Efficient lookup table using a linear function of inverse distance squared

The major bottleneck in molecular dynamics (MD) simulations of biomolecules exist in the calculation of pairwise nonbonded interactions like Lennard‐Jones and long‐range electrostatic interactions. Particle‐mesh Ewald (PME) method is able to evaluate long‐range electrostatic interactions accurately and quickly during MD simulation. However, the evaluation of energy and gradient includes time‐consuming inverse square roots and complementary error functions. To avoid such time‐consuming operations while keeping accuracy, we propose a new lookup table for short‐range interaction in PME by defining energy and gradient as a linear function of inverse distance squared. In our lookup table approach, densities of table points are inversely proportional to squared pair distances, enabling accurate evaluation of energy and gradient at small pair distances. Regardless of the inverse operation here, the new lookup table scheme allows fast pairwise nonbonded calculations owing to efficient usage of cache memory. © 2013 Wiley Periodicals, Inc.     

Studies of Nucleophilic Substitution Reactions of p‐Nitrophenyl Acetate with Some Dihydroxamate Ions in Cationic Micellar Media

Pseudo‐first‐order rate constants have been determined for the nucleophilic substitution reactions of p‐nitrophenyl acetate with oxalo, malono, and succinodihydroxamate ions (^?ONHC(O)(CH₂)_nC(O)NHO^?) in phosphate buffer (pH=7.9) at 27°C. The rate data of the reaction revealed that the nucleophilic reactivity sequence of these hydroxamate ions is generally ODHA>MDHA>SDHA. The k_obs value increases upon addition of cationic surfactants to the reaction medium which is typical behavior of micelle‐assisted bimolecular reactions. The pseudo‐phase ion exchange model has been successfully applied to determine binding constant.     

Recyclable N-heterocyclic carbene/palladium catalyst on graphene oxide for the aqueous-phase Suzuki reaction

Graphene oxide (GO) was functionalized with a N-heterocyclic carbene (NHC) precursor, 3-(3-aminopropyl)-1-methylimidazolium bromide ([APMIm][Br]) for the immobilization of palladium catalyst. The GO-supported NHC precursor (IMGO) formed a stable complex with Pd(OAc)₂ (GO–NHC–Pd), which showed excellent catalytic activity and fast reaction kinetics in the aqueous-phase Suzuki reaction of aryl bromides and chlorides at relatively mild conditions (1 h at 50 °C). The GO–NHC–Pd catalyst was reused several times without any loss of its catalytic activity in the Suzuki reaction of aryl bromide.     

Precise characterization method of antibody‐conjugated magnetic nanoparticles for pathogen detection using stuffer‐free multiplex ligation‐dependent probe amplification

Antibody‐conjugated magnetic nanoparticles (Ab‐MNPs) have potential in pathogen detection because they allow target cells to be easily separated from complex sample matrices. However, the sensitivity and specificity of pathogen capture by Ab‐MNPs generally vary according to the types of MNPs, antibodies, and sample matrices, as well as preparation methods, including immobilization. Therefore, achieving a reproducible analysis utilizing Ab‐MNPs as a pathogen detection method requires accurate characterization of Ab‐MNP capture ability and standardization of all handling processes. In this study, we used high‐resolution CE‐single strand conformational polymorphism coupled with a stuffer‐free multiplex ligation‐dependent probe amplification system to characterize Ab‐MNPs. The capture ability of Ab‐MNPs targeting Salmonella enteritidis and nine pathogens, including S. enteritidis, was analyzed in phosphate buffer and milk. The effect of storage conditions on the stability of Ab‐MNPs was also assessed. The results showed that the stuffer‐free multiplex ligation‐dependent probe amplification system has the potential to serve as a standard characterization method for Ab‐MNPs. Moreover, the precise characterization of Ab‐MNPs facilitated robust pathogen detection in various applications.     

Editorial Board: Electrophoresis 10'14

Electrophoresis 2014, 35, 1504–1508. DOI: 10.1002/elps.201400001 Combination of DNA biobarcode assay with micro‐capillary electrophoretic analysis on a chip allows us to perform breast and colorectal cancer cell detection with high sensitivity, multiplexity, and accuracy.

     

Reaction-based colorimetric and fluorogenic signaling of hydrogen sulfide using a 7-nitro-2,1,3-benzoxadiazole–coumarin conjugate

A novel reaction-based probe for the dual signaling of hydrogen sulfide (H₂S) was investigated. The selective H₂S-induced cleavage of the ether linkage of the 7-nitro-2,1,3-benzoxadiazole (NBD) and 7-hydroxycoumarin conjugate resulted in a dual signaling behavior. The colorimetric and fluorogenic signaling behaviors were attributed to the H₂S-induced generation of 7-nitrobenzo-2,1,3-oxadiazole-4-thiol (NBD-SH) and 7-hydroxycoumarin, respectively. The signaling behavior was analyzed by ratiometry. The selective signaling of H₂S over other common metal ions and anions was possible with a detection limit of 1.6 × 10⁻⁶ M in an aqueous DMSO solution.     

Dual Sulfide–Disulfide Crosslinked Networks with Rapid and Room Temperature Self‐Healability

Polymer‐based crosslinked networks with intrinsic self‐repairing ability have emerged due to their built‐in ability to repair physical damages. Here, novel dual sulfide–disulfide crosslinked networks (s‐ssPxNs) are reported exhibiting rapid and room temperature self‐healability within seconds to minutes, with no extra healing agents and no change under any environmental conditions. The method to synthesize these self‐healable networks utilizes a combination of well‐known crosslinking chemistry: photoinduced thiol‐ene click‐type radical addition, generating lightly sulfide‐crosslinked polysulfide‐based networks with excess thiols, and their oxidation, creating dynamic disulfide crosslinkages to yield the dual s‐ssPxNs. The resulting s‐ssPxN networks show rapid self‐healing within 30 s to 30 min at room temperature, as well as self‐healing elasticity with reversible viscoelastic properties. These results, combined with tunable self‐healing kinetics, demonstrate the versatility of the method as a new means to synthesize smart multifunctional polymeric materials.