A fast NMR method for resonance assignments: application to metabolomics

We present a new method for rapid NMR data acquisition and assignments applicable to unlabeled (C-12) or C-13-labeled biomolecules/organic molecules in general and metabolomics in particular. The method involves the acquisition of three two dimensional (2D) NMR spectra simultaneously using a dual receiver system. The three spectra, namely: (1) G-matrix Fourier transform (GFT) (3,2)D C-13, H-1] HSQC-TOCSY, (2) 2D H-1-H-1 TOCSY and (3) 2D C-13-H-1 HETCOR are acquired in a single experiment and provide mutually complementary information to completely assign individual metabolites in a mixture. The GFT (3,2)D C-13, H-1] HSQC-TOCSY provides 3D correlations in a reduced dimensionality manner facilitating high resolution and unambiguous assignments. The experiments were applied for complete H-1 and C-13 assignments of a mixture of 21 unlabeled metabolites corresponding to a medium used in assisted reproductive technology. Taken together, the experiments provide time gain of order of magnitudes compared to the conventional data acquisition methods and can be combined with other fast NMR techniques such as non-uniform sampling and covariance spectroscopy. This provides new avenues for using multiple receivers and projection NMR techniques for high-throughput approaches in metabolomics.

Cross-Linked, Biodegradable, Cytocompatible Salicylic Acid Based Polyesters for Localized, Sustained Delivery of Salicylic Acid: An In Vitro Study

In order to suppress chronic inflammation while supporting cell proliferation, there has been a continuous surge toward development of polymers with the intention of delivering anti-inflammatory molecules in a sustained manner. In the above backdrop, we report the synthesis of a novel, stable, cross-linked polyester with salicylic acid (SA) incorporated in the polymeric backbone and propose a simple synthesis route by melt condensation. The as-synthesized polymer was hydrophobic with a glass transition temperature of 1 degrees C, which increases to 17 degrees C upon curing. The combination of NMR and FT-IR spectral techniques established the ester linkages in the as-synthesized SA-based polyester. The pH-dependent degradation rate and the rate of release of salicylic acid from the as-synthesized SA-based polymer were studied at physiological conditions in vitro. The polyester underwent surface erosion and exhibited linear degradation kinetics in which a change in degradation rate is observed after 4-10 days and 24% mass loss was recorded after 4 months at 37 degrees C and pH 7.4. The delivery of salicylic acid also showed a similar change in slopes, with a sustained release rate of 3.5% in 4 months. The cytocompatibility studies of these polyesters were carried out with C2C12 murine myoblast cells using techniques like MTT assay and flow cytometry. Our results strongly suggest that SA-based polyester supports cell proliferation for 3 days in culture and do not cause cell death (<7%), as quantified by propidium iodide (PI) stained cells. Hence, these polyesters can be used as implant materials for localized, sustained delivery of salicylic acid and have applications in adjuvant cancer therapy, chronic wound healing, and as an alternative to commercially available polymers like poly(lactic acid) and poly(glycolic acid) or their copolymers.

Pure shift NMR approach for fast and accurate extraction of heteronuclear couplings

The direct and accurate determination of heteronuclear ((n)J(HX), X = F-19, P-31) couplings from the one dimensional H-1-NMR spectrum is severely hampered due to the simultaneous presence of large numbers of (n)J(HH). The present study demonstrates the utility of the pure shift NMR approach for spectral simplification, and precise and direct measurement of heteronuclear couplings. As a consequence of refocusing of homonuclear couplings ((n)J(HH)) by the pure shift NMR, only heteronuclear couplings ((n)J(HX)) appear as simple multiplets at the resonance position of each chemically non-equivalent proton, enabling their direct measurement from the 1D-H-1 spectrum. The experiment is demonstrated on a number of molecules containing either F-19 or P-31, where (n)J(HF) and (n)J(HP) could be precisely measured in a straightforward manner. The distinct advantage of the experiment is demonstrated on molecules containing more than one fluorine atom, where most of the available NMR experiments fail or have restricted utility.

Correlation between local structural dynamics of proteins inferred from NMR ensembles and evolutionary dynamics of homologues of known structure

Conformational changes in proteins are extremely important for their biochemical functions. Correlation between inherent conformational variations in a protein and conformational differences in its homologues of known structure is still unclear. In this study, we have used a structural alphabet called Protein Blocks (PBs). PBs are used to perform abstraction of protein 3-D structures into a 1-D strings of 16 alphabets (a-p) based on dihedral angles of overlapping pentapeptides. We have analyzed the variations in local conformations in terms of PBs represented in the ensembles of 801 protein structures determined using NMR spectroscopy. In the analysis of concatenated data over all the residues in all the NMR ensembles, we observe that the overall nature of inherent local structural variations in NMR ensembles is similar to the nature of local structural differences in homologous proteins with a high correlation coefficient of .94. High correlation at the alignment positions corresponding to helical and beta-sheet regions is only expected. However, the correlation coefficient by considering only the loop regions is also quite high (.91). Surprisingly, segregated position-wise analysis shows that this high correlation does not hold true to loop regions at the structurally equivalent positions in NMR ensembles and their homologues of known structure. This suggests that the general nature of local structural changes is unique; however most of the local structural variations in loop regions of NMR ensembles do not correlate to their local structural differences at structurally equivalent positions in homologues.

Mono- and Dialkyne Insertion Reactions of Cyclopalladated N,N `,N `'-Triarylguanidines kappa(2)(C,N)Pd(mu-Br)](2) and cis-/trans-kappa(2)(C,N)Pd(Lewis Base)Br]. Scaffolds for Enlarged, Rearranged, and Zwitterionic Palladacycles through Ring Contraction cum Amine-Imine Tautomerization

Insertion reactions of six-membered cyclopalladated N,N',N''-triarylguanidines, kappa(2)(C,N)Pd(mu-Br)](2) with various alkynes in CH2Cl2 under ambient conditions afforded diinserted eight-membered palladacycles, (kappa(2)(C,N):eta(2)(C=C)-PdBr] (1-11), in high yield (76-96%), while insertion reactions of six-membered cyclopalladated N,N',N''-triarylguanidines, kappa(2)(C,N)Pd(Lewis base)Br] (VI-XI), with various alkynes under the aforementioned conditions afforded monoinserted six-membered palladacycles, kappa(2)(C,N)-Pd(Lewis base)Br] (12-21), in high yield (81-91%) except for 14 (23%). The insertion reaction of VI with 2 equiv of dimethyl acetylenedicarboxylate (DMAD) and the insertion reaction of 12 with 1 equiv of DMAD in CH2Cl2 under ambient conditions resulted in the formation of a diinserted zwitterionic five-membered palladacycle, kappa(2)(C,C)Pd(2,6-lutidine)Br] (22), in 76% and 70% yields, respectively. Palladacycle 22 upon reaction with AgOTf in wet MeCN afforded the ionic palladacycle kappa(2)(C,C)Pd(2,6-lutidine)(H2O)]OTf] (23) in 78% yield. The ring size of the ``kappa(2)(C,N)Pd]'' unit in the structurally characterized diinserted palladacycles (1 center dot 2CH(2)Cl(2)center dot H2O, 2, 5, and 7), and monoinserted palladacycles (17, 18, and 20 center dot C7H8 H2O) is smaller than that anticipated for mono- and diinserted palladacycles, and this feature is mainly ascribed to the proclivity of III-XI to undergo ring contraction cum amine-imine tautomerization upon alkyne insertion. Palladacycle 22 represents the first diinserted product obtained in alkyne insertion reactions of kappa(2)(C,N)Pd(Lewis base)X] type palladarycles. The molecular structure of 22 center dot H2O determined by X-ray diffraction indicates that the positive charge on the guanidinium moiety is balanced by the negative charge on the palladium atom and thus represents the first structurally characterized zwitterionic palladacycle to be reported in alkyne insertion chemistry. Plausible mechanisms of formation of 12-21 and 22 have been outlined. The presence of more than one species in solution for some of the palladacycles in the series 1-7 and 12-21 was explained by invoking the C-N single-bond rotation of the CN3 unit of the guanidine moiety, while this process in conjunction with Pd-N(lutidine) bond rotation was invoked to explain the presence of four isomers of 15, as studied with the aid of variable-concentration H-1 NMR experiments carried out for 14 and 15.

Synthesis and antiproliferative effect of novel 4-thiazolidinone-, pyridine- and piperazine-based conjugates on human leukemic cells

The present work reveals the synthesis and antiproliferative effect of a series of 2, 3 disubstituted 4-thiazolidinone analogues on human leukemic cells. The chemical structures of newly synthesized compounds were confirmed by IR, H-1 NMR, C-13 NMR and mass spectral analysis. Compound methyl 3-methoxy-4-(4-oxo-3-(5-(piperazin-1-yl)pyridin-2-yl)thiazolidin-2-yl)be nzoate (5) displayed potent activity (IC50 9.71, 15.24 and 19.29 mu M) against Nalm6, K562, Jurkat cells. Cell cycle analysis and mitochondrial membrane potential further confirmed that compound 5 is cytotoxic and able to induce cell death. (C) 2014 Elsevier Masson SAS. All rights reserved.

High-Resolution Solid State C-13 NMR Studies of Bent-Core Mesogens of Benzene and Thiophene

Bent-core mesogens are an important class of thermotropic liquid crystals as they exhibit unusual properties as well as morphologies distinctly different from rodlike mesogens. Two bent-core mesogens with differing center rings namely benzene and thiophene are considered and investigated using high-resolution oriented solid state C-13 NMR method in their liquid crystalline phases. The mesogens exhibit different phase sequences with the benzene-based mesogen showing a B-1 phase, while the one based on thiophene showing nematic and smectic C phases. The 2-dimensional separated local field (2D-SLF) NMR method was used to obtain the C-13-H-1 dipolar couplings of carbons in the center ring as well as in the side-wing phenyl rings. Couplings, characteristic of the type of the center ring, that also provide orientational information on the molecule in the magnetic field were observed. Together with the dipolar couplings of the side-wing phenyl ring carbons from which the local order parameters of the different subunits of the core could be extracted, the bent angle of the mesogenic molecule could be obtained. Accordingly, for the benzene mesogen in its B-1 phase at 145 degrees C, the center ring methine C-13-H-1 dipolar couplings were found to be significantly larger (9.5-10.2 kHz) compared to those of the side-wing rings (1.6-2.1 kHz). From the local order parameter values of the center (0.68) as well as the side-wing rings (0.50), a bent-angle of 130.3 degrees for this mesogen was obtained. Interestingly, for the thiophene mesogen in its smectic C phase at 210 degrees C, the C-13-H-1 dipolar coupling of the center ring methine carbon (2.11 kHz) is smaller than those of the side-wing phenyl ring carbons (2.75-3.00 kHz) which is a consequence of the different structures of the thiophene and the benzene rings. These values correspond to local order parameters of 0.85 for the center thiophene ring and 0.76 for the first side-wing phenyl ring and a bent-angle of 149.2 degrees. Thus, the significant differences in the dipolar couplings and the order parameter values between different parts in the rigid core of the mesogens are a direct consequence of the nature of the center ring and the bent structure of the molecule. The present investigation thus highlights the ability of the C-13 2D-SLF technique to provide the geometry of the bent-core mesogens in a straightforward manner through the measurement of the C-13-H-1 dipolar couplings.

Efficient simulation of unitary operators by combining two numerical algorithms: An NMR simulation of the mirror-inversion propagator of an XY spin chain

Precise experimental implementation of unitary operators is one of the most important tasks for quantum information processing. Numerical optimization techniques are widely used to find optimized control fields to realize a desired unitary operator. However, finding high-fidelity control pulses to realize an arbitrary unitary operator in larger spin systems is still a difficult task. In this work, we demonstrate that a combination of the GRAPE algorithm, which is a numerical pulse optimization technique, and a unitary operator decomposition algorithm Ajoy et al., Phys. Rev. A 85, 030303 (2012)] can realize unitary operators with high experimental fidelity. This is illustrated by simulating the mirror-inversion propagator of an XY spin chain in a five-spin dipolar coupled nuclear spin system. Further, this simulation has been used to demonstrate the transfer of entangled states from one end of the spin chain to the other end.

Sensitivity enhancement in slice-selective NMR experiments through polarization sharing

The polarization sharing technique is utilized in gradient based slice selective experiments to transfer polarization from unutilized protons to selectively excited protons. This facilitates rapid data acquisition without any customary inter-scan relaxation delay, resulting in an average of 2-fold sensitivity enhancement per unit time.

A napthelene-pyrazol conjugate: Al(III) ion-selective blue shifting chemosensor applicable as biomarker in aqueous solution

A newly synthesized and crystalographically characterized napthelene-pyrazol conjugate, 1-(5-phenyl-1H-pyrazole-3-ylimino)-methyl]-naphthalen-2-ol (HL) behaves as an Al(III) ion-selective chemosensor through internal charge transfer (ICT)-chelation-enhanced fluorescence (CHEF) processes in 100 mM HEPES buffer (water-DMSO 5 : 1, v/v) at biological pH with almost no interference of other competitive ions. This mechanism is readily studied from electronic, fluorimetric and H-1 NMR titration. The probe (HL) behaved as a highly selective fluorescent sensor for Al(III) ions as low as 31.78 nM within a very short response time (15-20 s). The sensor (HL), which has no cytotoxicity, is also efficient in detecting the distribution of Al(III) ions in HeLa cells via image development under fluorescence microscope.

beta gamma-fused turn structures in sugar amino acid (SAA) containing cyclic tetrapeptides with alpha 3 delta architecture

The current manuscript describes conformational analysis of 15-membered cyclic tetrapeptides (CTPs), with alpha 3 delta architecture, containing sugar amino acids (SAA) having variation in the stereocenter at C5 carbon. Conformational analyses of both the series, in protected and deprotected forms, were carried out in DMSO-d(6) using various NMR techniques, supported by restrained MD calculations. It was intriguing to notice that the alpha 3 delta macrocycles got stabilized by both 10-membered beta-turn as well as a seven-membered gamma-turn, fused within the same macrocycle. The presence of fused sub-structures within a 15-membered macrocycle is rare to see. Also, the stereocenter variation at C5 did not affect the fused turn structures and exhibited similar conformations in both the series. The design becomes highly advantageous as fused reverse turn structures are occurring in the cyclic structure with minimalistic size macrocycle and this can be applied to develop suitable pharmacophores in the drug development process. (C) 2014 Elsevier Ltd. All rights reserved.

A versatile ternary ionic complex for chiral discrimination of molecules with diverse functionalities using H-1 NMR

This study reports a simple, efficient and versatile protocol developed for NMR spectroscopic enantiodiscrimination of molecules containing diverse functional -groups, such as amino alcohols, secondary alcohols, cyanohydrins, oxazolidones, diols, thiones and epoxides, using a phosphorous based three component mixture. The simple mixing and shaking of enantiopure 1,1'-binaphthyt-2,2'-diyl hydrogenphosphate (BNPA), 4-(dimethylamino)pyridine (DMAP) and a chiral analyte in the solvent CDCl3 served as a chiral solvating agent and resulted in well dispersed peaks for each enantiomer in the H-1 NMR spectrum. Discrimination could be achieved not only for the proton at the chiral centre, but also for multiple proton sites. The devised approach also permitted the precise measurement of the enantiomeric excess (ee).

Phenyl carbohydrazone conjugated 2-oxoindoline as a new scaffold that augments the DNA and BSA binding affinity and anti-proliferative activity of a 1,10-phenanthroline based copper(II) complex

A new type of copper(II) complex, CuL(phen)(2)](NO3) (CuIP), where L ((E)-N'-(2-oxoindolin-3-ylidene) benzohydrazide) is a N donor ligand and phen is the N, N-donor heterocyclic 1,10-phenanthroline, has been synthesized. The phenyl carbohydrazone conjugated isatin-based ligand L and CuIP were characterized by elemental analysis, infrared, UV-Vis, H-1 and C-13 NMR and ESI-mass spectral data, as well as single-crystal X-ray diffraction. The interaction of calf thymus DNA (CT DNA) with L and CuIP has been investigated by absorption, fluorescence and viscosity titration methods. The complex CuIP displays better binding affinity than the ligand L. The observed DNA binding constant (K-b = 4.15(+/- 0.18) x 10(5) M-1) and binding site size (s = 0.19), viscosity data together with molecular docking studies of CuIP suggest groove binding and/or a partial intercalative mode of binding to CT DNA. In addition, CuIP shows good binding propensity to the bovine serum albumin (BSA) protein, giving a K-BSA value of 1.25(+/- 0.24) x 10(6) M-1. In addition, the docking studies on DNA and human serum albumin (HSA) CuIP interactions are consistent with the consequence of binding experiments. The in vitro anti-proliferative study establishes the anticancer potency of the CuIP against the human cervical (HeLa) and breast (MCF7) cancer cells; noncancer breast epithelial (MCF10a) cells have also been investigated. CuIP shows better cytotoxicity and sensitivity towards cancer cells over noncancer ones than L under identical conditions, with the appearance of apoptotic bodies. (C) 2014 Elsevier B.V. All rights reserved.

Quick re-introduction of selective scalar interactions in a pure-shift NMR spectrum

A new 1D NMR experiment cited as `Quick G-SERF', which re-introduces selective proton-proton scalar interactions in a pure shift spectrum during real time data acquisition, is reported. The method provides information on multiple proton-proton couplings from a single experiment, analogous to the 2D G-SERF technique, while significantly shortening the experimental time by 1-2 orders of magnitude due to reduced dimension and enhanced sensitivity.