Hydrogen-bonded OH Research Articles

The significance of the 2' OH group and the influence of cations on the secondary structure of the RNA backbone.

In the IR spectra, the coupling of vibrations leads to band splitting and/or bands shifting in opposite directions which provides information on the mutual orientation of groupings. From such band shifts in the range 1800 to 1500 cm-1 one can draw conclusions on the double helix formation of polynucleotides. These band shifts are caused either by vibrational coupling of stretching vibrations within pairs of base residues or by coupling of stretching vibrations with the bending (scissor) vibration of the -NH2 groups; the latter is indicated by band shifts after deuterium substitution within the amino groups. Couplings of phosphate and 1 ibose vibrations in the range 1300 to 1000 cm-1 provide information on the secondary structure of the backbone. In order to obtain information of the structure of the RNA backbone, the IR spectra of poly(ribonucleotides) were studied in neutral media in which they were single-stranded. The shift due to coupling of the band of the 2'OD bending vibration and that of the antisymmetric stretching vibration of the ether group of the ribose residue proves that ribose residues of the backbone are cross-linked via hydrogen bonds. These are formed between the 2'OD or 2'OH groups, respectively, and the O atoms of the ether group of the neighboring ribose residues. This is the reason for the difference between DNA and RNA as regards the 2'OH group. The structure formation caused by these hydrogen bonds results in a stiffening of the RNA backbone. The tendency to form these hydrogen bonds increases in the order poly (U), poly(C), poly (A). This order of secondary structure stabilization is due to an interplay between the influences of (1) the 2'OH hydrogen bonds and (2) the base residues' stacking. Furthermore, the coupling of the antisymmetric stretching vibration of the greater than PO2- groups with a vibration involving the 2'OH group can result in a doublet structure of the band at about 1240 cm-1 if cations with strong fields are present. This probably shows that these cations can turn the greater than PO2-groups-which are usually turned outward at the backbone, as shown by construction of molecular models- towards the basic residues. Thus they cause stiff monohelices which are right-handed screws.

Lichen Substances VII. Identification of Orsellinate Derivatives from Lobaria linita

Lichen Substances VII. Identification of Orsellinate Derivatives from Lobaria linita

Chemical Stress-Relaxation and Other Studies on Styrene-Butadiene Rubber

Abstract The aging of styrene—butadiene rubber (SBR) was studied by three methods: stress relaxation, infrared spectroscopy, and swelling measurements, with the purpose of supplying information pertinent to understanding the basic mechanism of its aging. Stress-relaxation measurements in air and nitrogen at elevated temperatures indicated that atmospheric oxygen is the principal cause of chemical stress relaxation of SBR, rather than heat. Intermittent stress-relaxation measurements showed scission and crosslinking occurring simultaneously during network breakdown, and it was concluded that random scission in the backbone is indicated to take place in preference to scission in the crosslinks. Activation energies obtained from relaxation rates at several temperatures was 28 ± 0.5 kcal, comparable to literature values of 30 ± 2 kcals. The rates of carbonyl and hydroxyl group formation in SBR in air at various temperatures were determined by ir spectroscopy, both induction and maximum rates, νm, being measured. Activation energies calculated from these rates showed lower values compared to those obtained from stress-relaxation measurements. This may be due to the possibility that the processes being measured are not the same in each case. The three peaks appearing in the carbonyl region were ascribed to carboxyl, ketone, or aldehyde, and perester. The presence of these groups was confirmed by microanalytical methods. The absorption centered at 3450 cm−1 was attributed to hydrogen-bonded OH groups, i.e., alcohols and hydroperoxides. Positive chemical tests were obtained for hydroperoxide. The number of new network chains formed, νe, obtained from swelling measurements agreed well with those obtained from stress-relaxation measurements. It was found that the rate of the number of new network chains formed increased rapidly during the latter states of oxidation.

Physicochemical characterization of carbohydrate-solvent interactions by near-infrared spectroscopy

Near-infrared (n.i.r.) spectroscopy of carbohydrates in solvents of different proton-acceptor strengths shows splittings in the first-overtone, OH absorptions that are characteristic of a double minimum in the hydrogen-bond, potential-energy curve. On the basis of their specific, n.i.r. absorption maxima in methyl sulfoxide, N,N-dimethylformamide, and 19:1 HCONMe 2-water, α- D-glucose, β- D-glucose, and glycogen can be differentiated from each other. These carbohydrates also exhibit previously undefined absorption maxima that are assigned as nonsolvent, hydrogen-bonded OH groups, and the intensity of these bands decreases as the hydrogen-bonding strength of the solvent (Me 2SO☆19:1 HCONMe 2-water☆HCONMe 2) increases. A n.i.r. method for determination of the thermodynamic parameters of hydrogen bonding for cyclohexanol, α- D-glucose, and glycogen in hydrogen-bonding solvents has been designed on the basis of nonsolvent and solvent hydrogen-bonded species at various temperatures.

Hydrogen bond and proton transfer in complexes of trioctylamine with halogenoacetic acids

The infrared spectra of solutions containing trioctylamine and monohalogenoacetic acids have been investigated in the region 1500–1800 cm −1. Two forms of complexes 1: 1 acid-amine, the molecular complex with hydrogen bond OH N and the ionic pair, resulting from proton transfer from acid to amine, have been found to exist in equilibrium with each other.

OH Bending Vibrations and Hydrogen Bond in Crystalline p-Hydroxybenzaldehyde

OH Bending Vibrations and Hydrogen Bond in Crystalline <i>p</i>-Hydroxybenzaldehyde

IR spectra and structures of 3-hydroxyquinoline, 4-hydroxyisoquinoline, and their derivatives

From an examination of the frequencies, integral intensities, and half-widths of the absorption bands of the stretching vibrations of the hydroxyl groups in the IR spectra, it was concluded that 3-hydroxyquinoline, 4-hydroxyisoquinoline, and their derivatives exist in the phenol form in dilute CCl4 solutions. Strong intermolecular hydrogen bonds, which are destroyed on dilution, exist in 3-hydroxyquinoline, 4-methyl-3-hydroxyquinoline, 4-hydroxyisoquinoline, and 1-chloro-3-methyl-4-hydroxyquinoline at concentrations above 102 M in CCl4. From an examination of the values of halo derivatives of 3-hydroxyquinoline and 4-hydroxyisoquinoline, it was concluded that an intramolecular hydrogen bond of the OH...Hal type is present in these compounds. The shift in the OH band increases in the order Cl< Br< I. Weak bands of a free OH group that pertain to the s-trans form are observed in the spectrum. Strong intramolecular hydrogen bonds exist in 3-nitro-4-hydroxyisoquinoline and 3-piperidinomethyl-4-hydroxyisoquinoline.

Mechanical deformation of quartz

Abstract Quartz crystals obtained from three different sources have been strained in air a t atmospheric pressure, using compression rates of 10−3 to 10−5 sec−1. Of the three kinds of quartz tested, only the synthetic sample containing the highest amount of hydrogen-bonded OH groups (163 p.p.m.) was found to yield plastically, and then only at temperatures above 550°c. The deformation behaviour of this crystal changes over the different temperature ranges of < 700°c, 700°c-850°c, and >850°c respectively, coinciding with crystal phase chauges. Above 850°c, cristobalite and sometimes coesite phases appear and give rise to precipitation hardening. The orientation and temperature dependence of yield, and stress-strain relationships as a function of temperature are reported. Mechanisms to account for the ‘water-induced’ plasticity are also discussed.

Hydrogen Bond and19F NMR Chemical Shift Akisotropy in Apatite

Abstract The fluoroapatite minerals, Ca5-F(PO4)3 usually contain some hydroxyis, instead of fluorine. From infrared spectra it was concluded, that there are weak hydrogen bonds OH … F along apatite hexagonal axis1. In order to receive more detailed information about the character of F−and OH−bonds with the nearest atoms in apatites we studied the nuclear magnetic resonance (NMR) spectra of protons and fluorines in natural apatite single crystal, in which approximately 15% of fluorines is substituted by hydroxyis.

Infra-red study of the surface of rutile

An infra-red study of the surface of rutile has been carried out as a function of evacuation temperature (100–500°). Below 400° the surface was found to be composed of isolated and hydrogen bonded OH groups, molecular water being removed by evacuation at temperatures 200°. Above ca. 300° the hydrogen-bonded OH groups were progressively removed, the 450°-treated surface containing only isolated OH groups with a stretching frequency of 3740 cm–1. Absence of oxygen treatment of the surface after high-temperature evacuation markedly affects the OH region of the spectra. Rehydration experiments showed a strong interaction of the evacuated surface with water molecules but it has not been possible to decide conclusively whether surface OH groups are reformed on a 450°-treated surface.

CONTRIBUTION CONCERNING THE PROBLEM OF THE INTRAMOLECULAR HYDROGEN BONDS IN ORTHO HALOPHENOLS

The infrared spectra of the four ortho halophenols were measured in carbon tetrachloride solutions containing variable amounts of ether. The integrated intensities of the stretching band corresponding to the intermolecularly hydrogen-bonded OH groups were determined and plotted against ether concentration. From the curves obtained in this manner it was possible to deduce the relative strengths of the intramolecular hydrogen bonds which are present in these molecules. They are, in order of increasing strength: F &lt; I &lt; Br &lt; Cl. This result is compared to others, published in the literature, obtained using alternative methods.

Studies on N-substituted nortropane derivatives. VI. Intramolecular hydrogen bonds of 8-(2-hydroxyethyl)-3-nortropanone and related compounds.

The infrared spectral behaviors of 8-(2-hydroxyethyl)-3-nortropanone and related compounds in dilute nonpolar solution were examined. From the values of C=O and OH stretching frequencies it was concluded that all these compounds form intramolecular hydrogen bond of a type OH····N. The data obtained also agreed with those of OH····N hydrogen bond appearing in recent literature.

Nature of the Hydrogen Bond. III. The Measurement of the Infrared Absorption Intensities of Free and Hydrogen-Bonded OH Bands. Theory of the Increase of the Intensity Due to the Hydrogen Bond

The integrated intensities of the infrared OH bands of various compounds have been measured for the free and the hydrogen-bonded states. It is found that the integrated intensity of either the free or the hydrogen-bonded OH band increases as the frequency decreases. It is concluded that the main factor increasing the integrated intensity of the intermolecularly hydrogen-bonded OH bands is the charge transfer through the hydrogen bond. The sign of the change of the dipole moment of the free phenol with the OH distance is discussed. An explanation is given for the weakness of the OH bands of the chelate compounds.

Nature of the Hydrogen Bond. II. The Effect of Hydrogen Bonding and Other Solute-Solvent Interactions upon the Shape and Intensity of the Infrared OH Band of Phenol

The hydrogen-bonded OH bands of phenol are studied in ternary systems, each of which is composed of phenol, a proton acceptor, and a solvent. The acceptors used are ethyl ether, ethyl acetate, acetonitrile, and hexamethylene tetramine. It is confirmed that the frequency, shape, and molecular extinction coefficient of the band are not changed by the concentration of the acceptor, as far as the latter is smaller than ca 2 mole/liter. The spectra are slightly modified by further increase of the concentration of the acceptor. These modifications are in all cases far smaller than the modification due to the hydrogen bonding, and the peak intensities remain nearly constant. The equilibrium constants for the formation of the hydrogen bond are determined for all acceptors and the heat of formation is determined for the case of hexamethylene tetramine. It is found that the decrease of frequencies of the hydrogen-bonded OH bands is not strictly parallel to the increase of equilibrium constants.