Raman scattering of L‐tryptophan enhanced by surface plasmon of silver nanoparticles: vibrational assignment and structural determination

Vibrational bands of L ‐tryptophan which was adsorbed on Ag nanoparticles (∼10 nm in diameter) have been investigated in the spectral range of 200–1700 cm⁻¹ using surface‐enhanced Raman scattering (SERS) spectroscopy. Compared with the normal Raman scattering (NRS) of L ‐tryptophan in either 0.5 M aqueous solution (NRS‐AS) or solid powder (NRS‐SP), the intensified signals by SERS have made the SERS investigation at a lower molecular concentration (5 × 10⁻⁴ M ) possible. Ab initio calculations at the B3LYP/6‐311G level have been carried out to predict the optimal structure and vibrational wavenumbers for the zwitterionic form of L ‐tryptophan. Facilitated with the theoretical prediction, the observed vibrational modes of L ‐tryptophan in the NRS‐AS, NRS‐SP, and SERS spectra have been analyzed. In the spectroscopic observations, there are no significant changes for the vibrational bands of the indole ring in either NRS‐AS, NRS‐SP, or SERS. In contrast, spectral intensities involving the vibrations of carboxylate and amino groups are weak in NRS‐AS and NRS‐SP, but strong in SERS. The intensity enhancement in the SERS spectrum can reach 10³–10⁴‐fold magnification. On the basis of spectroscopic analysis, the carboxylate and amino groups of L ‐tryptophan are determined to be the preferential terminal groups to attach onto the surfaces of Ag nanoparticles in the SERS measurement. Copyright © 2008 John Wiley & Sons, Ltd.     

Reference database of Raman spectra of biological molecules

Raman spectra of biological materials are very complex, because they consist of signals from all molecules present in cells. In order to obtain chemical information from these spectra, it is necessary to know the Raman patterns of the possible components of a cell. In this paper, we present a collection of Raman spectra of biomolecules that can serve as references for the interpretation of Raman spectra of biological materials. We included the most important components present in a cell: (1) DNA and RNA bases (adenine, cytosine, guanine, thymine and uracil), (2) amino acids (glycine, L ‐alanine, L ‐valine, L ‐serine, L ‐glutamic acid, L ‐arginine, L ‐phenylalanine, L ‐tyrosine, L ‐tryptophan, L ‐histidine, L ‐proline), (3) fatty acids and fats (lauric acid, myristic acid, palmitic acid, stearic acid, 12‐methyltetradecanoic acid, 13‐methylmyristic acid, 14‐methylpentadecanoic acid, 14‐methylhexadecanoic acid, 15‐methylpalmitic acid, oleic acid, vaccenic acid, glycerol, triolein, trilinolein, trilinolenin), (4) saccharides (β‐D ‐glucose, lactose, cellulose, D ‐(+)‐dextrose, D ‐(+)‐trehalose, amylose, amylopectine, D ‐(+)‐mannose, D ‐(+)‐fucose, D ‐(−)‐arabinose, D ‐(+)‐xylose, D ‐(−)‐fructose, D ‐(+)‐galactosamine, N‐acetyl‐D ‐glucosamine, chitin), (5) primary metabolites (citric acid, succinic acid, fumarate, malic acid, pyruvate, phosphoenolpyruvate, coenzyme A, acetyl coenzyme A, acetoacetate, D ‐fructose‐6‐phosphate) and (6) others (β‐carotene, ascorbic acid, riboflavin, glutathione). Examples of Raman spectra of bacteria and fungal spores are shown, together with band assignments to the reference products. Copyright © 2007 John Wiley & Sons, Ltd.     

Identification of epidermal L‐tryptophan and its oxidation products by in vivo FT‐Raman Spectroscopy further supports oxidative stress in patients with vitiligo

In the past, non‐invasive in vivo FT‐Raman spectroscopy has been used to detect H₂O₂‐mediated oxidation of methionine to methionine sulfoxide and methionine sulfone, as well as cysteine to cysteic acid, in the sequence of proteins in the epidermis of patients with vitiligo. L ‐tryptophan (Trp) is another potential target for this oxidation. Owing to the presence of 10⁻³M epidermal albumin which contains one Trp residue, it was tempting to follow the oxidation of this amino acid. Using in vivo and in vitro FT‐Raman spectroscopy, we show for the first time that epidermal Trp is oxidised in patients with vitiligo, yielding 5‐OH‐Trp at 930 cm⁻¹ and other oxidation products (i.e. N‐formyl kynurenine and kynurenine) from indole ring oxidation peaking at 1050 cm⁻¹. On the basis of detailed in vitro results, we could conclude that 5‐OH‐Trp as well as formyl kynurenine and kynurenine are formed via H₂O₂‐mediated Fenton chemistry. These results once again bring out the strength of non‐invasive in vivo FT‐Raman Spectroscopy in dermatology to follow the effect of oxidative stress in the skin of patients with vitiligo. Copyright © 2008 John Wiley & Sons, Ltd.     

Vibrational spectroscopy and crystal structure analysis of two polymorphs of the di‐amino acid peptide cyclo(L‐Glu‐L‐Glu)

Cyclo(L ‐Glu‐L ‐Glu) has been crystallised in two different polymorphic forms. Both polymorphs are monoclinic, but form 1 is in space group P2₁ and form 2 is in space group C2. Raman scattering and FT‐IR spectroscopic studies have been conducted for the N,O‐protonated and deuterated derivatives. Raman spectra of orientated single crystals, solid‐state and aqueous solution samples have also been recorded. The different hydrogen‐bonding patterns for the two polymorphs have the greatest effect on vibrational modes with N H and CO stretching character. DFT (B3‐LYP/cc‐pVDZ) calculations of the isolated cyclo(L ‐Glu‐L ‐Glu) molecule predict that the minimum energy structure, assuming C₂ symmetry, has a boat conformation for the diketopiperazine ring with the two L ‐Glu side chains being folded above the ring. The calculated geometry is in good agreement with the X‐ray crystallographic structures for both polymorphs. Normal coordinate analysis has facilitated the band assignments for the experimental vibrational spectra. Copyright © 2009 John Wiley & Sons, Ltd.     

Vibrational spectra and crystal structure of the di‐amino acid peptide cyclo(L‐Met‐L‐Met): comparison of experimental data and DFT calculations

Experimental Raman and FT‐IR spectra of solid‐state non‐deuterated and N‐deuterated samples of cyclo(L ‐Met‐L ‐Met) are reported and discussed. The Raman and FT‐IR results show characteristic amide I vibrations (Raman: 1649 cm⁻¹, infrared: 1675 cm⁻¹) for molecules exhibiting a cis amide conformation. A Raman band, assigned to the cis amide II vibrational mode, is observed at ∼1493 cm⁻¹ but no IR band is observed in this region. Cyclo(L ‐Met‐L ‐Met) crystallises in the triclinic space group P1 with one molecule per unit cell. The overall shape of the diketopiperazine (DKP) ring displays a (slightly distorted) boat conformation. The crystal packing employs two strong hydrogen bonds, which traverse the entire crystal via translational repeats. B3‐LYP/cc‐pVDZ calculations of the structure of the molecule predict a boat conformation for the DKP ring, in agreement with the experimentally determined X‐ray structure. Copyright © 2009 John Wiley & Sons, Ltd.     

Vibrational spectroscopic studies of the structure of di‐amino acid peptides. Part II: cyclo(L‐Asp‐L‐Asp) in the solid state and in aqueous solution

Solid‐state protonated and N,O‐deuterated Fourier transform infrared (IR) and Raman scattering spectra together with the protonated and deuterated Raman spectra in aqueous solution of the cyclic di‐amino acid peptide cyclo(L ‐Asp‐L ‐Asp) are reported. Vibrational band assignments have been made on the basis of comparisons with previously cited literature values for diketopiperazine (DKP) derivatives and normal coordinate analyses for both the protonated and deuterated species based upon DFT calculations at the B3‐LYP/cc‐pVDZ level of the isolated molecule in the gas phase. The calculated minimum energy structure for cyclo(L ‐Asp‐L ‐Asp), assuming C₂ symmetry, predicts a boat conformation for the DKP ring with both the two L ‐aspartyl side chains being folded slightly above the ring. The CO stretching vibrations have been assigned for the side‐chain carboxylic acid group (e.g. at 1693 and 1670 cm⁻¹ in the Raman spectrum) and the cis amide I bands (e.g. at 1660 cm⁻¹ in the Raman spectrum). The presence of two bands for the carboxylic acid CO stretching modes in the solid‐state Raman spectrum can be accounted for by factor group splitting of the two nonequivalent molecules in a crystallographic unit cell. The cis amide II band is observed at 1489 cm⁻¹ in the solid‐state Raman spectrum, which is in agreement with results for cyclic di‐amino acid peptide molecules examined previously in the solid state, where the DKP ring adopts a boat conformation. Additionally, it also appears that as the molecular mass of the substituent on the C^α atom is increased, the amide II band wavenumber decreases to below 1500 cm⁻¹; this may be a consequence of increased strain on the DKP ring. The cis amide II Raman band is characterized by its relatively small deuterium shift (29 cm⁻¹), which indicates that this band has a smaller N H bending contribution than the trans amide II vibrational band observed for linear peptides. Copyright © 2009 John Wiley & Sons, Ltd.     

IR/Raman spectroscopy and DFT calculations of cyclic di‐amino acid peptides. Part III: comparison of solid state and solution structures of cyclo(L‐Ser‐L‐Ser)

B3‐LYP/cc‐pVDZ calculations of the gas‐phase structure and vibrational spectra of the isolated molecule cyclo(L ‐Ser‐L ‐Ser), a cyclic di‐amino acid peptide (CDAP), were carried out by assuming C₂ symmetry. It is predicted that the minimum‐energy structure is a boat conformation for the diketopiperazine (DKP) ring with both L ‐seryl side chains being folded slightly above the ring. An additional structure of higher energy (15.16 kJ mol⁻¹) has been calculated for a DKP ring with a planar geometry, although in this case two fundamental vibrations have been calculated with imaginary wavenumbers. The reported X‐ray crystallographic structure of cyclo(L ‐Ser‐L ‐Ser), shows that the DKP ring displays a near‐planar conformation, with both the two L ‐seryl side chains being folded above the ring. It is hypothesized that the crystal packing forces constrain the DKP ring in a planar conformation and it is probable that the lower energy boat conformation may prevail in the aqueous environment. Raman scattering and Fourier‐transform infrared (FT‐IR) spectra of solid state and aqueous solution samples of cyclo(L ‐Ser‐L ‐Ser) are reported and discussed. Vibrational band assignments have been made on the basis of comparisons with the calculated vibrational spectra and band wavenumber shifts upon deuteration of labile protons. The experimental Raman and IR results for solid‐state samples show characteristic amide I vibrations which are split (Raman: 1661 and 1687 cm⁻¹, IR: 1666 and 1680 cm⁻¹), possibly due to interactions between molecules in a crystallographic unit cell. The cis amide I band is differentiated by its deuterium shift of ∼30 cm⁻¹, which is larger than that previously reported for trans amide I deuterium shifts. A cis amide II mode has been assigned to a Raman band located at 1520 cm⁻¹. The occurrence of this cis amide II mode at a wavenumber above 1500 cm⁻¹ concurs with results of previously examined CDAP molecules with low molecular weight substituents on the C^α atoms, and is also indicative of a relatively unstrained DKP ring. Copyright © 2009 John Wiley & Sons, Ltd.     

Raman analysis of synthetic eritadenine

Eritadenine, 2(R),3(R)‐dihydroxy‐4‐(9‐adenyl)‐butyric acid, is a cholesterol‐reducing compound naturally occurring in the shitake mushroom (Lentinus edodes). To identify the unknown Raman spectrum of this compound, pure synthetic eritadenine was examined and the vibrational modes were assigned by following the synthesis pathway. This was accomplished by comparing the known spectra of the starting compounds adenine and D ‐ribose with the spectra of a synthesis intermediate, methyl 5‐(6‐Aminopurin‐9H‐9‐yl)‐2,3‐O‐isopropylidene‐5‐deoxy‐β‐D ‐ribofuranoside (MAIR) and eritadenine. In the Raman spectrum of eritadenine, a distinctive vibrational mode at 773 cm⁻¹ was detected and ascribed to vibrations in the carbon chain, ν(C C). A Raman line that arose at 1212 cm⁻¹, both in the Raman spectrum of MAIR and eritadenine, was also assigned to ν(C C). Additional Raman lines detected at 1526 and at 1583 cm⁻¹ in the Raman spectrum of MAIR and eritadenine were assigned to ν(N C) and a deformation of the purine ring structure. In these cases the vibrational modes are due to the linkage between adenine and the ribofuranoside moiety for MAIR, and between adenine and the carbon chain for eritadenine. This link is also the cause for the disappearance of adenine specific Raman lines in the spectrum of both MAIR and eritadenine. Several vibrations observed in the spectrum of D ‐ribose were not observed in the Raman spectrum of eritadenine due to the absence of the ribose ring structure. In the Raman spectrum of MAIR some of the D ‐ribose specific Raman lines disappeared due to the introduction of methyl and isopropylidene moieties to the ribose unit. With the approach presented in this study the so far unknown Raman spectrum of eritadenine could be successfully identified and is presented here for the first time. Copyright © 2008 John Wiley & Sons, Ltd.     

Proline and hydroxyproline deposited on silver nanoparticles. A Raman,SERS and theoretical study

The Raman and surface‐enhanced Raman scattering (SERS) spectra of l ‐proline (Pro) and trans‐4‐hydroxy‐ l ‐proline (Hyp) were recorded. SERS spectra were obtained on colloidal Ag prepared by reduction with hydroxylamine. Allowing sufficient time for Pro and Hyp to adjust in the colloidal solution resulted fundamentally in obtaining unique and reproducible SERS spectra. Hyp stabilizes on the surface more rapidly than Pro. The spectral analysis indicates that Pro interacts with the Ag surface through the carboxylate group. The interaction of Hyp with the metal surface occurs through the amino, methylene and carboxylate moieties of the molecule. The spectroscopic results are supported by quantum chemical calculations, performed using extended Hückel theory (EHT) of the title compounds interacting with an Ag cluster model. The assignment of the Raman bands was supported by a normal coordinate analysis performed through Becke, three‐parameter, Lee–Yang–Parr/6‐311 G* + calculations. Copyright © 2011 John Wiley & Sons, Ltd.     

Multiphonon resonant Raman scattering in N‐doped ZnO

Multiphonon resonant Raman scattering in N‐doped ZnO films was studied, and an enhancement of the resonant Raman scattering process as well as longitudinal optical (LO) phonon overtones up to the sixth order were observed at room temperature. The resonant Raman scattering intensity of the 1LO phonon in N‐doped ZnO appears three times as strong as that of undoped ZnO, which mainly arises from the defect‐induced Raman scattering caused by N‐doping. The nature of the 1LO phonon at 578 cm⁻¹ is interpreted as a quasimode with mixed A₁ and E₁ symmetry because of the defects formed in the ZnO lattice. In addition, the previously neglected impurity‐induced two‐LO‐phonon scattering process was clearly observed in N‐doped ZnO. Copyright © 2009 John Wiley & Sons, Ltd.     

Triple‐resonant two‐phonon Raman scattering in graphene

The triple‐resonant (TR) second‐order Raman scattering mechanism in graphene is re‐examined. It is shown that the magnitude of the TR contribution to the photon‐G′ mode coupling function in graphene is one order of magnitude larger than the widely accepted two‐resonant coupling. Enhancement of the order of 100 in the Raman intensity, with respect to the usual double‐resonant model, is found for the G′ band in graphene, and is expected in the related sp²‐based carbon materials, as well. Copyright © 2011 John Wiley & Sons, Ltd.     

The stimulated Raman scattering competition between solute and solvent in Rhodamine B solution

The competition between the stimulated resonance Raman scattering (SRRS) of Rhodamine B (RhB) and the stimulated Raman scattering (SRS) of ethanol (C₂H₅OH) is observed at the RhB in C₂H₅OH solution. For different concentrations of the solution, the peak wavelengths of the SRRS, the amplified spontaneous emission (ASE), the fluorescence and the absorption of RhB are different. The SRRS of RhB and the SRS of C₂H₅OH are simultaneously generated when the concentration of the solution is 10^-5 mol/L and the energy of the excitation laser is 20.4 mJ. Otherwise, only either the SRRS of RhB or the SRS of C₂H₅OH is generated. The SRRS can be amplified by the ASE gain when the SRRS is near the peak of the ASE, and the peak wavelength of the SRRS coincides with the wavelength of the maximal intensity ASE.     

Surface‐enhanced Raman measurements and DFT calculations for l‐tryptophan of varying pH in silver sol

The interaction of l ‐tryptophan (Trp) with silver colloids was investigated at between pH values of 6.11 and 10.6 of the sol. The measurements of surface‐enhanced Raman bands of Trp in the colloidal solution indicate the evolution of interaction between the metal particles and the molecules with increasing pH values for the sol. The experimental observations were explained using the estimated atomic charge distribution in the zwitterionic and anionic forms of the residue, obtained by density functional theory calculations. The variation in the ratio of the spectral intensities of the Fermi resonance bands with the pH reflects the effect of the colloidal environment on Trp. The results obtained can be used as a marker for describing the nature of the interaction of silver colloids with the specific terminus of the residue, at varying pH environments. Copyright © 2012 John Wiley & Sons, Ltd.     

Direct growth of graphene film on piezoelectric La3Ga5.5Ta0.5O14 crystal

For the first time, a few layer graphene was grown on the surface of the polar X ‐cut (110) of a piezoelectric La₃Ga_5.5Ta_0.5O₁₄ crystal by the CVD method. This polar X ‐cut is characterized by a good matching of the crystal lattice parameters of La₃Ga_5.5Ta_0.5O₁₄ and two‐dimensional graphene crystal, as well as the presence of piezoelectric fields on the surface of the substrate, which could affect the graphene growth process. Raman spectroscopy investigation has shown the ability for direct growth of graphene on the piezoelectric crystal. The NEXAFS spectroscopy studies of the film grown on the surface of the X ‐cut of an La₃Ga5_.5Ta_0.5O₁₄ crystal also confirmed that the grown film is graphene. Moreover, the NEXAFS spectra enable the conclusion that additional electron states are formed as a result of chemical bonding between the atoms of graphene and the substrate which proceeds through hybridization of the valence electron states of the substrate and graphene atoms. (© 2016 WILEY‐VCH Verlag GmbH &Co. KGaA, Weinheim)     

Comparison of adsorption mechanism on colloidal silver surface of alafosfalin and its analogs

This study reports the Raman (FT‐RS) and absorption infrared (FT‐IR) spectra, based on calculated wavenumbers and normal modes of vibrations, of the following compounds: L ‐Ala‐L ‐NH‐CH(Me)‐PO₃H₂ (alafosfalin, A1), L ‐Ala‐D ‐NH‐CH(Me)‐PO₃H₂ (A2), L ‐Ala‐L ‐NH‐CH(Et)‐PO₃H₂ (A3), D ,L ‐Ala‐D,L ‐NH‐CH(Et)‐PO₃H₂ (A4), L ‐Ala‐D ‐NH‐CH(iPr)‐PO₃H₂ (A5), L ‐Ala‐D,L ‐NH‐CH(iPr)‐PO₃H₂ (A6), L ‐Ala‐D,L ‐NH‐CH(tBu)‐PO₃H₂ (A7), L ‐Ala‐D,L ‐NH‐CH(iBu)‐PO₃H₂ (A8), L ‐Ala‐D,L ‐NH‐CH(cBu)‐PO₃H₂ (A9), L ‐Ala‐D,L ‐NH‐CH(nPA)‐PO₃H₂ (A10), β‐Ala‐D ‐NH‐CH(Me)‐PO₃H₂ (A11), and D,L ‐Ala‐NH‐C(Me,Me)‐PO₃H₂ (A12). The equilibrium geometries and vibrational wavenumbers are calculated using density functional theory (DFT) at the B3LYP; 6–31 + + G** level of theory using Gaussian'03, GaussSum 0.8, and GAR2PED software. We briefly compare and analyze the experimental and calculated vibrational wavenumbers in the range of 3600–400 cm⁻¹. In addition, Raman wavenumbers are compared to those from surface‐enhanced Raman scattering (SERS) for the phosphonodipeptides of alanine (Ala) adsorbed on a colloidal silver surface. The geometry of these molecules etched on the silver surface is deduce from the observed changes in both the intensity and breadth of Raman bands in the spectra of the bound vs free species. For example, A7, A8, A1, A3, and A4 appear to adsorb onto the colloidal silver particles mainly through the phosphonate terminus, and for A3 and A4, through the  C‐NH₂ and  CONH fragments. The most dominant SERS bands of A5, A6, A9, A10, and A11 are due to the amide bond vibrations, as well as to the vibrations of the  C‐NH₂ group (A9 and A10) and the C C group (A6 and A11). The differences recorded for the A5, A6, A9, A10, and A11 and those of A2 and A12 are due to interactions between the amine and methyl groups with the silver surface, and they reflect vibrational characteristic of these groups. Copyright © 2008 John Wiley & Sons, Ltd.     

UV resonance Raman study of TrpZip2 and related peptides: π‐π interactions of tryptophan

Aromatic interactions are important stabilizing forces in proteins but are difficult to detect in the absence of high‐resolution structures. Ultraviolet resonance Raman spectroscopy is used to probe the vibrational signatures of aromatic interactions in TrpZip2, a synthetic β‐hairpin peptide that is stabilized by edge‐to‐face and face‐to‐face tryptophan π‐π interactions. The vibrational markers of isolated edge‐to‐face π‐π interactions are investigated in the related β‐hairpin peptide W2W11. The bands that comprise the Fermi doublet exhibit systematic shifts in position and intensity for TrpZip2 and W2W11 relative to the model peptide, W2W9, which does not form aromatic interactions. Additionally, hypochromism of the B_b absorption band of tryptophan in TrpZip2 leads to a decrease in the relative Raman cross‐sections of B_b‐coupled Raman bands. These results reveal spectral markers for stabilizing tryptophan π‐π interactions and indicate that ultraviolet resonance Raman may be an important tool for the characterization of these biological forces. Copyright © 2012 John Wiley & Sons, Ltd.     

Raman spectra and simulation of cis‐ and trans‐cyclooctene for conformational analysis compared to inelastic neutron scattering

Simulated and measured Raman spectra are used to determine the molecular conformation of trans ‐cyclooctene. This is the first reported Raman spectrum of this highly strained species. A crown structure results in a computed Raman spectrum, which is in good agreement with the experiment; a chair structure does not. Comparison is made with the case of cis ‐cyclooctene. The computed structure and limitations of the method of conformational analysis are discussed. In particular, the relative merits of Raman spectroscopy in comparison with infrared and inelastic neutron scattering (INS) are evaluated using computed spectra for all three methods and comparison of the observed INS for cis ‐cyclooctene with that computed for two conformations. It is concluded that the combination of computed and observed Raman spectra provides a useful method for conformational analysis for cases of this type. Copyright © 2010 John Wiley & Sons, Ltd.     

Stimulated resonance Raman scattering of Rhodamine B

Stimulated resonance Raman scattering (SRRS) of the Rhodamine B (RhB) in the methanol (CH₃OH) or ethanol (C₂H₅OH) solutions have been observed. SRRS from RhB can be distinguished from the amplified spontaneous emission (ASE) of RhB with increasing the input laser energy. When the RhB is dissolved in the methanol or ethanol (10^?3 mol/L), the RhB have the different peak wavelengths of SRRS, ASE, fluorescence and absorption, respectively. SRRS can be amplified by the ASE gain when the SRRS is near the peak of the ASE, and the peak wavelength of SRRS coincides with the maximal intensity wavelength of ASE.     

Amphiphilic p‐tert‐butylthiacalix[4]arenes containing quaternary ammonium groups: from small molecules toward water‐soluble nanoscale associates

The formation of supramolecular associates based on water‐soluble p‐tert‐butylthiacalix[4]arenes with amino acids has been studied. It was shown that amphiphilic p‐tert‐butylthiacalix[4]arenes preferably formed supramolecular associates with aromatic α‐amino acids (tyrosine and tryptophan). Increasing size of the substituents of p‐tert‐butylthiacalix[4]arenes led to increase molecular weight of supramolecular associates based on the macrocycles and “guest” molecules. The spatial structures of p‐tert‐butylthiacalix[4]arenes and their associates with phenylalanine were studied by two‐dimensional ¹H‐¹H nuclear Overhauser effect NMR spectroscopy. The ability of aggregates based on p‐tert‐butylthiacalix[4]arenes and amino acids to effectively interact with bovine serum albumin with the formation of 7‐ to 8‐nm nanoparticles was shown. Copyright © 2015 John Wiley & Sons, Ltd.     

Vibrational spectroscopy and DFT calculations of di‐amino acid cyclic peptides. Part I: cyclo(Gly‐Gly), cyclo(L‐Ala‐L‐Ala) and cyclo(L‐Ala‐Gly) in the solid state and in aqueous solution

Investigations of the vibrational spectra of cyclo(Gly‐Gly), cyclo(L‐Ala‐L ‐Ala) and cyclo(L ‐Ala‐Gly) are reported. Raman scattering and Fourier transform infrared (FTIR) spectra of solid‐state and aqueous protonated samples, as well as their corresponding N‐deuterated isotopomers, have been examined. In addition, density functional theory (DFT) (B3‐LYP/cc‐pVDZ) calculations of molecular structures and their associated vibrational modes were carried out. In each case, the calculated structures of lowest energy for the isolated gas‐phase molecules have boat conformations. Assignments have been made for the observed Raman and FTIR vibrational bands of the cyclic di‐amino acid peptides (CDAPs) examined. Raman polarization studies of aqueous phase samples are consistent with C₂ and C₁ symmetries for the six‐membered rings of cyclo(L‐Ala‐L‐Ala) and cyclo(L‐Ala‐Gly), respectively. There is a good correlation between experimental and calculated vibrational bands for the three CDAPs. These data are in keeping with boat conformations for cyclo(L‐Ala‐L‐Ala) and cyclo(L‐Ala‐Gly) molecules, predicted by the ab initio calculations, in both the solid and aqueous solution states. However, Raman spectroscopic results might infer that cyclo(L‐Ala‐Gly) deviates only slightly from planarity in the solid state. The potential energy distributions of the amide I and II modes of a cis‐peptide linkage are shown to be significantly different from those of the trans‐peptides. For example, deuterium shifts have shown that the cis‐amide I vibrations found in cyclo(Gly‐Gly), cyclo(L‐Ala‐L‐Ala), and cyclo(L‐Ala‐Gly) have larger N‐H contributions compared to their trans‐amide counterparts. Compared to trans‐amide II vibrations, cis‐amide II vibrations show a considerable decrease in N H character. Copyright © 2009 John Wiley & Sons, Ltd.