Expanding diversity in dynamic combinatorial libraries: simultaneous exchange of disulfide and thioester linkages

Kinetic Control of Complexity in Multiple Dynamic Libraries

Multiple dynamic libraries of compounds are generated when more than one reversible reaction comes into play. Commonly, two or more orthogonal reversible reactions are used, leading to non-communicating dynamic libraries which share no building blocks. Only a few examples of communicating libraries have been reported, and in all those cases, building blocks are reversibly exchanged from one library to the other, constituting an antiparallel dynamic covalent system. Herein we report that communication between two different dynamic libraries through an irreversible process is also possible. Indeed, alkyl amines cancel the dynamic regime on the nucleophilic substitution of tetrazines, generating kinetically inert compounds. Interestingly, such amine can be part of another dynamic library, an imine-amine exchange. Thus, both libraries are interconnected with each other by an irreversible process which leads to kinetically inert structures that contain parts from both libraries, causing a collapse of the complexity. Additionally, a latent irreversible intercommunication could be developed. In such a way, a stable molecular system with specific host-guest and fluorescence properties, could be irreversibly transformed when the right stimulus was applied, triggering the cancellation of the original supramolecular and luminescent properties and the emergence of new ones.

Switching between Nonisoenergetic Dynamic Covalent Reactions Using Host-Guest Chemistry

CO2 reacts with simple amines in the presence of water to generate dynamic combinatorial libraries of majority (i.e., ammonium carbamates) and minority (i.e., ammonium carbonates) nonisoenergetic covalent adducts. Over the past two decades, our laboratory has reported on a new class of cavitands, namely, dyn[n]arenes, from which a polyanionic macrocycle is a highly efficient receptor for linear polyammoniums that forms [2]pseudorotaxanes in water at neutral pH. Herein, we demonstrate that the formation of [2]pseudorotaxanes shifts the equilibrium of CO2 capture by polyamines in water toward the quasi-exclusive formation of carbonate adducts, providing the first example of a switch between two competitive and reversible covalent processes triggered by host-guest interactions. In addition, this supramolecular approach to CO2 capture exhibits enhanced capture efficiency by increasing the state of protonation of complexed vs uncomplexed polyamines. Altogether, we report here that a templating approach can divert the outcome of two reversible covalent chemistries involving nucleophilic additions and acid-base reactions, challenging therefore the common knowledge that noncovalent and covalent bonds operate in separate energy frames.

Dual reactivity based dynamic covalent chemistry: mechanisms and applications

Dynamic covalent chemistry (DCC) focuses on the reversible formation, breakage, and exchange of covalent bonds and assemblies, setting a bridge between irreversible organic synthesis and supramolecular chemistry and finding wide utility. In order to enhance structural and functional diversity and complexity, different types of dynamic covalent reactions (DCRs) are placed in one vessel, encompassing orthogonal DCC without crosstalk and communicating DCC with a shared reactive functional group. As a means of adding tautomers, widespread in chemistry, to interconnected DCRs and combining the features of orthogonal and communicating DCRs, a concept of dual reactivity based DCC and underlying structural and mechanistic insights are summarized. The manipulation of the distinct reactivity of structurally diverse ring-chain tautomers allows selective activation and switching of reaction pathways and corresponding DCRs (C-N, C-O, and C-S) and assemblies. The coupling with photoswitches further enables light-mediated formation and scission of multiple types of reversible covalent bonds. To showcase the capability of dual reactivity based DCC, the versatile applications in dynamic polymers and luminescent materials are presented, paving the way for future functionalization studies.

Förster Resonance Energy Transfer Assay for Investigating the Reactivity of Thioesters in Biochemistry and Native Chemical Ligation

Thioesters are considered to be "energy-rich" functional groups that are susceptible to attack by thiolate and amine nucleophiles while remaining hydrolytically stable at neutral pH, which enables thioester chemistry to take place in an aqueous medium. Thus, the inherent reactivity of thioesters enables their fundamental roles in biology and unique applications in chemical synthesis. Here, we investigate the reactivity of thioesters that mimic acyl-coenzyme A (CoA) species and S-acylcysteine modifications as well as aryl thioesters applied in chemical protein synthesis by native chemical ligation (NCL). We developed a fluorogenic assay format for the direct and continuous investigation of the rate of reaction between thioesters and nucleophiles (hydroxide, thiolate, and amines) under various conditions and were able to recapitulate previously reported reactivity of thioesters. Further, chromatography-based analyses of acetyl- and succinyl-CoA mimics revealed striking differences in their ability to acylate lysine side chains, providing insight into nonenzymatic protein acylation. Finally, we investigated key aspects of native chemical ligation reaction conditions. Our data revealed a profound effect of the tris-(2-carboxyethyl)phosphine (TCEP) commonly used in systems where thiol-thioester exchange occurs, including a potentially harmful hydrolysis side reaction. These data provide insight into the potential optimization of native chemical ligation chemistry.

A scalable solid-state nanoporous network with atomic-level interaction design for carbon dioxide capture

Carbon capture and sequestration reduces carbon dioxide emissions and is critical in accomplishing carbon neutrality targets. Here, we demonstrate new sustainable, solid-state, polyamine-appended, cyanuric acid-stabilized melamine nanoporous networks (MNNs) via dynamic combinatorial chemistry (DCC) at the kilogram scale toward effective and high-capacity carbon dioxide capture. Polyamine-appended MNNs reaction mechanisms with carbon dioxide were elucidated with double-level DCC where two-dimensional heteronuclear chemical shift correlation nuclear magnetic resonance spectroscopy was performed to demonstrate the interatomic interactions. We distinguished ammonium carbamate pairs and a mix of ammonium carbamate and carbamic acid during carbon dioxide chemisorption. The coordination of polyamine and cyanuric acid modification endows MNNs with high adsorption capacity (1.82 millimoles per gram at 1 bar), fast adsorption time (less than 1 minute), low price, and extraordinary stability to cycling by flue gas. This work creates a general industrialization method toward carbon dioxide capture via DCC atomic-level design strategies.

Sulfur in Dynamic Covalent Chemistry

Sulfur has been important in dynamic covalent chemistry (DCC) since the beginning of the field. Mainly as part of disulfides and thioesters, dynamic sulfur-based bonds (DSBs) have a leading role in several remarkable reactions. Part of this success is due to the almost ideal properties of DSBs for the preparation of dynamic covalent systems, including high reactivity and good reversibility under mild aqueous conditions, the possibility of exploiting supramolecular interactions, access to isolable structures, and easy experimental control to turn the reaction on/off. DCC is currently witnessing an increase in the importance of DSBs. The chemical flexibility offered by DSBs opens the door to multiple applications. This Review presents an overview of all the DSBs used in DCC, their applications, and remarks on the interesting properties that they confer on dynamic chemical systems, especially those containing several DSBs.

Simultaneous Formation of a Fully Organic Triply Dynamic Combinatorial Library

Here we report the simultaneous formation of doubly and triply dynamic libraries as a result of exchange reactions between functionalized organic building blocks. A combination of three different reversible covalent linkages involving a boronate ester transesterification along with an imine and disulfide exchange was employed to generate a new type of fully organic triply dynamic molecular assembly.

Engineering multilayer chemical networks

Dynamic multilevel systems emerged in the last few years as new platforms to study thermodynamic systems. In this work, unprecedented fully communicated three-level systems are studied. First, different conditions were screened to selectively activate thiol/dithioacetal, thiol/thioester, and thiol/disulfide exchanges, individually or in pairs. Some of those conditions were applied, sequentially, to build multilayer dynamic systems wherein information, in the form of relative amounts of building blocks, can be directionally transmitted between different exchange pools. As far as we know, this is the first report of one synthetic dynamic chemical system where relationships between layers can be changed through network operations.

A tetrahedral molecular cage with a responsive vertex

Dynamic covalent chemistry (DCC) is a widely used method for the self-assembly of three-dimensional molecular architectures. The orthogonality of dynamic reactions is emerging as a versatile strategy for controlling product distributions in DCC, yet the application of this approach to the synthesis of 3D organic molecular cages is limited. We report the first system which employs the orthogonality of alkyne metathesis and dynamic imine exchange to prepare a molecular cage with a reversibly removable vertex. This study demonstrates the rational and controlled application of chemical orthogonality in DCC to prepare organic cages of expanded functionality which respond to chemical stimuli.

Coupling Metaloid-Directed Self-Assembly and Dynamic Covalent Systems as a Route to Large Organic Cages and Cyclophanes

The synthesis of large cyclic and caged disulfide structures was achieved by pnictogen-assisted iodine oxidation starting from self-assembled pnictogen thiolate complexes. The directing behavior of pnictogen enables rapid and selective syntheses of many discrete disulfide assemblies over competing oligomers/polymers, ranging from structures that are small and strained to those that are large and multifaceted, including 3D cages. Traditional cyclization reactions carried out under kinetic control are generally low-yielding, which often results in the formation of insoluble oligomers and polymers as unwanted side products. The prospect of self-assembling organic structures efficiently under thermodynamic control adds an attractive tool for the synthesis of cyclophanes and other large cage compounds. This method of metaloid-directed self-assembly within a dynamic covalent system allows for the rapid and discriminant self-assembly of disulfide cyclophanes without the consequences sometimes seen in traditional cyclophane syntheses such as poor yields, long reaction times, low ring-closing selectivity, and extensive purifications. The present paper provides an overview of this approach, explores the role of the pnictogen additive and solvent in this reaction, begins to test the limits of this strategy in complex 3D molecule formation, and extends our strategy to include one-pot syntheses that do not require the use of a pnictogen additive. This Viewpoint also includes an extended introduction to serve as a minireview highlighting the utility of a self-assembly approach to create organic cage structures. From a practical standpoint, the cyclophanes isolated from this method can serve as precursors in the production of insulating plastics (e.g., through the widely used parylene polymerization process, which uses derivatives of paracyclophane as monomers) or as potential hosts for molecular separations or capture.

Target-directed Dynamic Combinatorial Chemistry: A Study on Potentials and Pitfalls as Exemplified on a Bacterial Target

Target-directed dynamic combinatorial chemistry (DCC) is an emerging technique for the efficient identification of inhibitors of pharmacologically relevant targets. In this contribution, we present an application for a bacterial target, the lectin FimH, a crucial virulence factor of uropathogenic E. coli being the main cause of urinary tract infections. A small dynamic library of acylhydrazones was formed from aldehydes and hydrazides and equilibrated at neutral pH in presence of aniline as nucleophilic catalyst. The major success factors turned out to be an accordingly adjusted ratio of scaffolds and fragments, an adequate sample preparation prior to HPLC analysis, and the data processing. Only then did the ranking of the dynamic library constituents correlate well with affinity data. Furthermore, as a support of DCC applications especially to larger libraries, a new protocol for improved hit identification was established.

Dynamic Covalent Chemistry of Carbon Dioxide: Opportunities to Address Environmental Issues

Extraction and purification of basic chemicals from complex mixtures has been a persistent issue throughout the development of the chemical sciences. The chemical industry and academic research have grown over the centuries by following a deconstruction-reconstruction approach, reminiscent of the metabolism process. Chemists have designed and optimized extraction, purification, and transformation processes of molecules from natural deposits (fossil fuels, biomass, ores), in order to reassemble them into complex adducts. These highly selective and cost-effective techniques arose from developments in physical chemistry but also in supramolecular chemistry, long before the term was even coined. Thanks to the extremely diverse toolbox currently available to the scientific community, artificial molecular systems of increasing complexity can be built and integrated into high-technology products. If humanity has proven through the ages how gifted it can be at this deconstruction-reconstruction game, which has transformed the natural world to a human-shaped one, it has been confronted for more than a century by a new challenge: the deconstruction and reconstruction from a new type of deposit, the waste resulting from the mass production of disposable manufactured goods. In this Account, we will explore the potential contribution of controlled molecular and supramolecular self-assembly phenomena to the challenge of selective and efficient capture of valuable target molecules from mixtures found in postconsumer waste. While it may appear paradoxical to add more molecular ingredients to an already compositionally complex system in order to address a purification issue, we will compare the selectivity, yield, and cost of such an atypical procedure with traditional physical techniques. In the context of carbon dioxide capture or release, we will specifically focus on the coupling between this reversible covalent fixation of the gas by amines and an additional chemical equilibrium. This equilibrium may involve covalent or noncovalent bond formation between a supplementary species and either the unloaded reactant or the CO₂-loaded product. Thereby, this new reactive species may act as a CO₂ capture agonist or antagonist by either thermodynamically favoring the carbamation or decarbamation direction. Indeed, superagonism, the increase of CO₂ loading per amine site upon carbamation beyond the theoretical limit of 0.5, can be achieved using tightly bound cationic metal counterions. In all cases, upon binding and adduct formation, a mutual selection process occurs between one member of the CO₂-based dynamic combinatorial library and one agonist or antagonist, which can itself be contained in a complex mixture of analogues. If this adduct is the only species that, upon formation, can self-aggregate into a separate solid phase, selection and binding are accompanied by translocation, rendering the purification procedure operationally straightforward. This general strategy, based on a simple design of coupled molecular systems, may easily be implemented within new, disruptive technologies for selective extraction of target molecules, thereby providing a substantial environmental and economic benefit.

Proteintemplat-gesteuerte Fragmentligationen - von der molekularen Erkennung zur Wirkstofffindung

Proteintemplat‐gesteuerte Fragmentligationen sind ein neuartiges Konzept zur Unterstützung der Wirkstofffindung und können dazu beitragen, die Wirksamkeit von Proteinliganden zu verbessern. Es handelt sich dabei um chemische Reaktionen zwischen niedermolekularen Verbindungen (“Fragmenten”), die die Oberfläche eines Proteins als Reaktionsgefäß verwenden, um die Bildung eines Proteinliganden mit erhöhter Bindungsaffinität zu katalysieren. Die Methode nutzt die molekulare Erkennung kleiner reaktiver Fragmente durch die Proteine sowohl zur Assemblierung der Liganden als auch zur Identifizierung bioaktiver Fragmentkombinationen. Chemische Synthese und Bioassay werden dabei in einem Schritt vereint. Dieser Aufsatz diskutiert die biophysikalischen Grundlagen der reversiblen und irreversiblen Fragmentligationen und gibt einen Überblick über die Methoden, mit denen die durch das Proteintemplat gebildeten Ligationsprodukte detektiert werden können. Der chemische Reaktionsraum und aktuelle Anwendungen wie auch die Bedeutung dieses Konzeptes für die Wirkstofffindung werden erörtert.

Protein-Templated Fragment Ligations-From Molecular Recognition to Drug Discovery

Protein-templated fragment ligation is a novel concept to support drug discovery and can help to improve the efficacy of protein ligands. Protein-templated fragment ligations are chemical reactions between small molecules ("fragments") utilizing a protein's surface as a reaction vessel to catalyze the formation of a protein ligand with increased binding affinity. The approach exploits the molecular recognition of reactive small-molecule fragments by proteins both for ligand assembly and for the identification of bioactive fragment combinations. In this way, chemical synthesis and bioassay are integrated in one single step. This Review discusses the biophysical basis of reversible and irreversible fragment ligations and gives an overview of the available methods to detect protein-templated ligation products. The chemical scope and recent applications as well as future potential of the concept in drug discovery are reviewed.

Antiparallel Dynamic Covalent Chemistries

The ability to design reaction networks with high, but addressable complexity is a necessary prerequisite to make advanced functional chemical systems. Dynamic combinatorial chemistry has proven to be a useful tool in achieving complexity, however with some limitations in controlling it. Herein we introduce the concept of antiparallel chemistries, in which the same functional group can be channeled into one of two reversible chemistries depending on a controllable parameter. Such systems allow both for achieving complexity, by combinatorial chemistry, and addressing it, by switching from one chemistry to another by controlling an external parameter. In our design the two antiparallel chemistries are thiol-disulfide exchange and thio-Michael addition, sharing the thiol as the common building block. By means of oxidation and reduction the system can be reversibly switched from predominantly thio-Michael chemistry to predominantly disulfide chemistry, as well as to any intermediate state. Both chemistries operate in water, at room temperature, and at mildly basic pH, which makes them a suitable platform for further development of systems chemistry.

Dithioacetal Exchange: A New Reversible Reaction for Dynamic Combinatorial Chemistry

Reversibility of dithioacetal bond formation is reported under acidic mild conditions. Its utility for dynamic combinatorial chemistry was explored by combining it with orthogonal disulfide exchange. In such a setup, thiols are positioned at the intersection of both chemistries, constituting a connecting node between temporally separated networks.

A facile route to old and new cyclophanes via self-assembly and capture

Cyclophanes are a venerable class of macrocyclic and/or cage compounds that often feature high strain, unusual conformations and quite surprising properties, many of which are legendary in physical organic chemistry. However, the discovery of new, diverse cyclophanes and derivatives has been hindered by syntheses that are traditionally low-yielding, requiring long reaction times, laborious purification steps and often extreme conditions. Herein, we demonstrate a new self-assembly route to a variety of discrete cyclic and caged disulfide structures, which can then be kinetically captured upon sulfur extrusion at room temperature to give a diversity of new thioether (hetera)cyclophanes in high yield. In addition to the synthesis of novel macrocycles (dimers through hexamers), this process provides an improved route to a known macrobicyclic trithiacyclophane. This technique also enables the facile isolation of a tetrahedral macrotricyclic tetrathiacyclophane in two steps at an ambient temperature.

Doubly-dynamic-covalent polymers composed of oxime and oxanorbornene links

Two sets of reversible covalent linkages distributed in series along a polymer backbone were used to prepare a new class of doubly dynamic-covalent polymers capable of reversibly dissociatingviatwo distinct pathways.

Simultaneous Disulfide and Boronic Acid Ester Exchange in Dynamic Combinatorial Libraries

Dynamic combinatorial chemistry has emerged as a promising tool for the discovery of complex receptors in supramolecular chemistry. At the heart of dynamic combinatorial chemistry are the reversible reactions that enable the exchange of building blocks between library members in dynamic combinatorial libraries (DCLs) ensuring thermodynamic control over the system. If more than one reversible reaction operates in a single dynamic combinatorial library, the complexity of the system increases dramatically, and so does its possible applications. One can imagine two reversible reactions that operate simultaneously or two reversible reactions that operate independently. Both these scenarios have advantages and disadvantages. In this contribution, we show how disulfide exchange and boronic ester transesterification can function simultaneous in dynamic combinatorial libraries under appropriate conditions. We describe the detailed studies necessary to establish suitable reaction conditions and highlight the analytical techniques appropriate to study this type of system.

trans-Symmetric Dynamic Covalent Systems: Connected Transamination and Transimination Reactions

The development of chemical transaminations as a new type of dynamic covalent reaction is described. The key 1,3-proton shift is under complete catalytic control and can be conducted orthogonally to, or simultaneous with, transimination in the presence of an amine to rapidly yield two-dimensional dynamic systems with a high degree of complexity evolution. The transamination-transimination systems are proven to be fully reversible, stable over several days, compatible with a range of functional groups, and highly tunable. Kinetic studies show transamination to be the rate-limiting reaction in the network. Furthermore, it was discovered that readily available quinuclidine is a highly potent catalyst for aldimine transaminations. This study demonstrates how connected dynamic reactions give rise to significantly larger systems than the unconnected counterparts, and shows how reversible isomerizations can be utilized as an effective diversity-generating element.

Orthoester exchange: a tripodal tool for dynamic covalent and systems chemistry

Reversible covalent reactions have become an important tool in supramolecular chemistry and materials science. Here we introduce the acid-catalyzed exchange of O,O,O-orthoesters to the toolbox of dynamic covalent chemistry. We demonstrate that orthoesters readily exchange with a wide range of alcohols under mild conditions and we disclose the first report of an orthoester metathesis reaction. We also show that dynamic orthoester systems give rise to pronounced metal template effects, which can best be understood by agonistic relationships in a three-dimensional network analysis. Due to the tripodal architecture of orthoesters, the exchange process described herein could find unique applications in dynamic polymers, porous materials and host-guest architectures.

Dynamic combinatorial/covalent chemistry: a tool to read, generate and modulate the bioactivity of compounds and compound mixtures

Reversible covalent bond formation under thermodynamic control adds reactivity to self-assembled supramolecular systems, and is therefore an ideal tool to assess complexity of chemical and biological systems. Dynamic combinatorial/covalent chemistry (DCC) has been used to read structural information by selectively assembling receptors with the optimum molecular fit around a given template from a mixture of reversibly reacting building blocks. This technique allows access to efficient sensing devices and the generation of new biomolecules, such as small molecule receptor binders for drug discovery, but also larger biomimetic polymers and macromolecules with particular three-dimensional structural architectures. Adding a kinetic factor to a thermodynamically controlled equilibrium results in dynamic resolution and in self-sorting and self-replicating systems, all of which are of major importance in biological systems. Furthermore, the temporary modification of bioactive compounds by reversible combinatorial/covalent derivatisation allows control of their release and facilitates their transport across amphiphilic self-assembled systems such as artificial membranes or cell walls. The goal of this review is to give a conceptual overview of how the impact of DCC on supramolecular assemblies at different levels can allow us to understand, predict and modulate the complexity of biological systems.

The drive to life on wet and icy worlds

This paper presents a reformulation of the submarine alkaline hydrothermal theory for the emergence of life in response to recent experimental findings. The theory views life, like other self-organizing systems in the Universe, as an inevitable outcome of particular disequilibria. In this case, the disequilibria were two: (1) in redox potential, between hydrogen plus methane with the circuit-completing electron acceptors such as nitrite, nitrate, ferric iron, and carbon dioxide, and (2) in pH gradient between an acidulous external ocean and an alkaline hydrothermal fluid. Both CO2 and CH4 were equally the ultimate sources of organic carbon, and the metal sulfides and oxyhydroxides acted as protoenzymatic catalysts. The realization, now 50 years old, that membrane-spanning gradients, rather than organic intermediates, play a vital role in life's operations calls into question the idea of "prebiotic chemistry." It informs our own suggestion that experimentation should look to the kind of nanoengines that must have been the precursors to molecular motors-such as pyrophosphate synthetase and the like driven by these gradients-that make life work. It is these putative free energy or disequilibria converters, presumably constructed from minerals comprising the earliest inorganic membranes, that, as obstacles to vectorial ionic flows, present themselves as the candidates for future experiments. Key Words: Methanotrophy-Origin of life. Astrobiology 14, 308-343. The fixation of inorganic carbon into organic material (autotrophy) is a prerequisite for life and sets the starting point of biological evolution. (Fuchs, 2011 ) Further significant progress with the tightly membrane-bound H(+)-PPase family should lead to an increased insight into basic requirements for the biological transport of protons through membranes and its coupling to phosphorylation. (Baltscheffsky et al., 1999 ).

Thiazolidinones derived from dynamic systemic resolution of complex reversible-reaction networks

A complex dynamic system based on a network of multiple reversible reactions has been established. The network was applied to a dynamic systemic resolution protocol based on kinetically controlled lipase-catalyzed transformations. This resulted in the formation of cyclized products, where two thiazolidinone compounds were efficiently produced from a range of potential transformations.

Chloride-catalyzed, multicomponent self-assembly of arsenic thiolates

We present the observation that chloride serves as a simple catalyst for the acceleration of a self-assembly reaction between AsCl3 and dithiolate ligands (H2L) to form As2L3 assemblies. Studies on a model monomeric arsenic complex suggest that chloride may accelerate ligand exchange dynamics in pnictogen thiolates in general.

Dynamic molecular networks: from synthetic receptors to self-replicators

Dynamic combinatorial libraries (DCLs) are molecular networks in which the network members exchange building blocks. The resulting product distribution is initially under thermodynamic control. Addition of a guest or template molecule tends to shift the equilibrium towards compounds that are receptors for the guest. This Account gives an overview of our work in this area. We have demonstrated the template-induced amplification of synthetic receptors, which has given rise to several high-affinity binders for cationic and anionic guests in highly competitive aqueous solution. The dynamic combinatorial approach allows for the identification of new receptors unlikely to be obtained through rational design. Receptor discovery is possible and more efficient in larger libraries. The dynamic combinatorial approach has the attractive characteristic of revealing interesting structures, such as catenanes, even when they are not specifically targeted. Using a transition-state analogue as a guest we can identify receptors with catalytic activity. Although DCLs were initially used with the reductionistic view of identifying new synthetic receptors or catalysts, it is becoming increasingly apparent that DCLs are also of interest in their own right. We performed detailed computational studies of the effect of templates on the product distributions of DCLs using DCLSim software. Template effects can be rationalized by considering the entire network: the system tends to maximize global host-guest binding energy. A data-fitting analysis of the response of the global position of the DCLs to the addition of the template using DCLFit software allowed us to disentangle individual host-guest binding constants. This powerful procedure eliminates the need for isolation and purification of the various individual receptors. Furthermore, local network binding events tend to propagate through the entire network and may be harnessed for transmitting and processing of information. We demonstrated this possibility in silico through a simple dynamic molecular network that can perform AND logic with input and output in the form of molecules. Not only are dynamic molecular networks responsive to externally added templates, but they also adjust to internal template effects, giving rise to self-replication. Recently we have started to explore scenarios where library members recognize copies of themselves, resulting in a self-assembly process that drives the synthesis of the very molecules that self-assemble. We have developed a system that shows unprecedented mechanosensitive self-replication behavior: depending on whether the solution is shaken, stirred or not agitated, we have obtained a hexameric replicator, a heptameric replicator or no replication, respectively. We rationalize this behavior through a mechanism in which replication is promoted by mechanically-induced fragmentation of self-assembled replicator fibers. These results represent a new mode of self-replication in which mechanical energy liberates replicators from a self-inhibited state. These systems may also be viewed as self-synthesizing, self-assembling materials. These materials can be captured photochemically, converting a free-flowing fiber solution into a hydrogel through photo-induced homolytic disulfide exchange.

DCC in the development of nucleic acid targeted and nucleic acid inspired structures

Nucleic acids were one of the first biological targets explored with DCC, and research into the application has continued to yield novel and useful structures for sequence- and structure-selective recognition of oligonucleotides. This chapter reviews major developments in DNA- and RNA-targeted DCC, including methods under development for the conversion of DCC-derived lead compounds into probe molecules suitable for studies in vitro and in vivo. Innovative applications of DCC for the discovery of new materials based on nucleic acids and new methods for the modification of nucleic acid structure and function are also discussed.

The relative rates of thiol-thioester exchange and hydrolysis for alkyl and aryl thioalkanoates in water

This article reports rate constants for thiol-thioester exchange (k (ex)), and for acid-mediated (k (a)), base-mediated (k (b)), and pH-independent (k (w)) hydrolysis of S-methyl thioacetate and S-phenyl 5-dimethylamino-5-oxo-thiopentanoate-model alkyl and aryl thioalkanoates, respectively-in water. Reactions such as thiol-thioester exchange or aminolysis could have generated molecular complexity on early Earth, but for thioesters to have played important roles in the origin of life, constructive reactions would have needed to compete effectively with hydrolysis under prebiotic conditions. Knowledge of the kinetics of competition between exchange and hydrolysis is also useful in the optimization of systems where exchange is used in applications such as self-assembly or reversible binding. For the alkyl thioester S-methyl thioacetate, which has been synthesized in simulated prebiotic hydrothermal vents, k (a) = 1.5 × 10(-5) M(-1) s(-1), k (b) = 1.6 × 10(-1) M(-1) s(-1), and k (w) = 3.6 × 10(-8) s(-1). At pH 7 and 23°C, the half-life for hydrolysis is 155 days. The second-order rate constant for thiol-thioester exchange between S-methyl thioacetate and 2-sulfonatoethanethiolate is k (ex) = 1.7 M(-1) s(-1). At pH 7 and 23°C, with [R″S(H)] = 1 mM, the half-life of the exchange reaction is 38 h. These results confirm that conditions (pH, temperature, pK (a) of the thiol) exist where prebiotically relevant thioesters can survive hydrolysis in water for long periods of time and rates of thiol-thioester exchange exceed those of hydrolysis by several orders of magnitude.

Aqueous solution properties of disulfide-linked fluorinated gemini and cleaved monomeric thiol surfactants

We prepared a fluorinated gemini surfactant containing a disulfide bond in its spacer chain, [C₈F₁₇(CH₂)₃N(CH₃)₂CH₂CH₂SSCH₂CH₂N(CH₃)₂(CH₂)₃C₈F₁₇]2Cl, and its analogue with a hexamethylene spacer. Monomeric thiol surfactant, [C₈F₁₇(CH₂)₃N(CH₃)₂CH₂CH₂SH]Cl, was readily produced by the cleavage of the gemini surfactant using dithiothreitol in water. The critical micelle concentration was determined using surface tension, conductivity, and fluorescence probe methods. The critical micelle concentration of the monomeric surfactant was significantly larger than that of the gemini surfactant. The surface tension of aqueous solution for the cleaved monomeric thiol surfactant returned gradually to the original value through the formation of the disulfide bond via air oxidation.

Reversible covalent chemistries compatible with the principles of constitutional dynamic chemistry: new reactions to create more diversity

An approach to make chemical diversity space more manageable is to search for smaller molecules, or fragments, and then combine or elaborate these fragments. Dynamic Combinatorial Chemistry (DCC) is a powerful approach whereby a number of molecular elements each with binding potential can be reversibly combined via covalent or noncovalent linkages to generate a dynamic library of products under thermodynamic equilibrium. Once a target molecule has been added, the distribution of products can be shifted to favor products that bind to the target. Thus the approach can be employed to identify products that selectively recognize the target. Although the size of the repertoire of reversible covalent reactions suitable for DCC has increased significantly over the past 5-10 years, the discovery of new reactions that satisfy all the criteria of reversibility and biocompatibility remains an exciting challenge for chemists. Increasing the number of chemical reactions will enable the engineering of larger and more diverse DCLs, which remains a key step toward a broader use of DCC. In this review, we aim to provide a nonexhaustive list of reversible covalent reactions that are compatible with the concept of DCC, focusing mainly on the most recent examples that were reported in the literature in the past 5 years.