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.
In chemistry, a salt is an ionic compound that can be formed by the neutralization reaction of an acid and a base. Salts are composed of related numbers of cations and anions so that the product is electrically neutral; these component ions can be inorganic, such as organic, such as acetate. Salts can be classified in a variety of ways. Salts that produce hydroxide ions when dissolved in water are called alkali salts. Salts that produce acidic solutions are acidic salts. Neutral salts are those salts that are neither basic. Zwitterions contain an anionic and a cationic centres in the same molecule, but are not considered to be salts. Examples of zwitterions include amino acids, many metabolites and proteins. Solid salts tend to be transparent. In many cases, the apparent opacity or transparency are only related to the difference in size of the individual monocrystals. Since light reflects from the grain boundaries, larger crystals tend to be transparent, while the polycrystalline aggregates look like white powders.
Salts exist in many different colors, which arise either from the cations. For example: sodium chromate is yellow by virtue of the chromate ion potassium dichromate is orange by virtue of the dichromate ion cobalt nitrate is red owing to the chromophore of hydrated cobalt. copper sulfate is blue because of the copper chromophore potassium permanganate has the violet color of permanganate anion. Nickel chloride is green of sodium chloride, magnesium sulfate heptahydrate are colorless or white because the constituent cations and anions do not absorb in the visible part of the spectrumFew minerals are salts because they would be solubilized by water. Inorganic pigments tend not to be salts, because insolubility is required for fastness; some organic dyes are salts, but they are insoluble in water. Different salts can elicit all five basic tastes, e.g. salty, sour and umami or savory. Salts of strong acids and strong bases are non-volatile and odorless, whereas salts of either weak acids or weak bases may smell like the conjugate acid or the conjugate base of the component ions.
That slow, partial decomposition is accelerated by the presence of water, since hydrolysis is the other half of the reversible reaction equation of formation of weak salts. Many ionic compounds exhibit significant solubility in water or other polar solvents. Unlike molecular compounds, salts dissociate in solution into cationic components; the lattice energy, the cohesive forces between these ions within a solid, determines the solubility. The solubility is dependent on how well each ion interacts with the solvent, so certain patterns become apparent. For example, salts of sodium and ammonium are soluble in water. Notable exceptions include potassium cobaltinitrite. Most nitrates and many sulfates are water-soluble. Exceptions include barium sulfate, calcium sulfate, lead sulfate, where the 2+/2− pairing leads to high lattice energies. For similar reasons, most alkali metal carbonates are not soluble in water; some soluble carbonate salts are: potassium carbonate and ammonium carbonate. Salts are characteristically insulators.
Molten salts or solutions of salts conduct electricity. For this reason, liquified salts and solutions containing dissolved salts are called electrolytes. Salts characteristically have high melting points. For example, sodium chloride melts at 801 °C; some salts with low lattice energies are liquid near room temperature. These include molten salts, which are mixtures of salts, ionic liquids, which contain organic cations; these liquids exhibit unusual properties as solvents. The name of a salt starts with the name of the cation followed by the name of the anion. Salts are referred to only by the name of the cation or by the name of the anion. Common salt-forming cations include: Ammonium NH+4 Calcium Ca2+ Iron Fe2+ and Fe3+ Magnesium Mg2+ Potassium K+ Pyridinium C5H5NH+ Quaternary ammonium NR+4, R being an alkyl group or an aryl group Sodium Na+ Copper Cu2+Common salt-forming anions include: Acetate CH3COO− Carbonate CO2−3 Chloride Cl− Citrate HOC2 Cyanide C≡N− Fluoride F− Nitrate NO−3 Nitrite NO−2 Oxide O2− Phosphate PO3−4 Sulfate SO2−4 Salts with varying number of hydrogen atoms, with respect to the parent acid, replaced by cations can be referred to as monobasic, dibasic or tribasic salts: Sodium phosphate monobasic Sodium phosphate dibasic Sodium phosphate tribasic Salts are formed by a chemical reaction between: A base and an acid, e.g. NH3 + HCl → NH4Cl A metal and an acid, e.g. Mg + H2SO4 → MgSO4 + H2 A metal and a non-metal, e.g. Ca + Cl2 → CaCl2 A base and an a
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
In crystallography, crystal structure is a description of the ordered arrangement of atoms, ions or molecules in a crystalline material. Ordered structures occur from the intrinsic nature of the constituent particles to form symmetric patterns that repeat along the principal directions of three-dimensional space in matter; the smallest group of particles in the material that constitutes this repeating pattern is the unit cell of the structure. The unit cell reflects the symmetry and structure of the entire crystal, built up by repetitive translation of the unit cell along its principal axes; the translation vectors define the nodes of the Bravais lattice. The lengths of the principal axes, or edges, of the unit cell and the angles between them are the lattice constants called lattice parameters or cell parameters; the symmetry properties of the crystal are described by the concept of space groups. All possible symmetric arrangements of particles in three-dimensional space may be described by the 230 space groups.
The crystal structure and symmetry play a critical role in determining many physical properties, such as cleavage, electronic band structure, optical transparency. Crystal structure is described in terms of the geometry of arrangement of particles in the unit cell; the unit cell is defined as the smallest repeating unit having the full symmetry of the crystal structure. The geometry of the unit cell is defined as a parallelepiped, providing six lattice parameters taken as the lengths of the cell edges and the angles between them; the positions of particles inside the unit cell are described by the fractional coordinates along the cell edges, measured from a reference point. It is only necessary to report the coordinates of a smallest asymmetric subset of particles; this group of particles may be chosen so that it occupies the smallest physical space, which means that not all particles need to be physically located inside the boundaries given by the lattice parameters. All other particles of the unit cell are generated by the symmetry operations that characterize the symmetry of the unit cell.
The collection of symmetry operations of the unit cell is expressed formally as the space group of the crystal structure. Vectors and planes in a crystal lattice are described by the three-value Miller index notation; this syntax uses the indices ℓ, m, n as directional orthogonal parameters, which are separated by 90°. By definition, the syntax denotes a plane that intercepts the three points a1/ℓ, a2/m, a3/n, or some multiple thereof; that is, the Miller indices are proportional to the inverses of the intercepts of the plane with the unit cell. If one or more of the indices is zero, it means. A plane containing a coordinate axis is translated so that it no longer contains that axis before its Miller indices are determined; the Miller indices for a plane are integers with no common factors. Negative indices are indicated with horizontal bars, as in. In an orthogonal coordinate system for a cubic cell, the Miller indices of a plane are the Cartesian components of a vector normal to the plane. Considering only planes intersecting one or more lattice points, the distance d between adjacent lattice planes is related to the reciprocal lattice vector orthogonal to the planes by the formula d = 2 π | g ℓ m n | The crystallographic directions are geometric lines linking nodes of a crystal.
The crystallographic planes are geometric planes linking nodes. Some directions and planes have a higher density of nodes; these high density planes have an influence on the behavior of the crystal as follows: Optical properties: Refractive index is directly related to density. Adsorption and reactivity: Physical adsorption and chemical reactions occur at or near surface atoms or molecules; these phenomena are thus sensitive to the density of nodes. Surface tension: The condensation of a material means that the atoms, ions or molecules are more stable if they are surrounded by other similar species; the surface tension of an interface thus varies according to the density on the surface. Microstructural defects: Pores and crystallites tend to have straight grain boundaries following higher density planes. Cleavage: This occurs preferentially parallel to higher density planes. Plastic deformation: Dislocation glide occurs preferentially parallel to higher density planes; the perturbation carried by the dislocation is along a dense direction.
The shift of one node in a more dense direction requires a lesser distortion of the crystal lattice. Some directions and planes are defined by symmetry of the crystal system. In monoclinic, rhombohedral and trigonal/hexagonal systems there is one unique axis which has higher rotational symmetry than the other two axes; the basal plane is the plane perpendicular to the principal axis in these crystal systems. For triclinic and cubic crystal systems the axis designation is arbitrary and there is no principal axis. For the special case of simple cubic crystals, the lattice vectors are orthogonal and of equal length. So, in this common case, the Miller indices and both denote normals/directions in Cartesian coordinates. For cubic crystals with lattice constant a, the spacing d between adjacent l
Potassium is a chemical element with symbol K and atomic number 19. It was first isolated from the ashes of plants, from which its name derives. In the periodic table, potassium is one of the alkali metals. All of the alkali metals have a single valence electron in the outer electron shell, removed to create an ion with a positive charge – a cation, which combines with anions to form salts. Potassium in nature occurs only in ionic salts. Elemental potassium is a soft silvery-white alkali metal that oxidizes in air and reacts vigorously with water, generating sufficient heat to ignite hydrogen emitted in the reaction, burning with a lilac-colored flame, it is found dissolved in sea water, is part of many minerals. Potassium is chemically similar to sodium, the previous element in group 1 of the periodic table, they have a similar first ionization energy, which allows for each atom to give up its sole outer electron. That they are different elements that combine with the same anions to make similar salts was suspected in 1702, was proven in 1807 using electrolysis.
Occurring potassium is composed of three isotopes, of which 40K is radioactive. Traces of 40K are found in all potassium, it is the most common radioisotope in the human body. Potassium ions are vital for the functioning of all living cells; the transfer of potassium ions across nerve cell membranes is necessary for normal nerve transmission. Fresh fruits and vegetables are good dietary sources of potassium; the body responds to the influx of dietary potassium, which raises serum potassium levels, with a shift of potassium from outside to inside cells and an increase in potassium excretion by the kidneys. Most industrial applications of potassium exploit the high solubility in water of potassium compounds, such as potassium soaps. Heavy crop production depletes the soil of potassium, this can be remedied with agricultural fertilizers containing potassium, accounting for 95% of global potassium chemical production; the English name for the element potassium comes from the word "potash", which refers to an early method of extracting various potassium salts: placing in a pot the ash of burnt wood or tree leaves, adding water and evaporating the solution.
When Humphry Davy first isolated the pure element using electrolysis in 1807, he named it potassium, which he derived from the word potash. The symbol "K" stems from kali, itself from the root word alkali, which in turn comes from Arabic: القَلْيَه al-qalyah "plant ashes". In 1797, the German chemist Martin Klaproth discovered "potash" in the minerals leucite and lepidolite, realized that "potash" was not a product of plant growth but contained a new element, which he proposed to call kali. In 1807, Humphry Davy produced the element via electrolysis: in 1809, Ludwig Wilhelm Gilbert proposed the name Kalium for Davy's "potassium". In 1814, the Swedish chemist Berzelius advocated the name kalium for potassium, with the chemical symbol "K"; the English and French speaking countries adopted Davy and Gay-Lussac/Thénard's name Potassium, while the Germanic countries adopted Gilbert/Klaproth's name Kalium. The "Gold Book" of the International Union of Physical and Applied Chemistry has designated the official chemical symbol as K.
Potassium is the second least dense metal after lithium. It is a soft solid with a low melting point, can be cut with a knife. Freshly cut potassium is silvery in appearance, but it begins to tarnish toward gray on exposure to air. In a flame test and its compounds emit a lilac color with a peak emission wavelength of 766.5 nanometers. Neutral potassium atoms have 19 electrons, one more than the stable configuration of the noble gas argon; because of this and its low first ionization energy of 418.8 kJ/mol, the potassium atom is much more to lose the last electron and acquire a positive charge than to gain one and acquire a negative charge. This process requires so little energy that potassium is oxidized by atmospheric oxygen. In contrast, the second ionization energy is high, because removal of two electrons breaks the stable noble gas electronic configuration. Potassium therefore does not form compounds with the oxidation state of higher. Potassium is an active metal that reacts violently with oxygen in water and air.
With oxygen it forms potassium peroxide, with water potassium forms potassium hydroxide. The reaction of potassium with water is dangerous because of its violent exothermic character and the production of hydrogen gas. Hydrogen reacts again with atmospheric oxygen, producing water, which reacts with the remaining potassium; this reaction requires only traces of water. Because of the sensitivity of potassium to water and air, reactions with other elements are possible only in an inert atmosphere such as argon gas using air-free techniques. Potassium does not react with most hydrocarbons such as mineral kerosene, it dissolves in liquid ammonia, up to 480 g per 1000 g of ammonia at 0 °C. Depending on the concentration, the ammonia solutions are blue to yellow, their electrical conductivity is similar to that of liquid metals. In a pure solution, potassium reacts with ammonia to form KNH2, but this reaction is accelerated by minute amounts of transition metal s
The density, or more the volumetric mass density, of a substance is its mass per unit volume. The symbol most used for density is ρ, although the Latin letter D can be used. Mathematically, density is defined as mass divided by volume: ρ = m V where ρ is the density, m is the mass, V is the volume. In some cases, density is loosely defined as its weight per unit volume, although this is scientifically inaccurate – this quantity is more called specific weight. For a pure substance the density has the same numerical value as its mass concentration. Different materials have different densities, density may be relevant to buoyancy and packaging. Osmium and iridium are the densest known elements at standard conditions for temperature and pressure but certain chemical compounds may be denser. To simplify comparisons of density across different systems of units, it is sometimes replaced by the dimensionless quantity "relative density" or "specific gravity", i.e. the ratio of the density of the material to that of a standard material water.
Thus a relative density less than one means. The density of a material varies with pressure; this variation is small for solids and liquids but much greater for gases. Increasing the pressure on an object decreases the volume of the object and thus increases its density. Increasing the temperature of a substance decreases its density by increasing its volume. In most materials, heating the bottom of a fluid results in convection of the heat from the bottom to the top, due to the decrease in the density of the heated fluid; this causes it to rise relative to more dense unheated material. The reciprocal of the density of a substance is called its specific volume, a term sometimes used in thermodynamics. Density is an intensive property in that increasing the amount of a substance does not increase its density. In a well-known but apocryphal tale, Archimedes was given the task of determining whether King Hiero's goldsmith was embezzling gold during the manufacture of a golden wreath dedicated to the gods and replacing it with another, cheaper alloy.
Archimedes knew that the irregularly shaped wreath could be crushed into a cube whose volume could be calculated and compared with the mass. Baffled, Archimedes is said to have taken an immersion bath and observed from the rise of the water upon entering that he could calculate the volume of the gold wreath through the displacement of the water. Upon this discovery, he leapt from his bath and ran naked through the streets shouting, "Eureka! Eureka!". As a result, the term "eureka" entered common parlance and is used today to indicate a moment of enlightenment; the story first appeared in written form in Vitruvius' books of architecture, two centuries after it took place. Some scholars have doubted the accuracy of this tale, saying among other things that the method would have required precise measurements that would have been difficult to make at the time. From the equation for density, mass density has units of mass divided by volume; as there are many units of mass and volume covering many different magnitudes there are a large number of units for mass density in use.
The SI unit of kilogram per cubic metre and the cgs unit of gram per cubic centimetre are the most used units for density. One g/cm3 is equal to one thousand kg/m3. One cubic centimetre is equal to one millilitre. In industry, other larger or smaller units of mass and or volume are more practical and US customary units may be used. See below for a list of some of the most common units of density. A number of techniques as well as standards exist for the measurement of density of materials; such techniques include the use of a hydrometer, Hydrostatic balance, immersed body method, air comparison pycnometer, oscillating densitometer, as well as pour and tap. However, each individual method or technique measures different types of density, therefore it is necessary to have an understanding of the type of density being measured as well as the type of material in question; the density at all points of a homogeneous object equals its total mass divided by its total volume. The mass is measured with a scale or balance.
To determine the density of a liquid or a gas, a hydrometer, a dasymeter or a Coriolis flow meter may be used, respectively. Hydrostatic weighing uses the displacement of water due to a submerged object to determine the density of the object. If the body is not homogeneous its density varies between different regions of the object. In that case the density around any given location is determined by calculating the density of a small volume around that location. In the limit of an infinitesimal volume the density of an inhomogeneous object at a point becomes: ρ = d m / d V, where d V is an elementary volume at position r; the mass of the body t
Solubility is the property of a solid, liquid or gaseous chemical substance called solute to dissolve in a solid, liquid or gaseous solvent. The solubility of a substance fundamentally depends on the physical and chemical properties of the solute and solvent as well as on temperature and presence of other chemicals of the solution; the extent of the solubility of a substance in a specific solvent is measured as the saturation concentration, where adding more solute does not increase the concentration of the solution and begins to precipitate the excess amount of solute. Insolubility is the inability to dissolve in a liquid or gaseous solvent. Most the solvent is a liquid, which can be a pure substance or a mixture. One may speak of solid solution, but of solution in a gas. Under certain conditions, the equilibrium solubility can be exceeded to give a so-called supersaturated solution, metastable. Metastability of crystals can lead to apparent differences in the amount of a chemical that dissolves depending on its crystalline form or particle size.
A supersaturated solution crystallises when'seed' crystals are introduced and rapid equilibration occurs. Phenylsalicylate is one such simple observable substance when melted and cooled below its fusion point. Solubility is not to be confused with the ability to'dissolve' a substance, because the solution might occur because of a chemical reaction. For example, zinc'dissolves' in hydrochloric acid as a result of a chemical reaction releasing hydrogen gas in a displacement reaction; the zinc ions are soluble in the acid. The solubility of a substance is an different property from the rate of solution, how fast it dissolves; the smaller a particle is, the faster it dissolves although there are many factors to add to this generalization. Crucially solubility applies to all areas of chemistry, inorganic, physical and biochemistry. In all cases it will depend on the physical conditions and the enthalpy and entropy directly relating to the solvents and solutes concerned. By far the most common solvent in chemistry is water, a solvent for most ionic compounds as well as a wide range of organic substances.
This is a crucial factor in much environmental and geochemical work. According to the IUPAC definition, solubility is the analytical composition of a saturated solution expressed as a proportion of a designated solute in a designated solvent. Solubility may be stated in various units of concentration such as molarity, mole fraction, mole ratio, mass per volume and other units; the extent of solubility ranges from infinitely soluble such as ethanol in water, to poorly soluble, such as silver chloride in water. The term insoluble is applied to poorly or poorly soluble compounds. A number of other descriptive terms are used to qualify the extent of solubility for a given application. For example, U. S. Pharmacopoeia gives the following terms: The thresholds to describe something as insoluble, or similar terms, may depend on the application. For example, one source states that substances are described as "insoluble" when their solubility is less than 0.1 g per 100 mL of solvent. Solubility occurs under dynamic equilibrium, which means that solubility results from the simultaneous and opposing processes of dissolution and phase joining.
The solubility equilibrium occurs. The term solubility is used in some fields where the solute is altered by solvolysis. For example, many metals and their oxides are said to be "soluble in hydrochloric acid", although in fact the aqueous acid irreversibly degrades the solid to give soluble products, it is true that most ionic solids are dissolved by polar solvents, but such processes are reversible. In those cases where the solute is not recovered upon evaporation of the solvent, the process is referred to as solvolysis; the thermodynamic concept of solubility does not apply straightforwardly to solvolysis. When a solute dissolves, it may form several species in the solution. For example, an aqueous suspension of ferrous hydroxide, Fe2, will contain the series + as well as other species. Furthermore, the solubility of ferrous hydroxide and the composition of its soluble components depend on pH. In general, solubility in the solvent phase can be given only for a specific solute, thermodynamically stable, the value of the solubility will include all the species in the solution.
Solubility is defined for specific phases. For example, the solubility of aragonite and calcite in water are expected to differ though they are both polymorphs of calcium carbonate and have the same chemical formula; the solubility of one substance in another is determined by the balance of intermolecular forces between the solvent and solute, the entropy change that accompanies the solvation. Factors such as temperature and pressure will alter this balance. Solubility may strongly depend on the presence of other species dissolved in the solvent, for example, complex-forming anions in liquids. Solubility will depend on the excess or deficiency of a common ion in the solution, a phenomenon known as the common-ion effect. To a lesser extent, solubility will depend on the ionic strength of solutions; the last two effects can be quantified using the equation for solubility equilibrium. For a solid that dissolves in a redox reaction, solubility is expe