Deliberately Losing Control of C-H Activation Processes in the Design of Small-Molecule-Fragment Arrays Targeting Peroxisomal Metabolism.

Combined photochemical arylation, "nuisance effect" (SN Ar) reaction sequences have been employed in the design of small arrays for immediate deployment in medium-throughput X-ray protein-ligand structure determination. Reactions were deliberately allowed to run "out of control" in terms of selectivity; for example the ortho-arylation of 2-phenylpyridine gave five products resulting from mono- and bisarylations combined with SN Ar processes. As a result, a number of crystallographic hits against NUDT7, a key peroxisomal CoA ester hydrolase, have been identified.

Matrix-assisted DOSY.

The analysis of mixtures by NMR spectroscopy is challenging. Diffusion-ordered NMR spectroscopy enables a pseudo-separation of species based on differences in their translational diffusion coefficients. Under the right circumstances, this is a powerful technique; however, when molecules diffuse at similar rates separation in the diffusion dimension can be poor. In addition, spectral overlap also limits resolution and can make interpretation challenging. Matrix-assisted diffusion NMR seeks to improve resolution in the diffusion dimension by utilising the differential interaction of components in the mixture with an additive to the solvent. Tuning these matrix-analyte interactions allows the diffusion resolution to be optimised. This review presents the background to matrix-assisted diffusion experiments, surveys the wide range of matrices employed, including chromatographic stationary phases, surfactants and polymers, and demonstrates the current state of the art.

Using Small-Molecule Probes to Investigate Aggregation of Sunset Yellow FCF: What are the Concentration Limits?

The assembly of small molecules into larger structures, often driven by noncovalent interactions such as hydrogen bonding, aromatic stacking interactions, and burial of hydrophobic surface, is of widespread interest. The interaction of small molecules with aggregates also has a large range of applications from fluorescence aggregation assays to gas storage in framework materials. Here, we utilize nuclear magnetic resonance spectroscopy to investigate the interaction of a small-molecule probe on the assembly state of sunset yellow across a wide range of relative concentrations. Information from both macroscopic (diffusion) and microscopic (chemical shifts) measurements allows the interaction to be studied and the binding mode to be interrogated. Using fluorophenol as the small-molecule probe, we show that the aggregation behavior of sunset yellow is broadly unaffected by the relative amount of fluorophenol added.

Correction: Synthesis of kinase inhibitors containing a pentafluorosulfanyl moiety.

Correction for 'Synthesis of kinase inhibitors containing a pentafluorosulfanyl moiety' by Supojjanee Sansook et al., Org. Biomol. Chem., 2017, 15, 8655-8660.

Synthesis of kinase inhibitors containing a pentafluorosulfanyl moiety.

A series of 3-methylidene-1H-indol-2(3H)-ones substituted with a 5- or 6-pentafluorosulfanyl group has been synthesized by a Knoevenagel condensation reaction of SF5-substituted oxindoles with a range of aldehydes. The resulting products were characterized by X-ray crystallography studies and were tested for biological activity versus a panel of cell lines and protein kinases. Some exhibited single digit nM activity.

Size-exclusion chromatographic NMR under HR-MAS.

The addition of stationary phases or sample modifiers can be used to modify the separation achievable in the diffusion domain of diffusion NMR experiments or provide information on the nature of the analyte-sample modifier interaction. Unfortunately, the addition of insoluble chromatographic stationary phases can lead to line broadening and degradation in spectral resolution, largely because of differences in magnetic susceptibility between the sample and the stationary phase. High-resolution magic angle spinning (HR-MAS) techniques can be used to remove this broadening. Here, we attempt the application of HR-MAS to size-exclusion chromatographic NMR with limited success. Observed diffusion coefficients for polymer molecular weight reference standards are shown to be larger than those obtained on static samples. Further investigation reveals that under HR-MAS it is possible to obtain reasonably accurate estimates of diffusion coefficients, using either full rotor synchronisation or sophisticated pulse sequences. The requirement for restricting the sample to the centre of the MAS rotor to ensure homogeneous magnetic and RF fields is also tested. Copyright © 2016 John Wiley & Sons, Ltd.

A critical role for the self-assembly of Amyloid-ß1-42 in neurodegeneration.

Amyloid ß1-42 (Aß1-42) plays a central role in Alzheimer's disease. The link between structure, assembly and neuronal toxicity of this peptide is of major current interest but still poorly defined. Here, we explored this relationship by rationally designing a variant form of Aß1-42 (vAß1-42) differing in only two amino acids. Unlike Aß1-42, we found that the variant does not self-assemble, nor is it toxic to neuronal cells. Moreover, while Aß1-42 oligomers impact on synaptic function, vAß1-42 does not. In a living animal model system we demonstrate that only Aß1-42 leads to memory deficits. Our findings underline a key role for peptide sequence in the ability to assemble and form toxic structures. Furthermore, our non-toxic variant satisfies an unmet demand for a closely related control peptide for Aß1-42 cellular studies of disease pathology, offering a new opportunity to decipher the mechanisms that accompany Aß1-42-induced toxicity leading to neurodegeneration.

A synthetic, catalytic and theoretical investigation of an unsymmetrical SCN pincer palladacycle.

The SCN ligand 2-{3-[(methylsulfanyl)methyl]phenyl}pyridine, 1, has been synthesized starting from an initial Suzuki-Miyaura (SM) coupling between 3-((hydroxymethyl)phenyl)boronic acid and 2-bromopyridine. The C-H activation of 1 with in situ formed Pd(MeCN)4(BF4)2 has been studied and leads to a mixture of palladacycles, which were characterized by X-ray crystallography. The monomeric palladacycle LPdCl 6, where L-H = 1, has been synthesized, and tested in SM couplings of aryl bromides, where it showed moderate activity. Density functional theory and the atoms in molecules (AIM) method have been used to investigate the formation and bonding of 6, revealing a difference in the nature of the Pd-S and Pd-N bonds. It was found that S-coordination to the metal in the rate determining C-H bond activation step leads to better stabilization of the Pd(II) centre (by 13-28 kJ mol(-1)) than with N-coordination. This is attributed to the electron donating ability of the donor atoms determined by Bader charges. The AIM analysis also revealed that the Pd-N bonds are stronger than the Pd-S bonds influencing the stability of key intermediates in the palladacycle formation reaction pathway.

Influence of structural isomerism and fluorine atom substitution on the self-association of naphthoic acid.

The self-association of small aromatic systems driven by π-π stacking and hydrophobic interactions is well-known. Understanding the nature of these interactions is important if they are to be used to control association. Here, we present results of an NMR study into the self-association of two isomers of naphthoic acid along with an investigation into the role of a fluorine substituent on that self-association. We interpret the results in terms of a simple isodesmic model of self-association and show that the addition of the fluorine atom appears to increase the stability of the aggregates by an order of magnitude (e.g., 1-naphthoic acid vs 4-fluoro-1-naphthoic acid, Keq = 0.05 increases to 0.35 M(-1)), a result which is supported by computational studies in the literature on the role of substituent effects on interaction energy. The use of fluorinated isomers to probe the assembly is also presented, with differing trends in fluorine-19 chemical shifts observed depending on the isomer substitution pattern.

Size-exclusion chromatographic NMR of polymer mixtures.

The use of chromatographic stationary phases or solvent modifiers to modulate diffusion properties in NMR experiments is now well established. Their use can be to improve resolution in the diffusion domain or to provide an insight into analyte-modifier interactions and, hence, the chromatography process. Here, we extend previous work using size-exclusion chromatographic stationary phases to the investigation of polymer mixtures. We demonstrate that similar diffusion modulation behaviour is observed with a size-exclusion chromatographic stationary phase that can be understood in terms of size-exclusion behaviour.

Investigating the interaction of sunset yellow aggregates and 6-fluoro-2-naphthoic acid: increasing probe molecule complexity.

The interaction of small molecules with non-covalent assemblies is of wide interest. The use of a magnetically active reporter nucleus allows information to be obtained in the presence of spectral overlap or in cases of high dynamic range. In this paper, we explore the interaction of a larger probe molecule, 6-fluoro-2-naphthoic acid with assemblies of sunset yellow using (19)F chemical shifts and diffusion NMR methods. Comparing the observations with previous studies using fluorophenols, 6-fluoro-2-naphthoic acid prefers to associate as clusters at the ends of the sunset yellow stacks.

NMR investigations of the interaction between the azo-dye sunset yellow and fluorophenol.

The interaction of small molecules with larger noncovalent assemblies is important across a wide range of disciplines. Here, we apply two complementary NMR spectroscopic methods to investigate the interaction of various fluorophenol isomers with sunset yellow. This latter molecule is known to form noncovalent aggregates in isotropic solution, and form liquid crystals at high concentrations. We utilize the unique fluorine-19 nucleus of the fluorophenol as a reporter of the interactions via changes in both the observed chemical shift and diffusion coefficients. The data are interpreted in terms of the indefinite self-association model and simple modifications for the incorporation of a second species into an assembly. A change in association mode is tentatively assigned whereby the fluorophenol binds end-on with the sunset yellow aggregates at low concentration and inserts into the stacks at higher concentrations.

Insights into the mechanism for gold catalysis: behaviour of gold(I) amide complexes in solution.

We report the synthesis and activity of new mononuclear and dinuclear gold amide complexes 1-7. The dinuclear complexes 6b and 7 were characterised by single crystal X-ray analysis. We also report solution NMR and freezing point depression experiments to rationalise their behaviour in solution and question the de-ligation process invoked in gold catalysis.

Chromatographic NMR with size exclusion chromatography stationary phases.

Chromatographic NMR describes the use of stationary phases or solvent additives, such as polymers, to modify the diffusion properties of analyte molecules and thereby improve the observed resolution in the diffusion domain. This paper demonstrates similar ideas using size exclusion chromatographic media and characterises the changes in the observed diffusion coefficient using a series of polymer molecular weight reference standards of known polydispersity. The results are interpreted in terms of a simple description of the size exclusion phenomena.

The open-chain triphosphanes RMe2SiCH2P(PR'2)2 (R = Me, Ph; R' = SiMe3, Cy, Ph).

The triphosphanes RMe(2)SiCH(2)P(PR'(2))(2) (R = Me, Ph; R' = SiMe(3), Cy) are synthesised in good yield via metathesis of organodichlorophosphanes and LiPR'(2), while for R' = Ph a propensity to form (Ph(2)P)(2) precludes isolation of the in situ characterised triphosphanes. Where R = Me and R' = SiMe(3) the triphosphane has also been characterised by single crystal X-ray diffraction and exhibits a single geometric conformer in the solid state, though solution-phase NMR spectra are indicative of facile conformational exchange across a wide temperature range. All of the described triphosphanes exhibit comparable behaviour, with their respective (31)P{(1)H} NMR spectra manifesting anomalous 'second-order' characteristics, which are considered using full spin-Hamiltonian simulation. Preliminary studies of coordination chemistry and ancillary reactivity of the triphosphanes are described.

On the inversion of diffusion NMR data: Tikhonov regularization and optimal choice of the regularization parameter.

The analysis of diffusion NMR data in terms of distributions of diffusion coefficients is hampered by the ill-posed nature of the required inverse Laplace transformation. Naïve approaches such as multiexponential fitting or standard least-squares algorithms are numerically unstable and often fail. This paper updates the CONTIN approach of the application of Tikhonov regularization to stabilise this numerical inversion problem and demonstrates two methods for automatically choosing the optimal value of the regularization parameter. These approaches are computationally efficient and easy to implement using standard matrix algebra techniques. Example analyses are presenting using both synthetic data and experimental results of diffusion NMR studies on the azo-dye sunset yellow and some polymer molecular weight reference standards.

The effect of Alzheimer's Aß aggregation state on the permeation of biomimetic lipid vesicles.

Alzheimer's disease is characterized by the aggregation and deposition of the Aß peptide. This 40 or 42 residue peptide is the product of the proteolysis of the amyloid precursor protein membrane protein and is able to assemble to form ordered, stable amyloid fibrils as well as small, soluble, and potentially cytotoxic oligomers. The toxicity of the oligomers may be associated with the ability to bind to and affect the integrity of lipid membranes. In this novel work, we have monitored and compared the ability of the potent Aß42 peptide, the less amyloidogenic Aß40 peptide, and a variant with reduced amyloidogenicity to bind to and affect the integrity of membranes using dye-filled synthetic vesicles. We reveal that the potency of the assemblies reduces with incubation time of the peptide and that maximal effect occurs when a particular species is apparent by electron microscopy. We have investigated the effect of lipid vesicle composition, and our results suggest that charge on the vesicles is important and that binding may partly be mediated by the GM1 ganglioside receptors expressed in the outer leaflet of vertebrate membranes.

NMR characterization of the aggregation state of the azo dye sunset yellow in the isotropic phase.

The azo dye sunset yellow is known to form lyotropic liquid crystals as a function of both temperature and sample composition. Numerous studies have been performed to investigate the aggregation processes in these liquid crystals; however, less attention has been paid to the nature of the aggregates in the isotropic phase. In this study we employ diffusion nuclear magnetic resonance methods to investigate the hydrodynamic properties of sunset yellow aggregates at a range of concentrations in isotropic solution. The results of these experiments are interpreted in terms of a simple thermodynamic model for aggregation and suggest that the aggregates are comprised of tens to hundreds of monomer units at the concentrations investigated. The results also demonstrate that the average number of molecules per aggregate is a factor of approximately 5 larger than previously reported.

Topological frustration in beta alpha-repeat proteins: sequence diversity modulates the conserved folding mechanisms of alpha/beta/alpha sandwich proteins.

The thermodynamic hypothesis of Anfinsen postulates that structures and stabilities of globular proteins are determined by their amino acid sequences. Chain topology, however, is known to influence the folding reaction, in that motifs with a preponderance of local interactions typically fold more rapidly than those with a larger fraction of nonlocal interactions. Together, the topology and sequence can modulate the energy landscape and influence the rate at which the protein folds to the native conformation. To explore the relationship of sequence and topology in the folding of beta alpha-repeat proteins, which are dominated by local interactions, we performed a combined experimental and simulation analysis on two members of the flavodoxin-like, alpha/beta/alpha sandwich fold. Spo0F and the N-terminal receiver domain of NtrC (NT-NtrC) have similar topologies but low sequence identity, enabling a test of the effects of sequence on folding. Experimental results demonstrated that both response-regulator proteins fold via parallel channels through highly structured submillisecond intermediates before accessing their cis prolyl peptide bond-containing native conformations. Global analysis of the experimental results preferentially places these intermediates off the productive folding pathway. Sequence-sensitive Go-model simulations conclude that frustration in the folding in Spo0F, corresponding to the appearance of the off-pathway intermediate, reflects competition for intra-subdomain van der Waals contacts between its N- and C-terminal subdomains. The extent of transient, premature structure appears to correlate with the number of isoleucine, leucine, and valine (ILV) side chains that form a large sequence-local cluster involving the central beta-sheet and helices alpha2, alpha 3, and alpha 4. The failure to detect the off-pathway species in the simulations of NT-NtrC may reflect the reduced number of ILV side chains in its corresponding hydrophobic cluster. The location of the hydrophobic clusters in the structure may also be related to the differing functional properties of these response regulators. Comparison with the results of previous experimental and simulation analyses on the homologous CheY argues that prematurely folded unproductive intermediates are a common property of the beta alpha-repeat motif.

The double [3 + 2] photocycloaddition reaction.

A remarkable double [3 + 2] photocycloaddition reaction that results in the formation of fenestrane 2 from aromatic acetal 1 is reported. During the formation of 2, four carbon-carbon bonds, five new rings, and seven new stereocenters are created in a one-pot process. The reaction occurs in a sequential manner from the linear meta photocycloadduct 3, while the angular meta photocycloadduct 4 undergoes an alternative fragmentation-translocation photoreaction to afford angular tricycle 6.