In coordination chemistry, a ligand is an ion or molecule that binds to a central metal atom to form a coordination complex. The bonding with the metal involves formal donation of one or more of the ligand's electron pairs; the nature of metal–ligand bonding can range from covalent to ionic. Furthermore, the metal–ligand bond order can range from one to three. Ligands are viewed as Lewis bases, although rare cases are known to involve Lewis acidic "ligands". Metals and metalloids are bound to ligands in all circumstances, although gaseous "naked" metal ions can be generated in a high vacuum. Ligands in a complex dictate the reactivity of the central atom, including ligand substitution rates, the reactivity of the ligands themselves, redox. Ligand selection is a critical consideration in many practical areas, including bioinorganic and medicinal chemistry, homogeneous catalysis, environmental chemistry. Ligands are classified in many ways, including: charge, the identity of the coordinating atom, the number of electrons donated to the metal.
The size of a ligand is indicated by its cone angle. The composition of coordination complexes have been known since the early 1800s, such as Prussian blue and copper vitriol; the key breakthrough occurred when Alfred Werner reconciled isomers. He showed, among other things, that the formulas of many cobalt and chromium compounds can be understood if the metal has six ligands in an octahedral geometry; the first to use the term "ligand" were Alfred Stock and Carl Somiesky, in relation to silicon chemistry. The theory allows one to understand the difference between coordinated and ionic chloride in the cobalt ammine chlorides and to explain many of the inexplicable isomers, he resolved the first coordination complex called hexol into optical isomers, overthrowing the theory that chirality was associated with carbon compounds. In general, ligands are viewed as the metals as electron acceptors; this is because the ligand and central metal are bonded to one another, the ligand is providing both electrons to the bond instead of the metal and ligand each providing one electron.
Bonding is described using the formalisms of molecular orbital theory. The HOMO can be of ligands or metal character. Ligands and metal ions can be ordered in many ways. Metal ions preferentially bind certain ligands. In general,'hard' metal ions prefer weak field ligands, whereas'soft' metal ions prefer strong field ligands. According to the molecular orbital theory, the HOMO of the ligand should have an energy that overlaps with the LUMO of the metal preferential. Metal ions bound to strong-field ligands follow the Aufbau principle, whereas complexes bound to weak-field ligands follow Hund's rule. Binding of the metal with the ligands results in a set of molecular orbitals, where the metal can be identified with a new HOMO and LUMO and a certain ordering of the 5 d-orbitals. In an octahedral environment, the 5 otherwise degenerate d-orbitals split in sets of 2 and 3 orbitals. 3 orbitals of low energy: dxy and dyz 2 of high energy: dz2 and dx2−y2The energy difference between these 2 sets of d-orbitals is called the splitting parameter, Δo.
The magnitude of Δo is determined by the field-strength of the ligand: strong field ligands, by definition, increase Δo more than weak field ligands. Ligands can now be sorted according to the magnitude of Δo; this ordering of ligands is invariable for all metal ions and is called spectrochemical series. For complexes with a tetrahedral surrounding, the d-orbitals again split into two sets, but this time in reverse order. 2 orbitals of low energy: dz2 and dx2−y2 3 orbitals of high energy: dxy and dyzThe energy difference between these 2 sets of d-orbitals is now called Δt. The magnitude of Δt is smaller than for Δo, because in a tetrahedral complex only 4 ligands influence the d-orbitals, whereas in an octahedral complex the d-orbitals are influenced by 6 ligands; when the coordination number is neither octahedral nor tetrahedral, the splitting becomes correspondingly more complex. For the purposes of ranking ligands, the properties of the octahedral complexes and the resulting Δo has been of primary interest.
The arrangement of the d-orbitals on the central atom, has a strong effect on all the properties of the resulting complexes. E.g. the energy differences in the d-orbitals has a strong effect in the optical absorption spectra of metal complexes. It turns out that valence electrons occupying orbitals with significant 3 d-orbital character absorb in the 400–800 nm region of the spectrum; the absorption of light by these electrons can be correlated to the ground state of the metal complex, which reflects the bonding properties of the ligands. The relative change in energy of the d-orbitals as a function of the field-strength of the ligands is described in Tanabe–Sugano diagrams. In cases where the ligand has low energy LUMO, such orbitals participate in the bonding; the metal–ligand bond can be further stabilised by a formal donation of electron density back to the ligand in a process known as back-bonding. In this case a filled, c
A radionuclide is an atom that has excess nuclear energy, making it unstable. This excess energy can be used in one of three ways: emitted from the nucleus as gamma radiation. During those processes, the radionuclide is said to undergo radioactive decay; these emissions are considered ionizing radiation because they are powerful enough to liberate an electron from another atom. The radioactive decay can produce a stable nuclide or will sometimes produce a new unstable radionuclide which may undergo further decay. Radioactive decay is a random process at the level of single atoms: it is impossible to predict when one particular atom will decay. However, for a collection of atoms of a single element the decay rate, thus the half-life for that collection can be calculated from their measured decay constants; the range of the half-lives of radioactive atoms have no known limits and span a time range of over 55 orders of magnitude. Radionuclides occur or are artificially produced in nuclear reactors, particle accelerators or radionuclide generators.
There are about 730 radionuclides with half-lives longer than 60 minutes. Thirty-two of those are primordial radionuclides. At least another 60 radionuclides are detectable in nature, either as daughters of primordial radionuclides or as radionuclides produced through natural production on Earth by cosmic radiation. More than 2400 radionuclides have half-lives less than 60 minutes. Most of those are only produced artificially, have short half-lives. For comparison, there are about 253 stable nuclides. All chemical elements can exist as radionuclides; the lightest element, has a well-known radionuclide, tritium. Elements heavier than lead, the elements technetium and promethium, exist only as radionuclides. Unplanned exposure to radionuclides has a harmful effect on living organisms including humans, although low levels of exposure occur without harm; the degree of harm will depend on the nature and extent of the radiation produced, the amount and nature of exposure, the biochemical properties of the element.
However, radionuclides with suitable properties are used in nuclear medicine for both diagnosis and treatment. An imaging tracer made with radionuclides is called a radioactive tracer. A pharmaceutical drug made with radionuclides is called a radiopharmaceutical. On Earth occurring radionuclides fall into three categories: primordial radionuclides, secondary radionuclides, cosmogenic radionuclides. Radionuclides are produced in stellar nucleosynthesis and supernova explosions along with stable nuclides. Most decay but can still be observed astronomically and can play a part in understanding astronomic processes. Primordial radionuclides, such as uranium and thorium, exist in the present time because their half-lives are so long that they have not yet decayed; some radionuclides have half-lives so long that decay has only been detected, for most practical purposes they can be considered stable, most notably bismuth-209: detection of this decay meant that bismuth was no longer considered stable.
It is possible decay may be observed in other nuclides adding to this list of primordial radionuclides. Secondary radionuclides are radiogenic isotopes derived from the decay of primordial radionuclides, they have shorter half-lives than primordial radionuclides. They arise in the decay chain of the primordial isotopes thorium-232, uranium-238 and uranium-235. Examples include the natural isotopes of radium. Cosmogenic isotopes, such as carbon-14, are present because they are continually being formed in the atmosphere due to cosmic rays. Many of these radionuclides exist only in trace amounts in nature, including all cosmogenic nuclides. Secondary radionuclides will occur in proportion to their half-lives, so short-lived ones will be rare, thus polonium can be found in uranium ores at about 0.1 mg per metric ton. Further radionunclides may occur in nature in undetectable amounts as a result of rare events such as spontaneous fission or uncommon cosmic ray interactions. Radionuclides are produced as an unavoidable result of nuclear thermonuclear explosions.
The process of nuclear fission creates a wide range of fission products, most of which are radionuclides. Further radionuclides can be created from irradiation of the nuclear fuel and of the surrounding structures, yielding activation products; this complex mixture of radionuclides with different chemistries and radioactivity makes handling nuclear waste and dealing with nuclear fallout problematic. Synthetic radionuclides are deliberately synthesised using nuclear reactors, particle accelerators or radionuclide generators: As well as being extracted from nuclear waste, radioisotopes can be produced deliberately with nuclear reactors, exploiting the high flux of neutrons present; these neutrons activate elements placed within the reactor. A typical product from a nuclear reactor is iridium-
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
Simplified molecular-input line-entry system
The simplified molecular-input line-entry system is a specification in the form of a line notation for describing the structure of chemical species using short ASCII strings. SMILES strings can be imported by most molecule editors for conversion back into two-dimensional drawings or three-dimensional models of the molecules; the original SMILES specification was initiated in the 1980s. It has since been extended. In 2007, an open standard called. Other linear notations include the Wiswesser line notation, ROSDAL, SYBYL Line Notation; the original SMILES specification was initiated by David Weininger at the USEPA Mid-Continent Ecology Division Laboratory in Duluth in the 1980s. Acknowledged for their parts in the early development were "Gilman Veith and Rose Russo and Albert Leo and Corwin Hansch for supporting the work, Arthur Weininger and Jeremy Scofield for assistance in programming the system." The Environmental Protection Agency funded the initial project to develop SMILES. It has since been modified and extended by others, most notably by Daylight Chemical Information Systems.
In 2007, an open standard called "OpenSMILES" was developed by the Blue Obelisk open-source chemistry community. Other'linear' notations include the Wiswesser Line Notation, ROSDAL and SLN. In July 2006, the IUPAC introduced the InChI as a standard for formula representation. SMILES is considered to have the advantage of being more human-readable than InChI; the term SMILES refers to a line notation for encoding molecular structures and specific instances should be called SMILES strings. However, the term SMILES is commonly used to refer to both a single SMILES string and a number of SMILES strings; the terms "canonical" and "isomeric" can lead to some confusion when applied to SMILES. The terms are not mutually exclusive. A number of valid SMILES strings can be written for a molecule. For example, CCO, OCC and CC all specify the structure of ethanol. Algorithms have been developed to generate the same SMILES string for a given molecule; this SMILES is unique for each structure, although dependent on the canonicalization algorithm used to generate it, is termed the canonical SMILES.
These algorithms first convert the SMILES to an internal representation of the molecular structure. Various algorithms for generating canonical SMILES have been developed and include those by Daylight Chemical Information Systems, OpenEye Scientific Software, MEDIT, Chemical Computing Group, MolSoft LLC, the Chemistry Development Kit. A common application of canonical SMILES is indexing and ensuring uniqueness of molecules in a database; the original paper that described the CANGEN algorithm claimed to generate unique SMILES strings for graphs representing molecules, but the algorithm fails for a number of simple cases and cannot be considered a correct method for representing a graph canonically. There is no systematic comparison across commercial software to test if such flaws exist in those packages. SMILES notation allows the specification of configuration at tetrahedral centers, double bond geometry; these are structural features that cannot be specified by connectivity alone and SMILES which encode this information are termed isomeric SMILES.
A notable feature of these rules is. The term isomeric SMILES is applied to SMILES in which isotopes are specified. In terms of a graph-based computational procedure, SMILES is a string obtained by printing the symbol nodes encountered in a depth-first tree traversal of a chemical graph; the chemical graph is first trimmed to remove hydrogen atoms and cycles are broken to turn it into a spanning tree. Where cycles have been broken, numeric suffix labels are included to indicate the connected nodes. Parentheses are used to indicate points of branching on the tree; the resultant SMILES form depends on the choices: of the bonds chosen to break cycles, of the starting atom used for the depth-first traversal, of the order in which branches are listed when encountered. Atoms are represented by the standard abbreviation of the chemical elements, in square brackets, such as for gold. Brackets may be omitted in the common case of atoms which: are in the "organic subset" of B, C, N, O, P, S, F, Cl, Br, or I, have no formal charge, have the number of hydrogens attached implied by the SMILES valence model, are the normal isotopes, are not chiral centers.
All other elements must be enclosed in brackets, have charges and hydrogens shown explicitly. For instance, the SMILES for water may be written as either O or. Hydrogen may be written as a separate atom; when brackets are used, the symbol H is added if the atom in brackets is bonded to one or more hydrogen, followed by the number of hydrogen atoms if greater than 1 by the sign + for a positive charge or by - for a negative charge. For example, for ammonium. If there is more than one charge, it is written as digit.