The hydrogen bonding properties of cytosine: a computational study of cytosine complexed with hydrogen fluoride, water, and ammonia

Density functional theory is used to study the hydrogen bonding pattern in cytosine, which does not contain alternating proton donor and acceptor sites and therefore is unique compared with the other pyrimidines. Complexes between various small molecules (HF, H(2)O, and NH(3)) and four main binding sites in (neutral and (N1) anionic) cytosine are considered. Two complexes (O2(N1) and N3(N4)) involve neighboring cytosine proton acceptor and donor sites, which leads to cooperative interactions and bidendate hydrogen bonds. The third (less stable) complex (N4) involves a single cytosine donor. The final (O2-N3) complex involves two cytosine proton acceptors, which leads to an anticooperative hydrogen bonding pattern for H(2)O and NH(3). On the neutral surface, the anticooperative O2-N3 complex is less stable than those involving bidentate hydrogen bonds, and the H(2)O complex cannot be characterized when diffuse functions are included in the (6-31G(d,p)) basis set. On the contrary, the anionic O2-N3 structure is the most stable complex, while the HF and H(2)O N3(N4) complexes cannot be characterized with diffuse functions. B3LYP and MP2 potential energy surface scans are used to consider the relationship between the water N3(N4) and O2-N3 complexes. These calculations reveal that diffuse functions reduce the conversion barrier between the two complexes on both the neutral and anionic surfaces, where the reduction leads to a (O2-N3) energy plateau on the neutral surface and complete (N3(N4)) complex destabilization on the anionic surface. From these complexes, the effects of hydrogen bonds on the (N1) acidity of cytosine are determined, and it is found that the trends in the effects of hydrogen bonds on the (N1) acidity are similar for all pyrimidines.     

Fluorocyclohexanes-III 1H:4H/2H- and 1H/2H:4H-nonafluorocyclohexane and derived compounds

Two nonafluorocyclohexanes of b.p. 92° and 101°, made by fluorination of benzene,¹ have each been dehydrofluorinated to give the same six unsaturated products. These were identified by oxidation and other studies as 3H:4H- and 4H:5H-octafluorocyclohexene, 1H-1:4-, 1H-1:3-, and 2H-1:3-heptafluorocyclohexadiene, and hexafluorobenzene,² thus indicating a 1H:2H:4H-structure for the saturated precursors. The stereochemistry of the adjacent> CHF groups was established by resolution, via the brucine salt, of the 3H:4H-hexafluoroadipic acid obtained by oxidation of the 4H:5H-mono-olefin, showing that the hydrogens were trans. The complete stereochemistry of the nonafluorides was suggested by the dehydrofluorinations and confirmed by further fluorination³ to give known decafluorocyclohexanes. Treatment of 4H/5H-octafluorocyclohexene with lithium aluminium hydride in diethyl ether gave 1H,4H/5H-heptafluorocyclohexene, a precursor of pentafluorobenzene.⁴     

Total synthesis of (-)-tuberostemonine

The first total synthesis of the complex pentacyclic Stemona alkaloid tuberostemonine was accomplished in 24 steps and in 1.4% overall yield from a hydroindole intermediate which is readily obtained in three steps from Cbz-l-tyrosine. An innovative synthetic strategy was applied that relays the single stereocenter of the amino acid precursor into nine of the ten stereogenic carbons of the target molecule. Among the highlights of the synthetic methodology are the 3-fold use of ruthenium catalysis, first in an azepine ring-closing metathesis and then in an alkene isomerization followed by a cross-metathesis propenyl-vinyl exchange, as well as the stereoselective attachment of the gamma-butyrolactone moiety to the core tetracycle by use of a lithiated ortho ester.     

Microscale sample deposition onto hydrophobic target plates for trace level detection of neuropeptides in brain tissue by MALDI-MS

A sample preparation method that combines a modified target plate with a nanoscale reversed-phase column (nanocolumn) was developed for detection of neuropeptides by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). A gold-coated MALDI plate was modified with an octadecanethiol (ODT) self-assembled monolayer to create a hydrophobic surface that could concentrate peptide samples into a approximately 200-500-microm diameter spot. The spot sizes generated were comparable to those obtained for a substrate patterned with 200-microm hydrophilic spots on a hydrophobic substrate. The sample spots on the ODT-coated plate were 100-fold smaller than those formed on an unmodified gold plate with a 1-microl sample and generated 10 to 50 times higher mass sensitivity for peptide standards by MALDI-TOF MS. When the sample was deposited on an ODT-modified plate from a nanocolumn, the detection limit for peptides was as low as 20 pM for 5-microl samples corresponding to 80 amol deposited. This technique was used to analyze extracts of microwave-fixed tissue from rat brain striatum. Ninety-eight putative peptides were detected including several that had masses matching neuropeptides expected in this brain region such as substance P, rimorphin, and neurotensin. Twenty-three peptides had masses that matched peaks detected by capillary liquid chromatography with electrospray ionization MS.     

The MPE/UCB far-infrared imaging Fabry-Perot interferometer (FIFI)

FIFI is an imaging spectrometer with two or three Fabry-Perot interferometers (FPI) in series for airborne astronomical observations in the far-infrared range (=40...200m). It employs 5×5 arrays of photoconducting detectors and offers spectral resolutions as small as 2km/s. Resolution and bandwidth can be set over a wide range to match a variety of astronomical sources. Cryogenic optics minimizes thermal background radiation and provides for in-flight step tunable spatial resolution. At 158 m wavelength the background-limited NEP is 3 × 10^-15W/Hz at 40 km/s resolution and with two FPI's; with three FPI's the expected NEP is 10^-15WHz at 5 km/s resolution.The frequency-chopping mode of the high-resolution Fabry-Perot allows for line detection in extended objects. Absolute internal flux calibration ensures adequate flat fielding of the array elements.     

Synthesis of fused indoles by sequential palladium-catalyzed Heck reaction and N-heteroannulation

A route to 3,4-fused indoles via two consecutive palladium-catalyzed reactions; an intramolecular Heck reaction followed by a reductive N-heteroannulation is described. Using this route, a number of indoles have been prepared having a variety of ring sizes anchored to the 3- and 4-position of the indole nucleus. Furthermore, a number of functional groups, both carbon and heteroatom substituents can be introduced in (and on) the additional ring without any detrimental effects on the two reactions.     

Lexicographic products with high reconstruction numbers

The reconstruction number of a graph is the smallest number of vertex-deleted subgraphs needed to uniquely determine the graph up to isomorphism. Bollobás showed that almost all graphs have reconstruction number equal to three. McMullen and Radziszowski published a catalogue of all graphs on at most ten vertices with reconstruction number greater than three. We introduce constructions that generalize the examples identified in their work. In particular, we use lexicographic products of vertex transitive graphs with certain starter graphs from the work of Myrvold and from the work of Harary and Plantholt to generate new infinite families of graphs with high reconstruction numbers. In the process, we settle a question of McMullen and Radziszowski.     

pH tunable self-assembly of chicoric acid and their biocompatibility studies

We report for the first time, the pH tunable self-assembly of chicoric acid, an HIV-I integrase inhibitor, which displayed a remarkable tendency to self-assemble at room temperature into varying nano- and microstructures. Furthermore, those assemblies were then functionalised with gold (Au) nanoparticles. We then investigated the biocompatibility of the materials by conducting in vitro cell attachment and cytotoxicity studies using normal rat kidney cells. The studies revealed that the biomaterials were non-toxic and biocompatible, and showed considerable adhesion to the cells. These results suggest that the assemblies could potentially be used for a variety of applications, such as carriers for targeted drug delivery as well as optoelectronics and sensors. Furthermore, the formation of highly organised nano- and microstructures of medicinally significant phytohormones such as chicoric acid is of particular interest as it might help in further understanding the supramolecular assembly mechanism of higher organised biological structures for the development of building blocks for various device fabrications.