Segmented waves from a spatiotemporal transverse wave instability

We observe traveling waves emitted from Turing spots in the chlorine dioxide-iodine-malonic acid reaction. The newborn waves are continuous, but they break into segments as they propagate, and the propagation of these segments ultimately gives rise to spatiotemporal chaos. We model the wave-breaking process and the motion of the chaotic segments. We find stable segmented spirals as well. We attribute the segmentation to an interaction between front rippling via a transverse instability and front symmetry breaking by a fast-diffusing inhibitor far from the codimension-2 Hopf-Turing bifurcation, and the chaos to a secondary instability of the periodic segmentation.     

Phase transfer catalysis in N-alkylations of the pharmaceutical intermediates 5H-dibenz[b,f]azepine and 5H-10,11-dihydrodibenz[b,f]azepine

The two title compounds were alkylated under very mild phase-transfer-catalysis conditions. Differences in reactivities of the two heterocyclic nucleophiles, and in the reactivities of various alkyl halides are discussed.     

New insight into the electrochemical desorption of alkanethiol SAMs on gold

A combination of Polarization Modulation Infrared Reflection Absorption Spectroscopy (PMIRRAS) under electrochemical control, Electrochemical Scanning Tunneling Microscopy (ECSTM) and Molecular Dynamics (MD) simulations has been used to shed light on the reductive desorption process of dodecanethiol (C12) and octadecanethiol (C18) SAMs on gold in aqueous electrolytes. Experimental PMIRRAS, ECSTM and MD simulations data for C12 desorption are consistent with formation of randomly distributed micellar aggregates stabilized by Na(+) ions, coexisting with a lying-down phase of molecules. The analysis of pit and Au island coverage before and after desorption is consistent with the thiolate-Au adatoms models. On the other hand, PMIRRAS and MD data for C18 indicate that the desorbed alkanethiolates adopt a Na(+) ion-stabilized bilayer of interdigitated alkanethiolates, with no evidence of lying down molecules. MD simulations also show that both the degree of order and tilt angle of the desorbed alkanethiolates change with the surface charge on the metal, going from bilayers to micelles. These results demonstrate the complexity of the alkanethiol desorption in the presence of water and the fact that chain length and counterions play a key role in a complex structure.     

Weak polyelectrolytes tethered to surfaces: Effect of geometry,acid–base equilibrium and electrical permittivity

The structural and thermodynamical properties of weak polyelectrolytes end-tethered to surfaces of arbitrary geometry are studied using a molecular theory. The theory is based on writing down the free energy functional of the system including all the basic interactions and the explicit acid–base equilibrium for the chargeable groups of the polymer. The theory explicitly includes the size, shape, conformations, and charge distribution of all the molecular species. The electrostatic interactions include a density-dependent dielectric function, modeled with the Maxwell–Garnett mixing formula, to account for the composition-dependent permittivity. The minimization of the free energy leads to the distribution of all molecular species and their dependence on bulk pH and salt concentration. We apply the theory to polymer chains end-tethered to planar, cylindrical, and spherical surfaces. The radius of the curved surfaces is small to enhance the curvature effect. We find that when the grafting surfaces are uncharged, the approximation of a constant dielectric function works very well for both structural and thermodynamic properties. The structure of weak polyelectrolytes tethered on cylindrical and spherical surfaces is different from that of polymers tethered on planar surfaces due to the available volume as a function of the distance from the surface. Specifically, the degree of dissociation increases with increasing curvature of the surface. This is a manifestation of the coupling between the local density of protons, counterions, and polymer segments. The results can be interpreted in terms of the local Le Chatelier principle for the acid–base equilibrium, with proper account of the three local contributions: counterions, protons, and chargeable groups. We find that one can achieve local changes of pH between one to two units within 1–2 nm. The thickness of the tethered layers as a function of bulk pH shows a large increase when the pH is equal to the bulk pK. However, the variation with salt concentration is different for the different geometries. The largest swelling is found for cylindrical surfaces. The predictions from scaling theories of a maximum in the thickness of the film as a function of salt concentration is found for planar films, but not for curved surfaces. Finally, the interactions between cylinders with tethered polyelectrolytes is very different from the equivalent planar surfaces. These results are important for the interpretation of force measurements with nanoscale AFM tips. The implications of the results for the rational design of responsive tethered polymer layers is discussed together with the limitations of the theoretical approach. © 2006 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 44: 2638–2662, 2006     

Ion transport and molecular organization are coupled in polyelectrolyte-modified nanopores

Chemically modified nanopores show a strong and nontrivial coupling between ion current and the structure of the immobilized species. In this work we study theoretically the conductance and structure in polymer modified nanopores and explicitly address the problem of the coupling between ion transport and molecular organization. Our approach is based on a nonequilibrium molecular theory that couples ion conductivity with the conformational degrees of freedom of the polymer and the electrostatic and nonelectrostatic interactions among polyelectrolyte chains, ions, and solvent. We apply the theory to study a cylindrical nanopore between two reservoirs as a function of pore diameter and length, the length of the polyelectrolyte chains, their grafting density, and whether they are present or not on the outer reservoir walls. In the very low applied potential regime, where the distribution of polyelectrolyte and ions is similar to that in equilibrium, we present a simple analytical model based on the combination of the different resistances in the system that describes the conductance in excellent agreement with the calculations of the full nonequilibrium molecular theory. On the other hand, for a large applied potential bias, the theory predicts a dramatic reorganization of the polyelectrolyte chains and the ions. This reorganization results from the global optimization of the different interactions in the system under nonequilibrium conditions. For nanopores modified with long chains, this reorganization leads to two interesting physical phenomena: (i) control of polyelectrolyte morphology by the direction and magnitude of ion-fluxes and (ii) an unexpected decrease in system resistance with the applied potential bias for long chains due to the coupling between polyelectrolyte segment distribution and ion currents.     

Temperature dependence of ice critical nucleus size

We present a molecular dynamics study of ice growth from supercooled water. By performing a series of simulations with different initial conditions, we have quantitative established the relationship existing between the critical nucleus size and the temperature. The results show that ice embryos containing hundreds or thousands of molecules are needed for the system to crystallize macroscopically, even at high degrees of supercooling. Our findings explain the difficulty in observing spontaneous ice nucleation in atomistic simulations and the relative ease with which water droplets can be supercooled under controlled experiments.     

Crowding-induced structural alterations of random-loop chromosome model

We investigate structural alterations of random-loop polymers due to changes in the crowding condition, as a model to study environmental effects on the structure of chromosome subcompartments. The polymer structure is changed in a nonmonotonic fashion with an increasing density of crowders: condensed at small volume fractions; decondensed at high crowding volume fractions. The nonmonotonic behavior is a manifestation of the nontrivial distance dependence of the depletion interactions. We also show that crowding-induced structural alterations affect the access of binding proteins to the surface of polymer segments and are distinguished from structural changes due to the increased number of specific polymer loops.