Hantzsch synthesis of 2,6-dimethyl-3,5-dimethoxycarbonyl-4-(o-methoxyphenyl)-1,4-dihydropyridine; a novel cyclisation leading to an unusual formation of 1-amino-2-methoxy-carbonyl-3,5-bis(o-methoxyphenyl)-4-oxa-cyclohexan-1-ene

Hantzsch condensation of two equivalents of methyl-3-aminocrotonate with (m- and p)-methoxybenzaldehyde afforded the expected products 2,6-dimethyl-3,5-dimethoxycarbonyl-4-(m-methoxyphenyl)-1,4-dihydropyridine and 2,6-dimethyl-3,5-dimethoxycarbonyl-4-(p-methoxyphenyl)-1,4-dihydropyridine, whereas o-methoxy-benzaldehyde produced mainly 1-amino-2-methoxycarbonyl-3,5-bis(o-methoxy-phenyl)-4-oxa-cyclohexan-1-ene. The structure of the product, not previously reported in the literature, was determined by 1D and 2D NMR spectra and its MS fragmentation. This is the first example of cyclisation leading to a substituted pyran rather than 1,4-DHP under typical Hantzsch reaction conditions. A plausible mechanism for its formation is postulated.     

Electrochemical behavior and antioxidant and prooxidant activity of natural phenolics

We have investigated the electrochemical oxidation of a number natural phenolics (salicylic acid, m-hydroxybenzoic acid, p-hydroxybenzoic acid, protocatechuic acid, o-coumaric acid, m-coumaric acid, p-coumaric acid, caffeic acid, quercetin and rutin) using cyclic voltammetry. The antioxidant properties of these compounds were also studied. A structural analysis of the tested phenolics suggests that multiple OH substitution and conjugation are important determinants of the free radical scavenging activity and electrochemical behavior. Compounds with low oxidation potentials (Epa lower than 0.45) showed antioxidant activity, whereas compounds with high Epa values (>0.45) act as prooxidants.     

Evaluation of the activity of the sponge metabolites avarol and avarone and their synthetic derivatives against fouling micro- and macroorganisms

The sesquiterpene hydroquinone avarol (1) was isolated from the marine sponge Dysidea avara, whereas the corresponding quinone, avarone (2), was obtained by oxidation of avarol, and the significantly more lipophilic compounds [3'-(p-chloro-phenyl)avarone (3), 3',4'-ethylenedithioavarone (4), 4'-isopropylthioavarone (5), 4'-tert-butylthioavarone (6), 4'-propylthioavarone (7), 4'-octylthioavarone (8)] were obtained by nucleophilic addition of thiols or p-chloroaniline to avarone. All these compounds were tested, at concentrations ranging from 0.5 to 50 microg/mL, for their effect on the settlement of the cyprid stage of Balanus amphitrite, for toxicity to both nauplii and cyprids and for their growth inhibitory activity on marine bacteria (Cobetia marina, Marinobacterium stanieri, Vibrio fischeri and Pseudoalteromonas haloplanktis) and marine fungi (Halosphaeriopsis mediosetigera, Asteromyces cruciatus, Lulworthia uniseptata and Monodictys pelagica).     

Cross sections for low-energy electron scattering from adenine in the condensed phase

Measurements of the vibrational and electronic excitation of a sub-monolayer up to a monolayer film of adenine were performed with a high resolution electron energy-loss (HREEL) spectrometer. The integral cross sections (over the half-space angle) for excitation of the normal vibrational modes of the ground electronic state and electronically excited states are calculated from the measured reflectivity EEL spectra. Most cross sections for vibrational excitation are of the order of 10(-17) cm(2), the largest being the out-of-plane wagging of the amino-group and the six-member ring deformations. A wide resonance feature appears in the incident energy dependence of the vibrational cross sections at 3-5 eV, while a weak shoulder is present in this dependence for combined ring deformations and bending of hydrogen atoms. For the five excited electronic states, at 4.7, 5.0, 5.5, 6.1 and 6.6 eV, the cross sections are of the order of 10(-18) cm(2), except in the case of the state at the energy of 6.1 eV, for which it is two to three times higher.     

Optimising reaction performance in the pharmaceutical industry by monitoring with NMR

Quality assurance and process understanding are assuming increasing importance in the production of Active Pharmaceutical Ingredients (APIs). NMR has the potential to report on physical processes, quantities, structures, and speciation as chemical reactions progress. Following the progression of chemical reactions by placing the sample in an NMR tube, one can perform a large number of useful studies that provide chemical and mechanistic insight. But this simple approach can have limitations, and we have therefore constructed an apparatus comprising a laboratory reactor coupled with an NMR flow cell. The reactor duplicates the exact reaction conditions that will apply with large-scale production. This reaction mixture is sampled and pumped to a high-resolution NMR flow cell where the spectrum is recorded through the course of the reaction. We demonstrate the utility of reaction monitoring using NMR both for simple cases where tubes can be used, and describe the design of the on-flow apparatus and highlight its utility with an example.     

2-Aminopurine flipped into the active site of the adenine-specific DNA methyltransferase M.TaqI: crystal structures and time-resolved fluorescence

We report the crystal structure of the DNA adenine-N6 methyltransferase, M.TaqI, complexed with DNA, showing the fluorescent adenine analog, 2-aminopurine, flipped out of the DNA helix and occupying virtually the same position in the active site as the natural target adenine. Time-resolved fluorescence spectroscopy of the crystalline complex faithfully reports this state: base flipping is accompanied by the loss of the very short ( approximately 50 ps) lifetime component associated with fully base-stacked 2-aminopurine in DNA, and 2-aminopurine is subject to considerable quenching by pi-stacking interactions with Tyr108 in the catalytic motif IV (NPPY). This proves 2-aminopurine to be an excellent probe for studying base flipping by M.TaqI and suggests similar quenching in the active sites of DNA and RNA adenine-N6 as well as DNA cytosine-N4 methyltransferases sharing the conserved motif IV. In solution, the same distinctive fluorescence response confirms complete destacking from DNA and is also observed when the proposed key residue for base flipping by M.TaqI, the target base partner thymine, is substituted by an abasic site analog. The corresponding cocrystal structure shows 2-aminopurine in the active site of M.TaqI, demonstrating that the partner thymine is not essential for base flipping. However, in this structure, a shift of the 3' neighbor of the target base into the vacancy left after base flipping is observed, apparently replicating a stabilizing role of the missing partner thymine. Time-resolved fluorescence and acrylamide quenching measurements of M.TaqI complexes in solution provide evidence for an alternative binding site for the extra-helical target base within M.TaqI and suggest that the partner thymine assists in delivering the target base into the active site.     

Acetylcholinesterase: mechanisms of covalent inhibition of wild-type and H447I mutant determined by computational analyses

The reaction mechanisms of two inhibitors TFK+ and TFK0 binding to both the wild-type and H447I mutant mouse acetylcholinesterase (mAChE) have been investigated by using a combined ab initio quantum mechanical/molecular mechanical (QM/MM) approach and classical molecular dynamics (MD) simulations. In the wild-type mAChE, the binding reactions of TFK+ and TFK0 are both spontaneous processes, which proceed through the nucleophilic addition of the Ser203-Ogamma to the carbonyl-C of TFK+ or TFK0, accompanied with a simultaneous proton transfer from Ser203 to His447. No barrier is found along the reaction paths, consistent with the experimental reaction rates approaching the diffusion-controlled limit. By contrast, TFK+ binding to the H447I mutant may proceed with a different reaction mechanism. A water molecule takes over the role of His447 and participates in the bond breaking and forming as a "charge relayer". Unlike in the wild-type mAChE case, Glu334, a conserved residue from the catalytic triad, acts as a catalytic base in the reaction. The calculated energy barrier for this reaction is about 8 kcal/mol. These predictions await experimental verification. In the case of the neutral ligand TFK0, however, multiple MD simulations on the TFK0/H447I complex reveal that none of the water molecules can be retained in the active site as a "catalytic" water. Furthermore, our alchemical free energy calculation also suggests that the binding of TFK0 to H447I is much weaker than that of TFK+. Taken together, our computational studies confirm that TFK0 is almost inactive in the H447I mutant and also provide detailed mechanistic insights into the experimental observations.     

Spectroscopic and electronic structure studies of intermediate X in ribonucleotide reductase R2 and two variants: a description of the FeIV-oxo bond in the FeIII-O-FeIV dimer

Spectroscopic and electronic structure studies of the class I Escherichia coli ribonucleotide reductase (RNR) intermediate X and three computationally derived model complexes are presented, compared, and evaluated to determine the electronic and geometric structure of the FeIII-FeIV active site of intermediate X. Rapid freeze-quench (RFQ) EPR, absorption, and MCD were used to trap intermediate X in R2 wild-type (WT) and two variants, W48A and Y122F/Y356F. RFQ-EPR spin quantitation was used to determine the relative contributions of intermediate X and radicals present, while RFQ-MCD was used to specifically probe the FeIII/FeIV active site, which displayed three FeIV d-d transitions between 16,700 and 22,600 cm(-1), two FeIV d-d spin-flip transitions between 23,500 and 24,300 cm(-1), and five oxo to FeIV and FeIII charge transfer (CT) transitions between 25,000 and 32,000 cm(-1). The FeIV d-d transitions were perturbed in the two variants, confirming that all three d-d transitions derive from the d-pi manifold. Furthermore, the FeIV d-pi splittings in the WT are too large to correlate with a bis-mu-oxo structure. The assignment of the FeIV d-d transitions in WT intermediate X best correlates with a bridged mu-oxo/mu-hydroxo [FeIII(mu-O)(mu-OH)FeIV] structure. The mu-oxo/mu-hydroxo core structure provides an important sigma/pi superexchange pathway, which is not present in the bis-mu-oxo structure, to promote facile electron transfer from Y122 to the remote FeIV through the bent oxo bridge, thereby generating the tyrosyl radical for catalysis.     

Determination of ascorbic acid in pharmaceutical dosage forms and urine by means of an oscillatory reaction system using the pulse perturbation technique

A simple and reliable method for the determination of ascorbic acid (AA) is proposed and validated. It is based on potentiometric monitoring of the concentration perturbations of an oscillatory reaction system in a stable nonequilibrium stationary state close to the bifurcation point. The response of the Bray–Liebhafsky (BL) oscillatory reaction as a matrix, to the perturbation by different concentrations of AA, is followed by a Pt electrode. The linear relationship between maximal potential shift and the logarithm of the amount of AA is obtained between 0.01 and 1.0 μmol. The sensitivity of the proposed method (as the limit of detection) is 0.009 μmol and the method has excellent sample throughput (30 samples per hour). The procedure was used for AA determination in pharmaceutical formulations and urine. The results are in agreement with those obtained using the official method. Some aspects of the possible mechanism of AA action on the BL oscillating chemical system are discussed.     

Calculus of functors,operad formality,and rational homology of embedding spaces

Let M be a smooth manifold and V a Euclidean space. Let [`(\textEmb)] \overline{{{\text{Emb}}}} (M,V) be the homotopy fiber of the map Emb(M,V) → Imm(M,V). This paper is about the rational homology of [`(\textEmb)] \overline{{{\text{Emb}}}} (M,V). We study it by applying embedding calculus and orthogonal calculus to the bifunctor (M,V)↦ HQ ∧ [`(\textEmb)] \overline{{{\text{Emb}}}} (M,V)₊. Our main theorem states that if