Synthesis of NMP/RAFT inifers and preparation of block copolymers

Two different initiator/transfer agents (inifers) containing an alkoxyamine and a dithiobenzoate were synthetized and used to trigger out either reversible addition‐fragmentation chain transfer (RAFT) polymerization or nitroxide‐mediated polymerization (NMP). α‐Dithiobenzoate‐ω‐alkoxyamine‐difunctional polymers were produced in both cases which were subsequently used as precursors in the formation of block copolymers. This synthetic approach was applied to N‐isopropylacrylamide (NIPAM) or polyethylene oxide methacrylate (EOMA) to form α,ω‐heterodifunctional homopolymers via RAFT at 60°C which were chain extended with styrene by activating the alkoxyamine moiety at 120°C. Under such temperature conditions, it is proposed that a tandem NMP/RAFT polymerization is initiated producing a simultaneous growth of polystyrene blocks at both chain‐ends. Self‐assembled nanostructures of these amphiphilic block copolymers were evidenced by scanning electron microscopy. © 2012 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2012     

Unusual open chain quinolinyl peroxol and its alcohol counterpart obtained through a modified Skraup–Doebner–Von Miller quinoline synthesis: theoretical studies and complete 1H‐ and 13C‐NMR assignments

Because of their extreme instability, it is generally difficult to synthesize and fully characterize open chain peroxides, also known as peroxols. In our attempt to investigate the mechanism of the Skraup–Doebner–Von Miller quinoline synthesis, we were able to obtain an unusual open chain peroxy‐quinoline, namely, 4‐(8‐ethoxy‐2,3‐dihydro‐1H‐cyclopenta[c]quinolin‐4‐yl)butane‐1‐peroxol (1), and its alcohol counterpart, namely 4‐(8‐ethoxy‐2,3‐dihydro‐1H‐cyclopenta[c]quinolin‐4‐yl)butan‐1‐ol (2) obtained as a side product during the same reaction. Although structurally similar, these two compounds appeared to display some very distinct physical and spectroscopic characteristics. This work reports detailed NMR studies and full ¹H and ¹³ C NMR assignments for these two compounds. These assignments are based upon the analysis of the NMR spectra of these compounds including ¹H, ¹³ C, COSY, gHSQC and gHMBC. The effect of the peroxide functional group on the chemical shift of neighboring carbons and protons was also investigated by comparing the NMR data of these two compounds. Furthermore, the effects of potential hydrogen bondings in 1, 2, and possible 1–1 dimer, 2–2 dimer and in prototypical model systems, as well as the stability of these compounds, were investigated computationally. The computed dissociation energies and NMR data support the interpretation of the experimental data. Copyright © 2012 John Wiley & Sons, Ltd.     

Microscopic reversibility or detailed balance in ion channel models

Mass action type deterministic kinetic models of ion channels are usually constructed in such a way as to obey the principle of detailed balance (or, microscopic reversibility) for two reasons: first, the authors aspire to have models harmonizing with thermodynamics, second, the conditions to ensure detailed balance reduce the number of reaction rate coefficients to be measured. We investigate a series of ion channel models which are asserted to obey detailed balance, however, these models violate mass conservation and in their case only the necessary conditions (the so-called circuit conditions) are taken into account. We show that ion channel models have a very specific structure which makes the consequences true in spite of the imprecise arguments. First, we transform the models into mass conserving ones, second, we show that the full set of conditions ensuring detailed balance (formulated by Feinberg) leads to the same relations for the reaction rate constants in these special cases, both for the original models and the transformed ones.     

Monte Carlo structure simulations for aqueous 1,4-dioxane solutions

Monte Carlo simulations in the NpT ensembles have been performed for the structure exploration of aqueous 1,4-dioxane solutions. Three different systems with all-atom dioxane:TIP4P water molar compositions of 2:500 (code:D2), 8:465 (D8), and 17:425 (D17) modeled solutions of 0.22, 0.88, and 1.86 mol/dm3 concentrations, respectively, at T = 298 K and p = 1 atm. The calculated solution densities increase from 0.992 to 1.002 g/cm3 with increasing dioxane concentration and approach the experimentally determined densities within 1%. This close agreement was achieved by utilizing RESP charges fitted to the in-solution IEF-PCM/B3LYP/6-31G* electrostatic potential of dioxane taken in its chair conformation and recently developed C, H steric parameters for ethers for calculations with a 12-6-1 all-atom potential. Solution structure analyses pointed out that the dioxane molecules arrange in the solutions with favorable distances of 4-8 angstroms for the ring symmetry centers. Within this range not only pairs of rings but triangular triads and tetrads have also been observed with center-center distances <8 angstroms. For the D8 system, about 25% of the sampled configurations included such a triad. In the case of the D17 model, two simulations starting from different solution configuration predicted different degrees for the dioxane aggregation in aqueous solution. In the more aggregated structure 3-21 triads are consistently maintained and 1-2 tetrads are formed in 58% of the configurations. Each dioxane oxygen forms about one hydrogen bond, on average, to a water molecule in the 0.22-1.86 molar range. The most likely O(dioxane)...H(water) hydrogen bond distance is 1.75-1.80 angstroms compared to the optimal distance of 1.72 angstroms in the isolated dimer. The optimal dioxane-water interaction energy of -5.65 kcal/mol indicates a remarkable hydrogen-bond acceptor character for dioxane.     

Practical formal total synthesis of (rac)- and (S)-camptothecin

A practical, efficient and scalable formal total synthesis of (rac)- and (S)-camptothecin is described, which proceeds via the known DE ring building blocks 19 and (S)-19, respectively. The racemic synthesis starts from diethyl oxalate and uses straightforward carbonyl chemistry in order to generate the pyridone ring system. 19 was formed in 8.4% overall yield over 9 linear steps avoiding any chromatographic purification. The asymmetric version of this approach encompassed a diastereoselective Grignard addition to the enantiomerically pure alpha-ketoester 30 in order to generate the (S)-configured quaternary stereocenter. The auxiliary could be recycled in high yield and was successfully reused multiple times. The final steps paralleled the racemic approach. (S)-19 was thus prepared in 9.4% overall yield (er = 95 : 5) over 10 steps.     

Automatic kinetic model generation and selection based on concentration versus time curves

The goal of the paper is to automatize the construction and parameterization of kinetic reaction mechanisms that can describe a set of experimentally measured concentration versus time curves. Using the framework and theorems of formal reaction kinetics, first, we build a set of possible mechanisms with a given number of measured and unmeasured (real or fictitious) species and reaction steps that fulfill some chemically reasonable requirements. Then we fit all the corresponding mass-action kinetic models and offer the best one to the chemist to help explain the underlying chemical phenomenon or to use it for predictions. We demonstrate the use of the method via two simple examples: on an artificial, simulated set of data and on a small real-life data set. The method can also be used to do a kind of lumping to generate a model that can reproduce the simulation results of a detailed mechanism with less species and thereby can largely accelerate spatially inhomogeneous simulations.     

Fluorescence lifetime of Nile Red as a probe for the hydrogen bonding strength with its microenvironment

The fluorescence lifetime of Nile Red (NR) is not sensitive to dielectric solvent–solute interactions but markedly decreases with the increase of the hydrogen bond donating ability in alcohols because vibrations associated with hydrogen bonding are involved in the deactivation process. The negligible viscosity effect indicates that twisting of the diethylamino moiety of NR does not play significant role in the dissipation of the excitation energy.     

Estimation of Activation Energy from the Survival Yields: Fragmentation Study of Leucine Enkephalin and Polyethers by Tandem Mass Spectrometry

A simple collision model for multiple collisions occurring in quadrupole type mass spectrometers was derived and tested with leucine enkaphalin a common mass spectrometric standard with well-characterized properties. Implementation of the collision model and Rice-Ramsperger-Kassel-Marcus (RRKM) algorithm into a spreadsheet software allowed a good fitting of the calculated data to the experimental survival yield (SY) versus collision energy curve. In addition, fitting also ensured to estimate the efficiencies of the kinetic to internal energy conversion for Leucine enkephalin in quadrupole-time-of-flight and triple quadrupole instruments. It was observed that the experimental SY versus collision energy curves for the leucine enkephalin can be described by the Rice-Ramsperger-Kassel (RRK) formalism by reducing the total degrees of freedom (DOF) to about one-fifth. Furthermore, this collision model with the RRK formalism was used to estimate the critical energy (E _o ) of lithiated polyethers, including polyethylene glycol (PEG), polypropylene glycol (PPG), and polytetrahydrofurane (PTHF) with degrees of freedom similar to that of leucine enkephalin. Applying polyethers with similar DOF provided the elimination of the effect of DOF on the unimolecular reaction rate constant. The estimated value of E _o for PEG showed a relatively good agreement with the value calculated by high-level quantum chemical calculations reported in the literature. Interestingly, it was also found that the E _o values for the studied polyethers were similar.