Mean-field HP model, designability and alpha-helices in protein structures

Analysis of the geometric properties of a mean-field HP model on a square lattice for protein structure shows that structures with a large number of switchbacks between surface and core sites are chosen favorably by peptides as unique ground states. Global comparison of model (binary) peptide sequences with concatenated (binary) protein sequences listed in the Protein Data Bank and the Dali Domain Dictionary indicates that the highest correlation occurs between model peptides choosing the favored structures and those portions of protein sequences containing alpha helices.     

High-order kinetic flux vector splitting schemes in general coordinates for ideal quantum gas dynamics

A class of high-order kinetic flux vector splitting schemes are presented for solving ideal quantum gas dynamics based on quantum statistical mechanics. The collisionless quantum Boltzmann equation approach is adopted and both Bose–Einstein and Fermi–Dirac gases are considered. The formulas for the split flux vectors are derived based on the general three-dimensional distribution function in velocity space and formulas for lower dimensions can be directly deduced. General curvilinear coordinates are introduced to treat practical problems with general geometry. High-order accurate schemes using weighted essentially non-oscillatory methods are implemented. The resulting high resolution kinetic flux splitting schemes are tested for 1D shock tube flows and shock wave diffraction by a 2D wedge and by a circular cylinder in ideal quantum gases. Excellent results have been obtained for all examples computed.     

Use of multiplex PCR and CE for gene dosage quantification and its biomedical applications for SMN, PMP22, and alpha-globin genes

Many genetic diseases are caused by the presence of point mutations, small insertions, and deletions in respective genes, and the number of diseases known to be caused by deletions and duplications involving large DNA genomes is increasing. These changes lead to underexpression or overexpression of the gene, according to changes in gene dosage. The methods for the detection of point mutations, small insertions, and deletions are well established, but the detection of larger genomic deletions or duplications is more difficult. Due to the lack of efficient and technically feasible protocols for gene dosage quantification, we describe a diagnostic protocol employing a combination of available methods. The efficient and accurate gene dosage quantification platform is combined with multiplex PCR and CE, and applied to detect dosages of several genes, including SMN, PMP22, and alpha-globin genes. The reliability of this novel methodology shows that it is a relatively speedy and low-cost procedure and a significant tool for genetic diagnosis. Its sensitivity and specificity for identifying deletion and duplication genotypes approach 100%. Moreover, once we establish this powerful system, we will further apply this technique to the rapid detection of trisomy syndromes and microdeletion syndromes, including trisomy 13, Down syndrome, DiGeorge syndrome, and others.     

Carbazole-oxadiazole containing polyurethanes as phosphorescent host for organic light emitting diodes

New types of polyurethanes (PUs) were prepared from condensation polymerization of isophorone diisocyanate (IPDI) with various combination of 9-butyl-3,6-bis(4-hydroxyphenyl)carbazole (Cz) and 2,5-bis(4-hydroxyphenyl)-1,3,4-oxadiazole (OXD), and end-capped with 4-tert-butyl phenol. The Cz-OXD PUs can also be used as host for phosphorescent dye. Red EL emission was obtained when Ir(btp)₂(acac) or Ir(2-phq)₂(acac) was used as the phosphorescent dyes in Cz-OXD (3:1) PU. Maximum brightness of 394 cd/m² and EL efficiency of 1 cd/A were achieved for the Ir(2-phq)₂(acac) base device. In addition, white light PLED was demonstrated when co-dopant of Ir(btp)₂(acac) and Firpic were used.     

Analysis of Petroleum Distillates from Fire Debris Using Supercritical Fluid Extraction with a Two‐Level Orthogonal Array Experimental Design

A supercritical fluid extraction (SFE) method was developed in the present study as an effective sample pretreatment technique of petroleum distillates from fire debris. Three petroleum distillates were used as target analytes, including 95 unleaded gasoline, kerosene, and premium diesel. An orthogonal array (L16) experimental design was adopted to separately evaluate primary SFE experimental factors. The SFE efficiencies of petroleum distillates at various extraction conditions were examined and the optimized SFE conditions were identified. Experimental results demonstrated that the optimized SFE method not only provided an effective extraction method for the spiked sample, but also successfully recovered residues of petroleum distillates from fire debris.     

High Performance Nonvolatile Transistor Memories Utilizing Functional Polyimide‐Based Supramolecular Electrets

We report pentacene‐based organic field‐effect transistor memory devices utilizing supramolecular electrets, consisting of a polyimide, PI(6FOH‐ODPA), containing hydroxyl groups for hydrogen bonding with amine functionalized aromatic rings (AM) of 1‐aniline (AM1), 2‐naphthylamine (AM2), 2‐aminoanthracene (AM3), and 1‐aminopyrene (AM4). The effect of the phenyl ring size and composition of AM1–AM4 on the hole‐trapping capability of the fabricated devices was investigated systematically. Under an operating voltage under ±40 V, the prepared devices using the electrets of 100 % AM1–AM4/PI ratios exhibited a memory window of 0, 8.59, 25.97, and 29.95 V, respectively, suggesting that the hole‐trapping capability increased with enhancing phenyl ring size. The memory window was enhanced as the amount of AM in PI increased. Furthermore, the devices showed a long charge‐retention time of 10⁴ s with an ON/OFF current ratio of around 10³–10⁴ and multiple switching stability over 100 cycles. This study demonstrated that the electrical characteristics of the OFET memory devices could be manipulated through the chemical compositions of the supramolecular electrets.     

Thermodynamics of binding of 2-methoxy-3-isopropylpyrazine and 2-methoxy-3-isobutylpyrazine to the major urinary protein

In the present study we examine the thermodynamics of binding of two related pyrazine-derived ligands to the major urinary protein, MUP-I, using a combination of isothermal titration calorimetry (ITC), X-ray crystallography, and NMR backbone (15)N and methyl side-chain (2)H relaxation measurements. Global thermodynamics data derived from ITC indicate that binding is driven by favorable enthalpic contributions, rather than the classical entropy-driven hydrophobic effect. Unfavorable entropic contributions from the protein backbone and side-chain residues in the vicinity of the binding pocket are partially offset by favorable entropic contributions at adjacent positions, suggesting a "conformational relay" mechanism whereby increased rigidity of residues on ligand binding are accompanied by increased conformational freedom of side chains in adjacent positions. The principal driving force governing ligand affinity and specificity can be attributed to solvent-driven enthalpic effects from desolvation of the protein binding pocket.     

Nanocomposites of Tantalum‐Based Pyrochlore and Indium Hydroxide Showing High and Stable Photocatalytic Activities for Overall Water Splitting and Carbon Dioxide Reduction

Nanocomposites of tantalum‐based pyrochlore nanoparticles and indium hydroxide were prepared by a hydrothermal process for UV‐driven photocatalytic reactions including overall water splitting, hydrogen production from photoreforming of methanol, and CO₂ reduction with water to produce CO. The best catalyst was more than 20 times more active than sodium tantalate in overall water splitting and 3 times more active than Degussa P25 TiO₂ in CO₂ reduction. Moreover, the catalyst was very stable while generating stoichiometric products of H₂ (or CO) and O₂ throughout long‐term photocatalytic reactions. After the removal of In(OH)₃, the pyrochlore nanoparticles remained highly active for H₂ production from pure water and aqueous methanol solution. Both experimental studies and density functional theory calculations suggest that the pyrochlore nanoparticles catalyzed the water reduction to produce H₂, whereas In(OH)₃ was the major active component for water oxidation to produce O₂.     

Direct Synthesis of Chiral 3‐Arylsuccinimides by Rhodium‐Catalyzed Enantioselective Conjugate Addition of Arylboronic Acids to Maleimides

Chiral rhodium catalysts comprising 2,5‐diaryl‐ substituted bicyclo[2.2.1]diene ligands L1 – L10 were utilized in the enantioselective 1,4‐addition reaction of arylboronic acids to N‐substituted maleimides. In the presence of 2.5 mol % of Rh^I/ L2 , enantioenriched conjugate addition adducts were isolated in 72–99 % yields with 86–98 % ee. This protocol offers a convenient method to access a variety of 3‐arylsuccinimides in a highly enantioselective manner. Maleimides with readily cleavable N‐protecting groups were tolerated enabling the synthesis of useful synthetic intermediates. Pyrrolidine 4 , a biologically active compound, and pyrrolidine 5 , an ent‐precursor to an HSD‐1 inhibitor, were synthesized to demonstrate the utility of this method.