Bond length alternation and energy band gap of polyyne

The bond length alternation (BLA) and energy band gap of polyyne are investigated by various first-principles theories, including Hartree-Fock, MP2, hybrid, and nonhybrid density functional theories. Both solid-state calculations utilizing periodic boundary conditions on polymers and molecular quantum mechanical calculations on extra-long oligomers were performed with consistent results. By validation on similar linear conjugated polymers, polyacetylene and polydiacetylene, the combination of hybrid-DFT schemes, B3LYP//BHandHLYP or B3LYP//KMLYP, is shown to give the best predictions for both geometry and band gap of polyyne based on available experimental data. We conclude that the best estimate of the BLA of polyyne is about 0.13 A and that of the band gap is about 2.2 eV.     

Stepwise cope rearrangement of cyclo-biphenalenyl via an unusual multicenter covalent pi-bonded intermediate

Multicenter covalent pi-bonding between pi-conjugated radicals has been recently recognized as a novel and important bonding interaction. The Cope rearrangement of cyclo-biphenalenyl 9 is studied by exploring its potential energy surface with density functional theory (DFT), and it is found that pi-bonding plays a critical role in the rearrangement process. Affected by this, the rearrangement of 9 takes place by a stepwise mechanism through an unusual pi-intermediate 10, of C2h symmetry, which can be characterized as a 2 x 13pi + 2 x 2pi system. The pi-intermediate has a long inter-phenalenyl distance of R approximately 2.8 angstroms, which is shorter than the sum of the van der Waals radii displaying multicenter covalent pi-bonding between the two phenalenyl units. The energy of the pi-intermediate 10 is higher than that of the sigma-bonded reactant 9 by approximately 2 kcal/mol according to the employed spin-restricted DFT. NMR chemical shift calculations support the sigma-bonded 9 as the global minimum. The calculated activation barrier of approximately 6 kcal/mol for the Cope rearrangement is consistent with the stepwise mechanism. A covalent pi-bonding effect in the pi-intermediate 10 is demonstrated indirectly by the shortening of inter-naphthalene distance of the dianion and dication of the cyclophane 14 compared to that of its neutral counterpart. The unusual pi-bonded structure with a long inter-phenalenyl distance becomes the most stable structure for the ethano-bridged derivative 13, which should have observable paramagnetism according to the calculated paramagnetic susceptibility.     

Genotyping with microfluidic devices

In the past few years, electrophoresis microchips have been increasingly utilized to interrogate genetic variations in the human and other genomes. Microfluidic devices can be readily applied to speed up existing genotyping protocols, in particular the ones that require electric field-mediated separations in conjunction with restriction fragment analysis, DNA sequencing, hybridization-based techniques, allele-specific amplification, heteroduplex analysis, just to list the most important ones. As a result of recent developments, microfabricated electrophoresis devices offer several advantages over conventional slab-gel electrophoresis, such as small sample volume requirement, low reagent consumption, the option of system integration and easy multiplexing. The analysis speed of microchip electrophoresis is significantly higher than that of any other electric field-mediated separation techniques. State-of-the-art microfluidic bioanalytical devices already claim their place in most molecular biology laboratories. This review summarizes the recent developments in microchip electrophoresis methods of nucleic acids, particularly for rapid genotyping, that will most likely play a significant role in the future of clinical diagnostics.     

Molecular structure of silsesquioxanes determined by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry was used to deduce the three-dimensional structure of a complex silsesquioxane polymer. Four distinct levels of structure were observed in the mass spectrum. The overall shape of the peak distribution was typical of polymers formed by condensation reactions. The mass separation between major clusters of peaks, each major cluster corresponding to an oligomer with a unique number of repeat units, confirmed that the synthesis proceeded as expected with no side reactions. The mass separation between peaks within a major cluster showed that intramolecular reactions during synthesis resulted in the elimination of water. The loss of water was ascribed to the formation of closed loops in the polymer structure. A simple arithmetic algorithm is presented for identifying these peaks. Autocorrelation techniques were used to determine the number and distribution of intramolecular closed loops per oligomer. This knowledge was used to deduce whether a particular oligomer is branched-linear, ladder, polyhedral, or some combination of these. The single-oligomer isotopic distribution was used to determine that cationization was present from both sodium and potassium ions.     

Numerical errors and chaotic behavior in docking simulations

This work examines the sensitivity of docking programs to tiny changes in ligand input files. The results show that nearly identical ligand input structures can produce dramatically different top-scoring docked poses. Even changing the atom order in a ligand input file can produce significantly different poses and scores. In well-behaved cases the docking variations are small and follow a normal distribution around a central pose and score, but in many cases the variations are large and reflect wildly different top scores and binding modes. The docking variations are characterized by statistical methods, and the sensitivity of high-throughput and more precise docking methods are compared. The results demonstrate that part of docking variation is due to numerical sensitivity and potentially chaotic effects in current docking algorithms and not solely due to incomplete ligand conformation and pose searching. These results have major implications for the way docking is currently used for pose prediction, ranking, and virtual screening.     

Jet flavor tomography of quark gluon plasmas at RHIC and LHC

A new Monte Carlo model of jet quenching in nuclear collisions, CUJET1.0, is applied to predict the jet flavor dependence of the nuclear modification factor for fragments f=π,D,B,e(-) from quenched jet flavors g,u,c,b in central collisions at RHIC and LHC. The nuclear modification factors for different flavors are predicted to exhibit a novel level crossing pattern over a transverse momentum range 5相似文献   

Analysis of alpha-1-acid glycoprotein isoforms using CE-LIF with fluorescent thiol derivatization

The analysis of glycoprotein isoforms is of high interest in the biomedical field and clinical chemistry. Many studies have demonstrated that some glycoprotein isoforms could serve as biomarkers for several major diseases, such as cancers and vascular diseases, among others. Capillary zone electrophoresis (CZE) is a well-established technique to separate glycoprotein isoforms, however, it suffers from limited sensitivity when UV-Vis detection is used. On the other hand, with laser-induced fluorescence (LIF) detection, derivatization reaction to render the proteins fluorescent can destroy the resolution of the isoforms. In this work, a derivatization procedure through the thiol groups of glycoproteins using either 5-(iodoacetamide) fluorescein (5-IAF) or BODIPY iodoacetamide is presented with the model protein of alpha-1-acid glycoprotein (AGP). The derivatization process presented enabled high-resolution analysis of AGP isoforms by CZE-LIF. The derivatization procedure was successfully applied to label AGP from samples of serum and secretome of artery tissue, enabling the separation of the AGP isoforms by CE-LIF in natural samples at different concentration levels.     

Analytical solutions of N‐person games

The possibility of analytical solutions of N‐person games is presented. A simple formula provides valuable information about the outcomes of such games with linear payoff functions and Pavlovian agents. Experiments performed with our simulation tool for the multiagent stag hunt dilemma game are presented. For the case of Pavlovian agents the game has nontrivial but remarkably regular solutions. If both payoff functions are linear and the real solutions of Eq. (2) are both positive, then the analytical solutions are remarkably accurate. © 2012 Wiley Periodicals, Inc. Complexity, 2012     

High-throughput genotyping of repeat polymorphism in the regulatory region of serotonin transporter gene by gel microchip electrophoresis.

Large-scale genotyping of the repeat polymorphism in the regulatory region of the serotonin transporter gene (5-HTTLPR) was attempted by polymerase chain reaction (PCR) amplification followed by gel microchip electrophoresis analysis. The multilane (96) format of the gel microchip system allowed parallel separation of a large number of samples. The separation and visualization of the PCR amplicons from either the 5-HTTLPR short allele (number of repeats are 14) or the 5-HTTLPR long form (16 repeats) was completed in a few minutes. Genotyping of healthy Caucasian individuals showed that the short allele had a somewhat lower frequency (0.42) than the long form (0.58), and the genotype frequencies fulfilled the criteria of the Hardy-Weinberg equilibrium (chi = 0.012, p = 0.994). Based on these results, gel microchip electrophoresis system proved to be a powerful tool for high throughput genotyping of repeat polymorphism.     

Open retractions onto n-ods

We characterize dendrites which admit an open retraction onto an arbitrary n-od. The paper contains also several corollaries and two problems concerning the subject