Secondary-ion emission of amino acids

Secondary-ion mass spectroscopy (SIMS) is a hydrogen, isotope and compound sensitive analytical technique of extremely high absolute sensitivity. Continuing earlier measurements for carboxylic acids, adsorbed alcohols etc., we have carried out a systematical investigation of secondary-ion emission from metal-supported amino acids, containing various functional groups (e.g., alanine, phenylalanine, cysteine, arginine). In order to avoid damage effects we applied extremely small primary-ion current densities in the 10⁻⁹ A·cm⁻² range. The main results of our investigations can be summarized as follows:

Synergistic effect of probe sonication and ionic liquid for extraction of phenolic acids from oak galls

Phenolic acids of oak gall were extracted using ultrasonic-probe assisted extraction (UPAE) method in the presence of ionic liquid. It was compared with classical ultrasonic-bath assisted extraction (CUBAE) and conventional aqueous extraction (CAE) method, with and without the presence of ionic liquid. Remarkably, the UPAE method yielded two-fold higher extraction yield with the presence of ionic liquid, resulting 481.04 mg/g for gallic acids (GA) and 2287.90 mg/g for tannic acids (TA), while a decreased value of 130.36 mg/g for GA and 1556.26 mg/g for TA were resulted with the absence of ionic liquid. Intensification process resulted the highest yield of 497.34 mg/g and 2430.48 mg/g for GA and TA, respectively, extracted at temperature 50 °C with sonication intensity of 8.66 W/cm² and 10% duty cycle, diluted in ionic liquid, 1-Butyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide, [Bmim][Tf₂N] at concentration of 0.10 M with sample-to-solvent ratio 1:10 for 8 h. Peleg’s model successfully predicted the UPAE process confirming that extraction capacity is the controlling factor in extracting phenolic acids. Hence, it can be concluded that UPAE method and ionic liquid have synergistic effect as it effectively enhanced the extraction efficiency to increase the bioactive constituents yield.     

Enzymatic synthesis of some 15N-labelled l-amino acids

Our group has developed a stereospecific enzymatic method, which is very efficient for the in vitro synthesis of l-[¹⁵N]serine, l-[¹⁵N]methionine and l-[¹⁵N]glutamic acid. These amino acids were prepared from the corresponding α -ketoacids in the suitable enzymatic systems. The bacterial NAD-dependent amino acid dehydrogenases alanin dehydrogenase, leucin dehydrogenase and glutamate dehydrogenase were used as catalysts. Glucose dehydrogenase was used for the regeneration of NADH and ¹⁵NH₄Cl as isotopically labelled material at 99 at.% ¹⁵N. All reactions are inexpensive and easy to perform on a synthetically useful scale (1-10g) giving high yields of l-amino acids. The ¹⁵N isotope content was determined by mass spectrometry.     

Solvation properties of non-polar amino acids in water and methanol: a molecular dynamics study

Solvation properties of the amino acids alanine, valine, leucine and phenylalanine in water and in methanol at infinite dilution have been studied by using molecular dynamics simulations. The free energy transfer of the solutes from water to methanol has been calculated by means of a slow-growth technique and the results compared with diverse hydrophobicity scales available in the literature. Chothia's linear relation between the accessible surface area and the hydrophobicity is shown. The line obtained has a slope equivalent to 49cal mol^?1 Å^?2. The radial distribution of solvent molecules around the amino acids residues is considered, and a comparison is made of the number of hydrogen bonds formed between water molecules in the presence and in the absence, respectively, of the amino acids. The calculations show clearly that the solvation structure near the non-polar amino acids is richer for methanol than for water.     

Near-infrared characterization of N-tertiobutoxycarbonyl-L amino acids.

The near-infrared absorption spectra of open-chain secondary amides and smallring lactams have revealed the sensitivity of certain NH combination bands to conformation of the amide grouping^1,3 more specifically to the cis and trans conformations of the secondary amide grouping². Some near-infrared characteristics of the peptide groups have been reported a long time ago^4,5 but despite their biological interest, no data are available for N-tertiobutoxycarbonyl amino acids. In this work, the near infiared spectra of the following molecules have been investigated in the solid state and in carbon tetrachloride solution.     

Crystallization of carboxylic acids as studied by NMR Spectrometry

The temperature dependences of the narrow ¹H NMR signals, in the temperature range below phase transition point from the plastic to brittle crystal for pivalic acid (PA) confined in the controlled pore size glasses with mean diameters of 7.9 and 23.9 nm have been investigated in order to determine the depression of the crystallization temperature and the pore size distribution parameters. The obtained parameters and the temperature dependences of the narrow ¹H NMR signals in the solid phases of PA and other carboxylic acids (hexadecanoic (C₁₆), heptadecanoic (C₁₇), octadecanoic (C₁₈), nonadecanoic (C₁₉)) have been used for studying the pore size distributions appeared during the natural crystallization. It was found that the pore size distribution for the even-numbered acids (C₁₆ and C₁₈) is spread over much wider range of the sizes comparing with those for odd-numbered acids (C₁₇ and C₁₉). The maximal value of the pore radius R?=?40.4 nm has been found at the temperature just below the melting point of C₁₈, which is about eight times bigger than that found for C₁₇.     

Raman scattering in dried DNA and crystalline amino acids

Raman spectrum characteristics of dried deoxyribonucleic acid (DNA) and two types of crystalline amino acids (L-lysine, D-asparagine) are compared in a wide range of frequencies, including the regions of lattice (7 to 200 cm^?1) and intramolecular (200 to 4000 cm^?1) vibrations. It is found that the spectral position of the low-frequency band in the Raman spectrum of DNA with a peak near 26 cm^?1 correlates with the Raman spectrum of high-Q low-frequency modes that manifest themselves in the crystalline amino acids under investigation. The low-frequency band of DNA refers to a twist-like vibrational mode of nucleobases. The intensities of this DNA mode and the high-Q lattice modes of the crystalline amino acids L-lysine and D-asparagine are several times as high as those of the Raman lines corresponding to the intramolecular modes. Resonant coupling of low-frequency modes of DNA and amino acid molecular chains is analyzed.     

Spectroscopic Study on the Interaction of Pyronine Y with Nucleic Acids and Its Analytical Application

ABSTRACT

The interaction of pyronine Y (PY) with nucleic acids was studied by resonance Rayleigh scattering (RRS) for nucleic acid detection. The enhanced RRS intensity of nucleic acids reacted with PY was proportional to the concentration of nucleic acids in the ranges of 27.0–625 ng ml^?1 for fish sperm DNA, 39.0–500 ng ml^?1 for calf thymus DNA, and 59.0–375 ng ml^?1 for yeast RNA. The limits of determination were 0.2 ng ml^?1 for fish sperm DNA, 0.6 ng ml^?1 for calf thymus DNA, and 0.7 ng ml^?1 for yeast RNA. The method had been successfully applied to the quick determination of nucleic acids in synthetic and natural samples.     

57Fe-Mössbauer and13C-CP-MAS NMR spectroscopic studies of reaction products of ferrocenylruthenocene with Lewis acids

Adducts of ferrocenylruthenocene and biruthenocene with Lewis acids were studied by means of¹³C-CP-MAS NMR and⁵⁷Fe-Moessbauer spectroscopies. Large low-field shifts found in the¹³C-CP-MAS NMR and large quadrupole splitting (Q. S.) values found in the⁵⁷Fe-Moessbauer spectroscopies suggest the presence of a direct chemical bonding between the central metal atoms in the metallocenes and the Lewis acids.     

Comparative study on the photocatalytic mineralization of homologous aliphatic acids and alcohols

The photocatalytic mineralization of methanol, ethanol and 1-propanol is compared with those of their homologous carboxylic acids (formic, acetic and propanoic). The presence of S₂O₈²⁻ ions almost does not affect the alcohols mineralization. But, those of the acids are slowed down. In addition to this, adding H₂O₂ inhibits the alcohols mineralization and those of the acids, but to a lesser extent.FT-IR studies have shown that carboxylates generated from the oxidation of the corresponding alcohols adsorb at different centres from those where carboxylates directly generated from formic, acetic and propanoic acids do.From the obtained results, mineralizations of these compounds have been correlated with their proximity and accessibility to photoactive centres.     

Conductometric and fluorometric studies of sodium dodecyl sulphate in aqueous solution and in the presence of amino acids

The critical micelle concentration (CMC) of sodium dodecyl sulphate (SDS) in pure water and in the presence of amino acids (0.01, 0.02 and 0.03 mol kg^?1), L-valine (Val) and L-leucine (Leu) was determined from conductometric and fluorometric methods using pyrene as luminescence probe. Depression in the CMC at low concentration of amino acids is attributed to the increased hydrophobic–hydrophobic interaction between the non-polar groups of the surfactant, while, at high concentration, amino acids bind strongly with the anion, DS^?, head groups of SDS, thereby, delaying the micelle formation, resulting in increased CMC. A pronounced decrease in the CMC, while a marked increase in λ⁰₊, with decrease in the solvated radius (rather than crystal radius) of the counterions is observed. Negative values of ΔG⁰_m and ΔH⁰_m indicate that micellisation of SDS in the presence of amino acids is thermodynamically spontaneous and exothermic. Highest negative value of ΔH⁰_m in 0.01 m Val, with lowest CMC value, shows that 0.01 m aqueous Val is the most suitable medium favouring the micellisation of SDS. Decrease in I₁/I₃ from Val to Leu confirms the relative hydrophobicity of two amino acids. The observed values of the packing parameter, P, of SDS in water and in aqueous amino acids suggest that micelles formed are spherical in nature.     

Diffuse reflectance spectrum of some Nd3+ aromatic acids

The Nd³⁺ complexes of β-diketonates have been studied earlier, ^1–3 but those of aromatic acids have not been studied in detail. The present communication reports the study of two of such complexes.     

Understanding the complexation of aliphatic and aromatic acids guests with octa acid

In this study, inclusion of 10 guest molecules, adamantyl and naphthyl carboxylic acids with different structural and electronic properties, within a synthetic cavitand octa acid was probed by isothermal calorimetry, 1D and 2D ¹H nuclear magnetic resonance spectroscopy, and molecular dynamic simulations. Under the condition of the experiments (pH ~ 8.7), the guests were included as carboxylate anions with the polar anionic head group facing water and hydrophobic carbon skeleton buried within the cavitand, forming 1:1 host to guest complexes. Importance of weak interactions between the guest and the cavitand interior is reflected in the measured negative ΔH values. Although ΔH was negative for all guests, ΔS was positive for adamantyl guests and negative for naphthyl guests. Quite likely the difference in hydrophobicity between the 2 sets of molecules and the strength of interaction between the guest and the host are responsible for the sign difference in ΔS between the 2 series. The importance of steric factor during inclusion of naphthyl carboxylic acids within octa acid cavity is brought out by the difference in thermodynamic parameters between the 1‐ and 2‐substituted naphthyl carboxylic acids; 2‐naphthyl carboxylic acids that can penetrate deeply have larger ?ΔH and 1‐naphthyl carboxylic acids that can only enter the cavity in an angle have smaller ?ΔH. As expected, based on the well‐known concept of “enthalpy‐entropy compensation,” the molecules that have large ?ΔH are accompanied by large ?ΔS.     

Inelastic electron tunneling spectroscopy of carboxylic acids on alumina at low coverage

The difficulties in assigning certain modes of carboxylic acids adsorbed on alumina are discussed. The study of the spectra of marked acetic acid CH₃C¹⁸O¹⁸OH adsorbed on alumina has allowed us to clarify the assignments of the acetate ion formed. Then an examination of the spectra at very low coverages has enabled us to propose a model for the adsorption, which occurs on (at least) two different sites.     

Photoluminescence study of new lanthanide complexes with benzeneseleninic acids

New lanthanide complexes with benzeneseleninic (ABSe) and 4-chloro-benzeneseleninic (ABSeCl) acids have been synthesized and characterized by elemental analysis, infrared and UV–visible spectroscopies. The emission spectra of the trivalent europium complexes presented the typical electronic ⁵D₀→⁷F_J transitions of the ion (J=0–4). The ground-state geometries of the europium complexes have been calculated by using the Sparkle/AM1 model. From these results, the 4f–4f intensity parameters and energies of the ligand singlet and triplet excited states have been obtained. The lower emission quantum yield for the [Eu(ABSe)₃(H₂O)₂](H₂O)₂ compound, as compared to the [Eu(ABSeCl)₃(H₂O)₂] one, can be associated to the higher numbers of water molecules, in the first and second coordination spheres, that contribute to the luminescence quenching. The [Eu(ABSe)₃(H₂O)₂](H₂O)₂ complex presents an intermediate state whose energy difference with respect to the first excited singlet state is resonant with three phonons from the water molecules, favouring a multiphonon relaxation process from the singlet state followed by a fast internal conversion process; this effect is less pronounced in the complex with the ABSeCl ligand. The luminescence decay curves of the gadolinium complexes indicate that the level responsible for the intramolecular energy transfer process has a triplet character for both compounds. The nephelauxetic effect in these compounds was investigated under the light of a recently proposed covalency scale based on the concept of overlap polarizability of the chemical bond.     

Sample preparation techniques for the determination of natural 15N/14N variations in amino acids by gas chromatography-combustion-isotope ratio mass spectrometry (GC-C-IRMS)

In order to identify natural nitrogen isotope variations of biologically important amino acids four derivatization reactions (t-butylmethylsilylation, esterification with subsequent trifluoroacetylation, acetylation and pivaloylation) were tested with standard mixtures of 17 proteinogenic amino acids and plant (moss) samples using GC-C-IRMS. The possible fractionation of the nitrogen isotopes, caused for instance by the formation of multiple reaction products, was investigated. For biological samples, the esterification of the amino acids with subsequent trifluoroacetylation is recommended for nitrogen isotope ratio analysis. A sample preparation technique is described for the isotope ratio mass spectrometric analysis of amino acids from the non-protein (NPN) fraction of terrestrial moss. ¹⁴N/¹⁵N ratios from moss (Scleropodium spec.) samples from different anthropogenically polluted areas were studied with respect to ecotoxicologal bioindication.     

ToF-SIMS characterisation of diterpenoic acids after chromatographic separation

Microcolumn liquid chromatography (μHPLC) coupled on-line with time of flight secondary ion mass spectrometry (ToF-SIMS) was applied for mixture of diterpenoic acids (abietic, gibberellic and kaurenoic) analysis. Chromatographic effluent, with analytes separated, was carried out directly onto different, ToF-SIMS compatible surface substrates, for further ToF-SIMS analysis. Silica gel Si₆₀, aluminium backplate modified Si₆₀, monolithic silica gel and Raman spectroscopy chromatographic thin layers were used as the deposition substrates in this experiment. By ToF-SIMS surface imaging the deposition trace picture has been obtained. Effluent deposition surface area was scanned for diterpenoic acid fragment mass values based on mass spectrometric library. Measured ToF-SIMS dataset of fragment abundance and intensities were used for preliminary fragmentation schemes construction. The lowest substrate background activity has been established for monolithic silica gel thin layer and aluminium backplate modified Si₆₀ thin layer. In the case of Raman spectroscopy pre-treated thin layer or conventional chromatographic thin layer Si₆₀, the both, high background signal intensity and impossibility to construct negative ions surface image, were observed. Diterpenoic acids studied serve the similar mass spectrum but ToF-SIMS coupled with liquid chromatographic separation brings new impact to the positive identification of analytes studied.     

Theoretical study of14N pure quadrupole resonance in amino acids

The theoretical hybridization model of Vega is adapted to the tetrahedral environment around the nitrogen nucleus in eleven amino acids to estimate the orbital occupation numbers using the experimental values of the quadrupole coupling constant and asymmetry parameter of¹⁴N quadrupole resonance and the results are discussed.     

The effect of acids on fluorescence of coumarin-6 in organic solvents

The effect of acids (HCl, HClO₄, HNO₃, and CH₃COOH) on the fluorescence of coumarin-6 in organic solvents (acetonitrile, acetone, butanol-1, and ethanol) is studied. The regions of acid (HCl, HClO₄, HNO₃) concentrations that lead to a change in the fluorescence spectra are determined for each of the solvents. It is shown that, for all the solvents studied, acetic acid with a concentration within the region 10^?1–10^?6 M causes no significant changes in the fluorescence spectrum of coumarin-6. A mechanism of the coumarin-6 protonation is proposed.