Atomic-scale imaging and spectroscopy for in situ liquid scanning transmission electron microscopy

Observation of growth, synthesis, dynamics, and electrochemical reactions in the liquid state is an important yet largely unstudied aspect of nanotechnology. The only techniques that can potentially provide the insights necessary to advance our understanding of these mechanisms is simultaneous atomic-scale imaging and quantitative chemical analysis (through spectroscopy) under environmental conditions in the transmission electron microscope. In this study we describe the experimental and technical conditions necessary to obtain electron energy loss (EEL) spectra from a nanoparticle in colloidal suspension using aberration-corrected scanning transmission electron microscopy (STEM) combined with the environmental liquid stage. At a fluid path length below 400 nm, atomic resolution images can be obtained and simultaneous compositional analysis can be achieved. We show that EEL spectroscopy can be used to quantify the total fluid path length around the nanoparticle and demonstrate that characteristic core-loss signals from the suspended nanoparticles can be resolved and analyzed to provide information on the local interfacial chemistry with the surrounding environment. The combined approach using aberration-corrected STEM and EEL spectra with the in situ fluid stage demonstrates a plenary platform for detailed investigations of solution-based catalysis.     

Ab initio molecular dynamics using hybrid density functionals

Ab initio molecular dynamics simulations with hybrid density functionals have so far found little application due to their computational cost. In this work, an implementation of the Hartree-Fock exchange is presented that is specifically targeted at ab initio molecular dynamics simulations of medium sized systems. We demonstrate that our implementation, which is available as part of the CP2K/Quickstep program, is robust and efficient. Several prescreening techniques lead to a linear scaling cost for integral evaluation and storage. Integral compression techniques allow for in-core calculations on systems containing several thousand basis functions. The massively parallel implementation respects integral symmetry and scales up to hundreds of CPUs using a dynamic load balancing scheme. A time-reversible multiple time step scheme, exploiting the difference in computational efficiency between hybrid and local functionals, brings further time savings. With extensive simulations of liquid water, we demonstrate the ability to perform, for several tens of picoseconds, ab initio molecular dynamics based on hybrid functionals of systems in the condensed phase containing a few thousand Gaussian basis functions.     

A Dissipative Reaction Network Drives Transient Solid–Liquid and Liquid–Liquid Phase Cycling of Nanoparticles

Transient states maintained by energy dissipation are an essential feature of dynamic systems where structures and functions are regulated by fluxes of energy and matter through chemical reaction networks. Perfected in biology, chemically fueled dissipative networks incorporating nanoscale components allow the unique properties of nanomaterials to be bestowed with spatiotemporal adaptability and chemical responsiveness. We report the transient dispersion of gold nanoparticles in water, powered by dissipation of a chemical fuel. A dispersed state that is generated under non-equilibrium conditions permits fully reversible solid–liquid or liquid–liquid phase transfer. The molecular basis of the out-of-equilibrium process is reversible covalent modification of nanoparticle-bound ligands by a simple inorganic activator. Activator consumption by a coupled dissipative reaction network leads to autonomous cycling between phases. The out-of-equilibrium lifetime is tunable by adjusting the pH value, and reversible phase cycling is reproducible over several cycles.     

Formation and control of Turing patterns and phase fronts in photonics and chemistry

We review the main mechanisms for the formation of regular spatial structures (Turing patterns) and phase fronts in photonics and chemistry driven by either diffraction or diffusion. We first demonstrate that the so-called ‘off-resonance’ mechanism leading to regular patterns in photonics is a Turing instability. We then show that negative feedback techniques for the control of photonic patterns based on Fourier transforms can be extended and applied to chemical experiments. The dynamics of phase fronts leading to locked lines and spots are also presented to outline analogies and differences in the study of complex systems in these two scientific disciplines.     

Magnetic nanomaterials catalyzed synthesis of tetrazoles

Abstract

Tetrazoles are valuable molecules in pharmaceutical and agriculture chemistry, because they are excited in many drugs, natural products and biologically active molecules. During the last decade, magnetic nanomaterials have appeared as highly efficient catalysts in chemical science in general organic chemistry, because of their simple preparation, modification, and large surface area ratio. In this paper, we provide an overview of the utilization of magnetic nanomaterials as attractive and efficient catalytic systems in synthesis of biologically active tetrazoles.     

Bioorthogonal chemistry: a covalent strategy for the study of biological systems

The development of genetically encoded, wavelength-tunable fluorescent proteins has provided a powerful imaging tool to the study of protein dynamics and functions in cellular and organismal biology. However, many biological functions are not directly encoded in the protein primary sequence, e.g., dynamic regulation afforded by protein posttranslational modifications such as phosphorylation. To meet this challenge, an emerging field of bioorthogonal chemistry has promised to offer a versatile strategy to selectively label a biomolecule of interest and track their dynamic regulations in its native habitat. This strategy has been successfully applied to the studies of all classes of biomolecules in living systems, including proteins, nucleic acids, carbohydrates, and lipids. Whereas the incorporation of a bioorthogonal reporter site-selectively into a biomolecule through either genetic or metabolic approaches has been well established, the development of bioorthogonal reactions that allow fast ligation of exogenous chemical probes with the bioorthogonal reporter in living systems remains in its early stage. Here, we review the recent development of bioorthogonal reactions and their applications in various biological systems, with a detailed discussion about our own work—the development of the tetrazole based, photoinducible 1,3-dipolar cycloaddition reaction.     

Synthesis and assembly of rare earth nanostructures directed by the principle of coordination chemistry in solution-based process

In this review, several typical nanomaterials are selected to demonstrate the coordination effect on the control of structure/microstructure/texture, surface/interface, particle size and morphology. Based on the principle of coordination chemistry, with some solution-based methods including solvothermal treatment and the thermolysis of metal complex precursors, a series of novel nanostructured rare earth compounds, such as ultra-small colloidal ceria nanoparticles, highly homogenous and stable ceria–zirconia solid solutions, and high-quality rare earth oxide and fluoride nanocrystals, etc., have been prepared by elaborately controlling the synthetic parameters and reaction kinetics. In order to reveal the mechanisms of synthesis, assembly, and properties, the phase, microstructure, texture, and surface state have been characterized systematically. The main applications of coordination chemistry principle in the synthesis and assembly of rare earth nanocrystals have been summarized, which also can be extended to direct the fabrication of other nanomaterials.     

Lyotropic self-assembly of high-aspect-ratio semiconductor nanowires of single-crystal ZnO

Lyotropic nanowire dispersions are attractive precursors for semiconductor device fabrication because they permit the alignment control of active nanomaterials. The reliable production of nanowire-based mesophases, however, is very challenging in practice. We show that appropriately functionalized high-aspect-ratio nanowires of single-crystal ZnO spontaneously form nematic phases in organic and aqueous media. These systems show isotropic, biphasic, and nematic phases on increasing concentration, in reasonable agreement with Onsager's theory for rigid rods interacting via excluded volume. Suspensions were readily processed to produce films with large-area monodomains of aligned nanowires. Imprints of the director field in quiescently dried films display a propensity for bend deformation in the organic mesophase versus splay deformation in the aqueous case, suggesting that system elasticity may be tuned via surface functionalization. These results provide critical insight for the utilization of semiconductor nanowires as novel mesogens and further enable the use of solution-based routes for fabricating optoelectronic devices.     

Transient Metallo-Lipidoid Assemblies Amplify Covalent Catalysis of Aqueous and Non-Aqueous Reactions

Dissipative supramolecular assemblies are hallmarks of living systems, contributing to their complex, dynamic structures and emerging functions. Living cells can spatiotemporally control diverse biochemical reactions in membrane compartments and condensates, regulating metabolite levels, signal transduction or remodeling of the cytoskeleton. Herein, we constructed membranous compartments using self-assembly of lipid-like amphiphiles (lipidoid) in aqueous medium. The new double-tailed lipidoid features Cu(II) coordinated with a tetravalent chelator that dictates the binding of two amphiphilic ligands in cis-orientation. Hydrophobic interactions between the lipidoids coupled with intermolecular hydrogen bonding led to a well-defined bilayer vesicle structure. Oil-soluble S_NAr reaction is efficiently upregulated in the hydrophobic cavity, acting as a catalytic crucible. The modular system allows easy incorporation of exposed primary amine groups, which augments the catalysis of retro aldol and C−N bond formation reactions. Moreover, a higher-affinity chelator enables consumption of the Cu(II) template leveraging the differential thermodynamic stability, which allows a controllable lifetime of the vesicular assemblies. Concomitant temporal upregulation of the catalytic reactions could be tuned by the metal ion concentration. This work offers new possibilities for metal ion-mediated dynamic supramolecular systems, opening up a massive repertoire of functionally active dynamic “life-like” materials.     

Photoelectromagnetic Responsive Adaptive Porous Frameworks through Dynamic Covalent Chemistry of Tetraarylethylene-backboned Aryldicyanomethyl Radicals

Dynamic materials undergoing adaptive solid-state transitions are attractive for soft mechanics and information technology. Here, we report a novel porous framework system based on macrocyclic trimers assembled from open-shell tetraarylethylene building blocks with aryldicyanomethyl radicals as coupling linkers. Under mechanical, thermal, or chemical stimuli, the framework showed adaptability by activating conformational dynamics and radical-based transformations, thus displaying macroscopic responsiveness in terms of light absorption, luminescence, and magnetism. We studied the dynamic processes by variable-temperature nuclear magnetic resonance (VT-NMR), variable-temperature electron spin resonance (VT-ESR), and superconducting quantum interference device (SQUID) measurement and further established a proof-of-concept application for multi-modal information encryption. The strategy may open avenues for rational design of solid-state photoelectromagnetic dynamic materials by merging dynamic covalent coupling chemistry and functional aggregation principles.     

Multiphase microfluidics: from flow characteristics to chemical and materials synthesis

We review transport characteristics of pressure-driven, multiphase flows through microchannel networks tens of nanometres to several hundred of micrometres wide with emphasis on conditions resulting in enhanced mixing and reduced axial dispersion. Dimensionless scaling parameters useful in characterizing multiphase flows are summarized along with experimental flow visualization techniques. Static and dynamic stability considerations are also included along with methods for stabilizing multiphase flows through surface modifications. Observed gas-liquid and immiscible liquid-liquid flows are summarized in terms of flow regime diagrams and the different flows are related to applications in chemistry and materials synthesis. Means to completely separate multiphase flows on the microscale and guidelines for design of scalable multiphase systems are also discussed.     

In Situ Visualization of Block Copolymer Self‐Assembly in Organic Media by Super‐Resolution Fluorescence Microscopy

Analytical methods that enable visualization of nanomaterials derived from solution self‐assembly processes in organic solvents are highly desirable. Herein, we demonstrate the use of stimulated emission depletion microscopy (STED) and single molecule localization microscopy (SMLM) to map living crystallization‐driven block copolymer (BCP) self‐assembly in organic media at the sub‐diffraction scale. Four different dyes were successfully used for single‐colour super‐resolution imaging of the BCP nanostructures allowing micelle length distributions to be determined in situ. Dual‐colour SMLM imaging was used to measure and compare the rate of addition of red fluorescent BCP to the termini of green fluorescent seed micelles to generate block comicelles. Although well‐established for aqueous systems, the results highlight the potential of super‐resolution microscopy techniques for the interrogation of self‐assembly processes in organic media.     

Computational Chemistry techniques: covering orders of magnitude in space, time, and accuracy

Computational Chemistry is the branch of chemistry which uses extensively computer models to simulate real systems. Model systems are made to fit the real system in intended respects and with the intended accuracy of the creator or user of the model. The building blocks of model systems and the interactions between them are abstractions of the building blocks of real system and the interactions between them. In computer models a system must be represented by data which are stored in data structures, the interactions between them are represented by mathematical functions or sets of rules. Properties of the model system are calculated with various algorithms, both numerical and non-numerical. A computational chemist must decide which computer model is best suited to represent a real system so that its essential properties can be simulated as intended. Doing computational chemistry means to apply the right computer models to describe a real system or, if necessary, design new computer models.     

The chemistry of organic nanomaterials

The development of nanotechnology using organic materials is one of the most intellectually and commercially exciting stories of our times. Advances in synthetic chemistry and in methods for the investigation and manipulation of individual molecules and small ensembles of molecules have produced major advances in the field of organic nanomaterials. The new insights into the optical and electronic properties of molecules obtained by means of single-molecule spectroscopy and scanning probe microscopy have spurred chemists to conceive and make novel molecular and supramolecular designs. Methods have also been sought to exploit the properties of these materials in optoelectronic devices, and prototypes and models for new nanoscale devices have been demonstrated. This Review aims to show how the interaction between synthetic chemistry and spectroscopy has driven the field of organic nanomaterials forward towards the ultimate goal of new technology.     

Ab Initio Nonadiabatic Dynamics of Semiconductor Materials via Surface Hopping Method

Photoinduced carrier dynamic processes are without doubt the main driving force responsible for the efficient performance of semiconductor nanomaterials in applications like photoconversion and photonics. Nevertheless, establishing theoretical insights into these processes is computationally challenging owing to the multiple factors involved in the processes, namely reaction rate, material surface area, material composition etc. Modelling of photoinduced carrier dynamic processes can be performed via nonadiabatic molecular dynamics (NA-MD) methods, which are methods specifically designed to solve the time-dependent Schrodinger equation with the inclusion of nonadiabatic couplings. Among NA-MD methods, surface hopping methods have been proven to be a mighty tool to mimic the competitive nonadiabatic processes in semiconductor nanomaterials, a worth noticing feature is its exceptional balance between accuracy and computational cost. Consequently, surface hopping is the method of choice for modelling ultrafast dynamics and more complex phenomena like charge separation in Janus transition metal dichalcogenides-based van der Waals heterojunction materials. Covering latest stateof-the-art numerical simulations along with experimental results in the field, this review aims to provide a basic understanding of the tight relation between semiconductor nanomaterials and the proper simulation of their properties via surface hopping methods. Special stress is put on emerging state-ot-the-art techniques. By highlighting the challenge imposed by new materials, we depict emerging creative approaches, including high-level electronic structure methods and NA-MD methods to model nonadiabatic systems with high complexity.     

Photochemical Mechanisms of Fluorophores Employed in Single-Molecule Localization Microscopy

Decoding cellular processes requires visualization of the spatial distribution and dynamic interactions of biomolecules. It is therefore not surprising that innovations in imaging technologies have facilitated advances in biomedical research. The advent of super-resolution imaging technologies has empowered biomedical researchers with the ability to answer long-standing questions about cellular processes at an entirely new level. Fluorescent probes greatly enhance the specificity and resolution of super-resolution imaging experiments. Here, we introduce key super-resolution imaging technologies, with a brief discussion on single-molecule localization microscopy (SMLM). We evaluate the chemistry and photochemical mechanisms of fluorescent probes employed in SMLM. This Review provides guidance on the identification and adoption of fluorescent probes in single molecule localization microscopy to inspire the design of next-generation fluorescent probes amenable to single-molecule imaging.     

Real-time monitoring of cell migration,phagocytosis and cell surface receptor dynamics using a novel,live-cell opto-microfluidic technique

We report an opto-microfluidic method for continuous and non-interfering monitoring of cell movement and dynamic molecular processes in living cells enabled by the microfluidic “Lab-in-a-Trench” (LiaT) platform. To demonstrate real-time monitoring of heterogeneous cell–cell interactions, cell tracking and agent-induced cell activation dynamics, we observe phagocytosis of Escherichia coli by murine macrophages, migration of active macrophages and LPS-induced CD86 expression in macrophages. The visualization of phagocytosis is facilitated through the loading of green fluorescent protein (GFP) expressing E. coli to the array of cell capture modules before the introduction of macrophages. Simple migration tracking of active macrophages is enabled by a spatio-temporal control of the environment conditions within the LiaT platform. Furthermore, we report an interference-free monitoring of non-modified, endogenous changes in protein expression on the surface of living cells using traditional, antibody immuno-reagents. Throughout the experiment, murine macrophages were captured in the LiaT device and exposed to sub-background levels of fluorescently labeled anti-CD86 antibody. Upon lipopolysaccharide (LPS) stimulation, CD86 changes were visualized in real-time by time-lapse microscopy. This novel opto-microfluidic effect is controlled by the equilibrium of convective–diffusive replenishment of fluorescently labeled antibodies and antibody affinity. Overall, our non-interfering analysis method allows the studying of active cellular processes and endogenous protein dynamics in live cells in a simple and cost-efficient manner.     

Physical Chemistry of Cellular Liquid-Phase Separation

Compartmentalization of biochemical processes is essential for cell function. Although membrane-bound organelles are well studied in this context, recent work has shown that phase separation is a key contributor to cellular compartmentalization through the formation of liquid-like membraneless organelles (MLOs). In this Minireview, the key mechanistic concepts that underlie MLO dynamics and function are first briefly discussed, including the relevant noncovalent interaction chemistry and polymer physical chemistry. Next, a few examples of MLOs and relevant proteins are given, along with their functions, which highlight the relevance of the above concepts. The developing area of active matter and non-equilibrium systems, which can give rise to unexpected effects in fluctuating cellular conditions, are also discussed. Finally, our thoughts for emerging and future directions in the field are discussed, including in vitro and in vivo studies of MLO physical chemistry and function.     

Trialkoxysilane Exchange: Scope,Mechanism, Cryptates and pH-Response

The dynamic covalent chemistry (DCvC) of the Si−O bond holds unique opportunities, but has rarely been employed to assemble discrete molecular architectures. This may be due to the harsh conditions required to initiate exchange reactions at silicon in aprotic solvents. Herein, we provide a comprehensive experimental and computational account on the reaction of trialkoxysilanes with alcohols and identify mild conditions for rapid exchange in aprotic solvents. Substituent, solvent and salt effects are uncovered, understood and exploited for the construction of sila-orthoester cryptates. A sharp, divergent pH-response of the obtained cages renders this substance class attractive for future applications well beyond host-guest chemistry, for instance, in drug delivery.