FOURIER TRANSFORM INFRARED SPECTRAL STUDIES ON THE SCHIFF BASE MODE OF ALL-trans BACTERIORHODOPSIN and ITS PHOTOINTERMEDIATES,K and L*

Abstract– Difference Fourier transform infrared spectra were recorded for bacteriorhodopsin upon irradiation at 230, 170 or 77 K, which gave, respectively, the spectrum of the M, L or K intermediate minus unphotolyzed all-trans bacteriorhodopsin (denoted as BR). By replacement of the Schiff base nitrogen with ¹⁵N, or of either its hydrogen at N or C₁₅ with deuterium, the vibrational bands related to the Schiff base were identified and the isotope-shifts evaluated for BR, K and L. The 1348 cm^?l band of BR and K and the 1400 cm^?1 band of L were sensitive to each of these isotope substitutions. The 1254 cm^?1 band of BR, the 1245 cm^?1 band of K and the 1301 cm^?1 band of L were sensitive to either N- or C₁₅-deuteration but not to ¹⁵N-substitution. The N—D in-plane bending vibration of K and L appeared at 969 and 997 cm^?1, respectively, upon substitution with D₂O. All the results show that L is larger in frequencies related to the N—H in-plane bending vibration than K or BR and suggest that L has the strongest interaction with the protein. Among the bands containing an N—H bending vibration, the 1348 cm^?1 band of K was more intense than the corresponding band of L at 1400 cm^?1. The C₁₅-deuteration-induced upshift of the 1245 cm^?1 band of K was unobservable for the 1301 cm^?1 band of L. Such differences between L and K might be brought about by a distortion in the retinal moiety close to the protonated Schiff base of the 13-cis chromophore.     

IR-analysis of H-bonded H2O on the pure TiO2 surface

The surface state of optically pure polydisperse TiO₂ (anatase and rutile) was determined by infra-red (IR) spectroscopy analysis in the temperature range of 100–453 K. Anatase A300 spectrum, contrary to rutile R300 one, has a broad three-component absorption band with peaks at 1048, 1137 and 1222 cm⁻¹ in the spectral range of δ(Ti–O–H) deformation vibrations. For rutile R300 we observed a very weak band at 1047 cm⁻¹, and for the thermal treated rutile R900 these bands were not appeared at all. The analysis of temperature dependencies for the mentioned absorption bands revealed the spectral shift of 1222 cm⁻¹ band towards the high frequencies, when the temperature increased, but the spectral parameters of 1137 and 1048 cm⁻¹ bands remained the same. The temperature of 1222 cm⁻¹ band maximum shift was 373–393 K and correlated with DSC data. Obtained results allowed to assign 1222 cm⁻¹ band to the deformation vibrations of OH-groups, bounded to the surface adsorbed water molecules by weak hydrogen bonds (5 kcal/mol). During the temperature growth these molecules desorbed, which also resulted in the intensity decreasing of stretching OH-groups vibration IR-bands at 3420 cm⁻¹. The destruction and desorption of surface water complexes led to Ti–O–H bond strengthening. IR bands at 1137 and 1048 cm⁻¹ were attributed to the stronger bounded adsorbed water molecules, which are also characterized with stretching OH-groups vibration bands at 3200 cm⁻¹. These surface structure were additionally stabilized by hydrogen bonds with the neighbouring TiO₂ lattice anions and other OH-groups, and desorbed at higher temperatures.     

Optical absorption spectrum of Ni2+ in zinc cesium sulphate hexahydrate

The optical absorption spectrum of Ni²⁺ ion doped in zinc cesium sulphate hexahydrate has been studied at room and liquid nitrogen temperatures. From the nature and position of the bands a successful interpretation of all the bands could be made assuming octahedral symmetry for the Ni²⁺ ion in the crystal. The fine splitting of the ³T_1g (F) band at liquid nitrogen temperature has been interpreted due to spin—orbit interaction. A series of weak bands is found at 77 K at about 19,000 cm⁻¹. These bands are assigned as due to simultaneous electronic and vibrational transitions involving the HO stretching vibration.     

Vibrational spectra and reinvestigation of the crystal structure of a polymeric copper(II)-orotate complex, [Cu(μ-HOr)(H2O)2]n: The performance of new DFT methods, M06 and M05-2X, in theoretical studies

The crystal and molecular structure of a polymeric Cu(II)-orotate complex, [Cu(μ-HOr)(H₂O)₂]_n, has been reinvestigated by single crystal X-ray diffraction. It is shown that several synergistic interactions: two axial Cu-O interactions; intramolecular and intermolecular hydrogen bonds; and π-π stacking between the uracil rings contribute to the stability of the crystal structure. The Raman and FT-IR spectra of the title complex are reported for the first time. Comprehensive theoretical studies have been performed by using three unrestricted DFT methods: B3LYP; and the recently developed M06, and M05-2X density functionals. Clear-cut assignments of all the bands in the vibrational spectra have been made on the basis of the calculated potential energy distribution, PED. The very strong Raman band at 1219 cm⁻¹ is diagnostic for the N1-deprotonation of the uracil ring and formation of the copper-nitrogen bond, in this complex. The Cu-O (carboxylate) stretching vibration is observed at 287 cm⁻¹ in the IR spectrum, while the Cu-N (U ring) stretching vibration is assigned to the strong Raman band at 263 cm⁻¹. The molecular structure and vibrational spectra (frequencies and intensities) calculated by the M06 functional method are very similar to the results obtained by the B3LYP method, but M06 performs better than B3LYP in calculations of the geometrical parameters and vibrational frequencies of the interligand O-H?O hydrogen bonding. Unfortunately, the M05-2X method seriously overestimates the strength of interligand hydrogen bond.     

Vibrational spectroscopic study of syngenite formed during the treatment of liquid manure with sulphuric acid

Syngenite (K₂Ca(SO₄)₂·H₂O), formed during treatment of manure with sulphuric acid, was studied by infrared, near-infrared (NIR) and Raman spectroscopy. C_s site symmetry was determined for the two sulphate groups in syngenite (P2₁/m), so all bands are both infrared and Raman active. The split ν₁ (two Raman+two infrared bands) was observed at 981 and 1000 cm⁻¹. The split ν₂ (four Raman+four infrared bands) was observed in the Raman spectrum at 424, 441, 471 and 491 cm⁻¹. In the infrared spectrum, only one band was observed at 439 cm⁻¹. From the split ν₃ (six Raman+six infrared) bands three 298 K Raman bands were observed at 1117, 1138 and 1166 cm⁻¹. Cooling to 77 K resulted in four bands at 1119, 1136, 1144 and 1167 cm⁻¹. In the infrared spectrum, five bands were observed at 1110, 1125, 1136, 1148 and 1193 cm⁻¹. From the split ν₄ (six infrared+six Raman bands) four bands were observed in the infrared spectrum at 604, 617, 644 and 657 cm⁻¹. The 298 K Raman spectrum showed one band at 641 cm⁻¹, while at 77 K four bands were observed at 607, 621, 634 and 643 cm⁻¹. Crystal water is observed in the infrared spectrum by the OH-liberation mode at 754 cm⁻¹, OH-bending mode at 1631 cm⁻¹, OH-stretching modes at 3248 (symmetric) and 3377 cm⁻¹ (antisymmetric) and a combination band at 3510 cm⁻¹ of the H-bonded OH-mode plus the OH-stretching mode. The near-infrared spectrum gave information about the crystal water resulting in overtone and combination bands of OH-liberation, OH-bending and OH-stretching modes.     

Resonance raman scattering from metastable O2 molecules in γ-irradiated NaClO3

Resonance Raman scattering has been observed from metastable O₂ molecules produced in single crystals of NaClO₃ by γ-irradiation at 300 K. Evidence that the observed bands are due to O₂ is provided by the Raman spectrum of irradiated ¹⁸O enriched NaClO₃ in which bands due to ¹⁶O₂, ¹⁶O ¹⁸O, and ¹⁸O₂ were identified. The Raman band at 1544 cm^?1 ascribed to metastable O₂ disappears on bleaching with intense 4880 Å radiation enabling the identification of a weaker band at 1557 cm^?1 that is assigned to the stable form of O₂.     

Vibrational (i.r. and Raman) spectra and conformational studies of 1-formyl-3-thiosemicarbazide

The i.r. and Raman spectra (30–4000 cm⁻¹) of 1-formyl-3-thiosemicarbazide (FTSC) and deuterated ftsc-d₄, have been studied. Most of the vibration modes reveal pairs of bands and show strong temperature dependence. A band group {ν(NNH₂)} at ∼ 1100 cm⁻¹ exhibits well resolved doublet (1095 and 1112 cm⁻¹) structure below 100 k. The intensity in the 11 12 cm⁻¹ band decreases regularly (band disappears at 150 K) with the rise in temperature. Two new bands at 955 and 1070 cm⁻¹ appear while measured above 400 K. The system eventually exists in several conformers in simultaneous equilibria. Moreover, a few bands {e.g. ν(CO), ν(CS) and ν(CH)} that show strong intensifies in i.r. exhibit weak (or zero) intensifies in the Raman and vice-versa. The features (characteristic of u and g vibration species) could be explained by a C_2h pseudo symmetry space group proposed for the system. Both the FTSC and FTSC-d₄ represent strong molecular associations. This favours the maximum abundance in the dimer stabilized conformers.     

Neutron inelastic scattering spectra of strongly hydrogen bonded acid oxalates NaHC2O4, KHC2O4 and LiHC2O4

Neutron inelastic scattering spectra of NaHC₂O₄, KHC₂O₄ crystals at 80 K have been recorded in the 2200-200 cm^?1 range. The lithium acid salt was also studied at different temperatures. NIS spectra are compared to the corresponding infrared and Raman spectra and an assignment is proposed. Two strong bands near 1500 and 1100 cm^?1 are assigned to δ(OH) and γ(OH) vibrations, respectively, while five weak bands below 900 cm^?1 are associated with skeletal modes, mainly bending vibrations. The OH stretching vibration is not observed and is believed to be hidden by other bands; the peak intensity must be low because of its band width which is of the order of a few hundreds wavenumbers.     

Infrared Spectroscopic Studies on the Surface Chemistry of High‐Surface‐Area Gallia Polymorphs

Polymorphs α, β, and γ of Ga₂O₃ having hexagonal (corundum‐type), monoclinic and cubic (spinel‐type) structure, respectively, were prepared in a high‐surface‐area form, and characterized by powder X‐ray diffraction. Nitrogen adsorption at 77 K showed these gallia samples to have specific surface areas of 77 (α‐Ga₂O₃), 40 (β‐Ga₂O₃) and 120 m² g^?1 (γ‐Ga₂O₃). Fourier transform infrared spectroscopy of adsorbed carbon monoxide (at 77 K) and pyridine (at room temperature) showed that the three gallia polymorphs have a very similar surface Lewis acidity, regardless of their different crystal structures. This Lewis acidity was assigned, mainly, to coordinatively unsaturated tetrahedral Ga³⁺ ions situated on the surface of the small crystallites which constitute the different metal oxide varieties. Ga³⁺···CO adducts formed after CO adsorption gave (in all cases) a characteristic C–O stretching band at 2195–2200 cm^?1, while Lewis‐type adducts formed with adsorbed pyridine were characterized by IR absorption bands at 1610–1612 and 1446–1450 cm^?1. The three (partially hydroxylated) gallia polymorphs showed also a very weak Brønsted acidity, which they manifested by forming hydrogen‐bonded adducts with both CO and pyridine; however no protonation of adsorbed pyridine occurred.     

Raman spectrum from a single crystal of SnHPO4

The polarized Raman spectrum of a single crystal of SnHPO₄ has been obtained in order to ascertain the vibrational characteristics of HPO²⁻₄ dimers in a known configuration. Bands due to hydroxyl, OH, stretching, POH bending and the hydrogen bond were observed in addition to most of the predicted lattice modes.The OH stretching mode was observed at 2730 cm⁻¹, the in-plane POH bend at 1275 cm⁻¹ and the out-of-plane POH bend at 818 cm⁻¹. A band of 55 cm⁻¹ is assigned, on the basis of its deuterium shift, to a deformation of the hydrogen bond. Very low frequency bands at 18 and 30 cm⁻¹ reflect the layer structure of SnHPO₄ in which intra-layer forces are strong and inter-layer (hydrogen bonds) forces are weak.     

A thermal and structural study on Lanthanum Hexacyanocobaltate(III) pentahydrate,La[Co(CN)6]·5H2O. Part III

On dehydration of La[Co(CN)₆]·5H₂O, the color of the complex, changes from white to pale blue at around 230°C. Heating the pale blue specimen, the color changes to deep blue at around 290°C. This deep blue specimen is easily rehydrated to a pink one. As reported previously, in the pale blue specimen, Co³⁺ ions are situated in the center of the D_4h crystal field formed by six CN^- ions. The deep blue specimen is due to the presence of [Co(CN)₄]^2- ions in which Co²⁺ was situated in a T_d coordination field formed by four CN^- ions and the Co-C bond length is 1.67 Ĺ. The pink species corresponded to trans-[Co(CN)₄(H₂O)₂]^2- and the bond lengths of Co-C and Co-O are 1.89 and 1.85 Ĺ, respectively. The Raman spectra of the complex observed at 25°C displays two bands at 2157 and 2176 cm^-1 associated with the vibration of C-N bond, and the band of 2157 cm^-1 was split into two bands, 2150 and 2156 cm^-1, at around 100°C. When the complex was heated to around 230°C, three new bands were observed at 2103, 2116 and 2141 cm-1. The bands of 2103 and 2116 cm^-1 were assigned to the stretching vibration of C=N bonding to Co²⁺. The band of 2141 cm^-1 was assigned to the stretching vibration of the inverted CN^- as follows: Co-C=N-La→Co-N=C-La. The activation energy for the inversion of CN^- was estimated as 67 kJ mol^-1. This revised version was published online in August 2006 with corrections to the Cover Date.     

A Raman spectroscopic study of the uranyl phosphate mineral bergenite

Raman spectroscopy at 298 and 77 K of bergenite has been used to characterise this uranyl phosphate mineral. Bands at 995, 971 and 961 cm-1 (298 K) and 1006, 996, 971, 960 and 948 cm-1 (77K) are assigned to the nu1(PO4)3- symmetric stretching vibration. Three bands at 1059, 1107 and 1152 cm-1 (298 K) and 1061, 1114 and 1164 cm-1 (77 K) are attributed to the nu3(PO4)3- antisymmetric stretching vibrations. Two bands at 810 and 798 cm-1 (298 K) and 812 and 800 cm-1 (77 K) are attributed to the nu1 symmetric stretching vibration of the (UO2)2+ units. Bands at 860 cm-1 (298 K) and 866 cm-1 (77 K) are assigned to the nu3 antisymmetric stretching vibrations of the (UO2)2+ units. UO bond lengths in uranyls, calculated using the wavenumbers of the nu1 and nu3(UO2)2+ vibrations with empirical relations by Bartlett and Cooney, are in agreement with the X-ray single crystal structure data. Bands at (444, 432, 408 cm-1) (298 K), and (446, 434, 410 and 393 cm-1) (77 K) are assigned to the split doubly degenerate nu2(PO4)3- in-plane bending vibrations. The band at 547 cm-1 (298 K) and 549 cm-1 (77 K) are attributed to the nu4(PO4)3- out-of-plane bending vibrations. Raman bands at 3607, 3459, 3295 and 2944 cm-1 are attributed to water stretching vibrations and enable the calculation of hydrogen bond distances of >3.2, 2.847, 2.740 and 2.637 A. These bands prove the presence of structurally nonequivalent hydrogen bonded water molecules in the structure of bergenite.     

Vibrational spectroscopy of the sorosilicate mineral hemimorphite Zn4(OH)2Si2O7 · H2O

Raman spectroscopy complimented by infrared spectroscopy has been used to study the mineral hemimorphite from different origins. The Raman spectra show consistently similar spectra with only one sample showing additional bands due to the presence of smithsonite. Raman bands observed at 3510–3565 and 3436–3455 cm⁻¹ are assigned to OH stretching vibrations. Using a Libowitzky type formula, these OH bands provide hydrogen bond distances of 0.2910, 0.2825, 0.2762 and 0.2716 pm. Water bending modes are observed in the Raman spectrum at 1633 cm⁻¹. An intense Raman band at 930 cm⁻¹ is attributed to SiO symmetric stretching vibration of the Si₂O₇ units. Raman bands observed at 451 and 400 cm⁻¹are attributed to out-of-plane bending vibrations of the Si₂O₇ units. Raman bands at 330, 280, 168 and 132 cm⁻¹ are assigned to ZnO and OZnO vibrations.     

The intrinsic fluorescence of the mixed crystal system anthracene-perdeuteroanthracene, amalgamated exciton band

The fluorescence spectra of the mixed crystal system anthracene (A-h₁₀) - perdeuteroanthracene (A-d₁₀) have been studied over the full concentration range at temperatures between 1.6 and 77 K. There exists an amalgamated A-h₁₀ - A-d₁₀ S₁ exciton band at all concentrations. The intrinsic fluorescence starts from the lower edge this S₁ band at low temperatures. The edge shifts with a non-linear dependence with increasing concentration from 25097 cm⁻¹ in the neat A-h₁₀ crystal to 25156 cm⁻¹ in the neat A-d₁₀ crystal. The transition from the S₁ band edge to the S₀ ground state is always forbidden. Only transitions to levels intramolecular and lattice vibrations of the ground state have been observed. The fluorescence transitions take place to vibrational levels of both A-h₁₀ and A-d₁₀. This leads to a doublet structure of the vibrational bands. Due to the influence of quasi-resonance and exciton-superexchange the transitions to A-h₁₀ vibrational states at low temperatures are more probable than it would correspond to the A-h₁₀ concentration. Using the concentration shift of the lower S₁ band edge an approximative determination of the energy exchange integral square sum to Σ M² = 9600 cm⁻² ± 50% is possible.     

CO2 laser-induced decomposition of ethanol

The multiple photon absorption and decomposition of ethanol irradiated by pulsed 9P18 infrared radiation (1048.7 cm^?1) from a TEA CO₂ laser has been studied in the fluence range 15 to 5 J cm^?2. The absorption cross-section is pressure-dependent due to rapid collisional rotational hole-filling. At low pressures the only important decomposition channel following absorption is molecular dehydration of ethanol to yield ethene, but at higher pressures hydrogen, methane, carbon monoxide, ethane, and ethyne are also produced. In the irradiation of pure ethanol under ‘collision-free’ conditions, thermal decomposition following collisional redistribution of energy makes only a small contribution to the overall decomposition yield at fluences above 3.5 J cm^?2 but may become more significant at lower fluences. Modelling using RRKM calculations has been employed to link measured absorbed energies to extents of decomposition of ethanol. Both these calculations and the absorption measurements indicate that at low pressures only a fraction of the irradiated ethanol molecules absorb the 9P18 radiation. © 1993 John Wiley & Sons, Inc.     

Resonanzramanspektrum von matrixisoliertem Se3

Resonance Raman Spectrum of Matrixisolated Se₃ By the application of a double furnace it is possible to get a gas mixture of 90% Se₂ molecules and 10% Se atoms. By condensing this mixture in an inertgas matrix at 15 K followed by annealing to nearly 25 K we got Se₃ molecules by a matrix reaction In the resonance Raman spectrum of this molecule we observed 14 overtones of the symmetric stretching vibration. So we can calculate the following values of ω₁ an x₁₁ for ⁸⁰Se₃: 312.15 ± 0.2 cm^?1 and 0.53 ± 0.02 cm^?1. Using a mixture of 62% ⁷⁶Se and 38% ⁸²Se we got band structures in which the intensity of the bands and their frequency shift can only be explained by a bent Se₃ molecule (～115°). The value of the force constant f_r + f_rr is 310 ± 20 Nm^?1. — By a new construction it is possible to get the Raman and IR reflection spectrum of the same matrix.     

Near infrared electronic spectrum of TCNQ mono-valent anion

The high resolution near infrared electronic spectrum of TCNQ anion dissolved in 2-methyltetrahydrofuran glass at 77 K has been determined. The absorption bands are interpreted as simple progressions of two molecular vibrations in a single electronic excited state with ν₀₀ = 11661 cm^?1. The molecular vibrations (ω′₁ = 1264 ± 3 cm^?1, ω′₂ = 335 ± 3 cm^?1) of the vibrational progression agree well with observed Raman active transitions. The experimental data do not require the presence of two electronic transitions in the 1.3 to 2.1 eV region, contrary to what had been assumed previously on the basis of less well resolved room temperature spectra.     

Second-order spectrum of water in the K4Fe(CN)6.3H2O crystal

Second-order infrared spectra of the crystal K₄Fe(CN)₆.3H₂O are obtained in the region of 3700–7200 cm^?1 at 90 K. The bands corresponding to overtones and combinations of the stretching and bending modes of the different water molecules are discussed and interpreted. The anharmonicity constants are estimated using the observed frequencies.     

Absorption and emission spectra of the lowest triplet state in hexachloroacetone

T₁ ← S₀ absorption and T₁ → S₀ phosphorescence spectra of neat cystalline hexachloroacetone have been analyzed at 4.2°K. From the lifetime and energy the upper state is assigned as ³nπ^*. The spectra are sharp compared to other aliphatic ketones, with the 0-0 band at 26 248 ± 2 cm ^?1. The phosphorescence shows two strong progressions; one involving the CO stretching mode at 1784 cm^?1 (x), the other a long progression of at least 8 bands involving a mode at 143 cm^t-1 (a). The 143 cm^?1 progression forming mode can best be asigned to the CO out-of-plane wagging vibration. The absorption shows the same two strong progressions, reduced in frequency to 1270 cm^t-1 and 123 cm^?1, respectively, but with the progression in mode a broadened with increasing n. The broadening is interpreted as arising from inversion doublets; the close harmonicity up to n = 5 allowing the potential barrier to inversion to be estimated as > 700 cm^?1. A feature of the spectra is the absence of low frequency torsional modes suggesting lack of pseudo Jahn-Teller distortion of the triplet state potential surface. For comparison, the phosphorescence of crystalline hexafluoroacetone was also studied at 4.2°K. The spectrum exhibits broad bandedness with a 00 band tentatively assigned at 26 870 ± 20 cm^?1.     

Low-temperature photolysis of azidostyrylquinolines

Low-temperature photolysis of 2-and 4-(4′-azidostyryl)quinolines and azidohemicyanine dye, 1-methyl-4-(4′-azidostyryl)quinolinium iodide, was studied in an ether-ethanol matrix at 77 K and a methyltetrahydrofuran matrix at 5 K by means of electronic absorption spectroscopy and ESR technique. The formation of corresponding triplet nitrenes with absorption bands at 380–440 nm and zero-field splitting parameters of |D/h _cl = 0.781–0.790 cm^?1 and E = 0 was detected. It was found that the introduction of the positive charge into the azidostyrylquinoline molecule resulted in a bathochromic shift of the nitrene absorption band by ～40 nm and a decrease in the D by 0.005 cm^?1 due to charge transfer from the nitrene center to the quinoline moiety.