Supramolecular chemistrySupramolecular 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.
Host–guest chemistryIn 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.
CalixareneA calixarene is a macrocycle or cyclic oligomer based on a methylene-linked phenols. With hydrophobic cavities that can hold smaller molecules or ions, calixarenes belong to the class of cavitands known in host–guest chemistry. Calixarene nomenclature is straightforward and involves counting the number of repeating units in the ring and including it in the name. A calix[4]arene has 4 units in the ring and a calix[6]arene has 6.
Molecular recognitionThe 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.
Cation–π interactionCation–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.
CavitandIn chemistry, a cavitand is a container-shaped molecule. The cavity of the cavitand allows it to engage in host–guest chemistry with guest molecules of a complementary shape and size. The original definition proposed by Cram includes many classes of molecules: cyclodextrins, calixarenes, pillararenes and cucurbiturils. However, modern usage in the field of supramolecular chemistry specifically refers to cavitands formed on a resorcinarene scaffold by bridging adjacent phenolic units.
Supramolecular assemblyIn 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 (e.g., a DNA double helix or an inclusion compound), 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.
Molecular machineMolecular machines are a class of molecules typically described as an assembly of a discrete number of molecular components intended to produce mechanical movements in response to specific stimuli, mimicking macromolecular devices such as switches and motors. Naturally occurring or biological molecular machines are responsible for vital living processes such as DNA replication and ATP synthesis. Kinesins and ribosomes are examples of molecular machines, and they often take the form of multi-protein complexes.
Molecular motorMolecular motors are natural (biological) or artificial molecular machines that are the essential agents of movement in living organisms. In general terms, a motor is a device that consumes energy in one form and converts it into motion or mechanical work; for example, many protein-based molecular motors harness the chemical free energy released by the hydrolysis of ATP in order to perform mechanical work. In terms of energetic efficiency, this type of motor can be superior to currently available man-made motors.
Optical tweezersOptical tweezers (originally called single-beam gradient force trap) are scientific instruments that use a highly focused laser beam to hold and move microscopic and sub-microscopic objects like atoms, nanoparticles and droplets, in a manner similar to tweezers. If the object is held in air or vacuum without additional support, it can be called optical levitation. The laser light provides an attractive or repulsive force (typically on the order of piconewtons), depending on the relative refractive index between particle and surrounding medium.
MacrocycleMacrocycles are often described as molecules and ions containing a ring of twelve or more atoms. Classical examples include the crown ethers, calixarenes, porphyrins, and cyclodextrins. Macrocycles describe a large, mature area of chemistry. The formation of macrocycles by ring-closure is called macrocylization. Pioneering work was reported for studies on terpenoid macrocycles. The central challenge to macrocyclization is that ring-closing reactions do not favor the formation of large rings.
Molecular modellingMolecular modelling encompasses all methods, theoretical and computational, used to model or mimic the behaviour of molecules. The methods are used in the fields of computational chemistry, drug design, computational biology and materials science to study molecular systems ranging from small chemical systems to large biological molecules and material assemblies. The simplest calculations can be performed by hand, but inevitably computers are required to perform molecular modelling of any reasonably sized system.
Magnetic tweezersMagnetic tweezers (MT) are scientific instruments for the manipulation and characterization of biomolecules or polymers. These apparatus exert forces and torques to individual molecules or groups of molecules. It can be used to measure the tensile strength or the force generated by molecules. Most commonly magnetic tweezers are used to study mechanical properties of biological macromolecules like DNA or proteins in single-molecule experiments. Other applications are the rheology of soft matter, and studies of force-regulated processes in living cells.
Docking (molecular)In the field of molecular modeling, docking is a method which predicts the preferred orientation of one molecule to a second when a ligand and a target are bound to each other to form a stable complex. Knowledge of the preferred orientation in turn may be used to predict the strength of association or binding affinity between two molecules using, for example, scoring functions. The associations between biologically relevant molecules such as proteins, peptides, nucleic acids, carbohydrates, and lipids play a central role in signal transduction.
CatenaneIn macromolecular chemistry, a catenane () is a mechanically interlocked molecular architecture consisting of two or more interlocked macrocycles, i.e. a molecule containing two or more intertwined rings. The interlocked rings cannot be separated without breaking the covalent bonds of the macrocycles. They are conceptually related to other mechanically interlocked molecular architectures, such as rotaxanes, molecular knots or molecular Borromean rings.
SugarSugar is the generic name for sweet-tasting, soluble carbohydrates, many of which are used in food. Simple sugars, also called monosaccharides, include glucose, fructose, and galactose. Compound sugars, also called disaccharides or double sugars, are molecules made of two bonded monosaccharides; common examples are sucrose (glucose + fructose), lactose (glucose + galactose), and maltose (two molecules of glucose). White sugar is a refined form of sucrose. In the body, compound sugars are hydrolysed into simple sugars.
PHIn chemistry, pH (piːˈeɪtʃ ), also referred to as acidity, historically denotes "potential of hydrogen" (or "power of hydrogen"). It is a scale used to specify the acidity or basicity of an aqueous solution. Acidic solutions (solutions with higher concentrations of hydrogen () ions) are measured to have lower pH values than basic or alkaline solutions. The pH scale is logarithmic and inversely indicates the activity of hydrogen ions in the solution. where [H+] is the equilibrium molar concentration (mol/L) of H+ in the solution.
AromaticityIn chemistry, aromaticity means the molecule has cyclic (ring-shaped) structures with pi bonds in resonance (those containing delocalized electrons). Aromatic rings give increased stability compared to saturated compounds having single bonds, and other geometric or connective non-cyclic arrangements with the same set of atoms. Aromatic rings are very stable and do not break apart easily. Organic compounds that are not aromatic are classified as aliphatic compounds—they might be cyclic, but only aromatic rings have enhanced stability.
Linear combinationIn mathematics, a linear combination is an expression constructed from a set of terms by multiplying each term by a constant and adding the results (e.g. a linear combination of x and y would be any expression of the form ax + by, where a and b are constants). The concept of linear combinations is central to linear algebra and related fields of mathematics. Most of this article deals with linear combinations in the context of a vector space over a field, with some generalizations given at the end of the article.
X-ray tubeAn X-ray tube is a vacuum tube that converts electrical input power into X-rays. The availability of this controllable source of X-rays created the field of radiography, the imaging of partly opaque objects with penetrating radiation. In contrast to other sources of ionizing radiation, X-rays are only produced as long as the X-ray tube is energized. X-ray tubes are also used in CT scanners, airport luggage scanners, X-ray crystallography, material and structure analysis, and for industrial inspection.
