NMR analysis of Nile Blue (C. I. Basic Blue 12) and Thionine (C. I. 52000) in solution

The dyes Nile Blue (C. I. Basic Blue 12, NB) and Thionine (C. I. 52000, TH) were examined in both ionic and neutral forms in different solvents using NMR and UV-visible Spectroscopy to firmly establish the structures of the molecules and to assess the nature and extent of their aggregating characteristics. 1H and 13C NMR assignments and chemical shift data were used along with (for NB) nuclear Overhauser effect information enabling a structure for self-assembly to be proposed. In both cases these data were supplemented with variable temperature, dilution and diffusion-based experimental results using 1H NMR spectroscopy thereby enabling the extended aggregate structures to be assessed in terms of the relative strength of self-association and the extent to which extended aggregates could form. Full and detailed solution phase NMR analysis of such dyes, especially the two studied in this context, have either not been widely reported or have not been studied to the depth presented here. The data and their interpretation form an important addition to the analysis of this class of dye compounds and provide additional insight into the effects of self-assembly on the behaviour of such molecules in various solution-phase environments

Synthesis, structure and dynamics of NHC-based palladium macrocycles

A series of macrocyclic CNC pincer pro-ligands based on bis(imidazolium)lutidine salts with octa-, deca- and dodecamethylene spacers have been prepared and their coordination chemistry investigated. Using a Ag2O based transmetallation strategy, cationic palladium(II) chloride complexes [PdCl{CNC–(CH2)n}][BArF4] (n = 8, 10, 12; ArF = 3,5-C6H3(CF3)2) were prepared and fully characterised in solution, by NMR spectroscopy and ESI-MS, and in the solid-state, by X-ray crystallography. The smaller macrocyclic complexes (n = 8 and 10) exhibit dynamic behaviour in solution, involving ring flipping of the alkyl spacer across the Pd–Cl bond, which was interrogated by variable temperature NMR spectroscopy. In the solid-state, distorted coordination geometries are observed with the spacer skewed to one side of the Pd–Cl bond. In contrast, a static C2 symmetric structure is observed for the dodecamethylene based macrocycle. For comparison, palladium(II) fluoride analogues [PdF{CNC–(CH2)n}][BArF4] (n = 8, 10, 12) were also prepared and their solution and solid-state structures contrasted with those of the chlorides. Notably, these complexes exhibit very low frequency 19F chemical shifts (ca. −400 ppm) and the presence of C–HF interactions (2hJFC coupling observed by 13C NMR spectroscopy). The dynamic behaviour of the fluoride complexes is largely consistent with the smaller ancillary ligand; [PdF{CNC–(CH2)8}][BArF4] exceptionally shows C2v time averaged symmetry in solution at room temperature (CD2Cl2, 500 MHz) as a consequence of dual fluxional processes of the pincer backbone and alkyl spacer

Protein folding on the ribosome studied using NMR spectroscopy

NMR spectroscopy is a powerful tool for the investigation of protein folding and misfolding, providing a characterization of molecular structure, dynamics and exchange processes, across a very wide range of timescales and with near atomic resolution. In recent years NMR methods have also been developed to study protein folding as it might occur within the cell, in a de novo manner, by observing the folding of nascent polypeptides in the process of emerging from the ribosome during synthesis. Despite the 2.3 MDa molecular weight of the bacterial 70S ribosome, many nascent polypeptides, and some ribosomal proteins, have sufficient local flexibility that sharp resonances may be observed in solution-state NMR spectra. In providing information on dynamic regions of the structure, NMR spectroscopy is therefore highly complementary to alternative methods such as X-ray crystallography and cryo-electron microscopy, which have successfully characterized the rigid core of the ribosome particle. However, the low working concentrations and limited sample stability associated with ribosome-nascent chain complexes means that such studies still present significant technical challenges to the NMR spectroscopist. This review will discuss the progress that has been made in this area, surveying all NMR studies that have been published to date, and with a particular focus on strategies for improving experimental sensitivity

Structural and stereogenic properties of spiro- and ansa-substituted 1,3-propanedioxy derivatives of a spermine-bridged cyclotriphosphazene

Reaction of 1,3-propanediol with the achiral spermine-bridged cyclophosphazene 1 at various molar ratios in THF gives a number of spiro-and ansa-derivatives that exhibit different stereogenic properties, viz. racemic, meso or achiral forms. As expected, spiro forms are preferred (giving mono-, di-, tri- and tetra-substitution), although significant amounts of mono- and di-substituted ansa derivatives also occur. A number of new structures have been characterized by NMR spectroscopy and X-ray crystallography in this work; mono-spiro 2, di-mono-ansa 6 and di-spiro/mono-ansa 8. The mono-ansa compound 3 was observed in solution by NMR spectroscopy but no evidence was found for the monospiro/monoansa 5, a necessary precursor of compound 8. The tri-spiro derivative 7 has been isolated and characterized by 31P NMR spectroscopy, whereas the structures of the di-monospiro 4 (meso) and tetra-spiro 9 have been characterized previously. The stereogenic properties of many of the products have been confirmed by X-ray crystallography and/or by 31P NMR spectroscopy on addition of the chiral solvating agent, (S)-(+)-2,2,2-trifluoro-1-(9-anthryl)ethanol. Although the starting compound 1 is achiral, it is found that unsymmetrically-substituted derivatives with 1,3-propanediol give racemic mixtures for the mono-spiro 2 and tri-spiro 7 derivatives, whereas symmetrically-substituted derivatives such as di-mono-ansa 6 and di-spiro/mono-ansa 8 are meso. It is found that care must taken in interpreting the 'splitting' of 31P NMR signals on addition of CSA in terms of 'chirality' of molecules, because some meso compounds give false positive results due to changes from A2X-like to A2B or ABX spin systems

High-resolution NMR structure of an RNA model system : the 14-mer cUUCGg tetraloop hairpin RNA

We present a high-resolution nuclear magnetic resonance (NMR) solution structure of a 14-mer RNA hairpin capped by cUUCGg tetraloop. This short and very stable RNA presents an important model system for the study of RNA structure and dynamics using NMR spectroscopy, molecular dynamics (MD) simulations and RNA force-field development. The extraordinary high precision of the structure (root mean square deviation of 0.3 Å) could be achieved by measuring and incorporating all currently accessible NMR parameters, including distances derived from nuclear Overhauser effect (NOE) intensities, torsion-angle dependent homonuclear and heteronuclear scalar coupling constants, projection-angle-dependent cross-correlated relaxation rates and residual dipolar couplings. The structure calculations were performed with the program CNS using the ARIA setup and protocols. The structure quality was further improved by a final refinement in explicit water using OPLS force field parameters for non-bonded interactions and charges. In addition, the 2'-hydroxyl groups have been assigned and their conformation has been analyzed based on NOE contacts. The structure currently defines a benchmark for the precision and accuracy amenable to RNA structure determination by NMR spectroscopy. Here, we discuss the impact of various NMR restraints on structure quality and discuss in detail the dynamics of this system as previously determined

Conformational studies of various hemoglobins by natural-abundance 13C NMR spectroscopy

Studies of variously liganded hemoglobins (both from human and rabbit) by natural-abundance 13C NMR spectroscopy have revealed apparent conformational differences that have been interpreted on the basis of two quaternary structures for the α2ß2 tetramer, and variable tertiary structures for the individual α and ß subunits. In solution, rabbit hemoglobins appear to have somewhat more flexibility than human hemoglobins

Advanced NMR Methodology for the Investigation of Organometallic Compounds in Solution

The scope of this thesis was to investigate organometallic compounds by advanced solution state NMR methods in order to build a bridge from known solid state structures to their behaviour in solution. Since these reagents are mostly applied in solution, knowledge of the structural motives could improve the possibility to tune their reactivity. The projects presented in three separate chapters are dedicated to NMR spectroscopy in isotropic solution, NMR in anisotropic environment and combined approaches

\u3a0\u2011Stacking Signature in NMR Solution Spectra of Thiophene-Based Conjugated Polymers

Studies on conjugated polymers seldom report on their NMR characterization in solution. This paper shows how NMR experiments, both 1H NMR and routine 2D NMR spectra, can help in gaining a further insight into the aggregation behavior of conjugated polymers and could be used to flank the more employed solid-state NMR and other spectroscopy and microscopy techniques in the understanding of the aggregation processes. NMR spectroscopy allows distinguishing, within the class of poorly solvatochromic conjugated polymers, those highly prone to form \u3c0-stacked aggregates from the ones that have a low tendency toward \u3c0-stacking

High-Resolution 3D Structure Determination of Kaliotoxin by Solid-State NMR Spectroscopy

High-resolution solid-state NMR spectroscopy can provide structural information of proteins that cannot be studied by X-ray crystallography or solution NMR spectroscopy. Here we demonstrate that it is possible to determine a protein structure by solid-state NMR to a resolution comparable to that by solution NMR. Using an iterative assignment and structure calculation protocol, a large number of distance restraints was extracted from 1H/1H mixing experiments recorded on a single uniformly labeled sample under magic angle spinning conditions. The calculated structure has a coordinate precision of 0.6 Å and 1.3 Å for the backbone and side chain heavy atoms, respectively, and deviates from the structure observed in solution. The approach is expected to be applicable to larger systems enabling the determination of high-resolution structures of amyloid or membrane proteins