Net charge changes in the calculation of relative ligand‐binding free energies via classical atomistic molecular dynamics simulation

The calculation of binding free energies of charged species to a target molecule is a frequently encountered problem in molecular dynamics studies of (bio‐)chemical thermodynamics. Many important endogenous receptor‐binding molecules, enzyme substrates, or drug molecules have a nonzero net charge. Absolute binding free energies, as well as binding free energies relative to another molecule with a different net charge will be affected by artifacts due to the used effective electrostatic interaction function and associated parameters (e.g., size of the computational box). In the present study, charging contributions to binding free energies of small oligoatomic ions to a series of model host cavities functionalized with different chemical groups are calculated with classical atomistic molecular dynamics simulation. Electrostatic interactions are treated using a lattice‐summation scheme or a cutoff‐truncation scheme with Barker–Watts reaction‐field correction, and the simulations are conducted in boxes of different edge lengths. It is illustrated that the charging free energies of the guest molecules in water and in the host strongly depend on the applied methodology and that neglect of correction terms for the artifacts introduced by the finite size of the simulated system and the use of an effective electrostatic interaction function considerably impairs the thermodynamic interpretation of guest‐host interactions. Application of correction terms for the various artifacts yields consistent results for the charging contribution to binding free energies and is thus a prerequisite for the valid interpretation or prediction of experimental data via molecular dynamics simulation. Analysis and correction of electrostatic artifacts according to the scheme proposed in the present study should therefore be considered an integral part of careful free‐energy calculation studies if changes in the net charge are involved. © 2013 The Authors Journal of Computational Chemistry Published by Wiley Periodicals, Inc.     

化学工程:从基础研究到工业应用

本文介绍了我国中长期发展规划中所制定的化学化工学科发展目标,综述了化学工程学科近十余年来在队伍建设、平台建设和国家级奖励等方面所取得的成果,列举了若干化学工程在传递与过程强化、化工分离过程、精细与药物化工、能源化工和材料化工领域从基础研究到工业化应用的例子和成果,展望了化学工程学科今后发展的方向及目标.     

辉光放电质谱技术应用进展

对辉光放电质谱(GDMS)在金属与半导体、非导体、薄层与深度分析、分子信息分析方面的应用和一些新装置、新方法进行了综述.着重介绍了近20年来我国学者在辉光放电质谱方面的成就,并结合国际上的报道对该领域的发展现状进行了总结.     

基于思维模型建构的高三化学复习教学*—— 以“平衡原理的应用”为例

以高三复习课“平衡原理的应用”为例,通过真实情境的剖析让学生感知模型,引导学生分析归纳提炼模型,并进行针对练习运用模型,变式训练体会模型,让学生在实践中以模型思维为突破,深入领悟建构模型的实质,有序解决复杂化学问题,提升科学思维能力,发展化学学科核心素养。     

单原子材料类酶催化及生物医学应用研究进展

纳米酶因其经济、 稳定、 性质可调和可循环利用等诸多优势, 成功地克服了天然酶在实际应用中的不足. 单原子材料的出现使得对纳米酶的研究迈入原子水平, 其较高的原子利用率、 独特的配位环境和较强的金属-载体相互作用为揭示纳米酶构效关系及调控类酶活性提供了可能. 本文总结了近年来单原子材料类酶催化的研究进展, 重点讨论了单原子材料类酶活性的调控策略和催化机理, 概述了单原子类酶材料在癌症治疗、 抗氧化治疗、 抗菌以及生物传感等方面的应用, 并对单原子类酶材料的发展前景进行了展望.     

低共熔溶剂的应用研究现状

低共熔溶剂是两种或多种固体或液体物质通过氢键相互作用形成的液体溶剂,其熔点明显低于单一组分的熔点。与传统离子液体相比,低共熔溶剂成本更低,制备更容易,可生物降解,具有100%原子利用率和生物相容性及无毒无害等绿色特性,这些优点使其在许多研究领域被广泛研究。本文介绍了低共熔溶剂的最新分类,综述了低共熔溶剂在电化学、气体吸收、有机合成、功能材料合成、萃取分离、药物增溶及生物质预处理中的应用,并对低共熔溶剂的未来发展进行了展望。     

基于MXenes的功能纤维的制备及其在智能可穿戴领域的应用

在电子信息和物联网技术的推动下,人类对可穿戴电子器件和智能织物的需求愈发突出,功能纤维作为智能可穿戴设备的重要载体,近年来获得快速发展。功能纤维的性能很大程度上取决于纤维的基础构筑单元。过渡金属碳/氮化物(MXenes)作为一种新兴的二维材料,凭借其高电导率、优异的可加工性能、可调节的表面特性以及出色的机械强度等优点,受到了极大的关注,也逐渐成为构筑功能纤维的重要单元。本文将主要综述MXenes的湿化学、熔融盐、无氟试剂刻蚀等方法和力学、电学、光学和化学稳定性等性能,阐述基于该材料制备的功能纤维在传感、储能以及其他智能领域的应用,最后讨论了基于MXenes材料的功能纤维的未来应用前景和技术挑战。     

A Highly Sensitive and Selective Label-free Electrochemical Biosensor with a Wide Range of Applications for Bisphenol A Detection

A label-free DNA-based electrochemical biosensor owning high sensitivity and selectivity has been established for detecting bisphenol A in a wide range of applications. Coupling the high electrochemical performance of graphene oxide-thionine-Au nanomaterial with the specific binding capacity of the aptamers to BPA, the monitoring of trace amount of BPA was realized, the detection limit was 3.3 pg ⋅ mL⁻¹ with strong anti-interference. Besides, using molecular docking, it was found that BPA binds to the bases DC-49, DC-51, DG-52, DG-53 and DA-63 on the aptamer via hydrogen bonding and π-π stacking interactions. Finally, the biosensor had been successfully applied in different real samples.     

Green synthesis and characterization of copper and nickel hybrid nanomaterials: Investigation of their biological and photocatalytic potential for the removal of organic crystal violet dye

Nanotechnology deals with the materials at nanoscale to synthesize nanoparticles. The current study introduced a new green approach for the synthesis of Copper and Nickel hybrid nanoparticles by using Zingiber officinale rhizome extract as a capping and reducing agent. The nanoparticles were physico-chemically characterized by UV–visible spectroscopy, Fourier transform infrared spectroscopy, X-ray powder diffraction, Energy-dispersive X-ray spectroscopy, and Scanning electron microscopy. It was revealed by scanning electron micrograph that the Cu-Ni hybrid nanoparticles have spherical geometries with average grain size of 25.12 ± 1.2 nm. Furthermore, biocatalytic and photocatalytic applications of the biosynthesized nanoparticles were assessed. The results of antibacterial assay revealed that Cu-Ni hybrid nanoparticles had an inhibition zones of 28 ± 1.0, 25 ± 0.8, and 25 ± 1.5 mm against P. aeruginosa, E. coli and Proteus vulgaris. Commercially available antibiotics were purchased and coated with Cu-Ni hybrid nanoparticles, it was found that their antimicrobial efficacy was increased twice. To evaluate the antioxidant potential, nanoparticles having a concentration of 200 µg/mL were applied against 2,2-diphenyl-1-picrylhydrazyl free radicals and NPs showed 42.1 ± 0.71 % inhibition. Cu-Ni nanoparticles have shown a dose-dependent cytotoxicity against amastigote and promastigote in anti-leishmanial assay. The synthesized nanoparticles were found biocompatible and safe in nature to be used in vivo, as they showed no significant hemolysis of human red blood cells at their highest concentration. In antidiabetic assay, NPs inhibited alpha-amylase enzyme up to 38.07 ± 0.65 %. An organic crystal violet dye was successfully degraded by the synthesized nanoparticles in photocatalytic assay. Hence, it is concluded that Cu-Ni hybrid nanoparticles can be used both in vitro and in vivo for drug delivery in biomedical research. These nanoparticles can also be used in the remediation of organic dyes as a catalyst.