Supramolecular Chemistry

Supramolecular chemistry refers to the area of chemistry that focuses on the noncovalent bonding interactions of molecules. While traditional chemistry focuses on the covalent bond, supramolecular chemistry examines the weaker and reversible noncovalent interactions between molecules. These forces include hydrogen bonding, metal coordination, hydrophobic forces, van der Waals forces, pi-pi interactions and electrostatic effects. Important concepts that have been demonstrated by supramolecular chemistry include molecular self-assembly, folding, molecular recognition, host-guest chemistry, mechanically-interlocked molecular architectures, and dynamic covalent chemistry. The study of non-covalent interactions is crucial to understanding many biological processes from cell structure to vision that rely on these forces for structure and function. Biological systems are often the inspiration for supramolecular research.

Electrostatics

Electrostatics is the branch of science that deals with the phenomena arising from what seems to be stationary electric charges. Since ancient history it is known that some materials attract light particles after rubbing. The greek word for amber, (electron), gave name for many areas of natural science. Electrostatic phenomena arise from the forces that electric charges carry out on each other. Such forces are described by Coulomb's law. Electrostatic phenomena include such as simple as the attraction of plastic wrap to your hand after you remove it from a package to apparently spontaneous explosion of grain silos, to damage of electronic components during manufacturing, to the operation of photocopiers. Electrostatics involves the buildup of charge on the surface of objects due to contact with other surfaces. Although charge exchange happens whenever any two surfaces contact and separate, the effects of charge exchange are usually only noticed when at least one of the surfaces has a high resistance to electrical flow. This is because the charges that transfer to or from the highly resistive surface are more or less trapped there for a long enough time for their effects to be observed. These charges then remain on the object until they either bleed off to ground or are quickly neutralized by a discharge: e.g., the familiar phenomenon of a static 'shock' is caused by the neutralization of charge built up in the body from contact with nonconductive surface

Host-guest chemistry

In supramolecular chemistry, host-guest chemistry describes complexes that are composed of two or more molecules or ions held together in unique structural relationships by hydrogen bonding or by ion pairing or by Van der Waals force other than those of full covalent bonds.

The host component is defined as an organic molecule or ion whose binding sites converge in the complex and the guest component is defined as any molecule or ion whose binding sites diverge in the complex.

History

The existence of intermolecular forces was first postulated by Johannes Diderik van der Waals in 1873. However, it is with Nobel laureate Hermann Emil Fischer that supramolecular chemistry has its philosophical roots. In 1890, Fischer suggested that enzyme-substrate interactions take the form of a "lock and key", pre-empting the concepts of molecular recognition and host-guest chemistry. In the early twentieth century noncovalent 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 noncovalent 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 noncovalent 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 Vogtle 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. 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.

DNA

Deoxyribonucleic acid (DNA) is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms and some viruses. The main role of DNA molecules is the long-term storage of information. DNA is often compared to a set of blueprints or a recipe, since it contains the instructions needed to construct other components of cells, such as proteins and RNA molecules. The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in regulating the use of this genetic information.

Chemically, DNA is a long polymer of simple units called nucleotides, with a backbone made of sugars and phosphate groups joined by ester bonds. Attached to each sugar is one of four types of molecules called bases. It is the sequence of these four bases along the backbone that encodes information. This information is read using the genetic code, which specifies the sequence of the amino acids within proteins. The code is read by copying stretches of DNA into the related nucleic acid RNA, in a process called transcription.

Within cells, DNA is organized into structures called chromosomes. These chromosomes are duplicated before cells divide, in a process called DNA replication. Eukaryotic organisms (animals, plants, and fungi) store their DNA inside the cell nucleus, while in prokaryotes (bacteria and archae) it is found in the cell's cytoplasm. Within the chromosomes, chromatin proteins such as histones compact and organize DNA. These compact structures guide the interactions between DNA and other proteins, helping control which parts of the DNA are transcribed

Photochemistry

Photochemistry, a sub-discipline of chemistry, is the study of the interactions between atoms, small molecules, and light (or electromagnetic radiation.

Like most scientific disciplines, photochemistry utilizes the SI or metric measurement system. Important units and constants that show up regularly include the meter (and variants such as centimeter, millimeter, micrometer, nanometer, etc.), seconds, hertz, joules, moles, the gas constant R, and the Boltzmann constant. These units and constants are also integral to the field of physical chemistry.

The first law of photochemistry, known as the Grotthuss-Draper law (for chemists Theodor Grotthuss and John W. Draper), states that light must be absorbed by a chemical substance in order for a photochemical reaction to take place.

The second law of photochemistry, the Stark-Einstein law, states that for each photon of light absorbed by a chemical system, only one molecule is activated for a photochemical reaction. This is also known as the photoequivalence law and was derived by Albert Einstein at the time when the quantum (photon) theory of light was being developed.

Photochemistry may also be introduced to laymen as a reaction that proceeds with the absorption of light. Normally a reaction (not just a photochemical reaction) occurs when a molecule gains the necessary activation energy to undergo change. A simple example can be the combustion of gasoline (a hydrocarbon) into carbon dioxide and water. This is a chemical reaction where one or more molecules/chemical species are converted into others. For this reaction to take place activation energy should be supplied. The activation energy is provided in the form of heat or a spark. In case of photochemical reactions light provides the activation energy.

Nanoparticle

A nanoparticle which historically has included nanopowder, nanocluster, and nanocrystal is a small particle with at least one dimension less than 100 nm. This definition can be fleshed out further in order to remove ambiguity from future nano nomenclature. A nanoparticle is an amorphous or semicrystalline zero dimensional (0D) nano structure with at least one dimension between 10 and 100nm and a relatively large (≥ 15%) size dispersion. A nanocluster is an amorphous/semicrystalline nanostructure with at least one dimension being between 1-10nm and a narrow size distribution.This distinction is an extension of the term "cluster" which is used in inorganic/organometallic chemistry to indicate small molecular cages of fixed sizes. A nanopowder is an agglomeration of noncrystalline nanostructural subunits with at least one dimention less than 100nm. A nanocrystal is any nanomaterial with at least one dimension ≤ 100nm and that is singlecrystalline. Any particle which exhibits regions of crystallinity should be termed nanoparticle or nanocluster based on dimensions. Nanoparticle research is currently an area of intense scientific research, due to a wide variety of potential applications in biomedical, optical, and electronic fields. The National Nanotechnology Initiative of the United States government has driven huge amounts of state funding exclusively for nanoparticle research.

Chemical equilibrium

In a chemical process, chemical equilibrium is the state in which the chemical activities or concentrations of the reactants and products have no net change over time. Usually, this would be the state that results when the forward chemical process proceeds at the same rate as their reverse reaction. The reaction rates of the forward and reverse reactions are generally not zero but, being equal, there are no net changes in any of the reactant or product concentrations. This process is called dynamic equilibrium

Thermodynamics

Supramolecular chemistry deals with subtle interactions, and consequently control over the processes involved can require great precision. In particular, noncovalent bonds have low energies and often no activation energy for formation. As demonstrated by the Arrhenius equation, this means that, unlike in covalent bond-forming chemistry, the rate of bond formation is not increased at higher temperatures. In fact, chemical equilibrium equations show that the low bond energy results in a shift towards the breaking of supramolecular complexes at higher tem
However, low temperatures can also be problematic to supramolecular processes. Supramolecular chemistry can require molecules to distort into thermodynamically disfavored conformations (e.g. during the "slipping" synthesis of rotaxanes), and may include some covalent chemistry that goes along with the supramolecular. In addition, the dynamic nature of supramolecular chemistry is utilized in many systems (e.g. molecular mechanics), and cooling the system would slow these processes.

Thus, thermodynamics is an important tool to design, control, and study supramolecular chemistry. Perhaps the most striking example is that of warm-blooded biological systems, which cease to operate entirely outside a very narrow termperature range.

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.