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Aqueous-phase formation of N-containing secondary organic compounds affected by the ionic strength

Journal of Environmental Sciences 2024年第4期138卷 88-101页

作者： Yuqi Gan Xiaohui Lu Shaodong Chen xinghua Jiang Shanye Yang Xiewen Ma Mei Li Fan Yang Yewen shi Xiaofei Wang Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention Department of Environmental Science and EngineeringFudan UniversityShanghai 200433China Shanghai Institute of Pollution Control and Ecological Security Shanghai 200092China Guangdong Provincial Observation and Research Station for Coastal Atmosphere and Climate of the Great Bay Area Southern University of Science and TechnologyShenzhen 518055China Institute of Mass Spectrometry and Atmospheric Environment Guangdong Provincial Engineering Research Center for On-line Source Apportionment System of Air PollutionJinan UniversityGuangzhouChina Environmental Monitoring Station of Pudong New District Shanghai 201200China Shanghai Municipal Center for Disease Control&Prevention Shanghai 200336China

The reaction of carbonyl-to-imine/hemiaminal conversion in the atmospheric aqueous phase is a critical pathway to produce the light-absorbing N-containing secondary organic compounds(SOC).The formation mechanism of these compounds has been wildly investigated in bulk solutions with a low ionic strength.However,the ionic strength in the aqueous phase of the polluted atmosphere may be higher.It is still unclear whether and to what extent the inorganic ions can affect the SOC formation.Here we prepared the bulk solution with certain ionic strength,in which glyoxal and ammonium were mixed to mimic the aqueous-phase reaction.Molecular characterization by High-resolution Mass Spectrometry was performed to identify the N-containing products,and the light absorption of the mixtures was measured by ultraviolet-visible spectroscopy.Thirty-nine N-containing compounds were identified and divided into four categories(N-heterocyclic chromophores,high-molecular-weight compounds with N-heterocycle,aliphatic imines/hemiaminals,and the unclassified).It was observed that the longer reaction time and higher ionic strength led to the formation of more N-heterocyclic chromophores and the increasing of the lightabsorbance of the mixture.The added inorganic ions were proposed to make the aqueous phase somewhat viscous so that the molecules were prone to undergo consecutive and intramolecular reactions to form the heterocycles.In general,this study revealed that the enhanced ionic strength and prolonged reaction time had the promotion effect on the lightabsorbing SOC formation.It implies that the aldehyde-derived aqueous-phase SOC would contribute more light-absorbing particulate matter in the industrial or populated area where inorganic ions are abundant.

关键词： Ionic strength Carbonyl-to-imine/hemiaminal Heterocyclic Brown carbon Mass spectrometry Aqueous-phase reaction

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Enhanced sampling in molecular dynamics simulations and their latest applications--A review

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Nano Research 2023年第12期16卷 13474-13497页

作者： Wenhui Shen Tong Zhou xinghua shi Laboratory of Theoretical and Computational Nanoscience National Center for Nanoscience and TechnologyBeijing 100190China University of Chinese Academy of Sciences Beijing 100049China

Molecular dynamics(MD)simulations are capable of reproducing dynamic evolution at the molecular scale,but are limited by temporal scales.Enhanced sampling has emerged as a powerful tool to improve sampling efficiency,thereby extending the simulation timescales of a range of simulation studies in materials,chemistry,biology,nanoscience,and related fields.Here,we provide a systematic overview of established enhanced sampling methods and clarify the principles and interconnections between these methods.Furthermore,we categorically elaborate on the state-of-the-art applications of enhanced sampling in the last five years.Through these exemplified applications,we discuss the unique advantages of this technique,showing the prospects and challenges for its future development.This review could help researchers in different fields gain a comprehensive understanding of the enhanced sampling technique,and jointly facilitate its application and advancement.

关键词： molecular dynamics enhanced sampling free energy barrier time scale biological system

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Alteration of the health effects of bioaerosols by chemical modification in the atmosphere:A review

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Fundamental Research 2024年第3期4卷 463-470页

作者： Ailin Li xinghua Qiu Xing Jiang Xiaodi shi Jinming Liu Zhen Cheng Qianqian Chai Tong Zhu State Key Joint Laboratory for Environmental Simulation and Pollution Control College of Environmental Sciences and EngineeringPeking UniversityBeijing 100871China

Bioaerosols are a subset of important airborne particulates that present a substantial human health hazard due to their allergenicity and infectivity.Chemical reactions in atmospheric processes can significantly influence the health hazard presented by bioaerosols;however,few studies have summarized such alterations to bioaerosols and the mechanisms involved.In this paper,we systematically review the chemical modifications of bioaerosols and the impact on their health effects,mainly focusing on the exacerbation of allergic diseases such as asthma,rhinitis,and bronchitis.Oxidation,nitration,and oligomerization induced by hydroxyl radicals,ozone,and nitrogen dioxide are the major chemical modifications affecting bioaerosols,all of which can aggravate allergenicity mainly through immunoglobulin E pathways.Such processes can even interact with climate change including the greenhouse effect,suggesting the importance of bioaerosols in the future implementation of carbon neutralization strategies.In summary,the chemical modification of bioaerosols and the subsequent impact on health hazards indicate that the combined management of both chemical and biological components is required to mitigate the health hazards of particulate air pollution.

关键词： Bioaerosols Allergenicity Chemical modification Airpollution Climate change

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Full reaction mechanism of hydrogen peroxide catalyzed by reductive CoP nanoparticles:the enzyme-like activity

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Science China Chemistry 2023年第4期66卷 1221-1227页

作者： Kaiwei Wan Chang Long Bing Jiang Minmin Liang Zhiyong Tang Hui Wang xinghua shi Laboratory of Theoretical and Computational Nanoscience CAS Key Laboratory of Nanosystem and Hierarchical FabricationCAS Center for Excellence in NanoscienceNational Center for Nanoscience and TechnologyChinese Academy of SciencesBeijing 100190China University of Chinese Academy of Sciences Beijing 100049China Molecular Electrochemistry Laboratory Institute of Fundamental and Frontier SciencesUniversity of Electronic Science and Technology of ChinaChengdu 610054China Experimental Center of Advanced Materials School of Materials Science&EngineeringBeijing Institute of TechnologyBeijing 100081China

The hydrogen peroxide(H2O2)catalyzed by nanoparticles(NPs)demonstrates potential broad applications in the field of biomedicine and environmental protection.However,a systematic understanding of the catalytic mechanism severely limited the rational design of NPs with better enzyme-like activity and selectivity.Here,compared with the widely concerned Fe3O4NPs,the decomposition process of H_(2)O_(2) on reductive Co P NPs and p H-regulated peroxidase-and catalase-like activities with 3,3′,5,5′-tetramethylbenzidine(TMB)as reductive substrates were explored.All results show that OH·radical intermediates generated from the decomposition of H2O2*/OOH*at acidic conditions and complexed with TMB via H-bonds(complexed OH·)are the principal oxidant of TMB rather than free OH·as reported.Besides,the produced O*/OH*on Co P NPs shows negligible oxidation activity due to the strong reducibility of catalysts.The high coverage of O*/OH*from the dissociation of H2O2(H2O)at neutral(alkaline)p H conditions on Co P NPs enhances the dehydrogenation of H_(2)O_(2) to O2,leading to the transition between peroxidase-and catalase-like activities.

关键词： CoP nanoparticle peroxidase,catalase DFT calculations heterogeneous catalysis

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Mechanics of molecular beacons for mRNA detecting

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Acta Mechanica Sinica 2021年第2期37卷 187-193页

作者： Yulong Gong xinghua shi Laboratory of Theoretical and Computational Nanoscience CAS Center for Excellence in NanoscienceNational Center for Nanoscience and TechnologyChinese Academy of Sciences.Beijing 100190China University of Chinese Academy of Sciences Beijing 100049China

Decoding genetic information is crucial for gene therapy and cancer diagnosis,which has attracted growing interest in the field of clinical medicine and life science.In this study,we conducted a comprehensive exploration to obtain the detection mechanism of molecular beacons from a mechanics point of view.The potential energy function of molecular beacon/target system is established firstly,based on which the profile of molecular beacons is solved by genetic algorithm optimization.The length of stem and the total energy are further calculated when the target is hybridized with loop and stem.The results show that the hybridization between target and stem is energetically favorable compared with that between target and loop,indicating a new detection strategy.These analyses may cast light on understanding the mechanism of molecular beacons detection,and further help to design novel molecular beacons with high resolution and quantification.

关键词： Molecular beacon Detection mechanism Finite deformation model Energy release rate

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Molecular dynamics simulation of diffusion of nanoparticles in mucus

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Acta Mechanica Solida Sinica 2017年第3期30卷 241-247页

作者： Jiuling Wang xinghua shi LNM Institute of Mechanics Chinese Academy of Sciences Beijing 100190 China CAS Key Laboratory for Nanosystem and Hierarchy Fabrication CAS Center for Excellence in Nanoscience National Center for Nanoscience and Technology Chinese Academy of Sciences Beijing 100190 China University of Chinese Academy of Sciences Beijing 100049 China

The rapid diffusion of nanoparticles （NPs） through mucus layer is critical for efficient transportation of NPs-loaded drug delivery system. To understand how the physical and surface properties of NPs affect their diffusion in mucus, we have developed a coarse-grained molecular dynamics model to study the diffusion of NPs in modeled mucus layer. Both steric obstruction and hydrodynamic interaction are included in the model capable of capturing the key characteristics of NPs＇ diffusion in mucus. The results show that both particle size and surface properties significantly affect the diffusivities of NPs in mucus. Furthermore, we find rodlike NPs can gain a higher diffusivity than spherical NPs with the same hydrodynamic diameter. In addition, the disturbed environment can enhance the diffusivity of NPs. Our findings can be utilized to design mucus penetrating NPs for targeted drug delivery system.

关键词： Nanoparticle diffusion Mucus penetration Fibrous medium Molecular dynamics simulation Drug delivery

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Identifying MicroRNA and Gene Expression Networks Using Graph Communities

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Tsinghua Science and Technology 2016年第2期21卷 176-195页

作者： Benika Hall Andrew Quitadamo xinghua shi Department of Bioinformatics University of North Carolina at CharlotteCharlotteNC 28213USA.

Integrative network analysis is powerful in helping understand the underlying mechanisms of genetic and epigenetic perturbations for disease studies. Although it becomes clear that microRNAs, one type of epigenetic factors, have direct effect on target genes, it is unclear how microRNAs perturb downstream genetic neighborhood. Hence, we propose a network community approach to integrate microRNA and gene expression profiles, to construct an integrative genetic network perturbed by microRNAs. We apply this approach to an ovarian cancer dataset from The Cancer Genome Atlas project to identify the fluctuation of microRNA expression and its effects on gene expression. First, we perform expression quantitative loci analysis between microRNA and gene expression profiles via both a classical regression framework and a sparse learning model. Then, we apply the spin glass community detection algorithm to find genetic neighborhoods of the microRNAs and their associated genes. Finally, we construct an integrated network between microRNA and gene expression based on their community structure. Various disease related microRNAs and genes, particularly related to ovarian cancer, are identified in this network. Such an integrative network allows us to investigate the genetic neighborhood affected by microRNA expression that may lead to disease manifestation and progression.

关键词： network integration graph community detection spin glass algorithm microRNA networks

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Single site catalyst with enzyme-mimic micro-environment for electroreduction of CO_(2)

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Nano Research 2022年第3期15卷 1817-1823页

作者： Chang Long Kaiwei Wan Xueying Qiu Xiaofei Zhang Jianyu Han Pengfei An Zhongjie Yang Xiang Li Jun Guo xinghua shi Hui Wang Zhiyong Tang Shaoqin Liu School of Materials Science and Engineering MOE Key Laboratory of Micro-systems and Micro-structures ManufacturingHarbin Institute of TechnologyHarbin150080China CAS key Laboratory of Nanosystem and Hierarchical Fabrication CAS Center for Excellence in NanoscienceNational Center for Nanoscience and TechnologyBeijing100190China University of Chinese Academy of Sciences Beijing100049China Institute of High Energy Physics CAS Beijing100049China

Single site catalysts provide a unique platform for mimicking natural enzyme due to their tunable interaction between metal center and coordinated ligand.However,most works have focused on preparing structural and functional models of nature enzyme,with less reports also taking the local chemical environment,i.e.,functional/catalytic residues around the active site which is an essential feature of enzymes,into consideration.Herein,we report a Co-centered porphyrinic polymer containing the enzyme-mimic micro-environment,where the linker triazole over CoN4 site enables formation of hydrogen bond with the*COOH intermediate,thus promoting the electrocatalytic reduction of CO_(2).As-prepared catalyst achieves the CO_(2)-to-CO conversion of 5,788 h^(−1) turnover frequency value and near unit(~96%)faradaic efficiency at−0.61 V versus reversible hydrogen electrode.This strategy will bring new dimension of designing highly active single-site catalysts.

关键词： single-site catalyst CO_(2)electroreduction enzyme-mimic

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Coarse grained molecular dynamics and theoretical studies of carbon nanotubes entering cell membrane

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Acta Mechanica Sinica 2008年第2期24卷 161-169页

作者： xinghua shi Yong Kong H. Gao Division of Engineering Brown University 182 Hope Street Providence RI 02912 USA ICx Radiation GmbH Koelnerstrasse 99 42651 Solingen Germany

Motivated by recent experimental observations that carbon nanotubes （CNT） can enter animal cells, here we conduct coarse grained molecular dynamics and theoretical studies of the intrinsic interaction mechanisms between CNT＇s and lipid bilayer. The results indicate that CNT-cell interaction is dominated by van der Waals and hydrophobic forces, and that CNT＇s with sufficiently small radii can directly pierce through cell membrane while larger tubes tend to enter cell via a wrapping mechanism. Theoretical models are proposed to explain the observed size effect in transition of entry mechanisms.

关键词： Molecular dynamics Carbon nanotube Cell membrane Interaction mechanism

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Molecular dynamics simulation of peeling a DNA molecule on substrate

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Acta Mechanica Sinica 2005年第3期21卷 249-256页

作者： xinghua shi Yong Kong Yapu Zhao Huajian Gao Max-Planck Institut für Metallforschung Heisenbergstr. 3 D-70569 Stuttgart Germany State Key Laboratory of Nonlinear Mechanics (LNM) Institute of Mechanics Chinese Academy of Sciences. Beijing 100080 China

Molecular dynamics （MD） simulations are performed to study adhesion and peeling of a short fragment of single strand DNA （ssDNA） molecule from a graphite surface. The critical peel-off force is found to depend on both the peeling angle and the elasticity of ssDNA. For the short ssDNA strand under investigation, we show that the simulation results can be explained by a continuum model of an adhesive elastic band on substrate. The analysis suggests that it is often the peak value, rather than the mean value, of adhesion energy which determines the peeling of a nanoscale material.

关键词： Molecular dynamics simulation DNA Adhesion Peeling

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