A modular synthesis of annonaceous acetogenins

A synthesis of four Annonaceous acetogenins, asiminocin, asimicin, asimin, and bullanin, by a modular approach from seven fundamental subunits, A-G, is described. The approach employs a central core aldehyde segment, C, to which are appended an aliphatic terminus, A or B, a spacer subunit, D or E, and a butenolide terminus, F or G. Coupling of the A, B, D, and E segments to the core aldehyde unit is effected by highly diastereoselective additions of enantiopure allylic indium or tin reagents. The butenolide termini are attached to the ACD, BCE, or BCD intermediates by means of a Sonogashira coupling. The design of the core, spacer, and termini subunits is such that any of the C30, C10, or C4 natural acetogenins or stereoisomers thereof could be prepared. IC50 values for the four aforementioned acetogenins against H-116 human colon cancer cells were found to be in the 10(-3) to 10(-4) microM range. The IC90 activities were ca. 10(-3) microM for asimicin and asimin but only 0.1-1 microM for bullanin and asiminocin.     

Structure and properties of poly(ethylene terephthalate) crystallized by converging flow and high pressure

The structure and properties of a poly(ethylene terephthalate) extrudate, prepared by converging flow and high pressure, were examined. Relatively high levels of crystallinity and orientation were produced by the combination of an orienting flow and high-pressure quench. The fine structure was examined in detail by x-ray diffraction, negative staining–transmission electron microscopy, and amine etching–gel permeation chromatography. The morphology was directly relatable to this unique preparative technique. Modulus was determined by a compressive Rheovibron technique. Low shrinkage and the compressive modulus were related to the structure in the development of a structural model.     

General deoxyribozyme-catalyzed synthesis of native 3'-5' RNA linkages

An elusive goal for nucleic acid enzymology has been deoxyribozymes that ligate RNA rapidly, sequence-generally, with formation of native 3'-5' linkages, and in preparatively useful yield. Using in vitro selection, we have identified Mg2+- and Zn2+-dependent deoxyribozymes that simultaneously fulfill all four of these criteria. The new deoxyribozymes operate under practical incubation conditions and have modest RNA substrate sequence requirements, specifically D downward arrowRA for 9DB1 and A downward arrowR for 7DE5 (D = A, G, or U; R = A or G). These requirements are comparable to those of deoxyribozymes such as 10-23 and 8-17, which are already widely used as biochemical tools for RNA cleavage. We anticipate that the 9DB1 and 7DE5 deoxyribozymes will find immediate practical application for RNA ligation.     

Total synthesis of (-)-callystatin A

A total synthesis of the cytotoxic polyketide marine natural product callystatin A is described. The route features chiral allenylmetal additions to construct the polypropionate C15-22 segment and an sp(2)-sp(3) Suzuki coupling to join the C1-C11 and C12-C22 subunits.     

9-BBN: An amino acid protecting group for functionalization of amino acid side chains in organic solvents

9-Borabicyclononane (9-BBN) has been utilized to protect functionalized amino acids for potential chemoselective side chain manipulation. The 9-BBN group imparts organic solubility to otherwise hydrophilic molecules and is tolerant of a wide range of reaction conditions. The high degree of solubility of these molecules in THF is particularly noteworthy. It is cleaved with either aqueous HCl or by exchange with ethylenediamine in methanol. [reaction: see text]     

The determination of free ammonia in ambient air with diffusion/denuder tubes

Ammonia is important in atmospheric chemistry because it neutralises acidic species and increases the pH of cloud droplets. Data on the concentration of free ammonia in the atmosphere are sparse because it is difficult to separate free ammonia from particulate ammonium salt aerosol. A manual method for the determination of free ammonia in air is described based on diffusion/denuder tube separation of ammonia from ammonium salt aerosol. When air is drawn through a tube coated with a selective absorbent (here oxalic acid) separation is achieved because the gaseous species diffuses much more rapidly to the tube wall than the particles. After the sampling period (usually 1–4 h, depending on the free ammonia concentration expected), the sorbed ammonia is washed from the tube and measured potentiometrically with an ammonia probe. The method is tested theoretically and experimentally. The absorption efficiency of the coated tubes is ca. 90%. In samples of room air containing 12–28 μg m^?3, the standard deviation is estimated as 1.0 μg m^?3. In field use, ammonia contents were in the range 0.53–5.0 μg m^?3.     

Experimental evidence for a general model of modulated MOF nanoparticle growth

Nanoparticles of metal–organic frameworks (nanoMOFs) boast superior properties compared to their bulk analogs, yet little is known about how common synthetic parameters dictate particle sizes. Here, we provide experimental evidence for the “seesaw” model of nanoMOF growth. Solution acidity, ligand excess, and reactant concentrations are decoupled and shown to form the key independent determinants of nanoMOF sizes, thereby validating the proposal that nanoMOFs arise from coupled equilibria involving ligand deprotonation and metal–ligand complexation. By achieving the first demonstration of a seesaw relationship between nanoMOF sizes and ligand excess, these results provide further proof of the model, as they required deliberate manipulation of relationships outlined by the model. Exploring the relative impacts of these parameters reveals that ligand excess has the greatest ability to decrease sizes, although low acidity and high concentrations can exhibit similar effects. As a complement to existing models of polymer formation and crystal growth, the seesaw model therefore offers a powerful tool for reliable control over nanoMOF sizes.

Nanoparticles of metal–organic frameworks (nanoMOFs) boast superior properties compared to their bulk analogs, yet little is known about how common synthetic parameters dictate particle sizes.     

Mechanism of the oxidation of L-ascorbic acid by the bis(pyridine-2,6-dicarboxylate)cobaltate(III) ion in aqueous solution

A detailed investigation of the oxidation of L-ascorbic acid (H₂A) by the title complex has been carried out using conventional spectrophotometry at 510 nm, over the ranges: 0.010 [ascorbate] _T 0.045 mol dm^–3, 3.62 pH 5.34, and 12.0 30.0 °C, 0.50 I 1.00 mol dm^–3, and at ionic strength 0.60 mol dm^–3 (NaClO₄). The main reaction products are the bis(pyridine-2,6-dicarboxylate)cobaltate(II) ion and l-dehydroascorbic acid. The reaction rate is dependent on pH and the total ascorbate concentration in a complex manner, i.e., k _obs = (k ₁ K ₁)[ascorbate] _T /(K ₁ + [H⁺]). The second order rate constant, k ₁ [rate constant for the reaction of the cobalt(III) complex and HA^–] at 25.0 °C is 2.31 ± 0.13 mol^–1 dm³ s^–1. H = 30 ± 4 kJ mol^–1 and S = –138 ± 13 J mol^–1 K^–1. K ₁, the dissociation constant for H₂A, was determined as 1.58 × 10^–4 mol dm^–3 at an ionic strength of 0.60 mol dm^–3, while the self exchange rate constant, k ₁₁ for the title complex, was determined as 1.28 × 10^–5 dm³ mol^–1 s^–1. An outer-sphere electron transfer mechanism has been proposed.     

Nucleic acid analysis using an expanded genetic alphabet to quench fluorescence

Organic chemistry has made possible the synthesis of molecules that expand on Nature's genetic alphabet. Using the previously described nonstandard DNA base pair constructed from isoguanine and 5-methylisocytosine, we report a highly specific and sensitive method that allows for the fast and specific quantitation of genetic sequences in a closed tube format. During PCR amplification, enzymatic site-specific incorporation of a quencher covalently linked to isoguanine allows for the simultaneous detection and identification of multiple targets. The specificity of method is then established by analysis of thermal denaturation or melting of the amplicons. The appropriate functions of all reactions are further verified by incorporation of an independent target into the reaction mixture. We report that the method is sensitive down to the single copy level, and specificity is demonstrated by multiplexed end-point genotypic analysis of four targets simultaneously using four separate fluorescent reporters. The method is general enough for quantitative and qualitative analysis of both RNA and DNA using previously developed primer sets. Though the method described employs the commonly used PCR, the enzymatic incorporation of reporter groups into DNA site-specifically should find broad utility throughout molecular biology.     

Principles of rapid polymerase chain reactions: mathematical modeling and experimental verification

Polymerase chain reaction (PCR) is an important diagnostic tool for the amplification of DNA. The PCR process can be treated as a problem in biochemical engineering. This study focuses on the development of a mathematical model of the polymerase chain reaction. The PCR process consists of three steps: denaturation of target DNA, annealing of sequence-specific oligonucleotide primers and the enzyme-catalyzed elongation of the annealed complex (primer:DNA:polymerase). The denaturation step separates the double strands of DNA; this model assumes denaturation is complete. The annealing step describes the formation of a primer-fragment complex followed by the attachment of the polymerase to form a ternary complex. This step is complicated by competitive annealing between primers and incomplete fragments including primer-primer reactions. The elongation step is modeled by a stochastic method. Species that compete during the elongation step are deoxynucleotide triphosphates dCTP, dATP, dTTP, dGTP, dUTP, and pyrophosphate. Thermal deamination of dCTP to form dUTP is included in the model. The probability for a species to arrive at the active site is based on its molar fraction. The number of random insertion events depends on the average processing speed of the polymerase and the elongation time of the simulation. The numerical stochastic experiment is repeated a sufficient number of times to construct a probability density distribution (PDF). The moment of the PDF and the annealing step products provide the product distribution at the end of the elongation step. The overall yield is compared to six experimental values of the yield. In all cases the comparisons are very good.