Kinetic Trapping Research Articles

TPP Riboswitch Populates Holo-Form-like Structure Even in the Absence of Cognate Ligand at High Mg2+ Concentration.

Riboswitches are noncoding RNA that regulate gene expression by folding into specific three-dimensional structures (holo-form) upon binding by their cognate ligand in the presence of Mg2+. Riboswitch functioning is also hypothesized to be under kinetic control requiring large cognate ligand concentrations. We ask the question under thermodynamic conditions, can the riboswitches populate structures similar to the holo-form only in the presence of Mg2+ and absence of cognate ligand binding. We addressed this question using thiamine pyrophosphate (TPP) riboswitch as a model system and computer simulations using a coarse-grained model for RNA. The folding free energy surface (FES) shows that with the initial increase in Mg2+ concentration ([Mg2+]), the aptamer domain (AD) of TPP riboswitch undergoes a barrierless collapse in its dimensions. On further increase in [Mg2+], intermediates separated by barriers appear on the FES, and one of the intermediates has a TPP ligand-binding competent structure. We show that site-specific binding of the Mg2+ aids in the formation of tertiary contacts. For [Mg2+] greater than physiological concentration, AD folds into a structure similar to the crystal structure of the TPP holo-form even in the absence of the TPP ligand. The folding kinetics shows that TPP AD populates an intermediate due to the misalignment of two arms present in the structure, which acts as a kinetic trap, leading to larger folding timescales. The predictions of the intermediate structures from the simulations are amenable for experimental verification.

Helical bias in supramolecular polymers accounts for different stabilities of kinetically trapped states

AbstractThe idea to synthesize and self‐assemble nano‐graphenes with structural precision into supramolecular polymers is just one of Klaus Müllen's many pioneering contributions to the chemical sciences. To honor his impact in the field of polymer science, we here describe a study that combines experimental and computational methods in studying the stability of kinetically trapped states of supramolecular polymers. We show that the introduction of stereocenters in the sidechains allow helical supramolecular polymers based on chiral triphenylene‐2,6,10‐tricarboxamide monomers to escape a kinetic trap more efficiently than polymers based on their achiral analogs. Partial depolymerization of the kinetically trapped state by increasing the temperature followed by polymerization by lowering the temperature shows that monomers either polymerize on existing stacks or self‐nucleate to form the thermodynamically more stable state. Chiral monomers prefer the latter more than achiral monomers.

Visible-Light Switching of Metallosupramolecular Assemblies.

A photoswitchable ligand and palladium(II) ions form a dynamic mixture of self‐assembled metallosupramolecular structures. The photoswitching ligand is an ortho‐fluoroazobenzene with appended pyridyl groups. Combining the E‐isomer with palladium(II) salts affords a double‐walled triangle with composition [Pd3L6]6+ and a distorted tetrahedron [Pd4L8]8+ (1 : 2 ratio at 298 K). Irradiation with 410 nm light generates a photostationary state with approximately 80 % of the E‐isomer of the ligand and results in the selective disassembly of the tetrahedron, the more thermodynamically stable structure, and the formation of the triangle, the more kinetically inert product. The triangle is then slowly transformed back into the tetrahedron over 2 days at 333 K. The Z‐isomer of the ligand does not form any well‐defined structures and has a thermal half‐life of 25 days at 298 K. This approach shows how a thermodynamically preferred self‐assembled structure can be reversibly pumped to a kinetic trap by small perturbations of the isomer distribution using non‐destructive visible light.

Pegylation of the Galectin-3 carbohydrate recognition domain creates a kinetic trap protecting the protein from thermal unfolding

Proteins are widely used as therapeutics but often can be unstable, limiting their applications in the clinic. To improve the stability of protein drugs, synthetic polymers such as polyethylene glycol (PEG) can be covalently attached to specific protein side chains, creating protein-polymer conjugates. Though nearly thirty PEGylated proteins have been FDA-approved, our understanding is very limited of how PEG-protein interactions alter the fundamental chemical and physical properties of the conjugate.

CHARMM-GUI Enhanced Sampler for molecular dynamics simulations with collective variables and various enhanced sampling methods

Molecular dynamics (MD) simulation is a robust tool to investigate complex biomolecular systems with all-atomistic representation. MD trajectory based on accurate force field and equations of motion integration gives us the molecular-level understanding of the target systems. However, one might not observe rare-events or slow-processes within the typical simulation time if high free barrier or kinetic trap presents. Various enhanced sampling methods have been developed and utilized to resolve this issue by modifying temperatures, adding non-equilibrium forces to the subset of the system, or reshaping underlying potential energy functions.

Cellular growth during rapid directional solidification: Insights from quantitative phase field simulations

In this paper, columnar cellular growth with kinetic effects including kinetic undercooling and solute trapping in rapid directional solidification of alloys was investigated by using a recent quantitative phase-field model for rapid solidification. Morphological transition and primary spacing selection with and without kinetic effects were numerically investigated. Numerical results show that doublon structure is an intermediate state in the primary spacing adjustment of cellular arrays. It was found that the inclusions of kinetic effects result in the increase of the solute in the solid phase and the solute enrichment in the interdendritic liquid channel. Moreover, predicted results indicate that the growth directions of the cellular arrays in rapid directional solidification with and without kinetic effects are independent of the Péclet number. Therefore, the kinetic effects play important roles in numerical simulations of the growth pattern selection and solute distribution during rapid solidification. Neglecting them will result in the inaccurately predicted results.

Out-of-equilibrium supported Pt-Co core-shell nanoparticles stabilized by kinetic trapping at room temperature

The chemical stability of supported CoPt nanoparticles in out-of-equilibrium core-shell configurations was investigated mainly by anomalous grazing incidence small angle X-ray scattering (AGISAXS) in association with combined transmission electron microscopy and X-ray absorption spectroscopy. CoPt nanoparticles were prepared at room temperature by ultrahigh vacuum atom beam deposition using two different routes: simultaneous deposition of the two metals (CoPt) or sequential deposition. In this last case, Co deposition on a Pt-core (Pt@Co) and the reverse configuration (Co@Pt) are explored. In the Pt@Co case, our experimental analysis of 2.5 nm particles shows the stability of a Pt rich-core (80% Pt) surrounded by a two-monolayers-thick Co shell. In the reverse case, the core-shell structure is also stabilized, while the codeposited sample leads to an alloyed structure. These results suggest that the growth kinetics can trap the thermodynamically non-favorable core-shell structure even for this system which has a high alloying tendency. Besides the lack of atom mobility at room temperature, this stabilization can also be associated with core strain effects. Post thermal treatment of core-shell samples induces a structural transition from the core-shell configuration to the equilibrium alloyed configuration. This study demonstrates that the element-selective scattering technique, AGISAXS is highly efficient for the extraction of chemical segregation information from multi-component supported nanoparticles, such as core-shell structures, up to ultimate small sizes.

Tuning the fast generation of luminescent silver nanodots on a surface.

Silver nanodots, predominantly a near-IR emitter, can be instantly generated on a surface by silver cluster transfer. Kinetic trapping of ssDNA molecules on the surface limits the reorganization of the resulting silver nanodots for other silver nanodot emitters. Adjusting the freedom of the adsorbed ssDNA can tune the generation of various silver nanodots on the surface.

Timing matters: pre-assembly versus post-assembly functionalization of a polyoxovanadate-organic cuboid.

The pre-assembly and post-assembly approaches in the functionalization of a polyoxovanadate–organic cuboid, [{V6S}8(QPTC)8{V3}2]10−, are discussed. We have shown that the two pathways have led to distinctly different systems, with either an expanded or contracted interior void space, when phenylphosphonate is introduced at different stages of the self-assembly. One leaves the cuboid framework largely intact, whereas the other results in a compact, twisted cuboid. Kinetic factors will have to be considered in the equilibrium of these complex processes. Furthermore, the exceptional stability of these polyoxometalate–organic systems facilitates mass spectrometric characterization, which confirms the composition of the complexes and also indicates that the methoxide groups on the vanadium cluster nodes are labile. The results will help deepen the mechanistic understanding of the formation mechanisms of polyoxovanadate-based metal–organic cages and other functionalized polyoxovanadate clusters in general.

Living supramolecular polymerization of an amphiphilic aza-BODIPY dye realized by water-assisted kinetic trapping.

The kinetic assembly pathways of a newly synthesized amphiphilic aza-BODIPY dye 1 were tuned by using H2O as a co-solvent in MeOH. Accordingly, the biphasic aggregation pathways resulting in kinetically-trapped and thermodynamically stable aggregates of 1 were established and the multiple cyclic seeded living supramolecular polymerization of this dye was realized.

Differential repair enzyme-substrate selection within dynamic DNA energy landscapes.

We demonstrate that reshaping of the dynamic, bulged-loop energy landscape of DNA triplet repeat ensembles by the presence of an abasic site alters repair outcomes by the APE1 enzyme. This phenomenon depends on the structural context of the lesion, despite the abasic site always having the same neighbors in sequence space. We employ this lesion-induced redistribution of DNA states and a kinetic trap to monitor different occupancies of the DNA bulge loop states. We show how such dynamic redistribution and associated differential occupancies of DNA states impact APE1 repair outcomes and APE1 induced interconversions. We correlate the differential biophysical properties of the dynamic, DNA ensemble states, with their ability to be recognized and processed as substrates by the APE1 DNA repair enzyme. Enzymatic digestions and biophysical characterizations reveal that APE1 cuts a fraction (10-12%) of the dynamic, rollameric substrates within the initial kinetic distribution. APE1 interactions also 'induce' rollamer redistribution from a kinetically trapped distribution to an equilibrium distribution, the latter not containing viable APE1 substrates. We distinguish between kinetically controlled ensemble (re)distributions of potential DNA substrates, versus thermodynamically controlled ensemble (re)distribution; features of importance to DNA regulation. We conclude that APE1 activity catalyzes/induces ensembles that represent the thermodynamically optimal loop distribution, yet which also are nonviable substrate states for abasic site cleavage by APE1. We propose that by inducing substrate redistributions in a dynamic energy landscape, the enzyme actually reduces the available substrate competent species for it to process, reflective of a regulatory mechanism for enzymatic self-repression. If this is a general phenomenon, such a consequence would have a profound impact on slowing down and/or misdirecting DNA repair within dynamic energy landscapes, as exemplified here within triplet repeat domains. In short, APE1-instigated redistribution of potential substrates induces a preferred pathway to an equilibrium ensemble of enzymatically incompetent states.

How much does surface polymorphism influence the work function of organic/metal interfaces?

Molecules adsorbing on metal surfaces form a variety of different surface polymorphs. How strongly this polymorphism affects interface properties is a priori unknown. In this work we investigate how strongly the surface polymorphism influences the interface work functions for various organic/metal interfaces. To evaluate the whole bandwidth of possible polymorphs, we perform full theoretical structure search, probing millions of polymorph candidates. All of these candidates might be observed in reality, either by kinetic trapping or by thermodynamic occupation. Employing first-principles calculations and machine learning we predict and analyze the work function changes for those millions of candidates for three physically distinct model systems: the weakly interacting naphthalene on Cu(111), the strongly interacting anthraquinone on Ag(111), and tetracyanoethylene, which undergoes a reorientation from lying to standing polymorphs on the Cu(111) surface. These thorough investigations indicate that kinetic trapping of flat-lying molecules can lead to work function differences of a few hundred meV. If the molecules also reorientate, this can increase to a change of several eV. We further show that the spread in work function decreases when working in thermodynamic equilibrium, but thermally occupied phases still lead to an intrinsic uncertainty at elevated temperatures.

Toward Targeted Kinetic Trapping of Organic-Inorganic Interfaces: A Computational Case Study.

Properties of inorganic–organic interfaces, such as their interface dipole, strongly depend on the structural arrangements of the organic molecules. A prime example is tetracyanoethylene (TCNE) on Cu(111), which shows two different phases with significantly different work functions. However, the thermodynamically preferred phase is not always the one that is best suited for a given application. Rather, it may be desirable to selectively grow a kinetically trapped structure. In this work, we employ density functional theory and transition state theory to discuss under which conditions such a kinetic trapping might be possible for the model system of TCNE on Cu. Specifically, we want to trap the molecules in the first layer in a flat-lying orientation. This requires temperatures that are sufficiently low to suppress the reorientation of the molecules, which is thermodynamically more favorable for high dosages, but still high enough to enable ordered growth through diffusion of molecules. On the basis of the temperature-dependent diffusion and reorientation rates, we propose a temperature range at which the reorientation can be successfully suppressed.

Methylglyoxal Forms Diverse Mercaptomethylimidazole Crosslinks with Thiol and Guanidine Pairs in Endogenous Metabolites and Proteins.

Methylglyoxal (MGO) is a reactive byproduct formed by several metabolic precursors, the most notable being triosephosphates in glycolysis. While many MGO-mediated adducts have been described, the reactivity and specific biomolecular targets of MGO remain incompletely mapped. Based on our recent discovery that MGO can form stable mercaptomethylimidazole crosslinks between cysteine and arginine (MICA) in proteins, we hypothesized that MGO may participate in myriad reactions with biologically relevant guanidines and thiols in proteins, metabolites, and perhaps other biomolecules. Herein, we performed steady-state and kinetic analyses of MGO reactivity with several model thiols, guanidines, and biguanide drugs to establish the plausible and prevalent adducts formed by MGO in proteins, peptides, and abundant cellular metabolites. We identified several novel, stable MICA metabolites that form in vitro and in cells, as well as a novel intermolecular post-translational MICA modification of surface cysteines in proteins. These data confirm that kinetic trapping of free MGO by thiols occurs rapidly and can decrease formation of more stable imidazolone (MG-H1) arginine adducts. However, reversible hemithioacetal adducts can go on to form stable MICA modifications in an inter- and intramolecular fashion with abundant or proximal guanidines, respectively. Finally, we discovered that intracellular MICA-glutathione metabolites are recognized and exported by the efflux pump MRP1, providing a parallel and perhaps complementary pathway for MGO detoxification working alongside the glyoxalase pathway. These data provide new insights into the plausible reactions involving MGO in cells and tissues, as well as several new molecular species in proteins and metabolites for further study.

Protein-like particles through nanoprecipitation of mixtures of polymers of opposite charge

HypothesisPolymer nanoparticles (NPs) have a very high potential for applications notably in the biomedical field. However, synthetic polymer NPs cannot yet concurrence the functionalities of proteins, their natural counterparts, notably in terms of size, control over internal structure and interactions with biological environments. We hypothesize that kinetic trapping of polymers bearing oppositely charged groups in NPs could bring a new level of control and allow mimicking the surfaces of proteins. ExperimentsHere, the assembly of mixed-charge polymer NPs through nanoprecipitation of mixtures of oppositely charged polymers is studied. Two series of copolymers made of ethyl methacrylate and 1 to 25 mol% of either methacrylic acid or a trimethylammonium bearing methacrylate are synthesized. These carboxylic acid or trimethylammonium bearing polymers are then mixed in different ratios and nanoprecipitated. The influence of the charge fraction, mixing ratio of the polymers, and precipitation conditions on NP size and surface charge is studied. FindingsUsing this approach, NPs of less than 25 nm with tunable surface charge from +40 mV to −40 mV are assembled. The resulting NPs are sensitive to pH and certain NP formulations have an isoelectric point allowing repeated charge reversal. Encapsulation of fluorescent dyes yields very bright fluorescent NPs, whose interactions with cells are studied through fluorescence microscopy. The obtained results show the potential of nanoprecipitation of oppositely charged polymers for the design of NPs with precisely tuned surface properties.

Nano-sandwich composite by kinetic trapping assembly from protein and nucleic acid.

Design and preparation of layered composite materials alternating between nucleic acids and proteins has been elusive due to limitations in occurrence and geometry of interaction sites in natural biomolecules. We report the design and kinetically controlled stepwise synthesis of a nano-sandwich composite by programmed noncovalent association of protein, DNA and RNA modules. A homo-tetramer protein core was introduced to control the self-assembly and precise positioning of two RNA–DNA hybrid nanotriangles in a co-parallel sandwich arrangement. Kinetically favored self-assembly of the circularly closed nanostructures at the protein was driven by the intrinsic fast folding ability of RNA corner modules which were added to precursor complex of DNA bound to the protein. The 3D architecture of this first synthetic protein–RNA–DNA complex was confirmed by fluorescence labeling and cryo-electron microscopy studies. The synthesis strategy for the nano-sandwich composite provides a general blueprint for controlled noncovalent assembly of complex supramolecular architectures from protein, DNA and RNA components, which expand the design repertoire for bottom-up preparation of layered biomaterials.

Effects of boundary walls on the properties of settling spheres

Abstract Numerical Simulations are performed, using Eulerian two fluid model (TFM) to investigate the effects of solid volume fraction and no-slip side walls on the settling particles. It is found that average settling velocity decreases with increasing volume fraction for both gas-solid (GS) and liquid-solid (LS) systems, in good agreement with the Richardson-Zaki 1 − ϕ n ${\left(1-\phi \right)}^{n}$ law. It was also noted that average velocity is independent of the boundary condition for both gas-solid (GS) and liquid-solid (LS) systems. The root mean square value of the solid volume fraction shows the increasing trend with volume fraction, caused by the many particle interactions. Furthermore, no-slip sidewalls were found to damp the velocity fluctuations quantitively, while following the well-known ϕ 1 / 2 ${\phi }^{1/2}$ scaling with volume fraction. Side walls were found to act as kinetic trap for the particles, damping the fluctuation near the walls and plateauing in the mid plane. These simulations showed that the GS system shows the higher solid fraction fluctuations that the LS system at the same Reynolds number, mainly because of the higher collision frequency (higher Stokes number) among the particles.

How to Prepare Kinetically Stable Self-assembled Pt12 L24 Nanocages while Circumventing Kinetic Traps.

Supramolecular coordination‐based self‐assembled nanostructures have been widely studied, and currently various applications are being explored. For several applications, the stability of the nanostructure is of key importance, and this strongly depends on the metal used in the self‐assembly process. Herein, design strategies and synthetic protocols to access desirable kinetically stable Pt12L24 nanospheres are reported, and it is demonstrated that these are stable under conditions under which the palladium counterparts decompose. Descriptors previously used for palladium nanospheres are insufficient for platinum analogues, as the stronger metal–ligand bond results in a mixture of kinetically trapped structures. We report that next to the dihedral angle, the rigidity of the ditopic ligand is also a key parameter for the controlled formation of Pt12L24 nanospheres. Catalytic amounts of coordinating additives to labilise the platinum‐pyridyl bond to some extent are needed to selectively form Pt12L24 assemblies. The formed Pt12L24 nanospheres were demonstrated to be stable in the presence of chloride, amines and acids, unlike the palladium analogues.

Kinetic trapping of 3D-printable cyclodextrin-based poly(pseudo)rotaxane networks

<h2>Summary</h2> Synthetically trapping kinetically varied (super)structures of molecular assemblies and amplifying them to the macroscale is a promising, yet challenging, approach for the advancement of meta-stable materials. Here, we demonstrated a concerted kinetic trapping design to timely resolve a set of transient polypseudorotaxanes in solution and harness a crop of them via micro-crystallization. By installing stopper or speed bump moieties on the polymer axles, meta-stable polypseudorotaxanes with segmented cyclodextrin blocks were hierarchically amplified into crystalline networks of different crosslinking densities at mesoscale and viscoelastic hydrogels with 3D-printability in bulk. We demonstrated simultaneous 3D-printing of two polypseudorotaxane networks from one reactive ensemble and their conversion to heterogeneous polyrotaxane monoliths. Spatially programming the macroscale shapes of these heterogeneous polyrotaxanes enabled the construction of moisture-responsive actuators, in which the shape morphing originated from the different numbers of cyclodextrins interlocked in these polyrotaxane networks.

Competitive Binding-Modulated Metal–Phenolic Assemblies for Adaptable Nanofilm Engineering

Coordination-driven metal–phenolic assembly, a mechanism associated with many essential biological functions, is being actively exploited for engineering of advanced materials. However, a critical challenge remains in the regulation of the dynamic metal–phenolic networks to overcome the kinetic trapping for well-controlled nanofilm formation. This study presents an adaptable competitive binding strategy to shape the metal–phenolic complexes while modulating their assembly behaviors. Kinetically stable metal–phenolic assemblies with homogeneous hydrodynamic diameters are identified as a new class of metal–phenolic building blocks. Spectroscopic studies and density functional theory calculations reveal an inner-sphere complexation of the competitive ligands to the metal centers of bis-complex metal–phenolic species. Quantitative insights into the availability of competitive ligands are achieved, and a series of applicable ligands are located. Particularly, these kinetically stable building blocks, with good dispersibility in both aqueous and organic media, revolutionize the processing of metal–phenolic nanofilms, enabling the use of versatile industrially friendly methods including homogeneous spray coating, vertical deposition self-assembly, and ink-jet printing. The obtained films exhibit superior properties in terms of mechanical strength (EY = 13.7 GPa), surface smoothness, and reinforced adhesion force. This study provides new mechanistic understanding of the coordinative metal–phenolic assembly and activates the toolkit of supramolecular chemistry for controllable engineering of metal–organic hybrid films for multidisciplinary applications.