States of molecular assembly and physical properties of crystalline long-chain compounds studied by vibrational spectroscopy

Various types of molecular assembly of long-chain compounds in solid states were investigated by means of infrared absorption, Raman and Brillouin spectroscopic methods. As for the polymorphism in even-numbered n-fatty acids, three monoclinic modifications, B, C, and E, all consisting of the orthorhombic polyethylene sublattice, give rise to their characteristic infrared and Raman spectra. A dynamical equilibrium between cis and trans conformations of the hydrogen-bonded carboxyl groups in modification C, which is related to the high-temperature stable character of this phase, is reflected to a dramatic change with temperature in the low-frequency Raman spectra. A new type of reversible solid state phase transition was found between two A-type (triclinic) modifications of myristic, palmitic, and stearic acids. The γ→α phase transition of oleic acid was found to be caused by a conformational disordering of polymethylene chains at the lamellar interfacial region. Two basic polytype structures, Mon and Orth II, of stearic acid B were investigated, and it was found that the low-frequency phonon frequencies (below 50 cm⁻¹) were strongly influenced by the polytype structure. Based on the spectroscopic considerations, Orth II was predicted as the thermodynamically stable phase around room temperature compared with Mon, and the stability is responsible for the vibrational free energy term. Some experimental findings which support this prediction were obtained. The values of the stiffness tensor elements of Mon and Orth II, measured by Brillouin scattering, indicate that the mechanical behavior of bulk crystals is very dependent on the polytype structure. The relationship between the mobility of chain molecules and the width of the spectral bands was investigated in a quantitative manner for the case of n-alkane molecules entrapped in the urea inclusion adducts. The changes in the half-width for the polarization components of various Raman bands on the transition from the orthorhombic to the hexagonal phase are interpreted in terms of the correlation functions of the Raman tensor related to the rotational motion of the alkane molecules around the chain axes.     

A study of the structure of chemical compounds by nuclear magnetic resonance spectroscopy

The PMR spectra of the condensation products of N-arylsulfonylmonoimino sulfur dioxide with the dienes were studied. It was established that the reaction goes according to the condensation pattern of the Diels-Alder reaction, involving the nitrogen sulfur double bond with the formation of 1-oxo-2-arylsulfonyl-3, 6-dihydro-1, 2-thiazines.     

DNA vibrational coupling revealed with two-dimensional infrared spectroscopy: insight into why vibrational spectroscopy is sensitive to DNA structure

Two-dimensional infrared (2D IR) spectroscopy was used to study the carbonyl vibrational modes of guanine and cytosine bases in A- and B-form DNA. Located between 1600 and 1700 cm(-1), these modes are often used to monitor DNA secondary structure with traditional infrared spectroscopies such as FTIR, but traditional spectroscopies lack the necessary observables to unravel the coupling mechanisms that make these modes sensitive to secondary structure. By using 2D IR spectroscopy and electronic structure calculations on d(G(5)C(5)) and d(GC)(8) model nucleic acids, we find that hydrogen-bonded guanine/cytosine base pairs are primarily electrostatically coupled and that the coupling between these modes can be modeled with a transition dipole density approach. In comparison, electrostatics is insufficient to model stacked bases because of cooperative charge-sharing effects, but the coupling can be accurately calculated using a finite difference method. We find that the coupling is very strong for both hydrogen-bonded and stacked base geometries, creating vibrational modes that extend both across the base pairs and along the lengths of the helices. Our results provide a physical basis for understanding how strong coupling gives rise to the empirically established relationship between infrared spectroscopy and DNA/RNA secondary structure.     

Time-resolved vibrational spectroscopy of [FeFe]-hydrogenase model compounds

Model compounds have been found to structurally mimic the catalytic hydrogen-producing active site of Fe-Fe hydrogenases and are being explored as functional models. The time-dependent behavior of Fe(2)(μ-S(2)C(3)H(6))(CO)(6) and Fe(2)(μ-S(2)C(2)H(4))(CO)(6) is reviewed and new ultrafast UV- and visible-excitation/IR-probe measurements of the carbonyl stretching region are presented. Ground-state and excited-state electronic and vibrational properties of Fe(2)(μ-S(2)C(3)H(6))(CO)(6) were studied with density functional theory (DFT) calculations. For Fe(2)(μ-S(2)C(3)H(6))(CO)(6) excited with 266 nm, long-lived signals (τ = 3.7 ± 0.26 μs) are assigned to loss of a CO ligand. For 355 and 532 nm excitation, short-lived (τ = 150 ± 17 ps) bands are observed in addition to CO-loss product. Short-lived transient absorption intensities are smaller for 355 nm and much larger for 532 nm excitation and are assigned to a short-lived photoproduct resulting from excited electronic state structural reorganization of the Fe-Fe bond. Because these molecules are tethered by bridging disulfur ligands, this extended di-iron bond relaxes during the excited state decay. Interestingly, and perhaps fortuitously, the time-dependent DFT-optimized exited-state geometry of Fe(2)(μ-S(2)C(3)H(6))(CO)(6) with a semibridging CO is reminiscent of the geometry of the Fe(2)S(2) subcluster of the active site observed in Fe-Fe hydrogenase X-ray crystal structures. We suggest these wavelength-dependent excitation dynamics could significantly alter potential mechanisms for light-driven catalysis.     

Chemical tailoring of porous silica xerogels: local structure by vibrational spectroscopy

Monolithic porous silica xerogels were synthesized by the sol-gel process, and their local structure was analysed by vibrational spectroscopy. The silica alcogels were prepared by a two-step hydrolytic polycondensation of tetraethoxysilane (TEOS) in isopropanol, with a water/TEOS molar ratio of 4. The hydrolysis step was catalysed by hydrochloric acid (HCl), with different HCl/TEOS molar ratios (ranging from 0.0005 to 0.009), and the condensation step was catalysed by ammonia (NH(3)), with different NH(3)/HCl molar ratios (ranging from 0.7 to 1.7). After appropriate ageing, the alcogels were washed with isopropanol and subcritically dried at atmospheric pressure. The diffuse reflectance infrared Fourier transform (DRIFT) spectra were analysed in terms of the main siloxane rings that form the silica particles, taking into account the splitting of the nu(as)Sibond;Obond;Si mode into pairs of longitudinal and transverse optic components, by long-range Coulomb interactions. It was proven that the proportion of residual silanol groups (which correlates with hydrophilicity), and the fraction of siloxane 6-rings (which correlates with porosity) may be tailored by adequate catalytic conditions, mostly by the hydrolysis pH. This was explained in terms of the reactions' mechanisms taking place in the two-step sol-gel process followed.     

Determining the absolute configuration of two marine compounds using vibrational chiroptical spectroscopy

Chiroptical techniques are increasingly employed for assigning the absolute configuration of chiral molecules through comparison of experimental spectra with theoretical predictions. For assignment of natural products, electronic chiroptical spectroscopies such as electronic circular dichroism (ECD) are routinely applied. However, the sensitivity of electronic spectral parameters to experimental conditions and the theoretical methods employed can lead to incorrect assignments. Vibrational chiroptical methods (vibrational circular dichroism, VCD, and Raman optical activity, ROA) provide more reliable assignments, although they, in particular ROA, have been little explored for assignments of natural products. In this study, the ECD, VCD, and ROA chiroptical spectroscopies are evaluated for the assignment of the absolute configuration of a highly flexible natural compound with two stereocenters and an asymmetrically substituted double bond, the marine antibiotic Synoxazolidinone A (SynOxA), recently isolated from the sub-Arctic ascidian Synoicum pulmonaria. Conformationally averaged nuclear magnetic resonance (NMR), ECD, Raman, ROA, infrared (IR) and VCD spectral parameters are computed for the eight possible stereoisomers of SynOxA and compared to experimental results. In contrast to previously reported results, the stereochemical assignment of SynOxA based on ECD spectral bands is found to be unreliable. On the other hand, ROA spectra allow for a reliable determination of the configuration at the double bond and the ring stereocenter. However, ROA is not able to resolve the chlorine-substituted stereogenic center on the guanidinium side chain of SynOxA. Application of the third chiroptical method, VCD, indicates unique spectral features for all eight SynOxA isomers in the theoretical spectra. Although the experimental VCD is weak and restricted by the limited amount of sample, it allows for a tentative assignment of the elusive chlorine-substituted stereocenter. VCD chiroptical analysis of a SynOxA derivative with three stereocenters, SynOxC, results in the same absolute configuration as for SynOxA. Despite the experimental challenges, the results convincingly prove that the assignment of absolute configuration based on vibrational chiroptical methods is more reliable than for ECD.     

Solid state crystalline and liquid crystalline structure of semifluorinated 1-bromoalkane compounds

A series of semifluorinated 1-bromoalkane (SFBA) mesogens have been synthesized and characterized to better understand their solid state crystalline and liquid crystalline structures. In the solid state, the local conformation of the fluorocarbon segments becomes disordered once the fluorocarbon chain reaches a length above eight CF units. This is evident from the pronounced decrease of molar melting enthalpy. An increasing amount of helix and helix reverse conformations and increasingly disordered packing can also be observed with each addition of a fluorocarbon segment. X-ray diffraction peaks in the small angle region can be indexed by a tilted, two dimensional layered (herring bone) structure. The crystal structure is similar to a type of plastic crystal in which the amphiphilic character is clear, because the two segments of fluorocarbon and hydrocarbon are almost immiscible. Heating of F(CF2)12(CH2)10Br leads to a transition from plastic crystal to smectic B, as revealed by time-resolved XRD and FTIR analysis. At this solid-to-liquid transition temperature, conformational analysis confirmed an onset of the CH2 gauche conformation within the hexagonal lattice, most likely due to changes occurring in the hydrocarbon segment, and a sudden increase of helix defects along the fluorocarbon segment. The disordered helix rigid-rod structure of the fluorocarbon segment and its poor compatibility with the hydrocarbon segment play an important role in the crystalline solid and liquid crystalline structures.     

Gas-phase vibrational spectroscopy and ab initio study of organophosphorus compounds: discrimination between species and conformers

Gas phase vibrational spectra of dimethyl methylphosphonate (DMMP), trimethyl phosphate (TMP), and triethyl phosphate (TEP) have been measured using FTIR spectroscopy. For DMMP, TMP, and TEP, most of the infrared active vibrational modes have been observed in the 50-5000 cm (-1) spectral range, allowing an unambiguous discrimination between the three molecules. The vibrational analysis of the spectra was performed by comparing with MP2 and B3LYP harmonic and anharmonic force field ab initio calculations. The extension to anharmonic calculations provides the best agreement for the mid-infrared and the near-infrared spectra, but they do not improve the harmonic frequency predictions in the far-infrared domain. This part of the vibrational spectra associated with collective and nonlocalized vibrational modes presents the largest frequency differences between the two lowest energy conformers of DMMP and TMP. These two conformers were taken into account in the vibrational assignment of the spectra. Their experimental evidence was obtained by deconvoluting vibrational bands in the mid-infrared and in the far-infrared regions, respectively. For TEP, the conformational landscape appears very complicated at ambient temperature, and a further analysis at low temperature is required to explain the vibrational features of each conformer.     

Surface structure of protonated R-sapphire (1102) studied by sum-frequency vibrational spectroscopy

Sum-frequency vibrational spectroscopy was used to study the protonated R-plane (1102) sapphire surface. The OH stretch vibrational spectra show that the surface is terminated with three hydroxyl moieties, two from AlOH(2) and one from Al(2)OH functional groups. The observed polarization dependence allows determination of the orientations of the three OH species. The results suggest that the protonated sapphire (1102) surface differs from an ideal stoichiometric termination in a manner consistent with previous X-ray surface diffraction (crystal truncation rod) studies. However, in order to best explain the observed hydrogen-bonding arrangement, surface oxygen spacing determined from the X-ray diffraction study requires modification.