Dynamic covalent chemistry

Dynamic covalent chemistry relates to chemical reactions carried out reversibly under conditions of equilibrium control. The reversible nature of the reactions introduces the prospects of "error checking" and "proof-reading" into synthetic processes where dynamic covalent chemistry operates. Since the formation of products occurs under thermodynamic control, product distributions depend only on the relative stabilities of the final products. In kinetically controlled reactions, however, it is the free energy differences between the transition states leading to the products that determines their relative proportions. Supramolecular chemistry has had a huge impact on synthesis at two levels: one is noncovalent synthesis, or strict self-assembly, and the other is supramolecular assistance to molecular synthesis, also referred to as self-assembly followed by covalent modification. Noncovalent synthesis has given us access to finite supermolecules and infinite supramolecular arrays. Supramolecular assistance to covalent synthesis has been exploited in the construction of more-complex systems, such as interlocked molecular compounds (for example, catenanes and rotaxanes) as well as container molecules (molecular capsules). The appealing prospect of also synthesizing these types of compounds with complex molecular architectures using reversible covalent bond forming chemistry has led to the development of dynamic covalent chemistry. Historically, dynamic covalent chemistry has played a central role in the development of conformational analysis by opening up the possibility to be able to equilibrate configurational isomers, sometimes with base (for example, esters) and sometimes with acid (for example, acetals). These stereochemical "balancing acts" revealed another major advantage that dynamic covalent chemistry offers the chemist, which is not so easily accessible in the kinetically controlled regime: the ability to re-adjust the product distribution of a reaction, even once the initial products have been formed, by changing the reaction's environment (for example, concentration, temperature, presence or absence of a template). This highly transparent, yet tremendously subtle, characteristic of dynamic covalent chemistry has led to key discoveries in polymer chemistry. In this review, some recent examples where dynamic covalent chemistry has been demonstrated are shown to emphasise the basic concepts of this area of science.     

Par-delà la synthèse : l’auto-organisation

The evolution of the universe from the particle to the thinking organism has taken place through self-organization. Chemistry has a major role to play in understanding these processes leading to the generation of complex matter. Chemistry has developed a highly powerful molecular synthetic chemistry, mastering the combination and recombination of atoms into increasingly complex molecules through selective chemical reactions. Supramolecular chemistry is harnessing intermolecular forces for the generation of informed supramolecular systems and processes through supramolecular synthetic chemistry implementing molecular information carried by electromagnetic interactions. Supramolecular chemistry has been actively exploring systems undergoing self-organization, i.e., systems capable of spontaneously generating well-defined functional supramolecular architectures by self-assembly from their components, under the control of interactional molecular recognition events, thus behaving as programmed chemical systems. Molecular chemistry may similarly take advantage of the selectivity of covalent reactions to assemble complex molecular architectures through self-organization processes implementing functional molecular recognition. Supramolecular/non-covalent and molecular/covalent SELF-ORGANIZATION may thus be considered as the ULTIMATE SYNTHETIC CHEMISTRY, whereby chemical objects at both levels are generated on the basis of recognition processes involving either interactional or reactional features. Illustrations from the supramolecular domain will serve as illustrations. Supramolecular entities as well as molecules containing reversible bonds are able to undergo a continuous change in constitution by reorganization and exchange of building blocks. This capability defines a Constitutional Dynamic Chemistry (CDC) on both the molecular and supramolecular levels. CDC introduces a paradigm shift with respect to constitutionally static chemistry. It takes advantage of dynamic constitutional diversity to allow variation and selection and thus leads towards the emergence of adaptive and evolutive chemistry.     

Supramolecular polymer chemistry

Supramolecular chemistry aims at constructing highly complex chemical systems and advanced materials by designing arrays of components held together by intermolecular forces. The implementation of molecular recognition and information offers means for controlling the evolution and the architecture of supramolecular entities and of organised phases as they spontaneously build up from their components through self‐organisation.     

Supramolecular chemistry — Scope and perspectives: Molecules — Supermolecules — Molecular devices

Supramolecular chemistry is the chemistry of the intermolecular bond, covering the structures and functions of the entities formed by association of two or more chemical species. Molecular recognition in the supermolecules formed by receptor-substrate binding rests on the principles of molecular complementarity, as found in spherical and tetrahedral recognition, linear recognition by co-receptors, metallo-receptors, amphilic receptors and anion coordination. Supramolecular catalysis by receptors bearing reactive groups effects bond cleavage reactions as well as synthetic bond formation via co-catalysis. Lipophilic receptor molecules act as selective carriers for various substrates and allow the setting up of coupled transport processes linked to electron and proton gradients or to light. Whereas endo-receptors bind substrates in molecular cavities by convergent interactions, exo-receptors rely on interactions between the surfaces of the receptor and the substrate; thus new types of receptors such as the metallonucleates may be designed. In combination with polymolecular assemblies, receptors, carriers and catalysts may lead to molecular and supramolecular devices, defined as structurally organized and functionally integrated chemical systems built on supramolecular architectures. Their recognition, transfer and transformation features are analyzed specifically from the point of view of molecular devices that would operate via photons, electrons or ions, thus defining the fields of molecular photonics, electronics and ionics. Introduction of photosensitive groups yields photoactive receptors for the design of light conversion and charge separation centres. Redox active polyolefinic chains represent molecular wires for electron transfer through membranes. Tubular mesophases formed by stacking of suitable macrocyclic receptors may lead to ion channels. Molecular self-assembling occurs with acyclic ligands that form complexes with a double helical structure. Such developments in molecular and supramolecular design and engineering open perspectives towards the realization of molecular photonic, electronic and ionic devices, that would perform highly selective recognition, reaction and transfer operations for signal and information processing at the molecular level.     

Supramolecular chemistry and crystal engineering

Supramolecular chemistry is the chemistry of molecular ensembles and intermolecular interactions. Currently it is a major, interdisciplinary branch of science dealing with chemical, physical, biological and technological aspects of the creation and study of complex chemical systems based upon non-valent interactions. Crystal engineering is a direction of supramolecular chemistry aimed at the design of periodic structures with a desired supramolecular organization. This paper shortly reviews the goals and research objects of supramolecular chemistry and crystal engineering and lists the most important historical facts and the literature.     

Emerging supramolecular chemistry of gases

Molecular recognition of gases is an emerging area of chemistry. Supramolecular chemistry helps us to understand how gases interact with biological molecules and offers delicate insights into the mechanisms of their physiological activity. Principles of molecular recognition have been used for gas sensing, and have provided fundamental knowledge about the structure and dynamics of receptor-analyte complexes, and novel materials for gas sensing and storage have been developed. Supramolecular chemistry is also enabling us to learn how to transform gases into synthetically useful reagents. The rational design of novel catalysts for gas conversion and, more recently, encapsulation complexes with gases open novel directions in preparative synthetic chemistry.     

Dynamic combinatorial libraries: new opportunities in systems chemistry

Combinatorial chemistry is a tool for selecting molecules with special properties. Dynamic combinatorial chemistry started off aiming to be just that. However, unlike ordinary combinatorial chemistry, the interconnectedness of dynamic libraries gives them an extra dimension. An understanding of these molecular networks at systems level is essential for their use as a selection tool and creates exciting new opportunities in systems chemistry. In this feature article we discuss selected examples and considerations related to the advanced exploitation of dynamic combinatorial libraries for their originally conceived purpose of identifying strong binding interactions. Also reviewed are examples illustrating a trend towards increasing complexity in terms of network behaviour and reversible chemistry. Finally, new applications of dynamic combinatorial chemistry in self-assembly, transport and self-replication are discussed.     

Caught in Action: Visualizing Dynamic Nanostructures Within Supramolecular Systems Chemistry

Supramolecular systems chemistry has been an area of active research to develop nanomaterials with life-like functions. Progress in systems chemistry relies on our ability to probe the nanostructure formation in solution. Often visualizing the dynamics of nanostructures which transform over time is a formidable challenge. This necessitates a paradigm shift from dry sample imaging towards solution-based techniques. We review the application of state-of-the-art techniques for real-time, in situ visualization of dynamic self-assembly processes. We present how solution-based techniques namely optical super-resolution microscopy, solution-state atomic force microscopy, liquid-phase transmission electron microscopy, molecular dynamics simulations and other emerging techniques are revolutionizing our understanding of active and adaptive nanomaterials with life-like functions. This Review provides the visualization toolbox and futuristic vision to tap the potential of dynamic nanomaterials.     

Quantum chemistry simulation on quantum computers: theories and experiments

It has been claimed that quantum computers can mimic quantum systems efficiently in the polynomial scale. Traditionally, those simulations are carried out numerically on classical computers, which are inevitably confronted with the exponential growth of required resources, with the increasing size of quantum systems. Quantum computers avoid this problem, and thus provide a possible solution for large quantum systems. In this paper, we first discuss the ideas of quantum simulation, the background of quantum simulators, their categories, and the development in both theories and experiments. We then present a brief introduction to quantum chemistry evaluated via classical computers followed by typical procedures of quantum simulation towards quantum chemistry. Reviewed are not only theoretical proposals but also proof-of-principle experimental implementations, via a small quantum computer, which include the evaluation of the static molecular eigenenergy and the simulation of chemical reaction dynamics. Although the experimental development is still behind the theory, we give prospects and suggestions for future experiments. We anticipate that in the near future quantum simulation will become a powerful tool for quantum chemistry over classical computations.     

Noncovalent interactions in inorganic supramolecular chemistry based in heavy metals. Quantum chemistry point of view

Complexity is a concept that is being considered in chemistry as it has shown potential to reveal interesting phenomena. Thus, it is possible to study chemical phenomena in a new approach called systems chemistry. The systems chemistry has an organization and function, which are regulated by the interactions among its components. At the simplest level, noncovalent interactions between molecules can lead to the emergence of large structures. Consequently, it is possible to go from the molecular to the supramolecular systems chemistry, which aims to develop chemical systems highly complex through intra- and intermolecular forces. Proper use of the interactions previously mentioned allow a glimpse of supramolecular system chemistry in many tasks such as structural properties reflecting certain behaviors in the chemistry of materials, for example, electrical and optical, processes of molecular recognition and among others. In the last time, within this area, inorganic supramolecular systems chemistry has been developed. Those systems have a structural orientation which is defined by certain forces that predominate in the associations among molecules. It is possible to recognize these forces as hydrogen bonding, π-π stacking, halogen bonding, electrostatic, hydrophobic, charge transfer, metal coordination, and metallophilic interactions. The presence of these forces in supramolecular system yields certain properties such as light absorption and luminescence. The quantum theoretical modeling plays an important role in the designing of the supramolecular system. The goal is to apply supramolecular principles in order to understand the associated forces in many inorganic molecules that include heavy metals for instance gold, platinum, and mercury. Relevant systems will be studied in detail, considering functional aspects such as enhanced coordination of functionalized molecular self-assembly, electronic and optoelectronic properties.     

Supramolecular coordination chemistry: the synergistic effect of serendipity and rational design

Supramolecular coordination compounds bear exceptional advantages over their organic counterparts. They are available in one-pot reactions and in high yields and display physical properties that are generally inaccessible with organic species. Moreover, their weak, reversible, noncovalent bonding interactions facilitate error checking and self-correction. This Review emphasizes the achievements in supramolecular coordination chemistry initiated by serendipity and their materialization based on rational design. The recognition of similarities in the synthesis of different supramolecular assemblies allows prediction of potential results in related cases. Supramolecular synthesis obeys guidelines comparable to the "lead sheet" used by small jazz ensembles for improvisation and therefore more often leads to unpredicted results. The combination of detailed symmetry considerations with the basic rules of coordination chemistry has only recently allowed for the design of rational strategies for the construction of a variety of nanosized systems with specified size and shape.     

Supramolecular Chemistry—Scope and Perspectives Molecules,Supermolecules, and Molecular Devices (Nobel Lecture)

Supramolecular chemistry is the chemistry of the intermolecular bond, covering the structures and functions of the entities formed by association of two or more chemical species. Molecular recognition in the supermolecules formed by receptor-substrate binding rests on the principles of molecular complementarity, as found in spherical and tetrahedral recognition, linear recognition by coreceptors, metalloreceptors, amphiphilic receptors, and anion coordination. Supramolecular catalysis by receptors bearing reactive groups effects bond cleavage reactions as well as synthetic bond formation via cocatalysis. Lipophilic receptor molecules act as selective carriers for various substrates and make it possible to set up coupled transport processes linked to electron and proton gradients or to light. Whereas endoreceptors bind substrates in molecular cavities by convergent interactions, exoreceptors rely on interactions between the surfaces of the receptor and the substrate; thus new types of receptors, such as the metallonucleates, may be designed. In combination with polymolecular assemblies, receptors, carriers, and catalysts may lead to molecular and supramolecular devices, defined as structurally organized and functionally integrated chemical systems built on supramolecular architectures. Their recognition, transfer, and transformation features are analyzed specifically from the point of view of molecular devices that would operate via photons, electrons, or ions, thus defining fields of molecular photonics, electronics, and ionics. Introduction of photosensitive groups yields photoactive receptors for the design of light-conversion and charge-separation centers. Redox-active polyolefinic chains represent molecular wires for electron transfer through membranes. Tubular mesophases formed by stacking of suitable macrocyclic receptors may lead to ion channels. Molecular self-assembling occurs with acyclic ligands that form complexes of double-helical structure. Such developments in molecular and supramolecular design and engineering open perspectives towards the realization of molecular photonic, electronic, and ionic devices that would perform highly selective recognition, reaction, and transfer operations for signal and information processing at the molecular level.     

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

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

Self-organization of supramolecular microporous structures based on carbon nanotubes and benzene

The molecular dynamic has been used to study the self-organization of carbon nanotubes into an array in the presence of coordinating molecules. Methane adsorption on model systems has been calculated. It has been shown that secondary porosity formed by the nanotubes makes it possible to accumulate methane at the level of the best commercial adsorbents. Supramolecular systems have been synthesized on the basis of carbon nanotubes and benzene molecules used as coordinators according to a scheme realized in the numerical simulation. The specific adsorption of nitrogen at 293 K on the obtained supramolecular structure has been shown to increase by more than tenfold as compared with that on initial nanotubes.     

Solid-state NMR spectroscopic methods in chemistry

Over the last decades, NMR spectroscopy has grown into an indispensable tool for chemical analysis, structure determination, and the study of dynamics in organic, inorganic, and biological systems. It is commonly used for a wide range of applications from the characterization of synthetic products to the study of molecular structures of systems such as catalysts, polymers, and proteins. Although most NMR experiments are performed on liquid-state samples, solid-state NMR is rapidly emerging as a powerful method for the study of solid samples and materials. This Review outlines some of the developments of solid-state NMR spectroscopy, including techniques such as cross-polarization, magic-angle spinning, multiple-pulse sequences, homo- and heteronuclear decoupling and recoupling techniques, multiple-quantum spectroscopy, and dynamic angle spinning, as well as their applications to structure determination. Modern solid-state NMR spectroscopic techniques not only produce spectra with a resolution close to that of liquid-state spectra, but also capitalize on anisotropic interactions, which are often unavailable for liquid samples. With this background, the future of solid-state NMR spectroscopy in chemistry appears to be promising, indeed.     

Deoxyribonucleotides: the unusual chemistry and biochemistry of DNA precursors

Deoxyribonucleotides, monomers of macromolecular DNA and the chemical matter of genes, have received surprisingly little attention among chemists and molecular biologists alike, although their origin, properties, and mechanism of enzyme-catalyzed formation bear unique chemical traits which are the basis of DNA replication. Apart from providing insights in bioorganic free radical chemistry, present interest in deoxyribonucleotides stems from the expected demand of hundreds of kilograms per year for DNA chips and antisense constructs used in gene therapy, difficult to produce by conventional methods. A novel approach towards deoxyribonucleotide, and hence DNA formation in a putative primordial 'RNA world' has also recently emerged.     

Emergences of supramolecular chemistry: from supramolecular chemistry to supramolecular science

We describe the field of supramolecular chemistry as a consequence of the progress of chemistry from its premises to recent achievements. Supramolecular chemistry has been claimed to be an emergent field of research taking its roots in chemistry. According to the definitions of emergences related to hierarchy or more recently to scope, supramolecular chemistry is shown to have bottom-up or top-down emergences. The bottom-up emergence, directly related to hierarchy by definition, opens up the world of nanochemistry and nanomaterials while the top-down one, attributable to scope due to the implication of supramolecular chemistry in other fields of research, open the world of supramolecular biochemistry. Both emergences lead supramolecular chemistry to become a supramolecular science. Combining supramolecular chemistry with biology opens new direction in the study of life and it origin.     

Perspectives in Chemistry—Steps towards Complex Matter

Chemistry is progressively unraveling the processes that underlie the evolution of matter towards states of higher complexity and the generation of novel features along the way by self‐organization under the pressure of information. Chemistry has evolved from molecular to supramolecular to become adaptive chemistry by way of constitutional dynamics, which allow for adaptation, through component selection in an equilibrating set. Dynamic systems can be represented by weighted dynamic networks that define the agonistic and antagonistic relationships between the different constituents linked through component exchange. Such networks can be switched through amplification/up‐regulation of the best adapted/fittest constituent(s) in a dynamic set. Accessing higher level functions such as training, learning, and decision making represent future lines of development for adaptive chemical systems.     

Perspectives in Supramolecular Chemistry—From Molecular Recognition towards Molecular Information Processing and Self-Organization

The selective binding of a substrate by a molecular receptor to form a supramolecular species involves molecular recognition which rests on the molecular information stored in the interacting species. The functions of supermolecules cover recognition, as well as catalysis and transport. In combination with polymolecular organization, they open ways towards molecular and supramolecular devices for information processing and signal generation. The development of such devices requires the design of molecular components performing a given function (e.g., photoactive, electroactive, ionoactive, thermoactive, or chemoactive) and suitable for assembly into an organized array. Light-conversion devices and charge-separation centers have been realized with photoactive cryptates formed by receptors containing photosensitive groups. Eleclroactive and ionoactive devices are required for carrying information via electronic and ionic signals. Redox-active polyolefinic chains, like the “caroviologens”, represent molecular wires for electron transfer through membranes. Push-pull polyolefins possess marked nonlinear optical properties. Tubular mesophases, formed by organized stacking of suitable macro-cyclic components, as well as “chundle”-type structures, based on bundles of chains grafted onto a macrocyclic support, represent approaches to ion channels. Lipophilic macrocyclic units form Langmuir-Blodgett films that may display molecular recognition at the air-water interface. Supramolecular chemistry has relied on more or less preorganized molecular receptors for effecting molecular recognition, catalysis, and transport processes. A step beyond preorganization consists in the design of systems undergoing self-organization, that is, systems capable of spontaneously generating a well-defined supramolecular architecture by self-assembling from their components under a given set of conditions. Several approaches to self-assembling systems have been pursued: the formation of helical metal complexes, the double-stranded helicates, which result from the spontaneous organization of two linear polybipyridine ligands into a double helix by binding of specific metal ions; the generation of mesophases and liquid crystalline polymers of supramolecular nature from complementary components, amounting to macroscopic expression of molecular recognition; the molecular-recognition-directed formation of ordered solid-state structures. Endowing photo-, electro-, and ionoactive components with recognition elements opens perspectives towards the design of programmed molecular and supramolecular systems capable of self-assembly into organized and functional supramolecular devices. Such systems may be able to perform highly selective operations of recognition, reaction, transfer, and structure generation for signal and information processing at the molecular and supramolecular levels.