Activation of carboxyl group with cyanate: peptide bond formation from dicarboxylic acids

The reaction of cyanate with C-terminal carboxyl groups of peptides in aqueous solution was considered as a potential pathway for the abiotic formation of peptide bonds under the condition of the primitive Earth. The catalytic effect of dicarboxylic acids on cyanate hydrolysis was definitely attributed to intramolecular nucleophilic catalysis by the observation of the ¹H-NMR signal of succinic anhydride when reacting succinic acid with KOCN in aqueous solution (pH 2.2–5.5). The formation of amide bonds was noticed when adding amino acids or amino acid derivatives into the solution. The reaction of N-acyl aspartic acid derivatives was observed to proceed similarly and the scope of the cyanate-promoted reaction was analyzed from the standpoint of prebiotic peptide formation. The role of cyanate in activating peptide C-terminus constitutes a proof of principle that intramolecular reactions of adducts of peptides C-terminal carboxyl groups with activating agents represent a pathway for peptide activation in aqueous solution, the relevance of which is discussed in connexion with the issue of the emergence of homochirality.     

Proton and carbon-13 nuclear magnetic resonance studies on methyl (methyl d-galactosid)uronates and their per-O-acetyl derivatives

The ¹H- and ¹³C-n.m.r. spectra of the anomeric methyl (methyl d-galactosid)uronates, as well as the ¹H-n.m.r. spectra of their acetyl derivatives, were analyzed. The spectra of the unacetylated d-galactopyranosiduronates showed good correlation with those of the corresponding anomeric d-galactopyranuronic acids and their methyl esters, and with those of the anomeric methyl d-galactopyranosides. From the values of the chemical shifts and coupling constants, it was concluded that the anomeric methyl (methyl d-galactopyranosid)uronates and their corresponding peracetates are in the ⁴C₁(d) conformation. The chemical shifts in the ¹³C-n.m.r. spectra show good correlation with those of the methyl d-galactosides. The signals of the furanose derivatives appear at fields lower than those of the corresponding pyranose compounds.     

Structural analysis of comb-like,amylose derivatives by 13C-N.M.R. spectroscopy

¹³C-N.m.r. spectra have been recorded for previously reported, comb-like derivatives of amylose produced by orthoester and Helferich condensation of D-glucose to amylose. As known from monomeric studies, the Helferich condensation conditions (the presence of mercury salts) favor α-D-glucosylation, and orthoester condensation conditions favor β-D-glycosylation. It was anticipated that, for these polymer condensations, the Helferich and orthoester condensations would also favor α- or β-D-glycosylation, respectively. The ¹³C-n.m.r. spectra of representative products of the Helferich and orthoester condensations confirmed the presence of 4,6-di-O-substituted α-D-glucopyranosyl residues, and also the degree of polymer linearity derived from independent, analytical data. However, these spectra indicate extensive, if not exclusive, β-D-glycosylation for both the helferich and the orthoester conditions. These results were obtained by using the product from an enzymically synthesized, strictly linear amylose in the Helferich condensation reaction.     

Condensation of amino acids to form peptides in aqueous solution induced by the oxidation of sulfur(iv): An oxidative model for prebiotic peptide formation

Condensation of amino acids to peptides is an important step during the origin of life. However, up to now, successful explanations for plausible prebiotic peptide formation pathways have been limited. Here we report that the oxidation of sulfur (IV) can induce the condensation reaction of carboxylic acids and amines to form amides, and the condensation reaction of amino acids to form peptides. This might be a general reaction contributing to prebiotic peptide formation.     

The Effects of Borate Minerals on the Synthesis of Nucleic Acid Bases,Amino Acids and Biogenic Carboxylic Acids from Formamide

The thermal condensation of formamide in the presence of mineral borates is reported. The products afforded are precursors of nucleic acids, amino acids derivatives and carboxylic acids. The efficiency and the selectivity of the reaction was studied in relation to the elemental composition of the 18 minerals analyzed. The possibility of synthesizing at the same time building blocks of both genetic and metabolic apparatuses, along with the production of amino acids, highlights the interest of the formamide/borate system in prebiotic chemistry.     

Catalytic Role of Manganese Oxides in Prebiotic Nucleobases Synthesis from Formamide

Origin of life processes might have begun with the formation of important biomonomers, such as amino acids and nucleotides, from simple molecules present in the prebiotic environment and their subsequent condensation to biopolymers. While studying the prebiotic synthesis of naturally occurring purine and pyrimidine derivatives from formamide, the manganese oxides demonstrated not only good binding for formamide but demonstrated novel catalytic activity. A novel one pot manganese oxide catalyzed synthesis of pyrimidine nucleobases like thymine is reported along with the formation of other nucleobases like purine, 9-(hydroxyacetyl) purine, cytosine, 4(3 H)-pyrimidinone and adenine in acceptable amounts. The work reported is significant in the sense that the synthesis of thymine has exhibited difficulties especially under one pot conditions and also such has been reported only under the catalytic activity of TiO₂. The lower oxides of manganese were reported to show higher potential as catalysts and their existence were favored by the reducing atmospheric conditions prevalent on early Earth; thereby confirming the hypothesis that mineral having metals in reduced form might have been more active during the course of chemical evolution. Our results further confirm the role of formamide as a probable precursor for the formation of purine and pyrimidine bases during the course of chemical evolution and origin of life.     

Proteinogenic amino acids labelled with 15N and/or 13C for application in peptide synthesis: A short review with a comprehensive list of published derivatives

A review is given of the literature dealing with the most common protected derivatives of ¹⁵N- and/or ¹³C-labelled amino acids of interest in peptide synthesis. The list contains all such Boc-, Z- and Fmoc-amino acids as well as published methyl, ethyl, t-butyl and benzyl esters.     

Precursors and genetic control of anthocyanin synthesis in Matthiola incana R. Br.

After application of dihydroflavonols, naringenin, or suitable substituted chalcones, anthocyanins were synthesized in three genetically defined acyanic lines of Matthiola incana, indicating that the corresponding genetic block concerns the synthesis of the chalcone-flavanone intermediate. Independent of the precursors used, only cyanidin derivatives were produced. This supports the hypothesis that the oxygenation pattern of the B ring in anthocyanin formation is determined at a stage of a C₁₅ intermediate. In addition to the gene responsible for the oxygenation of the 3 position, the genes responsible for the glycosylation in the 3 and 5 positions of the anthocyanin molecule, and those responsible for the acylation with various hydroxycinnamic acids can still exert their influence. Two further genetically defined lines containing flavonol glycosides were not able to synthesize anthocyanins with any of the precursors tested. Their genetic blocks are assumed to be localized after dihydroflavonol synthesis but before anthocyanin formation.     

The structure of d-threo-2,5-hexodiulosonic acid and derivatives in solution

The structure of d-threo-2,5-hexodiulosonic acid (1) and various derivatives in solution was determined by ¹³C-n.m.r. spectroscopy to be a hydrated, pyranose form. The structures of the methyl ester of 1 and of its 5-(dimethyl acetal) were confirmed by chemical means and by X-ray structure analysis.     

Design and synthesis of vidarabine prodrugs as antiviral agents

5′-O-d- and l-amino acid derivatives and 5′-O-(d- and l-amino acid methyl ester phosphoramidate) derivatives of vidarabine (ara-A) were synthesized as vidarabine prodrugs. Some compounds were equi- or more potent in vitro than vidarabine against two pox viruses and their uptake by cultured cells was improved compared to the parent drug.     

A new route to cyclic urea derivatives of sugars via phosphinimines

Sugar phosphinimines and the corresponding aminophosphonium salts were prepared from 2-amino-2-deoxy-d-glucosyl azide derivatives and their structures were established by ¹³C- and ¹³P-n.m.r. spectroscopy. A simple one-pot procedure, involving reaction of the azides with triphenylphosphine and carbon dioxide, provides an efficient access to cyclic urea derivatives.     

Prebiotic synthesis of histidine

Summary The prebiotic formation of histidine (His) has been accomplished experimentally by the reacton of erythrose with formamidine followed by a Strecker synthesis. In the first step of this reaction sequence, the formation of imidazole-4-acetaldehyde took place by the condensation of erythrose and formamidine, two compounds that are known to be formed under prebiotic conditions. In a second step, the imidazole-4-acetaldehyde was converted to His, without isolation of the reaction products by adding HCN and ammonia to the reaction mixture. LC, HPLC, thermospray liquid chromatography-mass spectrometry, and tandem mass spectrometry were used to identify the product, which was obtained in a yield of 3.5% based on the ratio of His/erythrose. This is a new chemical synthesis of one of the basic amino acids which has not been synthesized prebiotically until now.     

Fast and efficient peptide bond formation using bis-[alpha,alpha-bis(trifluoromethyl)-benzyloxy]diphenylsulfur. Part I.

This study towards the development of sulfurane-based coupling agents shows that bis-[alpha,alpha-bis(trifluoromethyl)-benzyloxy]diphenylsulfur (BTBDS) can facilitate rapid amide bond formation between Nalpha-urethane-protected l-amino acids and l-phenylalanine ethyl ester in the absence of an external base. The corresponding dipeptide esters were obtained in excellent yields and with no detectable racemization, as judged by analysis of the formed dipeptides by chiral-phase HPLC. In addition, BTBDS-mediated condensation of benzoyl-l-phenylalanine with l-phenylalanine ethyl ester was also investigated. The results indicate that sulfuranes can be useful for application in racemization-sensitive systems, such as segment condensation.     

15N-NMR spectroscopy. 34. Stereospecificity of the polymerization of D,L-leucine N-carboxyanhydride and γ-OMe-D,L-glutamic acid N-carboxyanhydride

D ,L -Leucine-N-carboxyanhydride (D ,L -Leu-NCA) and γ-methyl-D ,L -glutamic acid N-carboxyanhydride (γ-OMe-D ,L -Glu-NCA) were synthesized with ca. 2.5% ¹⁵N enrichment. Their polymerizations were conducted under a variety of conditions using benzylamine, triethylamine potassium tert-butanolate, and pyridine as initiators. The 40.55-MHz ¹⁵N-nmr spectra of the resulting stereocopolypeptides measured in trifluoroacetic acid display at least four signals, representing the isotatic, syndiotactic, and two heterotactic triads. From the signal intensities it was concluded that these NCAs behave nearly identically. With benzylamine initiation the formation of isotactic blocks is slightly favored, and they are still more predominant when strong bases are used as initiators. Initiation by pyridine favors the formation of syndiotactic sequences. However, in all cases the average lengths of the stereoblocks never exceeded 4 monomer units. The low stereospecificity of most polymerizations of D ,L -NCAs is confirmed by the high degree of solubility of the resulting poly(D ,L -amino acids) in aprotic solvents. Penultimate effects are weak or absent, so that most polymerizations follow Bernoullian type statistics. Deviations from these statistics were found for polymerizations in pyridine.     

Analysis of problems encountered in the determination of amino acid enantiomeric ratios by gas chromatography

A previously described procedure for determining the enantiomeric ratios of amino acids has produced inconsistent results when determining relatively low (≤0.110) d/l ratios. The method involves synthesis of diastereomeric N-trifluoroacetyl-l-prolyl-d/l-amino acid ester dipeptides which are resolved by gas chromatography (GC). We have found that triethylamine, which is added to maintain a basic pH during the coupling reaction, racemizes the chiral reagent N-trifluoroacetyl-l-prolyl chloride (TPC). Coupling of partially racemized TPC to d/l-amino acid esters results in the formation of four dipeptides (two pairs of enantiomers) instead of the expected two diastereomeric dipeptides. The enantiomeric dipeptides coelute on an achiral GC column, resulting in erroneous d/l ratios. More accurate d/l ratios are obtained by preparing the volatile N-trifluoroacetyl-d/l-amino acid isopropyl ester derivative which can be separated into its enantiomers on a chiral GC column such as the Chirasil-Val III (registered trademark of Applied Science Laboratories).     

Production of α-keto acids: 2. Immobilized whole cells of Providencia sp. PCM 1298 containing l-amino acid oxidase

A number of bacteria belonging to the genera Proteus, Providencia, Pseudomonas and Erwinia have been tested for their capacity to oxidize l-amino acids to their corresponding α-keto acids. Members of the Proteus and the Providencia genera were active towards various l-amino acids. Immobilized cell preparations of Providencia sp. PCM 1298 were shown to form up to 80 mg α-keto-γ-methiol butyric acid from l-methionine per g of gel preparation (containing 4% w/w cells) per day. The productivity was highly dependent on the size of the beads. Oxygen appeared to be the rate-limiting substrate and oxygen transfer rates of 3–4 μmol cm^?2h^?1were calculated. The entrapment of activated charcoal to remove H₂O₂ formed during the oxidation extended the half-life of the immobilized biocatalyst considerably. A decrease in l-amino acid oxidase [l-amino acid: oxygen oxidoreductase (deaminating); EC 1.4.3.2] activity during operation could be compensated for by reinoculation of the alginate-entrapped cells in fresh growth medium, allowing use of these preparations of immobilized bacterial cells for more than one month.     

New Hydrazides and Hydrazide‐Hydrazones of 2,3‐Dihalogen Substituted Propionic Acids: Synthesis and in vitro Antimicrobial Activity Evaluation

The main aim of this research was the synthesis, spectral identification and in vitro antimicrobial evaluation of new hydrazides and hydrazide‐hydrazones of 2,3‐dihalogen substituted propionic acids. New hydrazides were obtained by the substitution reaction of appropriate ethyl esters of 2,3‐dihalogen substituted propionic acids with hydrazine hydrate. Then obtained hydrazides were subjected to condensation reaction with various aldehydes which yielded with new hydrazide‐hydrazone derivatives. All obtained compounds were identified on the basis of spectral methods (¹H‐NMR, ¹³C‐NMR) and in vitro screened against a panel of bacterial and fungal strains according to EUCAST and CLSI guidelines.     

An improved synthesis of 1,6-anhydro-2,4-dideoxy-β-D-threo-hexopyranose

Dextran fractions from NRRL strains Leuconostoc mesenteroides B-1299 and B-1399, and the native, structurally homogeneous dextrans from L. mesenteroides. B-640, B-1396, B-1422, and B-1424, were examined by ¹³C-n.m.r. spectroscopy at 34 and at 90°, and by g.l.c.-m.s. The ¹³C-n.m.r. data indicate that the dextrans of this series branch exclusively through α-d-(1→2)-linkages, and differ from one another only in degree of linearity. Diagnostic, ¹³C-n.m.r resonances, correlating with 2,6-di-O-substituted α-d-glucosyl residues at branch points, have chemical shifts that are independent of the degree of linearity of the dextran. The intensities of these diagnostic resonances from branching residues, compared to the resonances associated with linear dextran (low degree of branching), are generally proportional to the degree of branching established by methylation-fragmentation analysis. The validity of assignment of the diagnostic, ¹³C-n. m.r. resonances is substantiated by a critical review of methods previously used to provide structural information on dextrans having α-d-(1→2)-linkages, and by evaluation of the corresponding results on the basis of the ultimate standard-methylation structural analysis.     

The synthesis and N.M.R. spectroscopy of derivatives of 6-amino-6-deoxy-D-galactose-6-15N

Derivatives of 6-amino-6-deoxy-D-galactose-6-¹⁵N have been synthesized by reaction of the 6-deoxy-6-iodo (1) or 6-O-p-tolylsulfonyl derivative of 1,2:3,4-di-O-isopropylidene-α-D-galactopyranose with potassium phthalimide-¹⁵N. The reaction of 1 also yielded an elimination product, 6-deoxy-1,2:3,4-di-O-isopropylidene-β-L-arabino-hex-5-enopyranose. The structures of the 6-amino-6-deoxy-D-galactose derivatives and their precursors were characterized by proton- and ¹³C-n.m.r. spectroscopy, with confirmation of the ¹³C assignments by selective proton decoupling. Selective broadening of the C-1, C-4, C-5, and C-6 resonances of 6-amino-6-deoxy-1,2:3,4-di-O-isopropylidene-α-D-galactopyranose by low concentrations of cupric ion was observed, and studied by computerized measurements of the ¹³C linewidths. The application of this broadening to ¹³C-spectral assignments of amino sugar derivatives is indicated.     

The synthesis and chromatography of peptide nitriles

Di- and tripeptide nitriles, glycylaminoacetonitrile (Gly-AAN), diglycylaminoacetonitrile (Gly-Gly-AAN), alanyl--aminopropionitrile (Ala-APN), and dialanyl--aminopropionitrile (Ala-Ala-APN) were synthesized first.These peptide nitriles and related peptides and peptide amides were analyzed by means of ion-exchange chromatography. The every two diastereomers of dialanine, dialanine amide, and Ala-APN were separated into two peaks by using a pH 3.25 buffer as an eluent. The four isomers of trialanine, trialanine amide, and Ala-Ala-APN gave four, two, and one peak, respectively under the same conditions.The trimethylsilyl derivatives of alanyl peptides and related compounds were analyzed by means of gas chromatography combined with mass-spectrometry. The parent (M⁺ and/or M⁺-15) and other mass numbers observed in their mass-spectra supported the introduction of various numbers of trimethylsilyl groups.