A vibrational molecular force field of model compounds with biological interest. I. Harmonic dynamics of crystalline urea at 123 K

Normal coordinate calculations have been performed for urea and deuterated urea in the crystalline state. We have used the modified Urey–Bradley–Shimanouchi intramolecular potential energy function and a rather sophisticated intermolecular energy function to reproduce I.R. and Raman frequencies with an average error of 2 cm^–1. The general agreement between the calculation and experiment suggests that intermolecular interactions must be taken into account to determine reliable intramolecular parameters of the potential energy function, mainly the barrier to internal rotation around the C? N bond. The intermolecular energy function, which consists of the Buckingham function and an explicit harmonic function for hydrogen-bonding, then has the merit to reproduce quite well the observed frequencies of lattice vibrations.     

Champ de forces de symetrie locale de molecules cycliques: III. Interprétation des spectres de vibration du glucose cristallisé sous les deux formes α et β

This paper reports complete infrared and Raman spectra of crystalline α and β glucose. Some high frequency bands are shown to be characteristic of the anomeric forms but there are significant differences in the low frequency region, despite the fact that the two forms crystallize in the same space group.These spectral data have been interpreted using a normal coordinate treatment of intra and intermolecular vibrations. Firstly, it was necessary to take into account both “tree” and “cycle” redundancies. Concerning the intermolecular vibrations, hydrogen bonds and atom-atom contacts were considered. Assignments of frequencies are given. A relation between the observed differences and the molecular structure modification is established and it is shown that hydrogen bonding is responsible for the differentiation of the α and β glucose low frequency spectra.     

Force field and vibrational spectra of oligosaccharides with different glycosidic linkages—Part II. Maltose monohydrate,cellobiose and gentiobiose

Complete Raman and IR spectra of maltose monohydrate, cellobiose and gentiobiose have been recorded in the crystalline state. These three disaccharides present the same monosaccharide composition of the glucose molecule and the remaining studied position (1–4 and 1–6) of the glycosidic linkage. Moreover, maltose and cellobiose present the different configurations of the glycosidic linkage α, 1–4 and β, 1–4, respectively. These data will constitute the support for theoretical calculations of normal modes of vibration. The assignments of the calculated bands of vibration will be made on the basis of the potential energy distributions using a modified Urey—Bradley—Shimanouchi intramolecular potential energy combined with a specific intermolecular potential energy function. The calculations show that using a correct initial force field, it is possible to reproduce correctly the density of observed vibrational states for large molecules such as disaccharides. The standard deviation between calculated and observed frequencies, below 1500 cm⁻¹, leads to values of 4.7, 4.2 and 4.6 cm⁻ for maltose monohydrate, cellobiose and gentiobiose, respectively. Our previous investigations on trehalose dihydrate, sophorose monohydrate and laminaribiose are confirmed in this study and complete the previous assignments for the whole set of disaccharides.     

Quantum chemical calculation of exchange interactions in supramolecularly arranged N,N′‐dioxy‐2,6‐diazaadamantane organic biradical

Quantum mechanical exchange effects in purely organic N,N′‐dioxy‐2,6‐diazaadamantane biradical derivatives with promesogenic substituents have been studied. To determine intermolecular exchange energies, packing conditions of the radical core units in layered liquid crystalline phases are simulated using the Gaussian 09 program. The broken symmetry approach gives J ≈ 7 cm^?1 for intramolecular ferromagnetic exchange interactions between nitroxyl radical centers in one molecule. Both ferromagnetic and antiferromagnetic intermolecular interactions are possible in this kind of systems according to the obtained calculation results. Depending on the mutual positioning and orientation of molecules, the intermolecular antiferromagnetic exchange constant can reach a value of ?50 cm^?1, and the intermolecular ferromagnetic constant a value of 10 cm^?1. The simultaneous presence of intramolecular and intermolecular exchange between spin‐carrying centers in this kind of supramolecularly ordered multispin systems is favorable for the formation of magnetically interacting chains and two‐dimensional networks. © 2016 Wiley Periodicals, Inc.     

Description of the influence of intermolecular interaction on IR spectra's frequencies of simple dense fluids by Monte-Carlo simulation

The solvent-induced shift in IR spectrum of liquid CO is investigated by Monte-Carlo computer simulation. The intramolecular potential is Morse function, pair intermolecular potential includes short-range and dispertion parts. The calculated shift is 5 cm^?1 while the experimental value is 4 cm^?1.     

Study of the low-frequency motions in poly(ethylene terephthalate) (PET) by neutron inelastic scattering

By neutron inelastic scattering, a complex low-frequency spectrum is obtained for PET. This is attributed to the complicated structure of the monomer unit, a large number of intramolecular modes being possible. Most of them were identified using infrared and Raman data. Some indication of the presence of intermolecular modes below 200 cm^?1 was found in the dependence of resolution and intensity on temperature in this frequency domain. The existence of these intermolecular modes was further supported by the spectra obtained from oriented or annealed crystalline samples.     

A vibrational molecular force field of model compounds with biological interest. IV. Parameters for the different glycosidic linkages of oligosaccharides

The force field previously obtained for both anomers of glucose has been applied to six disaccharides that are molecules of _D-glucopyranosyl residues. These six disaccharides have different types of glycosidic linkages—that is, α, α trehalose dihydrate ( 1-1 ), sophorose monohydrate (β, 1-2 ), laminarabiose (β, 1-3 ), maltose monohydrate (α, 1-4 ) and cellobiose (β, 1-4 ), and gentiobiose (β, 1-6 ). From a careful analysis of the infrared and Raman spectra and from harmonic dynamics calculations in the crystalline state, the results show the reliability and the transferability of the set of parameters previously obtained for different carbohydrates. Below 1500 cm^?1, observed data and the corresponding calculated frequencies agreed within 5 cm^?1 for each of the six disaccharides. The vibrational density of states are well reproduced by these calculations for each molecule, particularly for the fingerprint regions. Moreover, as found by other workers who used sophisticated potential energy functions, no additional terms are needed to express the exoanomeric effect. Specific force constants characteristic of each glycosidic linkage have been derived, particularly for the glycosidic angle bending. More interesting are the values of the internal rotation barriers. It is shown that they are of the same size for both sides of the glycosidic linkage: VC₁O₁ = VO₁C_x′ = 3.29 kcal/mol for an alpha residue and 2.64 kcal/mol for a beta unit (x = 1–6 depends on the position of the glycosidic linkages of the considered disaccharide). © 1995 by John Wiley & Sons, Inc.     

Conformational Polymorphism in N‐(4′‐methoxyphenyl)‐ 3‐bromothiobenzamide

Three conformational polymorphs of N‐(4′‐methoxyphenyl)‐3‐bromothiobenzamide, yellow α, orange β, and yellow γ, have been identified by single‐crystal X‐ray diffraction. The properties and structure of the polymorphs were examined with FT Raman, FTIR (ATR), and UV/Vis spectroscopy, as well as differential scanning calorimetry. Computational data on rotational barriers in the isolated gas‐phase molecule indicate that the molecular conformation found in the α form is energetically preferred, but only by around 2 kJ mol^?1 over the γ conformation. The planar molecular structure found in the β form is destabilized by 10–14 kJ mol^?1, depending on the calculation method. However, experimental evidence suggests that the β polymorph is the most stable crystalline phase at room temperature. This is attributed to the relative planarity of this structure, which allows more and stronger intermolecular interactions, that is, more energetically effective packing. Calculated electronic‐absorption maxima were in agreement with experimental spectra.     

A simple method to determine the anomeric configuration of sialic acid and its derivatives by 13C-NMR

The anomeric configuration of sialic acid and its derivatives could be determined on the basis of the coupling pattern of C-1 in the gated proton-decoupled or selective proton decoupled ¹³C-NMR spectra; the α anomer gave a doublet C-1 signal while the β gave a singlet.The α-anomers gave a doublet C-1 signal while the β gave a singlet in their selective proton-decoupled spectra.     

Harmonic dynamics of alpha- and beta-methyl-D-galactopyranoside in the crystalline state

The study of the anomeric differences observed on the spectra of methyl-alpha- and methyl-beta-D-galactopyranoside is the essential goal of this investigation. Thus, after a careful examination of the IR and Raman spectra of these two compounds, several differences in the intensities and frequency shifts are observed. This is especially noted in the region 1000-700 cm(-1). In order to make some assignments with more precision, the normal modes analyses of the two compounds are performed in the crystalline state. For this purpose, a modified Urey-Bradley-Shimanouchi force field has been combined with an intermolecular potential energy function. The initial set of force constants comes from those of alpha- and beta-D-galactopyranosyl, then the force constants have been varied, so as to obtain a good agreement between the observed and the calculated vibrational frequencies. The obtained results have finally reproduced the experimental data and have confirmed the previous assignments made for the methyl-alpha- and methyl-beta-D-galactopyranoside. The calculations have demonstrated also the transferability of the set of parameters of the initial force field of D-galactose to methyl-D-galactopyranoside.     

Rate constants for the gas-phase reaction of OH radicals with a series of ketones at 299 ± 2 K

Relative rate constants for the reaction of OH radicals with a series of ketones have been determined at 299 ± 2 K, using methyl nitrite photolysis in air as a source of hydroxyl radicals. Using a rate constant for the reaction of OH radicals with cyclohexane of 7.57 × 10^?12 cm³ molecule^?1 s^?1, the rate constants obtained are (× 10¹² cm³ molecule^?1 s^?1): 2-pentanone, 4.74 ± 0.14; 3-pentanone, 1.85 ± 0.34; 2-hexanone, 9.16 ± 0.61; 3-hexanone, 6.96 ± 0.29; 2,4-dimethyl-3-pentanone, 5.43 ± 0.41; 4-methyl-2-pentanone, 14.5 ± 0.7; and 2,6-dimethyl-4-heptanone, 27.7 ± 1.5. These rate constants indicate that while the carbonyl group decreases the reactivity of C? H bonds in the α position toward reaction with the OH radical, it enhances the reactivity in the β position.     

Perturbation approach for frequency shifts in IR spectra of molecular clusters

A second order perturbation approach for the evaluation of the splitting and shifting of the infrared vibrational bands of molecular clusters, based on early publications of Buckingham, is presented. The Hamiltonian of the system comprises harmonic- and anharmonic intramolecular vibration terms, as well as the intermolecular potential. The anharmonic contributions of the intramolecular force field and the intermolecular potential are treated as a perturbation. In order to extend the applicability of the approach to homogeneous molecular clusters, the formalism of degenerate perturbation theory is employed. The new approach is applied to methanol clusters from dimer to hexamer for calculating the frequency shifts of the OH stretching mode (ω₁=3681.5 cm^?1), the CH₃ rocking mode (ω₇=1074.5 cm^?1), and the CO stretching mode (ω₈=1033.5 cm^?1). The numerical results compare favourably with experimental and previous theoretical data (except for ω₁), but with a tendency to overestimate the shifts.     

Submillimeter infrared absorption and chain conformations of poly(vinylidene fluoride) and copolymers. I. Crystalline and amorphous contributions

Far infrared spectra of poly(vinylidene fluoride) and several copolymers (with hexafluoropropylene, chlorotrifluoroethylene, and tetrafluoroethylene) have been obtained between 15 and 55 cm^?1. After correction of the interference phenomenon affecting the measurements, the absorption coefficient and the imaginary part of the dielectric constant have been calculated. We show how these parameters are affected by the chain conformation and copolymer composition. The behavior of the crystalline and amorphous phases have been studied. The effects of mechanical and electrical stresses are considered.     

Stereoselective Triplet‐Sensitised Radical Reactions of Furanone Derivatives

The stereo‐ and regioselectivity of triplet‐sensitised radical reactions of furanone derivatives have been investigated. Furanones 7 a , b were excited to the ³ππ* state by triplet energy transfer from acetone. Intramolecular hydrogen abstraction then occurred such that hydrogen was transferred from the tetrahydropyran to the β position of the furanone moiety. Radical combination of the tetrahydropyranyl and the oxoallyl radicals led to the final products 8 a , b . In the intramolecular reaction, overall, a pyranyl group adds to the α position of the furanone. The effect of conformation was first investigated with compounds 9 a , b carrying an additional substituent on the tether between the furanone and pyranyl moiety. Further information on the effect of conformation and the relative configuration at the pyranyl anomeric centre and the furanone moiety was obtained from the transformations of the glucose derivatives 12 , 14 , 17 and 18 . Radical abstraction occurred at the anomeric centre and at the 5′‐position of the glucosyl moiety. Computational studies of the hydrogen‐abstraction step were carried out with model structures. The activation barriers of this step for different stereoisomers and the abstraction at the anomeric centre and at the 6‘‐position of the tetrahydropyranyl moiety were calculated. The results of this investigation are in accordance with experimental observations. Furthermore, they reveal that the reactivity and regioselectivity are mainly determined in the hydrogen‐abstraction step. Intramolecular hydrogen abstraction (almost simultaneous electron and proton transfer) in ³ππ* excited furanones only takes place under restricted structural conditions in a limited number of conformations that are defined by the relative configuration of the substrates. It is observed that in the biradical intermediate, back‐hydrogen transfer occurs leading to the starting compound. In the case of glucose derivatives, this reaction led to epimerisation at the anomeric centre.     

Étude comparative,par spectroscopie infrarouge,des vibrations v(ch) de quelques alcools et thiols ne comportant qu'un seul vibrateur ch

Infrared spectra of some deuterated alcohols and thiols with only one α-CH or β-CH have been obtained in order to compare α and β heteroatom effects on v(CH). The spectra of RR'CHOH alcohols show two bands (Δv? 50 cm^?1) due to the α-CH bond trans to an oxygen lone-pair and the α-CH bond trans to OH.The α sulphur effect is found very weak or non-existent in thiols. The study of CD₂H-CD ₂OH and CD₂HCD₂SH spectra shows the same β-gauche effect of both the heteroatoms while only the sulphur atom seems to have a β-trans effect.     

Spectra and structure of gallium compounds: Part III. vibrational studies of trimethylgallane-phosphine and trimethylgallane-phosphine-d3

The IR (80–4000 cm^?1) and Raman (50–3500 cm^?1) spectra of (CH₃)₃GaPH₃ and (CH₃)₃GaPD₃ have been recorded for the solid state at low temperature. The spectra are interpreted on the basis of C_3v molecular symmetry. A modified valence force field model is utilized in calculating the frequencies and the potential energy distribution. The calculated potential constants for the adducts are compared to those previously reported for the Lewis base moiety, and the differences are shown to be consistent with structural changes upon adduct formation. Only very minor coupling is found between the Ga-C₃ stretches and the CH₃ deformations and the remaining normal modes are nearly pure. The relative values of the force constants are compared to the corresponding quantities in other Group IIIA-Group VA coordinated complexes.     

Structural changes in poly(L-alanine) induced by heat treatment

Structural changes in poly(L -alanine)(PLA), a model compound related to tussah silk fibroin, induced by heat treatment have been studied by differential thermal analysis, x-ray diffraction, and infrared spectroscopy. PLA heated below 300°C shows x-ray patterns very similar to those of the α-helix crystalline phase, in addition to the diffraction patterns due to the β structure. Samples heated at 368°C exhibit predominantly the diffraction patterns due to the β crystalline phase. From infrared spectra, PLA samples heated below 280°C are found to be composed of all three molecular conformations: β sheet, random coil, and α helix. The intensity of the infrared absorption at 650 cm^?1 (amide V) assigned to the random coil conformation is decreased by heat treatment above 325°C. The content of the β-sheet structure remains almost constant when the specimen is heated below 325°C, and increases abruptly on heating to around 335°C, while the random coil content is decreased abruptly by heat treatment above 335°C. The α-helix content does not change, regardless of heat treatment. It is suggested therefore that the random coil conformation of PLA transforms directly into the β sheet on heat treatment above 335°C.     

Raman scattering in uniaxially oriented samples of planar zigzag poly(vinylidiene fluoride)

Band assignments of phase-I PVF₂ have been Revised by using additional data obtained by laser Raman spectra of oriented samples. A set of least-squares refined force constants was obtained which reproduce the experimental data to an average error in frequencies of 1.3 cm^?1. In order to determine the effect of electrical polarization on the spectra, a Gaussian distribution of the dipole axis was assumed. The calculation shows that polarizations of less than 60% will not significantly affect the Raman spectra.     

The vibrational spectra of maleimide and N-D maleimide

The infrared spectra of maleimide as a vapour (160°C), melt (100°C), oriented polycrystalline film, pellet and when dissolved in various solvents were recorded between 4000 and 400 cm^?1. Also certain spectra in the far infrared region 400-40 cm^?1 were obtained. Raman spectra of the crystalline solid, melt and as a saturated solution in acetonitrile were recorded and semiquantitative polarization measurements carried out. For N-D maleimide infrared and Raman spectra of the solid compound were recorded.The fundamental frequencies have been assigned in terms of C_2v, symmetry on the basis of infrared vapour contours and dichroism of the oriented film as well as on Raman polarization data. A force field was derived for maleimide, by initially transferring force constants from maleic anhydride and subsequent refinement of the force constants. The agreement between observed and calculated frequencies for the in-plane modes was satisfactory whereas certain large discrepancies remained for the out-of-plane vibrations.     

Infrared studies of the reversible stress-induced crystal-crystal phase transition of poly(tetramethylene terephthalate)

The reversible stress-induced crystal-crystal phase transition of poly(tetramethylene terephthalate) (PTMT) has been studied using infrared spectroscopy. Two spectral regions were used to study this transition: the 900–1000 cm^?1 methylene rocking region and the 1300–1550 cm^?1 methylene bending region. The bands at 917 and 1456 cm^?1 are assigned to the ∝ phase. The bands at 935 and 1388 cm^?1 have components from the α phase and the β phase. Dynamic stretching experiments performed above and below the glass-transition temperature indicated different mechanisms of the phase transition.