The role of sulphur in chemical evolution

Summary Sulphur may have played an important role, mainly as an energy converter, during the initial steps of Chemical Evolution.In atmospheric processes, sulphur, in the form of H₂S might have been a primary energy acceptor and a source of hot hydrogen atoms. The presence of H₂S in the primeval earth atmosphere with a molar ratio of about 10^–2 could have allowed the formation of several volatile S-containing compounds without inhibiting the synthesis of the reactive products which are formed in the absence of H₂S. An evaluation of the quantity of H₂S which could have been included in the primeval atmosphere suggests that such a molar ratio may have been reached.In the primitive soup, the thiols and sulphides formed in the gaseous phase may have evolved, giving rise to various prebiotic syntheses. Studies on the addition reaction of alkanethiols on malonic nitriles in aqueous solutions show two different condensation processes: the formation of thioethers and the formation of iminothioesters. Taking into account the values of the specific rate constants for the two reactions, it is shown that these reactions may have taken place in the primitive earth conditions. These two compounds may have played an important role in the prebiochemical evolution. In particular, iminothioesters can be considered as the immediate precursors of thioesters.     

A new scaffold for amide ligation.

Highly chemoselective amide forming ligation reactions have facilitated the synthetic access to proteins and other amide-linked bioconjugates. In order to generalize this approach, a N(alpha)-2-phenyl ethanethiol scaffold has been developed to promote S to N acyl transfer in a manner analogous to native chemical ligation with N-terminal cysteine residues. Analysis of scaffold-mediated ligation reactions in aqueous solution indicate that the ligation rate at Xaa-Gly junctions is sufficient for the synthesis of large polypeptides. In addition, it was found that the ligation rate is independent of the stereocenter in the scaffold and S- to N-acyl transfer is rate limiting. These studies indicate that the N(alpha)-2-phenyl ethanethiol scaffold is a good candidate for the development of a ligation chemistry for the formation of Xaa-Gly peptides and other unhindered amides.     

A group contribution method for the estimation of equilibrium constants for biochemical reactions

Using Gibbs Energies of compounds, as well as Gibbs Energy changes and equilibrium constants of biochemical reactions, the contributions of functional groups to the Gibbs Energy (in aqueous solution, temperature 25°C, and pH=7) have been estimated. These contributions allow the estimation of the Gibbs Free Energy and the equilibrium constant of a biochemical reaction, given the structure of the reactants and products.     

The kinetics and mechanisms of the complex formation and antioxidant behaviour of the polyphenols EGCg and ECG with iron(III)

(-)-Epigallocatechin-gallate ((-)-EGCg) and (-)-epicatechin-gallate ((-)-ECG) are important antioxidants which are found in green tea. The kinetics and mechanisms of the reactions of a pseudo-first order excess of iron(III) with EGCg and ECG have been investigated in aqueous solution at 25 degrees C and an ionic strength of 0.5M NaClO(4). Mechanisms have been proposed which account satisfactorily for the kinetic data. These are consistent with a mechanism in which the 2:1 metal:ligand complex initially formed on reaction of iron(III) with the ligand subsequently decomposes in an electron transfer step. Complex formation takes place at two separate binding sites via coupled reactions. Rate constants of 4.28(+/-0.06) x 10(6) M(-2) s(-1) and 2.83(+/-0.04) x 10(6) M(-2) s(-1) have been evaluated for the reaction of monohydroxy Fe(OH)2+ species with EGCg and ECG, respectively while rate constants for of 2.94(+/-0.4) x 10(4) M(-2) s(-1) and 2.41(+/-0.25) x 10(4) M(-2) s(-1) have been evaluated for the reaction of Fe3+ species with EGCg and ECG, respectively. The iron(III) assisted decomposition of the initial iron(III) complex formed was also investigated and the rate constants evaluated. Both the complex formation and subsequent electron transfer reactions of iron(III) with EGCg and ECG were monitored using UV-visible spectrophotometry. All of the suggested mechanisms and calculated rate constants are supported by calculations carried out using global analysis of time dependant spectra. The results obtained show that one molecule of either EGCg or EGC is capable of reducing up to four iron(III) species, a fact which is consistent with the powerful antioxidant properties of the ligands.     

The kinetics and mechanisms of the reactions of aluminium(III) with gallic acid, gallic acid methyl ester and adrenaline

The kinetics and mechanisms of the reactions of gallic acid, gallic acid methyl ester and adrenaline with aluminium(III) have been investigated in aqueous solution at 25 degrees C and an ionic strength of 0.5 M. A mechanism has been proposed which accounts satisfactorily for the kinetic data. This is consistent with a mechanism in which complex formation takes place almost exclusively by reaction of [Al(H2O)5OH]2+ with the ligands. [Al(H2O)5OH]2+ reacts with gallic acid, gallic acid methyl ester and adrenaline with rate constants of 1145, 1330 and 316 M(-1) s(-1) respectively. These data together with the equilibrium data enable the rate constants for reaction of [Al(H2O)6]3+ with both gallic acid and gallic acid methyl ester to be calculated. In view of the dissociative nature of water exchange on [Al(H2O)6]3+ and [Al(H2O)5(OH)]2+ the complex formation rate constants are discussed in terms of the Eigen-Wilkins-Tamm mechanism. The overall mechanisms have been validated using global analysis. The results are compared with previously published data on the complex formation reactions of aluminium(III). In addition, the rate constants and mechanisms for replacement of maltol by gallic acid methyl ester and diethylenetriaminepentaacetic acid (dtpa) have been investigated.     

Prebiotic synthesis of diaminopyrimidine and thiocytosine

The reaction of guanidine hydrochloride with cyanoacetaldehyde gives high yields (40–85%) of 2,4-diaminopyrimidine under the concentrated conditions of a drying lagoon model of prebiotic synthesis, in contrast to the low yields previously obtained under more dilute conditions. The prebiotic source of cyanoacetaldehyde, cyanoacetylene, is produced from electric discharges under reducing conditions. The effect of pH and concentration of guanidine hydrochloride on the rate of synthesis and yield of diaminopyrimidine were investigated, as well as the hydrolysis of diaminopyrimidine to cytosine, isocytosine, and uracil. Thiourea also reacts with cyanoacetaldehyde to give 2-thiocytosine, but the pyrimidine yields are much lower than with guanidine hydrochloride or urea. Thiocytosine hydrolyzes to thiouracil and cytosine and then to uracil. This synthesis would have been a significant prebiotic source of 2-thiopyrimidines and 5-substituted derivatives of thiouracil, many of which occur in tRNA. The applicability of these results to the drying lagoon model of prebiotic synthesis was tested by dry-down experiments where dilute solutions of cyanoacetaldehyde, guanidine hydrochloride, and 0.5m NaCl were evaporated over varying periods of time. The yields of diaminopyrimidine varied from 1 to 7%. These results show that drying lagoons and beaches may have been major sites of prebiotic syntheses.     

Reactions of linoleic acid peroxyl radicals with phenolic antioxidants: a pulse radiolysis study

Linoleic acid peroxyl radicals (LOO.) can be viewed as model intermediates occurring during lipid peroxidation processes. Formation and reactions of these species were investigated in aqueous alkaline solution using the technique of pulse radiolysis combined with kinetic spectroscopy. Irradiation of linoleic acid in N2O/O2-saturated solutions leads to a mixture of peroxyl radical isomers, whereas reaction of 13-hydroperoxylinoleic acid (13-LOOH) with azide radicals in N2O-saturated solution produces 13-LOO. radicals specifically. These peroxyl radicals cannot be observed directly, but their reactions with the two flavonols, kaempferol and quercetin, acting as radical-scavenging antioxidants, produced strongly absorbing aroxyl radicals (ArO.). The same aroxyl radicals were generated by .OH and N3. with rate constants exceeding 10(9) dm3 mol-1 s-1. Applying a reaction scheme that includes competing generation and decay reactions of both LOO. and ArO. radicals, we derived individual rate constants for LOO. reactions with the phenols (greater than 10(7) dm3 mol-1 s-1), with the aroxyl radicals to form covalent adducts (greater than 10(8) dm3 mol-1 s-1), as well as for their bimilecular decay (3.0 X 10(8) dm3 mol-1 s-1). These results demonstrate the high reactivity of both fatty acid peroxyl radicals and the flavone antioxidants in aqueous solution.     

An evolutionary approach to enzyme kinetics: Optimization of ordered mechanisms

A theoretical investigation is presented which allows the calculation of rate constants and phenomenological parameters in states of maximal reaction rates for unbranched enzymic reactions. The analysis is based on the assumption that an increase in reaction rates was an important characteristic of the evolution of the kinetic properties of enzymes. The corresponding nonlinear optimization problem is solved taking into account the constraint that the rate constants of the elementary processes do not exceed certain upper limits. One-substrate-one-product reactions with two, three and four steps are treated in detail. Generalizations concern ordered uni-uni-reactions involving an arbitrary number of elementary steps. It could be shown that depending on the substrate and product concentrations different types of solutions can be found which are classified according to the number of rate constants assuming in the optimal state submaximal values. A general rule is derived concerning the number of possible solutions of the given optimization problem. For high values of the equilibrium constant one solution always applies to a very large range of the concentrations of the reactants. This solution is characterized by maximal values of the rate constants of all forward reactions and by non-maximal values of the rate constants of all backward reactions. Optimal kinetic parameters of ordered enzymic mechanisms with two substrates and one product (bi-uni-mechanisms) are calculated for the first time. Depending on the substrate and product concentrations a complete set of solutions is found. In all cases studied the model predicts a matching of the concentrations of the reactants and the corresponding Michaelis constants, which is in good accordance with the experimental data. It is discussed how the model can be applied to the calculation of the optimal kinetic design of real enzymes.     

The pH dependence of the reactions of flavin triplet states with amino acids: A laser flash photolysis study

The pH dependence of the rate constants of reaction of several amino acids with the triplet states of flavin mononucleotide in aqueous solution has been determined. In addition, the relative contributions of hydrogen atom transfer, electron transfer and physical deactivation to the overall process of triplet quenching by amino acids have been estimated.Analogous experiments to those with amino acids were carried out with EDTA as the substrate. The results indicate that the flavin triplet state abstracts an electron from EDTA but does not form an excited state flavin-EDTA complex as suggested in a previous study.     

Subzero temperature quenching and electrophoretic methods for the isolation of protein reaction intermediates

A quenching technique for the study of rapid protein reactions is described which consists of injecting a small volume of aqueous solution of reactants into a large volume (× 10) of hydro-organic solvent cooled at subzero temperature and mechanically shaken. The protein reaction intermediates, stabilized at subzero temperature and brought into a hydro-organic solution, can then be separated by subzero temperature electrophoretic methods, such as isoelectric focusing, in the same solvent. The alkaline hydrolysis of 2,4-dinitrophenylacetate was studied by the use of this quenching technique in order to compare the quenching and the rate constants of the reaction with those obtained by normal rapid quenching methods. It was found that first-order reactions having rate constants up to about 5 s^?1 can be satisfactorily studied by this technique. The technique is not suitable for the study of faster reactions because of the high value of the quenching time (40–100 ms). The hybridization reaction of carboxyhemoglobins A and C in aqueous solution at 22°C was studied as an example of the application of this quenching technique and of the isoelectric focusing method at subzero temperature to the isolation of unstable intermediates in a protein reaction.     

Investigations of S-transnitrosylation reactions between low- and high-molecular-weight S-nitroso compounds and their thiols by high-performance liquid chromatography and gas chromatography-mass spectrometry.

S-Transnitrosylation reactions are supposed to be the basic principle by which nitric oxide-related biological activities are regulated in vivo. Mechanisms of S-transnitrosylation reactions are poorly understood and equilibria constants for physiological S-nitroso compounds and thiols are rare. In the present study we investigated S-transnitrosylation reactions of the thiols homocysteine, cysteine, glutathione, N-acetylcysteine, N-acetylpenicillamine, and human plasma albumin and their corresponding S-nitroso compounds SNhC, SNC, GSNO, SNAC, SNAP, and SNALB utilizing high-performance liquid chromatographic and gas chromatographic-mass spectrometric techniques. These methods allowed to study S-transnitrosylation reactions in mixtures of several S-nitroso compound/thiol pairs, to determine equilibria constants, and to elucidate the mechanism of S-transnitrosylation reactions. We obtained the following order for the equilibria constants in aqueous buffered solution at pH 7.4: SNhC approximately SNAC > GSNO approximately SNALB > SNAP > SNC. Our results suggest that the mechanism of S-transnitrosylation reactions of these S-nitroso compounds and their thiols involve heterolytic cleavage of the S&sbond;N bond. Incubation of SNC with human red blood cells resulted in a dose-dependent formation of GSNO in the cytosol through S-transnitrosylation of intracellular GSH by the SNC transported into the cells. This reaction was accompanied with an almost complete disappearance of the SNC fraction transported into the cells. This finding is in full agreement with the equilibrium constant Keq of 1.9 for the reaction SNC + GSH <--> Cys + GSNO in aqueous buffer.     

The kinetics and mechanisms of the reactions of iron(III) with quercetin and morin

The kinetics and mechanisms of the reactions of a pseudo-first order excess of iron(III) with the flavonoids quercetin and morin have been investigated in aqueous solution at 25 degrees C and an ionic strength of 0.5M. Mechanisms have been proposed which account satisfactorily for the kinetic data. The data are consistent with a mechanism in which the metal:ligand complex formed initially on reaction of iron(III) with the ligand subsequently decomposes through an electron transfer step. Morin forms a 1:1 metal:ligand complex while quercetin forms a 2:1 metal:ligand complex. Both ligands showed evidence for the involvement of the iron hydroxo dimer Fe2(OH)2(4+) in the complex formation reaction at the hydroxy-carbonyl moiety. The iron(III) assisted decomposition of the initial iron(III) complex formed was also investigated and the rate constants evaluated. Both the complex formation and subsequent electron transfer reactions of iron(III) with these ligands were monitored using UV-visible spectrophotometry. All of the suggested mechanisms and calculated rate constants are supported by calculations carried out using global analysis of time dependant spectra.     

Direct monitoring of allosteric recognition of type IIE restriction endonuclease EcoRII

EcoRII is a homodimer with two domains consisting of a DNA-binding N terminus and a catalytic C terminus and recognizes two specific sequences on DNA. It shows a relatively complicated cleavage reaction in bulk solution. After binding to either recognition site, EcoRII cleaves the other recognition site of the same DNA (cis-binding) strand and/or the recognition site of the other DNA (trans-binding) strand. Although it is difficult to separate these two reactions in bulk solution, we could simply obtain the binding and cleavage kinetics of only the cis-binding by following the frequency (mass) changes of a DNA-immobilized quartz-crystal microbalance (QCM) responding to the addition of EcoRII in aqueous solution. We obtained the maximum binding amounts (Deltam(max)), the dissociation constants (K(d)), the binding and dissociation rate constants (k(on) and k(off)), and the catalytic cleavage reaction rate constants (k(cat)) for wild-type EcoRII, the N-terminal-truncated form (EcoRII N-domain), and the mutant derivatives in its C-terminal domain (K263A and R330A). It was determined from the kinetic analyses that the N-domain, which covers the catalytic C-domain in the absence of DNA, preferentially binds to the one DNA recognition site while transforming EcoRII into an active form allosterically, and then the secondary C-domain binds to and cleaves the other recognition site of the DNA strand.     

Studies of electron migration in DNA in aqueous solution using intercalating dyes.

The reactions of the hydrated electron (e-aq) and of the hydroxyl radical (OH) with double-stranded DNA in aqueous solution at room temperature have been studied through the use of the intercalating dyes, proflavine and ethidium. These dyes react with e-aq with rate constants of (2.5 +/- 0.2) - 10(10) M-1 - s-1 and (3.0 +/- 0.3) - 10(10) M-1 - s-1, respectively; the rate constant for the reaction of OH with proflavine is (1.0 +/- 0.2) - 10(10) M-1 - s-1. When these molecules are bound within the DNA structure both the yields and the rate constants of reaction with e-aq are reduced in a manner entirely consistent with a simple competition between the DNA bases and restricted dye molecules reacting with a bimolecular rate constant of about 2 - 10(9) M-1 - s-1. No evidence of free electron migration in the DNA was obtained, and an upper limit of five base pairs for the range of such migration was derived. Reactions of the hydroxyl radical with DNA-bound proflavine also lead to a rate constant of about 2 - 10(9) M-1 - s-1. These rate constants are in good agreement with rate predictions (per base unit) for a diffusion-controlled reaction with the DNA structure.     

A mathematical model for the synthesis of Gly-Phe by papain in an aqueous-organic system

The synthesis of the protected dipeptide BocGlyPheOMe, has been modellised when working in an aqueousorganic biphasic system, with papain as a catalyst. The mathematical model takes into account that one of the substrates, PheOMe, has parallel hydrolysis reactions and that the reaction only takes place in the aqueous phase while the whole reaction system is biphasic. The reaction system has been modellised when working in batch as well as when working in fed-batch mode, achieving a good prediction of the product evolution for both working strategies. When working in fed-batch mode, the extension of the undesired parallel reactions has been diminished, the model has been used for a computer aided optimisation of the addition sequence of PheOMe. The results obtained led to a process operation strategy with a compromise between yield and productivity.List of Symbols [i] concentration of any component i - [i] _aq concentration of i in the aqueous phase - [i] _bi concentration of i in the biphasic system - [E] ₀ initial concentration of enzyme - k _e, k_q first order kinetic constants - K _A, K_B equilibrium constants - r _m maximum rate of reaction This worked was financed by the Interministerial Commission for Science and Technology (CICYT)from the Spanish Government under projects number BIO/88-370 and SAF92-0261-CO2-02.     

Nitrosation of malononitrile by HONO,ClNO and N<Subscript>2</Subscript>O<Subscript>3</Subscript>: A theoretical study

Nitrosation reactions of malononitrile by three nitrosating agents, HONO, ClNO, and N₂O₃, have been theoretically investigated at the B3LYP/cc-pVTZ and MP2/cc-pVDZ levels. Two possible competitive paths for nitrosation of malononitrile to give 2-nitroso-malononitrile were proposed: (a) direct C-nitrosation and (b) N-nitrosation and subsequent nitroso transfer from N to C atom. The calculations show that at both B3LYP and MP2 levels, path b is kinetically favored over path a for nitrosations by HONO and N₂O₃. In the case of ClNO, the B3LYP predicts preference of path b, while the MP2 calculations suggest that both paths have similar rate-determining barriers. The data suggest that N₂O₃ is the preferred nitrosating agent for the nitrosation of malononitrile in aqueous solution. Transformation of 2-nitroso-malononitrile to form malononitrileoxime via intramolecular proton transfer has also been explored, and it is found that inclusion of an assistant water molecule can drastically accelerate the tautomerization.     

Kinetics of nitrification and denitrification reactions

Nitrification and denitrification are important microbiological reactions of nitrogen. In this work, the kinetics of these reactions have been investigated based on a Monod-type expression involving two growth limiting substrates: ammonium nitrogen and dissolved oxygen for nitrification and nitrate nitrogen and dissolved organic carbon for denitrification. The kinetic constants and yield coefficients were evaluated for both these reactions. Past experimental work was used to determine the constants for the nitrification reaction. For the denitrification reaction, experiments were performed in a stirred tank reactor under conditions such that only one substrate was growth limiting. Steady-state values of the substrate concentrations in the reactor were determined at various dilution rates. These data were analyzed to obtain the kinetic and stoichiometric constants. From these constants it was concluded that in the range of nitrate nitrogen concentrations encountered in waste water, the denitrification reaction can be considered a first-order reaction. It was also found that three times as much organic carbon is required as nitrate nitrogen for complete nitrogen removal.     

A comparative analysis of the interaction of borate ion with various polyols.

Although it is now generally accepted that borate ion, B(OH)₄^?, reacts with suitable polyols in aqueous solution to form two types of complexes with strongly acidic properties (1), several investigators have presented evidence to show the formation of two types of complexes is stoichiometrically unsatisfactory (2,3).Aside from its usefulness in structural studies, the reaction has important implications in numerous biochemical applications. Many compounds of biological importance contain hydroxyl groups in positions favorable for reaction with borate ion.As an extension of previous work (4) we report here the determination of solution stability constants of borate ion complexes with several biologically important polyols by means of a pH method and in two instances a calorimetric method.     

Enhanced hydrolysis of a phosphonate ester by mono-aquo metal cation complexes

The hydrolysis of the ester 2,4-dinitrophenyl- ethyl methylphosphonate has been examined by both stop-flow spectrophotometric and pH-stat techniques. These reactions have been carried out in the presence of several nucleophiles including simple non-labile (w.r.t. substitution) mono-aquo metal ion complexes. Comparison of reaction rates of the metal complexes with sterically hindered organic nucleophiles has led to the conclusion that the metal ions function predominantly as general base catalysts in dilute aqueous solution. Reaction rates for the various nucleophiles studied are tabulated together with solvolysis constants for hydroxide ion and water at 35 °C and I=0.1 mol dm⁻³ (KNO₃). These later two values are respectively 32.7 mol⁻¹ dm³ s⁻¹ and 1.37 x 10⁻⁴ s⁻¹. A Brönsted β value of 0.52 for the phosphonate ester studied has also been derived.     

The kinetics and mechanisms of reactions of iron(III) with caffeic acid, chlorogenic acid, sinapic acid, ferulic acid and naringin

The kinetics and mechanisms of the reactions of iron(III) with the hydroxy cinnamic acid based ligands caffeic, chlorogenic, sinapic and ferulic acids and the flavonoid naringin have been investigated in aqueous solution. The mechanisms for caffeic and chlorogenic acid are generally consistent with the formation of a 1:1 complex that subsequently decays through an electron transfer reaction. On reaction with iron(III), ferulic and sinapic acids undergo an electron transfer without the prior formation of any complex. There was no evidence of electron transfer occurring in the complex formed when iron(III) is reacted with naringin. Rate constants for k1 (formation) and k(-1) (dissociation) have been evaluated for the complex formation reactions of [Fe(H2O)6(OH)]2+ with caffeic acid, chlorogenic acid and naringin. Analysis of the kinetic data yielded stability constants, equilibrium constants for protonation of the iron(III) chlorogenic acid complex initially formed, together with the rate constants for complex decomposition through intramolecular electron transfers and in the case of caffeic acid and chlorogenic acid, rate constants for the iron(III) assisted decomposition of the initial complex formed. Some of the suggested mechanisms and calculated rate constants are validated by calculations carried out using global analysis of time dependent spectra.