary uncaging cross sections suitable for biological imaging applications

Photocaged fluorescent molecules are important research tools for tracking molecular dynamics with high spatiotemporal resolution in biological systems. We have designed and synthesized a new class of caged coumarin fluorophores. These coumarin cages displayed more than 200-fold fluorescence enhancement after UV photolysis. Remarkably, the uncaging cross section of a 1-(2-nitrophenyl)ethyl (NPE)-caged coumarin is 6600 at wavelength of 365 nm, about 2 orders of magnitude higher than previously described caged fluorophores. Product analysis of the photolytic reaction showed clean conversion of NPE-caged coumarin to 2-nitrosoacetophenone and the parent coumarin, suggesting that the mechanism of the photolysis follows the known photochemical reaction pathway of the 2-nitrobenzyl group. We have also measured the two-photon uncaging cross sections of NPE-caged coumarins 2a and 5 at 740 nm to be near 1 Goeppert-Mayer (GM). The mechanistic study, together with the two-photon uncaging data, suggested that the coumarin moiety serves as an antenna to enhance the light harvesting efficiency of the coumarin cage and that the photonic energy absorbed by coumarin was utilized efficiently to photolyze the NPE group. Future explorations of this type of "substrate-assisted photolysis" may yield other cages of high uncaging cross sections. For cellular imaging applications, we prepared a cell permeable and caged coumarin fluorophore, NPE-HCCC2/AM (10), which can be loaded into fully intact cells to high concentrations. Initial tests of this probe in a number of cultured mammalian cells showed desired properties for the in vivo imaging applications. The combined advantages of robust fluorescence contrast enhancement, remarkably high uncaging cross sections, noninvasive cellular delivery, and flexible chemistry for bioconjugations should generate broad applications of these caged coumarins in biochemical and biological research.     

Kinetics study of the photocleavage of (coumarin-4-yl)methyl esters

Photolabile coumarinylmethyl esters of biomolecules (caged compounds) are new tools for studying spatial and time-dependent aspects of signal transduction in living cells. Herein we describe a fluoresence spectroscopic method for the determination of the rate constants of the photolysis steps of such caged compounds using (6.7-dimethoxycoumarin-4-yl)methyl diethyl phosphate (DMCM-DEP) and sodium (6,7-dimethoxycoumarin-4-yl)methyl sulfate (DMCM-S). DMCM-DEP and DMCM-S are caged compounds which photorelease a proton, the corresponding acid anion, and the strongly fluorescent alcohol DMCM-OH upon excitation. The results of stationary and time-resolved measurements of the photochemistry and the luminescence of both caged compounds indicate that DMCM-OH is produced already during the excitation pulse. The quantitative analysis of the data demonstrates that the first step of the reaction--heterolytic bond cleavage of the coumarinylmethyl ester leading to the ion pair of a DMCM cation and an acid anion--is very fast with a rate constant of k1 approximately 2 x 10(10) s(-1). Recombination of the ion pair occurs with a rate constant of k(rec) approximately 2.3 x 10(9) s(-1) and is about 10 times faster than the competing hydrolysis reaction of the DMCM cation yielding DMCM-OH and a proton. Thus, both caged compounds belong to the fastest phototriggers known.     

Nickel complexes of carboxylate-containing polydentate ligands as models for the active site of urease

Two new carboxylate-containing polydentate ligands have been synthesized, the symmetric ligand 2,6-bis[N-(N-(carboxylmethyl)-N-((1-methylimidazol)methyl)amine)methyl]-4-methylphenolate (BCIMP) and the corresponding asymmetric ligand 2-(N-isopropyl-N-((1-aminomethyl)-4-methylphenol (ICIMP). The ligands have been used to prepare model complexes for the active site of the dinuclear nickel enzyme urease, viz. [Ni(2)(BCIMP)Ac(2)](-) (6), [Ni(2)(BCIMP)(Ph(2)Ac)(2)](-) (7), [Ni(2)(ICIMP)(Ph(2)Ac)(2)] (14), [Ni(4)(ICIMP)(2)(Ph(2)Ac)(2)][ClO(4)](2) (15), [Ni(4)(ICIMP)(2)(Ph(2)Ac)(2)(DMF)(2)][ClO(4)](2) (16), and [Ni(4)(ICIMP)(2)(Ph(2)Ac)(2)(urea)(H(2)O)][ClO(4)](2) (17), where the latter complex contains urea coordinated in a unidentate fashion through the carbonyl oxygen. The N(2)O-N(2)O(2) donor set of ICIMP provides a good framework for the preparation of urease models, but in some cases tetranuclear nickel complexes are formed due to coordination of the carboxylate moiety of one dinickel-ICIMP unit to one or both of the nickels of a second Ni(2) unit. Reactivity and kinetics studies of 7 and 15 show that these model complexes catalyze hydrolysis of 2-hydroxypropyl p-nitrophenyl phosphate (HPNP) at basic pH. In this assay, complexes based on the asymmetric ligand ICIMP exhibit a significantly faster rate of hydrolysis than the corresponding BCIMP complexes. Magnetic measurements indicate that there are weak antiferromagnetic interactions between the nickel ions in complex 16.     

New Urea Biosensor Based on Urease Enzyme Obtained from Helycobacter pylori

The urease enzyme of Helicobacter pylori was isolated from biopsy sample obtained from antrum big curvature cell extracts. A new urea biosensor was prepared by immobilizing urease enzyme isolated from Helicobacter pylori on poly(vinylchloride) (PVC) ammonium membrane electrode by using nonactine as an ammonium ionophore. The effect of pH, buffer concentration, and temperature for the biosensor prepared with urease from H. pylori were obtained as 6.0, 5 mM, and 25 °C, respectively. We also investigated urease concentration, stirring rate, and enzyme immobilization procedures in response to urea of the enzyme electrode. The linear working range of the biosensor extends from 1 × 10(-5) to 1 × 10(-2) M and they showed an apparent Nernstian response within this range. Urea enzyme electrodes prepared with urease enzymes obtained from H. pylori and Jack bean based on PVC membrane ammonium-selective electrode showed very good analytical parameters: high sensitivity, dynamic stability over 2 months with less decrease of sensitivity, response time 1-2 min. The analytical characteristics were investigated and were compared those of the urea biosensor prepared with urease enzyme isolated from Jack bean prepared at the same conditions. It was observed that rapid determinations of human serum urea amounts were also made possible with both biosensors.     

<Emphasis Type="Italic">N</Emphasis>-(4-methoxy-3-nitrobenzyl) derivatives of some nitrogen-containing heterocycles

A number of nitrogen heterocycles reacted with 4-methoxy-3-nitrobenzyl chloride in dimethyl-formamide in the presence of potassium carbonate to give the corresponding N-(4-methoxy-3-nitrobenzyl) derivatives. The reaction of 5-fluoro-1,3-bis(4-methoxy-3-nitrobenzyl)pyrimidine-2,4(1H,3H)-dione with aqueous methylamine afforded N,N′-bis(4-methylamino-3-nitrobenzyl)urea, whereas analogous reaction with 1-(4-methoxy-3-nitrobenzyl)-2-(methylsulfanyl)-1H-benzimidazole resulted in substitution of the methoxy group by methylamino.     

Photolabile precursors of cyclic nucleotides with high aqueous solubility and stability

Photolabile phosphotriester derivatives of cyclic AMP and cyclic GMP are described, where the additional group on the phosphate is a 2-nitrobenzyl that bears an electron-withdrawing and dianionic substituent. This confers high aqueous solubility and excellent resistance to hydrolysis of the phosphotriester (t(1/2) for hydrolysis at pH 7, 22 degrees C, is >3 months for the axial isomers 3a and 4a and >1 month for the equatorial isomers 3b and 4b). The photolysis quantum yields are in the range 0.15-0.24, and the product release rate upon flash photolysis is 1.7 s(-1) at pH 7.0, 20 degrees C.     

o-nitrobenzyl photolabile protecting groups with red-shifted absorption: syntheses and uncaging cross-sections for one- and two-photon excitation

We evaluated the o-nitrobenzyl platform for designing photolabile protecting groups with red-shifted absorption that could be photolyzed upon one- and two-photon excitation. Several synthetic pathways to build different conjugated o-nitrobenzyl backbones, as well as to vary the benzylic position, are reported. Relative to the reference 4,5-dimethoxy-2-nitrobenzyl group, several o-nitrobenzyl derivatives exhibit a large and red-shifted one-photon absorption within the near-UV range. Uncaging after one-photon excitation was studied by measuring UV-visible absorption and steady-state fluorescence emission on model caged ethers and esters. In the whole series investigated, the caged substrates were released cleanly upon photolysis. Quantum yields of uncaging after one-photon absorption lie within the 0.1-1 % range. We observed that these drop as the maximum wavelength absorption of the o-nitrobenzyl protecting group is increased. A new method based on fluorescence correlation spectroscopy (FCS) after two-photon excitation was used to measure the action uncaging cross section for two-photon excitation. The series of o-nitrobenzyl caged fluorescent coumarins investigated exhibit values within the 0.1-0.01 Goeppert-Mayer (GM) range. Such results are in line with the low quantum yields of uncaging associated with cross-sections of 1-50 GM for two-photon absorption. Although the cross-sections for one- and two-photon absorption of o-nitrobenzyl photolabile protecting groups can be readily improved, we emphasize the difficulty in enlarging the corresponding action uncaging cross-sections in view of the observed trend of their quantum yield of uncaging.     

Sequential determination of urea and HMTA in the process solution of sol-gel route of advanced nuclear fuel fabrication

Determinations of hexamethylene tetramine (HMTA) and urea in the process solutions are required to optimize their concentrations for obtaining high quality ceramic oxide microspheres, for monitoring the washing procedure and for their subsequent recovery, recycling or waste disposal. Determination of urea in the feed solution by conventional procedures is difficult as it contains HMTA. It is more so in the effluent as it contains hydrolytic products like formaldehyde, methylol derivatives of urea, ammonium nitrate and ammonium hydroxide used for washing the gel microspheres. This work describes a derivative potentiometric method using a microprocessor-based autotitrator. Peaks on the first derivative of the titration plot corresponded to constituents of different basicities. Urea was selectively hydrolyzed at room temperature by the catalytic action of urease enzyme leaving HMTA unaffected. Ammonium hydroxide and ammonium bicarbonate produced from urea and HMTA were sequentially titrated for the analysis of the feed solution to obtain the three corresponding peaks respectively. Two separate titrations were required for the analysis of the effluent solution, which contained free ammonia also. One aliquot was first titrated directly without adding urease (for free ammonia and HMTA) and another aliquot was titrated after treatment with urease. The end points due to the ammonia used for washing and that from urea hydrolysis merged resulting in the appearance of three peaks again. Using this sequential method the relative standard deviations were found to be 0.81% and 1.38% for urea and HMTA, respectively, in eight determinations when the aliquots contained 50 to 75 mg of urea and 75 to 125 mg of HMTA. Feed and effluent solutions of the process stream were analyzed.     

Enantiospecific inclusion of chiral 1,2-dichloroethane rotamers in the crystal lattice of chiral square-pyramidal Cu(II) complexes with perfectly polar alignment of guest and host molecules

The inclusion compounds, [CuL(1)2(H2O)].(P)-C2H4Cl2 and [CuL(2)2(H2O)].(M)-C2H4Cl2(HL1 = N-(2-hydroxy-5-nitrobenzyl)-(R)-alpha-methylbenzylamine and HL2 = N-(2-hydroxy-5-nitrobenzyl)-(S)-alpha-methylbenzylamine), crystallise in the non-centrosymmetric space group C2; intermolecular hydrogen bonding leads to a perfectly polar alignment of both host and guest molecules with enantioselectivity.     

Photochemical reaction mechanisms of 2-nitrobenzyl compounds: methyl ethers and caged ATP

The mechanism of methanol photorelease from 2-nitrobenzyl methyl ether (1) and 1-(2-nitrophenyl)ethyl methyl ether (2), and of ATP release from adenosine-5'-triphosphate-[P(3)-(1-(2-nitrophenyl)ethyl)] ester ('caged ATP', 3) was studied in various solvents by laser flash photolysis with UV-vis and IR detection. In addition to the well-known primary aci-nitro transients (A, lambda(max) approximately 400 nm), two further intermediates preceding the release of methanol, namely the corresponding 1,3-dihydrobenz[c]isoxazol-1-ol derivatives (B) and 2-nitrosobenzyl hemiacetals (C), were identified. The dependencies of the reaction rates of A-C on pH and buffer concentrations in aqueous solution were studied in detail. Substantial revision of previously proposed reaction mechanisms for substrate release from 2-nitrobenzyl protecting groups is required: (a) A novel reaction pathway of the aci-tautomers A prevailing in buffered aqueous solutions, e.g., phosphate buffer with pH 7, was found. (b) The cyclic intermediates B were identified for the first time as the products formed by the decay of the aci-tautomers A in solution. A recently proposed reaction pathway bypassing intermediates B (Corrie et al. J. Am. Chem. Soc., 2003, 125, 8546-8554) is shown not to be operative. (c) Hemiacetals C limit the release rate of both 1 (pH < 8) and 2 (pH < 10). This observation is in contrast to a recent claim for related 2-nitrobenzyl methyl ethers (Corrie et al.). Our findings are important for potential applications of the 2-nitrobenzyl protecting group in the determination of physiological response times to bioagents ('caged compounds').     

A NEW DIAZIRINE FOR PROTEIN MODIFICATION BY FLASH PHOTOLYSIS: COMPARISON WITH AN AZIDE

Abstract— A new photolabeling agent, N-[4–(3-chlorodiazirin-3-yl)benzoyl]glycine (CDBG), a carbene generator, was synthesized. The incorporation of its photolytic products into egg white lysozyme was studied using flash photolysis and compared with incorporation of N-(4-azido-2-nitro-phenyl)-2-amino ethane sulfonate (NAPT) products into lysozyme and bovine pancreatic ribonuclease A. There was considerable additional incorporation of photolysis products into ribonuclease and lysozyme after termination of flash photolysis when NAPT was used but no additional incorporation when CDBG was used. Protein labeled with NAPT retained the label poorly during electrophoresis in sodium dodecyl sulfate. Lysozyme labeled with CDBG lost little label upon electrophoresis. Neither label was well retained during electrophoresis in 8 M urea. Peptic and tryptic peptides from CDBG labeled lysozyme were differentially labeled.     

Rate constants for anilidyl radical cyclization reactions

[reaction: see text] N-Aryl-5,5-diphenyl-4-pentenamidyl radicals (3) were produced by 266 nm laser-flash photolysis of the corresponding N-(phenylthio) derivatives, and the rate constants for the cyclizations of these radicals were measured directly. The 5-exo cyclization reactions were fast (k(c) > 2 x 10(5) s(-1)), and radicals 3 generally behaved as electrophilic reactants with a Hammett correlation of rho = 1.9 for five of the six radicals studied. However, the p-methoxyphenyl-substituted radical 3f cyclized much faster than expected from the Hammett analysis. Variable temperature studies of parent radical 3a (aryl = phenyl) gave an Arrhenius function with log k = 9.2 - 4.4/2.3RT (kcal/mol). The rate constant for the reaction of p-ethylphenyl-substituted anilidyl radical 3b with Bu(3)SnH at 65 degrees C was k(T) = 4 x 10(5) M(-1) s(-1).     

Synthesis, Photoreactivity and Cytotoxic Activity of Caged Compounds of L-Leucyl-L-Leucine Methyl Ester, an Apoptosis Inducer

I,-Leucyl-L-leucine methyl ester (Leu-Leu-OMe), an apoptosis inducer in natural killer cells and macro-phages, was caged with trans -o-hydroxycinnamoyl (3ad), trans-o -mercaptocinnamoyl (4) and o -nitrobenzyl derivatives (5a, b), and the photochemical reactivity of these derivatives in phosphate-buffered saline containing 1% dimethyl sulfoxide and their immunological properties were studied. All of the derivatives exhibited absorplion at wavelengths longer than the UVB region. Although 3a–d and 4 were expected to isomerize to a cis isomer, which thgn cyclizes intramolecularly to give Leu-Leu-OMe and a coumarin derivative, cyclization efficiency was not satisfactory except for 3a. However, 3a itself caused necrosis (cell swelling) of U937 cells (a myeloid cell line). In contrast, 5a and b released Leu-Leu-OMe quickly and efficiently and did not affect U937 cells. Although irradiated 5b induced necrosis, irradiated 3a and 5a induced apoptosis in these cells, as evidenced by a decrease in cell size.     

A miniaturized urea sensor based on the integration of both ammonium based urea enzyme field effect transistor and a reference field effect transistor in a single chip

A urea biosensor prepared by covalent binding of urease directly to the surface of an ammonium-sensitive field effect transistor (FET) is described. Nonactin incorporated in carboxylated polyvinyl chloride was used to obtain the sensitive membrane of the ammonium-sensitive FET. The grafting of urease on the polyvinylchloride-COOH membrane surface was performed through carbodiimide coupling. The activity of the immobilized enzyme was spectrometrically controlled through the time-dependent disappearance of the absorbance of NADH at 340 nm. An apparent activity of 50% was found, compared with free enzyme. The sensitivity of the urea enzyme FET is 50 mV/pUrea working in a differential mode of 2 muM to 1 mM, this sensitivity being constant during 15 days. Finally, in order to test the potentialities of the urea biosensor for the environmental applications, the detection of heavy metal ions such as Cu(II) and Hg(II) in solution was performed by measuring the remaining activity of the inhibited enzyme.     

Deactivation of jack bean urease in urea hydrolysis

Deactivation studies of jack bean urease immobilized on porous alumina beads in the hydrolysis of urea were conducted in a continuously stirred tank reactor (CSTR) at a temperature of 25°C and pH 7.0. Though the mechanism of poisoning of urease by product ammonia is fairly well understood from the literature, the nature of the poisoning of urease by urea is presented in this article. These studies were conducted by adsorbing the ammonia formed in the hydrolysis reaction. The results indicate that, in the presence of the adsorbent Zeolite W, the deactivation rate is reduced by a factor of almost two, and thus provide a technique for prolonging the life of the enzyme. The deactivation model suggests that the free form of the enzyme is most susceptible to attack by the substrate urea. The experimental data suggest that deactivation by combined ammonia and urea is fairly complex.