Vibrational Study (Raman,SERS, and IR) of Plant Gallnut Polyphenols Related to the Fabrication of Iron Gall Inks

FT-Raman, FTIR, and SERS spectra of the structurally related gallnut polyphenols tannic acid, gallic acid, pyrogallol, and syringic acid are reported in this work aiming at performing a comparative assignation of the bands and finding specific marker features that can identify these compounds in complex polyphenol mixtures. Tannic and gallic acids are the principal components in oak gallnuts, and they can be found in iron gall inks. The different functional groups existing in these molecules and their spatial distribution lead to slight changes of the vibrations. The Raman spectra are dominated by bands corresponding to the ring vibrations, but the substituents in the ring strongly affect these vibrations. In contrast, the FTIR spectra of these molecules are dominated by the peripheral oxygen-containing substituents of the aromatic ring and afford complementary information. SERS spectroscopy can be used to analyze trace amounts of these compounds, but the spectra of these polyphenols show strong changes in comparison with the Raman spectra, indicating a strong interaction with the metal. The most significant modification observed in the SERS spectra of these compounds is the weakening of the benzene 8a ring vibration and the subsequent intensification of the 19a mode of the benzene ring. This mode is also more intense in the FTIR spectra, and its intensification in the SERS spectra could be related to a drastic change in the molecular polarizability associated with the interaction of the polyphenol with the metal in Ag NPs.     

Vibrational spectra and normal coordinate analysis of p-cresol and its deuterated analogs

I.r. and Raman spectra of p-cresol and its seven deuterated analogs were investigated in dilute solutions of hydrophobic solvents. Assignments of the observed i.r. and Raman bands were made on the basis of isotopic frequency shifts, Raman polarization properties, i.r. intensifies and normal coordinate calculations. The calculated normal frequencies are in good agreement with the experimental ones: the average error below 1700 cm⁻¹ is 3.8 cm⁻¹ for 164 in-plane vibrations and 3.3 cm⁻¹ for 59 out-of-plane vibrations. The calculated vibrational modes may be useful in analysing the vibrational spectra of tyrosine. It is suggested that several doublets due to Fermi resonance and a trio of Raman bands in the 1260-1160 cm⁻¹ region are potential probes for the micro-environments of tyrosine side chains in proteins.     

Polarized Raman spectra and intensities of aromatic amino acids phenylalanine,tyrosine and tryptophan

The prominent marker bands in the Raman spectra of the aromatic proteinogenic amino acids phenylalanine, tryptophan and tyrosine have been reinvestigated. Previous studies have been extended by measuring intensities against NaClO₄ as an external standard. Raman spectra were divided into isotropic (trace scattering of symmetric vibrations) and anisotropic (quadrupole scattering of antisymmetric or symmetric vibrations). These intensity and polarization properties of the marker bands were followed through pH changes from about 11–13 to 1–2.     

Internal reflectance spectra associated with staircase voltammetry in anodic oxidation of aromatic amines in acetonitrile

Dynamic transformation profiles of internal reflectance spectra were observed for anodic oxidation of triphenylamine, N-methyldiphenylamine, and N,N-dimethyl-aniline in acetonitrile. Absorption bands appearing in these spectra are compared with those in conventional absorption spectra of the electrolyzed aromatic amine solutions by controlled-potential electrolysis. From this comparison, the internal reflectance bands are assigned to a tetraphenylbenzidine radical monocation and dication, a dimethyl-diphenylbenzidine radical monocation and dication, etc.     

The study of Turnip Mosaic virus coat protein by surface enhanced Raman spectroscopy

Using Turnip Mosaic virus (TuMV) coat protein as material, the secondary structure has been studied by both normal Raman spectroscopy (NRS) and surface enhanced Raman spectroscopy (SERS). The NRS of TuMV coat protein under certain conditions showed the α-helix, β-sheet and random coil structure. The CSSC comformations are trans—gauche—gauche and gauche—gauche—gauche. The SERS spectrum of TuMV coat protein under certain conditions reveals the α-helix structure. By studying SERS at different adsorbing times, we have observed the amide III vibration of α-helix, β-sheet and random coil structure. The CSSC conformations drawn from the SERS spectra are trans—gauche—gauche and trans—gauche—trans. Besides the amide I, amide III and CSSC bands, the CαCN band, aromatic amino acid bands and some other bands can also be seen in the SERS spectra.     

Structure and molecular conformation of tussah silk fibroin films: Effect of methanol

Structural changes of tussah (Antheraea pernyi) silk fibroin films treated with different water-methanol solutions at 20°C were studied as a function of methanol concentration and immersion time. X-ray diffraction measurements showed that the α-helix structure, typical of untreated tussah films, did not change for short immersion times (2 min), regardless of methanol concentration. However, crystallization to β-sheet structure was observed following immersion of tussah films for 30 min in methanol solutions ranging from 20 to 60% (v/v). IR spectra of tussah films untreated and methanol treated for 2 min exhibited strong absorption bands at 1265, 892, and 622 cm^?1, typical of the α-helix conformation. The intensity of the bands assigned to the β-sheet conformation (1245, 965, and 698 cm^?1) increased for the sample treated with 40% methanol for 30 min. Raman spectra of tussah films with α-helix molecular conformation exhibited strong bands at 1657 (amide I), 1263 (amide III), 1106, 908, 530, and 376 cm^?1. Following α → β conformational transition, amide I and III bands shifted to 1668, and to 1241, 1230 cm^?1, respectively. The band at 1106 cm^?1 disappeared and new bands appeared at 1095 and 1073 cm^?1, whereas the intensity of the bands at 530 and 376 cm^?1 decreased significantly. ©1995 John Wiley & Sons, Inc.     

Vibrational and 1H NMR spectra of N-(2-pyridyl)-thioformamide and N-(2-pyridyl)thioacetamide

The Raman and infrared spectra of N-(2-pyridyl)thioformamide and N-(2-pyridyl)-thioacetamide have been measured. The assignment of the bands is aided by the complete normal coordinate treatment for all the vibrations of N-(2-pyridyl)thioformamide and its N-deuterated molecule using a Urey—Bradley force function for the in-plane vibrations and a valence force function for the out of plane vibrations. Variable temperature ¹H NMR study of the two pyridylthionamides has also been performed. It is inferred that while N-(2-pyridyl)thioformamide favours a cis —CSNH— group, the other compound favours a trans —CSNH— grouping at ambient temperature.     

Assignment problems of amino acids,di- and tripeptides and proteins in the near infrared region

Nine amino acids, four dipeptides, one tripeptide and several types of proteins were studied by reflectance and absorption FT-IR spectroscopy. Mid-IR and, where necessary, Raman frequencies were applied to assign the combination and overtone bands occurring in the near-IR region. On one occasion, an isotope effect (deuterization) was also employed for the recognition of the combinations involving N⁺H₃ vibrations. The overtone and combination bands of N⁺H₃, CH₃, CH₂, NH₂ and amide groups were, in part, assigned. On the basis of this assignment and with the use of second derivative and/or Fourier deconvolved spectra, attempts were made to recognize the characteristic features of glutamine and asparagine components of some proteins. The IR spectra were taken on an FT-IR spectrometer with a configuration allowing spectra to be measured in the 10,000 to 400 cm⁻¹ range.     

Structures of transient species in the photochromic reaction of 1′,3′,3′-trimethylspiro[2H-1-benzopyran-2,2′-indoline]: Time-resolved resonance Raman study of isotopically substituted analogues

Time-resolved resonance Raman spectra of seven kinds of isotopically substituted analogues of 1′,3′,3′-trimethylspiro[2H-1-benzopyran-2,2′-indoline] in the photomerocyanine form have disclosed that only the vibrations of the cleaved benzopyran part are resonance enhanced significantly in cyclohexane and in acetonitrile solutions with 460-390 nm probe light. Dramatic changes in the resonance Raman spectra of the photomerocyanine on going from non-hydrogen-bond donor solvents to hydrogen-bond donor solvents can be interpreted as being due to changes in the relative contribution of ortho-quinoidal and zwitterionic forms in the resonance hybrid structure of the photomerocyanine: in cyclohexane and in acetonitrile the contribution of the ortho-quinoidal form is substantial, while in methanol the zwitterionic form is stabilized by hydrogen bonding with the solvent and the photomerocyanine takes an almost zwitterionic structure.     

Application of the dimer approach for the analysis of vibrational spectra of BEDT—TTF-based charge-transfer salts

The dimer approach was proposed for the normal coordinate analysis of BEDT—TTF⁺ molecular vibrations. It was shown that, within the framework of the approximation used, the appearance of additional bands in the IR as well as in Raman spectra may be explained as due to the reduction of symmetry of the dimerized system in comparison with the monomeric one. The strength of intermolecular interaction in the dimer was estimated by adjusting the calculated frequencies to the observed positions of intense “vibronic” bands recorded in the IR spectra of BEDT—TTF-based monovalent charge transfer salts. It was found that for the reproduction of “vibronic shifts” observed for some vibrations it should be assumed that the intermolecular interaction takes effect not only on the totally symmetric a_g modes, but also on the vibrations of other symmetry species.     

Surface-enhanced Raman spectroscopic studies of coactivator-associated arginine methyltransferase 1

We report, for the first time, the surface-enhanced Raman spectra of an important enzyme, coactivator-associated arginine methyltransferase 1 (CARM1), involved in various biological activities such as tumor suppressor function and stem cell differentiation. We have employed surface-enhanced Raman scattering (SERS) to obtain insight into the structural details of CARM1 by adsorbing it to silver (Ag) nanoparticles. The enzyme retains its activity even after its adsorption onto Ag nanoparticles. We observe strong SERS modes arising from amide vibrations and aromatic ring amino acids. The SERS spectra revealed amide I bands at 1637 cm(-1) and 1666 cm(-1), which arise as a result of the alpha helix of the protein and the polypeptide backbone vibration of a random coil, respectively. In order to confirm the amide vibrations, we have performed SERS on deuterated CARM1, which exhibits a clear red shift in amide band positions. The SERS spectra may provide useful information, which could be harnessed to study the functional interactions of CARM1 with small molecule modulators.     

Synthesis and characterization of <Emphasis Type="Italic">D</Emphasis>-/<Emphasis Type="Italic">L</Emphasis>-methionine grafted PEDOTs for selective recognition of 3,4-dihydroxyphenylalanine enantiomers

Two pairs of amino-acid functionalized poly(3,4-ethylenedioxythiophene) (PEDOT) derivatives, namely, poly(N-(tert-butoxycarbonyl)-L-methionyl (3,4-ethylenedioxythiophene-2’-yl)methylamide) (L-PEDOT-Boc-Met) and poly(N-(tert-butoxycarbonyl)-D-methionyl (3,4-ethylenedioxythiophene-2’-yl)methylamide) (D-PEDOT-Boc-Met); poly(L-methionyl (3,4-ethylenedioxythiophene-2’-yl)methylamide) (L-PEDOT-Met) and poly(D-methionyl (3,4-ethylenedioxythiophene-2’-yl)methylamide) (D-PEDOT-Met) were synthesized via chemical oxidative polymerization of corresponding monomers. The structural characterization, spectroscopic properties and thermal stability of these monomers and polymers were systematically explored by FTIR spectra, Raman spectra, XRD spectra, UV-Vis spectra and thermogravimetric analysis. As chiral electrode materials, these polymers were employed to successfully recognize 3,4-dihydroxyphenylalanine (DOPA) enantiomers by cyclic voltammetry (CV) in sulphuric acid solution. The measurement results reveal that the tendency was hetero-chiral interaction between L-PEDOT-Met/PVA/GCE and D-DOPA, D-PEDOT-Met/PVA/GCE and L-DOPA, respectively. Also, the mechanism of chiral discrimination was discussed. All the results implied that the combination of electrochemical molecular recognition technology and chiral PEDOT materials can be a promising approach for chiral recognition and may open new opportunities for facile, biocompatible, sensitive and robust chiral assays in biochemical applications.     

Conformational isomerization of <Emphasis Type="Italic">N</Emphasis>-(naphthalen-1-yl)-<Emphasis Type="Italic">N</Emphasis>-(phenyl(quinolin-3-yl)methyl)amide derivatives

A series of N-(naphthalen-1-yl)-N-(phenyl(quinolin-3-yl)methyl)amide derivatives were designed and synthesized as anti-Mycobacterium tuberculosis drugs. NMR spectra showed that two conformational isomers of these compounds exist in solution, which is not due to cis-trans isomerization of amide bond. We proposed that the spatial interactions between three large aromatic groups caused the conformational isomerization, which was supported by molecular modeling and X-ray diffraction.     

Vibrational states of chlorophyll and related compound molecules. Metal complexes of octaethylchlorin

Fine-structure fluorescence spectra and i.r. spectra of the model compound chlorophyll-Zn-octaethylchlorin (Zn OEC), and its three deuterated derivatives at meso-positions and Zn OEC-¹⁵N₄ have been obtained. Polarization measurements for individual zero-phonon lines show that in the vibronic spectra of the above compounds the totally symmetric vibrations are mainly active. A joint analysis of the experimental data and calculation results of normal vibrations has served as a basis for the interpretation of the spectra obtained as well as resonance Raman spectra. It is pointed out that the vibrations of ethyl substituents largely form a vibrational structure of the vibronic Zn OEC spectrum. An assignment of some lines in a fine-structure spectrum of chlorophyll a is discussed.     

Investigations of the hydrophobic and hydrophilic interactions in polymer–water systems by ATR FTIR and Raman spectroscopy

ATR FTIR and Raman spectra of polymers containing amide groups in the main chain and in the side chain and of the amide low-molecular-weight model compounds in water media were measured. The hydrophobic and hydrophilic interactions of the dissolved compounds with the neighboring water molecules are reflected in the wavenumbers of the CH₃ stretching and of the Amide I and II vibrations. The possibility of the existence of β-sheet-like structures in polypeptides surrounded by water molecules is also discussed.     

Vibrational spectroscopic study on polymorphism and molecular aggregation states in polyoxymethylene

Polarized Raman spectra of the moth-shaped single-crystal of orthorhombic polyoxymethylene (metastable phase) have been investigated by means of the Raman microprobe technique in the frequency range covering both molecular and lattice vibrations. The observed polarizations of the Raman bands are found to be strongly influenced by the optical alignment in the microscope, mainly by the polarization scrambling effect. By taking the optical effect into account, the orientation of the crystal axes in the single-crystal is investigated. Normal mode analysis of the orthorhombic crystal is performed based on the newly obtained polarization data. Raman spectra of two crystalline samples of trigonal polyoxymethylene (stable phase) differing in their morphology and in their structural orderliness are compared. In the spectrum of the needle-like crystal consisting of the fully extended molecules, measured at low temperature, eight Raman bands due to the E₂ symmetry species are newly detected     

Uncoupled peptide bond vibrations in alpha-helical and polyproline II conformations of polyalanine peptides

We examined the 204-nm UV resonance Raman (UVR) spectra of the polyproline II (PPII) and alpha-helical states of a 21-residue mainly alanine peptide (AP) in different H2O/D2O mixtures. Our hypothesis is that if the amide backbone vibrations are coupled, then partial deuteration of the amide N will perturb the amide frequencies and Raman cross sections since the coupling will be interrupted; the spectra of the partially deuterated derivatives will not simply be the sum of the fully protonated and deuterated peptides. We find that the UVR spectra of the AmIII and AmII' bands of both the PPII conformation and the alpha-helical conformation (and also the PPII AmI, AmI', and AmII bands) can be exactly modeled as the linear sum of the fully N-H protonated and N-D deuterated peptides. Negligible coupling occurs for these vibrations between adjacent peptide bonds. Thus, we conclude that these peptide bond Raman bands can be considered as being independently Raman scattered by the individual peptide bonds. This dramatically simplifies the use of these vibrational bands in IR and Raman studies of peptide and protein structure. In contrast, the AmI and AmI' bands of the alpha-helical conformation cannot be well modeled as a linear sum of the fully N-H protonated and N-D deuterated derivatives. These bands show evidence of coupling between adjacent peptide bond vibrations. Care must be taken in utilizing the AmI and AmI' bands for monitoring alpha-helical conformations since these bands are likely to change as the alpha-helical length changes and the backbone conformation is perturbed.     

Cryochemistry : edited by M. Moskovits and G.A. Ozin,John Wiley & Sons,New York,London, Sydney and Toronto, 1976, pp. xi + 532, price £25.85

The IR spectra of N₂F₄ solutions in liquid argon and nitrogen have been recorded and reanalyzed in the 3300–3550 cm^?1 region. The fundamental absorption bands of NF-stretching modes of both the gauche and trans isomers and the bands of the second order transition have been observed. These new IR data on the spectra of cryosystems and published Raman data allowed us to make an unambiguous interpretation of the NF₂-stretching vibrational bands for both the N₂F₄ conformers.     

Vibrational spectroscopy of 5-amino-3-methyl-4-isoxazolecarbohydrazide and its N-deuterated isotopologue

Both spectral and structural studies of 5-amino-3-methyl-4-isoxazolecarbohydrazide (HIX) were done and compared to calculated parameters using ab initio DFT methods. A detailed interpretation of the infrared and Raman spectra of title molecule is reported on the basis of the calculated potential energy distribution (PED). The conformational search for possible conformers and tautomers of title compound has been conducted and widely discussed. N-deuterated isotopologue of 5-amino-3-methyl-4-isoxazolecarbohydrazide (HIXD) was synthesized to eliminate disturbing frequencies in carbonyl region of IR and Raman. Besides, N-deutaration enabled the unambiguous assignment some bands to specific vibrations. Moreover, the stability of the 5-amino-3-methyl-4-isoxazolecarbohydrazide arising from hyper conjugative interactions has been studied using natural bond orbital (NBO) analysis.     

Near-infrared excitation of Raman scattering by chromophoric proteins

Fourier-transformed Raman spectra of bacteriorhodopsin, the photosynthetic reaction center, and myoglobin in aqueous solution excited at 1064 nm are presented. These proteins are representative of three important classes of chromophoric proteins. The observed vibrational modes are assigned and discussed based on the known resonance Raman spectra of these proteins. In each case, chromophore vibrations dominate the Raman scattering, with little or no contribution from other protein vibrations. However, the limitations encountered in resonance Raman studies of chromophoric proteins due to sample fluorescence or sample photolability are circumvented. The relative intensities in the bacteriorhodopsin Raman spectrum excited at 1064 nm are nearly identical to the relative intensities previously observed by resonance excitation. The Raman spectrum of the reaction center of the photosynthetic bacterium Rhodobacter sphaeroides excited at 1064 nm contains contributions from both bacteriochlorophyll and bacteriopheophytin pigments, with possible preresonance enhancement of bacteriochlorophyll modes. The 1064-nm-excited Raman spectrum of myoglobin displays several marker bands that have been characterized previously in resonance Raman investigations with excitation in both the Soret and Q-band regions.