Structural characterisation of a uracil containing hairpin DNA by NMR and molecular dynamics

Three-dimensional (3D) structure of a hairpin DNA d-CTAGAGGATCCTTTUGGATCCT (22mer; abbreviated as U4-hairpin), which has a uracil nucleotide unit at the fourth position from the 5' end of the tetra-loop has been solved by NMR spectroscopy. The H-1 resonances of this hairpin have been assigned almost completely. NMR restrained molecular dynamics and energy minimisation procedures have been used to describe the 3D structure of the U4 hairpin. This study establishes that the stem of the hairpin adopts a right handed B-DNA conformation while the T-12 and U-15 nucleotide stack upon 3' and 5' ends of the stem, respectively. Further, T-14 stacks upon both T-12 and U-15 while T-13 partially stacks upon T-14. Very weak stacking interaction is observed between T-13 and T-12. All the individual nucleotide bases adopt 'anti' conformation with respect to their sugar moiety. The turning phosphate in the loop is located between T-13 and T-14. The stereochemistry of U-15 mimics the situation where uracil would stack in a B-DNA conformation. This could be the reason as to why the U4-hairpin is found to be the best substrate for its interaction with uracil DNA glycosylase (UDG) compared to the other substrates in which the uracil is at the first, second and third positions of the tetra-loop from its 5' end, as reported previously.

Catalytic oxidative polymerization of 1,1-diphenylethylene at ambient temperature and potential application of peroxide macroinitiator

The Co(II)TPP(Py) complex was used as an efficient dioxygen carrier for the radical polymerization of 1,1-diphenylethylene (DPE), which has a low ceiling temperature, at ambient temperature and low oxygen pressure. The mechanism of polymerization is discussed' on the basis of kinetic data, W-vis, ESR, and H-1 NMR studies. The rate of polymerization (RP) and number-average molecular weights (M) of poly(1,1-diphenylethylene peroxide) (PDPEP) are higher and the polydispersity is lower than in 2,2'-azobis(isobutyronitrile) (AIBN) initiated polymerization. PDPEP was further. used as a macroinitiator for the polymerization of MMA. The polymerization obeys classical kinetics. The K-2 value of the PDPEP has been determined from the slope of R-P(2) VS [M](2)[I], which reveals that it can also be used at higher temperature for the polymerization. An "active" PMMA was also synthesized, containing initiating segments in the polymer backbone.

Half-sandwich (eta(6)-arene)ruthenium(II) chiral Schiff base complexes: Analysis of the diastereomeric mixtures in solution by 2D-NMR spectroscopy

2D NMR spectroscopy has been used to determine the metal configuration in solution of three complexes, viz. [(eta(6)-p-cymene)Ru(L*)Cl] (1) and [(eta(6)-p-cymene)Ru(L*)(L')] (ClO4) (L' = H2O, 2; PPh3, 3), where L* is the anion of (S)-(1-phenylethyl)salicylaldimine. The complexes exist in two diastereomeric forms in solution. Both the (R-Ru,S-C)- and (S-Ru,S-C)-diastereomers display the presence of attractive, CH/pi interaction involving the phenyl group attached to the chiral carbon and the cymene ring hydrogens. This interaction restricts the rotation of the C*-N single bond and, as a result, two structural types with either the hydrogen atom attached to the chiral carbon (C*) or the methyl group attached to C* in close proximity of the cymene ring protons get stabilized. Using 2D NMR spectroscopy as a tool, the spatial interaction involving these protons are studied in order to obtain the metal configuration(s) of the diastereomeric complexes in solution. This technique has enabled us to determine the metal configuration as (R-Ru,S-C) for the major isomers of 1-3 in solution.

Implementation of conditional phase-shift gate for quantum information processing by NMR, using transition-selective pulses

Experimental realization of quantum information processing in the field of nuclear magnetic resonance (NMR) has been well established. Implementation of conditional phase-shift gate has been a significant step, which has lead to realization of important algorithms such as Grover's search algorithm and quantum Fourier transform. This gate has so far been implemented in NMR by using coupling evolution method. We demonstrate here the implementation of the conditional phase-shift gate using transition selective pulses. As an application of the gate, we demonstrate Grover's search algorithm and quantum Fourier transform by simulations and experiments using transition selective pulses. (C) 2002 Elsevier Science (USA). All rights reserved.

Solid state structural and solution studies on the formation of a flexible cavity for anions by copper(I) and 1,2-bis(diphenylphosphino)ethane

Copper(l) complexes of 1,2-bis(diphenylphosphino)ethane (dppe) with a stoichiometry Cu-2(dppe)(3)(X)(2) [X- = CN- (1), SCN- (2), NO3- (3)] are obtained from direct reactions of CuX and dppe. The complexes are structurally and spectroscopically (NMR and IR) characterized. The structure of the [Cu-2(dPPe)(3)](2+) dication is similar to the structural motif observed in many other complexes with a chelating dppe and a bridging dppe connecting two copper centers. In complexes 1 -3, the anions are confined to the cavity formed by the phosphines which force a monodentate coordination mode despite the predominant bidentate/bridging character of the anions. The coordination angles rather than the thermochemical radii dictate the steric requirement of anions. While the solution behavior of 3, with nitrate, is similar to complexes studied earlier, complexes with pseudohalides exhibit new solution behavior. (C) 2002 Elsevier Science Ltd. All rights reserved.

Twisted aromatics, 9-anthryl and 1-pyrenyl terpyridines organize into novel multi-directional 'ladder-like' motifs in the solid state

9-Anthryl and 1-pyrenyl terpyridines (1 and 2, respectively), key precursors for the design of novel fluorescent sensors have been synthesized and characterized by H-1 NMR, mass spectroscopy and X-ray crystallography. Twisted molecular conformations for each 1 and 2 were observed in their single crystal structures. Energy minimization calculations for the 1 and 2 using the semi-empirical AM1 method show that the 'twisted' conformation is intrinsic to these systems. We observe interconnected networks of edge-to-face CH...pi interactions, which appear to be cooperative in nature, in each of the crystal structures. The two twisted molecules, although having differently shaped polyaromatic hydrocarbon substituents, show similar patterns of edge-to-face CH...pi interactions.The presently described systems comprise of two aromatic surfaces that are almost orthogonal to each other. This twisted or orthogonal nature of the molecules leads to the formation of interesting multi-directional ladder like supramolecular organizations. A combination of edge-to-face and face-to-face packing modes helps to stabilize these motifs. The ladder like architecture in 1 is helical in nature. (C) 2002 Published by Elsevier Science B.V.

Synthesis, structural characterization, thermal studies and chain dynamics of poly(methacrylonitrile peroxide) by NMR spectroscopy

Poly(methacrylonitrile peroxide) (PMNP) has been synthesized from methacrylonitrile by free radical initiated oxidative polymerization and characterized by different spectroscopic methods. NMR spectroscopy confirmed the alternating copolymer structure with labile peroxy bonds in the main chain. The extreme instability of PMNP was noted from FTIR spectroscopy. Thermal degradation studies by using differential scanning calorimetry and thermogravimetry have revealed that PMNP degrades highly exothermically and the heat of degradation, 42.5 kcal mol−1, is of the same order as that reported for other vinyl polyperoxides. Mass spectral fragmentation pattern under electron impact (EI) condition has also been investigated. The mechanism of the primary exothermic degradation has been substantiated by thermochemical calculations. The chain dynamics of the polyperoxide chain has been studied by means of 13C spin–lattice relaxation times (T1) of the main chain as well as the side chain carbons. The temperature dependence of the spin–lattice relaxation times shows that the PMNP is more flexible compared to the analogous poly(styrene peroxide).

Synthesis and DNA binding studies of Ni(II), Co(II), Cu(II) and Zn(II) metal complexes of N(1),N(5)-bis[pyridine-2-methylene]-thiocarbohydrazone Schiff-base ligand

The thiocarbohydrazone Schiff-base ligand with a nitrogen and sulphur donor was synthesized through condensation of pyridine-2-carbaldehyde and thiocarbohydrazide. Schiff-base ligands have the ability to conjugate with metal salts. A series of metal complexes with a general formula [MCl(2)(H(2)L)]center dot nH(2)O (M=Ni, Co, Cu and Zn) were synthesized by forming complexes of the N(1),N5-bis[pyridine-2-methylene]thiocarbohydrazone (H2L) Schiff-base ligand. These metal complexes and ligand were characterized by using ultraviolet-visible (UV-Vis), Fourier Transform Infrared (FT-IR), (1)H and (13)C NMR spectroscopy and mass spectroscopy, physicochemical characterization, CHNS and conductivity. The biological activity of the synthesized ligand was investigated by using Escherichia coli DNA as target. The DNA interaction of the synthesized ligand and complexes on E. coli plasmid DNA was investigated in the aqueous medium by UV-Vis spectroscopy and the binding constant (K(b)) was calculated. The DNA binding studies showed that the metal complexes had an improved interaction due to trans-geometrical isomers of the complexes than ligand isomers in cis-positions. (C) 2011 Elsevier B.V. All rights reserved.

Spin State Selective Excitation of Single Quantum Transitions Using Multiple Quantum Spectroscopy- an Aid to Analyse Complex Proton NMR spectra of Oriented Molecules

NMR spectra of molecules oriented in liquid-crystalline matrix provide information on the structure and orientation of the molecules. Thermotropic liquid crystals used as an orienting media result in the spectra of spins that are generally strongly coupled. The number of allowed transitions increases rapidly with the increase in the number of interacting spins. Furthermore, the number of single quantum transitions required for analysis is highly redundant. In the present study, we have demonstrated that it is possible to separate the subspectra of a homonuclear dipolar coupled spin system on the basis of the spin states of the coupled heteronuclei by multiple quantum (MQ)−single quantum (SQ) correlation experiments. This significantly reduces the number of redundant transitions, thereby simplifying the analysis of the complex spectrum. The methodology has been demonstrated on the doubly 13C labeled acetonitrile aligned in the liquid-crystal matrix and has been applied to analyze the complex spectrum of an oriented six spin system.

Phase Characterization and Study of Molecular Order of a Three-Ring Mesogen by (13)C NMR in Smectic C and Nematic Phases

Molecules exhibiting a thermotropic liquid-crystalline property have acquired significant importance due to their sensitivity to external stimuli such as temperature, mechanical forces, and electric and magnetic fields. As a result, several novel mesogens have been synthesized by the introduction of various functional groups in the vicinity of the aromatic core as well as in the side chains and their properties have been studied. In the present study, we report three-ring mesogens with hydroxyl groups at one terminal. These mesogens were synthesized by a multistep route, and structural characterization was accomplished by spectral techniques. The mesophase properties were studied by hot-stage optical polarizing microscopy, differential scanning calorimetry, and small-angle X-ray scattering. An enantiotropic nematic phase was noticed for lower homologues, while an additional smectic C phase was found for higher homologues. Solid-state high-resolution natural abundance (13)C NMR studies of a typical mesogen in the solid phase and in the mesophases have been carried out. The (13)C NMR spectrum of the mesogen in the smectic C and nematic phases indicated spontaneous alignment of the molecule in the magnetic field. By utilizing the two-dimensional separated local field (SLF) NMR experiment known as SAMPI4, (13)C-(1)H dipolar couplings have been obtained, which were utilized to determine the orientational order parameters of the mesogen.

Exploring the spectral enantiodiscrimination potential of a DNA-based orienting medium using deuterium NMR spectroscopy

(2)H-{(1)H} 1D and 2D-NMR spectroscopy is used to evaluate the enantiodiscrimination potential of DNA-based, lyotropic chiral mesophases on a series of (pro) chiral amino acids.

NMR methods for fast data acquisition

NMR spectroscopy has witnessed tremendous advancements in recent years with the development of new methodologies for structure determination and availability of high-field strength spectrometers equipped with cryogenic probes. Supported by these advancements, a new dimension in NMR research has emerged which aims to increase the speed with data is collected and analyzed. Several novel methodologies have been proposed in this direction. This review focuses on the principles on which these different approaches are based with an emphasis on G-matrix Fourier transform NMR spectroscopy.

Study of liquid crystalline order by NMR

The liquid crystalline phase represents a unique state of matter where partial order exists on molecular and supra-molecular levels and is responsible for several interesting properties observed in this phase. Hence a detailed study of ordering in liquid crystals is of significant scientific and technological interest. NMR provides several parameters that can be used to obtain information about the liquid crystalline phase. Of these, the measurement of dipolar couplings between nuclei has proved to be a convenient way of obtaining liquid crystalline ordering since the coupling is dependent on the average orientation of the dipolar vector in the magnetic field which also aligns the liquid crystal.However, measurement of the dipolar coupling between a pair of selected nuclei is beset with problems that require special solutions. In this article the use of cross polarization for measuring dipolar couplings in liquid crystals is illustrated. Transient oscillations observed during cross polarization provide the dipolar couplings between essentially isolated nearest neighbor spins which can be extracted for several sites simultaneously by employing two-dimensional NMR techniques. The use of the method for obtaining heteronuclear dipolar couplings and hence the order parameters of liquid crystals is presented. Several modifications to the basic experiment are considered and their utility illustrated. A method for obtaining proton–proton dipolar couplings, by utilizing cross polarization from the dipolar reservoir, is presented. Some applications are also highlighted.

Three-Component Chiral Derivatizing Protocols for NMR Spectroscopic Enantiodiscrimination of Hydroxy Acids and Primary Amines

The novel three-component chiral derivatization protocols have been derived for (1)H and (19)F NMR spectroscopic discrimination of a series of chiral hydroxy acids by their coordination and self-assembly with optically active a-methylbenzylamine and 2-formylphenylboronic acid. In addition, the optically pure (S)-mandelic acid in combination with 2-formylphenylboronic acid permits visualization of enantiomers of primary amines. These protocols have been demonstrated on enantiodiscrimination of chiral amines and hydroxy acids.