Adaptive lambda square dynamics simulation: An efficient conformational sampling method for biomolecules

A novel, efficient sampling method for biomolecules is proposed. The partial multicanonical molecular dynamics (McMD) was recently developed as a method that improved generalized ensemble (GE) methods to focus sampling only on a part of a system (GEPS); however, it was not tested well. We found that partial McMD did not work well for polylysine decapeptide and gave significantly worse sampling efficiency than a conventional GE. Herein, we elucidate the fundamental reason for this and propose a novel GEPS, adaptive lambda square dynamics (ALSD), which can resolve the problem faced when using partial McMD. We demonstrate that ALSD greatly increases the sampling efficiency over a conventional GE. We believe that ALSD is an effective method and is applicable to the conformational sampling of larger and more complicated biomolecule systems. © 2013 Wiley Periodicals, Inc.     

Enhanced photoactivity of CdS nanorods by MXene and ZnSnO3: Application in photoelectrochemical biosensor for the effect of environmental pollutants on DNA hydroxymethylation in wheat tissues

The photoactivity of CdS nanorods was greatly improved by amino functionalized accordion-like MXene and spherical ZnSnO₃. MXene possesses good electron transfer capability and ZnSnO₃ presents matched energy band with CdS, which deeply accelerate the electron transfer and prevent the recombination of photogenerated electron-hole pair, leading to a strong photoelectrochemical (PEC) response. Taking the merit of the improved photoactivity of CdS nanorods, a novel PEC biosensor was constructed for DNA hydromethylation detection based on immune recognition of target molecule, where 5-hydroxymethyl-2′-deoxycytidine triphosphate (5hmdCTP) was employed as detect target, CdS/MXene was used as photoactive material, and ZnSnO₃ was adopted as signal amplification unit. Under enzymatic covalent reaction of –CH₂OH of 5hmdCTP with –NH₂ of MXene, 5hmdCTP was specifically recognized and captured. Then, taking advantages of the covalent reaction between phosphate group of 5hmdCTP and ZnSnO₃, the signal amplification unit was captured. Under the optimum conditions, this PEC biosensor presents wide linear range of 0.008–100 nM and low detection limit of 4.21 pM (3σ). The applicability of the developed method was evaluated by investigating the effect of Cd²⁺ and perfluorohexane compound pollutant on 5-hydroxymethylcytosine content in the genomic DNA of the roots and leaves of wheat seedlings.     

Localized surface plasmon resonance properties and biomedical applications of copper selenide nanomaterials

Nanomaterials with localized surface plasmon resonance (LSPR) locating in the near-infrared region have broad application prospects in the field of biomedicine. However, the biggest problem that limits the biomedical application of such nanomaterials lies in two aspects: First, the potential long-term in vivo toxicity caused by the metabolism of many nanomaterials with LSPR effect; Second, most of current nanomaterials with LSPR effect are difficult to achieve LSPR wavelength tunability in the near-infrared region to adapt to different biomedical applications. Copper selenide nanomaterials are composed of selenium and copper, which are necessary nutrient elements for human life. Because of the active and flexible chemical properties of selenium and copper, copper selenide nanomaterials can not only be effectively degraded and utilized in human body, but also be endowed with various physicochemical properties by chemical modification or doping. Recently, copper selenide nanomaterials have shown unique properties such as LSPR in the near-infrared region, making them attractive for near-infrared thermal ablation, photoacoustic imaging, disease marker detection, multimode imaging, and so on. Currently, to the best of our knowledge, there is no review on the LSPR properties of copper selenide nanomaterials and its biomedical applications. This review first discusses the relationship between the physicochemical properties and the LSPR of copper selenide nanomaterials and then summarizes the latest progress in the application of copper selenide nanomaterials in biological detection, diagnosis, and treatment of diseases. In addition, the advantages, and prospects of copper selenide nanomaterials in biomedicine are also highlighted.     

Experimental demonstration of the induction synchrotron

We report an experimental demonstration of the induction synchrotron, the concept of which has been proposed as a future accelerator for the second generation of neutrino factory or hadron collider. The induction synchrotron supports a superbunch and a superbunch permits more charge to be accelerated while observing the constraints of the transverse space-charge limit. By using a newly developed induction acceleration system instead of radio-wave acceleration devices, a single proton bunch injected from the 500 MeV booster ring and captured by the barrier bucket created by the induction step voltages was accelerated to 6 GeV in the KEK proton synchrotron.     

Palladium‐Catalyzed Direct CH Functionalization of Benzoquinone

A direct Pd‐catalyzed C? H functionalization of benzoquinone (BQ) can be controlled to give either mono‐ or disubstituted BQ, including the installation of two different groups in a one‐pot procedure. BQ can now be directly functionalized with aryl, heteroaryl, cycloalkyl, and cycloalkene groups and, moreover, the reaction is conducted in environmentally benign water or acetone as solvents.     

Synthesis and structure of novel 6-(pyrazol-1-yl)-4-methyl-1H-pyrazolo[3,4-b]pyridin-3-ol derivatives

New 6-(pyrazol-1-yl)pyrazolo[3,4-b]pyridin-3-ol compounds were synthesized by cyclization reaction from 2,6-dichloro-4-methylnicotinonitrile. Their derivatives exist as the 3-hydroxy tautomer. The structure of the compound 1a of one of the resulting compounds was studied in detail by X-ray diffraction.     

A Dual‐Ligand Porous Coordination Polymer Chemiresistor with Modulated Conductivity and Porosity

Single‐ligand‐based electronically conductive porous coordination polymers/metal–organic frameworks (EC‐PCPs/MOFs) fail to meet the requirements of numerous electronic applications owing to their limited tunability in terms of both conductivity and topology. In this study, a new 2D π‐conjugated EC‐MOF containing copper units with mixed trigonal ligands was developed: Cu₃(HHTP)(THQ) (HHTP=2,3,6,7,10,11‐hexahydrotriphenylene, THQ=tetrahydroxy‐1,4‐quinone). The modulated conductivity (σ≈2.53×10^?5 S cm^?1 with an activation energy of 0.30 eV) and high porosity (ca. 441.2 m² g^?1) of the Cu₃(HHTP)(THQ) semiconductive nanowires provided an appropriate resistance baseline and highly accessible areas for the development of an excellent chemiresistive gas sensor.     

High‐Tc Enantiomeric Ferroelectrics Based on Homochiral Dabco‐derivatives (Dabco=1,4‐Diazabicyclo[2.2.2]octane)

1,4‐Diazabicyclo[2.2.2]octane (dabco) and its derivatives have been extensively utilized as building units of excellent molecular ferroelectrics for decades. However, the homochiral dabco‐based ferroelectric remains a blank. Herein, by adding a methyl (Me) group accompanied by the introduction of homochirality to the [H₂dabco]²⁺ in the non‐ferroelectric [H₂dabco][TFSA]₂ (TFSA=bis(trifluoromethylsulfonyl)ammonium), we successfully designed enantiomeric ferroelectrics [R and S‐2‐Me‐H₂dabco][TFSA]₂. The two enantiomers show two sequential phase transitions with transition temperature (T_c) as high as 405.8 K and 415.8 K, which is outstanding in both dabco‐based ferroelectrics and homochiral ferroelectrics. To our knowledge, [R and S‐2‐Me‐H₂dabco][TFSA]₂ are the first examples of dabco‐based homochiral ferroelectrics. This finding opens an avenue to construct dabco‐based homochiral ferroelectrics and will inspire the exploration of more eminent enantiomeric molecular ferroelectrics.     

Aligning retention time shifts in HPLC three‐dimensional spectra by icoshift approach combined with data arrangement methods and the release of a graphical user interface

High‐performance liquid chromatography coupled with photodiode array detection has been extensively applied in many fields and the peaks among the analyzed samples can be shifted due to the variations of instrumental and experimental conditions. In multivariate analysis, retention time alignment is an important pretreatment step. Hence, the shifted peaks in high‐performance liquid chromatography coupled with photodiode array detection three‐dimensional spectra should be aligned for further analysis. Being motivated by this purpose, the interval correlated shifting method combined with the proposed data arrangement methods are recommended and employed on high‐performance liquid chromatography coupled with photodiode array detection data as a demonstration. We validate the alignment performance of the proposed method through comparison the consistency of the retention time before and after alignment. The obtained results demonstrated that the proposed method is capable of successful aligning the employed data. Additionally, the interval correlated shifting method combined with the data arrangement modes is implemented in an easy‐to‐use graphical user interface environment and so can be operated easily by users not familiar with programming languages.