Strong Hydrogen Bonds in Acetylenedicarboxylic Acid Dihydrate.

Acetylenedicarboxylic acid dihydrate (ADAD) represents a complex with strong hydrogen bonding between the carboxylic OH and the water molecule. An X-ray re-examination of the ADAD crystal structure confirms the O…O distance of the short hydrogen bonds, and clearly shows different bond lengths between the two oxygen atoms with respect to the carbon atom in the carboxyl group, indicating a neutral structure for the complex. The neutral structure was also confirmed by vibrational spectroscopy, as no proton transfer was observed. The diffraction studies also revealed two polymorph modifications: room temperature (α) and low temperature (ß), with a phase transition at approximately 4.9 °C. The calculated vibrational spectra are in satisfactory agreement with the experimental spectra. A comparison of the structure and the vibrational spectra between the ADAD and the oxalic acid dihydrate reveals some interesting details. The crystal structures of both crystal hydrates are almost identical; only the O…O distances of the strongest hydrogen bonds differ by 0.08 Å. Although it was expected that a larger O…O spacing in the ADAD crystal may significantly change the infrared and Raman spectra, especially for the frequency and the shape of the acidic OH stretching vibration, both the shape and frequency are almost identical, with all subpeaks topped on the broad OH stretching vibration. The O…O distance dependent are only in- and out-of-plane OH deformations modes. The presence of polarons due to the ionized defects was not observed in the vibrational spectra of ADAD. Therefore, the origin of the broad OH band shape was explained in a similar way to the acid dimers. The anharmonicity of a potential enhances the coupling of the OH stretching with the low-frequency hydrogen bond stretching, which, in addition to the Fermi resonance, structures the band shape of the OH stretching. The fine structure found as a superposition of a broad OH stretching is attributed to Davydov coupling.

Surface Enhanced Raman Spectroscopy for Quantitative Analysis: Results of a Large-Scale European Multi-Instrument Interlaboratory Study.

Surface-enhanced Raman scattering (SERS) is a powerful and sensitive technique for the detection of fingerprint signals of molecules and for the investigation of a series of surface chemical reactions. Many studies introduced quantitative applications of SERS in various fields, and several SERS methods have been implemented for each specific application, ranging in performance characteristics, analytes used, instruments, and analytical matrices. In general, very few methods have been validated according to international guidelines. As a consequence, the application of SERS in highly regulated environments is still considered risky, and the perception of a poorly reproducible and insufficiently robust analytical technique has persistently retarded its routine implementation. Collaborative trials are a type of interlaboratory study (ILS) frequently performed to ascertain the quality of a single analytical method. The idea of an ILS of quantification with SERS arose within the framework of Working Group 1 (WG1) of the EU COST Action BM1401 Raman4Clinics in an effort to overcome the problematic perception of quantitative SERS methods. Here, we report the first interlaboratory SERS study ever conducted, involving 15 laboratories and 44 researchers. In this study, we tried to define a methodology to assess the reproducibility and trueness of a quantitative SERS method and to compare different methods. In our opinion, this is a first important step toward a "standardization" process of SERS protocols, not proposed by a single laboratory but by a larger community.

Evidence of Polaron Excitations in Low Temperature Raman Spectra of Oxalic Acid Dihydrate.

Low temperature Raman spectra of oxalic acid dihydrate (8-300 K) for both the polycrystalline and single crystal phase show strong variation with temperature in the interval from 1200 to 2000 cm(-1). Previous low temperature diffraction studies all confirmed the stability of the crystal P21/n phase with no indications of any phase transition, reporting the existence of a strong hydrogen bond between the oxalic acid and a water molecule. A new group of Raman bands in the 1200-1300 cm(-1) interval below 90 K is observed, caused by possible loss of the center of inversion. This in turn could originate either due to disorder in hydroxyl proton positions or due to proton transfer from carboxylic group to water molecule. The hypothesis of proton transfer is further supported by the emergence of new bands centered at 1600 and 1813 cm(-1), which can be explained with vibrations of H3O(+) ions. The broad band at 1600 cm(-1) looses intensity, while the band at 1813 cm(-1) gains intensity on cooling. The agreement between quantum calculations of vibrational spectra and experimentally observed Raman bands of hydronium ions in oxalic acid sesquihydrate crystal corroborates this hypothesis.

Nitranilic acid hexahydrate, a novel benchmark system of the Zundel cation in an intrinsically asymmetric environment: spectroscopic features and hydrogen bond dynamics characterised by experimental and theoretical methods.

Nitranilic acid (2,5-dihydroxy-3,6-dinitro-2,5-cyclohexadiene-1,4-dione) as a strong dibasic acid in acidic aqueous media creates the Zundel cation, H5O2(+). The structural unit in a crystal comprises (H5O2)2(+) (2,5-dihydroxy-3,6-dinitro-1,4-benzoquinonate)(2-) dihydrate where the Zundel cation reveals no symmetry, being an ideal case for studying proton dynamics and its stability. The Zundel cation and proton transfer dynamics are studied by variable-temperature X-ray diffraction, IR and solid-state NMR spectroscopy, and various quantum chemical methods, including periodic DFT calculations, ab initio molecular dynamics simulation, and quantization of nuclear motion along three fully coupled internal coordinates. The Zundel cation features a short H-bond with the O···O distance of 2.433(2) Å with an asymmetric placement of hydrogen. The proton potential is of a single well type and, due to the non-symmetric surroundings, of asymmetric shape. The formation of the Zundel cation is facilitated by the electronegative NO2 groups. The employed spectroscopic techniques supported by calculations confirm the presence of a short H-bond with a complex proton dynamics.

Populations of the three major backbone conformations in 19 amino acid dipeptides.

The amide III region of the peptide infrared and Raman spectra has been used to determine the relative populations of the three major backbone conformations (P(II), ß, and α(R)) in 19 amino acid dipeptides. The results provide a benchmark for force field or other methods of predicting backbone conformations in flexible peptides. There are three resolvable backbone bands in the amide III region. The major population is either P(II) or ß for all dipeptides except Gly, whereas the α(R) population is measurable but always minor (≤ 10%) for 18 dipeptides. (The Gly ϕ,ψ map is complex and so is the interpretation of the amide III bands of Gly.) There are substantial differences in the relative ß and P(II) populations among the 19 dipeptides. The band frequencies have been assigned as P(II), 1,317-1,306 cm(-1); α(R), 1,304-1,294 cm(-1); and ß, 1,294-1,270 cm(-1). The three bands were measured by both attenuated total reflection spectroscopy and by Raman spectroscopy. Consistent results, both for band frequency and relative population, were obtained by both spectroscopic methods. The ß and P(II) bands were assigned from the dependence of the (3)J(H(N),H(α)) coupling constant (known for all 19 dipeptides) on the relative ß population. The P(II) band assignment agrees with one made earlier from Raman optical activity data. The temperature dependences of the relative ß and P(II) populations fit the standard model with Boltzmann-weighted energies for alanine and leucine between 30 and 60 °C.

Raman study of water deposited in solid argon matrix.

New Raman data are presented concerning H2O and D2O water aggregation in argon matrix having the ratio of number of argon atoms to water molecules close to 40:1. Experiments were conducted at temperatures from 8 K to 34 K allowing observation of OH and OD stretching vibrations of water monomers, dimers, trimers and higher multimers, as well as broad bands corresponding to solid amorphous water. Molecular dynamics simulations were performed for thirteen or sometimes fourteen water molecules dispersed among 500 argon atoms. Resulting final configurations included dimers, trimers, tetramers and pentamers, all in open chain configurations which upon optimization resulted in mostly cyclic conformations. Observed OH stretching vibrations were assigned by comparing calculated normal modes in harmonic approximation at the B3LYP/aug-cc-pVDZ and PBEPBE1/aug-cc-pVDZ level of theory with our data and previously observed bands from infrared matrix isolation studies and Raman jet cooled experiments. Raman bands assigned to water multimers in argon matrix are shifted 20 to 25 cm-1 towards lower wavenumbers with respect to the positions of OH stretching vibrations of almost free water clusters.

Glucosamine to gold nanoparticles binding studied using Raman spectroscopy.

The binding of glucosamine to gold in water solutions of glucosamine hydrochloride mixed with clean colloidal gold nanoparticles obtained by laser ablation in liquid was studied using surface-enhanced Raman scattering (SERS), dynamic light scattering (DLS) and UV-VIS spectroscopy. The purpose of this study was to establish whether the binding of charged aminogroup to gold nanoparticles (AuNPs) is taking place, and if it does, how can it be identified by means of SERS. The average size of dried gold nanoparticles was (20 ± 4) nm determined by averaging the sizes observed in transmission electron microscopy micrographs, which is smaller than the average size of gold nanoparticles in water solution as determined by DLS: (52 ± 2) nm. Upon adding the glucosamine solutions to gold colloid, average hydrodynamic diameter of ions was slightly larger for 0.1 mM glucosamine solution (55 ± 2 nm), while it increased to (105 ± 22) nm in the case of 1 mM solution, and was (398 ± 54) nm when 10 mM glucosamine solution was added. Most prominent Raman bands observed both for 0.1 mM and 1 mM glucosamine solutions were located at 1165 cm-1, 1532 and 1586 cm-1 and assigned to C-N coupled with C-C stretching, and C-NH3+ deformation angles bending. In SERS spectrum of 1 mM GlcN+ solution, two strong bands at 999 and 1075 cm-1 were found and attributed to C-Oring stretching coupled with C-NH3+ bending (999 cm-1) and to dominantly C-O stretching vibration. The differences in SERS spectra are attributed to different number of glucosamine molecules that attach to gold nanoparticles and their orientation with respect to the metal particle surface, partly due to presence of beta anomers protonated at anomeric oxygen position. The assignment of glucosamine bands was further corroborated by comparison with vibrational spectra of alpha and beta glucose and of polycrystalline powder of glucosamine hydrochloride. For all three substances comprehensive calculation of vibrational density of states was conducted using density functional theory. Benchmark bands for polycrystalline glucose anomers distinction are 846 and 915 cm-1 for alpha glucose, and 902 cm-1 for beta glucose. However, the bands observed in SERS spectra of 0.1 mM glucosamine solution at 831, 899, and 946 cm-1 or in 1 mM solution at 934 cm-1 cannot be easily identified as belonging either to alpha or beta glucosamine anomer, due to complexity of atomic motions involved. The identification of vibrational bands associated with -CNH3+ group will aid SERS studies on amino acids, especially in cases when several atomic groups could possibly bind to AuNPs.

Combining Raman Spectroscopy, DFT Calculations, and Atomic Force Microscopy in the Study of Clinker Materials.

Raman spectroscopy and Raman mapping analysis, combined with density functional theory calculations were applied to the problem of differentiating similar clinker materials such as alite and belite. The Portland cement clinker 217 (further: clinker) was analysed using colocalised Raman mapping and atomic force microscopy mapping, which provided both spatial and chemical information simultaneously. The main constituents found in the clinker were alite, belite, portlandite, amorphous calcium carbonate, and gypsum. Since phonon bands of alite and belite greatly overlap, and their distinction is important for the hydration process during cement setting, we provided the calculated phonon density of states for alite Ca3SiO5 (Pc structure) and belite Ca2SiO4 (ß P21/n structure) here for the first time. Both calculated phonon densities have similar distribution of phonon modes, with a gap between 560 and 810 cm-1. A comparison of the calculated phonon frequencies for Ca3SiO5 and Ca2SiO4 shows that the lowest calculated phonon frequency of ß-Ca2SiO4 lies at 102 cm-1, while for Pc alite the lowest phonon frequency is predicted at 27 cm-1. Low frequency Raman spectroscopy could therefore be used for a clearer distinction of these two species in a clinker material.

Vibrational dynamics of 1,3-propanediol in liquid, polycrystalline and glassy states: A Raman spectroscopic study.

Vibrational transitions of 1,3-propanediol in liquid and crystal phases are assigned on the basis of Raman and infrared spectra of liquid and low temperature (295K-10K) Raman spectra which are presented here for the first time. In the crystal, there are four molecules per unit cell, each having a gGGg' conformation. The vibrations for the P21/n crystal phase having four molecules in the unit cell are obtained by an ab initio calculation using CRYSTAL09 program, and are in good agreement with the observed Raman bands. Observed bands in Raman spectrum of liquid are in proximity of those observed for crystal phase, and it is tempting to assign them as belonging mainly to gGGg' conformer. However, quantum chemical ab initio calculations provide basis to ascertain that tGG'g and tGGt are two conformers having lowest energy at the B3LYP/6-31++G(d,p) level of theory. Several bands that disappear from Raman spectrum of liquid on solidification (384, 872 and 1040 cm-1) could give an insight into the nature of conformers present in liquid. Since the closest calculated vibrations are 386cm-1 for tGG'g and 1043cm-1 for tGG't conformer, we conclude that all three conformers: tGG'g, tGGt and gGGg', are present in the liquid.

Binding of p-mercaptobenzoic acid and adenine to gold-coated electroless etched silicon nanowires studied by surface-enhanced Raman scattering.

Modern diagnostic tools ever aim to reduce the amount of analyte and the time needed for obtaining the result. Surface-enhanced Raman spectroscopy is a method that could satisfy both of these requirements, provided that for each analyte an adequate substrate is found. Here we demonstrate the ability of gold-sputtered silicon nanowires (SiNW) to bind p-mercaptobenzoic acid in 10-3, 10-4 and 10-5M and adenine in 30 and 100µM concentrations. Based on the normal mode analysis, presented here for the first time, the binding of p-mercaptobenzoic acid is deduced. The intensity enhancement of the 1106cm-1 band is explained by involvement of the CS stretching deformation, and the appearance of the broad 300cm-1 band attributed to SAu stretching mode. Adenine SERS spectra demonstrate the existence of the 7H tautomer since the strongest band observed is at 736cm-1. The adenine binding is likely to occur in several ways, because the number of observed bands in the 1200-1600cm-1 interval exceeds the number of observed bands in the normal Raman spectrum of the free molecule.

Vibrational analysis of hydroxyacetone.

In order to be able to fully understand the vibrational dynamics of monosaccharide sugars, we started with hydroxyacetone CH2OHCOCH3, and glycolaldehyde CH2OHCOH, which are among the smallest molecules that contain hydroxyl and carbonyl group on neighboring carbon atoms. This sterical configuration is characteristic for saccharides and determines their biochemical activity. In this work vibrational analysis of hydroxyacetone was undertaken by performing the normal coordinate analysis for glycolaldehyde first, and transferring these force constants to hydroxyacetone. The observed Raman and infrared bands for 90 wt.% solution of hydroxyacetone in water (acetol) were used as a first approximation for the bands of free hydroxyacetone. The number of observed Raman and infrared bands for acetol exceeds the number of calculated values for the most stable hydroxyacetone conformer with Cs symmetry, which suggests more than one conformer of hydroxyacetone in water solution. In particular, there are two bands both in infrared (1083 and 1057 cm(-1)) and in Raman spectrum (1086.5 and 1053 cm(-1)) that are assigned to the CO stretching mode and this is one of the indicators of several hydroxyacetone conformers in the solution. Additional information was obtained from low temperature Raman spectra: at 240 K a broad asymmetric band centered around 280 cm(-1) appears, suggesting a disorder in the orientation of hydroxyl groups. Glassy state forms at approximately 150K. The broad band at 80 cm(-1) is assigned to frozen torsions of hydroxymethyl groups.

Raman spectroscopic evidence of low temperature stability of D,L-glycolic and L-(+)-lactic acid crystals.

Raman and infrared spectra of polycrystalline D,L-glycolic and L-(+) lactic acid are presented and assigned both by an ab initio calculation of normal modes of free conformers and by self-consistent-charge density-functional-theory computational program DFTB+. Temperature dependent Raman spectra from 295 K to 10 K reveal great stability of crystal lattices, since no soft modes and no band splittings that could be attributed to changes of the number of molecules per unit cell were observed. A semiempirical calculation with GULP program was used to estimate the strength of hydrogen bonds in crystals: in glycolic acid they have energies of -0.337 eV/mol, -0.329 eV/mol, -0.262 eV/mol and -0.242 eV/mol, while in lactic acid two hydrogen bonds have energies of -0.283 eV/mol and -0.202 eV/mol.

Luminescence and Raman spectra of acetylacetone at low temperatures.

Raman spectra of acetylacetone were recorded for molecules isolated in an argon matrix at 10 K and for a polycrystalline sample. In the solid sample, broad bands appear superimposed on a much weaker Raman spectrum corresponding mainly to the stable enol form. The position of these bands depends on the excitation wavelength (514.5 and 488.8 nm argon ion laser lines were used), sample temperature, and cooling history. They are attributed to transitions from an excited electronic state to various isomer states in the ground electronic state. Laser photons have energies comparable to energies of a number of excited triplet states predicted for a free acetylacetone molecule (Chen, X.-B.; Fang, W.-H.; Phillips, D. L. J. Phys. Chem. A 2006, 110, 4434). Since singlet-to-triplet photon absorption transitions are forbidden, states existing in the solid have mixed singlet/triplet character. Their decay results in population of different isomer states, which except for the lowest isomers SYN enol, TS2 enol (described in Matanovic I.; Doslic, N. J. Phys. Chem. A 2005, 109, 4185), and the keto form, which can be detected in the Raman spectra of the solid, are not vibrationally resolved. Differential scanning calorimetry detected two signals upon cooling of acetylacetone, one at 229 K and one at 217 K, while upon heating, they appear at 254 and 225 K. The phase change at higher temperature is attributed to a freezing/melting transition, while the one at lower temperature seems to correspond to freezing/melting of keto domains, as suggested by Johnson et al. (Johnson, M. R.; Jones, N. H.; Geis, A; Horsewill. A. J.; Trommsdorff, H. P. J. Chem. Phys. 2002, 116, 5694). Using matrix isolation in argon, the vibrational spectrum of acetylacetone at 10 K was recorded. Strong bands at 1602 and 1629 cm(-1) are assigned as the SYN enol bands, while a weaker underlying band at 1687 cm(-1) and a medium shoulder at 1617 cm(-1) are assigned as TS2 enol bands.