FTIR microscopy of biological cells and tissue: data analysis using resonant Mie scattering (RMieS) EMSC algorithm

Transmission and transflection infrared microscopy of biological cells and tissue suffer from significant baseline distortions due to scattering effects, predominantly resonant Mie scattering (RMieS). This scattering can also distort peak shapes and apparent peak positions making interpretation difficult and often unreliable. A correction algorithm, the resonant Mie scattering extended multiplicative signal correction (RMieS-EMSC), has been developed that can be used to remove these distortions. The correction algorithm has two key user defined parameters that influence the accuracy of the correction. The first is the number of iterations used to obtain the best outcome. The second is the choice of the initial reference spectrum required for the fitting procedure. The choice of these parameters influences computational time. This is not a major concern when correcting individual spectra or small data sets of a few hundred spectra but becomes much more significant when correcting spectra from infrared images obtained using large focal plane array detectors which may contain tens of thousands of spectra. In this paper we show that, classification of images from tissue can be achieved easily with a few (<10) iterations but a reliable interpretation of the biochemical differences between classes could require more iterations. Regarding the choice of reference spectrum, it is apparent that the more similar it is to the pure absorption spectrum of the sample, the fewer iterations required to obtain an accurate corrected spectrum. Importantly however, we show that using three different non-ideal reference spectra, the same unique correction solution can be obtained.     

Improving Internal Peptide Dynamics in the Coarse-Grained MARTINI Model: Toward Large-Scale Simulations of Amyloid- and Elastin-like Peptides

We present an extension of the coarse-grained MARTINI model for proteins and apply this extension to amyloid- and elastin-like peptides. Atomistic simulations of tetrapeptides, octapeptides, and longer peptides in solution are used as a reference to parametrize a set of pseudodihedral potentials that describe the internal flexibility of MARTINI peptides. We assess the performance of the resulting model in reproducing various structural properties computed from atomistic trajectories of peptides in water. The addition of new dihedral angle potentials improves agreement with the contact maps computed from atomistic simulations significantly. We also address the question of which parameters derived from atomistic trajectories are transferable between different lengths of peptides. The modified coarse-grained model shows reasonable transferability of parameters for the amyloid- and elastin-like peptides. In addition, the improved coarse-grained model is also applied to investigate the self-assembly of β-sheet forming peptides on the microsecond time scale. The octapeptides SNNFGAIL and (GV)(4) are used to examine peptide aggregation in different environments, in water, and at the water-octane interface. At the interface, peptide adsorption occurs rapidly, and peptides spontaneously aggregate in favor of stretched conformers resembling β-strands.     

Overgrowth of Rhodium on Gold Nanorods

This study focuses on the deposition and growth mode of rhodium (Rh) on gold (Au) seed nanorods (NRs). Using a combination of scanning transmission electron microscopy imaging, energy-dispersive X-ray spectroscopy, and UV-visible absorption spectroscopy, we show that Rh deposition results in an uneven overlayer morphology on the Au NR seeds, with a tendency for Rh deposition to occur preferentially on the Au NR ends. The results suggest that complex and kinetically driven metal-metal interactions take place in this system.     

Hexahomotrioxacalix[3]arene derivatives as ionophores for molecular recognition of dopamine, serotonin and phenylethylamine

The lower rim functionalized hexahomotrioxacalix[3]arene derivatives cone-3 and cone-5 bearing three benzyl and three N,N-diethyl-2-aminoethoxy groups, respectively, were synthesized from triol 1. Their complexation with 2-(3,4-dihydroxyphenyl)ethylamine (dopamine), 5-hydroxytryptamine (serotonin), and 2-phenylethylamine (phenethylamine), which have biologically important activities, has been studied by (1)H-NMR spectroscopy. The chemical shifts of the aromatic protons of the host and guest molecules and the up-field shifts of the ethyl protons of the guest molecules strongly suggest the formation of inclusion complexes in solution. The formation of the host-guest complexes is assisted by a hydrogen bond and/or an electrostatic interaction between the host and ammonium ion (RNH(3)(+)) of the guest. The structures of receptors cone-3 and cone-5 have been determined by X-ray crystallography.     

RNA and DNA association to zwitterionic and charged monolayers at the air-liquid interface

The objective of this work is to establish under which conditions short RNA molecules (similar to miRNA) associate with zwitterionic phospholipids and how this differs from the association with cationic surfactants. We study how the base pairing (i.e., single stranded versus double stranded nucleic acids) and the length of the nucleic acid and the charge of the lipid/surfactant monolayer affect the association behavior. For this purpose, we study the adsorption of nucleic acids to monolayers composed of dipalmitoyl phosphatidylcholine (DPPC) or dioctadecyl-dimethyl-ammoniumbromide (DODAB) using the surface film balance, neutron reflectometry, and fluorescence microscopy. The monolayer studies with the surface film balance suggested that short single-stranded ssRNA associates with liquid expanded zwitterionic phospholipid monolayers, whereas less or no association is detected for double-stranded dsRNA and dsDNA. In order to quantify the interaction and to determine the location of the nucleic acid in the lipid/surfactant monolayer we performed neutron reflectometry measurements. It was shown that ssRNA adsorbs to and penetrates the liquid expanded monolayers, whereas there is no penetration of nucleic acids into the liquid condensed monolayer. No adsorption was detected for dsDNA to zwitterionic monolayers. On the basis of these results, we propose that the association is driven by the hydrophobic interactions between the exposed hydrophobic bases of the ssRNA and the hydrocarbon chains of the phospholipids. The addition of ssRNA also influences domain formation in the DPPC monolayer, leading to fractal-like interconnected domains. The experimental results are discussed in terms of the implication for biological processes and new leads for applications in medicine and biotechnology.     

Synthesis of the HCV protease inhibitor Vaniprevir (MK-7009) using ring-closing metathesis strategy

A highly efficient synthesis of Vaniprevir (MK-7009) has been accomplished in nine linear steps and 55% overall yield. The key features of this synthesis include a cost-effective synthesis of the isoindoline subunit and efficient construction of the 20-membered macrocyclic core of Vaniprevir (MK-7009) utilizing ring-closing metathesis technology. A high-performing ring-closing metathesis protocol has been achieved by simultaneous slow addition of the ruthenium catalyst (0.2 mol %) and the diene substrate at a concentration of 0.13 M.     

The effect of reduction on rhenium(I) complexes with binaphthyridine and biquinoline ligands: a spectroscopic and computational study

A number of rhenium complexes with binaphthyridine and biquinoline ligands have been synthesized and studied. These are [Re(L)(CO)3Cl] where L = 3,3'-dimethylene-2,2'-bi-1,8-naphthyridine (dbn), 2,2'-bi-1,8-naphthyridine (bn), 3,3'-dimethylene-2,2'-biquinoline (dbq), and 3,3'-dimethyl-2,2'-biquinoline (diq). This series represents ligands in which the electronic properties and steric preferences are tuned. These complexes are modeled using density functional theory (DFT). An analysis of the resonance Raman spectra for these complexes, in concert with the vibrational assignments, reveals that the accepting molecular orbital (MO) in the metal-to-ligand charge transfer (MLCT) transition is the LUMO and causes bonding changes at the inter-ring section of the ligand. The electronic absorption spectroelectrochemistry for the reduced complexes of [Re(dbn)(CO)3Cl], [Re(dbq)(CO)3Cl], and [Re(diq)(CO)3Cl] suggest that the singly occupied MO is delocalized over the entire ligand structure despite the nonplanar nature of the diq ligand in [Re(diq)(CO)3Cl]. The IR spectroelectrochemistry for [Re(dbn)(CO)3Cl], [Re(dbq)(CO)3Cl], and [Re(bn)(CO)3Cl] reveal that reduction lowers the CO ligand vibrational frequencies to a similar extent in all three complexes. The substitution of naphthyridine for quinoline has little effect on the nature of the singly occupied MO. These data are supported by DFT calculations on the reduced complexes, which reveal that the ligands are flattened out by reduction: This may explain the similarity in the properties of the reduced complexes.     

Practical application of new catalytic methods: a concise synthesis of a potent PDE IV inhibitor

An efficient synthesis of a potent PDE IV inhibitor 1 is described. The synthesis is highlighted by two practical and efficient catalytic reactions: a highly selective catalytic palladium mediated carbonylation of the pyridine side chain and an efficient palladium-catalyzed Suzuki-Miyaura coupling of a chloropyridine-N-oxide.     

Fluorescence and Photochemistry of Recombinant Phytochrome from the Cyanobacterium Synechocystis

Fluorescence and photochemical properties of phytochrome from the cyanobacterium Synechocystis were investigated in the temperature interval from 293 to 85 K. The apoprotein was obtained by overexpression in Escherichia coli and assembled to a holophytochrome with phycocyanobilin (PCB) and phytochromobilin (PφB), Syn(PCB)phy and Syn(PφB)phy, respectively. Its red-absorbing form, Pr, is characterized at 85 K by the emission and excitation maxima at 682 and 666 nm in Syn(PCB)phy and at 690 and 674 nm in Syn(PφB)phy. At room temperature, the spectra are blue shifted by 5–10 nm. The fluorescence intensity dropped down by ?15–20-fold upon warming from 85 to 293 K and activation energy of the fluorescence decay was estimated to be ca 5.4 and 4.9 kJ mol^?1 in Syn(PCB)phy and Syn(PφB)phy, respectively. Phototransformation of Pr upon red illumination was observed at temperatures above 160–170 K in Syn(PCB)phy and above 140–150 K in Syn(PφB)phy with a 2–3 nm shift of the emission spectrum to the blue and increase of the intensity of its shorter wavelength part. This was interpreted as a possible formation of the photoproduct of the meta-Ra type of the plant phytochrome. At ambient temperatures, the extent of the Pr phototransformation to the far-red-absorbing form, Pfr, was ca 0.7–0.75 and 0.85–0.9 for Syn(PCB)phy and Syn(PφB)phy, respectively. Fluorescence of Pfr and of the photoproduct similar to lumi-R was not observed. With respect to the photochemical parameters, Syn(PCB)phy and Syn(PφB)phy are similar to each other and also to a small fraction of phyA (phyA″) and to phyB. The latter were shown to have low photochemical activity at low temperatures in contrast to the major phyA pool (phyA″), which is distinguished by the high extent (ca 50%) of Pr photoransformation at 85 K. These photochemical features are interpreted in terms of different activation barriers for the photoreaction in the Pr excited state.     

Do halogen and methyl substituents have electronic effects on the structures of simple disilanes? An experimental and theoretical study of the molecular structures of the series X3SiSiMe3 (X = H, F, Cl and Br)

The gas-phase molecular structures of a series of halogen-substituted disilanes [X₃SiSiMe₃ (X = H, F, Cl and Br)], 1,1,1-trimethyldisilane (H₃SiSiMe₃), 1,1,1-trifluoro-2,2,2-trimethyldisilane (F₃SiSiMe₃), 1,1,1-trichloro-2,2,2-trimethyldisilane (Cl₃SiSiMe₃) and 1,1,1-tribromo-2,2,2-trimethyldisilane (Br₃SiSiMe₃), have been determined in the gas phase by electron diffraction. Ab initio calculations at the HF and MP2 level were used to support the experimental investigation using the SARACEN method. All of the investigated structures were determined to adopt a staggered structure with C _3v symmetry. The effect of substitution on the Si–Si bond and the Si–Si–X bond angle was investigated and these results were compared to results obtained from a recent study of halogen-substituted disilanes [X₃SiSiXMe₂ (X = F, Cl, Br and I)] to consider the effect of the methyl groups on the substituted disilanes.