Chemically Fueled Autonomous Sol→Gel→Sol→Gel→Sol Transitions

Complex non-equilibrium phase behaviors are a hallmark of natural self-assembling systems. Here we show how intricate phase transitions can be achieved through a chemically fueled reaction cycle to yield autonomous sol→gel→sol→gel→sol transitions. A relay of chemical transformations based on thiazinane metathesis leads to two consecutive transient gelations in a closed system. Within seconds of fuel addition to deactivated thiazinane monomers, an imine-based hydrogel forms that consists of fibrillar microspheres. This gel quickly loses its mechanical strength and forms a solution, from which a second aldehyde-based gel nucleates and remains stable for over one day. Overall, our reaction cycle gives rise to two consecutive re-entrant phase transitions without any experimental intervention.     

Chemically artificial rovers based on self-propelled droplets in micrometer-scale environment

Self-propelled droplets made of organic materials can be an influential candidate for understanding cell migration from the viewpoint of nonequilibrium physics and have attracted significant attention with regard to soft-matter-type rovers. Because self-propelled droplets are soft enough to be easily deformed, they should be useful as chemically artificial rovers that can move in small areas with many obstacles in water and can be applied as ‘motile’ carriers for exploring and curing of biological bodies or remediation of the natural environment. Here, we review recent research progress on designing self-propelled droplets of micrometer size.     

Chemically Produced Excited States

Electronically excited states of organic molecules are formed in many chemical reactions. Such chemically produced excited states are (with one exception) identical to light produced excited states, and they undergo the molecular transformations expected of such states (“photochemistry without light”). The excited states can also be used in energy transfer experiments. This review covers the generation of chemically produced excited states, the chemical reactions they undergo, and the possible role of chemically produced excited states in biology.     

Plant protein-polysaccharide interactions in solutions: application of soft particle analysis and light scattering measurements

The soft particle analysis theory was applied to plant proteins and polysaccharides in solution, to determine the charge density of these polymers and the depth of the layer accessible by counterions according to pH conditions. In addition to the macromolecule shape characterized by light scattering measurements, these properties are also correlated with the optimum coacervation condition, so as to establish the prevalent plant protein-polysaccharide interactions governing the coacervate formation. Globulin was found to be highly charged and spherically shaped. The best coacervation condition was obtained at the pH value, which corresponds to the protein conformation with a dense and compact accessible layer. On the contrary, for the alpha gliadin, bearing a lower charge, a more extended conformation seems to be more favourable. For the plant proteins studied, the coacervation seems to be controlled by the structure of the counter polyanion used: from our model, it turns out that the rod-like structure of arabic gum observed at acidic pH allows the interaction with plant proteins to form coacervates, contrary to the highly charged and spherical structure of alginate.     

Electric Potential and Reaction Rates at Charged Surfaces in Asymmetric Electrolytes-An Analytic Approach

The electric potential and reaction rates of ions hitting the chemically active surfaces of microcrystals in an asymmetric electrolyte are computed analytically. Following ideas of Debye we start by solving the Poisson-Boltzmann equations and by determining the electric potential of the transport equations. We find distinct deviations when comparing our result with the Gouy-Chapman formula. In a simple model approximating a situation in which lead and hydrogen ions can react at goethite surfaces we compute analytically the currents of ions diffusing to the surfaces of microcrystals where they undergo a chemical reaction. We compute the reaction rates that can be controlled either by chemical reactions at the surface of the microcrystals or by diffusional transport. For realistic parameters of our model we find that the diffusional transport is the rate determining step. Copyright 2001 Academic Press.     

Fusion and sorting of two parallel trains of droplets using a railroad-like channel network and guiding tracks

We propose a robust droplet fusion and sorting method for two parallel trains of droplets that is relatively insensitive to frequency and phase mismatch. Conventional methods of droplet fusion require an extremely precise control of aqueous/oil flows for perfect frequency matching between two trains of droplets. In this work, by combining our previous two methods (i.e., droplet synchronization using railroad-like channels and manipulation of shape-dependent droplets using guiding tracks), we realized an error-free droplet fusion/sorting device for the two parallel trains of droplets. If droplet pairs are synchronized through a railroad-like channel, they are electrically fused and the fused droplets transit to a middle guiding track to flow in a middle channel; otherwise non-synchronized non-fused droplets will be discarded into the side waste channels by flowing through their own guiding tracks. The simple droplet synchronization, fusion, and sorting technology will have widespread application in droplet-based chemical or biological experiments, where two trains of the chemically or biologically treated or pre-formed droplets yield a train of 100% one-to-one fused droplets at the desired outlet channel by sorting all the non-synchronized non-fused droplets into waste outlets.     

Chemically reactive thin diffusion barriers

We assess the degree of protection against diffusion of an environmental pollutant afforded by a thin, chemically reactive surface film on a slab or membrane. For the case of an irreversible quasi-unimolecular reaction in such a surface film we derive a modified radiation boundary condition which adequately describes the presence of such a film. We show that the two extra parameters which appear in this boundary condition, an effective surface conductivity and an effective ambient concentration can be found from the permeation steady state flux and time lag through such a membrane. We compare our approximate boundary condition with that obtained for a chemically passive thin film and a newly derived boundary condition which exactly describes the transport in the composite medium — reactive film and body (slab or membrane). In certain instances such a thin, reactive film is effective as a diffusion barrier.     

Studying phase separation in confinement

Cells organize their interior through membrane-bound organelles and through membraneless condensates that are formed by liquid–liquid phase separation (LLPS). The complex process of coacervation that is involved in LLPS is challenging to study in living cells. Hence, studying coacervation in cell-mimicking synthetic containers can yield valuable insights. Here, we review recent progress with respect to studying LLPS (particularly coacervation) in artificial compartments, from water-in-oil droplets to membranous liposomes. We describe different strategies to form and control coacervates in microconfinements and to study their physicochemical and biological characteristics. We also describe how coacervation can itself be used in container formation. This review highlights the importance of in vitro coacervate studies for understanding cellular biology and for designing synthetic cells.     

Counter-ion activity and microstructure in polyelectrolyte complexes as determined by osmotic pressure measurements

We have investigated the activity of counter-ions at 60 degrees C through the osmotic coefficient K in solutions of anionic and cationic polyelectrolyte complexes of variable compositions. For excess of polyanion in the complexes (molar fraction of polycation f < 0.5), K increases as the polyanion is neutralized by the polycation (f getting closer to 0.5). By contrast, for an excess of polycation (f > 0.5), K stays constant or even slightly decreases as the polycation is getting neutralized by the polyanion. This asymmetric behavior depending on the charge of the complexes indicates that the globally negatively charged complexes are homogeneous and can be treated as a single polyelectrolyte of reduced linear charge density. On the other hand, the positively charged complexes show a micro-phase separation between neutral fully compensated microdomains and domains where the excess polycation is locally segregated. These two different microstructures are reminiscent of the coacervation and segregation regimes observed at higher concentrations and salinities, and also of polyelectrolyte complexes with oppositely charged surfactants. This interpretation is supported by two simple predictive models.     

Reversible pH-Responsive Coacervate Formation in Lipid Vesicles Activates Dormant Enzymatic Reactions

In situ, reversible coacervate formation within lipid vesicles represents a key step in the development of responsive synthetic cellular models. Herein, we exploit the pH responsiveness of a polycation above and below its pK_a, to drive liquid–liquid phase separation, to form single coacervate droplets within lipid vesicles. The process is completely reversible as coacervate droplets can be disassembled by increasing the pH above the pK_a. We further show that pH-triggered coacervation in the presence of low concentrations of enzymes activates dormant enzyme reactions by increasing the local concentration within the coacervate droplets and changing the local environment around the enzyme. In conclusion, this work establishes a tunable, pH responsive, enzymatically active multi-compartment synthetic cell. The system is readily transferred into microfluidics, making it a robust model for addressing general questions in biology, such as the role of phase separation and its effect on enzymatic reactions using a bottom-up synthetic biology approach.     

Enzymatic C−H Oxidation–Amidation Cascade in the Production of Natural and Unnatural Thiotetronate Antibiotics with Potentiated Bioactivity

The selective activation of unreactive hydrocarbons by biosynthetic enzymes has inspired new synthetic methods in C−H bond activation. Herein, we report the unprecedented two‐step biosynthetic conversion of thiotetromycin to thiotetroamide C involving the tandem oxidation and amidation of an unreactive ethyl group. We detail the genetic and biochemical basis for the terminal amidation in thiotetroamide C biosynthesis, which involves a uniquely adapted cytochrome P450–amidotransferase enzyme pair and highlights the first oxidation–amidation enzymatic cascade reaction leading to the selective formation of a primary amide group from a chemically inert alkyl group. Motivated by the ten‐fold increase in antibiotic potency of thiotetroamide C ascribed to the acetamide group and the unusual enzymology involved, we enzymatically interrogated diverse thiolactomycin analogues and prepared an unnatural thiotetroamide C analogue with potentiated bioactivity compared to the parent molecule.     

On the Separation of Timescales in Chemically Activated Reactions

Chemically activated reactions are important in describing the composition of reactive gases including flames, planetary atmospheres, and the interstellar medium (ISM). In a chemically activated reaction, two reactants combine to populate a vibrationally excited well that can undergo unimolecular transformations (isomerization, dissociation) or be thermalized through collisions with the bath gas. Once a well has been thermalized, it may still have sufficient energy to undergo further unimolecular reaction, in a purely thermal process. If the timescale for the thermally activated process is sufficiently short, such that it approaches that of the chemically activated reaction, the two concurrent processes become inseparable and the value of the phenomenological rate coefficient is no longer obvious. Here, we introduce the thermal decay (TD) procedure to determine phenomenological rate coefficients for chemically activated reactions proceeding on timescales approaching those of thermal reaction, principally for use in stochastic master equation simulations of multiple‐well multiple‐channel unimolecular reaction processes. By fitting the thermal decay of the initially activated well to a first‐order kinetic model, the would‐be thermal yield can be eliminated so as to arrive at the chemically activated component in a reliable and objective fashion. This technique is demonstrated here for the reaction of 1,3,6‐heptatriyne with H using the MultiWell code and a 16‐well 33‐channel C₇H₅ reaction model. A computer program implementing the TD method and for postprocessing of MultiWell output data, PPM, is provided.     

Chemically modified nylons as supports for enzyme immobilization

An isocyanide derivative of nylon, polyisonitrile-nylon (1,2), was used as a starting material whereby, through a series of modification reactions, different chemically reactive functional groups could be introduced on the polyamide backbone. The chemistry employed allowed for considerable flexibility in the choice of procedures for covalent fixation of proteins, all starting from the same chemically reactive parent polymer, polyisonitrile-nylon. Thus, polyisonitrilenylon could be used directly for the immobilization of enzymes via fourcomponent condensation reactions. The isocyanide functional groups of the parent polymer could be transformed, by treatment with bromine, into the strongly electrophilic dibromoisocyanide (—N=CBr^b2) groups. The selectivity of the —N=CBr^b2 group toward the various functional groups present in proteins could be regulated by appropriate control of the pH of the coupling reaction. Dibromoisocyanide-nylon was also further modified into other types of chemically reactive nylon derivatives.     

A Chemically Soldered Polyoxometalate Single-Molecule Transistor

Polyoxometalates have been proposed in the literature as nanoelectronic components, where they could offer key advantages with their structural versatility and rich electrochemistry. Apart from a few studies on their ensemble behaviour (as monolayers or thin films), this potential remains largely unexplored. We synthesised a pyridyl-capped Anderson–Evans polyoxometalate and used it to fabricate single-molecule junctions, using the organic termini to chemically “solder” a single cluster to two nanoelectrodes. Operating the device in an electrochemical environment allowed us to probe charge transport through different oxidation states of the polyoxometalate, and we report here an efficient three-state transistor behaviour. Conductance data fits a quantum tunnelling mechanism with different charge-transport probabilities through different charge states. Our results show the promise of polyoxometalates in nanoelectronics and give an insight on their single-entity electrochemical behaviour.     

Soy glycinin microcapsules by simple coacervation method

Encapsulation of a dispersed oil phase (hexadecane) was realized by simple coacervation method using soy glycinin as the wall forming material. Suitable emulsification and coacervation conditions, that favor the formation of microcapsules wall, were identified and investigated. Mild acid (pH 2.0) and heat (55 degrees C) treatments of the reaction medium during the emulsification step enhanced significantly the deposition of coacervated glycinin around oil droplets. A pronounced correlation between glycinin concentration in the continuous phase, specific surface of the dispersed phase and the microencapsulation efficiency was also observed. Coacervation step study concerned the morphology and the stability of microcapsules. Controlled initiation of the coacervation, by slow readjustment of the pH, allowed a homogeneous precipitation of glycinin around oil droplets as well as the absence of aggregation phenomena. Since the morphology of microcapsules was considerably affected by a prolonged stirring of the reaction medium, the coacervation and reticulation time were optimized in order to preserve the homogeneity of the microcapsules size distribution and the microencapsulation efficiency.     

Chemically programmed cell adhesion with membrane-anchored oligonucleotides

Cell adhesion organizes the structures of tissues and mediates their mechanical, chemical, and electrical integration with their surroundings. Here, we describe a strategy for chemically controlling cell adhesion using membrane-anchored single-stranded DNA oligonucleotides. The reagents are pure chemical species prepared from phosphoramidites synthesized in a single chemical step from commercially available starting materials. The approach enables rapid, efficient, and tunable cell adhesion, independent of proteins or glycans, by facilitating interactions with complementary labeled surfaces or other cells. We demonstrate the utility of this approach by imaging drug-induced changes in the membrane dynamics of non-adherent human cells that are chemically immobilized on a passivated glass surface.     

Hybrid modeling and simulation of stochastic effects on progression through the eukaryotic cell cycle

The eukaryotic cell cycle is regulated by a complicated chemical reaction network. Although many deterministic models have been proposed, stochastic models are desired to capture noise in the cell resulting from low numbers of critical species. However, converting a deterministic model into one that accurately captures stochastic effects can result in a complex model that is hard to build and expensive to simulate. In this paper, we first apply a hybrid (mixed deterministic and stochastic) simulation method to such a stochastic model. With proper partitioning of reactions between deterministic and stochastic simulation methods, the hybrid method generates the same primary characteristics and the same level of noise as Gillespie's stochastic simulation algorithm, but with better efficiency. By studying the results generated by various partitionings of reactions, we developed a new strategy for hybrid stochastic modeling of the cell cycle. The new approach is not limited to using mass-action rate laws. Numerical experiments demonstrate that our approach is consistent with characteristics of noisy cell cycle progression, and yields cell cycle statistics in accord with experimental observations.     

Reversible pH‐Responsive Coacervate Formation in Lipid Vesicles Activates Dormant Enzymatic Reactions

In situ, reversible coacervate formation within lipid vesicles represents a key step in the development of responsive synthetic cellular models. Herein, we exploit the pH responsiveness of a polycation above and below its pK_a, to drive liquid–liquid phase separation, to form single coacervate droplets within lipid vesicles. The process is completely reversible as coacervate droplets can be disassembled by increasing the pH above the pK_a. We further show that pH‐triggered coacervation in the presence of low concentrations of enzymes activates dormant enzyme reactions by increasing the local concentration within the coacervate droplets and changing the local environment around the enzyme. In conclusion, this work establishes a tunable, pH responsive, enzymatically active multi‐compartment synthetic cell. The system is readily transferred into microfluidics, making it a robust model for addressing general questions in biology, such as the role of phase separation and its effect on enzymatic reactions using a bottom‐up synthetic biology approach.     

Combining rails and anchors with laser forcing for selective manipulation within 2D droplet arrays

We demonstrate the combination of a rails and anchors microfluidic system with laser forcing to enable the creation of highly controllable 2D droplet arrays. Water droplets residing in an oil phase can be pinned to anchor holes made in the base of a microfluidic channel, enabling the creation of arrays by the appropriate patterning of such holes. The introduction of laser forcing, via laser induced thermocapillary forces to anchored droplets, enables the selective extraction of particular droplets from an array. We also demonstrate that such anchor arrays can be filled with multiple, in our case two, droplets each and that if such droplets have different chemical contents, the application of a laser at their interface triggers their merging and a chemical reaction to take place. Finally by adding guiding rails within the microfluidic structure we can selectively fill large scale arrays with monodisperse droplets with significant control over their contents. In this way we make a droplet array filled with 96 droplets containing different concentrations of fluorescent microparticles.     

Chemically induced phospholipid translocation across biological membranes

Chemical means of manipulating the distribution of lipids across biological membranes is of considerable interest for many biomedical applications as a characteristic lipid distribution is vital for numerous cellular functions. Here we employ atomic-scale molecular simulations to shed light on the ability of certain amphiphilic compounds to promote lipid translocation (flip-flops) across membranes. We show that chemically induced lipid flip-flops are most likely pore-mediated: the actual flip-flop event is a very fast process (time scales of tens of nanoseconds) once a transient water defect has been induced by the amphiphilic chemical (dimethylsulfoxide in this instance). Our findings are consistent with available experimental observations and further emphasize the importance of transient membrane defects for chemical control of lipid distribution across cell membranes.