Vibrational spectroscopic studies of the interaction of water with serine

The vibrational dynamics of water around serine was investigated by using Raman spectroscopy and inelastic incoherent neutron scattering. Experiments with serine in deuterium oxide were performed to assist the assignment. The study shows that for the serine, the exchange of protons-deuterons on the active -NH3+ and -OH groups were relatively easy, whereas there were hardly any exchanged on the -CH or -CH2- groups. The main features of the spectra for hydrated samples (versus the dry samples) were altered considerably; new sharp peaks in the measured spectra appeared, indicating that the hydrogen bonding between water and serine had disturbed the structure of the serine molecule.     

Analysis of cyclic pyrolysis products formed from amino acid monomer

Amino acid was mixed with silica and tetramethylammonium hydroxide (TMAH) to favor pyrolysis of amino acid monomer. The pyrolysis products formed from amino acid monomer were using GC/MS and GC. 20 amino acids of alanine, arginine, asparagine, aspartic acid, cysteine, glutamic acid, glutamine, glycine, histidine, isoleucine, leucine, lysine, methionine, phenylalanine, proline, serine, threonine, tryptophan, tyrosine, and valine were analyzed. The pyrolysis products were divided into cyclic and non-cyclic products. Among the 20 amino acids, arginine, asparagine, glutamic acid, glutamine, histidine, lysine, and phenylalanine generated cyclic pyrolysis products of the monomer. New cyclic pyrolysis products were formed by isolation of amino acid monomers. They commonly had polar side functional groups to 5-, 6-, or 7-membered ring structure. Arginine, asparagine, glutamic acid, glutamine, histidine, and phenylalanine generated only 5- or 6-membered ring products. However, lysine generated both 6- and 7-membered ring compounds. Variations of the relative intensities of the cyclic pyrolysis products with the pyrolysis temperature and amino acid concentration were also investigated.     

A comparative study of commercial liquid chromatographic detectors for the analysis of underivatized amino acids

This study compares the main commercial detectors that can detect amino acids in their underivatized form. The detectors tested are: the chemiluminescent nitrogen detector (CLND), the evaporative light scattering detector (ELSD), the nuclear magnetic resonance spectrometer, conductivity detector, refractive index, UV, and electrospray quadrupole mass spectrometry (in simple and tandem MS mode). As ELSD, CLND and MS require a volatile mobile phase, an ion-pair reversed-phase liquid chromatographic system was selected, consisting of an octadecyl column and an aqueous mobile phase containing pentadecafluorooctanoic acid as volatile ion-pairing reagent. Underivatized taurine, hypotaurine, aspartic acid, hydroxyproline, asparagine, serine, glycine, glutamine, cysteine, glutamic acid, threonine and alanine were simultaneously analysed with each detector. In order to test the applicability of these detectors to "real world" samples, the amino acid stoichiometry of the tetrapeptide Gly-Gly-Asp-Ala was determined with each detector after acid hydrolysis. The detectors were compared in terms of linearity, limit of detection, advantages and disadvantages as well as special features (capacity to provide structural information, specificity, quantification with single calibration curve, etc.).     

Determination of D- and L-amino acids in mouse kidney by high-performance liquid chromatography.

A method for the enantiomeric analysis of amino acids of mammalian tissues is described. An excellent resolution of D- and L-enantiomers of common protein amino acids was achieved by employing a combination of thin-layer chromatography and high-performance liquid chromatography. D-Enantiomers and L-enantiomers of glutamate, aspartate, glutamine, asparagine, serine, threonine, alanine, proline, tyrosine, valine, methionine, isoleucine, leucine, phenylalanine and histidine, as well as glycine were derivatized with 1-fluoro-2,4-dinitrophenyl-5-L-alanine amide. The amino acid diastereomers were separated by two-dimensional thin-layer chromatography. Each amino acid diastereomer was then analysed by reversed-phase high-performance liquid chromatography for the resolution of D- and L-enantiomers. Very sharp peaks were obtained using a conventional octadecylsilyl-bonded column, and the possibility of analysing these amino acids (except tyrosine and histidine) in subnanomole amounts was indicated. The method was used to demonstrate the presence of D-enantiomers of alanine, proline and serine in mouse kidney.     

Dynamics of water studied by coherent and incoherent inelastic neutron scattering

This paper reviews the more recent results obtained on the dynamics of water by neutron scattering and shows that some information can be obtained by this technique at the microscopic level of the hydrogen bond. It also accounts for some very recent results obtained with the hydrated protein C-phycocyanin.

Incoherent quasi-elastic and inelastic neutron scattering by water has been performed in a temperature range extending to the supercooled state. The analysis of the quasi-elastic spectrum separates two main components and gives two characteristic times, one of them being related to the hydrogen-bond lifetime. The inelastic spectra extend until 600 meV, i.e. covering the intramolecular vibration region, showing for the first time the stretching band.

Collective excitations propagating at 3310 m s⁻¹ have been observed by coherent inelastic neutron scattering. This result was predicted by previous computer molecular dynamics simulations of water. The data are interpreted as a manifestation of short wavelength collective modes propagating within patches of highly bonded water molecules, and distinct from the ordinary sound wave.     

Metastable Nitric Acid Trihydrate in Ice Clouds

The composition of high‐altitude ice clouds is still a matter of intense discussion. The constituents in question are ice and nitric acid hydrates, but the exact phase composition of clouds and its formation mechanisms are still unknown. In this work, conclusive evidence for a long‐predicted phase, alpha‐nitric acid trihydrate (alpha‐NAT), is presented. This phase was characterized by a combination of X‐ray and neutron diffraction experiments, allowing a convincing structure solution. Furthermore, vibrational spectra (infrared and inelastic neutron scattering) were recorded and compared with theoretical calculations. A strong interaction between water ice and alpha‐NAT was found, which explains the experimental spectra and the phase‐transition kinetics. On the basis of these results, we propose a new three‐step mechanism for NAT formation in high‐altitude ice clouds.     

TLC separation and derivative spectrophotometry of some amino acids

Chromatographic systems for the separation of amino acid mixtures on RP-18 as a stationary phase have been elaborated. The best results were obtained using methanol-water (1:1, v/v; 1:3, v/v; 1:5, v/v) as a mobile phase. The following amino acids have been examined: asparagine, arginine monohydrochloride, cystine, cysteine chloride, glycine, histidine monohydrochloride, hydroxyproline, isoleucine, leucine, lysine monochloride, methionine, ornithine monohydrochloride, phenylalanine, proline, threonine, tryptophan, tyrosine, serine, valine. Histidine (as monohydrochloride) and methionine were determined by first-, second- and third-derivative spectrophotometry in a mixture of several amino acids.     

Inelastic neutron scattering study of water in hydrated LTA-type zeolites

The vibrational dynamics of water molecules encapsulated in synthetic Na-A and Mg-exchanged A zeolites were studied versus temperature by inelastic neutron scattering (INS) measurements (30-1200 cm(-1)) as a function of the induced ion-exchange percentage by using the indirect geometry tof spectrometer TOSCA at the ISIS pulse neutron facility (RAL, UK). The experimental INS spectra were compared with those of ice Ih to characterize the structural changes induced by confinement on the H2O hydrogen-bonded network. We observed, after increasing the Mg2+ content, a tendency of water molecules to restore the bulklike arrangements together with more hindered dynamics. These results are confirmed by the analysis of the evaluated one-phonon amplitude-weighted proton vibrational density of states aimed, in particular, to follow the evolution of the water molecules librational mode region.     

The mass spectra of N-adamantoylpeptides

The N-adamantoyl derivatives of the esters of twenty-one di-peptides and eight tri-peptides containing the amino acids glycine, alanine, valine, leucine, isoleucine, proline, phenylalanine, glutamic acid, lysine, histidine, serine, threonine, methionine, S-benzylcysteine and tyrosine were prepared and their mass spectra determined. The spectra of all compounds were suitable for amino acid sequence determination. Mixtures containing N-adamantoyl dipeptide and tripeptide methyl esters were separated by thin-layer chromatography and the components identified by high resolution mass spectrometry. The mass spectrometric features of N-adamantoyl peptide esters are discussed and compared with those of other N-acyl peptide derivatives.     

Mutual interactions in a ternary protein/bioprotectant/water system

The dynamics of hydration water play a key role in many biological processes. The activity and function of proteins are strongly affected by the presence of water, which interacts primarily by means of hydrogen bonding. These interactions are examined in this work by a comparison of neutron vibrational spectra (Inelastic Neutron Scattering, INS) of dry lysozyme and hydrated lysozyme at h = 0.7 (g of H₂O/g of protein) with those of a lysozyme/water mixture at the same hydration value in the presence of the glass-forming bioprotectant trehalose. A difference spectrum, obtained by subtracting the dry lysozyme spectrum from that of the lysozyme/water mixture, yields the hydration water spectrum which is compared to the INS spectra of different kinds of ice in order to determine the changes induced by lysozyme on the hydrogen-bonded network of water. An additional comparison is performed by using a double-difference spectrum obtained by subtracting both the dry lysozyme and the trehalose spectra from the lysozyme/trehalose/water ternary spectrum. The effects of the mutual interactions among the three components, i.e. protein, disaccharide and water, are determined by comparison of the spectra of the dry systems (lysozyme, trehalose) with the difference spectra obtained from subtraction of the dry systems from the binary systems. It is concluded that the interfacial water more strongly affects the intermolecular mode region at low frequencies, whereas the vibrational spectra at high frequencies are more influenced by lysozyme and trehalose.     

Phonons and thermodynamics of unmixed and disordered Li0.6FePO4

The lithium-storage material Li(0.6)FePO(4) was studied by inelastic neutron scattering and differential scanning calorimetry. Li(0.6)FePO(4) undergoes a transformation from a two-phase mixture (heterosite and triphylite) to a disordered solid-solution at 200 degrees C. Phonon densities of states (DOS) obtained from the inelastic neutron scattering were similar for the two-phase sample measured at 180 degrees C and the disordered sample measured at 220 degrees C. The vibrational entropy of transformation is 1.8 +/-0.9 J/(K mol), which is smaller than the configurational entropy difference of approximately 3.1 J/(K mol). The measured enthalpy of the disordering transition was estimated as 2.5 kJ/mol. The phonon data show a small change in lattice dynamics upon disordering.     

An efficient synthesis of N-methyl amino acids by way of intermediate 5-oxazolidinones

N-Methyl amino acids occur in many natural products. Experimental strategies are presented for a unified approach to the synthesis of N-methyl derivatives through 5-oxazolidinones of the 20 common l-amino acids. The amino acids with reactive side chains that required protecting groups or devoted syntheses for side chain construction for N-methylation to proceed included serine, threonine, tyrosine, cysteine, methionine, tryptophan, asparagine, histidine, and arginine. The studies have provided improved methods for the preparation of N-methyl serine, threonine, and tyrosine. All 20 of the common l-amino acids are now available in suitable forms for solid or solution-phase peptide synthesis.     

Molecular Dynamics Simulations for Ice Modifications II and IX

Molecular vibrations of water (H₂O and D₂O) in crystals of ice II and ice IX are studied by molecular dynamics in a rigid bond approximation with a fixed bond angle. Using an atom-atomic potential PM for describing the interactions between water molecules in ice II (N = 576 molecules) and ice IX (N = 768) in an NVE ensemble leads to reproduction of the structure of both types of ice. For all water molecules and separately for each system of crystallographically equivalent water molecules in ice crystals, we defined the time dependence of the mean-square displacement of the center of mass of the molecule, the autocorrelation function of velocity for the center of mass, and the autocorrelation function of velocity for hydrogen (deuterium) atoms. The densities of vibrational states are calculated as Fourier integrals of the corresponding autocorrelation functions. In the case of ice II, the densities of states agree well with the experimental incoherent inelastic neutron scattering spectra. In the case of ice IX, agreement is worse. For both polymorphs, the mean-square displacement and the densities of vibrational states of the center of mass of the molecule and the hydrogen (deuterium) atom differ slightly between molecules belonging to different systems of crystallographic positions. This is explained by the difference in their environments.     

Gas-Phase Binding of Noncovalent Complexes Between α-cyclodextrin and Amino Acids Investigated by Mass Spectrometry

Noncovalent complexes between cyclodextrins and small molecules have been extensively studied recently because of their widespread application in the pharmaceutical industry for chiral and molecular recognition. To date, gas phase noncovalent binding affinities between α-cyclodextrin and amino acids have not been widely investigated. In this study, gas-phase binding of noncovalent complexes between α-CD and amino acids was investigated by electrospray ionization mass spectrometry (ESI-MS), demonstrating the formation of 1:1 stoichiometric noncovalent complexes. The binding of the complexes were further confirmed by collision-induced dissociation by tandem mass spectrometry. Mass spectrometric titrations between α-cyclodextrin and phenylalanine, glutamic acid, and arginine were performed to provide binding constants (lgK_a) as references for competitive ESI-MS. Calibration curves for the complexes of α-cyclodextrin with phenylalanine, glutamic acid, and arginine were plotted. Through competitive ESI-MS, the lgK_a for the complexes of α-CD with aspartic acid, lysine, proline, glycine, alanine, asparagine, cystine, glutamine, histidine, leucine, isoleucine, methionine, serine, threonine, and valine were measured directly. By comparison, it is seen that the measured binding constants for the complexes of α-cyclodextrin with basic amino acids such as arginine and lysine are lower than those for most complexes of neutral amino acids. The chiral selectivity of α-cyclodextrin for L- and D-isomers of methionine, threonine, asparagine, and phenylalanine determined by ESI-MS revealed its application as a chiral selector.     

Effect of UVB Radiation on Utilization of Inorganic Nitrogen by Antarctic Microalgae

Abstract— The impact of UVB (280-315 nm) radiation (WG 305) on uptake of ¹⁵N-ammonium and ¹⁵N-nitrate of marine phytoplankton from station 219 (47°W, 61.5°S) and sea ice-algae from station 265 (22.6°W, 73.29°S) was studied during the Polarstern Cruise (EPOS III, Leg 3) to the Weddell Sea, Antarctica 1989. Uptake rates of ¹⁵NH₄⁺ were higher and more affected by UVB radiation than those of ¹⁵N0₃-. Pool sizes of the main amino acids changed in response to the used inorganic nitrogen source and UV exposure. Pools of glutamine, serine and glycine decreased, whereas those of alanine, asparagine and glutamate increased after UVB irradiation. The ¹⁵N-incorporation into the amino acids was reduced as a result of UVB exposure of phytoplankton and ice algae. Results are discussed with reference to an inhibitory effect on the enzymes of both carbon and nitrogen metabolism as well as to adaptation strategies.     

A peptide containing aspartic acid, glutamic acid and serine in calf brain synaptic vesicles

Free amino acids and other amino compounds in calf brain synaptic vesicles were identified and determined by thin-layer chromatography and ion-exchange chromatography. The vesicles contained ten identified amino acids with glutamic acid, aspartic acid, taurine and gamma-aminobutyric acid in the highest concentrations, and also cysteic acid (or cysteinesulfinic acid), glutamine, alanine, serine, glycine and lysine. The vesicles also contained certain unknown acid-labile, ninhydrin-positive compounds, one of which was a peptide yielding, after acid hydrolysis, about 40% aspartic acid, 30% serine, 15% glutamic acid, 10% glycine and possibly some alanine and lysine. The concentration of the peptide in the vesicles was as high as that of all the other amino compounds together.     

An SFG study of interfacial amino acids at the hydrophilic SiO2 and hydrophobic deuterated polystyrene surfaces

Sum frequency generation (SFG) vibrational spectroscopy was employed to characterize the interfacial structure of eight individual amino acids--L-phenylalanine, L-leucine, glycine, L-lysine, L-arginine, L-cysteine, L-alanine, and L-proline--in aqueous solution adsorbed at model hydrophilic and hydrophobic surfaces. Specifically, SFG vibrational spectra were obtained for the amino acids at the solid-liquid interface between both hydrophobic d(8)-polystyrene (d(8)-PS) and SiO(2) model surfaces and phosphate buffered saline (PBS) at pH 7.4. At the hydrophobic d(8)-PS surface, seven of the amino acids solutions investigated showed clear and identifiable C-H vibrational modes, with the exception being l-alanine. In the SFG spectra obtained at the hydrophilic SiO(2) surface, no C-H vibrational modes were observed from any of the amino acids studied. However, it was confirmed by quartz crystal microbalance that amino acids do adsorb to the SiO(2) interface, and the amino acid solutions were found to have a detectable and widely varying influence on the magnitude of SFG signal from water at the SiO(2)/PBS interface. This study provides the first known SFG spectra of several individual amino acids in aqueous solution at the solid-liquid interface and under physiological conditions.     

Combined application of Monte Carlo method and neural networks to simulate qualitative prompt gamma neutron activation analysis

Prompt gamma spectrum produced by thermal neutron absorption and fast neutron inelastic scattering is simulated using Monte Carlo code MCNP4C. The simulated spectrum is analyzed with artificial neural network techniques. The neural network in our study is trained based on back-propagation algorithm with 138 gamma ray spectra. Elements existing in the 20 different substances are specified. The ANN could identify elements correctly in 96% of input cases.     

分析测试新方法(197~203)毛细管电泳-间接紫外法用于太子参中的非衍生化氨基酸检测

建立了一种简单、快速测定赖氨酸(Lys)、脯氨酸(Pro)、亮氨酸(Leu)、丙氨酸(Ala)、组氨酸(His)、苏氨酸(Thr)、蛋氨酸(Met)、丝氨酸(Ser)和甘氨酸(Gly)的毛细管电泳-间接紫外检测方法.通过研究缓冲液的种类和浓度、缓冲液的p H等分离条件对被测组分分离度和灵敏度的影响,从而优化了分析条件.实验结果表明,用0.1mol/L氢氧化钠溶液调节14 mmol/L的对氨基苯磺酸至p H为11.2做为运行缓冲液,当分离电压为20 k V时,9组分在12 min内实现了完全分离.实验结果表明,方法能成功用于不同产地太子参药材中9种氨基酸的含量测定.方法重现性良好,迁移时间和峰高的RSD分别小于2.6%和4.5%(n=7).