Dyeing uric acid crystals with methylene blue

The growth of anhydrous uric acid (UA) and uric acid dihydrate (UAD) crystals from supersaturated aqueous solutions containing methylene blue, a cationic organic dye, has been investigated. Low concentrations of dye molecules were found to be included in both types of crystal matrixes during the growth process. Incorporation of dye into UA crystals occurs with high specificity, affecting primarily [001] and [201] growth sectors, while UAD crystals grown from solutions of similar dye concentration show inclusion but little specificity. The orientation of the UA-trapped species was determined from polarization data obtained from visible light microspectrometry. To achieve charge neutrality, a second anionic species must also be included with the methylene blue into UA and UAD crystal matrices. Under high pH conditions, crystallization of 1:1 stoichiometric mixtures of methylene blue and urate yields methylene blue hexahydrate (MBU.6(H2O). The crystal structure of MBU.6(H2O) reveals continuous pi-pi stacks of planes of dye cations and urate anions mediated by water molecules. This structure provides an optimal geometry for methylene blue-urate pairs and additional support for the incorporation of these dimers in uric acid single-crystal matrices. The strikingly different inclusion patterns in UA and UAD demonstrate that subtle changes in the crystal surfaces and/or growth dynamics can greatly affect recognition events.     

Hydrothermal synthesis and extended structure of poly[aqua(μ5‐ethylenediaminetetraacetato)dizinc(II)]

In the extended structure of the title compound, [Zn₂(C₁₀H₁₂N₂O₈)(H₂O)], prepared under hydrothermal conditions, there are two distinct Zn^II sites. The first, with octahedral geometry, bonds to two N and three O atoms from one ethylenediaminetetraacetate tetraanion (EDTA) and one water molecule. The second, with tetrahedral geometry, coordinates to O atoms from four different EDTA ligands. The EDTA ligand almost encapsulates the octahedral Zn^II ion and binds to four symmetry‐related tetrahedral Zn^II ions, hence generating the extended structure. One noncoordinated O‐atom site on the EDTA ligand connects to the water molecule by hydrogen bonding. Structural comparisons are made with other compounds containing zinc, EDTA and water.     

Synthesis and biodistribution of p-iodophenyl analogues of a naturally occurring imidazole ribonucleoside

A model iodophenyl imidazole ribonucleoside has been synthesized to study biodistribution properties in laboratory animals. The key intermediate 5-amino-1-(2,3,5-tri-O-acetyl-β-D-ribofuranosyl)imidazole-4-[N-(p-iodophenyl)carboxamide] ( 5 ) was synthesized by coupling N-succinimidyl-5-amino-1-(2,3,5-tri-O-acetyl-β-D-ribofuranosyl)imidazole-4-carboxylate ( 4 ) and p-iodoaniline. Deacetylation of the intermediate compound gave 5-amino-1-β-D-ribofuranosylimidazole-4-[N-(p-iodophenyl)]carboxamide ( 6 ). Ring annulation via diazotization of 5 gave 7-(2,3,5-tri-O-acetyl-β-D-ribofuranosyl)imidazo[4,5-d]-v-triazin-[3-N-(p-iodophenyl)]-4-one ( 7 ). Subsequent deacetylation of 7 afforded 7-β-D-ribofuranosylimidazo[4,5-d]-v-triazin-[3-N-(p-iodophenyl)]-4-one ( 8 ). The radiolabeled compounds, [¹²⁵I] 5 and [¹²⁵I] 6 were prepared in a manner similar to the corresponding unlabeled compounds except that p-[¹²⁵I]iodoaniline was used for coupling with 4 . Biodistribution studies of iodine-125-labeled 5 and 6 were performed in female Fischer rats and tumor bearing nude mice. Compound 6 showed uptake in the brain and proliferating tissues such as tumor and bone-marrow.     

Ion atmosphere relaxation and percolative electron transfer in Co bipyridine DNA molten salts

Polypyridyl complexes of Co decorated with 350-Da polyether chains (Co(350)(2+)) form molten phases of nucleic acids when paired with DNA counterions (Co(350)DNA) or 25-mer oligonucleotides. Analysis of voltammetry and chronoamperometry of mixtures of these phases with complexes having ClO(4)(-) counterions (Co(350)(ClO(4))(2)) and no other diluent provides charge transport rates from the oxidation and reduction currents for the complexes. As the mole fraction of the Co(350)(ClO(4))(2) complex in the mixture is varied from ca. 0.25 to 1, the physical diffusion constants derived from the Co(III/II) wave increase from 1 x 10(-11) cm(2)/s to 5 x 10(-10) cm(2)/s, and apparent diffusion constants dominated by the Co(II/I) electron self-exchange increase from 1 x 10(-10) cm(2)/s to 2 x 10(-8) cm(2)/s. Pure Co(350)DNA melts, containing no Co(350)(ClO(4))(2) complex, do not exhibit recognizable voltammetric waves; DNA suppresses the Co(II/I) electron transfer reactions of Co complexes for which it is the counterion. There are therefore two microscopically distinct kinds of Co(350) complexes, those with DNA and those with ClO(4)(-) counterions, with respect to their Co(II/I) electron-transfer dynamics, leading to percolative behavior in their mixtures. The electron-transfer rates of the Co(II/I) couple are controlled by the diffusive relaxation of the ionic atmosphere around the reaction pair, and the inactivity of the bound Co complexes can be attributed to the very low mobility of the anionic phosphate groups in the DNA counterion. Substitution of sulfonated polystyrene for DNA produced similar results, suggesting that this phenomenon is general to other polymer counterions of low mobility. We conclude that the measured Co(II/I) charge transport and electron-transfer rate constants reflect more the diffusive mobility of the perchlorate counterion than the intrinsic Co(II/I) electron hopping rate.     

Design and characterization of a homodimeric antiparallel coiled coil

We report the first successful design of a self-associating antiparallel coiled coil, APH. The simultaneous application of Coulombic and hydrophobic components results in a decided preference for the antiparallel alignment as judged by HPLC, sedimentation equilibrium, and chemical denaturation data. The designed peptide is of comparable stability to naturally occurring leucine zipper peptides and can be expressed in bacteria. These properties of APH suggest potential in vivo protein fusion and biomaterials applications.     

Origin of the acidity enhancement of formic acid over methanol: resonance versus inductive effects

Density functional theory calculations were employed to study the relative contribution of resonance versus inductive effects toward the 37 kcal/mol enhanced gas-phase acidity (DeltaH degrees (acid)) of formic acid (1) over methanol (2). The gas-phase acidities of formic acid, methanol, vinyl alcohol (5), and their vinylogues (6, 8, and 9) were calculated at the B3LYP/6-31+G level of theory. Additionally, acidities were calculated for the formic acid and vinyl alcohol vinylogues in which the formyl group and the vinyl group, respectively, were perpendicular to the rest of the conjugated system. Comparisons among these calculated acidities suggest that inductive effects are the predominant effects responsible for the enhanced acidity of formic acid over methanol, accounting for between roughly 62% and 65% of the total enhanced acidity; the remaining 38% to 35% of the acidity enhancement appears to be due to resonance effects. Further comparisons suggest that resonance effects are between roughly 58% and 65% of the 26 kcal/mol calculated acidity enhancement of vinyl alcohol over methanol, and the remaining 42% to 35% are due to inductive effects.     

Photoinduced axial ligation and deligation dynamics of nonplanar nickel dodecaarylporphyrins

The ground- and excited-state metal-ligand dynamics of nonplanar nickel(II) 2,3,5,7,8,10,12,13,15,17,18,20-dodecaphenylporphyrin (NiDPP) and two fluorinated analogues (NiF(20)DPP and NiF(28)DPP) have been investigated using static and time-resolved absorption spectroscopy in toluene and in ligating media that differ in basicity, aromaticity, and steric encumbrance. Because of the electronic and steric consequences of nonplanarity, NiDPP does not bind axial ligands in the ground state, but metal coordination does occur after photoexcitation with multistep dynamics that depend on the properties of the ligand. Following the structural relaxations that occur in all nickel porphyrins within approximately 10 ps, ligand binding to photoexcited NiDPP is progressively longer in pyridine, piperidine, and 3,5-lutidine (25-100 ps) but does not occur at all in 2,6-lutidine in which the ligating nitrogen is sterically encumbered. The transient intermediate that is formed, which nominally could be either a five- or six-coordinate species, also has a ligand-dependent lifetime (200-550 ps). Decay of this intermediate occurs partially via ligand release to re-form the uncoordinated species, in competition with binding of the second axial ligand and/or conformational/electronic relaxations (of a six-coordinate intermediate) to give the ground state of the bis-ligated photoproduct. The finding that the photoproduct channel principally depends on ligand characteristics along with the time-evolving spectra suggests that the transient intermediate may involve a five-coordinate species. In contrast to NiDPP, the fluorinated analogues NiF(20)DPP and NiF(28)DPP do coordinate axial ligands in the ground state but eject them after photoexcitation. Collectively, these results demonstrate the sensitivity with which the electronic and structural characteristics of the macrocycle, substituents, and solvent (ligands) can govern the photophysical and photochemical properties of nonplanar porphyrins and open new avenues for exploring photoinduced ligand association and dissociation behavior.     

Glycosidation with a disarmed glycosyl iodide: promotion and scope

[reaction: see text] Glucuronyl iodide 1 has been studied in detail as a "disarmed" glycosyl donor. In a model reaction, using N-iodosuccinimide (NIS) as a promoter and 2-phenylethanol as acceptor, best results were obtained using NIS with I(2), followed by trimethylsilyltrifluoromethanesulfonate (TMSOTf). When a series of primary and secondary alcohols was glycosylated using these conditions, yields of 60-83% of beta-glucuronides were obtained. Various "nonheavy" metal salts also effectively catalyzed the model reaction but led to significant amounts of alpha-product with less reactive secondary alcohols.     

High-throughput manual parallel synthesis using SynPhase crowns and lanterns

The high-throughput manual solid-phase parallel synthesis of libraries comprising thousands of discrete samples using pellicular supports (i.e. SynPhase crowns and lanterns) and a suite of novel tools and techniques is described. Key aspects of this approach include the combination of a split-split-split synthesis strategy with spatial encoding to differentiate thousands of crowns, the rapid washing and filtration of up to 48 reaction vessels in parallel, the application of an inexpensive and environmentally friendly technique to remove trifluoroacetic acid from sixteen 96-well plates in parallel, and a high-throughput method for removing cleaved crowns from reusable pin racks. Tens of thousands of discrete samples have been produced in-house using this conceptually and operationally straightforward strategy.