Supramolecular chemistry

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Supramolecular chemistry refers to the branch of chemistry concerning chemical systems composed of a discrete number of molecules. The strength of the forces responsible for spatial organization of the system range from weak intermolecular forces, electrostatic charge, or hydrogen bonding to strong covalent bonding, provided that the electronic coupling strength remains small relative to the energy parameters of the component. [1] [2] [ page needed ] While traditional chemistry concentrates on the covalent bond, supramolecular chemistry examines the weaker and reversible non-covalent interactions between molecules. [3] These forces include hydrogen bonding, metal coordination, hydrophobic forces, van der Waals forces, pi–pi interactions and electrostatic effects. [4]

Contents

Important concepts advanced by supramolecular chemistry include molecular self-assembly, molecular folding, molecular recognition, host–guest chemistry, mechanically-interlocked molecular architectures, and dynamic covalent chemistry. [5] The study of non-covalent interactions is crucial to understanding many biological processes that rely on these forces for structure and function. Biological systems are often the inspiration for supramolecular research.

History

The existence of intermolecular forces was first postulated by Johannes Diderik van der Waals in 1873. However, Nobel laureate Hermann Emil Fischer developed supramolecular chemistry's philosophical roots. In 1894, [13] Fischer suggested that enzyme–substrate interactions take the form of a "lock and key", the fundamental principles of molecular recognition and host–guest chemistry. In the early twentieth century non-covalent bonds were understood in gradually more detail, with the hydrogen bond being described by Latimer and Rodebush in 1920.

The use of these principles led to an increasing understanding of protein structure and other biological processes. For instance, the important breakthrough that allowed the elucidation of the double helical structure of DNA occurred when it was realized that there are two separate strands of nucleotides connected through hydrogen bonds. The use of non-covalent bonds is essential to replication because they allow the strands to be separated and used to template new double stranded DNA. Concomitantly, chemists began to recognize and study synthetic structures based on non-covalent interactions, such as micelles and microemulsions.

Eventually, chemists were able to take these concepts and apply them to synthetic systems. The breakthrough came in the 1960s with the synthesis of the crown ethers by Charles J. Pedersen. Following this work, other researchers such as Donald J. Cram, Jean-Marie Lehn and Fritz Vögtle became active in synthesizing shape- and ion-selective receptors, and throughout the 1980s research in the area gathered a rapid pace with concepts such as mechanically interlocked molecular architectures emerging.

The importance of supramolecular chemistry was established by the 1987 Nobel Prize for Chemistry which was awarded to Donald J. Cram, Jean-Marie Lehn, and Charles J. Pedersen in recognition of their work in this area. [14] The development of selective "host–guest" complexes in particular, in which a host molecule recognizes and selectively binds a certain guest, was cited as an important contribution.

In the 1990s, supramolecular chemistry became even more sophisticated, with researchers such as James Fraser Stoddart developing molecular machinery and highly complex self-assembled structures, and Itamar Willner developing sensors and methods of electronic and biological interfacing. During this period, electrochemical and photochemical motifs became integrated into supramolecular systems in order to increase functionality, research into synthetic self-replicating system began, and work on molecular information processing devices began. The emerging science of nanotechnology also had a strong influence on the subject, with building blocks such as fullerenes, nanoparticles, and dendrimers becoming involved in synthetic systems.

Control

Thermodynamics

Supramolecular complexes are formed by non-covalent interactions between two chemical moieties, which can be described as an host and a guest. Most commonly, the interacting species are held together by hydrogen bonds. The definition excludes compounds formed by electrostatic interactions, which are called ion pairs.

In solution, the host H, guest G, and complexes HpGq, will be in equilibrium with each other. In the simplest case, p=q=1, the equilibrium can be written as

The value of the equilibrium constant, K, for this reaction can, in principle, be determined by any of the techniques described below. Some examples are shown in the following table. [15]

Log K1,1 values for complexes of medicinal interest in methanol at 25 °C
Li+Na+K+Rb+Cs+
Valinomycin <0.70.674.95.264.42
Enniatin 1.282.422.922.242.34
Nigericin -4.75.65.0-
Monensin 3.66.55.04.33.6

The Gibbs free energy change, , for this reaction is the sum of an enthalpy term, and an entropy term .

Both and values can be determined at a given temperature, , by means of Isothermal titration calorimetry. For an example, see Sessler. et.al. [16] In that example a macrocyclic ring with 4 protonated nitrogen atoms encapsulates a chloride anion; illustrations of ITC data and a titration curve are reproduced in Steed&Atwood. [15] (pp 15–16) The value of the equilibrium constant and the stoichiometry of the species formed were found to be strongly solvent-dependent. With nitromethane solutions values of ΔH = 8.55 kJmol−1 and ΔS = -9.1 JK−1mol−1 were obtained.

Environment

The molecular environment around a supramolecular system is also of prime importance to its operation and stability. Many solvents have strong hydrogen bonding, electrostatic, and charge-transfer capabilities, and are therefore able to become involved in complex equilibria with the system, even breaking complexes completely. For this reason, the choice of solvent can be critical.

Concepts

A ribosome is a biological machine that uses protein dynamics on nanoscales Protein translation.gif
A ribosome is a biological machine that uses protein dynamics on nanoscales

Molecular self-assembly

Molecular self-assembly is the construction of systems without guidance or management from an outside source (other than to provide a suitable environment). The molecules are directed to assemble through non-covalent interactions. Self-assembly may be subdivided into intermolecular self-assembly (to form a supramolecular assembly), and intramolecular self-assembly (or folding as demonstrated by foldamers and polypeptides). Molecular self-assembly also allows the construction of larger structures such as micelles, membranes, vesicles, liquid crystals, and is important to crystal engineering. [17]

Molecular recognition and complexation

Molecular recognition is the specific binding of a guest molecule to a complementary host molecule to form a host–guest complex. Often, the definition of which species is the "host" and which is the "guest" is arbitrary. The molecules are able to identify each other using non-covalent interactions. Key applications of this field are the construction of molecular sensors and catalysis. [18] [19] [20] [21]

Template-directed synthesis

Molecular recognition and self-assembly may be used with reactive species in order to pre-organize a system for a chemical reaction (to form one or more covalent bonds). It may be considered a special case of supramolecular catalysis. Non-covalent bonds between the reactants and a "template" hold the reactive sites of the reactants close together, facilitating the desired chemistry. This technique is particularly useful for situations where the desired reaction conformation is thermodynamically or kinetically unlikely, such as in the preparation of large macrocycles. This pre-organization also serves purposes such as minimizing side reactions, lowering the activation energy of the reaction, and producing desired stereochemistry. After the reaction has taken place, the template may remain in place, be forcibly removed, or may be "automatically" decomplexed on account of the different recognition properties of the reaction product. The template may be as simple as a single metal ion or may be extremely complex.[ citation needed ]

Mechanically interlocked molecular architectures

Mechanically interlocked molecular architectures consist of molecules that are linked only as a consequence of their topology. Some non-covalent interactions may exist between the different components (often those that were used in the construction of the system), but covalent bonds do not. Supramolecular chemistry, and template-directed synthesis in particular, is key to the efficient synthesis of the compounds. Examples of mechanically interlocked molecular architectures include catenanes, rotaxanes, molecular knots, molecular Borromean rings [22] and ravels. [23]

Dynamic covalent chemistry

In dynamic covalent chemistry covalent bonds are broken and formed in a reversible reaction under thermodynamic control. While covalent bonds are key to the process, the system is directed by non-covalent forces to form the lowest energy structures. [24]

Biomimetics

Many synthetic supramolecular systems are designed to copy functions of biological systems. These biomimetic architectures can be used to learn about both the biological model and the synthetic implementation. Examples include photoelectrochemical systems, catalytic systems, protein design and self-replication. [25]

Imprinting

Molecular imprinting describes a process by which a host is constructed from small molecules using a suitable molecular species as a template. After construction, the template is removed leaving only the host. The template for host construction may be subtly different from the guest that the finished host binds to. In its simplest form, imprinting uses only steric interactions, but more complex systems also incorporate hydrogen bonding and other interactions to improve binding strength and specificity. [26]

Molecular machinery

Molecular machines are molecules or molecular assemblies that can perform functions such as linear or rotational movement, switching, and entrapment. These devices exist at the boundary between supramolecular chemistry and nanotechnology, and prototypes have been demonstrated using supramolecular concepts. [27] Jean-Pierre Sauvage, Sir J. Fraser Stoddart and Bernard L. Feringa shared the 2016 Nobel Prize in Chemistry for the 'design and synthesis of molecular machines'. [28]

Building blocks

Supramolecular systems are rarely designed from first principles. Rather, chemists have a range of well-studied structural and functional building blocks that they are able to use to build up larger functional architectures. Many of these exist as whole families of similar units, from which the analog with the exact desired properties can be chosen.

Synthetic recognition motifs

Macrocycles

Macrocycles are very useful in supramolecular chemistry, as they provide whole cavities that can completely surround guest molecules and may be chemically modified to fine-tune their properties.

Structural units

Many supramolecular systems require their components to have suitable spacing and conformations relative to each other, and therefore easily employed structural units are required. [31]

Photo-chemically and electro-chemically active units

Biologically-derived units

Applications

Materials technology

Supramolecular chemistry has found many applications, [33] in particular molecular self-assembly processes have been applied to the development of new materials. Large structures can be readily accessed using bottom-up synthesis as they are composed of small molecules requiring fewer steps to synthesize. Thus most of the bottom-up approaches to nanotechnology are based on supramolecular chemistry. [34] Many smart materials [35] are based on molecular recognition. [36]

Catalysis

A major application of supramolecular chemistry is the design and understanding of catalysts and catalysis. Non-covalent interactions are extremely important in catalysis, binding reactants into conformations suitable for reaction and lowering the transition state energy of reaction. Template-directed synthesis is a special case of supramolecular catalysis. Encapsulation systems such as micelles, dendrimers, and cavitands [37] are also used in catalysis to create microenvironments suitable for reactions (or steps in reactions) to progress that is not possible to use on a macroscopic scale.

Medicine

Design based on supramolecular chemistry has led to numerous applications in the creation of functional biomaterials and therapeutics. [38] Supramolecular biomaterials afford a number of modular and generalizable platforms with tunable mechanical, chemical and biological properties. These include systems based on supramolecular assembly of peptides, host–guest macrocycles, high-affinity hydrogen bonding, and metal–ligand interactions.

A supramolecular approach has been used extensively to create artificial ion channels for the transport of sodium and potassium ions into and out of cells. [39]

Supramolecular chemistry is also important to the development of new pharmaceutical therapies by understanding the interactions at a drug binding site. The area of drug delivery has also made critical advances as a result of supramolecular chemistry providing encapsulation and targeted release mechanisms. [40] In addition, supramolecular systems have been designed to disrupt protein–protein interactions that are important to cellular function. [41]

Data storage and processing

Supramolecular chemistry has been used to demonstrate computation functions on a molecular scale. In many cases, photonic or chemical signals have been used in these components, but electrical interfacing of these units has also been shown by supramolecular signal transduction devices. Data storage has been accomplished by the use of molecular switches with photochromic and photoisomerizable units, by electrochromic and redox-switchable units, and even by molecular motion. Synthetic molecular logic gates have been demonstrated on a conceptual level. Even full-scale computations have been achieved by semi-synthetic DNA computers.

See also

Related Research Articles

<span class="mw-page-title-main">Molecular recognition</span> Type of non-covalent bonding

The term molecular recognition refers to the specific interaction between two or more molecules through noncovalent bonding such as hydrogen bonding, metal coordination, hydrophobic forces, van der Waals forces, π-π interactions, halogen bonding, or resonant interaction effects. In addition to these direct interactions, solvents can play a dominant indirect role in driving molecular recognition in solution. The host and guest involved in molecular recognition exhibit molecular complementarity. Exceptions are molecular containers, including e.g. nanotubes, in which portals essentially control selectivity.

<span class="mw-page-title-main">Host–guest chemistry</span> Supramolecular structures held together other than by covalent bonds

In supramolecular chemistry, host–guest chemistry describes complexes that are composed of two or more molecules or ions that are held together in unique structural relationships by forces other than those of full covalent bonds. Host–guest chemistry encompasses the idea of molecular recognition and interactions through non-covalent bonding. Non-covalent bonding is critical in maintaining the 3D structure of large molecules, such as proteins and is involved in many biological processes in which large molecules bind specifically but transiently to one another.

<span class="mw-page-title-main">Cucurbituril</span> Ring molecule able to store other molecules within itself

In host-guest chemistry, cucurbiturils are macrocyclic molecules made of glycoluril monomers linked by methylene bridges. The oxygen atoms are located along the edges of the band and are tilted inwards, forming a partly enclosed cavity (cavitand). The name is derived from the resemblance of this molecule with a pumpkin of the family of Cucurbitaceae.

<span class="mw-page-title-main">Supramolecular assembly</span> Complex of molecules non-covalently bound together

In chemistry, a supramolecular assembly is a complex of molecules held together by noncovalent bonds. While a supramolecular assembly can be simply composed of two molecules, or a defined number of stoichiometrically interacting molecules within a quaternary complex, it is more often used to denote larger complexes composed of indefinite numbers of molecules that form sphere-, rod-, or sheet-like species. Colloids, liquid crystals, biomolecular condensates, micelles, liposomes and biological membranes are examples of supramolecular assemblies, and their realm of study is known as supramolecular chemistry. The dimensions of supramolecular assemblies can range from nanometers to micrometers. Thus they allow access to nanoscale objects using a bottom-up approach in far fewer steps than a single molecule of similar dimensions.

In chemistry, a non-covalent interaction differs from a covalent bond in that it does not involve the sharing of electrons, but rather involves more dispersed variations of electromagnetic interactions between molecules or within a molecule. The chemical energy released in the formation of non-covalent interactions is typically on the order of 1–5 kcal/mol. Non-covalent interactions can be classified into different categories, such as electrostatic, π-effects, van der Waals forces, and hydrophobic effects.


Dynamic covalent chemistry (DCvC) is a synthetic strategy employed by chemists to make complex molecular and supramolecular assemblies from discrete molecular building blocks. DCvC has allowed access to complex assemblies such as covalent organic frameworks, molecular knots, polymers, and novel macrocycles. Not to be confused with dynamic combinatorial chemistry, DCvC concerns only covalent bonding interactions. As such, it only encompasses a subset of supramolecular chemistries.

<span class="mw-page-title-main">Salt bridge (protein and supramolecular)</span> Combination of hydrogen and ionic bonding in chemistry

In chemistry, a salt bridge is a combination of two non-covalent interactions: hydrogen bonding and ionic bonding. Ion pairing is one of the most important noncovalent forces in chemistry, in biological systems, in different materials and in many applications such as ion pair chromatography. It is a most commonly observed contribution to the stability to the entropically unfavorable folded conformation of proteins. Although non-covalent interactions are known to be relatively weak interactions, small stabilizing interactions can add up to make an important contribution to the overall stability of a conformer. Not only are salt bridges found in proteins, but they can also be found in supramolecular chemistry. The thermodynamics of each are explored through experimental procedures to access the free energy contribution of the salt bridge to the overall free energy of the state.

In chemistry, a resorcinarene is a macrocycle, or a cyclic oligomer, based on the condensation of resorcinol (1,3-dihydroxybenzene) and an aldehyde. Resorcinarenes are a type of calixarene. Other types of resorcinarenes include the related pyrogallolarenes and octahydroxypyridines, derived from pyrogallol and 2,6-dihydroxypyridine, respectively.

In chemistry, mechanically interlocked molecular architectures (MIMAs) are molecules that are connected as a consequence of their topology. This connection of molecules is analogous to keys on a keychain loop. The keys are not directly connected to the keychain loop but they cannot be separated without breaking the loop. On the molecular level, the interlocked molecules cannot be separated without the breaking of the covalent bonds that comprise the conjoined molecules; this is referred to as a mechanical bond. Examples of mechanically interlocked molecular architectures include catenanes, rotaxanes, molecular knots, and molecular Borromean rings. Work in this area was recognized with the 2016 Nobel Prize in Chemistry to Bernard L. Feringa, Jean-Pierre Sauvage, and J. Fraser Stoddart.

<span class="mw-page-title-main">Cation–π interaction</span>

Cation–π interaction is a noncovalent molecular interaction between the face of an electron-rich π system (e.g. benzene, ethylene, acetylene) and an adjacent cation (e.g. Li+, Na+). This interaction is an example of noncovalent bonding between a monopole (cation) and a quadrupole (π system). Bonding energies are significant, with solution-phase values falling within the same order of magnitude as hydrogen bonds and salt bridges. Similar to these other non-covalent bonds, cation–π interactions play an important role in nature, particularly in protein structure, molecular recognition and enzyme catalysis. The effect has also been observed and put to use in synthetic systems.

In polymer chemistry and materials science, the term "polymer" refers to large molecules whose structure is composed of multiple repeating units. Supramolecular polymers are a new category of polymers that can potentially be used for material applications beyond the limits of conventional polymers. By definition, supramolecular polymers are polymeric arrays of monomeric units that are connected by reversible and highly directional secondary interactions–that is, non-covalent bonds. These non-covalent interactions include van der Waals interactions, hydrogen bonding, Coulomb or ionic interactions, π-π stacking, metal coordination, halogen bonding, chalcogen bonding, and host–guest interaction. The direction and strength of the interactions are precisely tuned so that the array of molecules behaves as a polymer in dilute and concentrated solution, as well as in the bulk.

<span class="mw-page-title-main">Molecular sensor</span>

A molecular sensor or chemosensor is a molecular structure that is used for sensing of an analyte to produce a detectable change or a signal. The action of a chemosensor, relies on an interaction occurring at the molecular level, usually involves the continuous monitoring of the activity of a chemical species in a given matrix such as solution, air, blood, tissue, waste effluents, drinking water, etc. The application of chemosensors is referred to as chemosensing, which is a form of molecular recognition. All chemosensors are designed to contain a signalling moiety and a recognition moiety, that is connected either directly to each other or through a some kind of connector or a spacer. The signalling is often optically based electromagnetic radiation, giving rise to changes in either the ultraviolet and visible absorption or the emission properties of the sensors. Chemosensors may also be electrochemically based. Small molecule sensors are related to chemosensors. These are traditionally, however, considered as being structurally simple molecules and reflect the need to form chelating molecules for complexing ions in analytical chemistry. Chemosensors are synthetic analogues of biosensors, the difference being that biosensors incorporate biological receptors such as antibodies, aptamers or large biopolymers.

<span class="mw-page-title-main">Molecular self-assembly</span> Movement of molecules into a defined arrangement without outside influence

In chemistry and materials science, molecular self-assembly is the process by which molecules adopt a defined arrangement without guidance or management from an outside source. There are two types of self-assembly: intermolecular and intramolecular. Commonly, the term molecular self-assembly refers to the former, while the latter is more commonly called folding.

<span class="mw-page-title-main">Dynamic combinatorial chemistry</span>

Dynamic combinatorial chemistry (DCC); also known as constitutional dynamic chemistry (CDC) is a method to the generation of new molecules formed by reversible reaction of simple building blocks under thermodynamic control. The library of these reversibly interconverting building blocks is called a dynamic combinatorial library (DCL). All constituents in a DCL are in equilibrium, and their distribution is determined by their thermodynamic stability within the DCL. The interconversion of these building blocks may involve covalent or non-covalent interactions. When a DCL is exposed to an external influence, the equilibrium shifts and those components that interact with the external influence are stabilised and amplified, allowing more of the active compound to be formed.

Coordination cages are three-dimensional ordered structures in solution that act as hosts in host–guest chemistry. They are self-assembled in solution from organometallic precursors, and often rely solely on noncovalent interactions rather than covalent bonds. Coordinate bonds are useful in such supramolecular self-assembly because of their versatile geometries. However, there is controversy over calling coordinate bonds noncovalent, as they are typically strong bonds and have covalent character. The combination of a coordination cage and a guest is a type of inclusion compound. Coordination complexes can be used as "nano-laboratories" for synthesis, and to isolate interesting intermediates. The inclusion complexes of a guest inside a coordination cage show intriguing chemistry as well; often, the properties of the cage will change depending on the guest. Coordination complexes are molecular moieties, so they are distinct from clathrates and metal-organic frameworks.

<span class="mw-page-title-main">Two-dimensional polymer</span>

A two-dimensional polymer (2DP) is a sheet-like monomolecular macromolecule consisting of laterally connected repeat units with end groups along all edges. This recent definition of 2DP is based on Hermann Staudinger's polymer concept from the 1920s. According to this, covalent long chain molecules ("Makromoleküle") do exist and are composed of a sequence of linearly connected repeat units and end groups at both termini.

<span class="mw-page-title-main">Supramolecular catalysis</span> Field of chemistry

Supramolecular catalysis is not a well-defined field but it generally refers to an application of supramolecular chemistry, especially molecular recognition and guest binding, toward catalysis. This field was originally inspired by enzymatic system which, unlike classical organic chemistry reactions, utilizes non-covalent interactions such as hydrogen bonding, cation-pi interaction, and hydrophobic forces to dramatically accelerate rate of reaction and/or allow highly selective reactions to occur. Because enzymes are structurally complex and difficult to modify, supramolecular catalysts offer a simpler model for studying factors involved in catalytic efficiency of the enzyme. Another goal that motivates this field is the development of efficient and practical catalysts that may or may not have an enzyme equivalent in nature.

Cyclobis(paraquat-<i>p</i>-phenylene) Chemical compound

Cyclobis(paraquat-p-phenylene) belongs to the class of cyclophanes, and consists of aromatic units connected by methylene bridges. It is able to incorporate small guest molecule and has played an important role in host–guest chemistry and supramolecular chemistry.

Latticial metal complex or grid complex is a supramolecular complex of several metal atoms and coordinating ligands which form a grid-like structural motif. The structure formation usually occurs while on thermodynamic molecular self-assembly. They have properties that make them interesting for information technology as the future storage materials. Chelate ligands are used as ligands in tetrahedral or octahedral structures, which mostly use nitrogen atoms in pyridine like ring systems other than donor centers. Suitable metal ions are in accordance with octahedral coordinating transition metal ions such as Mn or rare tetrahedral Coordinating such as Ag used.

<span class="mw-page-title-main">Macromolecular cages</span>

Macromolecular cages have three dimensional chambers surrounded by a molecular framework. Macromolecular cage architectures come in various sizes ranging from 1-50 nm and have varying topologies as well as functions. They can be synthesized through covalent bonding or self-assembly through non-covalent interactions. Most macromolecular cages that are formed through self-assembly are sensitive to pH, temperature, and solvent polarity.

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