Effects of solvent and ionic medium on the kinetics of axial ligand substitution in vitamin B12. Part II. the reaction between aquocobalamin and thiourea in dioxane-water and acetonitrile-water mixtures

The rate constants for the reaction of aquocobalamin with thiourea were measured as a function of ionic strength, pH and solvent composition in dioxane-water and acetonitrile-water mixtures. With the help of solubility measurements a complete quantitative analysis of solvent effects on the reaction profile could be made. The transfer Gibbs energy of the initial state strongly depends on solvent composition. Because the transition state and the final state closely follow the initial state, this is not reflected in the rate constants.For the acetonitrile-water mixtures the transfer enthalpy and transfer entropy were determined and were found to exhibit the familiar compensation effect.It is concluded that, when the solvent changes, vitamin B₁₂ creates its own micro-environment around the active metal site, so that the reactivity is effectively solvent independent. The mechanism of activation is dissociative.     

Chemiluminescence of iron-chlorophyllin.

The iron-chlorophyllin complex was found to be chemiluminescent (CL) in an acetonitrile (22%)/water mixed solvent. In the presence of hydrogen peroxide, when iron-chlorophyllin was added to the mixed solvent, a sharp CL signal immediately appeared. Also, analysis of the absorption spectra revealed decomposition of iron-chlorophyllin (based on decrease in absorbance at 396 nm), hence iron-chlorophyllin is the CL substance. Moreover, the CL intensity decreased in the presence of potassium thiocyanate (KSCN), indicating that the axial coordinative position of iron-chlorophyllin acts as a point of catalytic activation. In addition, when fluorophores were present with iron-chlorophyllin CL, their CL intensity values were similar to or greater than that of the well-known trichlorophenylperoxalate ester (TCPO) CL. Thus, during the decomposition reaction of iron-chlorophyllin, the latter transfers its energy to the coexisting fluorophores. Moreover, since the decomposed compound in this CL reaction had a fluorescence, it was found that the iron-chlorophyllin also functions as an energy donor. Therefore, the iron-chlorophyllin complex acts not only as a CL substance, but also as a catalyst and energy donor in the reaction.     

Conversion of lipids to fatty alcohols and lysolipids by NaBH4

A variety of fatty acid esters were reacted with NaBH₄ in tetra-hydrofuran (THF) — water mixtures. Although triglycerides and free acids were stable under the conditions employed, more polar lipids were extensively reduced to the corresponding fatty alcohols. Thus when reacted with NaBH₄ for 60 min at 37°C, 94% and 64% respectively of the acyl groups in lecithin and monogalactosyl diglyceride were reduced to fatty alcohols. No discernible reduction or isomerisation of double bonds occurred during the reactions. Reductions in the reaction temperature, and in the THF content of the solvent, both resulted in slower reaction rates.The reactions with complex lipids proceded with the intermediate formation of the corresponding monoacyl (“lyso”) lipids, but the reagent showed no selectivity towards position or structure of the component ester groups.In its proposed form, the method for determining acyl thiolesters in biological tissues by their specific reduction with NaBH₄, is not satisfactory.     

Effects of solvent viscosity and different guanidine salts on the kinetics of ribonuclease A chain folding

The kinetics of folding of the two forms of unfolded ribonuclease A have been measured as a function of solvent viscosity by adding either glycerol or sucrose. The aim is to find out if either reaction is rate limited by segmental motion whose rate depends on external friction. The fast folding reaction (U₂ ? N) is known to be the direct folding process, and the slow folding reaction (U₁ ? N) is known to be rate limited by an interconversion between two forms (U₁ ? U₂) which are present after unfolding in strongly denaturing conditions. No dependence on solvent viscosity is found, either for the direct folding reaction or for the interconversion reaction. Each folding reaction has also been tested to see if its rate depends on the concentration of one or more partly folded intermediates, by adding denaturants destabilize any partly folded structures. Different guanidine salts are used as denaturants to vary the denaturing effectiveness of the salt while holding the guanidinium ion concentration constant. The rates both of the direct folding reaction and of the interconversion reaction decrease in relation to the denaturing effectiveness of the salt. However, there is a basic difference between the responses of the fast and slow folding reactions to low concentrations of denaturants. Although each folding reaction produces native protein, there is an 800-fold decrease in the rate of the fast folding reaction in 1M guanidine thiocyanate and only a 13-fold decrease in the rate of the slow folding reaction. This is consistent with the fast reaction being the direct folding process and the slow reaction being rate limited by the initial conversion of the slowrefolding to the fast-refolding form. Both the lack of viscosity dependence and the effects of denaturants indicate that the formation of structure is rate limiting in the direct folding reaction, U₂ ? N. The failure to find a viscosity dependence for the interconversion reaction, U₁ ? U₂, indicates that in this reaction also friction-limited segmental motion is not the rate-limiting process. Since the U₁ ? U₂ interconversion still occurs when the polypeptide chain is completely unfolded, the surprising result is that its rate in refolding conditions depends significantly on a reaction intermediate which is “denatured” by guanidine salts.     

Intramolecular and overall motion of proline: the influence of viscosity on carbon-13 spin-lattice relaxation times.

Nuclear magnetic resonance of ¹³C is used to probe the overall and internal motions of proline. Spin-lattice relaxation times (T₁) are reported for proline monomer dissolved in water/glycerol mixtures. Rates of overall molecular motion and internal motion depend on solvent composition but to different degrees. The effective correlation times (τ_eff) of the various proton-bearing carbon atoms in proline vary linearly as a function of solvent composition (%v/v) rather than of solution viscosity. The effective correlation time for molecular motion (τ_eff) is separated into contributions from overall molecular motion (τ_mol) and internal motion (τ_int). The γ-carbon of proline shows the smallest dependence of τ_int on solvent composition. The data indicate a high degree of intramolecular motion for the γ-carbon of proline. Inclusion of anisotropic molecular reorientation in the data analysis was found not to affect the above conclusions. The observed values of τ_eff indicate that the rotational diffusion model of molecular reorientations should apply to proline. The values of τ_eff calculated for proline using the Stokes-Einstein relation are larger than those observed; the discrepancy is discussed in terms of solvent-solute interactions.     

Thermodynamics of the helix-coil transition in polypeptides in mixed organic solvents: the influence of inert solvent and side chain

The thermally induced coil–helix transition of poly(γ-benzyl-L -glutamate) (PBLG) and poly(γ-methyl-L -glutamate) (PMLG) in binary solvent mixtures was investigated by calorimetric and optical rotatory dispersion (ORD) measurements. Dichloroacetic acid was the common active solvent, and the inert solvent was one of the chlorinated hydrocarbons, such as chloroform, 1,3-dichloropropane, 1-chlorobutane, or 1-chlorooctane. The thermodynamic parameters characterizing the intramolecular polypeptide and polypeptide–solvent interactions were calculated using the Karasz and Gajnos theoretical model [(1973) J. Phys. Chem. 77 , 1139–1145]. It was found that the enthalpy (ΔH₁) and entropy (ΔS₁) of helix stabilization in the absence of the active solvent depend on the inert solvent, but only in the case of PBLG. This is explained by the additional helix stabilization achieved by the stacking of the benzyl groups. The stacking is more pronounced in less polar chlorinated hydrocarbons with longer aliphatic chains. The results obtained indicate that the maximum helix stability is reached in chlorinated hydrocarbons with 12 C atoms. In the case PMLG, with an aliphatic ester side group, ΔH₁ and ΔS₁ are independent of the inert solvent. The ORD measurements were used to determine the maximum fraction of helicity attained at constant solvent composition and the transition temperature, T_c, at the point where f_H = 0.5. It was found that, for the same solvent composition, T_c was higher than the temperature of the midpoint of the calorimetric peak. This is explained by the fact that the maximum fraction of helicity is less than unity. The finite transition width was taken into account by calculating the phase boundaries for different fractions of helicity using the value of σ estimated from the calorimetric and van't Hoff enthalpies in the usual manner.     

Sub-nanosecond photolysis studies of Fe protoporphyrin IX solubilized in neat dimethyl sulfoxide

The present study examines the optical properties of the sub-nanosecond photolytic transient of Fe(II)protoporphyrin IX (Fe(II)PPIX) in neat dimethyl sulfoxide (DMSO). Previous nanosecond studies have revealed that photolysis of the (DMSO)₂Fe(II)PPIX complex in neat DMSO results in the formation of a five-coordinate high-spin (DMSO)Fe(II)PPIX complex within ∼100 ns which decayed with a pseudo-first order rate constant of 2 × 10⁶ s⁻¹ (Larsen et al. (1995) [19]). The results presented here demonstrate that the five-coordinate (DMSO)Fe(II)PPIX species is generated in <100 ps and that no significant changes occur in the kinetic difference between 100 ps and ∼100 ns. The 100 ps transient spectrum of the (DMSO)Fe(II)PPIX complex was also constructed from the kinetic difference spectrum and the equilibrium spectrum of the (DMSO)₂Fe(II)PPIX. The 100 ps transient spectrum exhibits a Soret maximum at ∼432 nm close to that of deoxyMb (435 nm, imidazole coordination) consistent with S-bonded DMSO occupying the fifth coordination site. Neither base elimination is detected on time scales down to 100 ps nor is there evidence for transient O-bonded DMSO followed by linkage isomerization to the equilibrium S-bonded form. The unusually slow rate of DMSO recombination is attributed to electrostatic interactions between DMSO and the five-coordinate heme iron as well as intermolecular interactions between solvent molecules in the bulk, as has been previously proposed.     

Catalytic effect of water,water dimer,HCOOH and H2SO4 on the isomerisation of HON(O)NNO2 to ON(OH)NNO2: a mechanism study

ABSTRACT

In this article, we report a theoretical investigation on the role of several catalysts in the isomerisation mechanisms of HON(O)NNO₂ to ON(OH)NNO₂ by theoretical method of CBS-QB3. The isomerisation reactions with catalyst X (X?=?H₂O, (H₂O)₂, HCOOH and H₂SO₄) are multi-hydrogen atom transfer reactions. Compared to the isomerisation mechanisms and rate constant of HON(O)NNO₂ to ON(OH)NNO₂ without catalysts, incorporation of the catalyst X shows different positive catalytic effects on affecting the reaction processes, with the H₂SO₄-assisted reaction being the most favourable. Such different catalytic effects are mainly related to the size of the ring structure in X-assisted transition states and the different values of pK_a and proton affinities for HCOOH and H₂SO₄. Besides, compared with the barrier height of the isomerisation process from HON(O)NNO₂ to ON(OH)NNO₂ with HN(NO₂)₂ and HON(O)NNO₂, the barrier of H₂SO₄-assisted reaction is lower by 9.3 and 4.5?kcal?·mol^?1, meanwhile, the rate constant of H₂SO₄ catalyzed is larger than water and water dimer–assisted by 3–5 and 2–3 orders of magnitude, respectively. So, H₂SO₄-assisted reaction is the most favourable.     

UPLC-MS profiling of low molecular weight phlorotannin polymers in Ascophyllum nodosum,Pelvetia canaliculata and Fucus spiralis

Phlorotannins are a group of complex polymers, found in particular brown macroalgae, composed solely of the monomer phloroglucinol (1,3,5-trihydroxybenzene). Their structural complexity arises from the number of possible linkage positions between each monomer unit. This study aimed to profile the phlorotannin metabolite composition and the complexity of isomerisation present in brown macroalgae Ascophyllum nodosum, Pelvetia canaliculata and Fucus spiralis using UPLC-MS utilising a tandem quadrupole mass spectrometer. Phlorotannin-enriched fractions from water and aqueous ethanol extracts were analysed by UPLC-MS performed in multiple reaction monitoring mode to detect molecular ions consistent with the molecular weights of phlorotannins. Ascophyllum nodosum and P. canaliculata appeared to contain predominantly larger phlorotannins (degree of polymerisation (DP) of 6–13 monomers) compared to F. spiralis (DP of 4–6 monomers). This is the first report observing the complex chromatographic separation and metabolomic profiling of low molecular weight phlorotannins consisting of more than ten monomers. Extracted ion chromatograms, for each of the MRM transitions, for each species were analysed to profile the level of isomerisation for specific molecular weights of phlorotannins between 3 and 16 monomers. The level of phlorotannin isomerisation within the extracts of the individual macroalgal species differed to some degree, resulting in substantially different numbers of phlorotannin isomers for particular molecular weights. A similar UPLC-MS/MS separation procedure, as outlined in this study, may be used in the future as a means of screening the metabolite profile of macroalgal extracts, therefore, allowing extract consistency to be monitored for standardisation purposes.     

Interaction of thiocyanate with horseradish peroxidase. 1H and 15N nuclear magnetic resonance studies

Interaction of thiocyanate with horseradish peroxidase (HRP) was investigated by relaxation rate measurements (at 50.68 MHz) of the 15N resonance of thiocyanate nitrogen and by following the hyperfine shifted ring methyl proton resonances (at 500 MHz) of the heme group of SCN-.HRP solutions. At pH 4.0, the apparent dissociation constant (KD) for thiocyanate binding to HRP was deduced to be 158 mM from the relaxation rate measurements. Chemical shift changes of 1- and 8-ring methyl proton resonances in the presence of various amounts of thiocyanate at pH 4.0 yielded KD values of 166 and 136 mM, respectively. From the pH dependence of KD and the 15N resonance line width, it was observed that thiocyanate binds to HRP only under acidic conditions (pH less than 6). The binding was found to be facilitated by protonation of an acid group on the enzyme with pKa 4.0. The pH dependence of the 15N line width as well as the apparent dissociation constant were quantitatively analyzed on the basis of a reaction scheme in which thiocyanate in deprotonated ionic form binds to the enzyme in protonated acidic form. The KD for thiocyanate binding to HRP was also evaluated in the presence of an excess of exogenous substrates such as resorcinol, cyanide, and iodide ions. It was found that the presence of cyanide (which binds to heme iron at the sixth coordination position) and resorcinol did not have any effect on the binding of thiocyanate, indicating that the binding site of the thiocyanate ion is located away from the ferric center as well as from the aromatic donor binding site. The KD in the presence of iodide, however, showed that iodide competes with thiocyanate for binding at the same site. The distance of the bound thiocyanate ion from the ferric center was deduced from the 15N relaxation time measurements and was found to be a 6.8 A. From the distance as well as the change in the chemical shifts and line width of 1- and 8-methyl proton resonances, it is suggested that the binding site of thiocyanate may be located near heme, placed symmetrically with respect to 1- and 8-methyl groups of the heme of HRP. Similarity in the modes of binding of iodide and thiocyanate suggests that the oxidation of thiocyanate ion by H2O2 may also proceed via the two-electron transfer pathway under acidic conditions, as is the case for iodide.     

The formation and reactivity of sulfito complexes of tetraethylenepentamine-cobalt(III): X-ray structure of αα-[co(tetren)SO3]ClO4

The synthesis of complexes of the type Co(tetren)-OH₂³⁺ (tetren = tetraethylenepentamine) and their reactions with sulfite to produce O- and S-bonded isomers were studied in detail. The linkage isomerization reaction of αβS-Co(tetren)OSO₂⁺ to αβS-Co(tetren)SO₃⁺ is accompanied by a geometrical isomerization to αα-Co(tetren)SO₃⁺. The latter species was isolated as pure crystals and an X-ray structure was determined. The structure data clearly show the strong trans effect of the sulfito ligand, which may account for the geometrical isomerization process.     

An improved chemical approach toward the C-terminal sequence analysis of proteins containing all natural amino acids.

An improved chemical method, capable of derivatizing all natural amino acids to their corresponding thiohydantoins, is described. This involves activation by acetyl chloride in TFA followed by derivatization with ammonium thiocyanate. Possible interference of reactive side chains was investigated by reacting N-acetylamino acids as well as several peptides with propionyl chloride instead of acetyl chloride. The products were characterized by PDMS mass spectrometry and 1H-NMR. This chemical method allows, for the first time, complete derivatization of N-acetylproline to proline thiohydantoin. Applying this chemistry to peptides with a C-terminal proline, the yields for formation of proline thiohydantoin were found to be up to 60%, depending on the peptide sequence. The previous inability to derivatize C-terminal proline to thiohydantoin was thought to stem from the fact that proline cannot form the oxazolonium ion required for efficient reaction with the thiocyanate ion. However, we have found mass spectrometric evidence for the existence of a proline oxazolonium ion, under basic as well as under acidic conditions. This improvement in derivatization of C-terminal amino acids including proline is a major step forward in the development of a general chemical C-terminal sequencing method that permits the C-terminal sequence analysis of proteins of any amino acid composition.     

The mechanism of the rearrangement of linoleate hydroperoxides

Linoleate hydroperoxides undergo rearrangement leading to their isomerisation in which the OOH group is relocated or the stereochemistry of a double bond changed, or both. The reaction was studied mainly with pure isomers of methyl hydroperoxylinoleates since conditions could be found in which rearrangement occurred with little accompanying decomposition. The rearrangement was found to be non-stereoselective and took place by a free-radical chain mechanism. Using ¹⁸O-labelled hydroperoxide on ¹⁸O₂, it was shown that the oxygen atoms of the OOH group of the hydroperoxides exchanged with surrounding molecular oxygen during the rearrangement. A mechanism for the rearrangement is proposed.     

Effects of solvent and ionic medium on the kinetics of axial ligand substitution in vitamin B12. Part III. Reactions of aquocobalamin and aquamethylcobaloxime with sulfur-coordinating ligands

Rate constants for the reactions of aquocobalamin and aquamethylcobaloxime with a series of uncharged sulfur-coordinating ligands were measured in the solvents water and 50 vol% dioxane-water. For both complexes in both solvent systems a linear free energy relationship was found with unit slope, indicating a dissociative mode of activation. With the help of solubility measurements a complete quantitative analysis of solvent effects on the reaction profile could be made. For both cobalt complexes the solvent effects on the reaction profiles are comparable, but in the case of aquocobalamin the kinetic parameters are more influenced by steric factors and hydrogen bonding. From the quantitative analysis of the reactivity of aquocobalamin and aquamethylcobaloxime it is concluded, that for biological reactions where steric effects and/or hydrogen bonding play an important role, aquamethylcobaloxime is not a good model compound for vitamin B₁₂.     

Effects of solvent and ionic medium on the kinetics of axial ligand substitution in vitamin B12. Part VI. Partial molar volumes of some cobalamin derivates

Apparent molar volumesφ_v, were measured at 25 °C in 0.1 molal NaClO₄ for aquocobalamin chloride, methylcobalamin, 5′-deoxyadenosylcobalamin and aquanitrocobaloxime. For the organocobalamins the pH dependence of φ_v was studied, and for aquocobalamin and aquanitrocobaloxime the dependence on solvent composition was studied. The base-off forms of the organocobalamins have the same volumes as the base-on forms. The apparent molar volume of aquocobalamin chloride is almost independent of solvent composition in dioxane-water mixtures, but increases dramatically in acetonitrile-water mixtures.     

Ru(phen)2(bis-thioether) complexes: Synthesis and photosubstitution reactions

Three new ruthenium(II) complexes which contain two 1,10-phenanthroline units and a third bis-thioether chelate have been prepared and characterized. For two complexes, the X-ray structure shows a perfect fit between the two phen ligands and the bis-thioethers, with almost perfect C₂ symmetry for the Ru(phen)₂ unit and the S-containing ligand. This geometrical complementarity is also reflected by π-π stacking between the phen nuclei and the S-borne phenyl rings. In relatively harsher preparation conditions a ruthenium complex composed of one phenanthroline and two bis-thioethers is formed as a result of a scrambling reaction. When a bis-thioether chelate incorporated in a macrocycle also including a 6,6′-disubstituted-2,2′-bipyridine unit is used, ¹H NMR study shows that an exo S-bonded ruthenium(II) complex is obtained. In presence of chloride anions a photosubstitution reaction of the bis-thioether chelate takes place selectively and efficiently.     

13C-NMR and transient kinetic studies on lactate dehydrogenase [Cys(13CN)165]. Direct measurement of a rate-limiting rearrangement in protein structure

Chemical modification of cysteine-165 in pig heart lactate dehydrogenase to produce lactate dehydrogenase [Cys(13CN)165] introduces an covalently bound, enriched 13C probe at a position adjacent to the active cen. The signal from the thiocyanate probe is clearly visible at 47 ppm relative to dioxane. On formation of binary complexes with NAD+ and NADH, no signal change is detected. Formation of the ternary complexes E-NADH-oxamate and E-NAD+-oxalate results in an upfield shift of the signal of 1.2 ppm. These results interpreted as demonstrating that binding of the substrate analogue induces a conformational change a position adjacent to the active centre. Exchange experiments in which the enzyme is poised in dynamic equilibrium between binary and ternary complexes show that the rate at which the probe senses a change environment is the same as the kinetically observed unimolecular event which limits the enzyme-catalyst reduction of pyruvate. The two processes show the same dependence on temperature, solvent composition and pH. These results indicate that the rate-limiting isomerisation corresponds to a rearrangement of the protein in the region of cysteine-165.     

Purification, properties, and kinetic observations on the isoenzymes of NADP isocitrate dehydrogenase of maize.

A successful method for the purification of NADP isocitrate dehydrogenase from a plant source, Zea mays, is reported. Two mitochondrial isoenzymes were found and purified to homogeneity by a course of acetone fractionation, bulk exchange on DEAE-cellulose, cellulose hydroxylapatite column chromatography, and continuous elution electrophoresis. The mitochondrial isoenzymes are very similar with respect to kinetic properties, response to solvent perturbation, and temperature dependence of the pH/V relationship of isocitrate dehydrogenation. The Michaelis constant for isocitrate is identical for both isoenzymes. The enzymes have a molecular weight of 81,000 as estimated by permeation chromatography and an isoelectric point of 5.5 as extrapolated from gel-electrophoretic mobilities. Detectable differences are confined to differences in electrophoretic mobilities and heat denaturation. In D₂O the rate of the overall reaction from isocitrate to α-ketoglutarate and CO₂ was about 3.6 times slower than the same reaction in H₂O. Both the forward and reverse reactions, in which isocitrate is dehydrogenated or generated from oxalosuccinate, were observed to decrease by this amount in D₂O. The decarboxylation of oxalosuccinate was found to decrease by only about 25% in D₂O relative to the velocity of the reaction in H₂O. Thus the slow step in the overall reaction must be the initial dehydrogenation step rather than the decarboxylation of oxalosuccinate. The pK of the overall reaction did not change in D₂O as compared to H₂O.     

Studies on silk fibroin of the silkworm Bombyx mori

A procedure has been developed to obtain native fibroin in a pure state from the reservoir part of the silk gland. The purified protein has a sedimentation coefficient of 10 S as determined on sucrose density gradients and the amino acid composition is similar to that reported for fibroin from the cocoons. The effects of various solvents has been studied; lithium thiocyanate was found to be the solvent of choice. By in vivo labeling of fibroin with [³H]glycine and [¹⁴C]alanine it was demonstrated that fibroin synthesized in the posterior part of the gland and that stored in the reservoir part are identical.