Low-temperature FTIR spectra and hydrogen bonds in polycrystalline adenosine and uridine

FTIR spectra of polycrystalline samples of adenosine and uridine, pure and containing small (<10%) quantity of N(O)H or N(O)D groups, were measured in KBr pellets from 4000 to 400 cm(-1) at temperatures from 300 to 20 K. For the first time, the bands of narrow isotopically decoupled proton stretching vibration nu1 mode of NH- and OH- groups were found and assigned to ordered hydrogen bonds according to crystal structural data for both nucleosides. The FTIR adenosine spectra in the out-of-plane bending proton nu4 mode range (lower than 1000 cm(-1)) of N(O)H groups revealed at low temperature at least twice more bands, than in the nu1 range, which are influenced by isotopic exchange and (or) cooling. Almost all of them have their counterparts in the N(O)D substance spectrum with an isotopic frequency ratio of 1.30-1.40. These bands were assigned to the differently H-bound disordered NH and OH protons, which could not be seen with crystal structural methods. The energy and length of different H-bonds were estimated from peak positions of both mode bands (as the red shift of nu1 or blue shift of nu4 relatively free molecules) with well-established empirical correlations between spectral, thermodynamic and structural parameters of hydrogen bonds. The results were compared with independent experimental data.     

Low temperature Fourier transform infrared spectra and hydrogen bonding in polycrystalline uracil and thymine

The FTIR spectra of pure NH and isotopically diluted (NH/ND and ND/NH) polycrystalline uracil and thymine were measured in the range 4000-400 cm(-1) at temperatures from 300 to 10K. For the first time, the essentially narrow bands corresponding to the uncoupled stretching (nu(1)) and out of plane bending (nu(4)) NH proton modes of uracil and thymine were observed in the solid phase. It was found that in the nu(4) region the spectra reveal more details on the H-bond interactions present in both solids than in the nu(1) range. The frequencies of the various bands observed in both spectral regions were used for estimation of the H-bond energy, using empirical correlations between this property and both the red shift of nu(1) and the blue shift of nu(4) that occur upon crystallization due to the establishment of the H-bonds. The results are compared with known thermodynamic, structural and theoretical data. The IR data also suggest that the H-bond networks of both crystals contain, besides the two NH...O=C bonds revealed by X-ray experiments, additional types of H-bonds, which do not show long range periodicity and, thus, cannot be detected by the conventional structural methods. The assignment of some other bands in the spectra of both substances was also reviewed.     

Low temperature FTIR spectroscopy and hydrogen bonding in cytosine polycrystals

The FTIR spectra of both the pure NH and isotopically substituted ND (<10% and >90% D) polycrystalline cytosine were recorded in the range 400-4000 cm(-1) as a function of temperature (10-300 K). For the first time, uncoupled NH(D) stretching mode bands of amine and imine groups were observed in the spectra of isotopically diluted cytosine at low temperatures. These bands correspond to the three distinct H-bonds that are present in the crystal, in agreement with the available data obtained by structural methods. At least nine bands were observed below 1000 cm(-1) and, in consonance with their temperature and isotopic exchange behavior, were assigned to the NH proton out-of-the-plane bending modes. Six of these bands were found to correspond to additional "disordered" H-bonds, which could not be observed by structural methods. Empirical correlations of spectral and thermodynamic parameters enabled to estimate the contribution of the H-bonds to the sublimation enthalpy of the crystal, in agreement with independent experimental data.     

Calculated vibrational spectra of weak hydrogen bonds

Potential energy and dipole moment surfaces for the H-bond SH... S in the dimeric methanethiol have been calculated by the SCF-MO-LCGO method, and the vibrational spectrum — transition frequencies and IR absorption intensities at 20 °K — computed. This spectrum is compared with that of the monomeric species and with experimental results. The resulting dimerization energy is 1.4 kcal/mole.     

Low-temperature Fourier transform infrared spectra and hydrogen bonding in polycrystalline L-alanine

The 400-4000 cm(-1) FTIR spectra of pure NH and isotopically substituted (10 and 90% doped ND/NH) polycrystalline L-alanine were recorded in the temperature range 10-300 K. The observed temperature dependence and isotopic shifts behavior enabled to identify, in the spectra of the doped crystals, three well-separated bands ascribable to either the NH or ND stretching vibrations associated with the three different types of hydrogen bonds existing in the crystal. The observed red shifts of these bands relative to the frequency of a reference "free" NH (or ND) stretching mode were found to correlate well with the H-bond distances found in the crystal and provide an indirect way of estimating the enthalpies associated with each type of H-bond found in the crystal. In the low-frequency deformation and torsional spectral region (below 2000 cm(-1)), several bands, which were found to be affected by isotopic substitution, were identified as belonging to the NH3(+) group. Several bands show splitting at low temperatures, indicating the occurrence of a significant reorganization in the crystal structure, which with all probability results mainly from changes in the proton positions. Finally, the literature assignments of the IR spectra of both crystalline NH3(+) and ND3(+) L-alanine were revised taking into consideration their temperature dependence and behavior upon deuteration.     

Hydrogen bonds, improper hydrogen bonds and dihydrogen bonds

The structures, interaction energies and vibrational spectra of a large number of molecular complexes, formed by binary combination of the covalent hydrides of some of the elements of the first two rows of the periodic table, have been determined by means of ab initio molecular orbital theory at the MP2 level, using the 6-311++G(d,p) basis set. The results are discussed in terms of a variety of different types of interaction experienced by the monomer species as they undergo association, namely conventional hydrogen bonding, improper hydrogen bonding, dihydrogen bonding and electron donor–acceptor interaction.     

Multiple hydrogen bonds. Mass spectra of hydrogen bonded heterodimers. A comparison of ESI- and REMPI-ReTOF-MS

Resonance enhanced multi-photon ionization-reflectron time of flight mass spectrometry is the analytical method of choice to observe hydrogen bonded supramolecules in the gas phase when protonation of basic centers competes with cluster formation.     

Stability of hydrogen bonds upon polymerization and color transition of diacetylenes: An FTIR spectroscopy study

FTIR spectra (400–7500 cm⁻¹) have been recorded for polycrystalline films and single crystals of the diacetylene 4BCMU in the monomer, blue and red polymer states, and of 3BCMU monomer. Particular attention was paid to the amide bands associated to the urethanes in the side groups, which form one-dimensional H-bond linear chains quite similar to those found in peptides and proteins. The positions and strengths of these absorptions are practically unchanged by polymerization or blue to red polymer color transition. This suggests that the H-bond linear chains are the main constitutive interactions in these crystals, and that the conjugated parts must and do “adapt” to the unchanged H-bond lines. No evidence of side group disordering was observed at the irreversible blue to red transition in poly-4BCMU crystal.     

Hydrogen bonds in fluorosubstituted dicarboxylic acids: vibrational spectra and crystal structure of potassium hydrogen difluorofumarate and potassium hydrogen difluoromaleate

The crystal structures of potassium hydrogen difluoromaleate (KHDFM) and potassium hydrogen difluorofumarate (KHDFF) have been determined by single crystal X-ray methods. The hydrogen difluoromaleate ion has a closed ring structure with a short intramolecular hydrogen bond. The O· O distance is 2.415(1) Å The hydrogen difluorofumarate ions form infinite chains via short intermolecular hydrogen bonds.The O· ;O distance is 2.450(5) Å. In both compounds the hydrogen bonds are across crystallographic symmetry elements. The vibrational spectra of both compounds and their deuterated derivatives have been recorded and assigned. The IR spectrum of KHDFF is of Speakman's A₂ type. The spectra of KHDFM and potassium hydrogen maleate are very similar.     

Infrared and resonance enhanced Raman spectra of some metal vic-dioximes with short hydrogen bonds

Infrared and enhanced Raman spectra were recorded of bis(2,3-butanonedioximato-N,N′) nickel (II) and palladium (NiDMG, PdDMG) as well as the i.r. spectra of bis(ethanedialdioximato-N,N′) nickel (II) (NiHG), bis(2,3-pentanonedioximato-N,N′) nickel (II) (NiEMG), and of bis(2,3-butanonedioximato-N,N′) copper (II) (CuDMG). The mutual exclusion of i.r. and Raman active modes of NiDMG and PdDMG prove the existence of an inversion centre whereas the coupling of the in-plane OH deformation with two skeletal modes of CN stretching character indicates that the molecular symmetry is likely to be C_2h only. The B _u OHO stretching mode has been identified in the nickel complexes with a strong, broad band near 900 cm⁻¹. The resonance Raman enhancement is observed mainly with skeletal vibrations of CN character and, less, with those having NO character. The effects of high pressure upon i.r. spectra were observed. The possible symmetry of the hydrogen bond is discussed.     

Low temperature fluorescence spectra of atropisomeric perylene dyes

The site selection spectra of highly photostable perylene fluorescent dyes at 4.2 K in a glassy matrix of three different organic solvents (ethanol, methyl tetrahydrofuran, n-butyl acetate) are presented. The spectra ofthe two isomers are identical for a given solvent and only very minute differences are detectable between different solvents. We conclude that the influence of the matrix on the fluorescence spectra is of only minor importance. The influence of the orientation in the matrix is negligible.     

Integrated intensity of continuous absorption in infrared spectra of complexes with medium-strong and strong hydrogen bonds

A simple, nongraphical and reproducible method of separation of the complex absorption due to strong hydrogen bonds from that due to the skeleton is proposed. The method has been tested on 17 complexes of pyridine N-oxide, triphenylphosphine oxide and DMSO-d₆ with dichloroacetic acid in dry dichloromethane and acetonitrile. The integrated intensity (A_CPA) and the centre of gravity (mathtype1) of complex absorption due to protonic vibration were measured and correlated with pK_a values of bases and chemical shifts of the hydrogen-bonded protons (δ), and discussed with respect to hydrogen bond strength variations. TheA^CPA values vary from 17.5 to 46 x 10⁴ cm mmol^-1 and were reproducible to within ± 1 x 10⁴ cm mmol⁻¹ (5-15 %). A nonlinear correlation between A_CPA and (mathtype2) has been found in wide region of data; (mathtype3) varies from 500 to 2300 cm⁻¹. A gradual proton transfer has been considered from the acid to pyridine N-oxides via strengthening intermolecular H-bonds, AH⋯ON, and further via weakening interionic H-bonds, A⁻⋯ HON⁺. The obtained correlations suggest that variations of hydrogen bond strength caused similar changes of A_CPA and (mathtype4) both in molecular (A–H⋯B) and ionic (A⁻⋯H–B⁺) species.     

Influence of temperature on FTIR spectra of various organic compounds analyzed by on-line carbon dioxide SFC/FTIR

The development of an on-line SFC-FTIR method with supercritical carbon dioxide as mobile phase requires information about the nature of the FTIR spectrum of a solute dissolved in supercritical or liquid CO₂. The wavenumber of maximum absorbance of the carbonyl stretching vibration was quantitatively studied versus temperature and CO₂ density. FTIR spectra recorded in supercritical or liquid CO₂ have been compared to their vapor-phase and condensed-phase spectra for various solutes.     

Low temperature absorption spectra of KMnO4 in KClo4

The permanganate spectrum has been remeasured at liquid hydrogen and helium temperatures using spectrographs with reasonably high dispersion. Evidence is found for four absorption band systems. The first one is assigned as ¹ A ₁ ¹ T ₂ and displays a great deal of vibrational structure starting with the 0–0 line located at 18,072 cm^–1. The second transition found at 25,000 to 30,000 cm^–1 is rather featureless. The third transition with maximum at 33,000 cm^–1 shows a simple progression in quanta of 750 cm^–1. The fourth band is completely featureless with maximum intensity at 43,500 cm^–1. These findings are compared with a simplified SCF LCAO MO calculation.

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Zusammenfassung Das Permanganat-Spektrum wurde bei Temperaturen von flüssigem Wasserstoff und Helium unter Verwendung eines ausreichend auflösenden Spektrographen neu vermessen, wobei vier Absorptionssysteme gefunden wurden. Dem ersten von ihnen wurde ein ¹ A ₁ ¹ T ₂-Übergang zugeordnet; es besitzt eine ausgeprägte Vibrationsstruktur (0–0-Bande bei 18,072 cm^–1, während das folgende zwischen 25,000 und 30,000 cm^–1 kaum eine Struktur zeigt. Der dritte Übergang mit Maximum bei 33,000 cm^–1 zeigt einfache Progressionen entsprechend Quanten von 750 cm^–1. Die vierte Bande schließlich ist vollkommen strukturlos und hat ihr Maximum bei 43,500 cm^–1. Diesen Daten wurden die Ergebnisse einer einfachen SCF-LCAO-MO-Rechnung gegenübergestellt.

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Résumé Le spectre du permanganate de potassium a été réétudié aux températures de l'hydrogène et de l'hélium liquide en utilisant des spectrographes à dispersion raissonnablement élevée. On trouve la preuve de la présence de quatre systèmes de bandes d'absorption. Le premier, attribué à ¹ A ₁ ¹ T ₂, possède une forte structure vibrationnelle commencant à la bande 0–0 située à 18.072 cm^–1. La seconde transition située entre 25.000 et 30.000 cm^–1 est plutot sans structure. La troisième transition avec un maximum à 33.000 cm^–1 présente une progression simple de 750 cm^–1. La quatrième bande est complètement sans structure et a son maximum vers 43.500 cm^–1. Ces observations sont comparées avec un calcul simplifié SCF LCAO MO.

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NATO Postdoctoral Fellow 1965–66.     

Infrared and raman spectra of crystalline quinuclidin-3-one hemiperchlorate with symmetrical NHN hydrogen bonds

Infrared and Raman studies have been performed on polycrystalline and monocrystalline samples of quinuclidin-3-one hemipercholate which at low temperature contain symmetric [NHN]⁺ hydrogen bonds. The most characteristic feature of the IR spectrum is a continuous broad absorption polarized parallel to the hydrogen bond direction.The Evans holes in the low-frequency range are most probably due to the coupling of protonic vibrations with internal modes of quinuclidine moieties leading to a modulation of the bridge geometry. Unusual isotopic and temperature effects could indicate a particular shape of the potential for the proton motion.     

Quantum-chemical study,IR spectra,and intramolecular hydrogen bonds in dimeric 5- and 6-methyluracils

Comparative analysis of the geometry, atomic charges, force constants, and IR spectra of crystals of isomeric 5- and 6-methyluracils was performed by quantum-chemical methods. Dimeric and trimeric associates of C-methyluracil molecules and their dimers with adenine were calculated in order to estimate the energies of intramolecular hydrogen bonds. Thymine in DNA is impossible to replace by 6-methyluracillargely by steric reasons.Translated from Zhurnal Obshchei Khimii, Vol. 74, No. 12, 2004, pp. 2038–2047.Original Russian Text Copyright © 2004 by Naumov, Tafipolskii, Reznik.This revised version was published online in April 2005 with a corrected cover date.     

Effect of the resonance of molecular vibrations on the ir spectra of hydrogen bonds

The effects are considered of the vibrations occurring with the group of atoms peripheral towards the hydrogen bond on the IR spectrum of the model hydrogen bond. It. is shown that the resonance of the v_OHv_CH stretching vibrations in a hydrogen bonded molecule result in the division of the v_OH band into two other bands having different polarizations. The resonance interaction leads to redistribution of the intensity and perturbs the regular Franck—Condon type envelope of the spectrum.