Performing probe experiments in the SEM

A four nanoprobe system has been installed inside a FEI XL30 F scanning electron microscope (SEM), and shown to be fully compatible with the normal functions of the SEM and also a Gatan cold stage (model C1003, -185-400 degrees C). With some selected examples of applications, we have shown that this nanoprobe system may be used effectively for gripping, moving and manipulating nanoobjects, e.g. carbon nanotubes, setting up electric contacts for electronic measurements, tailoring the structure of the nanoobject by cutting, etc. and even for making unexpected nanostructures, e.g. a nanohook. Applications in other areas have also been speculated, limitations or disadvantages of the current design of the probe system were discussed, and methods for possible improvement were suggested.     

Gelation of octadecyltrimethoxysilane at the air/water interface: effect of perfluorotetradecanoic acid and divalent cadmium ions

The effect of an acidic surfactant, perfluorotetradecanoic acid (PFTDA), on the gelation of octadecyltrimethoxysilane (ODTMS) monolayers at the air/water interface was investigated using a Langmuir film balance, attenuated total reflection (ATR) infrared spectroscopy, and atomic force microscopy (AFM). The gelation of ODTMS was greatly accelerated by adding only 2 mol % PFTDA into the monolayer; in this case, the hydrolysis of ODTMS was completed within a few minutes, whereas otherwise it took 18 h. ATR-IR spectroscopy clearly demonstrated that the gelation of a 49:1 ODTMS/PFTDA monolayer proceeded on a pure water subphase mainly via hydrolysis followed by condensation. In the presence of PFTDA, the local acidity at specific sites is presumed to be very high, catalyzing the hydrolysis of ODTMS. The extremely fast rate is attributed not only to the lateral diffusion of PFTDA in the mixed monolayer but also to proton propagation where the proton(s) involved in the initial hydrolysis are transposed rapidly to the nearby methoxy groups for subsequent hydrolysis. The catalytic activity of PFTDA can be neutralized, however, simply by the addition of multivalent metallic ions such as Cd2+ to form saltlike complexes with PFTDA; the rate of 2-D sol-gel processes can thus be easily regulated by a minute amount of PFTDA and/or Cd2+ added into the reaction system.     

Parallel identification of O-GlcNAc-modified proteins from cell lysates

We report a new strategy for the parallel identification of O-GlcNAc-glycosylated proteins from cell lysates. The approach permits specific proteins of interest to be rapidly interrogated for the modification in any tissue or cell type and can be extended to peptides to facilitate the mapping of glycosylation sites. As an illustration of the approach, we identified four new O-GlcNAc-glycosylated proteins of low cellular abundance (c-Fos, c-Jun, ATF-1, and CBP) and two short regions of glycosylation in the enzyme O-GlcNAc transferase (OGT). The ability to target specific proteins across various tissue or cell types complements emerging proteomic technologies and should advance our understanding of this important posttranslational modification.     

BioSimGrid: towards a worldwide repository for biomolecular simulations

BioSimGrid is a database for biomolecular simulations, or, a "Protein Data Bank extended in time" for molecular dynamics trajectories. We describe the implementation details: architecture, data schema, deposition, and analysis modules. We encourage the simulation community to explore BioSimGrid and work towards a common trajectory exchange format.     

Copper(II) acetate promoted oxidative cyclization of arylsulfonyl-o-allylanilines

Tosyl-o-allylaniline 1 undergoes oxidative cyclization to produce tetracycle 2 upon treatment with Cu(OAc)(2) and Cs(2)CO(3) at 120 degrees C. The scope of the reaction was extended to other N-sulfonylated aromatic systems.     

VUV spectroscopic properties of Ce and Pr-doped AREP2O7-type alkali rare earth diphosphates (A=Na, K, Rb, Cs; RE=Y, Lu)

Spectroscopic properties of Ce³⁺ and Pr³⁺-doped AREP₂O₇-type alkali rare earth diphosphates (A=Na, K, Rb, Cs; RE=Y, Lu) have been investigated using VUV spectroscopy technique. Ce³⁺-doped samples show typical Ce³⁺ emission in the range of 325-450 nm. The strong host absorption band starting at around 160 nm indicates that the optical band gap of AREP₂O₇ hosts is at least 7.7 eV, and the host→Ce³⁺ energy transfer process is rather efficient. However, AREP₂O₇:Pr³⁺ samples show less efficient host→Pr³⁺ energy transfer. The direct Pr³⁺ 4f²→4f¹5d¹ excitation, which are 12160±640 cm⁻¹ higher respect to that of Ce³⁺, leads to strong 4f¹5d¹→4f² emission bands in the range of 230-325 nm but no obvious 4f²→4f² emission lines.     

Application of the VESCF method to calculation of the electronic spectra of pyridine,pyrrole, and furan

The partial neglect of differential overlap (PNDO) method has been applied to the heterocycles in the title to obtain total charge distributions. These have then been used to construct (semi-empirical) molecular cores, which have been used in the VESCF treatment of the -systems. Configuration interaction treatments have then been carried out using the ground configuration, and all singly- and doubly-excited configurations. While the treatment is a semiempirical one, care has been taken to introduce no parameters which would be inconsistent with our earlier treatments of hydrocarbons and carbonyl compounds by the same methods. The results indicate that following this kind of scheme, it will probably be finally possible to calculate in a general a priori way the electronic spectra of -systems of heterocycles, as well as hydrocarbons and carbonyl compounds, with an accuracy comparable with that of experiment.

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Zusammenfassung Die Methode der teilweisen Vernachlässigung der differentiellen Überlappung (PNDO) wurde auf die im Titel genannten Heterozyklen angewandt, um totale Ladungsverteilungen zu erhalten. Diese wurden benutzt, um (halb-empirisch) molekulare Kerne zu konstruieren, die bei der VESCF Behandlung von -Systemen benötigt wurden. CI-Verfahren wurden dann durchgeführt unter Verwendung der Grundkonfiguration und aller einfach und doppelt angeregten Konfigurationen. Da das Verfahren semiempirisch ist, muß man darauf achten, keine Parameter einzuführen, die inkonsistent sind mit unseren früheren Behandlungen von Kohlenwasserstoffen und Carbonylverbindungen mittels derselben Methoden. Die Resultate zeigen an, daß bei Verfolgung dieser Art von Schema, es wahrscheinlich endgültig möglich sein wird, auf einem allgemeinen a priori Weg die Elektronenspektren von -Systemen bei Heterozyklen ebenso wie bei Kohlenwasserstoffen und Carbonylverbindungen mit einer dem Experiment vergleichbaren Genauigkeit auszurechnen.

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Résumé La méthode du recouvrement différentiel partiellement nul (PNDO) a été appliquée aux hétérocycles afin d'obtenir des distributions de charge totale. Celles ci on été ensuite utilisées pour construire des squelettes moléculaires (semi-empiriques), employés dans la traitement VESCF des systèmes d'électrons . L'interaction de configurations a été réalisée en utilisant toutes les configurations mono et di-excitées. Malgré le caractère semi-empirique de ce traitement, on a pris la précaution de ne pas introduire de paramètres qui présenteraient une incohérence avec notre traitement analogue des hydrocarbures et des composés carbonyles. Les résultats obtenus montrent qu'en suivant un tel schéma de calcul il serait probablement possible de calculer d'une manière générale à priori les spectres électroniques des systèmes des hétérocycles, des hydrocarbures et des composés carbonyles, à la précision expérimentale.

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This research was supported by Research Grant GP 6763 from the National Science Foundation.     

Information leakage through a passive optical channel

From the basic entropy of information, the information leakage through a passive coherent channel is calculated. In the course of the derivation, the optical channel is decomposed into a series of cascaded subchannels. It is shown that the amount of information decreases as the information flows through the cascaded channels. The best a passive channel can achieve, in principle, is to preserve the entire input information. It is possible to obtain at the output an amount of information greater than the input, but only through the use of active channels. However, an active channel requires an external source of energy which in some cases could lead to an enormous amount of energy.     

Mechanism of acetylcholinesterase inhibition by fasciculin: a 5-ns molecular dynamics simulation

Our previous molecular dynamics simulation (10 ns) of mouse acetylcholinesterase (EC 3.1.1.7) revealed complex fluctuation of the enzyme active site gorge. Now we report a 5-ns simulation of acetylcholinesterase complexed with fasciculin 2. Fasciculin 2 binds to the gorge entrance of acetylcholinesterase with excellent complementarity and many polar and hydrophobic interactions. In this simulation of the protein-protein complex, where fasciculin 2 appears to sterically block access of ligands to the gorge, again we observe a two-peaked probability distribution of the gorge width. When fasciculin is present, the gorge width distribution is altered such that the gorge is more likely to be narrow. Moreover, there are large increases in the opening of alternative passages, namely, the side door (near Thr 75) and the back door (near Tyr 449). Finally, the catalytic triad arrangement in the acetylcholinesterase active site is disrupted with fasciculin bound. These data support that, in addition to the steric obstruction seen in the crystal structure, fasciculin may inhibit acetylcholinesterase by combined allosteric and dynamical means. Additional data from these simulations can be found at http://mccammon.ucsd.edu/.