Infrared absorption and raman scattering of sulfate groups of heparin and related glycosaminoglycans in aqueous solution

The i.r. spectra for aqueous solutions of sulfated glycosaminoglycans and model compounds in the transmittance “window” region of the solvent (1400-950 cm^?1) are dominated by the strong and complex absorption centered at ～1230 cm^?1 and associated with the antisymmetric stretching vibrations of the SO groups. Primary and secondary O-sulfate groups absorb at somewhat higher frequencies (1260-1200 cm^?1) than N-sulfates (～1185 cm^?1). Each sulfate band lends itself to quantitative applications, especially within a given class of sulfated polysaccharide. Laser-Raman spectra of heparin and model compounds have been obtained in aqueous solution and in the solid state. The most-prominent Raman peak (at ～1060 cm^?1) is attributable to the symmetrical vibration of the SO groups, with N-sulfates emitting at somewhat lower frequencies (～1040 cm^?1) than O-sulfates. The Raman pattern in the 950-800 cm^?1 region (currently used in the i.r. for distinguishing between types of sulfate groups) also involves vibrations that are not localized only in the COS bonds.     

Raman study of crystalline peptides containing beta turns

The Raman spectra of crystalline H-ProLeuGlyNH₂ which has a type II β turn, crystalline S-benzylCysProLeuGlyNH₂ which has a type I β-turn, and crystalline gramicidin S which has two β turns and β-sheet structure in its conformation, were investigated. The amide I and amide III bands of the peptides with β turns were generally different from those which are diagnostic for α-helix and β-sheet conformations. The patterns of the amide I and amide III bands, when examined together, indicate that Raman spectra can provide diagnostic evidence for β-turn structure in peptides.     

Resonance Raman spectroscopy of chemically modified retinals: Assigning the carbon-methyl vibrations in the resonance Raman spectrum of rhodopsin

To assign the observed vibrationsl modes in the resonance Raman spectrum of the retinylidene chromophore of rhodopsin, we have studied chemically modified retinals. The series of analogs investigated are the n-butyl retinals substituted at C₉ and C₁₃. The results obtained for the 11-cis isomer have clearly assigned the CCH₃ vibrational frequencies observed in the spectrum of the retinylidene chromophore. The data show that the C₍₉₎CH₃ stretching vibration can be assigned to the vibrational mode observed in the 1017 cm^?1 region, and the vibration detected at 997 cm^?1 can be assigned to the C₍₁₃CH₃ vibration. The C₍₅₎CH₃ stretching mode does not contribute to the vibrations observed in this region. The splitting in the C_(n)CH₃ (n = 9, 13) vibration is characteristic of the 11-cis conformation. The results on the modified retinals do not support the hypothesis that the splitting arises from equilibrium mixtures of 11-cis, 12-s-cis and 11-cis, 12-s-trans in solution. Thus, this splitting cannot be used to determine whether the chromophore in rhodopsin is in a 12-s-cis or 12-s-trans conformation. However, our results demonstrate that there are other vibrational modes in the spectra which are sensitive to this conformational equilibrium and we use the presence of a strong ~ 1271 cm^?1 mode in bovine and squid rhodopsin spectra as an indication that the chromophore in these pigments is 11-cis, 12-s-trans.     

Electrostatically induced change of the conformational order of charged lipid membranes

Raman spectroscopy and X-ray diffraction are used to investigate the influence of surface charges on the structure of ionizable lipid membranes of dimyristoylmethylphosphatidic acid. The membrane surface charge density is regulated by varying the pH of the aqueous phase. Changes of the conformational order of the lipid chains are determined from the intensity of the CC stretch chain vibrations around 1100 cm^?1 in a lipid Raman spectrum. In going from an electrical neutral to a negatively charged membrane, the conformational order is reduced by 5% in the ordered and by 9% in the fluid membrane phase, corresponding to 0.6 and 0.8 CC bonds, respectively, which change from a trans to a gauche conformation. The electrostatically induced conformational change is mainly concentrated at the lipid chain ends as indicated by the spectral variations of the 890 cm^?1 CH₃ rocking band of the chain termini. The X-ray diffraction experiments show that increasing the surface charge density in the ordered membrane phase leads to a lateral expansion of the packing of the lipid polar groups, whereas the packing of the lipid chains in a plane perpendicular to the chain axes remains constant, indicating an increase of the tilt of the lipid chains from δ = 10° (pH 3) to δ = 27° (pH 9).     

Structural and vibrational characteristics of the tetrasulfatodimolybdenum ions with MoMo bond orders of 3.5 and 4.0

The compound K₄[Mo₂(SO₄)₄]Br·4H₂O has been made and its crystal structure determined. Space group P4/mnc; unit cell dimensions, a = 11.903(2), c = 8.021(1) Å, V = 1136(1) ų. The compound is isomorphous with the analogous chloride whose structure has been reported. The MoMo and MoBr distances are 2.169(2) and 2.926(1) Å, respectively and the [Mo₂(SO₄)₄] ³⁻ ions reside on crystallographic special positions with 4/m symmetry. The Raman spectra of both the bromo and chloro compounds have been measured and the MoMo stretching frequency is 370 ± 1.5 cm⁻¹ in each, for the compounds containing the natural isotopic distribution of molybdenum. The chloro compound has been prepared containing the pure isotope ⁹²Mo as well, and the Raman spectra recorded. The v(MoMo) band is shifted by 6.8 ± 0.5 cm⁻¹. The compound K₄[Mo₂(SO₄)₄]·2H₂O has also been prepared with Mo at natural abundance and with the pure isotope ¹⁰⁰Mo, whereby a shift of 8.5 ± 0.5 cm⁻¹ was found. These and other results will be discussed with regard to the similarity of the Raman spectra of the Mo₂(S0₄)₄³⁻ and M0₂(S0₄)₄⁴⁻ species.     

MonodentateN coordination of 1aza4oxo1,3butadienes [R1NC(R2)C(R3)O] to platinum(II). X-ray structure of trans-[PtCl2(PEt3){σ-N-(t-BuNCHC(Me)O)}]

Reaction of dimeric trans-[PtCl₂(PR₃)]₂ with 1-aza-4-oxo-1,3-butadienes [R¹NC(R²)C(R³)O, R³ = Me, Ph, OMe, NEt₂] in a 1:2 molar ratio results in almost quantitative formation of mononuclear complexes trans·[PtCl₂(PR₃){σ-N-(R¹NC(R²)C(R³)O)}]. The ligands are bonded in the monodentate σ-N bonding mode to the platinum(II) centre. This has been established by an X-ray structure determination of trans-[PtCl₂(PEt₃){σ-N-(t-BuNCHC(Me)O)}]. Crystals of the latter compound are orthorhombic with space group Pc2₁n; cell constants are a = 14.712(3), b = 15.053(2), c = 9.025(5) Å, Z= 4 and R_w = 0.056 for 3281 reflections. The 1aza4oxol,3butadiene (α-iminoketone for R³ is alkyl or aryl) has the E-configuration about the imine bond (CN 1.34(4) Å), with a C(5)C(6) distance of 1.44(5) Å and a NC(5)/ C(6)O torsion angle of 89(4)°. As a result of this ligand conformation, the acetyl hydrogen atoms are positioned (on average) into the neighbourhood of the Pt-atom above the Pt-coordination plane. Infrared and NMR (¹H, ¹³C, ³¹p) data show that these structural features are also predominant in solution.     

Laser-raman spectroscopic study of carbohydrates: 1-thio-β-d-hexopyranosides

Some β-d-hexopyranosides of 1-thio-d-glucose, 2-acetamido-2-deoxy-1-thio-d-glucose, and 1-thio-d-galactose were examined by laser-Raman spectroscopy. An anomeric CH bending vibration was found at 891 ± 7 cm^-1 for all compounds investigated; thus, the anomers of these sugars can be differentiated by Raman spectroscopy. The N-acetyl group and carboxyl group can also be detected by Raman spectroscopy. Unlike protein samples, the carbohydrates in aqueous solution yield less useful information from Raman spectra than in the solid state; this is due to the extensive overlapping of carbohydrate OH bands with water OH bands.     

Pre-resonance Raman spectra and conformations of nystatin in powder,solution and phospholipid-cholesterol multilayers

A Raman scattering study of the channel-forming polyene antibiotic nystatin, is reported in the solid state, in organic and aqueous solutions as well as in phospholipid and phospholipid-cholesterol multilayers. Measurements of the solid and solution spectra as a function of excitation wavelengths in the 459.7–514.5 nm range, and the phospholipid spectra as a function of temperature in the 10–60°C range, have also been made. The spectral features indicate a pre-resonance-enhanced Raman spectrum in which the CC and CC stretching modes of the polyene segment of nystatin are dominant. However, in contrast to previously published results on the nearly isostructural polyene antibiotic amphotericin B, a line at 1610 cm^?1 assignable to the CO stretching mode is also observed to be strongly resonance enhanced. This is explained by a postulated ground-state conformation model in which a twisting of the molecule is facilitated by the break in the polyene chain. This allows the CO group at one end of the molecule to be aligned along the polyene unit at the other end, and the CC stretching vibration, which is strongly modulated by the polyene π → π1 excited state, to mix with the CO stretching vibration. The peak frequencies and intensities of the CC and CC stretching modes in nystatin, however, remain essentially unchanged compared with amphotericin B, indicating that the polyene units in nystatin remain planar and trans both in the ground and excited states.The intensity of the CO mode with respect to the CC stretching mode was observed to vary appreciably with nystatin environment, indicating a     

Infrared and raman study of matrix isolated M(SO2) molecules. The structure of the molecular ion SO2−

The IR and Raman spectra of Cs(SO₂), K(SO₂) and Na(SO₂) molecules were studied by ³²S/³⁴S and ¹⁶O/¹⁸O isotopic substitution technique. These molecules have a planar ring configuration of C_2v symmetry with the OSO angle equal to 109°±5° and the SO bond length of 0.149±0.001 nm. The alkali metal atom interacts symmetrically with the oxygen atoms of the SO₂⁻ group. The doubling observed for the vibrations of Cs(S¹⁶O¹⁸O) was attributed to a matrix effect.     

Synthesis,structural characterization,and properties of the organothorium alkylthiolate complex [(CH3)5C5]2Th(SCH2CH2CH3)2

This contribution reports the synthesis and characterization of the organothorium alkylthiolate complex [(CH₃)₅C₅]₂Th(SCH₂CH₂CH₃)₂. This compound crystallizes in the monoclinic space group C2/c (#15) with four molecules in a cell of dimensions a=19.066(2), b=11.603(1), c=16.379(2) Å, and β=130.08(1)°. Least-squares refinement led to a value for the conventional R index (on F_o) of 0.040 for 132 variables and 2030 observations having F_o²⩾3σ(F_o²). The molecular structure consists of an unexceptional ‘bent sandwich’ [(CH₃)₅C₅]₂Th fragment coordinated to two n-propylthiolate ligands. The ThS bond distance is 2.718(3) Å; the SC(α) distance, 1.78(2) Å; the ThSC(α) angle, 108.3(5)°; and the SThS′ angle, 102.5(2)°. Contrasts are drawn with the structures of analogous actinide alkoxides     

IR and Raman spectroscopy in the study of carotenoids of <Emphasis Type="Italic">Cladophora rivularis</Emphasis> algae

Using Raman and infrared spectroscopy it has been found that during the normal life of algae (pH changes from 8.0 to 9.0) the content of carotenoids increases and the molecules change their conformation: the contribution of–C=C–bonds of the polyene chain of a carotenoid molecule (Raman spectroscopy) is reduced and the contribution of methyl groups (～2940 cm^–1) and aromatic C–H-plane deformation vibrations (band at 1050 cm^–1) of carotenoid molecules (infrared spectroscopy) decreases as well. It is the opinion of the authors that a change in the extracellular pH within the normal range has no influence on the content of chlorophyll a and b, but tends to increase the content and alter the conformation or structure of carotenoid molecules.     

Conformational characteristics of polypeptides containing isolated L-proline residues with cis peptide bonds

The conformational characteristics of the peptide sequence X-l-Pro, where X  Gly or l-Ala and the peptide bond joining X and l-Pro is cis, are evaluated. Semi-empirical potential functions are used to estimate the contributions to the conformational energy made by the non-bonded van der Waals' and electrostatic interactions and the intrinsic torsional potentials about the NC^a and C^aC′ bonds. Rotations φ₁ and ψ₁ about the NC^a and C^aC′ bonds in residue X and rotation ψ₂ about the C^aC′ bond in l-Pro are permitted, while the angle of rotation φ₂ about the NC^a bond in l-Pro is fixed at 120 ° by the pyrrolidine ring. The presence of the cis peptide bond connecting X and l-Pro renders the backbone rotations φ₁, ψ₁ in X dependent upon the rotation ψ₂ about the C^aC′ bond in l-Pro. (Interdependence of rotations in neighboring residues joined by a cis peptide bond was previously observed in l-alanine oligomers.) The number of energetically allowed conformations for the Gly and l-Ala residues preceding a cis peptide bond l-Pro residue are found to be substantially reduced from those permitted when the peptide bond is trans or when l-Pro is replaced by an amino acid residue. On the other hand, ψ₂ = 100 to 160 ° (cis′) and 300 to 0 ° (trans′) are found to be the lowest energy conformations of the l-Pro residue irrespective of the cis or trans conformation of the X-l-Pro peptide bond.     

Crystal structure of methyl 2,6-dichloro-2,6-dideoxy-3,4-O-isopropylidene-α-D-altropyranoside. A pyranoside system close to a skew-boat conformation

The crystal structure of methyl 2,6-dichloro-2,6-dideoxy-3,4-O-isopropylidene-α-D-altropyranoside (1) has been determined by X-ray diffraction. The compound crystallizes in the orthorhombic system, space group P2₁2₁2₁, with unit-cell dimensions a  7.932, b  8.133, and c  20.447 Å. The structure was solved by the heavy-atom method and refined by the least-squares technique to an R value of 0.047 by using 736 intensities measured on a diffractometer. The pyranoside ring is close to a skew-boat conformation, with C-2 and C-5 being maximally displaced from the least-squares plane through the remaining four atoms. The H-1H-2 dihedral angle of  158° is in agreement with the J_1,2 value of 4.5 Hz. Thus the solid-state conformation appears to correspond with the conformation in solution. The dioxolane ring is in a twist form, with O-4 and, C-8 puckered on opposite sides of the plane of the other ring atoms. The pyranose-ring substituents are in equatorial and pseudoequatorial orientations. The hydrogen atoms at C-3 and C-4 are in a cis arrangement. The orientations of both the methoxyl group and the chloromethyl group with respect to the ring are gauche—trans. The exocyclic anomeric C-1O-1 bond-distance (1.39 Å) is the shortest CO bond in the structure. The intracyclic CO bonds are significantly different, C-1O-5 being less than C-5O-5.     

Etude cristallographique des β-d-glucopyranosyl- et β-d-mannopyranosyl-benzènes acétylés,analogues de nucléosides pyrimidiques

The structures of the two title C-glycopyranosylarene nucleosides have been determined by X-ray diffraction. The aim of this work was to relate the conformation around the extracyclic C-1C-7 bond to steric hindrance between the pyranose and benzene rings. The torsion angles observed in the two compounds (O-5C-1C-7C-8: +61,7° for 1, ?13,4° for 2) signify of a C-2 configurational modification. Moreover, the interaction between O-5 and an o-phenyl hydrogen could explain the particular conformation of the aryl substituent in 2.     

Direct electrochemical oxidation of Clostridium pasteurianum ferredoxin: Identification of facile electron-transfer processes relevant to cluster degradation

Rapid oxidation processes relevant to the degradation of [4Fe4S] clusters in Clostridium pasteurianum ferredoxin were studied via direct (unmediated) heterogeneous electron transfer at a pyrolytic graphite electrode. Differential-pulse voltammograms of native [4Fe4S] ferredoxin showed two well-defined oxidation peaks corresponding to apparent E-values of +793 and +1120 mV at 5°C. Direct involvement of the cluster was established through parallel experiments with the 2[4Fe4Se] derivative for which peak positions were shifted. Square-wave voltammetry showed that the product of the first electron transfer, which may correspond to the ‘super-oxidised’ [4Fe4S]³⁺ oxidation level, undergoes rapid degradation (t_{$\text{1}\text{2}$} < 1.6 ms at 5°C). The second oxidation process, as characterised by a significant (?100 mV) negative shift upon selenium substitution, very likely represents oxidation of S(Se) still associated with the protein and possibly contained within the remaining FES(Se) substructure.     

Raman intensities of carbon-carbon stretching modes in a model membrane

Laser-Raman spectra of L-α-dimyristoylphosphatidylcholine (DMPC) liposomes in the spectral range 1000–1200 cm^?1 were obtained as a function of temperature from ?80 to +50°C. The triplet found in this spectral region was resolved into Lorentzian components by means of an iterative computer program. The peak intensities, band widths, and band areas of the resolved 1062 cm^?1 and 1130 cm^?1 bands, assigned to CC stretching vibrations of trans segments, were evaluated as a function of temperature. While the peak intensities of the bands decrease substantially with temperature, the band widths show a considerable increase. The change in band areas is therefore smaller than the change in peak heights. Experiments with all trans carboxylic acids showed that in these compounds the area of the Raman bands at 1062 cm^?1 and 1130 cm^?1 is proportional to the number of trans bonds. The variation with temperature of the number of trans and gauche bonds in the studied phospholipid is reflected by the change of the area of the 1130 cm^?1 Raman band.     

6-Azauridine, a nucleoside with unusual ribose conformation. The molecular and crystal structure

The cytostatic analogue ribo-6-azauridine crystallizes in the orthorhombic space group P2₁2₁2₁ with eight molecules per unit cell of dimensions $\text{a = 20.230, b = 7.709, c = 12.863}\text{A}\text{?}$. A trial structure was obtained by direct methods. Least-squares refinement of co-ordinates and anisotropic thermal parameters based on 1998 reflections measured on a four-circle diffractometer led to a discrepancy index R = 4.0%. Like uridine, 6-azauridine has the anti conformation about the glycosidic bond and a C(3′)-endo sugar pucker. Unlike uridine, it exhibits a close approach of N(6) to C(2′) at only 2.814 and 2.844 Å in the two independent molecules, and a C(5′)(5′) bond that is gauche to C(4′)O(1′) but trans to C(4′)C(3′); this conformation about a C(4′)C(5′) bond has never been observed before for C(3′)-endo puckered riboses in the crystalline state. The crystal structure displays a pseudo-A face centering and very similar conformational parameters for the two independent molecules. Every OH and NH group in the structure serves as a proton donor in a hydrogen bond, including an unusual N(3)—H(3) … O(1′) link. Molecular orbital calculations by the extended Hückel method indicate that from uridine to 6-azauridine the net charge changes sign at ring positions 5 and 6 and disappears at 1.     

Main group metal halide complexes with sterically hindered thioureas. IX. New complexes of selected post-transition metals and 1,3-dimethyl-2(3H)-imidazolethione and a structural investigation of infrared peak shifts associated with coordination

Five new complexes of sterically hindered 1,3- dimethyl-2(3H)-imidazolethione (dmit) with the chlorides of Cd(II), Hg(II), Te(II), Sn(IV) and Sb(V) have been synthesized and characterized. The previously reported Zn(II) adduct was also synthesized and further characterized. These complexes were of the general formula MX_n(dmit)_m where n = 2 and m = 2 when M = Zn, Cd, Hg and Sn; and n = 2 and m = 4 for Te(II). The only 1:1 adduct observed was SbCl₅dmit, and its chemistry is more complex giving rise to unique redox products upon heating in solution. Solid state spectra of these complexes as well as for dmit complexes are reported and discussed with regard to the coordination sensitive NCN asymmetric stretch and the CS stretch observed not only for dmit complexes but for tetramethylthiourea (tmtu) complexes reported in the literature as well. Greatest shifts on coordination are observed with the NCN asymmetric stretch for tmtu causing shifts to higher wave numbers ranging from 55 to 95 cm⁻¹ relative to free tmtu. Shifts are explained on the basis of observed crystal structures of tmtu adducts showing a greater CN double bond character. Dmit adducts show much smaller shifts both to higher and lower wave numbers for this mode relative to free ligand, and the CS stretch shows little change also. Comparison to known crystal structures show little change in the bond distances of the dmit ligand upon coordination. Inductive effects based on correlations of shift magnitude to the Sanderson group electronegativity (SGEN) of the acceptor seem to be unrelated with the exception of a small positive correlation observed for the NCN asymmetric stretch of tmtu.     

Kristallstruktur von 2,3,4-tri-O-acetyl-β-D- xylopyranosylchlorid

Although 2,3,4-tri-O-acetyl-β-D-xylopyranosyl chloride is shown by n.m.r. data to be 80 percent in the ¹C₄ conformation in chloroform solution, it crystallizes in the normal ⁴C₁ conformation as shown by a three-dimensional, X-ray structure analysis. The crystals are orthorhombic, space group P2₁2₁2₁. The phase problem was solved by the heavy-atom method. The parameters were refined to an R-value of 0.039 for 1101 structure factors. With the chlorine atom being in equatorial position in the ⁴C₁ conformation, the C-1O-6 bond is not shortened and the C-1Cl-1 bond is not lengthened. These results are in agreement with comparable values for cis-2,3-dichloro-1,4-dioxane.