Powder XRD investigations on dotriacontane in mixtures: Phase strength and super lattices

Powder XRD investigations on dotriacontane-decane and dotriacontane-decanol mixtures are made. Phase strength, phase separation and formation of superlattices are discussed. The role of tunnel-like defects is considered.     

Crystal structure of 2-chloro-3-(beta-nitrovinyl)quinoline.

2-Chloro-3-(beta-nitrovinyl)quinoline (CNQ) was crystallographically studied owing to its medicinal properties and its occurrance in numerous commercial products, including pharmaceuticals, fragrances and dyes. The vinyl group is planar, and takes up an extended conformation. An hydrogen bonding of C-H...N type helps to stabilize the molecules in the unit cell.     

Gas-phase regiocontrolled generation of charged amino acid and peptide radicals

The combined use of advanced mass spectrometry experiments, condensed-phase synthesis of serine and homoserine nitrate ester radical precursors, and high-level ab initio calculations provides a powerful way of examining the fundamental reactivity of radicals derived from peptides.     

FT‐IR,FT‐Raman,and computational calculations of 4‐chloro‐2‐(3‐chlorophenyl carbamoyl)phenyl acetate

FT‐IR and FT‐Raman spectra of 4‐chloro‐2‐(3‐chlorophenylcarbamoyl) phenyl acetate were studied. Vibrational wavenumbers and corresponding vibrational assignments were examined theoretically using the Gaussian03 set of quantum chemistry codes and the normal modes are assigned by potential energy distribution (PED) calculations. Simultaneous IR and Raman activation of the CO stretching mode shows the charge transfer interaction through a π‐conjugated path. Optimized geometrical parameters of the title compound are in agreement with the reported values. Analysis of the phenyl ring modes shows that C C stretching mode is equally active as strong bands in both IR and Raman, which can be interpreted as the evidence of intramolecular charge transfer via conjugated ring path and is responsible for hyperpolarizability enhancement leading to nonlinear optical activity. The red‐shift of the NH‐stretching wavenumber in the infrared spectrum from the computed wavenumber indicates the weakening of the NH bond resulting in proton transfer to the neighboring oxygen atom. Copyright © 2009 John Wiley & Sons, Ltd.     

pH as a trigger of peptide beta-sheet self-assembly and reversible switching between nematic and isotropic phases

The hierarchical self-assembly of rationally designed synthetic peptides into beta-sheet tapes, ribbons, fibrils, and fibers opens up potentially useful routes to soft-solidlike materials such as hydrogels, organogels, or liquid crystals. Here, it is shown how incorporation of Glu (-CH(2)CH(2)COOH) or Orn (-CH(2)CH(2)CH(2)NH(2)) into the primary structure of an 11 amino acid peptide enables self-assembly to be rapidly (seconds) and reversibly controlled by simply changing pH. Solutions of monomeric peptide, typically at concentrations in excess of 0.003 v/v, can be switched within seconds to, for example, nematic gel states comprised of interconnected orientationally ordered arrays of fibrils or vice versa. This is to be compared with the lyophilized peptide dissolution route to nematic fluids and gels which is impracticably long, taking many hours or even days. An important design principle, that stabilization of fibrillar dispersions requires of the order of one unit of net positive or negative charge per peptide molecule, is first demonstrated and then used to design an 11 amino acid peptide P(11)-3 (CH(3)CO-Gln-Gln-Arg-Phe-Gln-Trp-Gln-Phe-Gln-Gln-Gln-NH(2)) whose self-assembly behavior is independent of pH (1 < pH < 10). pH control is then incorporated by appropriately positioning Glu or Orn side chains so that the peptide-peptide free energy of interaction in the tapelike substructure is strongly influenced by direct electrostatic forces between gamma-COO(-) in Glu(-) or delta-NH(3)(+) in Orn(+), respectively. This design principle is illustrated by the behavior of two peptides: P(11)-4 (CH(3)CO-Gln-Gln-Arg-Phe-Glu-Trp-Glu-Phe-Glu-Gln-Gln-NH(2)) which can be switched from its nematic to its isotropic fluid state by increasing pH and P(11)-5 (CH(3)CO-Gln-Gln-Orn-Phe-Orn-Trp-Orn-Phe-Gln-Gln-Gln-NH(2)) designed to exhibit the converse behavior. Acid-base titrations of fibrillar dispersions reveal deprotonation of the gamma-COOH of Glu or of the delta-NH(3)(+) of Orn(+) occurs over wide bands of up to 5 pH units, a feature of polyelectrolytes. The values of the energy parameters controlling self-assembly can therefore be smoothly and continuously varied by changing pH. This enables isotropic fluid-to-nematic transitions to be triggered by relatively small additions of acid or base, typically 1 part in 10(3) by volume of 1 M HCl or NaOH.     

Structural insights into the polymorphism of amyloid-like fibrils formed by region 20-29 of amylin revealed by solid-state NMR and X-ray fiber diffraction

Many unrelated proteins and peptides can assemble into amyloid or amyloid-like nanostructures, all of which share the cross-beta motif of repeat arrays of beta-strands hydrogen-bonded along the fibril axis. Yet, paradoxically, structurally polymorphic fibrils may derive from the same initial polypeptide sequence. Here, solid-state nuclear magnetic resonance (SSNMR) analysis of amyloid-like fibrils of the peptide hIAPP 20-29, corresponding to the region S (20)NNFGAILSS (29) of the human islet amyloid polypeptide amylin, reveals that the peptide assembles into two amyloid-like forms, (1) and (2), which have distinct structures at the molecular level. Rotational resonance SSNMR measurements of (13)C dipolar couplings between backbone F23 and I26 of hIAPP 20-29 fibrils are consistent with form (1) having parallel beta-strands and form (2) having antiparallel strands within the beta-sheet layers of the protofilament units. Seeding hIAPP 20-29 with structurally homogeneous fibrils from a 30-residue amylin fragment (hIAPP 8-37) produces morphologically homogeneous fibrils with similar NMR properties to form (1). A model for the architecture of the seeded fibrils is presented, based on the analysis of X-ray fiber diffraction data, combined with an extensive range of SSNMR constraints including chemical shifts, torsional angles, and interatomic distances. The model features a cross-beta spine comprising two beta-sheets with an interface defined by residues F23, A25, and L27, which form a hydrophobic zipper. We suggest that the energies of formation for fibril form containing antiparallel and parallel beta-strands are similar when both configurations can be stabilized by a core of hydrophobic contacts, which has implications for the relationship between amino acid sequence and amyloid polymorphism in general.     

Investigating the Structural Compaction of Biomolecules Upon Transition to the Gas-Phase Using ESI-TWIMS-MS

Collision cross-section (CCS) measurements obtained from ion mobility spectrometry-mass spectrometry (IMS-MS) analyses often provide useful information concerning a protein’s size and shape and can be complemented by modeling procedures. However, there have been some concerns about the extent to which certain proteins maintain a native-like conformation during the gas-phase analysis, especially proteins with dynamic or extended regions. Here we have measured the CCSs of a range of biomolecules including non-globular proteins and RNAs of different sequence, size, and stability. Using traveling wave IMS-MS, we show that for the proteins studied, the measured CCS deviates significantly from predicted CCS values based upon currently available structures. The results presented indicate that these proteins collapse to different extents varying on their elongated structures upon transition into the gas-phase. Comparing two RNAs of similar mass but different solution structures, we show that these biomolecules may also be susceptible to gas-phase compaction. Together, the results suggest that caution is needed when predicting structural models based on CCS data for RNAs as well as proteins with non-globular folds.

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Designing copper(II) ternary complexes to generate radical cations of peptides in the gas phase: role of the auxiliary ligand

A series of ternary copper(II) complexes of the type [Cu(II)(L)(M)](2+), where M represents the hexapeptides GGGFLR, YGGFLR and WGGFLR and L a set of 12 nitrogen donor ligands have been evaluated for their ability to form cationic peptide radicals, M(+)*, in the gas phase. Although the fragmentation chemistry of these ions is complex, two main conclusions emerge: (i) Complexes containing a tri- or tetra-dentate ligand were found to be more effective at producing the peptide radical because in these instances competitive loss of the ligand from the complex is inhibited; (ii) The ligands ought not possess any acidic protons in order to prevent competitive loss of the protonated peptide, [M + H](+). There is significant interaction of the N-terminal aromatic residues in YGGFLR and WGGLFR with the copper(ii) ion in several of the complexes as revealed by the formation of [Cu(I)(L)(p-quinomethide)](+) and [Cu(I)(L)(3-methyleneindoline)](+) fragment ions. Following its dissociation from the ternary complex, CID of the YGGFLR(+)* radical cation shows a dependence on the ligand in the complex from which it was formed. This 'memory effect' most likely reflects differences in the coordinated peptide structure induced by the ligand in the precursor complex which are maintained following dissociation.     

Gas-phase ligand loss and ligand substitution reactions of platinum(II) complexes of tridentate nitrogen donor ligands

The source of protons associated with the ligand loss channel of HX((n - 1)+) from [Pt(II)(dien)X](n+) (X = Cl, Br and I for n = 1 and X = NC(5)H(5) for n = 2) in the gas phase was investigated by deuterium-labelling studies. The results of these studies indicate that these protons originate from both the amino groups and the carbon backbone of the dien ligand. In some instances (e.g. X = Br and I), the protons lost from the carbon backbone can be even more abundant than the protons lost from the amino groups. The gas-phase substitution reactions of coordinatively saturated [Pt(II)(L(3))L(a)](2+) complexes (L(3) = tpy or dien) were also examined using ion-molecule reactions. The outcome of the ion-molecule reactions depends on both the ancillary ligand (L(3)) as well as the leaving group (L(a)). [Pt(II)(tpy)L(a)](2+) complexes undergo substitution reactions, with a faster rate when L(a) is a good leaving group, while the [Pt(II)(dien)L(a)](2+) complex undergoes a proton transfer reaction.     

OXIDATION PRODUCTS OF CYCLIC THIONES

Abstract

A large number of cyclic thiones has been synthesized. These include alicyclic and heterocyclic thiones, the latter including those with potential aromatic character. It is the intention of this paper to summarize the reactions of a number of simple systems of this type with a variety of reagents which lead to modification of the thione function. Reactions may either lead to oxidation of the molecule, replacement of the thione sulfur atom by oxygen, or even replacement by hydrogen. Data are also included for some thiols which are capable of tautomerism with thiones and give similar or related products.