Ultrasonic and IR study of intermolecular association through hydrogen bonding in ternary liquid mixtures

Complex formation in ternary liquid mixtures of dimethylsulfoxide (DMSO) with phenol and o-cresol in carbontetrachloride has been studied by measuring ultrasonic velocity at 2 MHz, in the concentration range of 0.019-0.162 (in mole fraction of DMSO) at varying temperatures of 20, 30 and 40 degrees C. Using measured values of ultrasonic velocity, other parameters such as adiabatic compressibility, intermolecular free length, molar sound velocity, molar compressibility, specific acoustic impedance and molar volume have been evaluated. These parameters have been utilized to study the solute-solute interactions in these systems. The ultrasonic velocity shows a maxima and adiabatic compressibility a corresponding minima as a function of concentration for these mixtures. The results indicate the occurrence of complex formation between unlike molecules through intermolecular hydrogen bonding between oxygen atom of DMSO molecule and hydrogen atom of phenol and o-cresol molecules. The excess values of adiabatic compressibility and intermolecular free length have also been evaluated. The variation of both these parameters with concentration also indicates the possibility of the complex formation in these systems. Further, to investigate the presence of O-HO bond complexes and the strength of molecular association with concentrations, the infrared spectra of both the systems, DMSO-phenol and DMSO-o-cresol, have been recorded for various concentrations at room temperature (20 degrees C). The results obtained using infrared spectroscopy for both the systems also support the occurrence of complex formation through intermolecular hydrogen bonding in these ternary liquid mixtures.     

Revealing interactions between polyaza pyridinophane compounds and DNA/RNA polynucleotides by SERS spectroscopy

Surface‐enhanced Raman scattering spectroscopy (SERS) in the near‐infrared region had been applied to study interactions of polyaza pyridinophanes with single stranded RNA and double stranded DNA and RNA polynucleotides. Studied compounds, PYPOD and PHENPOD, differed in the central aromatic moiety, pyridine and phenanthroline, respectively, which linked two cyclic amines. An intense scattering was obtained from molecules adsorbed onto the silver nanoparticles, showing nonlinear concentration dependence in the 6.5 × 10⁻⁸−6.5 × 10⁻⁵ M range. New bands in spectra of PYPOD/polynucleotide and PHENPOD/polynucleotide mixtures were assigned to vibrational modes of polynucleotide moieties involved in interactions. SERS spectra of both polyaza pyridinophanes with single stranded RNA polynucleotides indicated hydrogen bonding between the small molecules and the nucleic bases of poly A, poly C and poly U, whereas an interaction of only PYPOD with poly G was suggested. SERS spectra implied that both compounds bound into the minor groove of the helical poly dAdT–poly dAdT polynucleotide, while none of polyaza pyridinophanes interacted with the grooves of the poly dGdC–poly dGdC polynucleotide. Nevertheless, intensity ratios suggested intercalation of the phenanthroline moiety of the PHENPOD molecules into the double helix of the guanine‐cytosine polynucleotide. Spectral features also indicated binding of the PYPOD molecules within the major groove of the double stranded RNA analog. Copyright © 2014 John Wiley & Sons, Ltd.     

Molecular mechanism of gelation upon the addition of water to a solution of poly(acrylonitrile) in dimethylsulfoxide

The solidification of a solution of poly(acrylonitrile) (PAN) in dimethylsulfoxide (DMSO) upon introduction of water into the solution is studied by Raman spectroscopy. In the absence of water, DMSO molecules are found to produce dipole-dipole bonds with PAN molecules. Upon the introduction of water, DMSO molecules produce hydrogen bonds with it and bands at 1005 and 1015 cm⁻¹ appear in the Raman spectrum, which are assigned to the valence vibrations of S=O bonds involved in the hydrogen bonds. Simultaneously, water molecules produce hydrogen bonds with PAN molecules: R-C≡N...H-O-H...N≡C-R, where R is the carbon skeleton of a PAN molecule. Accordingly, a band at 2250 cm⁻¹ arises in the Raman spectrum, which is assigned to the valence vibrations of C≡N bonds producing hydrogen bonds with a water molecule. When the water content is low and the DMSO concentration is high, the length of the hydrogen bonds varies in wide limits and the band at 2250 cm⁻¹ is wide. As the water content rises, DMSO molecules come out of PAN, the variation of the hydrogen bond length in it decreases (the band at 2250 cm⁻¹ narrows), and a high-viscosity system (gel) arises that consists of PAN molecules bonded to water molecules via “equally strong” hydrogen bonds.     

Interpretation of the vibrational spectra of polycrystalline adenine

The infrared and Raman spectra of the tetramer of the adenine N₉H are calculated and analyzed. The vibrational spectra of polycrystalline adenine are interpreted. It is demonstrated that the method for calculating the vibrational spectra of molecular complexes formed by hydrogen bonds can be used for interpreting the vibrational spectra of polyatomic molecules in the solid state.     

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.     

Raman spectroscopy of dawsonite NaAl(CO3)(OH)2

Raman spectroscopy both at 298 and 77 K complemented with infrared spectroscopy was used to study the structure of dawsonite. Previous crystallographic studies concluded that the structure of dawsonite was a simple one; however, both Raman and infrared spectroscopy show that this conclusion is incorrect. Multiple bands are observed in both the Raman and infrared spectra in the antisymmetric stretching and bending regions, showing that the symmetry of the carbonate anion is reduced and in all probability the carbonate anions are not equivalent in the dawsonite structure. Multiple OH deformation vibrations centred around 950 cm⁻¹ in both Raman and infrared spectra show that the OH units in the dawsonite structure are non‐equivalent. Calculations using the position of the Raman and infrared OH stretching vibrations enabled estimates of the hydrogen‐bond distances of 0.2735 and 0.27219 pm at 298 K, and 0.27315 and 0.2713 pm at 77 K to be made. This indicates strong hydrogen bonding of the OH units in the dawsonite structure. Copyright © 2007 John Wiley & Sons, Ltd.     

FT‐Raman,FT‐IR spectra and DFT calculations on monomeric and dimeric structures of 5‐fluoro‐ and 5‐chloro‐salicylic acid

The experimental and theoretical study on the structures and vibrations of 5‐fluoro‐salicylic acid and 5‐chloro‐salicylic acid (5‐FSA and 5‐ClSA, C₇H₅FO₃ and C₇H₅ClO₃) is presented. The Fourier transform infrared spectra (4000–400 cm⁻¹) and the Fourier transform Raman spectra (4000–50 cm⁻¹) of the title molecules in the solid phase were recorded. The molecular structures, vibrational wavenumbers, infrared intensities, Raman intensities and Raman scattering activities were calculated for a pair of molecules linked by the intermolecular O H···O hydrogen bond. The geometrical parameters and energies of 5‐FSA and 5ClSA were obtained for all eight conformers/isomers from density functional theory (DFT) (B3LYP) with 6‐311++G(d,p) basis set calculations. The computational results identified the most stable conformer of 5‐FSA and 5‐ClSA as the C1 form. The complete assignments were performed on the basis of the total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanics (SQM) method. The spectroscopic and theoretical results were compared with the corresponding properties for 5‐FSA and 5‐ClSA monomers and dimer of C1 conformer. The optimized bond lengths, bond angles and calculated wavenumbers showed the best agreement with the experimental results. Copyright © 2010 John Wiley & Sons, Ltd.     

Structure and conformation of Arg8 vasopressin modified analogs

Fourier‐transform Raman and infrared spectra were acquired for four arginine vasopressin (AVP) analogs containing L ‐diphenylalanine (Dpa): [Dpa²]AVP, [Cpa¹,Dpa²]AVP, [Dpa³]AVP, and [Cpa¹,Dpa³]AVP (where Cpa denotes 1‐mercaptocyclohexaneacetic acid). We compared and analyzed these spectra. In addition, the Raman spectra were compared to the corresponding surface‐enhanced Raman scattering spectra recorded in an aqueous silver colloidal dispersion. Silver colloidal dispersions prepared by the simple borohydride reduction of silver nitrate were used as substrates. The geometry of these molecules etched on the silver surface was deduced from the observed changes in the intensity enhancement, breadth, and shift in wavenumber of the Raman bands in the spectra of the bound versus free species. Based on the obtained data, adsorption mechanisms were proposed for each case, and the suggested adsorbate structures were compared. All the molecules were thought to adsorb onto a silver surface via a phenyl ring, free electron pairs on the sulfur atom, and CO and  CONH‐bonds. However, the orientation of these fragments on the colloidal silver surface and the strength of the interactions with this surface are different. For [Dpa³]AVP and [Cpa¹,Dpa³]AVP, a strong interaction among the—CCN‐peptide fragment and the colloidal silver surface occurs. Copyright © 2011 John Wiley & Sons, Ltd.     

Vibrational spectroscopy of self‐assembling aromatic peptide derivates

Peptides can assemble to supramolecular structures, of which fibers are of special biochemical and medical relevance. We employed Raman and infrared spectroscopy to elucidate the chemical integrity of fibers built from peptides and peptide derivates that contain the aromatic side groups fluorenyl and phenyl. Because the observed spectra compare very well with simulation results of the respective single molecules in vacuum, we were able to assign all observed vibrations. We found the main differences between solid phase and single molecule for O‐H and N‐H stretching and bending vibrations, owing to hydrogen bonding in solids. The fluorenyl and phenyl residues cause π‐stacking of the molecules, which barely manifests in the spectra, but clearly in the structures. Whereas hydrogen bonds provide the principal stability of the fiber backbone, aromatic π‐stacking supports the assembly to fibers, especially when electrospinning assists the molecular alignment. Copyright © 2012 John Wiley & Sons, Ltd.     

Effect of hydrogen bonding in the vibrational spectra of trans‐cinnamic acid

A computationally‐assisted methodology to assign the vibrational spectra of molecular materials (PiMM) has been successfully applied to the Raman and infrared (IR) spectra of trans‐cinnamic acid (t‐CIA) in the solid state. The effects of molecular association through O H···O hydrogen‐bonding in both the wavenumber and the intensity of the bands are accurately described by a single dimer structure. This supports the discrimination between the possible conformers in the solid, the complete evaluation of hydrogen‐bonding effects, and the full assignment of the vibrational spectra of t‐CIA. Copyright © 2008 John Wiley & Sons, Ltd.     

Raman spectroscopy of hydrogen arsenate group (AsO3OH)2− in solid‐state compounds: cobalt‐containing zinc arsenate mineral,koritnigite (Zn,Co)(AsO3OH)·H2O

Raman spectra of two well‐defined types of koritnigite crystals from the Jáchymov ore district, Czech Republic, were recorded and interpreted. No substantial differences were observed between both crystal types. The observed Raman bands were attributed to the (AsO₃OH)²⁻ stretching and bending vibrations as well as stretching and bending vibrations of water molecules and hydroxyl ions. The non‐interpreted Raman spectra of koritnigite from the RRUFF database and the published infrared spectra of cobaltkoritnigite were used for comparison. The O H···O hydrogen bond lengths in the crystal structure of koritnigite were inferred from the Raman spectra and compared with those derived from the X‐ray single‐crystal refinement. The presence of (AsO₃OH)²⁻ units in the crystal structure of koritnigite was proved from the Raman spectra, which supports the conclusions of the X‐ray structure analysis. Copyright © 2010 John Wiley & Sons, Ltd.     

Surface enhanced Raman scattering of trans‐p‐coumaric and syringic acids

The vibrational spectra of trans‐p‐coumaric acid (pCA) and syringic acid (SA) are discussed. The spectral fingerprints of the organic acids observed in the infrared and Raman spectra are assigned to fundamental vibrational wavenumbers supported by quantum chemical computations. The average surface‐enhanced Raman scattering spectra of both acids have been obtained on silver colloidal solutions and the interpretation of the spectra is presented based on complementary Raman spectra and computational results for the silver salts. Copyright © 2009 John Wiley & Sons, Ltd.     

Theoretical and vibrational spectral investigation of sodium salt of acenocoumarol

The FT‐IR and FT‐Raman spectra of sodium salt of 4‐hydroxy‐3[1‐(4‐nitrophenyl)‐3‐oxobutyl]‐2H‐1‐benzopyran‐2‐one (acenocoumarol sodium salt) in solid phase have been recorded and analyzed. The optimization geometry, intramolecular hydrogen bonding, and harmonic vibrational wavenumbers of acenocoumarol sodium salt have been investigated with the help of B3LYP density functional theory (DFT) methods. The infrared and Raman spectra were predicted theoretically from the calculated intensities. Natural bond orbital (NBO) analysis indicates the presence of C H···O hydrogen bonding in the molecule. The first static hyperpolarizability of the molecule has been computed. Copyright © 2009 John Wiley & Sons, Ltd.     

Infrared and Far Infrared Spectra of Crystalline Phenol-p-benzoquinone Complexes

The infrared and far infrared spectra of complexes formed between p-benzoquinone and phenol derivatives were studied in the crystalline state. The spectra showed the compounds to be weakly polar charge transfer complexes with hydrogen bonds. In the far infrared region hydrogen bond vibrations and internal vibrations forbidden in the free molecules were observed.     

Adsorption of 1,2,4‐triazole on a silver electrode: surface‐enhanced Raman spectroscopy and density functional theory studies

The pH‐dependent surface‐enhanced Raman scattering (SERS) of 1,2,4‐triazole adsorbed on silver electrode and normal Raman (NR) spectra of this compound in the aqueous solutions were investigated. The observed bands in the NR and SERS spectra were assigned with the help of density functional theory calculations for model molecules in the neutral, anionic, and cationic forms and their complexes with silver. The Raman wavenumbers and intensities were computed at the optimized molecular geometry. Vibrational assignments of the SERS and NR spectra are provided by calculated potential energy distributions. The combination of experimental SERS results and density functional theory calculations provide an insight into the molecular structure of adlayers formed by 1,2,4‐triazole on a silver surface at varying pH values and enable the determination of molecular orientation with respect to the surface. Copyright © 2012 John Wiley & Sons, Ltd.     

Vibrational spectra and scaled quantum chemical studies of the structure of Martius yellow sodium salt monohydrate

The FT‐IR and Raman spectra of Martius Yellow sodium salt Monohydrate (MYM) [2, 4‐dinitro‐1‐naphthol sodium salt] in solid‐phase have been measured. The geometry, intramolecular hydrogen bonding and harmonic vibrational wavenumbers of MYM have been investigated with the help of B3LYP density functional theory (DFT) methods. The detailed interpretation of the vibrational spectra has been carried out with the aid of normal coordinate analysis (NCA) following the scaled quantum mechanical force field methodology (SQMFF). The existence of intramolecular C H···O improper, blue‐shifted hydrogen bonding was investigated by means of the NBO analysis. The infrared and Raman spectra were predicted theoretically from the calculated intensities. The observed and the calculated spectra were found to be in good agreement. Copyright © 2009 John Wiley & Sons, Ltd.     

Raman spectroscopy of hydrogen‐arsenate group (AsO3OH) in solid‐state compounds: cobalt mineral phase burgessite Co2(H2O)4[AsO3OH]2·H2O

Raman spectrum of burgessite, Co₂(H₂O)₄[AsO₃OH]₂· H₂O, was studied, interpreted and compared with its infrared spectrum. The stretching and bending vibrations of (AsO₃) and As‐OH units, as well as the stretching, bending and libration modes of water molecules and hydroxyl ions were assigned. The range of O H···O hydrogen bond lengths was inferred from the Raman and infrared spectra of burgessite. The presence of (AsO₃OH)²⁻ units in the crystal structure of burgessite was proved, which is in agreement with its recently solved crystal structure. Raman and infrared spectra of erythrite inferred from the RRUFF database are used for comparison. Copyright © 2010 John Wiley & Sons, Ltd.     

Experimental vibrational spectra (Raman,infrared) and DFT calculations on monomeric and dimeric structures of 2‐ and 6‐bromonicotinic acid

In this work, the Fourier transform infrared and Raman spectra of 2‐bromonicotinic acid and 6‐bromonicotinic acid (abbreviated as 2‐BrNA and 6‐BrNA, C₆H₄BrNO₂) have been recorded in the region 4000–400 and 3500–50 cm⁻¹. The optimum molecular geometry, normal mode wavenumbers, infrared intensities and Raman scattering activities, corresponding vibrational assignments and intermolecular hydrogen bonds were investigated with the help of B3LYP density functional theory (DFT) method using 6‐311++G(d,p) basis set. Reliable vibrational assignments were made on the basis of total energy distribution (TED) calculated with scaled quantum mechanical (SQM) method. From the calculations, the molecules are predicted to exist predominantly as the C1 conformer. Copyright © 2009 John Wiley & Sons, Ltd.     

DFT simulations and vibrational analysis of FTIR and FT‐Raman spectra of 2‐amino‐4,6‐dihydroxypyrimidine

This work deals with the vibrational spectroscopy of 2‐amino‐4,6‐dihydroxy pyrimidine (ADHP) by means of quantum chemical calculations. The mid‐ and far FTIR and FT‐Raman spectra were measured in the condensed state. The fundamental vibrational wavenumbers and intensity of vibrational bands were evaluated using density functional theory (DFT) with the standard B3LYP/6‐311 + G** methods and basis set combinations, and were scaled using various scale factors, which yielded good agreement between the observed and calculated wavenumbers. The vibrational spectra were interpreted with the aid of normal coordinate analysis based on the scaled density functional force field. The results of the calculations were applied to simulate the infrared and Raman spectra of the title compound, which showed excellent agreement with the observed spectra. Copyright © 2008 John Wiley & Sons, Ltd.     

Hydrogen bonding in nitrofurantoin polymorphs: a computation‐assisted spectroscopic study

The importance of hydrogen‐bond formation in the molecular packing arrangements of two anhydrous forms of nitrofurantoin is investigated, combining computational methods and spectroscopic data. The overall results indicate, as expected, that the vibrational modes related to the CO, N H and C H groups are strongly affected by intermolecular hydrogen‐bond formation. Moreover, the importance of weak C‐H···O interactions in conferring additional stability to molecular associations in biological systems is evidenced in this study. The complete assignment of the Raman and infrared spectra of both polymorphs is accomplished by means of a computationally based methodology, which accounts for the effects of intermolecular interactions in the crystal. The vibrational shifts due to crystal packing interactions are evaluated from DFT calculations for a set of suitable molecular pairs, using the B3LYP/6‐31G* approach. This methodology provides an answer to the current demand for a reliable and complete assignment of the vibrational spectra of pharmaceutically active compounds such as nitrofurantoin. Copyright © 2009 John Wiley & Sons, Ltd.