Singlet-state creation and universal quantum computation in NMR using a genetic algorithm

The experimental implementation of a quantum algorithm requires the decomposition of unitary operators. Here we treat unitary-operator decomposition as an optimization problem, and use a genetic algorithm-a global-optimization method inspired by nature's evolutionary process-for operator decomposition. We apply this method to NMR quantum information processing, and find a probabilistic way of performing universal quantum computation using global hard pulses. We also demonstrate the efficient creation of the singlet state (a special type of Bell state) directly from thermal equilibrium, using an optimum sequence of pulses.

High resolution methyl selective C-13-NMR of proteins in solution and solid state

New C-13-detected NMR experiments have been devised for molecules in solution and solid state, which provide chemical shift correlations of methyl groups with high resolution, selectivity and sensitivity. The experiments achieve selective methyl detection by exploiting the one bond J-coupling between the C-13-methyl nucleus and its directly attached C-13 spin in a molecule. In proteins such correlations edit the C-13-resonances of different methyl containing residues into distinct spectral regions yielding a high resolution spectrum. This has a range of applications as exemplified for different systems such as large proteins, intrinsically disordered polypeptides and proteins with a paramagnetic centre.

H-1, C-13, N-15 assignment and secondary structure determination of glutamine amido transferase subunit of gaunosine monophosphate synthetase from Methanocaldococcus jannaschii

Sequence specific resonance assignments have been obtained for H-1, C-13 and N-15 nuclei of the 21 kDa (188 residues long) glutamine amido transferase subunit of guanosine monophosphate synthetase from Methanocaldococcus jannaschii. From an analysis of H-1 and C-13(alpha), C-13(beta) secondary chemical shifts, (3) JH(N)H(alpha) scalar coupling constants and sequential, short and medium range H-1-H-1 NOEs, it was deduced that the glutamine amido transferase subunit has eleven strands and five helices as the major secondary structural elements in its tertiary structure.

GFT projection NMR for efficient H-1/C-13 sugar spin system identification in nucleic acids

A newly implemented G-matrix Fourier transform (GFT) (4,3)D HC(C)CH experiment is presented in conjunction with (4,3)D HCCH to efficiently identify H-1/C-13 sugar spin systems in C-13 labeled nucleic acids. This experiment enables rapid collection of highly resolved relay 4D HC(C)CH spectral information, that is, shift correlations of C-13-H-1 groups separated by two carbon bonds. For RNA, (4,3)D HC(C)CH takes advantage of the comparably favorable 1'- and 3'-CH signal dispersion for complete spin system identification including 5'-CH. The (4,3)D HC(C)CH/HCCH based strategy is exemplified for the 30-nucleotide 3'-untranslated region of the pre-mRNA of human U1A protein.

Crowding, molecular volume and plasticity: An assessment involving crystallography, NMR and simulations

The discrepancy between the X-ray and NMR structures of Mycobacterium tuberculosis peptidyl-tRNA hydrolase in relation to the functionally important plasticity of the molecule led to molecular dynamics simulations. The X-ray and the NMR studies along with the simulations indicated an inverse correlation between crowding and molecular volume. A detailed comparison of proteins for which X-ray and the NMR structures appears to confirm this correlation. In consonance with the reported results of the investigations in cellular compartments and aqueous solution, the comparison indicates that the crowding results in compaction of the molecule as well as change in its shape, which could specifically involve regions of the molecule important in function. Crowding could thus influence the action of proteins through modulation of the functionally important plasticity of the molecule. Selvaraj M, Ahmad R, Varshney U and Vijayan M 2012 Crowding, molecular volume and plasticity: An assessment involving crystallography, NMR and simulations. J. Biosci. 37 953-963] DOI 10.1007/s12038-012-9276-5

NMR Analysis of Cross Strand Aromatic Interactions in an 8 Residue Hairpin and a 14 Residue Three Stranded beta-Sheet Peptide

Cross strand aromatic interactions between a facing pair of phenylalanine residues in antiparallel beta-sheet structures have been probed using two structurally defined model peptides. The octapeptide Boc-(LFVPPLFV)-P-D-P-L-OMe (peptide 1) favors the beta-hairpin conformation nucleated by the type II' beta-turn formed by the (D)Pro-(L)Pro segment, placing Phe2 and Phe7 side chains in proximity. Two centrally positioned (D)Pro-(L)Pro segments facilitate the three stranded beta-sheet formation in the 14 residue peptide Boc-LFV(D)P(L)PLFVA(D)P(L)PLFV-OMe (peptide 2) in which the Phe2/Phe7 orientations are similar to that in the octapeptide. The anticipated folded conformations of peptides 1 and 2 are established by the delineation of intramolecularly hydrogen bonded NH groups and by the observation of specific cross strand NOEs. The observation of ring current shifted aromatic protons is a diagnostic of close approach of the Phe2 and Phe7 side chains. Specific assignment of aromatic proton resonances using HSQC and HSQC-TOCSY methods allow an analysis of interproton NOEs between the spatially proximate aromatic rings. This approach facilitates specific assignments in systems containing multiple aromatic rings in spectra at natural abundance. Evidence is presented for a dynamic process which invokes a correlated conformational change about the C-alpha-C-beta(chi(1)) bond for the pair of interacting Phe residues. NMR results suggest that aromatic ring orientations observed in crystals are maintained in solution. Anomalous temperature dependence of ring current induced proton chemical shifts suggests that solvophobic effects may facilitate aromatic ring clustering in apolar solvents.

Chiral discrimination and the measurement of enantiomeric excess from a severely overcrowded NMR spectrum

NMR spectroscopic chiral visualization, unambiguous assignment of peaks pertaining to R and S enantiomers and the subsequent measurement of enantiomeric composition demands a highly resolved spectrum. The method fails when the spectrum is severely overcrowded or highly complex, thereby hampering the determination of enantiomeric excess. In order to circumvent such problems we propose the utility of pure shift spectrum obtained by resolving the chemical shift and coupling information in two orthogonal dimensions. The skew projected spectrum yields singlet's at the respective chemical shift positions, permitting the unravelling of the superimposed spectral transitions for each enantiomer and measurement of enantiomeric composition. (C) 2012 Elsevier B. V. All rights reserved.

The Coil-to-Helix Transition in IlvN Regulates the Allosteric Control of Escherichia coli Acetohydroxyacid Synthase I

The solution structure of IlvN, the regulatory subunit of Escherichia coil acetohydroxyacid synthase I, in the valine-bound form has been determined using high-resolution multidimensional, multinuclear nuclear magnetic resonance (NMR) methods. IlvN in the presence or absence of the effector molecule is present as a 22.5 kDa dimeric molecule. The ensemble of 20 low-energy structures shows a backbone root-mean-square deviation of 0.73 +/- 0.13 angstrom and a root-mean-square deviation of 1.16 +/- 0.13 angstrom for all heavy atoms. Furthermore, more than 98% of the backbone phi and psi dihedral angles occupy the allowed and additionally allowed regions of the Ramachandran map, which is indicative of the fact that the structures are of high stereochemical quality. Each protomer exhibits a beta alpha beta beta alpha beta alpha topology that is a characteristic feature of the ACT domain seen in metabolic enzymes. In the valine-bound form, IlvN exists apparently as a single conformer. In the free form, IlvN exists as a mixture of conformational states that are in intermediate exchange on the NMR time scale. Thus, a large shift in the conformational equilibrium is observed upon going from the free form to the bound form. The structure of the valine-bound form of IlvN was found to be similar to that of the ACT domain of the unliganded form of IlvH. Comparisons of the structures of the unliganded forms of these proteins suggest significant differences. The structural and conformational properties of IlvN determined here have allowed a better understanding of the mechanism of regulation of branched chain amino acid biosynthesis.

NMR studies of preimplantation embryo metabolism in human assisted reproductive techniques: a new biomarker for assessment of embryo implantation potential

There has been growing interest in understanding energy metabolism in human embryos generated using assisted reproductive techniques (ART) for improving the overall success rate of the method. Using NMR spectroscopy as a noninvasive tool, we studied human embryo metabolism to identify specific biomarkers to assess the quality of embryos for their implantation potential. The study was based on estimation of pyruvate, lactate and alanine levels in the growth medium, ISM1, used in the culture of embryos. An NMR study involving 127 embryos from 48 couples revealed that embryos transferred on Day 3 (after 72 h in vitro culture) with successful implantation (pregnancy) exhibited significantly (p < 10(-5)) lower pyruvate/alanine ratios compared to those that failed to implant. Lactate levels in media were similar for all embryos. This implies that in addition to lactate production, successfully implanted embryos use pyruvate to produce alanine and other cellular functions. While pyruvate and alanine individually have been used as biomarkers, the present study highlights the potential of combining them to provide a single parameter that correlates strongly with implantation potential. Copyright (C) 2012 John Wiley & Sons, Ltd.

Effect of chlorine substitution on triplet state structure of thioxanthone: A time-resolved resonance Raman study

Substitution plays an important role in determining the triplet state reactivity. In this paper, we have studied the effect of chlorine substitution on the triplet state structure and the reactivity of thioxanthone (TX). We have employed time-resolved resonance Raman technique to understand the structure of the lowest triplet excited state of 2-chlorothioxanthone (CTX). The experimental findings have been corroborated with the computational results using density functional theory. Akin to the parent compound (TX), coexistence of two lowest triplet states has been observed in case of CTX, which has been substantiated using resonant probe wavelength dependence study. The relative contribution of 3n-pi* to 3 pi-pi* to the equilibrated triplet state has been found to be more for CTX compared to TX suggesting increase in the triplet state reactivity after the substitution. The above observation has been further supported by the flash photolysis experiments. Copyright (C) 2013 John Wiley & Sons, Ltd.

Sensory-organ-like response determines the magnetism of zigzag-edged honeycomb nanoribbons

We present an analytical effective theory for the magnetic phase diagram for zigzag-edge terminated honeycomb nanoribbons described by a Hubbard model with an interaction parameter U. We show that the edge magnetic moment varies as ln U and uncover its dependence on the width W of the ribbon. The physics of this owes its origin to the sensory-organ-like response of the nanoribbons, demonstrating that considerations beyond the usual Stoner-Landau theory are necessary to understand the magnetism of these systems. A first-order magnetic transition from an antiparallel orientation of the moments on opposite edges to a parallel orientation occurs upon doping with holes or electrons. The critical doping for this transition is shown to depend inversely on the width of the ribbon. Using variational Monte Carlo calculations, we show that magnetism is robust to fluctuations. Additionally, we show that the magnetic phase diagram is generic to zigzag-edge terminated nanostructures such as nanodots. Furthermore, we perform first-principles modeling to show how such magnetic transitions can be realized in substituted graphene nanoribbons. DOI: 10.1103/PhysRevB.87.085412

Engagement of CF3 Group in N-H center dot center dot center dot F-C Hydrogen Bond in the Solution State: NMR Spectroscopy and MD Simulation Studies

Unambiguous evidence for the engagement of CF3 group in N-H center dot center dot center dot F-C hydrogen bond in a low polarity solvent, the first observation of its kind, is reported. The presence of such weak molecular interactions in the solution state is convincingly established by one and two-dimensional H-1, F-19, and natural abundant N-15 NMR spectroscopic studies. The strong and direct evidence is derived by the observation of through-space couplings, such as, (1h)J(FH), (1h)J(FN), and (2h)J(FF), where the spin polarization is transmitted through hydrogen bond. In an interesting example of a molecule containing two CF3 groups getting simultaneously involved in hydrogen bond, where hydrogen bond mediated couplings are not reflected in the NMR spectrum, F-19-F-19 NOESY experiment yielded confirmatory evidence. Significant deviations in the strengths of (1)J(NH), variable temperature, and the solvent induced perturbations yielded additional support. The NMR results are corroborated by both DFT calculations and MD simulations, where the quantitative information on different ways of involvement of fluorine in two and three centered hydrogen bonds, their percentage of occurrences, and geometries have been obtained. The hydrogen bond interaction energies have also been calculated.

Selective excitation and detection of maximum quantum coherence of a group of scalar coupled protons in chiral molecules: an NMR experiment for enantiodiscrimination

The H-1 NMR spectroscopic discrimination of enantiomers in the solution state and the measurement of enantiomeric composition is most often hindered due to either very small chemical shift differences between the discriminated peaks or severe overlap of transitions from other chemically non-equivalent protons. In addition the use of chiral auxiliaries such as, crown ether and chiral lanthanide shift reagent may often cause enormous line broadening or give little degree of discrimination beyond the crown ether substrate ratio, hampering the discrimination. In circumventing such problems we are proposing the utilization of the difference in the additive values of all the chemical shifts of a scalar coupled spin system. The excitation and detection of appropriate highest quantum coherence yields the measurable difference in the frequencies between two transitions, one pertaining to each enantiomer in the maximum quantum dimension permitting their discrimination and the F-2 cross section at each of these frequencies yields an enantiopure spectrum. The advantage of the utility of the proposed method is demonstrated on several chiral compounds where the conventional one dimensional H-1 NMR spectra fail to differentiate the enantiomers.

Electronic energy transfer between long-range resonance states of 3-mercaptopropionic acid capped CdTe quantum dots in aqueous media

We demonstrate electronic energy transfer between resonance states of 2 and 2.8 nm CdTe quantum dots in aqueous media using steady-state photoluminescence spectroscopy without using any external linker molecule. With increasing concentration of larger dots, there is subsequent quenching of luminescence in smaller dots accompanied by the enhancement of luminescence in larger dots. Our experimental evidence suggests that there is long-range resonance energy transfer among electronic excitations, specifically from the electronically confined states of the smaller dots to the higher excited states of the larger dots.

Synthesis and characterisation of novel alkoxycyanobiphenyl-substituted rufigallols

Microwave-assisted synthesis of novel alkoxycyanobiphenyl-substituted rufigallols are reported by systematically replacing one, two, four, five or six cyanobiphenyl-tethered alkoxy chains. The synthesis of the target compounds was challenging since classical reactions failed to produce these hybrids. Chemical structures of the hybrids were determined by H-1 nuclear magnetic resonance (NMR), C-13 NMR, infrared, ultraviolet spectroscopy and elemental analysis. The thermotropic liquid crystalline properties of the new compounds were investigated by polarising optical microscopy, differential scanning calorimetry and X-ray diffractometry.