Controlling the DNA binding specificity of bHLH proteins through intramolecular interactions

Reversible control of the conformation of proteins was employed to probe the relationship between flexibility and specificity of the basic helix-loop-helix protein MyoD. A fusion protein (apaMyoD) was designed where the basic DNA binding helix of MyoD was stablized by an amino-terminal extension with a sequence derived from the bee venom peptide apamin. The disulfide-stabilized helix from apamin served as a nucleus for a helix that extended for a further ten residues, thereby holding apaMyoD's DNA recognition helix in a predominantly alpha-helical conformation. The thermal stability of the DNA complexes of apaMyoD was increased by 13 degrees C relative to MyoD-bHLH. Measurements of the fluorescence anisotropy change on DNA binding indicated that apaMyoD bound to E-box-containing DNA sequences with enhanced affinity relative to MyoD-bHLH. Consequently, the DNA binding specificity of apaMyoD was increased 10-fold.     

Cyclodextrin catalysis of the smiles rearrangement of 4-nitrophenyl salicylate

α- and β-Cyclodextrins accelerate the Smiles rearrangement of 4-nitrophenyl salicylate which proceeds through the mechanism of intramolecular aromatic nucleophilic substitution. The binding and catalytic rate constants were calculated from the dependences of the observed pseudo-first-order rate constants of the rearrangement reaction on cyclodextrin concentration obtained at various pH values. The catalysis was interpreted in terms of a tighter binding of the anionic, highly delocalized δ-complex intermediate than that of the substrate to cyclodextrins.     

Absolute rate constants for some hydrogen atom abstraction reactions by a primary fluoroalkyl radical in water

A combination of laser flash photolysis and competitive kinetic methods have been used to measure the absolute bimolecular rate constants for hydrogen atom abstraction in water from a variety of organic substrates including alcohols, ethers, and carboxylic acids by the perfluoroalkyl radical, *CF(2)CF(2)OCF(2)CF(2)SO(3)(-) Na(+). Comparison, where possible, of these rate constants with those previously measured for analogous reactions in the non-polar organic solvent, 1,3-bis(trifluoromethyl)benzene (J. Am. Chem. Soc, 1999, 121, 7335) show that the alcohols react 2-5 times more rapidly in the water solvent and that the ethers react at the same rate in both solvents. A transition state for hydrogen abstraction that is more reminiscent of an "intimate ion pair" than a "solvent separated ion pair" is invoked to explain these modest solvent effects.     

Retention of Cr(III) by high-performance chelation ion chromatography interfaced to inductively-coupled plasma mass spectrometric detection with collision cell

High-performance chelation ion chromatography (HPCIC) was employed to retain cationic Cr(III) on an anion-exchange column and hence allow the separation of the two most prevalent forms of chromium, Cr(II) and Cr(VI). A mobile phase of nitric acid was utilized at pH = 1.5; additionally, 2,6-pyridinedicarboxylic acid was used at a concentration of 6 mM. Additives with different structural characteristics were used in an effort to elucidate retention mechanisms. Inductively-coupled plasma mass spectrometry was used for chromium detection. A collision cell was utilized to reduce chloride-based polyatomic ions that may interfere with the detection of Cr(III), and a detection limit study yielded levels in the low part-per-billion range. The newly developed method was applied to the chromatographic analysis of samples of an incubation medium containing Cr(VI) incubated with cell nuclei.     

Three 4‐amino­quinolines of anti­malarial interest

The structures of three compounds with potential anti­malarial activity are reported. In N,N‐diethyl‐N′‐(7‐iodo­quinolin‐4‐yl)ethane‐1,2‐diamine, C₁₅H₂₀IN₃, (I), the mol­ecules are linked into ribbons by N—H⋯N and C—H⋯N hydrogen bonds. In N‐(7‐bromo­quinolin‐4‐yl)‐N′,N′‐diethyl­ethane‐1,2‐diamine dihydrate, C₁₅H₂₀BrN₃·2H₂O, (II), two amino­quino­line mol­ecules and four water mol­ecules form an R₅⁴(13) hydrogen‐bonded ring which links to its neighbours to form a T5(2) one‐dimensional infinite tape with pendant hydrogen bonds to the amino­quinolines. The phosphate salt 7‐chloro‐4‐[2‐(diethyl­ammonio)ethyl­amino]quinolinium bis­(dihydrogen­phosphate) phospho­ric acid, C₁₅H₂₂ClN₃²⁺·2H₂PO₄⁻·H₃PO₄, (III), was prepared in order to establish the protonation sites of these compounds. The phosphate ions form a two‐dimensional hydrogen‐bonded sheet, while the amino­quino­line cations are linked to the phosphates by N—H⋯O hydrogen bonds from each of their three N atoms. While the conformation of the quinoline region hardly varies between (I), (II) and (III), the amino side chain is much more flexible and adopts a significantly different conformation in each case. Aromatic π–π stacking inter­actions are the only supramolecular inter­actions seen in all three structures.     

Wetting of surfactant solutions by alkanes.

Ellipsometry, surface tensiometry, and contact-angle measurement have been used to study the transition between partial wetting and pseudo-partial wetting of surfactant solutions by alkanes. In the partial wetting regime, the air-water surface tension is the same with and without alkane. In the pseudo-partial wetting regime, the air-water surface tension is lowered by the presence of alkane, showing that oil is solubilised into the surfactant monolayer. A discontinuous change in the coefficient of ellipticity with increasing surfactant concentration provides unequivocal evidence for the first-order nature of the wetting transitions. Ellipsometry has been used to explore the generality of wetting transitions of alkanes (dodecane, hexadecane, and squalane) on surfactant solutions [dodecyltrimethylammonium bromide, tetredecyltrimethylammonium bromide, dibucaine hydrochloride, and Aerosol OT (AOT)]. Of the systems studied, only hexadecane on AOT solutions did not show a wetting transition. Excess alkane remains as a lens on the surface of the surfactant solutions at all concentrations, but the contact angle is a minimum at the wetting transition. A semiquantitative model for the variation of the contact angle with surfactant concentration is provided.     

Comparison of total folate concentrations in foods determined by microbiological assay at several experienced U.S. commercial laboratories

Analysis of total folate concentration measured by microbiological assay in a variety of foods submitted in a routine manner to experienced laboratories that regularly perform folate analysis on fee-for-service basis was evaluated. Homogenates of fresh strawberries, frozen spinach, orange juice, frozen meat and vegetable pizza, dry macaroni, and dried pinto beans were prepared and stored under conditions previously determined to maintain stability of folate content. An aliquot of each composite and of 3 certified reference materials were sent on each of 4 occasions to 4 laboratories. Results for macaroni and pizza, the only folic acid-fortified foods, had considerably lower between-laboratory variation (CV(B)) with CV(B) of 9-11% versus >45% for other foods. Mean total folate ranged from 14 to 279 microg/100 g for a mixed vegetable reference material, from 5 to 70 microg/100 g for strawberries, and from 28 to 81 microg/100 g for wholemeal flour. Only 1 laboratory reported using a tri-enzyme extraction, and all laboratories used folic acid fortified foods as internal control materials. Users of commercial total folate analysis should understand the uncertainty in values determined by microbiological assay, particularly for foods containing primarily naturally occurring folate, which may not be apparent when replicate samples are not submitted for analysis.     

Protonated (protosolvated) onium ions (onlum dications)

In this short review we have shown the importance of protosolvation of onium ions (containing non-bonded pairs of electrons) in superacid catalyzed reactions. Such activation can result in unusual reactions such as aromatic alkylation with Meerwein’s salts, aliphatic nitration with nitronium ion, alkylation of saturated hydrocarbons, greatly enhanced activity of acyl cations, etc. Possibly such phenomena may be operative in hydroxylation reactions using protonated hydrogen peroxide in strong acid solutions. Even the reactivity of halonium ions could be enhanced by protosolvation. Consequently, electrophilic protosolvation may play a significant role in strogg acid catalyzed reactions.     

Thermal and electrochemical C-X activation (X = Cl,Br, I) by the strong Lewis acid Pd3(dppm)3(CO)2+ cluster and its catalytic applications

The stoichiometric and catalytic activations of alkyl halides and acid chlorides by the unsatured Pd(3)(dppm)(3)(CO)(2+) cluster (Pd(3)(2+)) are investigated in detail. A series of alkyl halides (R-X; R = t-Bu, Et, Pr, Bu, allyl; X = Cl, Br, I) react slowly with Pd(3)(2+) to form the corresponding Pd(3)(X)(+) adduct and "R(+)". This activation can proceed much faster if it is electrochemically induced via the formation of the paramagnetic species Pd(3)(+). The latter is the first confidently identified paramagnetic Pd cluster. The kinetic constants extracted from the evolution of the UV-vis spectra for the thermal activation, as well as the amount of electricity to bring the activation to completion for the electrochemically induced reactions, correlate the relative C-X bond strength and the steric factors. The highly reactive "R(+)" species has been trapped using phenol to afford the corresponding ether. On the other hand, the acid chlorides react rapidly with Pd(3)(2+) where no induction is necessary. The analysis of the cyclic voltammograms (CV) establishes that a dissociative mechanism operates (RCOCl --> RCO(+) + Cl(-); R = t-Bu, Ph) prior to Cl(-) scavenging by the Pd(3)(2+) species. For the other acid chlorides (R = n-C(6)H(13), Me(2)CH, Et, Me, Pr), a second associative process (Pd(3)(2+) + RCOCl --> Pd(3)(2+.....)Cl(CO)(R)) is seen. Addition of Cu(NCMe)(4)(+) or Ag(+) leads to the abstraction of Cl(-) from Pd(3)(Cl)(+) to form Pd(3)(2+) and the insoluble MCl materials (M = Cu, Ag) allowing to regenerate the starting unsaturated cluster, where the precipitation of MX drives the reaction. By using a copper anode, the quasi-quantitative catalytic generation of the acylium ion ("RCO(+)") operates cleanly and rapidly. The trapping of "RCO(+)" with PF(6)(-) or BF(4)(-) leads to the corresponding acid fluorides and, with an alcohol (R'OH), to the corresponding ester catalytically, under mild conditions. Attempts were made to trap the key intermediates "Pd(3)(Cl)(+)...M(+)" (M(+) = Cu(+), Ag(+)), which was successfully performed for Pd(3)(ClAg)(2+), as characterized by (31)P NMR, IR, and FAB mass spectrometry. During the course of this investigation, the rare case of PF(6)(-) hydrolysis has been observed, where the product PF(2)O(2)(-) anion is observed in the complex Pd(3)(PF(2)O(2))(+), where the substrate is well-located inside the cavity formed by the dppm-Ph groups above the unsatured face of the Pd(3)(2+) center. This work shows that Pd(3)(2+) is a stronger Lewis acid in CH(2)Cl(2) and THF than AlCl(3), Ag(+), Cu(+), and Tl(+).