DFT study on the nucleophilic addition reaction of water and ammonia to the thymine radical cation

The nucleophilic addition reactions of water and ammonia molecules toward the C5-C6 double bond of thymine radical cations were investigated using density functional theory. We predicted that the nucleophilic addition favored the C5-site of thymine radical cations, in contrast to the previous experimental observations in bulk solution where the addition product to the C6-site was dominant. Considering the molecular orbital factors, we estimated the relative reactivity of the C5- and C6-sites of thymine radical cations for the nucleophilic addition of ammonia. We found that the C5 was more reactive than the C6 for the small-size clusters of Thy1(NH3)n+, n = 0-2, in the gas phase and even in aqueous solution, though the difference in the reactivity between the two sites became smaller as the number of ammonia molecules increased. This variation of the reactivity was attributed to the electron density redistribution within the thymine radical cations induced by the ammonia molecules as a nucleophile. We suggest that the dominance of the C6-addition product in bulk solution is mainly due to the higher stability of the C6-addition product by solvation, rather than to the higher reactivity of the C6-site for the nucleophilic addition.     

Development of a data-mining methodology for spent nuclear fuel forensics

The purpose of this study is to categorize the type of spent nuclear fuels using simulation data-based classification methods. Considering the practical conditions making the full analysis of radioactive nuclides difficult, the classification methods were designed to be robust to noise and missing information. The strength and weakness of three classifiers, linear discriminant analysis, quadratic discriminant analysis and support vector classification were compared, which is developed by the history information such as burnup, enrichment, and cooling type generated from ORIGEN-ARP upon fuel assembly types. Auto-Associative Kernel Regression improved outlier management as a pre-processing technique.     

Sagnac interference in carbon nanotube loops

In this Letter we study electron interference in nanotube loops. The conductance as a function of the applied voltage is shown to oscillate due to interference between electron beams traversing the loop in two opposite directions, with slightly different velocities. The period of these oscillations with respect to the gate voltage, as well as the temperatures required for the effect to appear, are shown to be much larger than those of the related Fabry-Perot interference. We calculate interaction effects on the period of the oscillations, and show that even though interactions destroy much of the near degeneracy of velocities in the symmetric spin channel, the slow interference effects survive.     

Development of Imidazoline‐2‐Thiones Based Two‐Photon Fluorescence Probes for Imaging Hypochlorite Generation in a Co‐Culture System

We designed and prepared the imidazoline‐2‐thione containing OCl^? probes, PIS and NIS , which operate through specific reactions with OCl^? that yield corresponding fluorescent imidazolium ions. Importantly, we demonstrated that PIS can be employed to image OCl^? generation in macrophages in a co‐culture system. We have also employed two‐photon microscopy and PIS to image OCl^? in live cells and tissues, indicating that this probe could have wide biological applications.     

Hydrated alizarin complexes: hydrogen bonding and proton transfer

We investigated the hydrogen bonding structures and proton transfer for the hydration complexes of alizarin (Az) produced in a supersonic jet using fluorescence excitation (FE), dispersed laser induced fluorescence (LIF), visible-visible hole burning (HB), and fluorescence detected infrared (FDIR) spectroscopy. The FDIR spectrum of bare Az with two O-H groups exhibits two vibrational bands at 3092 and 3579 cm(-1), which, respectively, correspond to the stretching vibration of O1-H1 that forms a strong intramolecular hydrogen bond with the C9=O9 carbonyl group and the stretching vibration of O2-H2 that is weakly hydrogen-bonded to O1-H1. For the 1:1 hydration complex Az(H(2)O)(1), we identified three conformers. In the most stable conformer, the water molecule forms hydrogen bonds with the O1-H1 and O2-H2 groups of Az as a proton donor and proton acceptor, respectively. In the other conformers, the water binds to the C10=O10 group in two nearly isoenergetic configurations. In contrast to the sharp vibronic peaks in the FE spectra of Az and Az(H(2)O)(1), only broad, structureless absorption was observed for Az(H(2)O)(n) (n≥ 2), indicating a facile decay process, possibly due to proton transfer in the electronic excited state. The FDIR spectrum with the wavelength of the probe laser fixed at the broad band exhibited a broad vibrational band near the O2-H2 stretching vibration frequency of the most stable conformer of Az(H(2)O)(1). With the help of theoretical calculations, we suggest that the broad vibrational band may represent the occurrence of proton transfer by tunnelling in the electronic ground state of Az(H(2)O)(n) (n≥ 2) upon excitation of the O2-H2 vibration.     

Single-stage anaerobic codigestion for mixture wastes of simulated Korean food waste and waste activated sludge

Korean food waste was treated with a single-stage anaerobic codigester (SSAD) using waste activated sludge (WAS) generated from a municipal wastewater treatment plant. The stability and performance of the system was analyzed. The C/N ratio was improved with increasing food waste fraction of feed mixture. The pH, alkalinity, and free ammonia nitrogen concentration were the parameters used to evaluate the digester’s stability. The experimentally determined values of the parameters indicated that there were no methane inhibitions in the digester. Digester performance was determined by measuring the total chemical oxygen demand TCOD), volate solids (VS) removal, methane content in biogas, methane production rate (MPR), and specific methane productivity. Methane content in biogas and MPR were significantly dependent on hydraulic retention time (HRT) and ratio of food waste to WAS. The methane content in biogas decreased at shorter HRT or higher organic loading rate (OLR) with increased food waste fraction. Concerning the performance of the codigester, the optimum operating condition of the SSAD was found to be at an HRT of 10 d with a feed mixture ratio of 50% food waste and 50% WAS. A TCOD removal efficiency of 53.6% and a VS removal efficiency of 53.7% were obtained at an OLR of 5.96 kg of TCOD/(m³·d) and 3.14 kg of VS/(m³·d), respectively. A maximum MPR of 1.15 m³ CH₄/(m³·d) and an SMP of 0.37 m³ CH₄/kg of VS_feed were obtained at an HRT of 10 d with a methane content of 63%.     

Predicted structures and dynamics for agonists and antagonists bound to serotonin 5-HT2B and 5-HT2C receptors

Subtype 2 serotonin (5-hydroxytryptamine, 5-HT) receptors are major drug targets for schizophrenia, feeding disorders, perception, depression, migraines, hypertension, anxiety, hallucinogens, and gastrointestinal dysfunctions. (1) We report here the predicted structure of 5-HT2B and 5-HT2C receptors bound to highly potent and selective 5-HT2B antagonist PRX-08066 3, (pKi: 30 nM), including the key binding residues [V103 (2.53), L132 (3.29), V190 (4.60), and L347 (6.58)] determining the selectivity of binding to 5-HT2B over 5-HT2A. We also report structures of the endogenous agonist (5-HT) and a HT2B selective antagonist 2 (1-methyl-1-1,6,7,8-tetrahydro-pyrrolo[2,3-g]quinoline-5-carboxylic acid pyridine-3-ylamide). We examine the dynamics for the agonist- and antagonist-bound HT2B receptors in explicit membrane and water finding dramatically different patterns of water migration into the NPxxY motif and the binding site that correlates with the stability of ionic locks in the D(E)RY region.     

Transition metal ion directed supramolecular assembly of one- and two-dimensional polyrotaxanes incorporating cucurbituril

This paper reports a synthetic strategy to construct one- and two-dimensional (1D and 2D) polyrotaxanes, in which a number of rings are threaded onto a coordination polymer, by the combination of self-assembly and coordination chemistry. Our approach to construct polyrotaxanes with high structural regularity involves threading a cucurbituril (CB) "bead" with a short "string" to form a stable pseudorotaxane, followed by linking the pseudorotaxanes with metal ions as "linkers" to organize into a 1D or 2D polyrotaxane. A 4- or 3-pyridylmethyl group is attached to each end of 1,4-diaminobutane or 1,5-diaminopentane to produce the short "strings", which then react with the cucurbituril "bead" to form stable pseudorotaxanes. The reaction of the pseudorotaxanes with various transition metal ions including CuII, CoII, NiII, AgI, and CdII produces 1D or 2D polyrotaxanes, in which many molecular "beads" are threaded onto 1D or 2D coordination polymers as confirmed by X-ray crystallography. The overall structure of a polyrotaxane is the result of interplay among various factors that include the coordination preferences of the metal ion, spatial disposition of the donor atoms with respect to the CB beads in the pseudorotaxane, and the size and coordination ability of the counteranion.     

Controlled loading of cryoprotectants (CPAs) to oocyte with linear and complex CPA profiles on a microfluidic platform

Oocyte cryopreservation has become an essential tool in the treatment of infertility by preserving oocytes for women undergoing chemotherapy. However, despite recent advances, pregnancy rates from all cryopreserved oocytes remain low. The inevitable use of the cryoprotectants (CPAs) during preservation affects the viability of the preserved oocytes and pregnancy rates either through CPA toxicity or osmotic injury. Current protocols attempt to reduce CPA toxicity by minimizing CPA concentrations, or by minimizing the volume changes via the step-wise addition of CPAs to the cells. Although the step-wise addition decreases osmotic shock to oocytes, it unfortunately increases toxic injuries due to the long exposure times to CPAs. To address limitations of current protocols and to rationally design protocols that minimize the exposure to CPAs, we developed a microfluidic device for the quantitative measurements of oocyte volume during various CPA loading protocols. We spatially secured a single oocyte on the microfluidic device, created precisely controlled continuous CPA profiles (step-wise, linear and complex) for the addition of CPAs to the oocyte and measured the oocyte volumetric response to each profile. With both linear and complex profiles, we were able to load 1.5 M propanediol to oocytes in less than 15 min and with a volumetric change of less than 10%. Thus, we believe this single oocyte analysis technology will eventually help future advances in assisted reproductive technologies and fertility preservation.     

Multifunctional hybrid nanoconjugates for efficient in vivo delivery of immunomodulating oligonucleotides and enhanced antitumor immunity

A winning combination: Multifunctional hybrid nanoconjugates (HNCs) based on polymer nanoparticles containing quantum dots (QDs) conjugated with CpG oligonucleotides (as a ligand for TLR9) and STAT3 siRNAs (to suppress the immune response) have been synthesized. These HNCs were shown to synergistically enhance the antitumor immune response in dendritic cells and in tumor-bearing mice.