Phase diagram of the D3/D5 system in a magnetic field and a BKT transition

We study the full temperature and chemical potential dependence of the D3/D5 2+1$2+1$-dimensional theory in the presence of a magnetic field. The theory displays separate transitions associated with chiral symmetry breaking and melting of the bound states. We display the phase diagram which has areas with first and second order transitions meeting at two critical points similar to that of the D3/D7 system. In addition there is the recently reported BKT transition at zero temperature leading to distinct structure at low temperatures.     

Synthesis of substituted isoquinolines via Pd-catalyzed cross-coupling approaches

Palladium complexes incorporating ligands based on a 1,3,5,7-tetramethyl-2,4,8-trioxa-6-phosphaadamantanyl scaffold were used to catalyze the arylation of ethyl cyanoacetate, malononitrile, and various ketones. The products from these reactions can be elaborated to substituted β-arylethylamines and used in microwave-assisted Pictet-Spengler reactions. The protocol developed is suitable for the synthesis of libraries of substituted isoquinolines.     

Affinity‐Based Drug Delivery

Affinity‐based drug delivery systems utilize interactions between the therapeutic drug and the delivery system to manipulate drug loading and to control drug release. In this paper, affinity‐based drug delivery system syntheses, types of therapeutic factors delivered, and delivery system loading and release are discussed in detail. The paper is divided into three subsections, based on the type of delivery system: molecular imprinting systems, growth‐factor delivery, and cyclodextrin‐based delivery. The objective of this paper is to examine the current state of research, highlight the breakthroughs and challenges, point out potential impacts of this relatively new technology, and explore future developmental areas.

     

Protein side chain modeling with orientation-dependent atomic force fields derived by series expansions

We describe the development of new force fields for protein side chain modeling called optimized side chain atomic energy (OSCAR). The distance‐dependent energy functions (OSCAR‐d) and side‐chain dihedral angle potential energy functions were represented as power and Fourier series, respectively. The resulting 802 adjustable parameters were optimized by discriminating the native side chain conformations from non‐native conformations, using a training set of 12,000 side chains for each residue type. In the course of optimization, for every residue, its side chain was replaced by varying rotamers, whereas conformations for all other residues were kept as they appeared in the crystal structure. Then, the OSCAR‐d were multiplied by an orientation‐dependent function to yield OSCAR‐o. A total of 1087 parameters of the orientation‐dependent energy functions (OSCAR‐o) were optimized by maximizing the energy gap between the native conformation and subrotamers calculated as low energy by OSCAR‐d. When OSCAR‐o with optimized parameters were used to model side chain conformations simultaneously for 218 recently released protein structures, the prediction accuracies were 88.8% for χ₁, 79.7% for χ_{1 + 2}, 1.24 Å overall root mean square deviation (RMSD), and 0.62 Å RMSD for core residues, respectively, compared with the next‐best performing side‐chain modeling program which achieved 86.6% for χ₁, 75.7% for χ_{1 + 2}, 1.40 Å overall RMSD, and 0.86 Å RMSD for core residues, respectively. The continuous energy functions obtained in this study are suitable for gradient‐based optimization techniques for protein structure refinement. A program with built‐in OSCAR for protein side chain prediction is available for download at http://sysimm.ifrec.osaka‐u.ac.jp/OSCAR/ . © 2011 Wiley Periodicals, Inc. J Comput Chem 2011     

Characteristics of microwaves on second generation nitrogen-doped TiO2 nanoparticles and their effect on photoassisted processes

Characteristics of 2.45-GHz microwave radiation were examined on two second generation nitrogen-doped TiO₂ nanomaterials prepared by annealing Degussa P-25 TiO₂ and Ishihara ST-01 TiO₂ at 400 °C and 500 °C, respectively, in air in the presence of urea, and for comparison on the undoped pristine samples. Band gaps of all four samples were determined by diffuse reflectance spectroscopy. Both the sizes and the BET specific surface areas of the TiO₂ particles were determined, together with dielectric constants and dielectric loss factors. Nitrogen doping caused the size to increase and surface area to decrease. Temperature–time profiles showed that the heating efficiency of the N-doped specimens by the microwaves was greater, particularly significant for the N-doped P25 sample, but rather small for the N-ST01 sample. The effect of microwaves on the surface optical phonons of the samples, with and without UV–vis irradiation, was examined by an in situ Raman spectroscopic technique; for the undoped P-25 and nitrogen-doped N-P25 TiO₂ systems the effect was negligible. By contrast, microwave irradiation of Ishihara ST-01 and nitrogen-doped N-ST01 TiO₂ samples showed significant changes in the 144-cm^?1 optical phonons. Results infer a microwave thermal effect on the Ishihara ST-01 and N-ST01 specimens, whereas for the Degussa P-25 samples the microwaves also imparted a specific effect as the microwaves influenced the N-dopant sites in contrast to the ST-01 systems where the dopant sites were unaffected as evidenced by temperature–time profiles. The microwave-/photo-assisted degradation of 4-chlorophenol under various conditions of UV–vis irradiation and conventional heating, as opposed to microwave heating, confirms the specific microwave effect for the P-25 systems.     

Diagnostic NH and OH Vibrations for Oxazolone and Diketopiperazine Structures: b<Subscript>2</Subscript> from Protonated Triglycine

We present infrared multiple photon dissociation (IRMPD) spectra in the hydrogen stretching region of the simplest b fragment, b₂ from protonated triglycine, contrasted to that of protonated cyclo(Gly-Gly). Both spectra confirm the presence of intense, diagnostic vibrations linked to the site of proton attachment. Protonated cyclo(Gly-Gly) serves as a reference spectrum for the diketopiperazine structure, showing a diagnostic O-H⁺ stretch of the protonated carbonyl group at 3585 cm^–1. Conversely, b₂ from protonated triglycine exhibits a strong band at 3345 cm^–1, associated with the N-H stretching mode of the protonated oxazolone ring structure. Other weaker N-H stretches can also be discerned, such as the amino NH₂ and amide NH bands. These results demonstrate the usefulness of the hydrogen stretching region, and hence benchtop optical parametric oscillator/amplifier (OPO/A) set-ups, in making structural assignments of product ions in collision-induced dissociation (CID) of peptides.     

On the dynamics of fragment isomerization in collision-induced dissociation of peptides

The structures of peptide collision-induced dissociation (CID) product ions are investigated using ion mobility/mass spectrometry techniques combined with theoretical methods. The cross-section results are consistent with a mixture of linear and cyclic structures for both b4 and a4 fragment ions. Direct evidence for cyclic structures is essential in rationalizing the appearance of fragments with scrambled (i.e., permutated) primary structures, as the cycle may not open up where it was initially formed. It is demonstrated here that cyclic and linear a4 structures can interconvert freely as a result of collisional activation, implying that isomerization takes place prior to dissociation.     

Distinguishing Aspartic and Isoaspartic Acids in Peptides by Several Mass Spectrometric Fragmentation Methods

Six ion fragmentation techniques that can distinguish aspartic acid from its isomer, isoaspartic acid, were compared. MALDI post-source decay (PSD), MALDI 157 nm photodissociation, tris(2,4,6-trimethoxyphenyl)phosphonium bromide (TMPP) charge tagging in PSD and photodissociation, ESI collision-induced dissociation (CID), electron transfer dissociation (ETD), and free-radical initiated peptide sequencing (FRIPS) with CID were applied to peptides containing either aspartic or isoaspartic acid. Diagnostic ions, such as the y–46 and b+H₂O, are present in PSD, photodissociation, and charge tagging. c^?+57 and z–57 ions are observed in ETD and FRIPS experiments. For some molecules, aspartic and isoaspartic acid yield ion fragments with significantly different intensities. ETD and charge tagging appear to be most effective at distinguishing these residues.

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Difference estimates for continuous and discrete operator semigroups

For suitable bounded operator semigroups (e ^tA ) _t≥0 in a Banach space, we characterize the estimate ‖Ae ^tA ‖≤c/F(t) for large t, where F is a function satisfying a sublinear growth condition. The characterizations are by holomorphy estimates on the semigroup, and by estimates on powers of the resolvent. We give similar characterizations of the difference estimate ‖T ⁿ −T ⁿ⁺¹‖≤c/F(n) for a power-bounded linear operator T, when F(n) grows faster than n ^1/2 for large n.