Intensities of DNA ion-phosphate modes in the low-frequency Raman spectra

The Raman intensities of counterion vibrations with respect to the phosphate groups of the double-helix backbone (ion-phosphate modes) in the low-frequency spectra (< 200 cm^-1) of B -DNA with different alkali metal counterions have been calculated using the model for DNA conformational vibrations and the valence-optic approach. The results have showed that the spectra of DNA with heavy counterions ( Rb⁺ and Cs⁺ differ from the spectra of DNA with light counterions ( Na⁺ and K⁺ . The calculated spectra of DNA with heavy counterions are characterized by intensive modes of ion-phosphate vibrations that form one united band near 115cm^-1. Ion-phosphate modes in the spectra of DNA with light counterions are characterized by higher frequencies (near 180cm^-1) and much lower intensity. Our calculations explain why the modes of ion-phosphate vibrations are observed in Cs-DNA spectra rather than in Na-DNA. The determined sensitivity of the intensities of DNA low-frequency spectra to the counterion type proves the existence of the ion-phosphate modes.     

Raman spectra of lithium hydroxide single crystals

First order Raman frequencies, linewidths, intensities and assignments to the symmetry species of all modes predicted by group theory at 20°C and at 78 K are reported for the first time. Assignments of the fundamental frequencies to stretching vibrations or librations of the OH^? ions, internal vibrations of Li⁺ ions of the same layer or translational modes of the Li⁺ and OH^? layers are derived from factor group analysis and correlation methods. They correspond to the constructions of unit cell modes by Wickersheim[2].     

The fluctuation hypothesis of hydrogen bonding

To describe the distortion perturbations of the water molecules in solutions the quantum-mechanical method of partial oscillators has been developed. This method allows one to separate in a simple manner two types of influences on vibrations of OH oscillators, viz. the intermolecular perturbations resulting in the different strengths of hydrogen bonds and intramolecular coupling between stretching vibrations. Here the coupling is treated quite strictly, whereas the intermolecular perturbations are introduced phenomenologically. The calculation of the distribution of distortions among molecules in liquid H₂O and D₂O induced by non-equivalency of the two hydrogen bonds of the water molecule has been made on the basis of the method developed, and the parameters of the mean statistical molecule have been found from the experimental spectrum of HOD. The depolarization ratios of vibrations in Raman spectra of the mean statistical molecules H₂O and D₂O have been computed as an illustration of the possibilities of the proposed calculation method. All the estimates show that the stretching oscillators of H₂O and D₂O molecules are significantly coupled in spite of the great distortion of the symmetry of water molecules in the liquid state.     

Infrared spectra of catalysts and adsorbed molecules

The infrared absorption spectra of water adsorbed on Al₂O₃ and NiO-Al₂O₃ catalysts have been studied in the range 4000–1200 cm^–1. For all the catalysts, broad bands are observed at 3400 and 1640 cm^–1, characteristic of the stretching and bending vibrations of the OH groups in liquid water. The bands observed in the spectrum of alumina prepared from suspension in isopropyl alcohol are produced by water molecules and isopropyl alcohol molecules absorbed on the catalyst surface. The influence of treatment with heavy water and thermal treatment on the position of the infrared absorption bands in the spectrum of alumina is discussed.     

HXD中XH拉伸振动的振动跃迁偶极矩方向的理论研究

本文利用局域模研究了“重轻”体系简单分子XH伸缩振动的实验振动光谱. 键偶极方法进一步为实验光谱分析提供了帮助(假设XH伸缩振动的跃迁偶极矩沿着XH键方向排列). 通过局域模和多维简正模对HOD,HND^-,HCD,HSD,HPD^-和HSiD的XH伸缩振动的理论计算, XH伸缩振动的局部1D图片可以用于分析跃迁偶极矩倾斜角度. 在HOD分子中,OH伸缩振动的跃迁偶极矩远离OH键并且向远离OD键的方向倾斜;在HSD,HND^-,HPD^-,HCD和HSiD分子中的XH伸缩振动远离OH键,但朝向OD键,表明键偶极近似法不能很好地适用于“重轻体系”分子,重原子X可以影响跃迁偶极矩方向. 利用分子中原子理论分析了偶极矩的变化.     

Infrared intensities of the fundamental vibrations of liquid H2O

Infrared absorption intensities of the fundamental vibrations of liquid H₂O have been obtained by measuring transmissions at two sample thicknesses (about 9 and 0.9 μ). The effect of multiple internal reflections on the observed absorptions is examined in terms of thin-film optics. It is shown that this simple method yields precise absorption intensities, without corrections for the effects of multiple internal reflections. The resulting intensities are 89.9 × 10³ cm/mmol and 5.91 × 10³ cm/mmol for the stretching and bending vibrations, respectively. The latter value was estimated after eliminating the absorption of intermolecular vibrations from the 1400–2400 cm^-1 region by means of computer simulation.     

A study of the molecular structure of DL-serine with the method of low-temperature IR spectroscopy

Use of low-temperature IR spectroscopy in studies of compounds with a developed system of hydrogen bonds such as DL-serine revealed a complete set of vibrational frequencies. The region of manifestation of stretching vibrations of OH groups involved in the formation of strong hydrogen bonds was found. It is shown experimentally that in a crystal some of the molecules of SL-serine exist in the nonionized form. On the basis of analysis of experimental data, frequency ranges of stretching deformation and torsional vibrations of NH ₃ ⁺ , COO⁻, and OH groups were determined more accurately. It is found that in the crystals there exist molecules of DL-serine with different spatial orientation of NH ₃ ⁺ COO⁻, and COH groups. It is shown that conformational diversity of molecular structures is also preserved at T=18 K. Translated from Zhurnal Prikladnoi Spektroskopii, Vol. 65, No. 6, pp. 864–868, November–December, 1998.     

The numerical determination of dipole hyperpolarizabilities

The paper is devoted to calculations of the contour shapes in the infra-red and Raman spectra of the 1 : 1 and 1 : 2 type complexes of ordinary and heavy water with two organic bases, dioxane and dimethyl sulphoxide, by means of a computer. The calculations have been made using the mathematical formalism developed in the previous papers of this series which takes into account the coupling between two stretching vibrations of the water molecule and the overtone of its bending vibration for a set of the liquid molecules variously perturbed by non-equal H-bonds. The basic parameters of the model are obtained from the spectra of HOD molecules involved in the same complex as the one considered, and from empirical correlations discussed in the previous papers. Starting from a set of parameters determined in this manner we calculate three spectra simultaneously for each of the above-mentioned complexes, namely the infra-red spectrum and the isotropic and anisotropic components of the Raman spectrum. Every spectrum is composed of three contours belonging to the overtone of the bending vibrations, and also to the in-phase and out-of-phase stretching vibrations respectively. These contours are asymmetrical and have different half-widths, maximum frequencies and intensities in all three types of spectra. The model demonstrates the inadequacy of the widespread interpretation of such spectra in terms of the symmetric and antisymmetric vibrations of undistorted water molecules characterized by the symmetry C _2v . Good agreement between calculated and experimental spectra is considered to provide strong evidence of the fluctuation model.     

Fourier Transform Vibrational Spectra of Magnesium Hydrogenphosphate Trihydrate. I. The O-H Stretching Region∗

Abstract

The Fourier transform (FT) infrared and Raman spectra of newberyite, MgHPH₄ - 3H₂O are studied in the region where the stretching vibrations of the water molecules (protiated and deuterated) and the O-H/O-D stretches of the hydrogenphosphate anions are expected to appear. The O-H stretching vibrations give rise to a complex feature known as the A,B,C trio. Since neither of the maxima found below 3000 cm^?1 represents a true band arising from a given fundamental, it is pointless to correlate their frequencies with the observed O…O distances. In the water stretching region, the two bands with highest frequencies undoubtedly correspond to the anti symmetric and symmetric stretch of one type of the water molecules. The stretching vibrations of one of the remaining two types of H₂O molecules are clearly uncoupled and the O-H oscillator involved in the weaker hydrogen bond is responsible for a band at 3376 cm^?1 whereas the rest of the water stretchings are apparently overlapped yielding the complex band below 3320 cm^?1. Thus the situation is again complicated and the correlations between the frequencies and the O_w…O distances are inappropriate. The two bands at highest frequencies (3522 and 3483 cm^?1 at RT) exhibit a positive temperature coefficient.

     

Calculation of conformations and vibrational spectra of a monomeric fragment of the 2,6-carboxymethyl cellulose molecule

A theoretical conformational analysis has been carried out for the side substituents of a fragment of the molecule for 2,6-carboxymethyl cellulose (a water-soluble cellulose ether), and the frequencies and the potential energy distribution of the normal vibrations have been calculated for the most stable conformers of the ether groups of this fragment in the approximation of the molecular mechanics method. It has been shown that the most stable conformers are those that have the conformations gg, t, g⁻, g⁻, g⁻-for the groups of atoms on the bonds C5-C6, C6-O6, C13-O6, C10-C13, C10-O9 and the conformations g⁺g⁻, g⁺, g⁻, g⁻; g⁺g⁻, g⁻, g⁻, g⁻; g⁺g⁻, g⁻, g⁺, t for the groups of atoms on the bonds C2-O2, C11-O2, C7-C11, C7-O8. Comparative analysis of the calculated frequencies and the potential energy distribution of the normal vibrations for 13 of the most stable conformers showed, as in the case of the 2,6-hydroxyethyl cellulose molecule, that the frequencies and modes of the normal vibrations are highly sensitive to conformational transitions in the analyzed spectral region (800–1500 cm⁻¹). The characteristic patterns for the change in the frequencies and modes of the normal vibrations have been established in connection with conformational transitions within both side substituents. The observed conformational lability of the bulky substituents in the cellulose ether molecules and its manifestations in the vibrational spectrum provide a basis for hypothesizing that one of the major mechanisms for the process of their thermal gelation in aqueous solutions is conformational transitions within these substituents. __________ Translated from Zhurnal Prikladnoi Spektroskopii, Vol. 74, No. 1, pp. 5–15, January–February, 2007.     

Raman spectra of various polymorphs of isotactic polypropylene

The Raman spectra of the α, γ, and smectic modifications of isotactic polypropylene (PP) are studied. The most significant spectral differences are observed in the frequency range around 2960 cm⁻¹ for the spectral doublet assigned to the asymmetric stretching vibrations of the CH₃ groups and in the frequency range around 800 cm⁻¹, which is used for analysis of the phase composition of isotactic PP. It is demonstrated that the peak positions and relative intensities of the doublet assigned to the asymmetric stretching vibrations of the CH₃ groups can be used to identify the polymorph modifications of isotactic PP.     

Raman spectroscopic study of the hydrogen‐arsenate mineral pharmacolite Ca(AsO3OH)·2H2O—implications for aquifer and sediment remediation

The removal of arsenate anions from aqueous media, sediments and wasted soils is of environmental significance. The reaction of gypsum with the arsenate anion results in pharmacolite mineral formation, together with related minerals. Raman and infrared (IR) spectroscopy have been used to study the mineral pharmacolite Ca(AsO₃OH)· 2H₂O. The mineral is characterised by an intense Raman band at 865 cm⁻¹ assigned to the ν₁ (AsO₃)²⁻ symmetric stretching mode. The equivalent IR band is found at 864 cm⁻¹. The low‐intensity Raman bands in the range from 844 to 886 cm⁻¹ provide evidence for ν₃ (AsO₃) antisymmetric stretching vibrations. A series of overlapping bands in the 300‐450 cm⁻¹ region are attributed to ν₂ and ν₄ (AsO₃) bending modes. Prominent Raman bands at around 3187 cm⁻¹ are assigned to the OH stretching vibrations of hydrogen‐bonded water molecules and the two sharp bands at 3425 and 3526 cm⁻¹ to the OH stretching vibrations of only weakly hydrogen‐bonded hydroxyls in (AsO₃OH)²⁻ units. Copyright © 2009 John Wiley & Sons, Ltd.     

Vibrational spectra of Na4P2O7·10H2O

The IR and Raman spectra are measured and analysed for sodium pyrophosphate decahydrate. The spectra are interpreted on the basis of P₂O ₇ ⁴⁻ ion and water vibrations. The observed results fit with the features predicted for the factor goup model. The appearance of two sets of frequencies in the stretching and bending regions of water suggests the existence of two kinds of water molecules in the crystal. This is confirmed by deuterium substitution.     

Understanding the influence of external perturbation on aziridinium ion formation

A density functional theory study is performed to understand the effect of discrete water molecules during Az⁺ ion formation in nitrogen mustards. A comparative study in gas phase, and implicit and explicit solvation models of three drug molecules (mustine, chlorambucil and melphalan) is reported. Noteworthy changes in the structure and C–N stretching frequencies of the transition states have been observed in the presence of explicit water molecules. Presence of explicit water molecules reduces the positive charge around the tricyclic Az⁺ ring, and hence stabilising it. Both activation energy and rate constants are seen to be significantly affected in the presence of discrete water molecules.     

The values of <L 2> in diatomic molecules: implications for adiabatic and molecular fine structure calculations

The possibility of using calculated ab initio values of <L ²> to assess convergence of second order sums in molecular fine structure parameters is investigated for several diatomic molecules with ³Σ^- ground states. Values of <L ²> for a number of molecules in ¹Σ⁺ states have also been obtained. The calculated values of <L ²> are in general very large, especially for non-hydride molecules, and they show a marked dependence on the internuclear separation R. The implications of these large values of <L ²> are discussed both for the calculation of molecular fine structure parameters (where the convergence criterion is seen to be of little use) and for the adiabatic corrections often needed in discussing isotopic effects. In this latter context, ab initio values of have also been calculated and found to be an important term in adiabatic corrections, contrary to some assertions in the literature. The implications of the strong dependence of <L ²> on the internuclear separation are also discussed.     

The bonding of water molecules to platinum surfaces

Using high resolution electron energy loss spectroscopy in ultra-high vacuum we have studied the vibrational spectrum of submonolayer and multilayer quantities of water adsorbed on platinum (100) surfaces. For adsorbed multilayers the spectrum resembles the spectrum of ice I. For submonolayer quantities of H₂O we find three different OH stretching vibrations, 2850, 3380, and 3670 cm^?1. The highest frequency is attributed to free OH groups. The vibration around 3380 cm^?1 indicates H bonding between oxygen atoms. It is therefore concluded that the water molecules cluster even at low coverage. The lowest OH stretching frequency is attributed to H bonding to platinum. We find also evidence for additional oxygen lone pair orbital bonding to the surface which disappears however when the first monolayer is completed. The relation to currently considered models in electrochemistry of aqueous solutions is discussed.     

Infrared absorption of aligned H−Na+H− complexes in Kcl crystals

The localized vibrations of a complex in KCl consisting of a triangular array of two H^? ions and one Na⁺ ion in substitutional, neighboring positions have been observed in infrared absorption. As one would expect for such a molecule, five modes are observed: two longitudinal modes at 365 and 508 cm^-1, two complanar transverse modes along <110> at 459 and 562 cm^?1, and one transverse mode along <100> at 551 cm^?1.     

Effective spin-spin interactions and singlet-triplet transition intensities in a class of open-shell diatomic molecules

Ab initio calculations of the effective spin-spin parameter λ, and of electric dipole intensities for the forbidden ¹Σ⁺-³Σ^- transition, are reported for NH, NF, PH, PF, NCl and SO, and values of λ alone are calculated for O₂ and S₂. In general the values of λ agree to within 10 per cent with the experimental values, and the calculations enable the apparently irregular variation of λ within this class of molecules to be explained. The effect on λ of several approximations has been investigated, and it is found that the simplest model considered gives reasonable agreement with experiment, as others have found in comparable cases. This model employs single configuration wavefunctions in which the ³Σ^- orbitals are used to represent the isoconfigurational ¹Σ⁺ state; only the interaction with this one ¹Σ⁺ state is included, and only one-centre spin-orbit integrals are retained. Values of λ were calculated at three internuclear separations bracketing the experimental equilibrium separation, so that the vibrational and rotational dependence of λ could be studied. The agreement of the calculated transition intensities with experiment is surprisingly good. Although the level of approximation of the calculation makes it necessary to treat these theoretical transition moments with caution, they suggest that the ¹Σ⁺-³Σ^- transition in PH, hitherto unobserved, should be at least as strong as the corresponding known transition in NH.     

Raman and infrared study of phyllosilicates containing heavy metals (Sb,Bi): bismutoferrite and chapmanite

The kaolinite‐like phyllosilicate minerals bismutoferrite BiFe³⁺₂Si₂O₈(OH) and chapmanite SbFe³⁺₂Si₂O₈(OH) have been studied by Raman spectroscopy and complemented with infrared spectra. Tentatively interpreted spectra were related to their molecular structure. The antisymmetric and symmetric stretching vibrations of the Si O Si bridges, δ SiOSi and δ OSiO bending vibrations, ν (Si O_terminal)⁻ stretching vibrations, ν OH stretching vibrations of hydroxyl ions, and δ OH bending vibrations were attributed to the observed bands. Infrared bands in the range 3289–3470 cm⁻¹ and Raman bands in the range 1590–1667 cm⁻¹ were assigned to adsorbed water. O H···O hydrogen‐bond lengths were calculated from the Raman and infrared spectra. Copyright © 2009 John Wiley & Sons, Ltd.     

A Raman spectroscopic study of bukovskýite Fe2(AsO4)(SO4)(OH)· 7H2O,a mineral phase with a significant role in arsenic migration

The Raman spectrum of bukovskýite [Fe³⁺₂(OH)(SO₄)(AsO₄)· 7H₂O] has been studied and compared with that of an amorphous gel containing specifically Fe, As and S, which is understood to be an intermediate product in the formation of bukovskýite. The observed bands are assigned to the stretching and bending vibrations of (SO₄)²⁻ and (AsO₄)³⁻ units, stretching and bending vibrations and vibrational modes of hydrogen‐bonded water molecules, stretching and bending vibrations of hydrogen‐bonded (OH)⁻ ions and Fe³⁺ (O,OH) units. The approximate range of O H···O hydrogen bond lengths was inferred from the Raman spectra. Raman spectra of crystalline bukovskýite and of the amorphous gel differ in that the bukovskýite spectrum is more complex, the observed bands are sharp and the degenerate bands of (SO₄)²⁻ and (AsO₄)³⁻ are split and more intense. Lower wavenumbers of δ H₂O bending vibrations in the spectrum of the amorphous gel may indicate the presence of weaker hydrogen bonds compared to those in bukovskýite. Copyright © 2011 John Wiley & Sons, Ltd.