New-generation amber united-atom force field

We have developed a new-generation Amber united-atom force field for simulations involving highly demanding conformational sampling such as protein folding and protein-protein binding. In the new united-atom force field, all hydrogens on aliphatic carbons in all amino acids are united with carbons except those on Calpha. Our choice of explicit representation of all protein backbone atoms aims at minimizing perturbation to protein backbone conformational distributions and to simplify development of backbone torsion terms. Tests with dipeptides and solvated proteins show that our goal is achieved quite successfully. The new united-atom force field uses the same new RESP charging scheme based on B3LYP/cc-pVTZ//HF/6-31g** quantum mechanical calculations in the PCM continuum solvent as that in the Duan et al. force field. van der Waals parameters are empirically refitted starting from published values with respect to experimental solvation free energies of amino acid side-chain analogues. The suitability of mixing new point charges and van der Waals parameters with existing Amber covalent terms is tested on alanine dipeptide and is found to be reasonable. Parameters for all new torsion terms are refitted based on the new point charges and the van der Waals parameters. Molecular dynamics simulations of three small globular proteins in the explicit TIP3P solvent are performed to test the overall stability and accuracy of the new united-atom force field. Good agreements between the united-atom force field and the Duan et al. all-atom force field for both backbone and side-chain conformations are observed. In addition, the per-step efficiency of the new united-atom force field is demonstrated for simulations in the implicit generalized Born solvent. A speedup around two is observed over the Duan et al. all-atom force field for the three tested small proteins. Finally, the efficiency gain of the new united-atom force field in conformational sampling is further demonstrated with a well-known toy protein folding system, an 18 residue polyalanine in distance-dependent dielectric. The new united-atom force field is at least a factor of 200 more efficient than the Duan et al. all-atom force field for ab initio folding of the tested peptide.     

Two-photon absorption chromophores with a tunable [2,2′]bithiophene core

Sonogashira coupling between 3,5,3′,5′-tetrabromo-[2,2′]bithiophene and various terminal alkynes provides two-photon absorption (TPA) chromophores 1-6, which possess electron donor (D) and/or acceptor (A) alkynyl substituents at 3(3′) and 5(5′) sites of the bithiophene core. The up-converted fluorescence emission excited at 800 nm (Ti:sapphire femtosecond laser, ∼100 fs pulses) was used to determine the two-photon absorption cross-sections (σ) of these compounds. The corresponding TPA cross-section (σ) values ranging from 132 to 1120 GM (10⁻⁵⁰ cm⁴ s photon⁻¹) can be fine-tuned by the substitutents. The quadrupolar-type (A-π-D-π-A) chromophore 5 exhibits the largest σ value (1120 GM) in CH₂Cl₂ upon 800 nm excitation.     

Fabrication of microfluidic devices using dry film photoresist for microchip capillary electrophoresis

An inexpensive, disposable microfluidic device was fabricated from a dry film photoresist using a combination of photolithographic and hot roll lamination techniques. A microfluidic flow pattern was prefabricated in a dry film photoresist tape using traditional photolithographic methods. This tape became bonded to a poly(methyl methacrylate) (PMMA) sheet with prepouched holes when passed through a hot roll laminator. A copper working electrode and platinum decoupler was readily incorporated within this microchip. The integrated microchip device was then fixed in a laboratory-built Plexiglas holder prior to its use in microchip capillary electrophoresis. The performance of this device with amperometric detection for the separation of dopamine and catechol was examined. The separation was complete within 50 s at an applied potential of 200 V/cm. The relative standard deviations (RSD) of analyte migration times were less than 0.71%, and the theoretical plate numbers for dopamine and catechol were 3.2 x 10(4) and 4.1 x 10(4), respectively, based on a 65 mm separation channel.     

Impact of halides on the simultaneous separation of aromatic amines and their acidic metabolites by capillary electrophoresis with laser-induced native fluorescence detection under acidic conditions

This paper describes a simple, sensitive, efficient, and rapid method for simultaneous analysis of biologically active amines and acids by capillary electrophoresis in conjunction with laser-induced native fluorescence detection (CE-LINF) using a diode pumped solid state nanolaser at 266 nm. In order to optimize resolution of the amines that were prepared in 10.0 mM formate-Tris (FT) solutions, 10.0 mM FT solutions with and without containing halides were used to fill the capillary and reservoirs, respectively. The electrophoretic mobilities of tryptamine (TA) and serotonin (5-HT) at pH 4.0 decrease with the increase in halide concentration (0-10.0 mM). Taken together with a great effect of iodide than other halides, we suggest that the formation of ion pairs is a main contributor for altering the migration of the amines. In order to simultaneously analyze the amines and their metabolites (acids) at low pH, a high bulk EOF is required. The analysis of 10 anlytes including amines and acids was completed within 12 min by CE-LINF using a capillary treated with 0.5M NaOH and then filled with 10.0 mM FT solutions (pH 4.0) containing 10.0 mM KCl prior to analysis. The limits of detection for TA and 5-hydroxyindole-3-acetic acid (5-HIAA) are 0.12 and 6.0 nM, respectively. The present method has been further validated by analyzing urine samples, with an RSD less than 3.1% (migration times) and 3.9% (concentration).     

Electrowetting-induced capillary flow in a parallel-plate channel

This paper investigated, theoretically and experimentally, the electrowetting-induced capillary rise in a parallel-plate channel. The measured equilibrium height of the meniscus was proportional to the square of the applied potential. A model, based on the kinetic equation of capillary flow with the consideration of an electrowetting dynamic contact angle, was established to simulate the capillary rise. The effects of the electrostatic charge and the contact-line friction were linearly added to describe the electrowetting dynamic contact angle. The model was found to be able to adequately describe the experimental data under different initial heights and applied voltages. The non-Poseuille flow effect had little influence in the meniscus rising phenomenon studied in this work.     

Orbitally driven spin-singlet dimerization in S=1 La4Ru2O10

Using x-ray absorption spectroscopy at the Ru-L2,3 edge we reveal that the Ru4+ ions remain in the S=1 spin state across the rare 4d-orbital ordering transition and spin-gap formation. We find using local spin density approximation + Hubbard U band structure calculations that the crystal fields in the low-temperature phase are not strong enough to stabilize the S=0 state. Instead, we identify a distinct orbital ordering with a significant anisotropy of the antiferromagnetic exchange couplings. We conclude that La4Ru2O10 appears to be a novel material in which the orbital physics drives the formation of spin-singlet dimers in a quasi-two-dimensional S=1 system.     

Determination of aristolochic acid in Chinese herbal medicine by capillary electrophoresis with laser-induced fluorescence detection

We have demonstrated the analysis of aristolochic acids (AAs) that are naturally occurring nephrotoxin and carcinogen by capillary electrophoresis in conjunction with laser-induced fluorescence detection (CE-LIF). Owing to lack of intrinsic fluorescence characteristics of oxidized AAs (OAAs), reduction of the analytes by iron powder in 10.0 mM HCl is required prior to CE analysis. The reduced AAs (RAAs) exhibit fluorescence at 477 nm when excited at 405 nm using a solid-state blue laser. By using 50.0 mM sodium tetraborate (pH 9.0) containing 10.0 mM SDS, the determination of AA-I and AA-II by CE-LIF has been achieved within 12 min. The CE-LIF provides the LODs of 8.2 and 5.4 nM for AA-I and AA-II, respectively. The simple CE-LIF method has been validated by the analysis of 61 Chinese herbal samples. Prior to CE analysis, OAAs were extracted by using 5.0 mL MeOH, and then the extracts were subjected to centrifugation at 3,000 rpm for 5 min. After reduction, extraction, and centrifugation, the supernatants were collected and subjected to CE analysis. Of the 61 samples, 14 samples contain AA-I and AA-II, as well as 10 samples contain either AAI or AAII. The relative standard deviation (RSD) values of the migration times for AA-I and AA-II are less than 2.5% and 2.1% for three consecutive measurements of each sample. The RSD values for the peak heights corresponding to AA-I and AA-II in most samples are about 8.0% and 10.0%, respectively. The result shows that the present CE-LIF approach is sensitive, simple, efficient, and accurate for the determination of AAs in real samples.     

On-line preconcentration and determination of ketamine and norketamine by micellar electrokinetic chromatography. Complementary method to gas chromatography/mass spectrometry

We have investigated a rapid, simple, and highly efficient on-line preconcentration method using in micellar electrokinetic chromatography (MEKC) for the analysis of abused drugs. Ketamine is an anesthetic that has been abused as a hallucinogen. We applied the sample sweeping technique first to ketamine and its major metabolite, norketamine, and separated the analytes with MEKC. Several of the sweeping MEKC parameters to effect successful separations, such as the concentration of sodium dodecyl sulfate (SDS), the injection time, and the applied voltage were optimized. The improvements in the number of theoretical plates under the different separation conditions are presented clearly in a three-dimensional representation. The limits of detection were 2.8, 3.4, and 3.3 ng/mL for ketamine, norketamine, and ketamine-D(4), respectively. The enrichment factor for each compound was within the range of 540-800. Experimental results are in agreement with those of analysis conducted by gas chromatography/mass spectroscopy (GC/MS). Therefore, we believe that sweeping, combined with MEKC, represents a suitable complementary method to GC/MS for use in clinical and forensic analyses of ketamine and norketamine.     

Characterization of natural chitosan membranes from the carapace of the soldier crab Mictyris brevidactylus and its application to immobilize glucose oxidase in amperometric flow-injection biosensing system

This study investigated characteristics of a chitosan membrane from the carapace of the soldier crab Mictyris brevidactylus intended to construct an amperometric biosensor. Electrochemical impedance spectroscopy (EIS) and cyclic voltammetry (CV) were used in this study to characterize these chitosan membranes intended for constructing enzymatic biosensors. Chitosan membranes suffering various durations (>10 min) of deacetylation had small charge-transfer resistances (<7.88 kohms) but large double-layer capacitances (>0.55 microF). They were found in EIS where both the solution resistance and Warburg impedance upon electrode interface were almost independent of the durations and degree of deacetylation. The degree of deacetylation and the thickness of chitosan membranes were also determined. Membrane thickness was slightly dependent with the duration but degree of deacetylation was slightly dependent on the duration. Chitosan membranes with various thicknesses suffered various durations of deacetylation, but this did not influence their electrochemical characteristics. The chitinous membrane was covalently immobilized with glucose oxidase (EC 1.3.4.3) and then attached onto the platinum electrode of a homemade amperometric flow cell. Sensor signal was linearly related to glucose concentration (r=0.999 for glucose up to 1.0 mM). The system was sensitive (S/N>5 for 10 microM glucose) and reproducible (CV<1.3% for 50 microM glucose, n=5).     

Promotion of cell affinity of porous PLLA scaffolds by immobilization of RGD peptides via plasma treatment

In the present work, RGDS (Arg-Gly-Asp-Ser) was immobilized on PLLA scaffolds with plasma treatment. The amount of immobilization, determined by HPLC, was confirmed to be in the effective order. Results from the culture of rat osteosarcoma (ROS), osteoblastic-like cells, demonstrate that the immobilization of RGDS could effectively enhance the attachment of ROS cells on PLLA and increase the cell density in PLLA scaffolds. In addition, experiments of in vitro mineralization indicate that there were more cells and mineralization focci in the RGDS-immobilized scaffolds, suggesting a tendency to form bone-like tissues, compared with the unmodified PLLA scaffold. On the other hand, the PLLA scaffolds immobilized with RGES (Arg-Gly-Glu-Ser) were much less effective in promotion of ROS attachment, suggesting that the enhancement on cell attachment was mainly due to the recognition of RGDS by the adhesion receptors on the cell membrane. The results presented in this work demonstrate that RGDS could be successfully immobilized on PLLA scaffolds with plasma treatment and such modification can make PLLA scaffolds more suitable for culture of osteoblast-like cells and for generation of bone-like tissues.