NCIPLOT: a program for plotting non-covalent interaction regions

Non-covalent interactions hold the key to understanding many chemical, biological, and technological problems. Describing these non-covalent interactions accurately, including their positions in real space, constitutes a first step in the process of decoupling the complex balance of forces that define non-covalent interactions. Because of the size of macromolecules, the most common approach has been to assign van der Waals interactions (vdW), steric clashes (SC), and hydrogen bonds (HBs) based on pairwise distances between atoms according to their van der Waals radii. We recently developed an alternative perspective, derived from the electronic density: the Non-Covalent Interactions (NCI) index [J. Am. Chem. Soc. 2010, 132, 6498]. This index has the dual advantages of being generally transferable to diverse chemical applications and being very fast to compute, since it can be calculated from promolecular densities. Thus, NCI analysis is applicable to large systems, including proteins and DNA, where analysis of non-covalent interactions is of great potential value. Here, we describe the NCI computational algorithms and their implementation for the analysis and visualization of weak interactions, using both self-consistent fully quantum-mechanical, as well as promolecular, densities. A wide range of options for tuning the range of interactions to be plotted is also presented. To demonstrate the capabilities of our approach, several examples are given from organic, inorganic, solid state, and macromolecular chemistry, including cases where NCI analysis gives insight into unconventional chemical bonding. The NCI code and its manual are available for download at http://www.chem.duke.edu/~yang/software.htm.     

Induced polymersome formation from a diblock PS-b-PAA polymer via encapsulation of positively charged proteins and peptides

In contrast to simple salts or negatively charged macromolecules, positively charged proteins and peptides including cytochrome c (yeast) and poly-L-lysine are efficiently encapsulated while inducing the formation of polymersomes from polystyrene(140)-b-poly(acrylic acid)(48) (PS(140)-b-PAA(48)).     

H atom adsorption and diffusion on Si(110)-(1×1) and (2×1) surfaces

We present a periodic density-functional study of hydrogen adsorption and diffusion on the Si(110)-(1×1) and (2×1) surfaces, and identify a local reconstruction that stabilizes the clean Si(110)-(1×1) by 0.51 eV. Hydrogen saturates the dangling bonds of surface Si atoms on both reconstructions and the different structures can be identified from their simulated scanning tunneling microscopy/current image tunneling spectroscopy (STM/CITS) images. Hydrogen diffusion on both reconstructions will proceed preferentially along zigzag rows, in between two adjacent rows. The mobility of the hydrogen atom is higher on the (2×1) reconstruction. Diffusion of a hydrogen vacancy on a monohydride Si(110) surface will proceed along one zigzag row and is slightly more difficult (0.2 eV and 0.6 eV on (1×1) and (2×1), respectively) than hydrogen atom diffusion on the clean surface.     

Spontaneous waveguide Raman spectroscopy of self-assembled monolayers in silica micropores

Advances in nanoscience are critically dependent on the ability to control and probe chemical and physical phenomena in confined geometries. A key challenge is to identify confinement structures with high surface area to volume ratios and controlled surface boundaries that can be probed quantitatively at the molecular level. Herein we report an approach for probing molecular structures within nano- to microscale pores by the application of spontaneous Raman spectroscopy. We demonstrate the method by characterization of the structural features of picomole quantities of well-organized octadecyltrichlorosilane (OTS) monolayers self-assembled on the interior pore surfaces of high aspect ratio (1 μm diameter × 1-10 cm length), near-atomically smooth silica microstructured optical fibers (MOFs). The simple Raman backscattering collection geometry employed is well suited for a wide variety of diagnostic applications as demonstrated by tracking the combustion of the hydrocarbon chains of the OTS self-assembled monolayer (SAM) and spectral confirmation of the formation of an adsorbed monolayer of human serum albumin (HSA) protein. Using this MOF Raman approach, molecular processes in precisely defined, highly confined geometries can be probed at high pressures and temperatures, with a wide range of excitation wavelengths from the visible to the near-IR, and under other external perturbations such as electric and magnetic fields.     

Core-Clickable PEG-Branch-Azide Bivalent-Bottle-Brush Polymers by ROMP: Grafting-Through and Clicking-To

The combination of highly efficient polymerizations with modular "click" coupling reactions has enabled the synthesis of a wide variety of novel nanoscopic structures. Here we demonstrate the facile synthesis of a new class of clickable, branched nanostructures, polyethylene glycol (PEG)-branch-azide bivalent-brush polymers, facilitated by "graft-through" ring-opening metathesis polymerization of a branched norbornene-PEG-chloride macromonomer followed by halide-azide exchange. The resulting bivalent-brush polymers possess azide groups at the core near a polynorbornene backbone with PEG chains extended into solution; the structure resembles a unimolecular micelle. We demonstrate copper-catalyzed azide-alkyne cycloaddition (CuAAC) "click-to" coupling of a photocleavable doxorubicin (DOX)-alkyne derivative to the azide core. The CuAAC coupling was quantitative across a wide range of nanoscopic sizes (～6-～50 nm); UV photolysis of the resulting DOX-loaded materials yielded free DOX that was therapeutically effective against human cancer cells.     

Determining partial differential cross sections for low-energy electron photodetachment involving conical intersections using the solution of a Lippmann-Schwinger equation constructed with standard electronic structure techniques

A method for obtaining partial differential cross sections for low energy electron photodetachment in which the electronic states of the residual molecule are strongly coupled by conical intersections is reported. The method is based on the iterative solution to a Lippmann-Schwinger equation, using a zeroth order Hamiltonian consisting of the bound nonadiabatically coupled residual molecule and a free electron. The solution to the Lippmann-Schwinger equation involves only standard electronic structure techniques and a standard three-dimensional free particle Green's function quadrature for which fast techniques exist. The transition dipole moment for electron photodetachment, is a sum of matrix elements each involving one nonorthogonal orbital obtained from the solution to the Lippmann-Schwinger equation. An expression for the electron photodetachment transition dipole matrix element in terms of Dyson orbitals, which does not make the usual orthogonality assumptions, is derived.     

Lung assist device technology with physiologic blood flow developed on a tissue engineered scaffold platform

There is no technology available to support failing lung function for patients outside the hospital. An implantable lung assist device would augment lung function as a bridge to transplant or possible destination therapy. Utilizing biomimetic design principles, a microfluidic vascular network was developed for blood inflow from the pulmonary artery and blood return to the left atrium. Computational fluid dynamics analysis was used to optimize blood flow within the vascular network. A micro milled variable depth mold with 3D features was created to achieve both physiologic blood flow and shear stress. Gas exchange occurs across a thin silicone membrane between the vascular network and adjacent alveolar chamber with flowing oxygen. The device had a surface area of 23.1 cm(2) and respiratory membrane thickness of 8.7 ± 1.2 μm. Carbon dioxide transfer within the device was 156 ml min(-1) m(-2) and the oxygen transfer was 34 ml min(-1) m(-2). A lung assist device based on tissue engineering architecture achieves gas exchange comparable to hollow fiber oxygenators yet does so while maintaining physiologic blood flow. This device may be scaled up to create an implantable ambulatory lung assist device.     

Controlling the duality of the mechanism in liquid-phase oxidation of benzyl alcohol catalysed by supported Au-Pd nanoparticles

In the solvent-free oxidation of benzyl alcohol to benzaldehyde using supported gold-palladium nanoparticles as catalysts, two pathways have been identified as the sources of the principal product, benzaldehyde. One is the direct catalytic oxidation of benzyl alcohol to benzaldehyde by O(2), whereas the second is the disproportionation of two molecules of benzyl alcohol to give equal amounts of benzaldehyde and toluene. Herein we report that by changing the metal oxide used to support the metal-nanoparticles catalyst from titania or niobium oxide to magnesium oxide or zinc oxide, it is possible to switch off the disproportionation reaction and thereby completely stop the toluene formation. It has been observed that the presence of O(2) increases the turnover number of this disproportionation reaction as compared to reactions in a helium atmosphere, implying that there are two catalytic pathways leading to toluene.     

The Grob/Eschenmoser fragmentation of cycloalkanones bearing β-electron withdrawing groups: a general strategy to acyclic synthetic intermediates

Introduction of a β-electron withdrawing group to cycloalkanones allows facile C-C bond fragmentation. The reaction has been demonstrated with a large range of ring sizes, bearing various leaving and electron withdrawing groups, and using a variety of nitrogen and oxygen containing nucleophiles (>30 examples). The application of fragmentation products to the preparation of substituted γ-lactones has been demonstrated. Mechanistic studies are reported which are suggestive of a Grob/Eschenmoser type reaction.     

Size-selective concentration and label-free characterization of protein aggregates using a Raman active nanofluidic device

Trace detection and physicochemical characterization of protein aggregates have a large impact in understanding and diagnosing many diseases, such as ageing-related neurodegeneration and systemic amyloidosis, for which the formation of protein aggregates is one of the pathological hallmarks. Here we demonstrate an innovative label-free method for detecting and characterizing small amounts of early stage protein aggregates using a Raman active nanofluidic device. Sub-micrometre channels formed by a novel elastomeric collapse technique enable the separation and concentration of matured protein aggregates from small protein molecules. The Raman enhancement by gold nanoparticle clusters fixed below a micro/nanofluidic junction allows characterization of intrinsic properties of protein aggregates at concentration levels (～fM) much lower than can be done with traditional analytical tools. With our device we show for the first time the concentration dependence of protein aggregation over these low concentration ranges. We expect that our method could facilitate definitive diagnosis and possible therapeutics of diseases at early stages.