Synthesis of 19F nucleic acid–polymer conjugates as real-time MRI probes of biorecognition

Polymer-DNA conjugates in which one nucleic acid strand contains fluorine-substituted nucleobases have been prepared and characterised. The efficacy of these novel F-19 nucleic acid-polymer conjugates as sensitive and selective in vitro reporters of DNA binding events is demonstrated through a number of rapid-acquisition MR sequences. The conjugates respond readily and in a sequence specific manner to external target oligonucleotide sequences by changes in hybridisation. In turn, these structural changes in polymer-nucleotide conjugates translate into responses which are detectable in fluorine relaxation and diffusion switches, and which can be monitored by in vitro Spin Echo and DOSY NMR spectroscopy. Although complementary to conventional FRET methods, the excellent diagnostic properties of fluorine nuclei make this approach a versatile and sensitive probe of molecular structure and conformation in polymeric assemblies.

Nickel(II) meso-hydroxyporphyrin complexes revisited: Palladium-catalysed synthesis, electronic structures of derived oxy radicals, and oxidative coupling to a dioxoporphodimethene dyad

We report the synthesis and characterisation of new examples of meso-hydroxynickel(II) porphyrins with 5,15-diphenyl and 10-phenyl-5,15-diphenyl/diaryl substitu- tion. The OH group was introduced by using carbonate or hydroxide as nucleophile by using palladium/phosphine cat- alysis. The NiPor OHs exist in solution in equilibrium with the corresponding oxy radicals NiPor OC. The 15-phenyl group stabilises the radicals, so that the 1H NMR spectra of {NiPor OH} are extremely broad due to chemical exchange with the paramagnetic species. The radical concentration for the diphenylporphyrin analogue is only 1%, and its NMR line-broadening was able to be studied by variable-tempera- ture NMR spectroscopy. The EPR signals of NiPor OC are con- sistent with somewhat delocalised porphyrinyloxy radicals, and the spin distributions calculated by using density func- tional theory match the EPR and NMR spectroscopic obser- vations. Nickel(II) meso-hydroxy-10,20-diphenylporphyrin was oxidatively coupled to a dioxo-terminated porphodimethene dyad, the strongly red-shifted electronic spectrum of which was successfully modelled by using time-dependent DFT calculations.

Structural studies of the hen's egg lipovitellins. NMR and fluorescence investigations

The pH dependent reversible association-dissociation reaction of α- and β-lipovitellins from egg yolk has been studied by 1H NMR and fluorescence probe methods. Increased mobility of the choline methyl groups has been demonstrated on dissociation. The lipid methylene resonance of β-lipovitellin shows clear doublet character suggesting that the fatty acid chains exist in distinct environments. The high field component increases with temperature but is suppressed on treatment with pronase, suggesting a significant role for proteins in maintaining the differences in lipid environments. 1-Anilino-8-naphthalene sulfonate has been shown to bind less effectively to the monomeric lipovitellins. This is in agreement with earlier results suggesting that dissociation may be accompanied by increased hydration and conformational changes.

Synthetic and conformational studies on dehydroalanine-containing model peptides

Three model dipeptides containing a dehydroalanine residue (Ala) at the C-terminal, Boc-X-Ala-NHCH3 [X = Ala, Val, and Phe,] have been synthesized and their solution conformations investigated by 1H-NMR, IR, and CD spectroscopy. NMR studies on these peptides in CDCl3 clearly indicate that the NH group of dehydroalanine is involved in an intramolecular hydrogen bond. This conclusion is supported by IR studies also. Nuclear Overhauser effect (NOE) studies are also accommodative of an inverse -turn-type of conformation that is characterised by conformational angles of -70° and +70° around the X residue, and a C[stack i+1 ]H-Ni+2H interproton distance of 2.5 Å. It appears that unlike dehydrophenylalanine or dehydroleucine, which tend to stabilize -turn type of structures occupying the i + 2 position of the turn, dehydroalanine favors the formation of an inverse -turn, centered at the proceeding L-residue in such solvents as CDCl3 and (CD3)2SO. A comparison of solution conformation of Boc Val-Ala-NHCH3 with the corresponding saturated analogue, Boc-Val-Ala-NHCH3, is also presented and shows that dehydroalanine is responsible for inducing the turn structure. It may be possible to design peptides with different preferred conformations using the suitable dehydroamino acid.

Unraveling the packing pattern leading to gelation using SS NMR and X-ray diffraction: direct observation of the evolution of self-assembled fibers

A detailed understanding of the mode of packing patterns that leads to the gelation of low molecular mass gelators derived from bile acid esters was carried out using solid state NMR along with complementary techniques such as powder X-ray diffraction (PXRD), differential scanning calorimetry (DSC), thermogravimetric analysis (TGA) and polarizing optical microscopy (POM). Solid state C-13{H-1} cross polarization (CP) magic angle spinning (MAS) NMR of the low molecularmass gel in its native state was recorded for the first time. A close resemblance in the packing patterns of the gel, xerogel and bulk solid states was revealed upon comparing their C-13{H-1} CPMAS NMR spectral pattern. A doublet resonance pattern of C-13 signals in C-13{H-1}CPMAS NMR spectra were observed for the gelator molecules, whereas the non-gelators showed simple singlet resonance or resulted inthe formation of inclusion complexes/solvates. PXRD patterns revealed a close isomorphous nature of the gelators indicating the similarity in the mode of the packing pattern in their solid state. Direct imaging of the evolution of nanofibers (sol-gel transition) was carried out using POM, which proved the presence of self-assembled fibrillar networks (SAFINs) in the gel. Finally powder X-ray structure determination revealed the presence of two non-equivalent molecules in an asymmetric unit which is responsible for the doublet resonance pattern in the solid state NMR spectra.

Scanning Tunneling Spectroscopy on Pr0.68Pb0.32MnO3 single crystals

Scanning tunneling microscopy/spectroscopy studies were carried out on single crystals of colossal magnetoresistive manganite Pr0. 68Pb0.32MnO3 at different temperatures in order to probe their spatial homogeneity across the metal-insulator transition temperature TM-I(similar to 255 K). A metallic behavior of the local conductance was observed for temperatures T < TM-I. Zero bias conductance (dI/dV)v=(0), which is directly proportional to the local surface density of states at the Fermi level, shows a single distribution at temperatures T < 200 K suggesting a homogeneous electronic phase at low temperatures. In a narrow temperature window of 200 K < T < TM-I, however, an inhomogeneous distribution of (dI/dV)v=(0) has been observed. This result gives evidence for phase separation in the transition region in this compound.

Identification and characterization of a library of microheterogeneous cyclohexadepsipeptides from the fungus Isaria

Ten new cyclic hexadepsipeptides, six isariins and four isaridins, from the fungus Isaria have been identified and characterized by high-performance liquid chromatography, coupled to tandem electrospray ionization mass spectrometry (LC-ESIMS/MS). The isariins possess a beta-hydroxy acid residue and five alpha-amino acids, while isaridins contain a beta-amino acid, an alpha-hydroxy acid, and four alpha-amino acids. One- and two-dimensional NMR spectroscopy confirmed the chemical identity of some of the isariin fractions. Mass spectral fragmentation patterns of [M + H](+) ions reveal clear diagnostic fragment ions for the isariins and isaridins. Previously described cyclic depsipeptides, isarfelins from Isaria felina (Guo, Y. X.; Liu, Q. H.; Ng, T. B.; Wang H. X. Peptides 2005, 26, 2384), are now reassigned as members of the isaridin family. Examination of isaridin sequences revealed significant similarities with cyclic hexadepsipeptides such as destruxins and roseotoxins. The structure of an isariin (isariin A) investigated by NMR spectroscopy indicated the presence of a hybrid alpha beta C-11 turn, formed by the beta-hydroxy acid and glycine residues and a (D)Leu-(L)Ala type II' beta-turn. Additionally, the inhibitory effect of isariins and an isaridin on the intra-erythrocytic growth of Plasmodium falciparum is presented.

Structural Insights into the Acyl Intermediates of the Plasmodium falciparum Fatty Acid Synthesis Pathway THE MECHANISM OF EXPANSION OF THE ACYL CARRIER PROTEIN CORE

Acyl carrier protein (ACP) plays a central role in fatty acid biosynthesis. However, the molecular machinery that mediates its function is not yet fully understood. Therefore, structural studies were carried out on the acyl-ACP intermediates of Plasmodium falciparum using NMR as a spectroscopic probe. Chemical shift perturbation studies put forth a new picture of the interaction of ACP molecule with the acyl chain, namely, the hydrophobic core can protect up to 12 carbon units, and additional carbons protrude out from the top of the hydrophobic cavity. The latter hypothesis stems from chemical shift changes observed in C-alpha and C-beta of Ser-37 in tetradecanoyl-ACP. C-13, N-15-Double-filtered nuclear Overhauser effect (NOE) spectroscopy experiments further substantiate the concept; in octanoyl (C-8)- and dodecanoyl (C-12)-ACP, a long range NOE is observed within the phosphopantetheine arm, suggesting an arch-like conformation. This NOE is nearly invisible in tetradecanoyl (C-14)-ACP, indicating a change in conformation of the prosthetic group. Furthermore, the present study provides insights into the molecular mechanism of ACP expansion, as revealed from a unique side chain-to-backbone hydrogen bond between two fairly conserved residues, Ile-55 HN and Glu-48 O. The backbone amide of Ile-55 HN reports a pK(a) value for the carboxylate, similar to 1.9 pH units higher than model compound value, suggesting strong electrostatic repulsion between helix II and helix III. Charge-charge repulsion between the helices in combination with thrust from inside due to acyl chain would energetically favor the separation of the two helices. Helix III has fewer structural restraints and, hence, undergoes major conformational change without altering the overall-fold of P. falciparum ACP.

The syntheses, characterizations, X-ray crystal structures and properties of Cu(I) complexes of a bis-bidentate schiff base ligand

Bis-bidentate Schiff base ligand L and its two mononuclear complexes [CuL(CH3CN)(2)]ClO4 (1)and [CuL(PPh3)(2)]ClO4 (2)have been prepared and thoroughly characterized by elemental analyses, IR, UV-Vis, NMR spectroscopy and X-ray diffraction analysis. In both the complexes the metal ion auxiliaries adopt tetrahedral coordination environment. Their reactivity, electrochemical and photophysical behavior have been studied. Complex 1 shows reversible Cu-II/I couple with potential 0.74 V versus Ag/AgCl in CH2Cl2. At room temperature L is weakly fluorescent in CH2Cl2, however in Cu(I)complexes 1 and 2 the emission in quenched. (C) 2009 Elsevier B. V. All rights reserved.

Study of molecular reorientation and quantum rotational tunneling in tetramethylammonium selenate by H-1 NMR

H-1 NMR spin-lattice relaxation time measurements have been carried out in [(CH3)(4)N](2)SeO4 in the temperature range 389-6.6K to understand the possible phase transitions, internal motions and quantum rotational tunneling. A broad T, minimum observed around 280K is attributed to the simultaneous motions of CH3 and (CH3)(4)N groups. Magnetization recovery is found to be stretched exponential below 72 K with varying stretched exponent. Low-temperature T-1 behavior is interpreted in terms of methyl groups undergoing quantum rotational tunneling. (c) 2007 Elsevier Inc. All rights reserved.

NMR study of internal motions in certain iron group fluosilicates

NMR study of ferrous fluosilicate hexahydrate indicated the presence of motion of both proton and fluorine nuclei. Only a single narrow line was observed for protons for any arbitrary orientation of a single crystal with respect to the applied magnetic field. This can be interpreted in terms of a phase-correlated flip motion of the interproton vectors between two disordered orientations or in terms of a hindered rotation of the Fe(H2O) 6 octahedron about the fourfold axes, together with the flip motion. The fluorine second moment indicated that the SiF6 octahedron also is undergoing reorientation. The temperature variation of the powder linewidth showed a transition around 195°K and led to rather low values for the potential barriers hindering the motions. No significant temperature variation of the linewidth was observed for hexahydrated cobalt fluosilicate in the temperature range between 90°K and room temperature. Similar observations in a powder sample of tetrahydrated copper fluosilicate also showed the presence of internal motions. The linewidth transition in this case took place at about 220°K and was found to be rather abrupt. The potential barrier for the motion was found to be relatively high.

Synthesis and characterization of polyaniline salts with phenoxy acetic acids by emulsion polymerization

Polyaniline salts have been synthesized by chemical oxidative polymerization of aniline in the presence of phenoxy acetic acid and its two derivatives using emulsion method at room temperature and characterized by different techniques such as infrared, H-1 and C-13 NMR, UV-visible spectroscopy, SEM, wide angle X-ray diffractograms and conductivity measurements. These polyaniline salts have the desirable property of high solubility for processibility in solvents such as DNIF, DMSO and a mixture of CHCl3 and acetone and they exhibit fairly good conductivity of similar to 3.0 x 10(-3) S cm(-1). The variations in solubility, conductivity and morphology with the protonating strength of the dopants are examined.

Spectroscopy of tissue triglyceride composition : In vitro and in vivo studies

Lipid analysis is commonly performed by gas chromatography (GC) in laboratory conditions. Spectroscopic techniques, however, are non-destructive and can be implemented noninvasively in vivo. Excess fat (triglycerides) in visceral adipose tissue and liver is known predispose to metabolic abnormalities, collectively known as the metabolic syndrome. Insulin resistance is the likely cause with diets high in saturated fat known to impair insulin sensitivity. Tissue triglyceride composition has been used as marker of dietary intake but it can also be influenced by tissue specific handling of fatty acids. Recent studies have shown that adipocyte insulin sensitivity correlates positively with their saturated fat content, contradicting the common view of dietary effects. A better understanding of factors affecting tissue triglyceride composition is needed to provide further insights into tissue function in lipid metabolism. In this thesis two spectroscopic techniques were developed for in vitro and in vivo analysis of tissue triglyceride composition. In vitro studies (Study I) used infrared spectroscopy (FTIR), a fast and cost effective analytical technique well suited for multivariate analysis. Infrared spectra are characterized by peak overlap leading to poorly resolved absorbances and limited analytical performance. In vivo studies (Studies II, III and IV) used proton magnetic resonance spectroscopy (1H-MRS), an established non-invasive clinical method for measuring metabolites in vivo. 1H-MRS has been limited in its ability to analyze triglyceride composition due to poorly resolved resonances. Using an attenuated total reflection accessory, we were able to obtain pure triglyceride infrared spectra from adipose tissue biopsies. Using multivariate curve resolution (MCR), we were able to resolve the overlapping double bond absorbances of monounsaturated fat and polyunsaturated fat. MCR also resolved the isolated trans double bond and conjugated linoleic acids from an overlapping background absorbance. Using oil phantoms to study the effects of different fatty acid compositions on the echo time behaviour of triglycerides, it was concluded that the use of long echo times improved peak separation with T2 weighting having a negligible impact. It was also discovered that the echo time behaviour of the methyl resonance of omega-3 fats differed from other fats due to characteristic J-coupling. This novel insight could be used to detect omega-3 fats in human adipose tissue in vivo at very long echo times (TE = 470 and 540 ms). A comparison of 1H-MRS of adipose tissue in vivo and GC of adipose tissue biopsies in humans showed that long TE spectra resulted in improved peak fitting and better correlations with GC data. The study also showed that calculation of fatty acid fractions from 1H-MRS data is unreliable and should not be used. Omega-3 fatty acid content derived from long TE in vivo spectra (TE = 540 ms) correlated with total omega-3 fatty acid concentration measured by GC. The long TE protocol used for adipose tissue studies was subsequently extended to the analysis of liver fat composition. Respiratory triggering and long TE resulted in spectra with the olefinic and tissue water resonances resolved. Conversion of the derived unsaturation to double bond content per fatty acid showed that the results were in accordance with previously published gas chromatography data on liver fat composition. In patients with metabolic syndrome, liver fat was found to be more saturated than subcutaneous or visceral adipose tissue. The higher saturation observed in liver fat may be a result of a higher rate of de-novo-lipogenesis in liver than in adipose tissue. This thesis has introduced the first non-invasive method for determining adipose tissue omega-3 fatty acid content in humans in vivo. The methods introduced here have also shown that liver fat is more saturated than adipose tissue fat.

Selective Homonuclear Decoupling in H-1 NMR: Application to Visualization of Enantiomers in Chiral Aligning Medium and Simplified Analyses of Spectra in Isotropic Solutions

The proton NMR spectral complexity arising due to severe overlap of peaks hampers their analyses in diverse situations, even by the application of two-dimensional experiments. The selective or complete removal of the couplings and retention of only the chemical shift interactions in indirect dimension aids in the simplification of the spectrum to a large extent with little investment of the instrument time. The present study provides precise enantiodiscrimination employing more anisotropic NMR parameters in the chiral liquid crystalline medium and differentiates the overlapped peaks of many organic molecules and peptides dissolved in isotropic solvents.