R. Withnall

Vibrational Spectra of α-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.

Surface-enhanced Raman scattering studies of rhodanines: evidence for substrate surface-induced dimerization

The surface-enhanced Raman scattering (SERS) spectra of rhodanine adsorbed on silver nanoparticles have been examined using 514.5 and 632.8 nm excitation. There is evidence that, under the experimental conditions used, rhodanine undergoes a nanoparticle surface-induced reaction resulting in the formation of a dimeric species via the active methylene group in a process which is analogous to the Knoevenagel reaction. The experimental observations are supported by DFT calculations at the B3-LYP/cc-pVDZ level. Calculated energies for the interaction of the E and Z isomers of the dimers of rhodanine with silver nanoparticles support a model in which the (intra-molecular hydrogen bonded) E isomer dimer is of lower energy than the Z isomer. A strong band, at 1566 cm(-1), in the SERS spectrum of rhodanine is assigned to the nu(C double bond C) mode of the dimer species.

Vibrational spectra and structures of the anions of urazole and 4-methylurazole: DFT calculations of the normal modes and the influence of hydrogen bonding

Solid state IR and Raman as well as aqueous solution state Raman spectra are reported for the anions of urazole and 4-methylurazole, and their N-deuterated derivatives. DFT calculations, at the B3-LYP/cc-pVTZ level, established that the structures and vibrational spectra of both anions can be interpreted using a model that incorporates hydrogen-bonded water molecules, in conjunction with the polarizable continuum solvation method. In the case of the urazole anion it is shown that deprotonation occurs primarily at N1 rather than N4, but there is also evidence for the second tautomer both in the solid state and in aqueous solution. The vibrational spectra were computed at the optimised molecular geometry in each case, enabling normal coordinate analysis, which yielded satisfactory agreement with the experimental IR and Raman data. Computed potential energy distributions of the normal modes provided detailed vibrational assignments.

Analysis of microgels as a function of temperature by SERS

There is a paucity of data relating to the use of SERS for the investigation of temperature dependent phenomena, particularly in relation to cross-linked supra-molecular polymeric systems. Microgels-also known as SMART materialsundergo a reversible volume phase transition (VPT) [1] as a function of temperature (Fig.1). Macroscopically the VPT results from a combination of effects: the loss of interstitial bulk water molecules, changes in non-covalent molecular interactions (microgel-solvent, solvent-solvent and intra/inter-polymer chain) and conformational changes in the polymer backbone [2]. A silver sol was employed as the SERS substrate [3, 4].

Experimental vibrational spectroscopic and theoretical (ab initio calculations) studies of the di-amino acid peptide cyclo(L-Val-L-Val)

The primary focus of our studies is an ongoing research programme examining the experimental and theoretically calculated vibrational spectra (Raman and FT-IR) of cyclic and linear di-amino acid peptides. The Raman spectrum, fig. 2a, of cyclo(L-Val-L-Val) shows a weak, broad band located at 1658 cm assigned to an amide I vibration. It is noticeable that on Ndeuteriation this vibrational band increases in intensity and is shifted down in wavenumber by ~ 43 cm. The deuterium shift is in keeping with other cyclic dipeptides investigated [3, 4] and is probably typical for the N-H contribution to the potential energy distribution of the amide I mode for cyclic dipeptides adopting a cis amide conformation. For example, cyclo(L-Met-L-Met), cyclo(L-Ala-L-Ala) and cyclo(L-Ala-Gly) show an amide I shift of approximately 33, 32 and 39 cm respectively.

Experimental vibrational spectroscopic and theoretical (ab initio calculations) studies of the peptide L-Met-L-Met

The X-ray structure of L-Met-L-Met has been reported [1], showing that the molecule crystallises in the orthorhombic space group and that the peptide is planar. Aside from intrinsic interest, applied interest in the physico-chemical properties of this molecule has stemmed, in part, from its potential bacteriocidal activity [2] and involvement in cellular biosynthetic pathways [3]. Studies of L-Met-L-Met are part of a long term investigation (which also involve theoretical ab initio calculations) of the vibrational spectroscopic properties of cis and trans amides in cyclic and linear peptides respectively. It can clearly be seen, in Fig. 2, that there is a sharp N-H stretch located at 3325 cm and a less intense, broader band located at 3213 cm due to the N-H group being involved in intermolecular hydrogen bonds of different strengths. Both bands show a considerable shift in wavenumber on N-deuteriation. Indeed it has been reported that the amine protons are involved in strong hydrogen bonds, to the carboxyl groups [1], which is indicative of the broad N-H stretch located at 3213 cm. Additionally it is proposed [1] that the amide N-H’s are weakly hydrogen bonded to the neighbouring amide carbonyl molecules and hence the presence of a sharp vibrational band located at 3325 cm. In the Raman spectra shown in Fig. 2, the trans amide I band is clearly evident at 1650 cm. This vibrational band shows a small downward shift on Ndeuteriation, of about 7 cm indicative of an amide I band with a small contribution from the N-H bend. In contrast cyclo(L-Met-L-Met), in which the amide moiety adopts the cis configuration, displays an amide I band located at 1650 cm [4]; upon N-deuteriation this vibrational mode shows a downward shift of ~19 cm.

Synthesis and analysis of the dye indigo carmine from indigo using SERRS

Surface enhanced resonance Raman spectroscopy (SERRS) has found wide utility as a sensitive analytical tool in a multitude of interdisciplinary scientific investigations (including e.g. chemical analysis, clinical, forensic, environmental and biological sciences, archaeological/historical applications and drug analysis) [1]. There has been a growing interest in the use of SERRS for highly sensitive quantitative chemical analyses, in a wide range of matrices, even down to the single molecule level [2, 3]. In an attempt to extend and develop novel applications of SERRS (using a silver sol) the technique has been used to monitor and analyse the synthesis of the dye indigo carmine from indigo (see Fig.1).

Raman spectroscopic studies of chemically modified pullulans

In the studies reported herein pullulan has been structurally modified by chemical incorporation of various functional moieties and analysed by Raman spectroscopy. One reason for conducting such an investigation is to compare and contrast the usefulness of Raman compared to NMR [2] techniques for the analysis of the structural composition of the derivatized pullulans. Raman spectroscopy has proved to be particularly useful in identifying different chemical functionalities and assessing the degree of polymer modification.

A novel use of Raman spectroscopy: analysis of the structural composition of comonomer microgels

Co-monomer microgels, which have molecular weights of tens of millions of Daltons, present scientific challenges in attempts to analyse their monomer composition both qualitatively and quantitatively. However, uniquely, Raman spectroscopy may be a potentially useful technique for such purposes. Colloidal polymeric microgel systems [1] are particularly appealing from a research perspective because they provide an opportunity to investigate conformational changes in cross-linked polymeric systems. Microgels composed of co-monomers are currently of significant academic and industrial interest [2] due to their potential uses in diverse interdisciplinary areas of scientific interest [3] including drug delivery and as scaffolds for catalysis [4]. However the analysis of the structural composition of microgels is a non-trivial experimental problem. It is proposed that in the case of co-monomer microgels, Raman spectroscopy can be used as a quick and easy method to ensure that co-polymerization has occurred and also to determine, semi-quantitatively, the percentage incorporation of the monomers. Poly(N-isopropylacrylamide/methylenebisacrylamide) [poly(NIPAM/BA)] and poly(4vinylpyridine/methylenethylenebisacrylamide) [poly(4-VP/BA)] as well as poly(Nisopropylacrylamide/methylenebisacrylamide/4vinylpyridine) [poly(NIPAM/BA/4-VP)] microgels (the latter synthesized using 0.15 0.55 mole fraction of 4-VP) were prepared by surfactant-free emulsion polymerization followed by purification and characterization as described previously [2]. Freeze-dried samples of the microgels were subjected to analysis by Raman spectroscopy, at room temperature, using 632.8 nm exciting radiation from a helium-neon laser. Freeze-dried microgels differing in co-monomer composition (with constant mole fraction of BA) differ substantially in their Raman spectral profiles. An example (Fig. 1) shows the difference in Raman spectroscopic output between poly(NIPAM/BA) and poly(4-VP/BA) homopolymer microgels in the 2600-3200 cm region. Note the clear presence of the Raman band at ~3050 cm due to aromatic C-H stretching vibrational modes of 4-VP. In addition it is noteworthy that there are two low intensity (weak) bands at 2723 and 2766 cm (tentatively assigned to overtones of C-H bending vibrations in the 1300-1400 cm region) present in the Raman spectrum of poly(NIPAM/BA), but absent in the spectrum of poly(4-VP/BA) microgels.

Raman spectroscopy of 1, 3-dicyclohexylcarbodiimide

As a prelude to examining structurally and functionally related molecules particularly in terms of the kinetics of reactions in which such compounds are involved, using vibrational spectroscopy, the Raman spectral profile of DCC has been examined. Vibrational band assignments have been made on the basis of group frequency considerations and ab initio calculations performed using the hybrid SCF-DFT (B3-LYP) method incorporating a cc-pVDZ basis set.