Reversible covalent bonding is often used for the creation of novel supramolecular structures, multi-component assemblies and sensing ensembles. Despite the remarkable success of dynamic covalent ...systems, the reversible binding of a mono-alcohol with high strength is challenging. Here, we show that a strategy of carbonyl activation and hemiaminal ether stabilization can be embodied in a four-component reversible assembly that creates a tetradentate ligand and incorporates secondary alcohols with exceptionally high affinity. Evidence is presented that the intermediate leading to binding and exchange of alcohols is an iminium ion. To demonstrate the use of this assembly process we also explored chirality sensing and enantiomeric excess determinations. An induced twist in the ligand by a chiral mono-ol results in large Cotton effects in the circular dichroism spectra indicative of the handedness of the alcohol. The strategy revealed in this study should prove broadly applicable for the incorporation of alcohols into supramolecular architecture construction.
Chiral mono-ols are among the most sought after targets in asymmetric synthesis, and therefore, their chemical characterization and associated enantiomeric excess (ee) values are commonly reported. A ...simple optical method for determining alcohol identity and ee could be widely used. Toward this end, an in situ-generated multicomponent assembly that creates diastereomeric tris(pyridine) metal complexes incorporating chiral secondary alcohols was explored using exciton-coupled circular dichroism (ECCD). Qualitative models were proposed to predict the preferential diastereomer and its twist, and computational studies provided a rationalization of the CD spectra. Different ECCD spectra found for diastereomers formed in the self-assembled tris(pyridine) complexes were used to determine the absolute configurations of chiral mono-ols. Linear discriminant analysis was successfully employed to classify the alcohol analytes, thereby allowing identification of the alcohols. Conformational effects imparted by heteroatoms were also explored, further expanding the substrate scope. Finally, ee calibration curves allowed the determination of the ee of unknown samples of three chiral secondary alcohols with an average error of 3%. The assay described here is unique because no preparation of structurally elaborated chiral hosts is needed.
The site-specific incorporation of noncanonical monomers into polypeptides through genetic code reprogramming permits synthesis of bio-based products that extend beyond natural limits. To better ...enable such efforts, flexizymes (transfer RNA (tRNA) synthetase-like ribozymes that recognize synthetic leaving groups) have been used to expand the scope of chemical substrates for ribosome-directed polymerization. The development of design rules for flexizyme-catalyzed acylation should allow scalable and rational expansion of genetic code reprogramming. Here we report the systematic synthesis of 37 substrates based on 4 chemically diverse scaffolds (phenylalanine, benzoic acid, heteroaromatic, and aliphatic monomers) with different electronic and steric factors. Of these substrates, 32 were acylated onto tRNA and incorporated into peptides by in vitro translation. Based on the design rules derived from this expanded alphabet, we successfully predicted the acylation of 6 additional monomers that could uniquely be incorporated into peptides and direct N-terminal incorporation of an aldehyde group for orthogonal bioconjugation reactions.
Conspectus Gels assembled from solvent-dispersed nanocrystals are of interest for functional materials because they promise the opportunity to retain distinctive properties of individual nanocrystals ...combined with tunable, structure-dependent collective behavior. By incorporating stimuli-responsive components, these materials could also be dynamically reconfigured between structurally distinct states. However, nanocrystal gels have so far been formed mostly through irreversible aggregation, which has limited the realization of these possibilities. Meanwhile, gelation strategies for larger colloidal microparticles have been developed using reversible physical or chemical interactions. These approaches have enabled the experimental navigation of theoretically predicted phase diagrams, helping to establish an understanding of how thermodynamic behavior can guide gel formation in these materials. However, the translation of these principles to the nanoscale poses both practical and fundamental challenges. The molecules guiding assembly can no longer be safely assumed to be vanishingly small compared to the particles nor large compared to the solvent. In this Account, we discuss recent progress toward the assembly of tunable nanocrystal gels using two strategies guided by equilibrium considerations: (1) reversible chemical bonding between functionalized nanocrystals and difunctional linker molecules and (2) nonspecific, polymer-induced depletion attractions. The effective nanocrystal attractions, mediated in both approaches by a secondary molecule, compete against stabilizing repulsions to promote reversible assembly. The structure and properties of the nanocrystal gels are controlled microscopically by the design of the secondary molecule and macroscopically by its concentration. This mode of control is compelling because it largely decouples nanocrystal synthesis and functionalization from the design of interactions that drive assembly. Statistical thermodynamic theory and computer simulation have been applied to simple models that describe the bonding motifs in these assembling systems, furnish predictions for conditions under which gelation is likely to occur, and suggest strategies for tuning and disassembling the gel networks. Insights from these models have guided experimental realizations of reversible gels with optical properties in the infrared range that are sensitive to the gel structure. This process avoids time-consuming and costly trial-and-error experimental investigations to accelerate the development of nanocrystal gel assemblies. These advances highlight the need to better understand interactions between nanocrystals, how interactions give rise to gel structure, and properties that emerge. Such an understanding could suggest new approaches for creating stimuli-responsive and dissipative assembled materials whose properties are tunable on demand through directed reconfiguration of the underlying gel microstructure. It may also make nanocrystal gels amenable to computationally guided design using inverse methods to rapidly optimize experimental parameters for targeted functionalities.
CRISPR-Cas systems confer an adaptive immunity against viruses. Following viral injection, Cas1-Cas2 integrates segments of the viral genome (spacers) into the CRISPR locus. In type I CRISPR-Cas ...systems, efficient “primed” spacer acquisition and viral degradation (interference) require both the Cascade complex and the Cas3 helicase/nuclease. Here, we present single-molecule characterization of the Thermobifida fusca (Tfu) primed acquisition complex (PAC). We show that TfuCascade rapidly samples non-specific DNA via facilitated one-dimensional diffusion. Cas3 loads at target-bound Cascade and the Cascade/Cas3 complex translocates via a looped DNA intermediate. Cascade/Cas3 complexes stall at diverse protein roadblocks, resulting in a double strand break at the stall site. In contrast, Cas1-Cas2 samples DNA transiently via 3D collisions. Moreover, Cas1-Cas2 associates with Cascade and translocates with Cascade/Cas3, forming the PAC. PACs can displace different protein roadblocks, suggesting a mechanism for long-range spacer acquisition. This work provides a molecular basis for the coordinated steps in CRISPR-based adaptive immunity.
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•Cascade diffuses on DNA and transiently engages potential targets•Cascade/Cas3 stalling at protein roadblocks results in DNA double strand breaks•Cascade, Cas3, and Cas1-Cas2 form the primed acquisition complex (PAC)•The PAC displaces protein roadblocks in search of downstream protospacers
Single-molecule studies illuminate how the type I-E CRISPR-Cas interference and adaptation complexes interact and function to achieve primed spacer acquisition.
Porphyrins have been used frequently to construct supramolecular assemblies. In contrast, noncovalent ensembles derived from expanded porphyrins, larger congeners of naturally occurring tetrapyrrole ...macrocycles, are all but unknown. Here we report a series of expanded porphyrin-anion supramolecular assemblies. These systems display unique environmentally responsive behavior. Addition of polar organic solvents or common anions to the ensembles leads to either a visible color change, a change in the fluorescence emission features, or differences in solubility. The actual response, which could be followed easily by the naked eye, was found to depend on the specifics of the assembly, as well as the choice of analyte. Using the ensembles of this study, it proved possible to differentiate between common solvents, such as diethyl ether, THF, ethyl acetate, acetone, alcohol, acetonitrile, DMF, and DMSO, identify complex solvent systems, as well as distinguish between the fluoride, chloride, bromide, nitrate, and sulfate anions.
A simple and highly selective chromogenic and fluorogenic detection of sulfur mustard (SM) simulants is reported. Dithiol 1, in the presence and absence of a mustard simulant behaves differently ...toward a squaraine dye (SQ), and thus provides a visual and spectroscopic signal for mustard gas. The sensor responds to the SM simulant, but not to the O-analog of mustard stimulant or nerve agent mimics and other electrophilic agents. The visual and fluorescent detection with less than 50 mu M of SM simulant shows good sensitivity. The utility of the sensor was demonstrated by analysis of SM simulant on surfaces, in soil, and in the gas phase.
Axial chirality is a prevalent and important phenomenon in chemistry. Herein we report a combination of dynamic covalent chemistry and axial chirality for the development of a versatile platform for ...the binding and chirality sensing of multiple classes of mononucleophiles. An equilibrium between an open aldehyde and its cyclic hemiaminal within biphenyl derivatives enabled the dynamic incorporation of a broad range of alcohols, thiols, primary amines, and secondary amines with high efficiency. Selectivity toward different classes of nucleophiles was also achieved by regulating the distinct reactivity of the system with external stimuli. Through induced helicity as a result of central‐to‐axial chirality transfer, the handedness and ee values of chiral monoalcohol and monoamine analytes were reported by circular dichroism. The strategies introduced herein should find application in many contexts, including assembly, sensing, and labeling.
Talking sense: A convergence of the concepts of dynamic covalent chemistry and axial chirality enabled the reversible incorporation and chirality sensing of multiple classes of mononucleophiles (see picture). Selectivity toward different classes of nucleophiles could also be induced by regulating the distinct reactivity of the system with external stimuli.
The coupling and decoupling of molecular units is a fundamental undertaking of organic chemistry. Herein we report the use of a very simple conjugate acceptor, derived from Meldrum's acid, for the ...sequential 'clicking' together of an amine and a thiol in aqueous conditions at neutral pH. Subsequently, this linkage can be 'declicked' by a chemical trigger to release the original amine and thiol undisturbed. The reactivity differs from that of other crosslinking agents because the selectivity for sequential functionalization derives from an altering of the electrophilicity of the conjugate acceptor on the addition of the amine. We describe the use of the procedure to modify proteins, create multicomponent libraries and synthesize oligomers, all of which can be declicked to their starting components in a controlled fashion when desired. Owing to the mild reaction conditions and ease of use in a variety of applications, the method is predicted to have wide utility.
Differential sensing is continuing to develop as an alternative to traditional, selective chemosensing techniques. This technique takes a cue from how the human senses of taste and smell operate in ...order to obtain qualitative and even quantitative data on single analytes and mixtures. Whereas classical chemosensing techniques inspired by the ‘lock-and-key’ approach depend on the development of a selective receptor for a target analyte, pattern-based sensing depends on the development of an array of cross-reactive receptors, which produce a collection of responses upon the array's interaction with a target analyte. This review focuses on an approach to differential sensing that diversifies synthetic receptors to be used in an array via appending combinatorial peptidic arms, metal ions, and indicators to a core binding unit.
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