Genomics of selected human odorant receptors

Single nucleotide polymorphisms (SNPs) in odorant receptor genes may influence the protein sequence and consequently also the function of the receptors. An analysis of the HapMap data for human OR3A1 was performed and provided evidence that genetic differences subject to ancestry and gender can be recognized. A genomic comparison of individuals shows the diversity of odorant receptor genes and therefore potentially the variety of the sense of smell. At this time, two complete human genomes are available in public domain, which we used for this purpose. Correspondence: Anton Beyer, Institute of Theoretical Chemistry, University of Vienna, A-1090 Vienna, Austria.     

Anthracene-Porphyrin Nanoribbons

π-Conjugated nanoribbons attract interest because of their unusual electronic structures and charge-transport behavior. Here, we report the synthesis of a series of fully edge-fused porphyrin-anthracene oligomeric ribbons (dimer and trimer), together with a computational study of the corresponding infinite polymer. The porphyrin dimer and trimer were synthesized in high yield, via oxidative cyclodehydrogenation of singly linked precursors, using 2,3-dichloro-5,6-dicyano-1,4-benzoquinone (DDQ) and trifluoromethanesulfonic acid (TfOH). The crystal structure of the dimer shows that the central π-system is flat, with a slight S-shaped wave distortion at each porphyrin terminal. The extended π-conjugation causes a dramatic red-shift in the absorption spectra: the absorption maxima of the fused dimer and trimer appear at 1188 nm and 1642 nm, respectively (for the nickel complexes dissolved in toluene). The coordinated metal in the dimer was changed from Ni to Mg, using p-tolylmagnesium bromide, providing access to free-base and Zn complexes. These results open a versatile avenue to longer π-conjugated nanoribbons with integrated metalloporphyrin units.     

Synthetic and mechanistic aspects of a new method for ruthenium-metalation of porphyrins and Schiff-bases

A new method is presented for metalation of a wide range of free-base, neutral, cationic, and anionic porphyrins in refluxing dimethylformamide (DMF) using an easily prepared [Ru(DMF) 6](OTf) 3 complex, and comparisons are made with the more familiar metalation procedure using Ru 3(CO) 12. Both procedures generate Ru (II)(porp)(CO)L complexes (L = solvent); use of the Ru (III)-triflate precursor gives yields comparable to, or greater than, those obtained with the carbonyl, and generates no Ru-chlorin impurities. Mechanistic studies on the meso-tetraphenylporphyrin system reveal that the DMF furnishes the CO, which in the presence of essential water reduces the metal, and metalation likely occurs via a Ru (II)-CO species. Corresponding metalation of tetradentate Schiff-bases gives trans-[Ru (III)(Schiff- base)(DMF) 2]OTf complexes in yields of approximately 50%, a limitation being the accompanying hydrolysis of the Schiff-base through the presence of trace water.     

Design of open-framework germanates by combining different building units

Open-framework germanates with extra-large channels are built from two different types of clusters. The two different clusters are connected in such a way to form a pseudo-body-centered cluster aggregate (PBCCA). The different packing of PBCCAs resulted in different 3D open-framework germanates.     

Measurement of deamidation of intact proteins by isotopic envelope and mass defect with ion cyclotron resonance Fourier transform mass spectrometry

After synthesis and folding, proteins undergo many post-synthetic modifications, including cleavage, oxidation, glycosylation, methylation, racemization, phosphorylation, and deamidation. Of these modifications, non-enymatic deamidation is the most prevalent. Each asparaginyl and glutaminyl residue in a protein is a miniature molecular clock that deamidates with a genetically determined half-time. These half-times vary from a few hours to more than a century, depending on a primary, secondary, tertiary, and quaternary structure near the amide residue. It has been suggested that these clocks regulate many biological processes. A few such processes have been discovered. These discoveries have been difficult because deamidation is inconvenient to measure. While most post-synthetic changes are easily measured by mass spectrometry, deamidation increases molecular mass by only one nominal Dalton, so the deamidated isotopic envelope overlaps the undeamidated isotopic envelope. While peptide deamidation rate determination through deconvolution of these envelopes has been accomplished for several hundred peptides, deconvolution becomes more difficult as the molecular weight increases. In high-resolution mass spectrometers, this deconvolution is possible for larger molecules and an alternative method based on the 19 mDa mass defect between the deamidated envelope and the isotopic envelope of protein fragments can also be utilized. We herein report a comparison of the envelope deconvolution and the mass defect methods for measurement of deamidation in human eye lens crystallins, with special emphasis on betaB2 crystallin and gammaS crystallin. Measurement of extent of deamidation of betaB2 crystallin in a 7 Tesla ion cyclotron resonance Fourier transform mass spectrometer is found to be accurate to a relative standard deviation in a single measurement of about 4% for each method. The envelope deconvolution method is further illustrated by detection of deamidation in intact gammaS crystallin, a 20 904 Da protein, and discovery of the principal gammaS deamidation site.     

Formation of silver nanoparticles at the air-water interface mediated by a monolayer of functionalized hyperbranched molecules

Nanofibrillar micellar structures formed by the amphiphilic hyperbranched molecules within a Langmuir monolayer were utilized as matter for silver nanoparticle formation from the ion-containing water subphase. We observed that silver nanoparticles were formed within the multifunctional amphiphilic hyperbranched molecules. The diameter of nanoparticles varied from 2-4 nm and was controlled by the core dimensions and the interfibrillar free surface area. Furthermore, upon addition of potassium nitrate to the subphase, the Langmuir monolayer templated the nanoparticles' formation along the nanofibrillar structures. The suggested mechanism of nanoparticle formation involves the oxidation of primary amino groups by silver catalysis facilitated by "caging" of silver ions within surface areas dominated by multibranched cores. This system provides an example of a one-step process in which hyperbranched molecules with outer alkyl tails and compressed amine-hydroxyl cores mediated the formation of stable nanoparticles placed along/among/beneath the nanofibrillar micelles.     

Langmuir-Blodgett monolayers of gold nanoparticles with amphiphilic shells from V-shaped binary polymer arms

Gold nanoparticles functionalized with amphiphilic polybutadiene-poly(ethylene glycol) (PB-PEG) V-shaped arms formed stable Langmuir monolayers at the air-water and the air-solid interfaces. At these interfaces, the binary arms vertically segregated into a dense polymer corona, which surrounded the gold nanoparticles, preventing their large-scale agglomeration and keeping individual nanoparticles well-separated from each other and forming flattened, pancake nanostructures. The presence of both PEG and PB chains in the close proximity to the gold core was confirmed by surface enhanced Raman spectroscopy, whereas the AFM phase contrast images revealed the presence of 2 nm gold cores surrounded by the polymer shell with the diameter of 11 nm. We suggest that the amphiphilic shell drives their spontaneous organization into discrete 2D pancake-like hybrid structures that measured up to 10 microm in diameter and had a high packing density of gold clusters.     

Phane properties of [2.2]paracyclophane/dehydrobenzoannulene hybrids

A series of [2.2]paracyclophane/dehydrobenzo[14]annulene (PC/DBA) hybrids (hydrocarbons 5, 6, 9, 10 b, and 10 c), [2.2]paracyclophane/dehydro[14]annulene (PC/DA) hybrids (7 and 8) and suitable model systems (11, 12, and 33) has been synthesized. Comparison of the electronic absorption spectra in each series of compounds provides further insight into the global communication between the decks in the [2.2]paracyclophane unit.     

Experimental and theoretical characterization of the valence isomerization of Bi-2H-azirin-2-yls to diazabenzenes

3,4-diazidocyclobutenes 16 were prepared from the corresponding dihalides. Some of these diazides, such as parent compound 16 d and phenyl-substituted derivatives 16 c,f, underwent spontaneous stereoselective electrocyclic ring opening below room temperature, whereas the tetraalkyl derivatives of 16 had to be heated to force the same reaction. In most cases, the resulting 1,4-diazidobuta-1,3-dienes 8 were isolated to study their photochemical transformation into bi-2H-azirin-2-yls 9 via intermediate mono-azirines 17. Except for starting materials with a low number of substituents such as 9 d and 9 f, title compounds 9 underwent a thermal valence isomerization which led exclusively to pyridazines 18 at surprisingly low temperatures. Based on quantum-chemical calculations for the parent bi-2H-azirinyl-2-yl 9 d at the UB3LYP/6-31+G(d) and MR-MP2/TZV(2df,2p) levels, the valence isomerization process is best explained by simultaneous homolytic cleavage of both C--N single bonds of 9 to generate energetically favorable N,N' diradicals 26, which cyclize to 18. The theoretical studies indicate also that one stereoisomer of 9, namely, the rac compound, should undergo valence isomerization more easily than the other, which is in conformity with different rates of these rearrangement reactions found experimentally. For the tetramethyl-bi-2H-azirin-2-yls 9 g, which are better models for the experimentally studied compounds, simultaneous homolytic cleavage of both C--N single bonds is also predicted by the calculations, although the intermediate diradicals 26 g are significantly higher in energy than those of the parent system 9 d.