The infrared spectra and structures of the valyl-glycine zwitterion isolated in a KBr matrix

The IR absorption spectrum of zwitterions of l-valyl-glycine isolated in a KBr matrix has been measured using a novel dissolution, spray and deposition technique. The number of conformers, their molecular structures and their vibrational spectra have been determined by ab initio molecular orbital calculations of the non-aqueous self-consistent reaction field type, using the Onsager dipole-sphere model at both the density functional theory and Hartree–Fock levels. Six conformers were determined. Although differences in their relative energies were found to be small, one conformer Tg2 was consistently the lowest for a range of cavity radii and for both levels of theory. From comparison of the observed and predicted spectra it is concluded that one or more of the trans group of conformers is present in the KBr matrix. Good agreement between measured and calculated spectra has been obtained for the majority of the prominent bands in the spectrum.     

Qualitative and quantitative evaluation of chrysotile and crocidolite fibers with IR-spectroscopy: application to asbestos-cement products

Infrared (IR) spectrophotometry allows simple and quick qualitative and quantitative evaluations of different kinds of asbestos, as well as of other inorganic particles. In particular, chrysotile and crocidolite have characteristic IR spectra and optical density measures of 2,710 nm band for chrysotile, of 12,820 nm band for crocidolite permit quantitative evaluation of each fiber alone or in mixture. IR spectra also give informations about changes of fiber structure and of chemical composition due, for example, to thermal treatment or acid leaching. The analytical method we developed can detect levels as low as 0.1 mg of fiber in a 300 mg disk of KBr using a low cost IR spectrophotometer. The use of a Fourier Transform IR spectrophotometer (FTIR) improves dramatically the sensitivity and selectivity. Computer assisted analysis of spectra offers the possibility to reduce matrix interferences and to compare different spectra. Examples of IR technique applied to asbestos-cement products and insulating materials are presented.     

Correlation of structure and vibrational spectra of the zwitterion L-alanine in the presence of water: an experimental and density functional analysis

Infrared vibrational spectra were collected along with the vibrational circular dichroism (VCD) spectra for the zwitterions alpha-D-alanine, alpha-L-alanine, alpha-D-mannose and alpha-L-mannose as potassium bromide (KBr) pressed samples. VCD for D- and L-alanine dissolved in water was also measured and compared against the spectra resulting from KBr pressed samples. The experimental data were compared against the ab initio B3LYP/6-31G* optimized geometry. The zwitterion structure of alpha-L-alanine was stabilized by the addition of water molecules. Computationally, beta-L-mannose was studied and resulting expected VCD bands assigned. We present the molecular structures resulting VCD spectra and infrared vibrational spectra from experimentation as compared with the computed results.     

Surface adsorption‐induced conformational ordering and crystallization of polyethylene oxide

The conformational ordering and crystallization of polyethylene oxide (PEO) in the presence of KBr surface were studied with in situ Fourier transform infrared spectroscopy (FTIR). KBr was chosen because of its low absorption on IR, which allows adding large amounts KBr into PEO matrix without sacrificing IR signal significantly. The presence of KBr enhances conformational order well above the melting temperature of PEO, which can further accelerate or decelerate the crystallization process. Low concentrations of KBr powder in the PEO melt promotes crystallization process, whereas high concentration of KBr restricts large portion of PEO chains on KBr surfaces, which hinder the diffusion and rearrangement of conformation and consequently slow down the crystallization process. Acceleration of crystallization requires a synergetic effect between the adsorbed chains with ordered conformation and the free chains with a fast diffusion rate, where the former and the later are responsible to lower the nuclei barrier and to maintain the low activation energy of diffusion, respectively. © 2009 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 48: 106–112, 2010     

Computational Exploration of Conformations of Glycine-Arginine and a Deduced Model on Global Minimum Configurations of Dipeptides in Gas Phase

An extensive computational study on the conformations of gaseous dipeptide glycinearginine, GlyArg, has been performed. A large number of trail structures were generated by systematically sampling the potential energy surface (PES) of GlyArg. The trial structures were successively optimized with the methods of PM3, HF/3-21G^*, BHandHLYP/6-31G^*, and BHandHLYP/6-311++G^** in order to reliably find the low energy conformations. The conformational energies were finally determined with the methods of BHandHLYP, camB3LYP, B97D, and MP2 using the basis set of 6-311++G(3df,3pd). The results establish firmly that gaseous GlyArg exists primarily in its canonical form, in sharp contrast with ArgGly that adopts the zwitterionic form. Important data such as the rotational constants, dipole moments, vertical ionization energies, temperature distributions and IR spectra of the low energy conformers are represented for the understanding of the future experiments. Moreover, considering the global minima of all amino acids and many dipeptides, combined with the hydrophobicities of amino acids, a model predicting whether the global minimum configuration of a dipeptide is canonical or zwitterionic is developed.     

Vibrational spectra of alpha-amino acids in the zwitterionic state in aqueous solution and the solid state: DFT calculations and the influence of hydrogen bonding

The zwitterionic forms of the two simplest alpha-amino acids, glycine and l-alanine, in aqueous solution and the solid state have been modeled by DFT calculations. Calculations of the structures in the solid state, using PW91 or PBE functionals, are in good agreement with the reported crystal structures, and the vibrational spectra computed at the optimized geometries provide a good fit to the observed IR and Raman spectra in the solid state. DFT calculations of the structures and vibrational spectra of the zwitterions in aqueous solution at the B3-LYP/cc-pVDZ level were found to require both explicit and implicit solvation models. Explicit solvation was modeled by inclusion of five hydrogen-bonded water molecules attached to each of the five possible hydrogen-bonding sites in the zwitterion and the integration equation formalism polarizable continuum model (IEF-PCM) was employed, providing a satisfactory fit to observed IR and Raman spectra. Band assignments are reported in terms of potential-energy distributions, which differ in some respects to those previously reported for glycine and l-alanine.     

Reaction of γ-pyrones with 1,3-bis(dicyanomethylene)indan

The condensation of -pyrones with 1,3-bis(dicyanomethylene)indan leads to the corresponding deeply colored 2-(pyran-4-ylidene)-1,3-bis(dicyanomethylene)indans. The reaction of the latter with primary aliphatic or aromatic amines leads to replacement of the pyran oxygen by an amino group. The resulting compounds are zwitterions and possesses dichroic properties. The IR and UV spectra, and also the dichroic spectra of the compounds obtained in a liquid crystal are given. A qualitative explanation of the nature of the absorption bands of these compounds in the visible region of the spectrum is presented.Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 5, pp. 603–608, May, 1985.     

碳纳米管为基质对氨基酸的MALDI-FT MS分析

Twenty common amino acids have been analyzed successfully by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) using carbon nanotubes as matrix. From the spectra, little or no background interference or fragmentation of the analytes has been observed. This method was also applied to the analysis of amino acid mixture successfully. Carbon nanotubes have some features such as large surface area to disperse the analyte molecules sufficiently and prevent the sample aggregation and strong ultraviolet absorption to transfer energy easily to the analyte molecules. The present method has potential application for the rapid and sensitive analysis of amino acids and their mixture.     

Effect of sample packing on the scattering properties of the reference material in diffuse reflectance infrared spectrometry

Effect of the sample packing on the scattering properties of KBr, one of the most conventional matrix used in diffuse reflectance Fourier transform infrared (IR) spectrometry (DRIFTS), has been studied. The particle size of KBr ranged between 2 and 15 mum with a mean of 9.9 mum. The average particle size of quartz and calcite used as analytes were 2 mum and 6 mum, respectively. The scattering coefficient of KBr has been found to increase with increasing pressure applied during sample packing. 1 MPa pressure was necessary for reproducible scattering properties and quantitative results. The scattering coefficient of KBr using 1 MPa pressure for 1 min during sample packing has been determined from calibration curves and found to be as s = 107 +/- 11 cm(-1). It has been experimentally demonstrated that using 2 mm deep sample cups, the criteria of infinite sample thickness is practically fulfilled. It has been also shown that band intensities of reflectance spectra were strongly influenced by the change of the reflectance of the reference material and the less the sample concentration (c) the greater the effect. If c < 0.1 w/w%, that often occurs in practice, the RSD of band intensities can vary upto +/- 10-60%. Therefore, in quantitative analysis all spectra should be measured against one and same sample of reference material.     

鸟嘌呤红外光谱的密度泛函理论研究──标度量子力学(SQM)力场处理

用密度泛函理论DFT(B3LYP)/6-31G^*方法对鸟嘌呤分子的酮-胺式和醇-胺式异构体的几何结构、振动谐性力场和红外光谱进行了研究.理论力场由迁移自相关分子异胞嘧啶和咪唑的力常数标度因子进行标度.算得振动频率与鸟嘌呤的实验基质隔离IR光谱比较平均偏差对酮-胺式和醇-胺式分别为6.6和6.0cm^-1.根据振动频率的势能分布和DFT计算的光谱强度值对鸟嘌呤分子的实验振动基频进行了理论归属.     

Multilayer adsorption of amino acids on oxidized cellulose

The adsorption of amino acids (AA) (glycine, L-alanine, L-proline) on oxidized cellulose (OC) with various carboxyl contents and degrees of crystallinity from aqueous and water/ethanol solutions was studied. It was found that multilayer adsorption occurs in concentrated solutions of AA. It proceeds according to successive mechanisms via adsorption of AA zwitterions onto carboxyls of already adsorbed AA. This leads to formation of chain AA associates in the OC phase. A sharp increase in swelling accompanies multilayer adsorption. It was established that structural characteristics and degree of polymerization of OC are the main factors that affect multilayer adsorption. The distribution of carboxyls in the OC phase also plays an important role. Multilayer adsorption does not proceed in water/ethanol solutions and in the case of the cationic form of AA.     

Temperature dependence of peptide carboxylic group IR spectra in the amide I′ region at neutral and acidic pH

Analysis of the temperature-dependent amide I′ bands of peptides and proteins can be complicated by their overlap with other IR bands, particularly those of carboxylic groups of amino acid side-chains and the C-terminus. Previously, we reported IR spectra of charged carboxylic side-chains in Asp and Glu amino acids, and C-terminal groups of several amino acids and dipeptides at neutral pH. To complement these results, here we investigate the IR absorptions of Asp and Glu side-chains in capped amino acids (AcAspNMe and AcGluNMe), at both neutral and acidic pH. Spectra of protonated (acidic pH) C-terminal group absorptions are also investigated, using three dipeptides (AlaGly GlyAla and GlyGly) as model compounds. Sets of temperature-dependent experimental IR spectra were analyzed using pseudo-Voigt lineshape profiles. We find that the temperature-dependent behavior of the IR bands of deprotonated (neutral pH) side-chains in AcAspNMe and AcGluNMe dipeptides are generally similar to those reported previously for Asp and Glu. Protonated carboxylic group (acidic pH) IR bands behave uniformly with respect to temperature, showing very similar magnitude frequency shifts and intensity changes. Implications for analyses of amide I′ bands of peptides and proteins are discussed.     

Infrared depletion spectra of 2-aminopyridine2-pyridone, a Watson-Crick mimic of adenine.uracil

The 2-aminopyridine2-pyridone (2AP2PY) dimer is linked by N-H...O=C and N-H...N hydrogen bonds, providing a model for the Watson-Crick hydrogen bond configuration of the adenine.thymine and adenine.uracil nucleobase pairs. Mass-specific infrared spectra of 2AP2PY and its seven N-H deuterated isotopomers have been measured between 2550 and 3650 cm(-1) by IR laser depletion combined with UV two-color resonant two-photon ionization. The 2PY amide N-H stretch is a very intense band spread over the range 2700-3000 cm(-1) due to large anharmonic couplings. It is shifted to lower frequency by 710 cm(-1) or approximately 20% upon H bonding to 2AP. On the 2AP moiety, the "bound" amino N-H stretch gives rise to a sharp band at 3140 cm(-1), which is downshifted by 354 cm(-1) or approximately 10% upon H bonding to 2PY. The amino group "free" N-H stretch and the H-N-H bend overtone are sharp bands at approximately 3530 cm(-1) and 3320 cm(-1). Ab initio structures and harmonic vibrations were calculated at the Hartree-Fock level and with the PW91 and B3LYP density functionals. The PW91/6-311++G(d,p) method provides excellent predictions for the frequencies and IR intensities of all the isotopomers.     

Ionic Composition of the MK-40 Cation-Exchange Membrane in Amino Acid Solutions: A Conductimetric Study

The ionic composition of a cation-exchange membrane in solutions of amino acids of three types is studied by measuring its conductivity. The concentration constants of equilibrium of the protonation of zwitterions of these acids in the membrane are estimated. The membrane's ionic composition substantially depends on the type of amino acid.     

Application of Fourier transform Raman spectroscopy to a range of compounds of pharmaceutical interest

Fourier transform (FT) Raman spectra have been obtained for a range of synthetic and semisynthetic samples to evaluate the utility of the technique for the characterization of compounds of pharmaceutical interest. These spectra are compared with the IR KBr disc spectra. Examples of the additional, important information which may be extracted from Raman data in comparison with IR spectroscopy are reported for the range of chemical structures studied. The superior ability of Raman to characterize the stretching modes of the CH bond compared with IR spectroscopy is demonstrated for several compounds.The characterization of highly symmetric vibrational modes is one of the most prominent and useful advantages of Raman spectroscopy and several examples of this primary application are also cited. These include the assignment of the ring breathing frequency of monosubstituted benzene rings, the CCC symmetric skeletal mode of a tricyclic fused ring system, the NO symmetric stretch of aromatic nitro groups and the stretching vibrations of various double bonds, several of which possess a high degree of local symmetry.     

Synthesis of a pair of novel receptors and their properties of enantioselective recognition for amino acid zwitterions

A pair of artificial enantiotopic receptors la and lb composed of ( S, S) or (R,R) chiral bicyclic guanidinium, azacrown ether and (t-butyldiphenylsilyloxy) methyl group for amino acid zwitterions have been synthesized. The liquid-liquid competition extraction experiments and 1H NMR studies indicate that the receptor 1a with (S, S) configuration and lb with (R,R) configuration selectively recognize L- and Z)-aromatic amino acids respectively.     

Determination of amino acids in rat vitreous perfusates by capillary electrophoresis

In vivo determinations of amino acids are important for improving our understanding of physiological states of biological tissue function and dysfunction. However, the chemically complex matrix of different biological fluids complicates the assay of this important class of molecules. We introduce a method for characterizing the amino acid composition of submicroliter volumes of vitreous humor perfusates. Low-flow push-pull perfusion sampling is compatible with collecting small volume samples in a complicated matrix that are potentially difficult to separate. An efficient, sensitive, and rapid analysis of amino acids from in vivo perfusates of the vitreous is presented with 3-(4-carboxybenzoyl)-2-quinoline-carboxaldehyde (CBQCA) derivatitation and capillary electrophoresis (CE) separation with laser-induced fluorescence detection (LIF). Derivatization with CBQCA for up to 2 h provided high sensitivity and low detection limits at the nM level. Seventeen amino acids including D-serine (D-Ser) and D-aspartate (D-Asp) were resolved in less than 10 min. Importantly, D-Ser is separated from its enantiomeric pair. Characterization of vitreal amino acids with this assay technique will be useful for understanding ocular diseases and physiological mechanisms in vision.     

Vibrational and photoionization spectroscopy of biomolecules: aliphatic amino acid structures

The aliphatic amino acids glycine, valine, leucine, and isoleucine are thermally placed into the gas phase and expanded into a vacuum system for access by time of flight mass spectroscopy and infrared (IR) spectroscopy in the energy range of 2500-4000 cm(-1) (CH, NH, OH, and stretching vibrations). The isolated neutral amino acids are ionized by a single photon of 10.5 eV energy (118 nm), which exceeds by less than 2 eV their reported ionization thresholds. As has been reported for many hydrogen bonded acid-base systems (e.g., water, ammonia, alcohol, acid clusters, and acid molecules), the amino acids undergo a structural rearrangement in the ion state (e.g., in simplest form, a proton transfer) that imparts sufficient excess vibrational energy to the ion to completely fragment it. No parent ions are observed. If the neutral ground state amino acids are exposed to IR radiation prior to ionization, an IR spectrum of the individual isomers for each amino acid can be determined by observation of the ion intensity of the different fragment mass channels. Both the IR spectrum and fragmentation patterns for individual isomers can be qualitatively identified and related to a particular isomer in each instance. Thus, each fragment ion detected presents an IR spectrum of its particular parent amino acid isomer. In some instances, the absorption of IR radiation by the neutral amino acid parent isomer increases a particular fragmentation mass channel intensity, while other fragmentation mass channel intensities decrease. This phenomenon can be rationalized by considering that with added energy in the molecule, the fragmentation channel populations can be modulated by the added vibrational energy in the rearranged ions. This observation also suggests that the IR absorption does not induce isomerization in the ground electronic state of these amino acids. These data are consistent with theoretical predictions for isolated amino acid secondary structures and can be related to previous IR spectra of amino acid conformers.     

Simple conversion of fully protected amino acids to zwitterions

An operationally simple and efficient method under mild acidic conditions was developed to convert fully protected amino acids to the corresponding zwitterions without either isoelectric precipitation or ion exchange chromatography.