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1.
FTIR spectra of polycrystalline samples of cytidine, pure and containing a small quantity of N(O)H or N(O)D groups (<20%), were measured in KBr pellets from 4000 to 400 cm(-1) at temperatures from 300 to 20K. For the first time the bands of the narrow isotopically decoupled proton stretching vibration mode (nu(1)) of OH- and NH- groups were found; their number corresponds to the number of H-bonds in crystal according to structural data. The FTIR spectra at low temperature in the out-of-plane bending nu(4) proton mode range (lower than 1000 cm(-1)) of N(O)H groups revealed narrow bands, which correspond to nu(1) bands together with several "extra" bands, which are influenced by the isotopic exchange and (or) cooling. All of them have their counterparts in the N(O)D-substance spectrum with an isotopic frequency ratio of 1.30-1.40. The "extra" bands are assigned to the H-bound OH and NH protons, which are disordered and cannot be seen with X-ray crystal structure analysis. The peak positions of both mode bands (expressed as the red shift of nu(1) or blue shift of nu(4) modes relatively free molecules) were used for the estimation of the energy of different H-bonds using previously established empirical correlations between spectral and thermodynamic parameters of hydrogen bonds. The correlation of the red shift and H-bond length is also confirmed for all five H-bonds of cytidine.  相似文献   

2.
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.  相似文献   

3.
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.  相似文献   

4.
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.  相似文献   

5.
FTIR spectra of solid samples of co-crystallized adenine and uracil were measured at 10K in the range below 1000cm(-1). New bands ascribable to the N3H (uracil) and NH(2) (adenine) out of plane vibrations, which disappear upon D-exchange, were revealed in comparison with the spectra of pure polycrystalline adenine and uracil obtained in the same conditions. The observed changes relate to the same groups that establish the H-bonds in base pairs of naturally occurring nucleic acids, despite the presence of an extra proton donor NH-group in both molecules. The well-established empirical correlation between the out of plane NH vibrational frequencies and H-bond energies was successfully applied for estimation of the latter in the mixed crystal.  相似文献   

6.
The structure of dl-serine.HCl was studied by three complementary techniques. Experimental Fourier transform infrared (FT-IR) spectra of pure NH/OH polycrystalline dl-serine.HCl [HO-CH2-CH(NH3+)-COOH.Cl(-)] and the respective deuterated derivatives [ND/ODAlcohol/Acid (<10% and ca. 60% D)] were recorded in the region 4000-400 cm(-1) in the temperature range 300-10 K and interpreted. The assignments were confirmed by comparison with the vibrational spectra of crystalline dl- and l-serine zwitterions [HO-CH 2-CH(NH3+)-COO(-)]. Further insight into the structure of the title compound was provided by theoretical DFT(B3LYP)/6-311++G(d,p) calculations of the infrared spectra and energies of 13 different conformers. Potential energy distributions resulting from normal co-ordinate analysis were calculated for the most stable conformer ( I) in its hydrogenated and deuterated modification. Frequencies of several vibrational modes were used in the estimation of enthalpies of individual H-bonds present in the crystal, using empirical correlations between enthalpy and the frequency shift that occurs as a result of the establishment of the H-bonds. X-ray crystallography data for dl-serine.HCl were recorded for the first time and, together with the experimental vibrational spectra and the theoretical calculations, allowed a detailed characterization of its molecular structure.  相似文献   

7.
Effect of water on the formamide-intercalation of kaolinite   总被引:12,自引:0,他引:12  
The molecular structures of low defect kaolinite completely intercalated with formamide and formamide-water mixtures have been determined using a combination of X-ray diffraction, thermoanalytical techniques, DRIFT and Raman spectroscopy. Expansion of the kaolinite to 10.09 A was observed with subtle differences whether the kaolinite was expanded with formamide or formamide-water mixtures. Thermal analysis showed that greater amounts of formamide could be intercalated into the kaolinite in the presence of water. New infrared bands were observed for the formamide intercalated kaolinites at 3648, 3630 and 3606 cm(-1). These bands are attributed to the hydroxyl stretching frequencies of the inner surface hydroxyls hydrogen bonded to formamide with water, formamide and interlamellar water. Bands were observed at similar positions in the Raman spectrum. At liquid nitrogen temperature, the 3630 cm(-1) Raman band separated into two bands at 3633 and 3625 cm(-1). DRIFT spectra showed the hydroxyl deformation mode at 905 cm(-1). Changes in the molecular structure of the formamide are observed through both the NH stretching vibrations and the amide 1 and 2 bands. Upon intercalation of kaolinite with formamide, bands are observed at 3460, 3344, 3248 and 3167 cm(-1) attributed to the NH stretching vibration of the NH involved with hydrogen bonded to the oxygens of the kaolinite siloxane surface. In the DRIFT spectra of the formamide intercalated kaolinites bands are observed at 1700 and 1671 cm(-1) and are attributed to the amide 1 and amide 2 vibrations.  相似文献   

8.
Infrared photodissociation action spectra of protonated ammonia cluster ions, NH(4) (+)(NH(3))(n) (n=5-8), were measured in the range of 1020-1210 cm(-1) by using a tunable infrared free electron laser. Analyses by the density functional theory (DFT) show that the spectral features observed can be assigned to the nu(2) vibrational mode of the NH(3) molecules in NH(4) (+)(NH(3))(n). Size dependence of the spectra supports structural models obtained by the DFT calculations, in which the NH(4) (+) ion is solvated by the four nearest-neighbor NH(3) molecules. For NH(4) (+)(NH(3))(5), the spectrum between 1000 and 1700 cm(-1) was measured. The nu(4) bands of the NH(3) molecules and the NH(4) (+) ion were found in the range of 1420-1700 cm(-1).  相似文献   

9.
The conformational preferences and infrared and ultraviolet spectral signatures of two model beta-peptides, Ac-beta3-hPhe-beta3-hAla-NHMe (1) and Ac-beta3-hAla-beta3-hPhe-NHMe (2), have been explored under jet-cooled, isolated-molecule conditions. The mass-resolved, resonant two-photon ionization spectra of the two molecules were recorded in the region of the S0-S1 origin of the phenyl substituents (37,200-37,800 cm(-1)). UV-UV hole-burning spectroscopy was used to determine the ultraviolet spectral signatures of five conformational isomers of both 1 and 2. Transitions due to two conformers (labeled A and B) dominate the R2PI spectra of each molecule, while the other three are minor conformers (C-E) with transitions a factor of 3-5 smaller. Resonant ion-dip infrared spectroscopy was used to obtain single-conformation infrared spectra in the 3300-3700 cm(-1) region. The infrared spectra showed patterns of NH stretch transitions characteristic of the number and type of intramolecular H-bonds present in the beta-peptide backbone. For comparison with experiment, full optimizations of low-lying minima of both molecules were carried out at DFT B3LYP/6-31+G*, followed by single point MP2/6-31+G* and selected MP2/aug-cc-pVDZ calculations at the DFT optimized geometries. Calculated harmonic vibrational frequencies and infrared intensities for the amide NH stretch vibrations were used to determine the beta-peptide backbone structures for nine of the ten observed conformers. Conformers 1B, 1D, and 2A were assigned to double ring structures containing two C6 H-bonded rings (C6a/C6a), conformers 1A and 2B are C10 single H-bonded rings, conformers 1C and 2D are double ring structures composed of two C8 H-bonded rings (C8/C8), and conformers 1E and 2E are double ring/double acceptor structures in which two NH groups H-bond to the same C=O group, thereby weakening both H-bonds. Both 1E and 2E are tentatively assigned to C6/C8 double ring/double acceptor structures, although C8/C12 structures cannot be ruled out unequivocally. Finally, no firm conformational assignment has been made for conformer 2C whose unusual infrared spectrum contains one very strong H-bond with NH stretch frequency at 3309 cm(-1), a second H-bonded NH stretch fundamental of more typical value (3399 cm(-1)), and a third fundamental at 3440 cm(-1), below that typical of a branched-chain free NH. The single conformation spectra provide characteristic wavenumber ranges for the amide NH stretch fundamentals ascribed to C6 (3378-3415 cm(-1)), C8 (3339-3369 cm(-1)), and C10 (3381-3390 cm(-1)) H-bonded rings.  相似文献   

10.
《Vibrational Spectroscopy》2007,43(2):395-404
The IR spectra (4000–400 cm−1) of neat and isotopically substituted (ND/OD  10% D and ≅30% D) polycrystalline l-serine (α-amino-β-hydroxypropionic acid; HO–CH2–CH(NH3)+–COO) were recorded in the temperature range 300–10 K and assigned. The isotopic-doping/low-temperature methodology, which allows for decoupling of individual proton vibrational modes from the crystal bulk vibrations, was used for estimating the lengths and energies of the different H-bonds present in l-serine crystal. To this end, the frequency shifts observed in both the NH/OH stretching and out-of-plane bending spectral regions (relatively to reference values for these vibrations in non-hydrogen-bonded l-serine molecules) were used, together with previously developed empirical correlations between these spectral parameters and the H-bond properties. In addition, the room-temperature Raman spectrum (4000–150 cm−1) of a single crystal of neat l-serine was also recorded and interpreted. A systematic comparison was made between the spectroscopic data obtained currently for l-serine and previously for dl-serine, revealing that the vibrational spectra of the two crystals reflect well the different characteristics of their hydrogen-bond networks, and also correlate accurately with the different susceptibility of the two crystals to pressure-induced strain.  相似文献   

11.
The Raman and IR spectra of NH3(CH2)5NH3SnCl6 have been measured at ambient temperature. It is shown that the cations in the compound assume a symmetry lower than C2v. Combination bands observed in the 2100-1800 cm(-1) region in the IR spectrum of NH3(CH2)5NH3SnCl6 indicate that the compound contains the C-NH3 grouping, the bands are discussed and their assignment are suggested. No evidence of existence of hydrogen bonding is found from the infrared spectrum in the region of 2800-3200 cm(-1); anions and cations are found not connected by hydrogen bonding and are therfore isolated. The Raman spectrum of anions can be interpreted in terms of disordered groups, not clearly showing the predicted splitting of bands.  相似文献   

12.
The NIR spectra of reichenbachite, scholzite and parascholzite have been studied at 298 K. The spectra of the minerals are different, in line with composition and crystal structural variations. Cation substitution effects are significant in their electronic spectra and three distinctly different electronic transition bands are observed in the near-infrared spectra at high wavenumbers in the 12,000-7600 cm(-1) spectral region. Reichenbachite electronic spectrum is characterised by Cu(II) transition bands at 9755 and 7520 cm(-1). A broad spectral feature observed for ferrous ion in the 12,000-9000 cm(-1) region both in scholzite and parascholzite. Some what similarities in the vibrational spectra of the three phosphate minerals are observed particularly in the OH stretching region. The observation of strong band at 5090 cm(-1) indicates strong hydrogen bonding in the structure of the dimorphs, scholzite and parascholzite. The three phosphates exhibit overlapping bands in the 4800-4000 cm(-1) region resulting from the combinations of vibrational modes of (PO(4))(3-) units.  相似文献   

13.
The NH-He van der Waals complex was characterized via laser excitation of bands associated with the NH A (3)Pi-X (3)Sigma(-) transition. It was demonstrated that the ground state supports a bound level with a rotational constant of B"=0.334(2) cm(-1). These results are in agreement with the predictions of recent high-level theoretical calculations. Spin-orbit predissociation of the excited complex was observed, and the spectra yield insights regarding the NH(A)+He potential energy surfaces.  相似文献   

14.
The Raman spectra at 77 K of the hydroxyl stretching of kaolinite were obtained along the three axes perpendicular to the crystal faces. Raman bands were observed at 3616, 3658 and 3677 cm(-1) together with a distinct band observed at 3691 cm(-1) and a broad profile between 3695 and 3715 cm(-1). The band at 3616 cm(-1) is assigned to the inner hydroxyl. The bands at 3658 and 3677 cm(-1) are attributed to the out-of-phase vibrations of the inner surface hydroxyls. The Raman spectra of the in-phase vibrations of the inner-surface hydroxyl-stretching region are described in terms of transverse and longitudinal optic splitting. The band at 3691 cm(-1) is assigned to the transverse optic and the broad profile to the longitudinal optic mode. This splitting remained even at liquid nitrogen temperature. The transverse optic vibration may be curve resolved into two or three bands, which are attributed to different types of hydroxyl groups in the kaolinite.  相似文献   

15.
The two water gas OH stretch vibrations that absorb in the infrared (IR) near 3700 cm(-1) are redshifted to near 3300 cm(-1) upon liquefaction. The bathochromic shift is due to the formation of four H-bonds: two are from the labile hydrogen atoms to neighbors and two are received from neighbors by the oxygen free electron pairs. Therefore, the water oxygen atom is surrounded by four hydrogen atoms, two of these make covalent bonds that make H-bonds and two are oxygen H-bonded. However, these permute at rate in the ps range. When the water molecules are isolated in acetonitrile (MeCN) or acetone (Me(2)CO), only the labile hydrogen atoms make H-bonds with the solvent. The bathochromic shift of the OH stretch bands is then almost 130 cm(-1) with, however, the asymmetric (ν(3)) and symmetric (ν(1)) stretch bands maintained. When more water is added to the solutions, the oxygen lone doublets make H-bonds with the available labile hydrogen atoms from neighboring water molecules. With one bond accepted, the bathochromic shift is further displaced by almost 170 cm(-1). When the second oxygen doublet is filled, another bathochromic shift by almost 100 cm(-1) is observed. The total bathochromic shift is near 400 cm(-1) with a full width at half height of near 400 cm(1). This is the case of pure liquid water. Notwithstanding the shift and the band broadness, the ν(3) and ν(1) band individualities are maintained with, however, added satellite companions that come from the far IR (FIR) absorption. These added to the fundamental bands are responsible for the band broadness and almost featureless shape of the massive OH stretch absorption of liquid water. Comparison of light and heavy water mixture spectra indicates that the OH and OD stretch regions show five different configurations: OH(4); OH(3)D; OH(2)D(2); OHD(3); and OD(4) [J. Chem. Phys. 116, 4626 (2002)]. The comparison of the OH bands of OH(4) with that of OHD(3) indicates that the main component in OHD(3) is ν(OH), whereas in OH(4) two main components are present: ν(3) and ν(1). Similar results are obtained for the OD bands of OD(4) and ODH(3). These results indicate that the C(2) (v) symmetry of H(2)O and D(2)O is preserved in the liquid and aqueous solutions whereas C(s) is that of HDO.  相似文献   

16.
The IR spectra for various sizes of pyrrole clusters were measured in the NH stretching vibration region by infrared cavity ringdown spectroscopy. The hydrogen-bonded structures and normal modes of the pyrrole clusters were analyzed by a density functional theory calculation of the B3LYP/6-311+G(d,p) level. Two types of pulsed nozzles, a slit and a large pinhole, were used to generate different cluster size distributions in a supersonic jet. A rotational contour analysis of the NH stretching vibration for the monomer revealed that the slit nozzle provides a warmer jet condition than the pinhole one. The IR spectra, measured under the warmer condition, showed the intense bands at 3444, 3392, and 3382 cm(-1), which were assigned to hydrogen-bonded NH stretching vibrations due to the dimer, the trimer, and the tetramer, respectively. On the other hand, the IR spectra measured under a lower temperature condition by a pinhole nozzle showed a broad absorption feature in addition to sharp bands. This broad absorption was reproduced by the sum of two Gaussians peaks at 3400 and 3372 cm(-1) with widths of 30 and 50 cm(-1) (FWHM), respectively. Compared with the spectra of the condensed phase, two bands at 3400 and 3372 cm(-1) were assigned to hydrogen-bonded NH stretching vibrations of larger clusters having liquid-like and solid-like structures, respectively.  相似文献   

17.
Infrared (IR) spectra have been measured for a liquid crystal (LC) consisting of one trans-butene diacid (BD) molecule as a proton donor and two 4-(2,3,4-tridecyloxybenzoyloxy)-4'-stilbazoles (DBS) molecules as a proton acceptor (DBS:BD:DBS) linked together with each other by inter-molecular hydrogen bonds over a temperature range from 20 to 120 degrees C to explore its phase transition and heat-induced structural variations. The temperature-dependent IR spectra have shown that the inter-molecular hydrogen bonds are stable in the liquid crystalline phase but become slightly decoupled with temperature increasing. Two kinds of two-dimensional (2D) correlation spectroscopy, variable-variable (VV) and sample-sample (SS) 2D spectroscopy, have been employed to analyze the observed temperature-dependent spectral variations more efficiently. The SS 2D correlation analysis in the spectral range of 2700-1800 cm(-1) has demonstrated that a change in hydrogen bonds in the LC starts from 40 degrees C, which is not clarified by differential scanning calorimetry (DSC) and conventional IR and Raman spectroscopic analyses. On the other hand, the phase transition of LC revealed by SS 2D spectroscopy in the specific spectral regions of 1750-1650 and 3000-2700 cm(-1) is in a good agreement with that revealed by DSC for the heating process. The VV 2D correlation spectroscopy analysis has provided information about the structural variations of inter-molecular hydrogen bonds. The different species of hydrogen-bonded and free -COOH and -COO- groups in the LC have been clarified by the VV 2D correlation analysis. It has also elucidated the specific order of the temperature-induced structural changes in the intra- and inter-molecular hydrogen bonds concerning with the -COOH and/or -COO- groups in the LC.  相似文献   

18.
The infrared (IR) and Raman spectra of 3,5-dimethylpyrazole have been recorded in the vapor, liquid (melt and solution) and solid states. Two deuterated derivatives, C5H7N-ND and C5D7N-NH, were also studied in solid state and in solutions. Instrumental resolution was relatively low, 2.0 cm(-1) in the IR and approximately 2.7 cm(-1) in the Raman spectra. The solids are made of cyclic hydrogen-bonded trimers. These trimers, present also in chloroform and acetone solutions, give rise to characteristic high absorption IR spectra in the 3200-2500 cm(-1) region, related to Fermi resonance involving nu(NH) vibrations. Bands from trimers are not present in water solutions but these solutions show spectral features similar in several ways to those of the trimer, attributable to solvent-bonded complexes. Evidence of H-bonding interactions with the other solvents is also visible in the high-frequency region. The two very intense bands in the Raman spectra of the solids appearing at 115 and 82 cm(-1) in the parent compound are also connected with a trimer formation. To interpret the experimental data, ab initio computations of the harmonic vibrational frequencies and IR and Raman intensities were carried out using the Gaussian 94 program package after full optimization at the RHF/6-31G* level for the three monomeric compounds as well as for three models of the trimer, with C3h, C3 and C1 symmetry. The combined use of experiments and computations allow a firm assignment of most of the observed bands for all the systems. In general, the agreement between theory and experiment is very good, with the exception of the IR and Raman intensities of some transitions. Particularly noticeable is the failure of the theoretical calculation in accounting for the high intensity of the Raman bands of the solid about 115 and 82 cm(-1).  相似文献   

19.
The X-ray crystal structure of 1H-pyrazole-3-(N-tert-butyl)-carboxamide was determined. In the solid state, the 13C and 15N CP/MAS NMR spectra correspond to this tautomer. In solution, both tautomers are present in a ratio that depends on the temperature (at 293 K, 90% 3-substituted/10% 5-substituted). Some unusual 1H, 1H couplings involving the NH proton were observed. DFT (GIAO) calculations were carried out.  相似文献   

20.
The Raman spectra at 300 and 77 K of beryl, columbite-tantalite and topaz single crystals from pegmatites in the Iveland-Evje area are described in detail. The beryl is shown to contain mainly water type I and less of type II in its channels, while CO2 is only a very minor channel constituent. Cooling to 77 K results in minor shifts towards higher wavenumbers for most bands. The Si-O vibrations at 1009 and 1066 cm(-1) show a doubling to four bands at 1015, 1072, 1087 and 1149 cm(-1) due to structural rearrangements in the hexameric rings forming the channels in the beryl crystal structure. In addition a new band becomes visible around 1155 cm(-1). The tantalite could not be analysed in detail due to strong fluorescence. The Raman spectrum of the yellow topaz from Sol?s is comparable to that of the colourless topaz from Topaz Mountain, Thomas Range, Utah. Upon cooling to 77 K, two OH-stretching bands become visible around 3644 and 3655 cm(-1), which were not observed at room temperature.  相似文献   

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