COordinated Responsive Arrays of Surface-Linked polymer islands (CORALS) allow for the creation of molecular surfaces with novel and switchable properties. Critical components of CORALs are the uniformly distributed islands of densely grafted polymer chains (nanoislands) separated by regions of bare surface. The grafting footprint and separation distances of nanoislands are comparable to that of the constituent polymer chains themselves. Herein, we characterize the structural features of the nanoislands and semiflexible polymers within to better understand this critical constituent of CORALs. We observe different characteristics of grafted semiflexible polymers depending on the polymer island's size and distance from the center of the island. Specifically, the characteristics of the chains at the island periphery are similar to isolated tethered polymer chains (full flexible chains), while chains in the center of the island experience the neighbor effect such as chains in the classic polymer brush. Chains close to the edge of the islands exhibit unique structural features between these two regimes. These results can be used in the rational design of CORALs with specific interfacial characteristics and predictable responses to external stimuli. It is hoped that this the discussion of the different morphologies of the polymers as a function of distance from the edge of the polymer will find applications in a wide variety of systems.

An improved time correlation function (TCF) description of sum frequency generation (SFG) spectroscopy was developed and applied to theoretically describing the spectroscopy of the ambient water/vapor interface. A more general TCF expression than was published previously is presented-it is valid over the entire vibrational spectrum for both the real and imaginary parts of the signal. Computationally, earlier time correlation function approaches were limited to short correlation times that made signal processing challenging. Here, this limitation is overcome, and well-averaged spectra are presented for the three independent polarization conditions that are possible for electronically nonresonant SFG. The theoretical spectra compare quite favorably in shape and relative magnitude to extant experimental results in the O-H stretching region of water for all polarization geometries. The methodological improvements also allow the calculation of intermolecular SFG spectra. While the intermolecular spectrum of bulk water shows relatively little structure, the interfacial spectra (for polarizations that are sensitive to dipole derivatives normal to the interface--SSP and PPP) show a well-defined intermolecular mode at 875 cm(-1) that is comparable in intensity to the rest of the intermolecular structure, and has an intensity that is approximately one-sixth of the magnitude of the intense free O-H stretching peak. Using instantaneous normal mode methods, the resonance is shown to be due to a wagging mode localized on a single water molecule, almost parallel to the interface, with two hydrogens displaced normal to the interface, and the oxygen anchored in the interface. We have also uncovered the origin of another intermolecular mode at 95 cm(-1) for the SSP and PPP spectra, and at 220 cm(-1) for the SPS spectra. These resonances are due to hindered translations perpendicular to the interface for the SSP and PPP spectra, and translations parallel to the interface for the SPS spectra. Further, by examining the real and imaginary parts of the SFG signal, several resonances are shown to be due to a single spectroscopic species while the "donor" O-H region is shown to consist of three distinct species-consistent with an earlier experimental analysis.

Molecular dynamics simulations were used to study the structural perturbations of lipids surrounding transmembrane ion channel forming helices/helical bundles and the movement of water within the pores of the ion-channels/bundles. Specifically, helical monomers to hexameric helical bundles embedded in palmitoyl-oleoyl-phosphatidyl-choline (POPC) lipid bilayer were studied. Two amphipathic α-helices with the sequence Ac-(LSLLLSL)3-NH2 (LS2), and Ac-(LSSLLSL)3-NH2 (LS3), which are known to form ion channels, were used. To investigate the surrounding lipid environment, we examined the hydrophobic mismatch, acyl chain order parameter profiles, lipid head-to-tail vector projection on the membrane surface, and the lipid headgroup vector projection. We find that the lipid structure is perturbed within approximately two lipid solvation shells from the protein bundle for each system (~15.0 Å). Beyond two lipid “solvation” shells bulk lipid bilayer properties were observed in all systems. To understand water flow, we enumerated each time a water molecule enters or exited the channel, which allowed us to calculate the number of water crossing events and their rates, and the residence time of water in the channel. We correlate the rate of water crossing with the structural properties of these ion channels and find that the movements of water are predominantly governed by the packing and pore diameter, rather than the topology of each peptide or the pore (hydrophobic or hydrophilic). We show that the crossing events of water fit quantitatively to a stochastic process and that water molecules are traveling diffusively through the pores. These lipid and water findings can be used for understanding the environment within and around ion channels. Furthermore, these findings can benefit various research areas such as rational design of novel therapeutics, in which the drug interacts with membranes and transmembrane proteins to enhance the efficacy or reduce off-target effects.

The concept of co-ordinated responsive arrays of surface-linked islands (polymer CORALs) is introduced. This study targets a responsive system capable of revealing or covering the substrate surface in response to environmental changes in a reversible way. A convenient method of fabrication of polymer CORALs is proposed. It is based on microphase separation that occurs in thin films of supramolecular assemblies of block copolymers with reactive blocks. Such blocks form nanometer-size domains that may serve as anchors for surface-linked polymer islands. Two characteristics of the islands are critically important for the switching function: high grafting density within the islands and small lateral separation that allows interactions between polymer chains grafted to the neighboring islands. This combination permits complete coverage of the substrate surface upon exposure to a good solvent (relaxed state). In a weak solvent, the chains collapse within the islands, thus revealing the substrate (compact state). The morphology of the CORALs in both states and some details of the switching process were studied with atomic force microscopy, grazing incidence small-angle scattering, and coarse-grained molecular dynamic simulations.