Derivatives of orotic acid and its analogs

The synthesis of oxo derivatives of pyrrolo[3, 4-d]pyrimidine has been effected by the reaction of the lactone of 5-(hydroxymethyl)-orotic acid with ammonia or primary amines. In a number of cases, in place of the free organic bases their salts with mineral acids were used successfully. A number of 2, 4, 7-trioxo derivatives of pyrrolo[3, 4-d]pyrimidine and some new derivatives of orotic acid have been synthesized.     

Theoretical study of the mechanism of hantzsch ester hydrogenation of imines catalyzed by chiral BINOL-phosphoric acids

The mechanism of the Hantzsch ester hydrogenation of imines catalyzed by chiral BINOL-phosphoric acid has been investigated using DFT methods. Despite the importance of this reaction, there are a number of possible detailed mechanisms, and the preferred pathway has not been firmly established. Our calculations show that the catalyst not only activates the imine group for the reaction by acting as a Br?nsted acid but also establishes an interaction with the Hantzsch ester that can lead to an explanation for the enantioselectivity.     

The Theoretical and Experimental Studies on Oxidation of Straight Chain Amino Acids in Moderately Concentrated Sulfuric Acid Medium

The kinetics of the permanganic oxidation process of some straight chain amino acids in moderately concentrated sulfuric acid medium have been investigated using a spectrophotometric technique. Conclusive evidences have proven autocatalytic activity of Mn(II) for these reactions. It is determined that even and odd effects of the number carbon atom in a carbon chain are annihilated when it's the number of carbon atoms is increased more than of three in a noncatalytic oxidation pathway. Thus, rate constants belonging to glycine, l ‐α‐amino‐n‐butyric acid, l ‐norleucine, and l ‐α‐amino‐n‐heptanoic acid satisfy Taft's equation involving the induction factor in the noncatalytic pathway, whereas l ‐α‐amino‐n‐heptanoic acid has an odd number of carbon atom in its chain carbon. On the other hand, in the catalytic pathway, rate constants satisfy Taft' equation including inductive and steric factors, when rate constants belonging to amino acids with an even number of carbon atoms are separated from those with an odd number of carbon atoms. The oxidation process of amino acids in the noncatalytic pathway and those with the even number of carbon atoms in the carbon chain in the catalytic pathway speeds up by an increase in the length of chain that is accompanied with an increase in the carbon chain's electron‐donating characteristic. On the other hand, an increase in the length of the carbon chain is accompanied with more steric hindrance, which counteracts its electron‐donating character, thereby decreasing reaction rate in the catalytic pathway. Finally, amino acid–Mn(II) complexes were studied using a density functional theory method. Results obtained show that such a complex is less stable than reactants, namely it is formed in an endothermic reaction. The number and strength of hydrogen bonding belonging to amino acid is more than those of the amino acid–Mn(II) complex. Besides, it has been illustrated that natural bond orbital analysis and molecular orbital calculations satisfy the findings.     

The Potential of a Protein Model Synthesized Absent of Methionine

Methionine is an amino acid long thought to be essential, but only in the case of protein synthesis initiation. In more recent years, methionine has been found to play an important role in antioxidant defense, stability, and modulation of cell and protein activity. Though these findings have expanded the previously held sentiment of methionine having a singular purpose within cells and proteins, the essential nature of methionine can still be challenged. Many of the features that give methionine its newfound functions are shared by the other sulfur-containing amino acid: cysteine. While the antioxidant, stabilizing, and cell/protein modulatory functions of cysteine have already been well established, recent findings have shown a similar hydrophobicity to methionine which suggests cysteine may be able to replace methionine in all functions outside of protein synthesis initiation with little effect on cell and protein function. Furthermore, a number of novel mechanisms for alternative initiation of protein synthesis have been identified that suggest a potential to bypass the traditional methionine-dependent initiation during times of stress. In this review, these findings are discussed with a number of examples that demonstrate a potential model for synthesizing a protein in the absence of methionine.     

Electronic structure of carbon nanotube network

Covalently cross-linked carbon nanotube network has been synthesized using spark plasma sintering followed by nitric acid treatment. EPR investigation of its electronic structure in comparison with pristine carbon nanotubes has revealed that the covalent cross-linking leads to a decrease in the number of paramagnetic centers, while the oxidation results in an increase in their number. The oxidation affects the cross-linked and pristine materials in a different manner     

Preparation of Functionalized Carbon-Coated Cobalt Nanoparticles with Sulfonated Arene Derivatives,a Study on Surface Functionalization and Stability

The functionalization of magnetic nanoparticles has been an important field in the last decade due to the versatile applications in catalysis and biomedicine. Generally, a high degree of functionalities on the surface of the nanoparticles is desired. In this study, covalent functionalization of various aromatic sulfonic acids on carbon-coated cobalt nanoparticles are investigated on surface functionalization yield and stability. The nanoparticles are prepared via covalent linkage of an in situ generated diazonium on the graphene-like surface. Adsorption and wash experiments were performed to confirm a covalent bonding of the naphthalene derivatives on the nanoparticle surface. With an increased number of sulfonic acid groups on the aromatic compound a significantly lower loading is observed on the corresponding functionalized nanoparticles. This can be counteracted by a change of nitrite species. With this method, nanoparticles with a high number of sulfonic acid groups can be produced.     

Comparison of global-minimum-energy conformations of phospholipids

The Monte Carlo technique in combination with the procedure of “slow cooling” of a configurational ensemble has been used to establish the conformations of the global energy minima of phosphatidylcholine and phosphatidylethanolamine molecules with saturated and unsaturated fatty acid residues. Substituents of the ammonium group in saturated phospholipids have been shown to affect the head group only. In the case of 1-stearoyl-2-arachidonyl glycerol the type of the head group dramatically affects the geometry of the nearest region of the first fatty acid residue and leaves the second fatty acid residue practically intact. This fact is accounted for by electrostatic bonding between the ammonium group and the keto oxygen atom of the first fatty acid residue in an unsaturated lipid. It is the electrostatic force field that stipulates the specificity of head groups in lipids. It is shown that the minimum energy conformations of saturated fatty acid residues in double-chain lipids contain a large number of gauche-type defects.     

Catalytic asymmetric synthesis of phthioceranic acid, a heptamethyl-branched acid from Mycobacterium tuberculosis

The first total synthesis of phthioceranic acid (1) has been achieved by an iterative catalytic asymmetric 1,4-addition protocol. This method provides a robust and high-yielding route for the preparation of 1,3-oligomethyl (deoxypropionate) arrays. After the desired number of methyl groups has been introduced, these arrays can be further functionalized at both ends to polymethyl-substituted lipids such as phthioceranic acid, a heptamethyl-branched fatty acid from the virulence factor Sulfolipid-I (2), found in Mycobacterium tuberculosis.     

Reduction of Tosylamino Acids and Related Compounds with Sodium in Liquid Ammonia; stoichiometry and products

Using an extraction procedure which permits determination of end-points, the reduction of a number of tosylamino acids, their derivatives, and model compounds with sodium in liquid ammonia has been investigated. When the molecule contains a single acidic group in addition to the tosylamino group (as in the case of the simple mono-tosylamino monocarboxylic acids) reduction proceeds with the consumption of 2 g-at. Na per tosyl group and the formation of toluene-4-sulphinic acid. If the number of acidic groups in the products is insufficient to accommodate the number of electrons consumed in the reduction, the reduction of ionisable tosylamino groups is incomplete unless an acid is added. If the number of acidic groups is higher, or excess acid is added, the sulphur-containing products include thiocresol and sulphite. This last reaction course is also observed whenever calcium is used in place of sodium. A partial interpretation of the results is offered.     

Extraction-fluorimetric determination of microgram amounts of thallium with 2-phenylbenzo[8,9]quinolizino[4,5,6,7-fed]phenanthridinylium perchlorate

In 0.5 M hydrochloric acid medium, thallium(III) forms with 2-phenylbenzo [8,9]quinolizino[4,5,6,7-fed]phenanthridinylium perchlorate (PQPP) an ion-association compound which is extractable in isoamyl acetate. The extracted ion-pair has a mole ratio Tl/PQPP in 1:1 and has been used for the spectrofluorimetric determination of thallium in the concentration range 0.06–1.6 μg per 5 ml of organic layer. The interference of a large number of foreign ions has been investigated. The method is sensitive, accurate, precise, and specially useful for the determination of thallium in different materials with low contents of this element.     

Novel way of separating polyfluorocarboxylic acids by ion-exclusion chromatography

Ion-exclusion chromatography has been successfully applied to the separation of a number of polyfluorocarboxylic acids. The separation of various mono- and dibasic polyfluorocarboxylic acids having a different alkyl group was investigated using a polymethacrylate-based weakly acidic cation-exchange resin (TSK gel OApak-A) in the H -form and conductimetric detection. When water was used as the eluent, polyfluorocarboxylic acids could not be resolved. When an aqueous solution of sulfuric acid, benzoic acid, o-phthalic acid, 1,3,5-benzenetricarboxylic acid, 1,2,4,5-benzenetetracarboxylic acid, and tartaric acid was used, the separation of polyfluorocarboxylic acids occurred for monobasic ones. While, for fluorine-containing dibasic acids, imperfect separation of peaks occurred. In order to improve their separation, the effect of an addition of organic modifiers such as methanol, 2,2,2-trifluoroethanol and 2H-hexafluoro-2-propanol in the eluent was also investigated.     

Determination of fatty acid amides as trimethylsilyl derivatives by gas chromatography with mass spectrometric detection.

Fatty acid amides are a newly emerging class of compounds with biological activity. The amides are formed enzymatically in vivo. Analysis of fatty acid amides has been accomplished by gas chromatography coupled with mass spectrometry. Fatty acid amides required derivatization prior to analysis at high temperatures due to thermal instability. Trimethylsilylation of fatty acid amides has been accomplished under optimum reaction conditions. The limit of detection for the silylated amides is approximately 1 pmol, with the lowest detected level being 700 fmol for the lauramide derivative. Quantitation of fatty acid amide derivatives can be accomplished by monitoring m/z 59 or m/z M-71, the only two major fragments formed in the ion trap mass spectrometer with electron impact ionization. The smaller fragment is the result of a newly reported, McLafferty-type rearrangement; M-71 resulted from loss of an n-pentyl fragment. Either peak gave four-five orders of magnitude linear dynamic range. Numerous trimethylsilylamides from C7 to C20 were separated under standard conditions. Elution was linear with the number of carbons and was systematically affected by the number and position of the double bonds.     

Organic Brønsted acid-catalyzed cycloadditions of o-quinone methides with 1, 3-dicarbonlys: Facile access to xanthenones and chromanones

The in-situ generation of o-quinone methides and their inverse-electron-demand Diels–Alder reaction in the presence of pentacarboxycyclopentadiene—an organic Brønsted acid—has been reported. The synthesis of xanthenones and chromanones in good to excellent yields from the [4 + 2] cycloaddition of quinone methides with 1, 3-dicarbonyls and Meldrum's acid has been accomplished. The development of this method helps in generating a number of biologically potent heterocycles with medicinal applications.     

Kinetik und Mechanismus der Substitutionsreaktionen von Komplexverbindungen. XXIII. Die Wasserstoff-bis-nyoximato-diselenocyanatokobaltiat(III)-Säure und die Kinetik der Aquotisierung des [Co(NioxH)2(NCSe)2]-Ions

A new monobasic complex acid has been obtained by oxydizing a mixture of 1,2-cyclohexane-dione-dioxime (nyoxime), cobalt(II)-acetate and KCNSe. It is the hydrogen-bis-nyoximato-diselenocyanato cobaltiat: H[Co(NioxH)₂(NCSe)₂]. A number of 34 new complex salts of this acid have been isolated in crystalline form. In order to clear up some structural problems, a spectrophotometric study has been made in UV, and IR region. In aqueous solutions of the complexion takes place an aquation reaction, which leads to the substitution of a selenocyanation by water. Kinetics of this reaction has been followed at different temperatures (Activation energy of the reaction E_a = 32.5 ± 0.9 kcal/mole, pre-exponential factor in ARRHENIUS' equation lg Z = 15.5 ± 2.5). Results are compared with the kinetic parameters of the aquation of the analogous bis-dimethyl-glyoximato-diselenocyanato-cobalt(III)-ion.     

Probing the Binding Region of the Single-Stranded DNA-Binding Domain of Rat DNA Polymerase β Using Nanosecond-Pulse Laser-Induced Cross-Linking and Mass Spectrometry

In recent years, there has been a significant number of studies in which UV light has been used as a reagent to induce cross-links in nucleic acid-protein complexes. An area of considerable interest among those interested in structural biology is the garnering of information about the sites of cross-linking within the protein and nucleic acid members of photolinked conjugates, under the assumption that such knowledge should lead to identification of contact regions or sites within the native complexes. In this paper, we present our results from a photocross-linking study of the complex of the single-stranded DNA-binding domain of rat DNA polymerase β (pol β-ss) with the oligonucleotide d(ATATATA). In this study, we have used single nanosecond laser pulses as the cross-linking reagent and matrix-assisted laser desorp-tion/ionization-time of flight mass spectrometry as an analytical tool to identify cross-linked peptides purified from proteolytic digests of the cross-linked complex. Six cross-linked peptides have been identified in tryptic digests of the protein-oligonucleotide conjugates that result from irradiation of the pol β-ss-d(ATATATA) complex with a single laser pulse. Comparisons with NMR data in the literature for the same complex show that each of the cross-linked peptides contains amino acids that are in contact with the nucleic acid component of the complex.     

Structural studies on the hydration of L-glutamic acid in solution

A combination of neutron diffraction augmented with isotopic substitution and computer modeling using empirical potential structure refinement has been used to extract detailed structural information for L-glutamic acid dissolved in 2 M NaOH solution. This work shows that the tetrahedral hydrogen bonding network in water is severely disrupted by the addition of glutamic acid and NaOH, with the number of water-water hydrogen bonds being reduced from 1.8 bonds per water molecule in pure water to 1.4 bonds per water molecule in the present solution. In the glutamic acid molecule, each carboxylate oxygen atom forms an average of three hydrogen bonds with the surrounding water solvent with one of these hydrogens being shared between the two oxygen atoms on each carboxylate group, while each amine hydrogen forms a single hydrogen bond with the surrounding water solvent. Additionally, the average conformation of the glutamic acid molecules in these solutions is extracted.     

Studies in sesquiterpenes—XIX Action of perbenzoic acid on longifolene

Oxidation of longifolene, a mono-olefinic sesquiterpene, with a chloroform solution of perbenzoic acid proceeded to almost two mole consumption of the peracid to furnish a number of products, important ones being an -ketol, a norketone (longicamphenilone) and the corresponding C₁₄-alcohols. Under certain conditions it has been possible to arrest the reaction at one mole consumption and to isolate longifolene--epoxide, which is the major product; some amounts of epimeric longifolaldehydes and longicamphenilone were also formed. Further action of perbenzoic acid on longifolene oxide and longifolaldehydes has been investigated and the results used to interpret the mechanism of abnormal peracid oxidation of longifolene.     

Further studies on the postpolymerization of methyl methacrylate

A search has been made for electroinitiators of postpolymerization. A number of hydroxycarboxylic acids and some of their sodium salts have been found to be quite efficient. Factors controlling the rate of polymerization and yield have been described. Surprisingly, citric acid, though not an electroinitiator of polymerization, is a good initiator of postpolymerization. Other active species that deserve mention are tartaric acid and its salts. A free radical mechanism involving formation of oligomeric initiator fragments, growth by attachment of imbibed monomer, and termination by chain transfer has been proposed to explain the observed facts.     

3,4-Dihydroxy-7,8-dihydro-beta-ionone 3-O-beta-D-glucopyranoside and other glycosidic constituents from apple leaves

3,4-Dihydroxy-7,8-dihydro-beta-ionone 3-O-beta-D-glucopyranoside 1 has been isolated from a methanolic extract of apple (Malus domestica) leaves by XAD-2 adsorption chromatography and subsequent purification by high speed countercurrent chromatography (HSCCC) and HPLC. Under acidic conditions this glycoside gives rise to a number of volatile compounds including 1,1,6-trimethyl-1,2-dihydronaphthalene (TDN) 2, which is known as an off-flavor compound in wine. In the course of the study, six additional glycoconjugates were isolated from apple leaves, i.e. roseoside 3, 3-oxo-alpha-ionol beta-D-glucopyranoside 4, benzoic acid beta-D-glucose ester 5, kaempferol 3-O-rhamnoside 6, (+)-syringaresinol beta-D-glucopyranoside 7 and 4-hydroxy-5-(3'-methyl-2'-butenyl)-benzoic acid methylester 3-beta-D-glucopyranoside 8. The latter compound has been isolated for the first time in nature. In order to avoid the 'kerosene-off-flavor' caused by TDN, the methanolic extract has been subjected to yeast fermentation. This treatment reduced the amount of TDN formed and resulted in an improved flavor impression of the methanolic extract.