Supramolecular chemistry

supramolecular chemistry is the branch of chemistry that studies supramolecular interactions, that is, between molecules. His study is inspired by biology and is based on the mechanisms of synthetic organic and inorganic chemistry.

Supramolecular chemistry studies molecular recognition and the formation of supramolecular aggregates, which gives us the opportunity to understand and interface the biological world, complex systems and nanotechnology. Supramolecular chemistry is defined as:

"Supramolecular chemistry is the chemistry of intermolecular bonds, covering the structures and functions of entities formed by association of two or more chemical species" J-M- Lehn

"Supramolecular chemistry is defined as chemistry beyond the molecular, a chemistry of designed intermolecular interactions" F. Vögtle

The supramolecular aggregates that are the object of study by supramolecular chemistry are very diverse, ranging from biological systems involving a large number of molecules that spontaneously organize themselves to form larger structures, such as monolayers, bilayers, micelles, complexes enzymes and lipoproteins, to assemblies of few molecules that undergo a phenomenon of molecular self-assembly, such as catenanes, rotaxanes, molecular polyhedra and other related architectures.

History

The concept of supramolecular chemistry was defined for the first time in 1978 by Nobel Prize winner Jean-Marie Lehn, who defined it as “the chemistry of intermolecular bonds” but before that, various works were carried out that led to the development of supramolecular chemistry as we know it today.

In 1810 Humphry Davy proved that chlorine is a chemical element and gave it that name because of its greenish-yellow color. In 1823 the studies on chlorine continued and Michael Faraday designed the formula for chlorine hydrates. In 1891, the scientists Villiers and Hebd carried out research where they discovered cyclodextrins, which are considered host molecules; These concepts gave way to the most important contributions such as the one made by Alfred Werner in 1893, introducing the term coordination chemistry, a basic concept for understanding supramolecular chemistry.

In 1894 Nobel laureate Hermann Emil Fischer developed the philosophical roots of supramolecular chemistry, suggesting that enzyme-substrate interactions resemble a "lock-key" interaction, a fundamental principle of molecular recognition and host-guest chemistry. In the early 20th century, noncovalent bonds were understood in more detail, such as the hydrogen bond described by Latimer and Rodebush in 1920.

The use of these principles led to a greater understanding of the structure of proteins and other biological processes. For example, the breakthrough that led to the elucidation of the double helix structure of DNA occurred when it was found that there are two distinct strands of nucleotides connected by hydrogen bonds. The use of non-covalent bonds is essential for replication, as they allow the strands to be separated and used for new double-stranded DNA template. At the same time, chemists began to recognize and study synthetic structures based on noncovalent interactions, such as micelles and microemulsions.

Over time, chemists were able to take these concepts and apply them to synthetic systems. The breakthrough came in the 1960s with the synthesis of crown ethers by Charles J. Pedersen. Following this work, other researchers such as Donald James Cram, Jean-Marie Lehn, and Fritz Vögtle continued to work with this chemistry throughout the 1980s, winning them the Nobel Prize in Chemistry in 1987.

Bottom-Up

The systems Supramoleculars work particularly because of the arrangement of their components. using molecules as building blocks, in the same way you can create molecules independent with different species of atoms to create complex molecules of which will be used to create a system with properties based on those of the molecules.

The only alternatives that have been found to create complex systems are by bottom-up means the which offers a great diversity of methods of which are still being investigated to create nano-structures that could not be understood if we use top-bottom media due to the difficulty of manipulation at that scale.

The sources from which we can ensure that the bottom-up approximation is reliable if found primarily in biological systems or originating in nature. These systems do not use covalent interactions, so their formation entropy costs are practically nil since most of them are reversible interactions, how to create nanostructures synthetic mimicking biological systems so that they can recognize components of molecules is the targets that are want to achieve with the bottom-up approach.

Molecular Recognition

Molecular recognition explains the unions that develop in a specific way in a molecule towards its molecular receptor. Molecules that achieve efficient and selective recognition are called host molecules (host) which can be cyclic compounds called macrocyles that have cavities of specific sizes inside, useful for housing other defined smaller molecules. as guests (host)

This molecular recognition is related to the catalytic processes either through the use of synthetic or natural catalysts such as enzymes that form supramolecular compounds together with the substrate through three essential steps that are:

• Molecular recognition between catalyst and substrate to form a complex, the selectivity of the catalyst is defined.
• The reaction speed is accelerated while the activation energy decreases in order to stabilize the reaction and define the state of transition.
• Regeneration of the catalyst with the release of the producer starting a new cycle, where the speed will define the number of catalytic cycles to be carried out for a while of time.

A concept that concretely explains molecular recognition is the lock-key model proposed in 1884 by the German biochemist E.Fisher

Car assembly.

Some of the best-known biological systems that use self-assembly is DNA replication in a structure with double helixes linked by hydrogen bonds where the interactions are made by 4 molecules that join 2 by 2: Guanine (G) with Cytosine (C) forming 3 hydrogen bonds and Adenine (A) with Thiamine (T) forming 2 hydrogen bonds, creating the binding interactions between the 2 DNA helices.

In this structure, it only depends on the affinity of the molecules so that the hydrogen bonds are created, the different combinations between the molecules being nothing effective so that they unite as they do with the conventional combination. The errors that could occur in the formation of the DNA structure are highly null since the formation entropy prevents the molecules from being arranged in wrong combinations, which would provide us with a much more efficient, optimal and faster way to create nano systems. structured in the future so that there are no costs due to manufacturing errors.

Metalosupramolecular

Coordination compounds are used in inorganic chemistry to be able to create structures composed of an organic part with some ion or metal which remain for the purposes of their properties to create nanostructures, these systems depend on the factors in which they are synthesized Since by varying their general dimensions large changes in the way in which they will interact with molecules that are willing to change.

These structures are generally polygons in two dimensions where the size and Angle where the ligands make connection with other structures will make the system optimal for the molecules that have affinity with it, in this way the selectivity will have a specific spectrum with possible species that are in its environment.

Grids

They involve a series of parallel components in an orientation orthogonal to another series of ligand metal ions in a cross section creating a lattice as more ions are added to the grids.

Entropy of formation

Entropy costs are take into consideration when creating nano-structures for their arrangement and adequate aggregation and are not unstable on which their degrees of freedom and can be estimated in different ways in different types of aggregation.

Entropy of translation

The magnitude of the entropy of translation reflects the possibility of different arrangements in a molecule in a given space but in liquid environments where the same can be applied to gases, however, being a gas, its entropy will be much greater than that of a so liquid makes it more difficult to predict the entropy of formation in such structures in computational modelling.

Rotational Entropy

The molecular density of a molecule is defined as its molecular mass in KG/molecule divided by its volume in organic compounds composed mainly of carbon, nitrogen and oxygen given in spherical structures in solution, the aggregation of other components will depend on the inertia in which the molecule rotates in a solution.

Vibrational Entropy

The frequency of the vibrations to which a molecule can be subjected can have effects when adding other molecules, some of them need vibrations to be able to be added correctly in the appropriate places of others, that is why the high Frequencies will increase entropy and in some cases it may be favorable for linking or aggregation, on the other hand, low frequencies will favor systems that need a slight vibration.

Supramolecular interactions

Non-covalent interaction forces

Supramolecular interactions help us understand how species are held together through a variety of non-covalent interactions where their strength ranges from 2-300 kJmol-1. The non-covalent interactions used for the formation of supramolecular systems are:

• Ionics

Ion-Ion: This interaction occurs when two species with opposite charges are in contact, so they do not show dependence on directionality. One aspect that affects the stability of the interaction is the ionic strength of the medium, which can be analyzed using the DebyeHückel equation. For the development of these interactions, solvents with low dielectric constants such as chloroform, acetonitrile or dichloromethane are usually used and avoiding water in the medium is highly competitive.

ion-dipole: These interactions are established between a neutral species and another that will be charged, so they will show dependence on the orientation of the dipole in such a way that when the molecule orients its dipole towards the charged species, a bond force of about 5-200 kJmol-1

In Supramolecular chemistry, there are systems that explain this interaction, such as complexes formed by crown ethers with different ammonium derivatives, where the interaction will be established between the oxygens of the ether and the hydrogen of the host, which will be positively charged, and the complexation of the hosts with alkali and alkaline earth metals. The formation of rotaxanes has also been observed through cyclodextrins used as macrocilles and bipyridine cations as axes.

• Population

Dipole-dipole: There are two types of dipole-dipole interactions, one is when the two adjacent molecules align their dipoles where it is only necessary that only one of the molecules is properly oriented, the other type is when both molecules align simultaneously its two dipole moments, in this case it is dependent on directionality. The systems most frequently detected as forming these interactions are polar neutrals and are usually those with carbonyl, nitro and amine groups, such as C=O/C=O,C=O/CN,

• De Van Der Waals

Within these interactions there are three types of associations between dipoles, which arise from fluctuations in the distribution of electrons between two species that are close; these interactions will show dependence on the polarization of the molecules, being the most polarizable those that form the strong interactions.

The Keersom interaction is when molecules are interacting at certain distances and have permanent dipoles, so they align to those dipoles in an attractive way, on the other hand when a molecule with a permanent dipole induces a dipole in another nearby one are known as Debye interaction and by Ultimately the interaction between two nonpolar but polarizable molecules is known as the London interaction. In supramolecular chemistry, more specifically in host-guest systems, these interactions play important roles.

• Interactions π-π stacking

Hydrogen Bridge Representation

Supramolecular chemistry is based on biological behaviors to imitate them and develop reaction techniques. π-π bonds are of great importance as they can be observed in protein stacking and the structure of DNA.

• hydrogen bridge

This interaction occurs between partially negative donor species with other proton acceptors and a hydrogen located between them. It is considered that hydrogen bonds with linear geometry are stronger, so the directionality requirement makes it selective when forming complexes, so within Supramolecular chemistry the interaction that will be responsible for an organized and stable assembly is considered but it is difficult to do this in an aqueous system since water is an excellent donor and acceptor of hydrogen bonds

Supramolecular aggregates

As an example:

• Macrocycle
• Criptizing
• Enzima
• Coloid
• Micela
• Cyclodextrin
• Liposoma
• Plasma membrane
• Lipoprotein
• Ribosome
• Chromatin
• Cyclofane
• I can