Crystal nucleation, growth, and morphology of the synthetic malaria pigment beta-hematin and the effect thereon by quinoline additives: the malaria pigment as a target of various antimalarial drugs

The morphology of micrometer-sized beta-hematin crystals (synthetic malaria pigment) was determined by TEM images and diffraction, and by grazing incidence synchrotron X-ray diffraction at the air-water interface. The needle-like crystals are bounded by sharp {100} and {010} side faces, and capped by {011} and, to a lesser extent, by {001} end faces, in agreement with hemozoin (malaria pigment) crystals. The beta-hematin crystals grown in the presence of 10% chloroquine or quinine took appreciably longer to precipitate and tended to be symmetrically tapered toward both ends of the needle, due to stereoselective additive binding to {001} or {011} ledges. Evidence, but marginal, is presented that additives reduce crystal mosaic domain size along the needle axis, based on X-ray powder diffraction data. Coherent grazing exit X-ray diffraction suggests that the mosaic domains are smaller and less structurally stable than in pure crystals. IR-ATR and Raman spectra indicate molecular based differences due to a modification of surface and bulk propionic acid groups, following additive binding and a molecular rearrangement in the environment of the bulk sites poisoned by occluded quinoline. These results provided incentive to examine computationally whether hemozoin may be a target of antimalarial drugs diethylamino-alkoxyxanthones and artemisinin. A variation in activity of the former as a function of the alkoxy chain length is correlated with computed binding energy to {001} and {011} faces of beta-hematin. A model is proposed for artemisinin activity involving hemozoin nucleation inhibition via artemisinin-beta-hematin adducts bound to the principal crystal faces. Regarding nucleation of hemozoin inside the digestive vacuole of the malaria parasite, nucleation via the vacuole's membranous surface is proposed, based on a reported hemozoin alignment. As a test, a dibehenoyl-phosphatidylcholine monolayer transferred onto OTS-Si wafer nucleated far more beta-hematin crystals, albeit randomly oriented, than a reference OTS-Si.     

Modeling the kinetics of gas adsorption in multilayer porphyrin films

A kinetic model is proposed to describe the diffusion and adsorption behavior of gas in multilayer films. Numerical solutions are attained on time scales of seconds using a finite differencing approximation to the kinetic equations. Predictions of this model are compared to experimental data for the case of NO2 diffusing through a porphyrin film. The model predicts a binding energy for the NO2 porphyrin interaction of 0.72 eV. It also predicts that for this system diffusion is the limiting factor for the adsorption response time of the film, although the recovery time is determined by both the diffusion coefficient and NO2 binding energy. Comparison with experiment gives a predicted diffusion coefficient of approximately 10(-14) m2.s-1.     

Raman, infrared and computational analysis of genistein and its methoxy derivatives

Structural vibrational analyses of four 5-hydroxyisoflavones: genistein, biochanin A, prunetin and 4′,7-dimethoxygenistein have been performed using a combination of computational and experimental investigations of Raman and infrared spectra. Normal vibrational modes in the Raman and infrared spectra were assigned and correlated with the aid of calculations using density functional theory (DFT), adopting the B3LYP functional with the 6-31+G(d) basis set. As the four isoflavones differ by methoxy substitutions of the hydroxyl groups, shifts between phenol and anisole were also used to assist in the assignments. This work offers insight into some of the variations observed in the vibrational spectra of genistein and other isoflavones and lays the foundation for analysis of related compounds as well as further spectral analysis of the present isoflavones.     

Label-acquired magnetorotation for biosensing: An asynchronous rotation assay

This paper presents a novel application of magnetic particles for biosensing, called label-acquired magnetorotation (LAM). This method is based on a combination of the traditional sandwich assay format with the asynchronous magnetic bead rotation (AMBR) method. In label-acquired magnetorotation, an analyte facilitates the binding of a magnetic label bead to a nonmagnetic solid phase sphere, forming a sandwich complex. The sandwich complex is then placed in a rotating magnetic field, where the rotational frequency of the sandwich complex is a function of the amount of analyte attached to the surface of the sphere. Here, we use streptavidin-coated beads and biotin-coated particles as analyte mimics, to be replaced by proteins and other biological targets in future work. We show this sensing method to have a dynamic range of two orders of magnitude.     

Reactivity between acetone and single-stranded DNA containing a 5′-capped 2′-fluoro-N7-methyl guanine

DNA-mediated catalysis is an emerging field in bioorganic chemistry and chemical biology. However, the functional group diversity and known reactivity of DNA (A, T, C, and G) is relatively limited in scope. This relatively defined reactivity can limit the utility of DNA as a catalyst. In an effort to expand the functional group diversity and chemical reactivity of DNA, we sought to explore reactions involving single-stranded DNA equipped with a stabilized variant of N7-methyl guanine (2′-fluoro-5′-N7-methyl guanine). Here, we show that 5′-capped 2′-fluoro-N7-methyl guanine-labeled single-stranded DNA reacts with a ketone to afford a ketone-labeled DNA. This reaction likely proceeds through a reactive ylide or N-heterocyclic carbene. Taken together, our findings suggest that 2′-fluoro-5′-N7-methyl guanine is a stable adduct that can be selectively incorporated into ssDNA and functionalized with a ketone moiety by reaction with a simple ketone. Incorporation of this nucleoside into ssDNA may be useful for the evolution of novel deoxyribozymes that catalyze new reactions, including those which proceed via a reactive ylide or N-heterocyclic carbene-mediated chemistry.     

Synchrotron far infrared spectroscopy of the ground, ν(5), and ν(15) states of thiirane

The high-resolution (0.001 cm(-1)) spectrum of thiirane has been recorded at the far-infrared beamline at the Australian synchrotron between 760-400 cm(-1) and 170-10 cm(-1). Ro-vibrational transitions of the highly Coriolis coupled ν(5) (628.1 cm(-1)) and ν(15) (669.7 cm(-1)) fundamentals, as well as pure rotational far-IR transitions have been assigned, and rotational, centrifugal distortion, and Coriolis interaction parameters determined. ν(15) gains the vast majority of its intensity from an interesting Coriolis intensity stealing mechanism, which is also outlined.     

Resin-bound dynamic combinatorial chemistry

[reaction: see text] Dynamic combinatorial chemistry (DCC) is a promising technique for receptor-aided selection of high-affinity ligands from equilibrating combinatorial libraries. Identification of the specific ligand(s) selected is often challenging, however, due to difficulties associated with chromatographic separation and/or mass degeneracy within the library. Herein, we describe proof-of-concept experiments demonstrating a new technique termed resin-bound DCC (RB-DCC), which provides a solution to this problem.     

Comment on gas phase infrared spectrum and ab initio calculations of phosphorus(III) thiocyanide, SPCN

We show that two of the three bands assigned to SPCN are assignable to cyanogen and that the bands assigned to SPCl are done so in error, with the 712 cm(-1) band in the spectrum of Allaf and Odeh assignable to HCN. There is no evidence for either ClPS or SPCN in the spectra shown. Finally low resolution IR spectroscopy by itself, whilst useful in assisting in the identification of pyrolysis products does not provide unambiguous identification and requires support by rigorous computation, band modelling and correct use of the literature. None of these are evidenced in the present paper of Allaf and Odeh nor indeed in the work that was the subject of our previous criticism and re-analysis.