Supramolecular chemistry is the domain 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. Whereas traditional chemistry concentrates on the covalent bond, supramolecular chemistry examines the weaker and reversible non-covalent interactions between molecules; these forces include hydrogen bonding, metal coordination, hydrophobic forces, van der Waals forces, pi–pi interactions and electrostatic effects. Important concepts advanced by supramolecular chemistry include molecular self-assembly, molecular folding, molecular recognition, host–guest chemistry, mechanically-interlocked molecular architectures, dynamic covalent chemistry; 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 the inspiration for supramolecular research. 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, 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 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. 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, 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, awarded to Donald J. Cram, Jean-Marie Lehn, 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 more sophisticated, with researchers such as James Fraser Stoddart developing molecular machinery and complex self-assembled structures, Itamar Willner developing sensors and methods of electronic and biological interfacing. During this period and photochemical motifs became integrated into supramolecular systems in order to increase functionality, research into synthetic self-replicating system began, work on molecular information processing devices began; the emerging science of nanotechnology had a strong influence on the subject, with building blocks such as fullerenes and dendrimers becoming involved in synthetic systems. Supramolecular chemistry deals with subtle interactions, control over the processes involved can require great precision. In particular, non-covalent bonds have low energies and 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 temperatures. However, low temperatures can be problematic to supramolecular processes. Supramolecular chemistry can require molecules to distort into thermodynamically disfavored conformations, may include some covalent chemistry that goes along with the supramolecular. In addition, the dynamic nature of supramolecular chemistry is utilized in many systems, cooling the system would slow these processes. Thus, thermodynamics is an important tool to design and study supramolecular chemistry; the most striking example is that of warm-blooded biological systems, which cease to operate outside a narrow temperature range. The molecular environment around a supramolecular system is of prime importance to its operation and stability. Many solvents have strong hydrogen bonding and charge-transfer capabilities, are therefore able to become involved in complex equilibria with the system breaking complexes completely.
For this reason, the choice of solvent can be critical. Molecular self-assembly is the construction of systems without guidance or management from an outside source; the molecules are directed to assemble through non-covalent interactions. Self-assembly may be subdivided into intermolecular self-assemb
A rotaxane is a mechanically interlocked molecular architecture consisting of a "dumbbell shaped molecule", threaded through a "macrocycle". The name is derived from the Latin for axle; the two components of a rotaxane are kinetically trapped since the ends of the dumbbell are larger than the internal diameter of the ring and prevent dissociation of the components since this would require significant distortion of the covalent bonds. Much of the research concerning rotaxanes and other mechanically interlocked molecular architectures, such as catenanes, has been focused on their efficient synthesis or their utilization as artificial molecular machines. However, examples of rotaxane substructure have been found in occurring peptides, including: cystine knot peptides, cyclotides or lasso-peptides such as microcin J25; the earliest reported synthesis of a rotaxane in 1967 relied on the statistical probability that if two halves of a dumbbell-shaped molecule were reacted in the presence of a macrocycle that some small percentage would connect through the ring.
To obtain a reasonable quantity of rotaxane, the macrocycle was attached to a solid-phase support and treated with both halves of the dumbbell 70 times and severed from the support to give a 6% yield. However, the synthesis of rotaxanes has advanced and efficient yields can be obtained by preorganizing the components utilizing hydrogen bonding, metal coordination, hydrophobic forces, covalent bonds, or coulombic interactions; the three most common strategies to synthesize rotaxane are "capping", "clipping", "slipping", though others do exist. Leigh and co-workers described a new pathway to mechanically interlocked architectures involving a transition-metal center that can catalyse a reaction through the cavity of a macrocycle. Synthesis via the capping method relies upon a thermodynamically driven template effect; this dynamic complex or pseudorotaxane is converted to the rotaxane by reacting the ends of the threaded guest with large groups, preventing disassociation. The clipping method is similar to the capping reaction except that in this case the dumbbell shaped molecule is complete and is bound to a partial macrocycle.
The partial macrocycle undergoes a ring closing reaction around the dumbbell-shaped molecule, forming the rotaxane. The method of slipping is one. If the end groups of the dumbbell are an appropriate size it will be able to reversibly thread through the macrocycle at higher temperatures. By cooling the dynamic complex, it becomes kinetically trapped as a rotaxane at the lower temperature. Leigh and co-workers began to explore a strategy in which template ions could play an active role in promoting the crucial final covalent bond forming reaction that captures the interlocked structure. Rotaxane-based molecular machines have been of initial interest for their potential use in molecular electronics as logic molecular switching elements and as molecular shuttles; these molecular machines are based on the movement of the macrocycle on the dumbbell. The macrocycle can rotate around the axis of the dumbbell like a wheel and axle or it can slide along its axis from one site to another. Controlling the position of the macrocycle allows the rotaxane to function as a molecular switch, with each possible location of the macrocycle corresponding to a different state.
These rotaxane machines can be manipulated both by photochemical inputs. Rotaxane based systems have been shown to function as molecular muscles. In 2009, there was a report of a "domino effect" from one extremity to the other in a Glycorotaxane Molecular Machine. In this case, the 4C1 or 1C4 chair-like conformation of the mannopyranoside stopper can be controlled, depending on the localization of the macrocycle. In 2012, unique pseudo-macrocycles consisting of double-lasso molecular machines were reported in Chem. Sci; these structures can be tightened or loosened depending on pH. A controllable jump rope movement was observed in these new molecular machines. Potential application as long-lasting dyes is based on the enhanced stability of the inner portion of the dumbbell-shaped molecule. Studies with cyclodextrin-protected rotaxane azo dyes established this characteristic. More reactive squaraine dyes have been shown to have enhanced stability by preventing nucleophilic attack of the inner squaraine moiety.
The enhanced stability of rotaxane dyes is attributed to the insulating effect of the macrocycle, able to block interactions with other molecules. In a nanorecording application, a certain rotaxane is deposited as a Langmuir–Blodgett film on ITO-coated glass; when a positive voltage is applied with the tip of a scanning tunneling microscope probe, the rotaxane rings in the tip area switch to a different part of the dumbbell and the resulting new conformation makes the molecules stick out 0.3 nanometer from the surface. This height difference is sufficient for a memory dot, it is not yet known. Accepted nomenclature is to designate the number of components of the rotaxane in brackets as a prefix. Therefore, the a rotaxane consisting of a single dumbbell-shaped axial molecule with a single macrocycle around its shaft is called a rotaxane, two cyanostar molecules around the central
The melting point of a substance is the temperature at which it changes state from solid to liquid. At the melting point the solid and liquid phase exist in equilibrium; the melting point of a substance depends on pressure and is specified at a standard pressure such as 1 atmosphere or 100 kPa. When considered as the temperature of the reverse change from liquid to solid, it is referred to as the freezing point or crystallization point; because of the ability of some substances to supercool, the freezing point is not considered as a characteristic property of a substance. When the "characteristic freezing point" of a substance is determined, in fact the actual methodology is always "the principle of observing the disappearance rather than the formation of ice", that is, the melting point. For most substances and freezing points are equal. For example, the melting point and freezing point of mercury is 234.32 kelvins. However, certain substances possess differing solid-liquid transition temperatures.
For example, agar melts at 85 °C and solidifies from 31 °C. The melting point of ice at 1 atmosphere of pressure is close to 0 °C. In the presence of nucleating substances, the freezing point of water is not always the same as the melting point. In the absence of nucleators water can exist as a supercooled liquid down to −48.3 °C before freezing. The chemical element with the highest melting point is tungsten, at 3,414 °C; the often-cited carbon does not melt at ambient pressure but sublimes at about 3,726.85 °C. Tantalum hafnium carbide is a refractory compound with a high melting point of 4215 K. At the other end of the scale, helium does not freeze at all at normal pressure at temperatures arbitrarily close to absolute zero. Many laboratory techniques exist for the determination of melting points. A Kofler bench is a metal strip with a temperature gradient. Any substance can be placed on a section of the strip, revealing its thermal behaviour at the temperature at that point. Differential scanning calorimetry gives information on melting point together with its enthalpy of fusion.
A basic melting point apparatus for the analysis of crystalline solids consists of an oil bath with a transparent window and a simple magnifier. The several grains of a solid are placed in a thin glass tube and immersed in the oil bath; the oil bath is heated and with the aid of the magnifier melting of the individual crystals at a certain temperature can be observed. In large/small devices, the sample is placed in a heating block, optical detection is automated; the measurement can be made continuously with an operating process. For instance, oil refineries measure the freeze point of diesel fuel online, meaning that the sample is taken from the process and measured automatically; this allows for more frequent measurements as the sample does not have to be manually collected and taken to a remote laboratory. For refractory materials the high melting point may be determined by heating the material in a black body furnace and measuring the black-body temperature with an optical pyrometer. For the highest melting materials, this may require extrapolation by several hundred degrees.
The spectral radiance from an incandescent body is known to be a function of its temperature. An optical pyrometer matches the radiance of a body under study to the radiance of a source, calibrated as a function of temperature. In this way, the measurement of the absolute magnitude of the intensity of radiation is unnecessary. However, known temperatures must be used to determine the calibration of the pyrometer. For temperatures above the calibration range of the source, an extrapolation technique must be employed; this extrapolation is accomplished by using Planck's law of radiation. The constants in this equation are not known with sufficient accuracy, causing errors in the extrapolation to become larger at higher temperatures. However, standard techniques have been developed to perform this extrapolation. Consider the case of using gold as the source. In this technique, the current through the filament of the pyrometer is adjusted until the light intensity of the filament matches that of a black-body at the melting point of gold.
This establishes the primary calibration temperature and can be expressed in terms of current through the pyrometer lamp. With the same current setting, the pyrometer is sighted on another black-body at a higher temperature. An absorbing medium of known transmission is inserted between this black-body; the temperature of the black-body is adjusted until a match exists between its intensity and that of the pyrometer filament. The true higher temperature of the black-body is determined from Planck's Law; the absorbing medium is removed and the current through the filament is adjusted to match the filament intensity to that of the black-body. This establishes a second calibration point for the pyrometer; this step is repeated to carry the calibration to hi
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. Catenane is derived from the Latin catena meaning "chain", they are conceptually related to other mechanically interlocked molecular architectures, such as rotaxanes, molecular knots or molecular Borromean rings. The terminology "mechanical bond" has been coined that describes the connection between the macrocycles of a catenane. Catenanes have been synthesised in two different ways: statistical synthesis and template-directed synthesis. There are two primary approaches to the organic synthesis of catenanes; the first is to perform a ring-closing reaction with the hope that some of the rings will form around other rings giving the desired catenane product. This so-called "statistical approach" led to the first successful synthesis of a catenane.
The second approach relies on supramolecular preorganization of the macrocyclic precursors utilizing hydrogen bonding, metal coordination, hydrophobic effect, or coulombic interactions. These non-covalent interactions offset some of the entropic cost of association and help position the components to form the desired catenane upon the final ring-closing; this "template-directed" approach, together with the use of high-pressure conditions, can provide yields of over 90%, thus improving the potential of catenanes for applications. An example of this approach used bis-bipyridinium salts which form strong complexes threaded through crown ether bis-34-crown-10. Template directed syntheses are performed under kinetic control, when the macrocyclization reaction is irreversible. More the groups of Sanders and Otto have shown that dynamic combinatorial approaches using reversible chemistry can be successful in preparing new catenanes of unpredictable structure; the thermodynamically controlled synthesis provides an error correction mechanism.
The approach provides information on the affinity constants between different macrocycles thanks to the equilibrium between the individual components and the catenanes, allowing a titration-like experiment. A interesting property of many catenanes is the ability of the rings to rotate with respect to one another; this motion can be detected and measured by NMR spectroscopy, among other methods. When molecular recognition motifs exist in the finished catenane, the catenane can have one or more thermodynamically preferred positions of the rings with respect to each other. In the case where one recognition site is a switchable moiety, a mechanical molecular switch results; when a catenane is synthesized by coordination of the macrocycles around a metal ion removal and re-insertion of the metal ion can switch the free motion of the rings on and off. If there are more than one recognition sites it is possible to observe different colors depending on the recognition site the ring occupies and thus it is possible to change the color of the catenane solution by changing the preferred recognition site.
Switching between the two sites may be achieved by the use of chemical, electrochemical or visible light based methods. Catenanes have been synthesized incorporating many functional units, including redox-active groups, photoisomerizable groups, fluorescent groups and chiral groups; some such units have been used to create molecular switches as described above, as well as for the fabrication of molecular electronic devices and molecular sensors. There are a number of distinct methods of holding the precursors together prior to the ultimate ring-closing reaction in a template-directed catenane synthesis; each noncovalent approach to catenane formation results in what can be considered different families of catenanes. Another family of catenanes are called pretzelanes or bridged catenanes after their likeness to pretzels with a spacer linking the two macrocycles. In one such system one macrocycle is an electron deficient oligo Bis-bipyridinium ring and the other cycle is crown ether cyclophane based on para phenylene or naphthalene.
X-ray diffraction shows that due to pi-pi interactions the aromatic group of the cyclophane is held inside the pyridinium ring. A limited number of conformers exist for this type of compound. In handcuff-shaped catenanes, two connected rings are threaded through the same ring; the bis-macrocycle contains two phenanthroline units in a crown ether chain. The interlocking ring is self-assembled when two more phenanthroline units with alkene arms coordinate through a copper complex followed by a metathesis ring closing step. In catenane nomenclature, a number in square brackets precedes the word "catenane" in order to indicate how many rings are involved. Discrete catenanes up to a catenane have been synthesised. Olympiadane Polycatenane
Naphthalenetetracarboxylic dianhydride is an organic compound related to naphthalene. The compound is a beige solid. NTDA is most used as a precursor to naphthalenediimides, a family of compounds with many uses. Naphthalenetetracarboxylic dianhydride is prepared by oxidation of pyrene. Typical oxidants are chromic chlorine; the unsaturated tetrachloride hydrolyzes to enols that tautomerize to the bis-dione, which in turn can be oxidized to the tetracarboxylic acid. Symmetrical naphthalene diimides are synthesized by the condensation reaction of primary amines and the dianhydride. Unsymmetrical derivatives, i.e. those derived from two different amines, are obtained by hydrolysis of one of the two anhydride groups prior to the condensation with the first amine. These diimides are members of a broader class of compounds called rylenes, oligomers of naphthalene with bonds between the 1 and 1' and 8 and 8' positions; the resulting materials have rigidly planar conjugated cores. They exhibit good processing characteristics for fabrication of soft electronic devices.
Aside from the NDIs, other members include the diimide derivatives of perylene-3,4:9,10-tetracarboxylic dianhydride and terrylene-3,4:11,12-tetracarboxylic dianhydride. Naphthalene diimides are fluorescent, although the intensity is sensitive to substituents. NDIs are redox-active, forming stable radical anions near -1.10 V vs. Fc/Fc+, their ability to accept electrons reflects the presence of an extended conjugated ring system and the electron withdrawing groups. NDIs are used ins supramolecular chemistry due to their tendency to form charge-transfer complexes with crown ethers, e.g. to give rotaxanes and catenanes. As another consequence of their planar structure and electron-acceptor properties, NDIs intercalate into DNA; because a range of amines can be condensed with the dianhydride. For example, two useful pigments of the perinone class are generated by condensation with phenylenediamine. A variety of ligands with NDI backbones have been prepared
Crown ethers are cyclic chemical compounds that consist of a ring containing several ether groups. The most common crown ethers are cyclic oligomers of ethylene oxide, the repeating unit being ethyleneoxy, i.e. –CH2CH2O–. Important members of this series are the tetramer, the pentamer, the hexamer; the term "crown" refers to the resemblance between the structure of a crown ether bound to a cation, a crown sitting on a person's head. The first number in a crown ether's name refers to the number of atoms in the cycle, the second number refers to the number of those atoms that are oxygen. Crown ethers are much broader than the oligomers of ethylene oxide. Crown ethers bind certain cations, forming complexes; the oxygen atoms are well situated to coordinate with a cation located at the interior of the ring, whereas the exterior of the ring is hydrophobic. The resulting cations form salts that are soluble in nonpolar solvents, for this reason crown ethers are useful in phase transfer catalysis; the denticity of the polyether influences the affinity of the crown ether for various cations.
For example, 18-crown-6 has high affinity for potassium cation, 15-crown-5 for sodium cation, 12-crown-4 for lithium cation. The high affinity of 18-crown-6 for potassium ions contributes to its toxicity. Crown ethers are not the only macrocyclic ligands. Ionophores such as valinomycin display a marked preference for the potassium cation over other cations. Crown ethers have been shown to coordinate to Lewis acids through electrostatic, σ-hole interactions, between the Lewis basic oxygen atoms of the crown ether and the electrophilic Lewis acid center. In 1967, Charles Pedersen, a chemist working at DuPont, discovered a simple method of synthesizing a crown ether when he was trying to prepare a complexing agent for divalent cations, his strategy entailed linking two catecholate groups through one hydroxyl on each molecule. This linking defines a polydentate ligand that could envelop the cation and, by ionization of the phenolic hydroxyls, neutralize the bound dication, he was surprised to isolate a by-product that complexed potassium cations.
Citing earlier work on the dissolution of potassium in 16-crown-4, he realized that the cyclic polyethers represented a new class of complexing agents that were capable of binding alkali metal cations. He proceeded to report systematic studies of the synthesis and binding properties of crown ethers in a seminal series of papers; the fields of organic synthesis, phase transfer catalysts, other emerging disciplines benefited from the discovery of crown ethers. Pedersen popularized the dibenzo crown ethers. Pedersen shared the 1987 Nobel Prize in Chemistry for the discovery of the synthetic routes to, binding properties of, crown ethers. Apart from its high affinity for potassium cations, 18-crown-6 can bind to protonated amines and form stable complexes in both solution and the gas phase; some amino acids, such as lysine, contain a primary amine on their side chains. Those protonated amino groups can bind to the cavity of 18-crown-6 and form stable complexes in the gas phase. Hydrogen-bonds are formed between the three hydrogen atoms of protonated amines and three oxygen atoms of 18-crown-6.
These hydrogen-bonds make the complex a stable adduct. By incorporating luminescent substituents into their backbone, these compounds have proved to be sensitive ion probes, as changes in the absorption or fluorescence of the photoactive groups can be measured for low concentrations of metal present; some attractive examples include macrocycles, incorporating oxygen and/or nitrogen donors, that are attached to polyaromatic species such as anthracenes or naphthalenes. 21- and 18-membered diazacrown ether derivatives exhibit excellent calcium and magnesium selectivities and are used in ion-selective electrodes. Some or all of the oxygen atoms in crown ethers can be replaced by nitrogens to form cryptands. A well-known tetrazacrown is cyclen. Lariat crown ethers have sidearms; the lariat is attached to an amine centre in an azacrown. 9-Crown-3 Cryptand Metallacrown Pedersen, Charles. "Nobel Lecture". Nobel Prize. Molecular crown
The Jmol applet, among other abilities, offers an alternative to the Chime plug-in, no longer under active development. While Jmol has many features that Chime lacks, it does not claim to reproduce all Chime functions, most notably, the Sculpt mode. Chime requires plug-in installation and Internet Explorer 6.0 or Firefox 2.0 on Microsoft Windows, or Netscape Communicator 4.8 on Mac OS 9. Jmol operates on a wide variety of platforms. For example, Jmol is functional in Mozilla Firefox, Internet Explorer, Google Chrome, Safari. Chemistry Development Kit Comparison of software for molecular mechanics modeling Jmol extension for MediaWiki List of molecular graphics systems Molecular graphics Molecule editor Proteopedia PyMOL SAMSON Official website Wiki with listings of websites and moodles Willighagen, Egon. "Fast and Scriptable Molecular Graphics in Web Browsers without Java3D". Doi:10.1038/npre.2007.50.1