The cytotoxic response of cells in culture is dependant on the degree of functionalization of the single-walled carbon nanotube (SWNT). After characterizing a set of water-dispersible SWNTs, we performed in vitro cytotoxicity screens on cultured human dermal fibroblasts (HDF). The SWNT samples used in this exposure include SWNT-phenyl-SO3H and SWNT-phenyl-SO3Na (six samples with carbon/-phenyl-SO3X ratios of 18, 41, and 80), SWNT-phenyl-(COOH)2 (one sample with carbon/-phenyl-(COOH)2 ratio of 23), and underivatized SWNT stabilized in 1% Pluronic F108. We have found that as the degree of sidewall functionalization increases, the SWNT sample becomes less cytotoxic. Further, sidewall functionalized SWNT samples are substantially less cytotoxic than surfactant stabilized SWNTs. Even though cell death did not exceed 50% for cells dosed with sidewall functionalized SWNTs, optical and atomic force microscopies show direct contact between cellular membranes and water-dispersible SWNTs; i.e. the SWNTs in aqueous suspension precipitate out and selectively deposit on the membrane.

Abstract: The review discusses the molecular origins of the forces and free energies that determine several things about proteins, and how experiment and theory reveal this information. The first subject is the stability of the folded, native structures. The second is the range of molecular mechanisms by which proteins find their way to those folded structures in laboratory environments. The third is the much more complex problem of how folding occurs in the cellular environment. This topic includes a discussion of crowding and of the roles of chaperone molecules. The review concludes with a discussion of protein aggregation and fibril formation and of misfolding and therapies associated with it.

Single-walled carbon nanotubes functionalized by phenyl groups can be sulfortated in oleum (H2SO4, 20% free SO3) to give materials that exhibit high solubility in water as determined by centrifugation in conjunction with UV-vis-near-infrared measurements. Cryo-transmission electron microscopy images show that extensive debundling occurs during the sulfonation step.

The simultaneous decomposition of bis(cyclooctadiene)nickel (0) [Ni(COD)2] and tetraphenyldibismuthine [Bi2Ph4] in tetrahydrofuran (THF) at reflux temperature leads to nickel−bismuth alloy nanoparticles with an average size of 8−10 nm. Transmission electron microscopy (TEM) diffraction methods show that these nanoparticles adopt the hexagonal structure of β-NiBi. Magnetic characterization shows a superparamagnetic behavior at temperatures above 45 K and the presence of antiferromagnetic dipolar interactions between the particles. XRD confirms the crystallization of the β-NiBi at temperatures above 600 °C. When the decomposition is carried out at a higher temperature (200 °C) in the presence of trioctylamine and oleic acid, NiBi nanowires were observed in addition to the nanoparticles.

We use an integrated computational approach to reconstruct accurately the transition state ensemble (TSE) for folding of the src-SH3 protein domain. We first identify putative TSE conformations from free energy surfaces generated by importance sampling molecular dynamics for a fully atomic, solvated model of the src-SH3 protein domain. These putative TSE conformations are then subjected to a folding analysis using a coarse-grained representation of the protein and rapid discrete molecular dynamics simulations. Those conformations that fold to the native conformation with a probability (Pfold) of approximately 0.5, constitute the true transition state. Approximately 20% of the putative TSE structures were found to have a Pfold near 0.5, indicating that, although correct TSE conformations are populated at the free energy barrier, there is a critical need to refine this ensemble. Our simulations indicate that the true TSE conformations are compact, with a well-defined central β sheet, in good agreement with previous experimental and theoretical studies. A structured central β sheet was found to be present in a number of pre-TSE conformations, however, indicating that this element, although required in the transition state, does not define it uniquely. An additional tight cluster of contacts between highly conserved residues belonging to the diverging turn and second β-sheet of the protein emerged as being critical elements of the folding nucleus. A number of commonly used order parameters to identify the transition state for folding were investigated, with the number of native Cβ contacts displaying the most satisfactory correlation with Pfold values.

Control over size and size distribution of nanoparticles has been the subject of much interest during the past decade. In the present study, a simple strategy is described for obtaining monodisperse Pd nanoparticles with size less than 5 nm and size distribution around 10%. Without size-selective precipitation but with a simple reducing agent, hypophosphite, the synthesized Pd nanoparticles can form 2D well-ordered arrays on the TEM grids. When reducing agents were changed, no obvious size change of Pd nanoparticles was observed within experimental errors but the size distribution varied dramatically. In addition, stability, self-organized pattern, and solubility can be controlled by changing the capping agent. The present route is very simple and reproducible, and further study on the properties of the Pd nanoparticles is underway.

The temperature dependence of the free energy landscape of the src‐SH3 protein domain is investigated through fully atomic simulations in explicit solvent. Simulations are performed above and below the folding transition temperature, enabling an analysis of both protein folding and unfolding. The transition state for folding and unfolding, identified from the free energy surfaces, is found to be very similar, with structure in the central hydrophobic sheet and little structure throughout the rest of the protein. This is a result of a polarized folding (unfolding) mechanism involving early formation (late loss) of the central hydrophobic sheet at the transition state. Unfolding simulations map qualitatively well onto low‐temperature free energy surfaces but appear, however, to miss important features observed in folding simulations. In particular, details of the folding mechanism involving the opening and closing of the hydrophobic core are not captured by unfolding simulations performed under strongly denaturing conditions. In addition, free energy surfaces at high temperatures do not display a desolvation barrier found at lower temperatures, involving the expulsion of water molecules from the hydrophobic core. Proteins 2004;55:000–000. © 2004 Wiley‐Liss, Inc.

Single-wall carbon nanotubes (SWNTs) were arranged in a membrane similar to a "bed-of-nails", in which a single layer of parallel SWNTs was densely packed and aligned along the normal to the membrane. The planar, free-standing, ultrathin SWNT membranes were prepared by milling a neat SWNT fiber with a gallium focused ion beam. The approach is readily applicable to cutting nanotubes to a desirable and precise length and enables further fabrication of devices using the "bed-of-nails" membranes to test the transport properties of SWNTs.

The folding thermodynamics of the src-SH3 protein domain were characterized under refolding conditions through biased fully atomic molecular dynamics simulations with explicit solvent. The calculated free energy surfaces along several reaction coordinates revealed two barriers. The first, larger barrier was identified as the transition state barrier for folding, associated with the formation of the first hydrophobic sheet of the protein. phi values calculated from structures residing at the transition state barrier agree well with experimental phi values. The microscopic information obtained from our simulations allowed us to unambiguously assign intermediate phi values as the result of multiple folding pathways. The second, smaller barrier occurs later in the folding process and is associated with the cooperative expulsion of water molecules between the hydrophobic sheets of the protein. This posttransition state desolvation barrier cannot be observed through traditional folding experiments, but is found to be critical to the correct packing of the hydrophobic core in the final stages of folding. Hydrogen exchange and NMR experiments are suggested to probe this barrier.