Active site labeling of cysteine cathepsins by a straightforward diazomethylketone probe derived from the N-terminus of human cystatin C

We designed a straightforward biotinylated probe using the N-terminal substrate-like region of the inhibitory site of human cystatin C as a scaffold, linked to the thiol-specific reagent diazomethylketone group as a covalent warhead (i.e. Biot-(PEG)2-Ahx-LeuValGly-DMK). The irreversible activity-based probe bound readily to cysteine cathepsins B, L, S and K. Moreover affinity labeling is sensitive since active cathepsins were detected in the nM range using an ExtrAvidin®-peroxidase conjugate for disclosure. Biot-(PEG)2-Ahx-LeuValGly-DMK allowed a slightly more pronounced labeling for cathepsin S with a compelling second-order rate constant for association (kass = 2,320,000 M−1 s−1). Labeling of the active site is dose-dependent as observed using 6-cyclohexylamine-4-piperazinyl-1,3,5-triazine-2-carbonitrile, as competitive inhibitor of cathepsins. Finally we showed that Biot-(PEG)2-Ahx-LeuValGly-DMK may be a simple and convenient tool to label secreted and intracellular active cathepsins using a myelomonocytic cell line (THP-1 cells) as model.

Lanthanide luminescent logic gate mimics in soft matter: [H(+)] and [F(-)] dual-input device in a polymer gel with potential for selective component release

The non-covalent incorporation of responsive luminescent lanthanide, Ln(iii), complexes with orthogonal outputs from Eu(iii) and Tb(iii) in a gel matrix allows for in situ logic operation with colorimetric outputs. Herein, we report an exemplar system with two inputs ([H(+)] and [F(-)]) within a p(HEMA-co-MMA) polymer organogel acting as a dual-responsive device and identify future potential for such systems.

Efficient simulations with electronic open boundaries

We present a reformulation of the hairy-probe method for introducing electronic open boundaries that is appropriate for steady-state calculations involving nonorthogonal atomic basis sets. As a check on the correctness of the method we investigate a perfect atomic wire of Cu atoms and a perfect nonorthogonal chain of H atoms. For both atom chains we find that the conductance has a value of exactly one quantum unit and that this is rather insensitive to the strength of coupling of the probes to the system, provided values of the coupling are of the same order as the mean interlevel spacing of the system without probes. For the Cu atom chain we find in addition that away from the regions with probes attached, the potential in the wire is uniform, while within them it follows a predicted exponential variation with position. We then apply the method to an initial investigation of the suitability of graphene as a contact material for molecular electronics. We perform calculations on a carbon nanoribbon to determine the correct coupling strength of the probes to the graphene and obtain a conductance of about two quantum units corresponding to two bands crossing the Fermi surface. We then compute the current through a benzene molecule attached to two graphene contacts and find only a very weak current because of the disruption of the π conjugation by the covalent bond between the benzene and the graphene. In all cases we find that very strong or weak probe couplings suppress the current.

Ultrafast charge-transfer in organic photovoltaic interfaces: geometrical and functionalization effects

Understanding the microscopic mechanisms of electronic excitation in organic photovoltaic cells is a challenging problem in the design of efficient devices capable of performing sunlight harvesting. Here we develop and apply an ab initio approach based on time-dependent density functional theory and Ehrenfest dynamics to investigate photoinduced charge transfer in small organic molecules. Our calculations include mixed quantum–classical dynamics with ions moving classically and electrons quantum mechanically, where no experimental external parameter other than the material geometry is required. We show that the behavior of photocarriers in zinc phthalocyanine (ZnPc) and C60 systems, an effective prototype system for organic solar cells, is sensitive to the atomic orientation of the donor and the acceptor units as well as the functionalization of covalent molecules at the interface. In particular, configurations with the ZnPc molecules facing on C60 facilitate charge transfer between substrate and molecules that occurs within 200 fs. In contrast, configurations where ZnPc is tilted above C60 present extremely low carrier injection efficiency even at longer times as an effect of the larger interfacial potential level offset and higher energetic barrier between the donor and acceptor molecules. An enhancement of charge injection into C60 at shorter times is observed as binding groups connect ZnPc and C60 in a dyad system. Our results demonstrate a promising way of designing and controlling photoinduced charge transfer on the atomic level in organic devices that would lead to efficient carrier separation and maximize device performance.

First-Principles Study of the Electronic and Magnetic Properties of Defects in Carbon Nanostructures

Understanding the magnetic properties of graphenic nanostructures is instrumental in future spintronics applications. These magnetic properties are known to depend crucially on the presence of defects. Here we review our recent theoretical studies using density functional calculations on two types of defects in carbon nanostructures: Substitutional doping with transition metals, and sp$^3$-type defects created by covalent functionalization with organic and inorganic molecules. We focus on such defects because they can be used to create and control magnetism in graphene-based materials. Our main results are summarized as follows: i)Substitutional metal impurities are fully understood using a model based on the hybridization between the $d$ states of the metal atom and the defect levels associated with an unreconstructed D$_{3h}$ carbon vacancy. We identify three different regimes, associated with the occupation of distinct hybridization levels, which determine the magnetic properties obtained with this type of doping; ii) A spin moment of 1.0 $\mu_B$ is always induced by chemical functionalization when a molecule chemisorbs on a graphene layer via a single C-C (or other weakly polar) covalent bond. The magnetic coupling between adsorbates shows a key dependence on the sublattice adsorption site. This effect is similar to that of H adsorption, however, with universal character; iii) The spin moment of substitutional metal impurities can be controlled using strain. In particular, we show that although Ni substitutionals are non-magnetic in flat and unstrained graphene, the magnetism of these defects can be activated by applying either uniaxial strain or curvature to the graphene layer. All these results provide key information about formation and control of defect-induced magnetism in graphene and related materials.