Interaction of acetone with single wall carbon nanotubes at cryogenic temperatures: a combined temperature programmed desorption and theoretical study

The interaction of acetone with single wall carbon nanotubes (SWCNTs) at low temperatures was studied by a combination of temperature programmed desorption (TPD) and dispersion-augmented density-functional-based tight binding (DFTB-D) theoretical simulations. On the basis of the results of the TPD study and theoretical simulations, the desorption peaks of acetone can be assigned to the following adsorption sites: (i) sites with energy of approximately 75 kJ mol (-1) ( T des approximately 300 K)endohedral sites of small diameter nanotubes ( approximately 7.7 A); (ii) sites with energy 40-68 kJ mol (-1) ( T des approximately 240 K)acetone adsorption on accessible interstitial, groove sites, and endohedral sites of larger nanotubes ( approximately 14 A); (iii) sites with energy 25-42 kJ mol (-1) ( T des approximately 140 K)acetone adsorption on external walls of SWCNTs and multilayer adsorption. Oxidatively purified SWCNTs have limited access to endohedral sites due to the presence of oxygen functionalities. Oxygen functionalities can be removed by annealing to elevated temperature (900 K) opening access to endohedral sites of nanotubes. Nonpurified, as-received SWCNTs are characterized by limited access for acetone to endohedral sites even after annealing to elevated temperatures (900 K). Annealing of both purified and as-produced SWCNTs to high temperatures (1400 K) leads to reduction of access for acetone molecules to endohedral sites of small nanotubes, probably due to defect self-healing and cap formation at the ends of SWCNTs. No chemical interaction between acetone and SWCNTs was detected for low temperature adsorption experiments. Theoretical simulations of acetone adsorption on finite pristine SWCNTs of different diameters suggest a clear relationship of the adsorption energy with tube sidewall curvature. Adsorption of acetone is due to dispersion forces, with its C-O bond either parallel to the surface or O pointing away from it. No significant charge transfer or polarization was found. Carbon black was used to model amorphous carbonaceous impurities present in as-produced SWCNTs. Desorption of acetone from carbon black revealed two peaks at approximately 140 and approximately 180-230 K, similar to two acetone desorption peaks from SWCNTs. The characteristic feature of acetone desorption from SWCNTs was peak at approximately 300 K that was not observed for carbon black. Care should be taken when assigning TPD peaks for molecules desorbing from carbon nanotubes as amorphous carbon can interfere.     

FRET-based direct and continuous monitoring of human fucosyltransferases activity: an efficient synthesis of versatile GDP-L-fucose derivatives from abundant D-galactose

We have developed a facile and versatile protocol for the continuous monitoring of human fucosyltransferases activity by using fluorescence energy resonance transfer (FRET), and have explored the feasibility of its use in an inhibitor screening assay. A convenient sugar nucleotide with a fluorogenic probe, 6-deoxy-6-N-(2-naphalene-2-yl-acetamide)-beta-L-galactopyranos-1-yl-guanosine 5'-diphosphate disodium salt (1), was efficiently synthesized from naturally abundant D-galactopyranose via a key intermediate, 6-azide-1,2,3,4-tetra-O-benzoyl-6-deoxy-beta-L-galactopyranose (10). It was demonstrated that the combined use of the glycosyl donor 1 and a dansylated acceptor substrate, sialyl-alpha2,3-LacNAc derivative (2) allowed us to carry out highly sensitive, direct, and continuous in vitro monitoring of the generation of sialyl Lewis X (SLe x), which is catalyzed by human alpha-1,3-fucosyltransferase VI (FUT-VI). A kinetic analysis revealed that compound 1 was an excellent donor substrate (KM=0.94 microM and Vmax=0.14 microM min(-1)) for detecting human FUT-VI activity. To the best of our knowledge, this synthetic fluorogenic probe is the most sensitive and selective donor substrate for FUT-VI among all of the known GDP-Fuc analogues, including the parent GDP-Fuc. When a dansylated asparagine-linked glycopeptide 20, which is derived from egg yolk was employed as an alternate acceptor substrate, a FRET-based assay with compound 1 could be used to directly monitor the alpha1,6-fucosylation at the reducing terminal GlcNAc residue by human FUT-VIII (KM=175 microM and Vmax=0.06 microM/ min); this indicates that the present method might become a general protocol for the characterization of various mammalian fucosyltransferases in the presence of designated fluorogenic acceptor substrates. The present protocol revealed that compound 23, which was obtained by a 1,3-dipolar cycloaddition between the disodium salt 16 and 1-ethynyl-naphthalene exhibits highly potent inhibitory effects against the FUT-VI-mediated sialyl Lewis X synthesis (IC50=5.4 microM).     

A fluorescent molecular switch driven by the input sequence of metal cations: an azamacrocyclic ligand containing bipolar anthracene fragments

An azamacrocyclic ligand (L) containing two anthracene (AN) fragments connected through two triethylenetetramine bridges has been synthesized, in which each of the bridges can coordinate with one metal cation. The effects of pH and metal cations (Zn2+ and Cd2+) on the emission properties of L were studied in water. Without metal cations, L does not show any emission at basic pH values. The addition of Zn2+ leads to the production of excimer emission, which is due to a static excimer formed by direct excitation of the intramolecular ground-state dimer of the bipolar AN fragments that approach each other by Zn2+ binding. In contrast, Cd2+ addition does not result in excimer emission because the Cd2+-AN pi complex, formed by donation of a pi electron of the AN fragments to the adjacent Cd2+, suppresses pi-stacking interactions of the AN fragments. The most notable feature is the appearance of excimer emission controlled by the input sequence of metal cations: Zn2+-->Cd2+ sequential addition (each one equivalent) allows excimer emission, whereas the reverse sequence (Cd2+-->Zn2+) does not. In the Zn2+-->Cd2+ sequence, Cd2+ coordination is structurally restricted by the first Zn2+ coordination with the other polyamine bridge, leading to the formation of a weak Cd2+-AN pi complex. In contrast, for the reverse sequence, the first Cd2+ coordination forms a stable Cd2+-AN pi complex, which is not weakened by sequential Zn2+ coordination, resulting in no excimer emission.     

Photophysical properties of acene DCDHF fluorophores: long-wavelength single-molecule emitters designed for cellular imaging

We report the solvatochromic, viscosity-sensitive, and single-molecule photophysics of the fluorophores DCDHF-N-6 and DCDHF-A-6. These molecules are members of the dicyanomethylenedihydrofuran (DCDHF) class of single-molecule emitters that contain an amine electron donor and a DCDHF acceptor linked by a conjugated unit; DCDHF-N-6 and DCDHF-A-6 have naphthalene- and anthracene-conjugated linkers, respectively. These molecules maintain the beneficial photophysics of the phenylene-linked DCDHF (i.e., photostability, emission wavelength dependence on solvent polarity, and quantum yield sensitivity to solvent viscosity), yet offer absorption and emission at longer wavelengths that are more appropriate for cellular imaging. We demonstrate that these new fluorophores are less photolabile in an aqueous environment than several other commonly used dyes (rhodamine 6G, Texas Red, and fluorescein). Finally, we image single copies of the acene DCDHFs diffusing in the plasma membrane of living cells.     

One-pot solid-phase glycoblotting and probing by transoximization for high-throughput glycomics and glycoproteomics

The development of rapid and efficient methods for high-throughput protein glycomics is of growing importance because the glycoform-focused reverse proteomics/genomics strategy will greatly contribute to the discovery of novel biomarkers closely related to cellular development, differentiation, growth, and aging as well as a variety of diseases such as cancers and viral infection. Recently, we communicated that rapid and efficient purification of carbohydrates can be achieved by employing sugar-specific chemical ligation with aminooxy-functionalized polymers, which we termed "glycoblotting" (see S.-I. Nishimura et al., Angew. Chem. 2005, 117, 93-98; Angew. Chem. Int. Ed. 2005, 44, 91-96). The chemoselective blotting of oligosaccharides present in crude biological materials onto synthetic polymers relies on the unique oxime-bond formation between aminooxy group displayed on the supporting materials and aldehyde/ketone group at the reducing terminal of all oligosaccharides, thus enabling highly selective and rapid oligosaccharide purification. Aiming to improve the detection sensitivity of the released oligosaccharides, we introduce here a novel strategy for one-pot solid-phase glycoblotting and probing by transoximization. We found that oligosaccharides captured by the polymer supports via the oxime bond can be released in the presence of excess O-substituted aminooxy derivatives in a weakly acidic condition. The released oligosaccharides could be recovered as newly formed oxime derivatives of the O-substituted aminooxy compound added, thus demonstrating the simultaneous releasing and probing. In addition, we synthesized a novel aminooxy-functionalized monomer, N-[2-[2-(2-tert-butoxycarbonylaminooxyacetylamino-ethoxy)ethoxy]ethyl]-2-methacrylamide, which allows for the large-scale preparation of a versatile polymer characterized by its high stability, high blotting capacity, and easy use. The one-pot protocol allowed to profile 23 kinds of N-glycan chains of human serum glycoproteins. This concept was further applied for the glycopeptides analysis in a crude mixture followed by galactose oxidase treatment to generate free aldehyde group at the non-reducing terminal of oligosaccharide moiety of glycopeptides. Our technique may be implemented in existing biochemistry and molecular diagnostics laboratories because enriched oligosaccharides and glycopeptides by solid-phase transoximization with high-sensitive labeling reagents are widely applicable in a variety of common analytical methods using two-dimensional HPLC, LC/MS, and capillary electrophoresis as well as modern mass spectrometry.     

Specific isolation of N-terminal fragments from proteins and their high-fidelity de novo sequencing

A new method to determine N-terminal amino acid sequences of multiple proteins at low pmol level by a parallel processing has been developed. The method contains the following five steps: (1) reduction, S-alkylation and guanidination for targeted proteins; (2) coupling with sulfosucccimidyl-2-(biotinamido)ethyl-1,3-dithiopropionate(sulfo-NHS-SS-biotin) to N(alpha)-amino groups of proteins; (3) digestion of the modified proteins by an appropriate protease; (4) specific isolation of N-terminal fragments of proteins by affinity capture using the biotin-avidin system; (5) de novo sequence analysis of peptides by MALDI-TOF-/MALDI-TOF-PSD mass spectrometry with effective utilization of the CAF (chemically assisted fragmentation) method.1 This method is also effective for N-terminal sequencing of each protein in a mixture of several proteins, and for sequencing components of a multiprotein complex. It is expected to become an essential proteomics tool for identifying proteins, especially when used in combination with a C-terminal sequencing method.     

Cholesterol biosensor based on amino-undecanethiol self-assembled monolayer using surface plasmon resonance technique

Cholesterol oxidase has been covalently immobilized onto 11-amino-1-undecanethiol hydrochloride (AUT) self-assembled monolayer (SAM) fabricated on gold (Au) substrates using glutaraldehyde as a cross-linker. These ChOx/AUT/Au bioelectrodes characterized using contact angle (CA) measurements; electrochemical technique and atomic force microscopy (AFM) have been utilized for the estimation of cholesterol in solution using the surface plasmon resonance (SPR) technique. These biosensing electrodes exhibiting linearity from 50 to 500 mg/dL of cholesterol in solution and sensitivity of 1.23 m0/(mg dL), can be used more than 20 times and have a shelf life of about 10 weeks when stored at 4 degrees C.     

Effects of metal cation coordination on fluorescence properties of a diethylenetriamine bearing two end pyrene fragments

Fluorescence properties of a diethylenetriamine bearing two end pyrene fragments (L) have been studied in water, where effects of adding metal cations (Zn2+, Cd2+, Cu2+, Hg2+, Ag+) on the emission properties of L have been studied. Without metal cations, L shows dual-mode fluorescence consisting of monomer and excimer emissions. The monomer emission intensity (I(M)) is strong at acidic pH but decreases with a pH increase because of an electron transfer (ET) from the unprotonated nitrogen atoms to the excited pyrene fragment. The excimer emission is due to the static excimer formed via a direct photoexcitation of the intramolecular ground-state dimer (GSD) of the end pyrene fragments. The excimer emission intensity (I(E)) is weak at acidic pH but increases with a pH increase because of the GSD stability increase associated with the deprotonation of the polyamine chain. Addition of metal cations leads to I(M) decrease, where chelation-driven I(M) enhancement does not occur even with diamagnetic Zn2+ and Cd2+ at any pH. This is because a pyrene-metal cation pi-complex, formed via a donation of pi-electron of the pyrene fragment to the adjacent metal center, suppresses the monomer photoexcitation. I(E) also decreases upon addition of metal cations because the pyrene-metal cation pi-complex weakens pi-stacking interaction of the end pyrene fragments, leading to GSD stability decrease. The emission properties of L-Zn2+ complexes were studied by means of time-resolved fluorescence decay measurements, and the effects of adding a less-polar organic solvent were also studied to clarify the detailed emission properties.