A molecule grouping class that groups the different ion forms of the base of an acid
A molecule grouping class that can groups an acid together with all its conjugate bases. physiological
A grouping class that refines a charge-neutral entity
A grouping class for a chemical salt named by anion
A grouping class for a chemical salt named by cation
a stereocenter consisting of an atom holding a set of ligands (atoms or groups of atoms) in a spatial arrangement which is not superimposable on its mirror image.
This utility class serves to collect a set of domain entities, and to be the top level object in tree-based representations such as JSON.
A grouping class defined as a derivative of another molecule or molecular grouping class
molecule grouping class defined by addition of a group
A grouping class defined in terms of a derivative of a molecule and the addition of a group
molecule grouping class defined by components
A grouping class defined as an exhaustive list of components
A deterministic SMILES string. Note there is no unique system for canonical smiles strings
The carbohydrate structure format used by the Complex Carbohydrate Structure Database (CCSD) originally developed at the University of Georgia. This is a 2D structure where bars and hyphens are used to indicate linkages, and monosaccharides are specified in the following order, separated by hyphens: anomer - configuration symbol - monosaccharide abbreviation.
A CHEBI formular combines aspects of molecular and generalized molecular formulae, and may also be an atom symbol
CurlySMILES is a chemical line notation which extends SMILES with annotations for storage, retrieval and modeling of interlinked, coordinated, assembled and adsorbed molecules in supramolecular structures and nanodevices. https://jcheminf.biomedcentral.com/articles/10.1186/1758-2946-3-1
a stereoisomer relationship where the two forms are mirror images of one another
A diastereoisomer of relationship in which the isomers differ at only one stereocenter
structural isomers that have the same molecular formula (that is, the same number of atoms of the same elements), but the atoms are connected in different ways so that the groupings are dissimilar.
A variant of an empirical formula where numbers are replaced by generic ns; e.g. CnH2n+2 for alkane
This is a multiline format used by GlycomeDB, among others, and uses a graph notation to represent glycans, similar to KCF. Monosaccharides are specified more strictly to be able to map the monosaccharides between different representations. Substituents, such as N-acetyl, are specified as separate nodes from their basetypes and are linked together in the edge section. If newlines are removed, this format can be made linear.
A linear notation proposed by GlycoMinds, Ltd., where monosaccharides are indicated by a one- or two-letter code, linkages are indicated by “a” or “b” for anomers and a single number for the carbon number linkage on the reducing end, and branches are indicated by parentheses. This format is the most compact among existing formats, and several databases use a modified form of this format to accommodate additional codes and varying carbohydrate structures (such as ambiguous structures).
connects a base to the acid form. E.g. citrate(3-) has acid form citric acid
true if the molecule possesses a cycle in the atom connectivity graph
Location of a MolFile representing a chemical structure
has physiologically stable form (Deprecated)
Different term for the concept of a major microspecies at pH 7.3.
Relation between a polymer and all instances of a repeated polymeric unit
Auxhiliary information on top of a RInChi
A half-reaction, such as a RInChI with starting materials and no identified products, is a valid RInChI
A reaction transform language that is a superset of reaction SMILES and a subset of reaction SMARTS
A hashed representation of an InChi2D string
A hashed representation of an InChi string
relationship that holds between two isotones, always holds if the isotones have a different atomic number and the same neutron number.
a relationship that holds between two forms of a parent molecule with identical chemical formulas but are differentiated by the number of neutrons in at least one atom
isomers which differ by isotopic substitution, and which have the same number of atoms of each isotope but in a different arrangement.
The maximum number of substrate molecules converted to product per enzyme molecule per unit time, when the enzyme is saturated with substrate. It represents the maximum catalytic efficiency of an enzyme under ideal conditions.
A multiline format used by the KEGG GLYCAN database and represents glycans as graphs. Monosaccharides are represented as nodes, and glycosidic linkages are represented as edges. Each node is given a unique number, and x- and y- coordinates are specified such that the glycan structure can be drawn on a 2D plane. Edge information uses the node numbers to specify anomeric and carbon number information. Monosaccharide names are specified as text, and no particular rules are specified to represent these names.
A unique linear notation proposed and used by GLYCOSCIENCES.de, with the reducing end specified on the left. Monosaccharides, written according to CarbBank rules, are surrounded by square brackets and anomers, and stereochemistry is specified and separated by hyphens. Glycosidic linkages are also surrounded by hyphens, and carbon numbers of the linkages are separated by the plus sign. Branches are indicated by curly brackets.
logP partition coefficient calculated from 2D structure using contributions from pre-defined structure fragments. It corresponds to: log(Poctanol/Pwater) = log(SoluteInOctanol/SoluteInWater)
the substrate concentration at which the reaction rate is half of its maximum value (Vmax)
A lower Km indicates higher affinity (the enzyme needs less substrate to achieve half its maximum rate
Km is typically expressed in units of concentration (e.g., mol/L, μM, mM)
Molar refractivity calculated from 2D structure using contributions from pre-defined structure fragments.
The electric charge of a molecule, typically expressed as multiples of the elementary charge.
molecular electronic absorption spectroscopy
A molecular property describing absorption or emission of electromagnetic radiation due to electronic transitions.
A chemical formula where numbers denote atom count. E.g. C6H12O6 for glucose
The amount of heat required to raise the temperature of one mole of a molecule by one Kelvin.
The number of water molecules associated with or bound to a molecule.
The geometric configuration or three-dimensional arrangement of atoms within a molecule.
A property reflecting the spatial dimensions or volume occupied by a molecule.
The specific arrangement of atoms in a molecule, usually represented by chemical notation or structural formulas.
Next in a sequence of compounds with the same functional group and similar chemical properties in which the members of the series can be branched or unbranched. E.g. ethane (C2H6) next in homologous series from methane (CH4)
relationship that holds between two nuclear isomers, always holds if the isomers have the same nucleon number but different energy states
number of hydrogen bond acceptors corresponding to sum of nitrogen atoms without any any implicit/explicit hydrogen atom and all oxygen atoms
number of hydrogen bond donors corresponding to sum of nitrogen and oxygen atoms with at least one implicit/explicit hydrogen atom
number of rotatable bonds corresponds to single bonds excluding following types of single bonds terminal bonds; attached to triple bonds; amide, thioamide and sulfonamide bonds.
a functional group or other substituent changes position on a parent structure.
components of the (usually carbon) skeleton are distinctly re-ordered to create different structures. Pentane exists as three isomers: n-pentane (often called simply "pentane"), isopentane (2-methylbutane) and neopentane (dimethylpropane).
structural isomers (constitutional isomers) of chemical compounds that readily interconvert. Examples: a neutral amino acid and its zwitterion
Topological Polar Surface Area corresponding to nitrogen and oxygen atoms calculated from 2D structure using contributions from pre-defined structure fragments containing these atoms
van der Waals molecular volume calculated from 2D structure using atomic radii with adjustments for number of bonds, aromatic and non-aromatic rings
A relationship between two or more chemical entities where there is some degree of similarity between these entities on their similarity
A mixin for an entity that consists of one or more atoms where the atoms and the number of occurrences is counted (corresponding to the chemical layer in InChI)
A mixin for an entity where the charge is explicitly specified (corresponding to the /q layer in InChI)
A mixin for an entity that consists of two or more atom occurrences where the connectivity is specified (corresponding to the /c layer in InChI)
A mixin for an entity where the stereochemistry is explicitly specified (corresponding to the /t, m/, and /s layers in InChI)
A molecule grouping class that can be written using a chemical formula using variables (e.g. n), or arithmetic expressions uing variables (e.g. 2n+2), plus optionally constraints on those variables (e.g. n>3). An example is alkane; CnH2n+2, which groups specific molecules such as methane
A representation of an InChI string as an object, composed of distinct sublayers
Abstract grouping for entities that represent abstract or concrete locations of chemical entities or their parts.
A grouping class that classifies materials
A grouping class that classifies molecular components. Example: inorganic anion group
An abstract part of a polymer that is all instances of a repeated monomer of a single type
A grouping class for reactions, for example, dehalogenase; breaking of covalent bond
A subtype_of relationship holds between I and C if I is a specific entity of type C. Here I and C denotes instances of OWL classes, where I is a specific class and C is a grouping class
A stereoisomer non-mirror image non-identical stereoisomers
Diastereomers differ from enantiomers in that the latter are pairs of stereoisomers that differ in all stereocenters and are therefore mirror images of one another
The subject of this link is the most common protonation state for this chemical at a pH of 7.3. The link may point to it's source.
Elementary particle not affected by the strong force having a spin 1/2, a negative elementary charge and a rest mass of 0.000548579903(13) u, or 0.51099906(15) MeV.
A boson that is its own antiparticle, has no spin, zero electric charge and zero colour charge.
The general name for the hydrogen nucleus, to be used without regard to the hydrogen nuclear mass (either for hydrogen in its natural abundance or where it is not desired to distinguish between the isotopes).
Nuclear particle of charge number +1, spin 1/2 and rest mass of 1.007276470(12) u.
Particle of zero charge, zero rest mass, spin quantum number 1, energy hnu and momentum hnu/c (h is the Planck constant, nu the frequency of radiation and c the speed of light), carrier of electromagnetic force.
Elementary particle not affected by the strong force having a spin 1/2, a positive elementary charge and a rest mass of 0.113428913(17) u, or 105.658389(34) MeV.
Nuclear particle of zero charge, spin 1/2 and rest mass of 1.008664904(14) u.
Elementary particle not affected by the strong force having a spin 1/2, a positive elementary charge and a rest mass of 0.000548579903(13) u, or 0.51099906(15) MeV.
A particle not known to have substructure.
Heavy nuclear particle: proton or neutron.
Lepton is a fermion that does not experience the strong force (strong interaction). The term is derived from the Greek lambdaepsilonpitauomicronsigma (small, thin).
Baryon is a fermion that does experience the strong force (strong interaction). The term is derived from the Greek betaalpharhoupsilonsigma (heavy).
Particle of half-integer spin quantum number following Fermi-Dirac statistics. Fermions are named after Enrico Fermi.
Particle of integer spin quantum number following Bose-Einstein statistics. Bosons are named after Satyendra Nath Bose.
A subatomic particle known to have substructure (i.e. consisting of smaller particles).
Hadron is a subatomic particle which experiences the strong force.
A hadron with zero or integer spin; a strongly interacting boson. The term is derived from the Greek muepsilonsigmaomicronsigma (medium, middle).
Quarks comprise one of two classes of the fundamental particles. Quarks possess fractional electric charges and are not observed in free state.
A nucleus or any of its constituents in any of their energy states.
The collective name for zero-spin mesons pi(+), pi(-) and pi(0).
A subatomic particle of charge number +1, zero spin and rest mass of 0.1498323(8) u, or 139.5679(7) MeV.
A subatomic particle of charge number -1, zero spin and rest mass of 0.1498323(8) u, or 139.5679(7) MeV.
A subatomic particle of zero charge, zero spin and rest mass of 0.1449008(9) u, or 134.9743(8) MeV.
An elementary particle of spin 1/2, zero electric charge and negligible rest mass. Three known types (flavors) of neutrino are electron neutrino, muon neutrino and tau neutrino, named after their charged partner leptons.
Elementary particle not affected by the strong force having a spin 1/2, a negative elementary charge and a rest mass of 1777.05 MeV.
Elementary particle not affected by the strong force having a spin 1/2, a negative elementary charge and a rest mass of 0.113428913(17) u, or 105.658389(34) MeV.
A baryon which contain one or more strange quarks. Hyperons are short-lived and heavier than nucleons.
A first-generation quark with a charge of +2/3. The up and down quarks are the fundamental constituents of the nucleons.
A first-generation quark with a charge of -1/3. The up and down quarks are the fundamental constituents of the nucleons.
A second-generation quark with a charge of -1/3 and a strangeness of -1.
A second-generation quark with a charge of +2/3.
A third-generation quark with a charge of -1/3.
A third-generation quark with a charge of +2/3.
A reaction in which two or more reactants yield a single main product with accompanying formation of a small molecule
Formation of cyclic structures from linear precursors
A functional group modification reaction where a functional group is oxidised
Formation of an acyl group bond, typically involving carboxylic acid derivatives
Reactions that form new carbon-carbon bonds
Alkylation or arylation of heteroatoms such as nitrogen, oxygen, or sulfur
Rearrangement reactions that convert one isomer to another
A functional group modification reaction where a functional group is reduced
Reactions that add atoms or groups across multiple bonds
A reaction step where one atom or group is replaced with another
A solvolysis reaction where the solvent material is water
A molecular process where two groups are lost with concomitant formation of an unsaturation in the molecule or formation of a new ring
A covalent bond is a chemical bond that involves the sharing of pairs of electrons between atoms. This sharing results in a stable balance of attractive and repulsive forces between those atoms.
A monoatomic ion that is positive, e.g Cu(2+)
atom grouping by periodic table placement
A grouping class that classifies atoms. For example, metal atom
A connection between two atoms. Note this is the reified form of 'atomically connected to'.
A characteristic of a chemical entity that is realized under particular conditions
a polymer with a more than one type of repeating unit
An ester is a chemical compound derived from an acid (organic or inorganic) in which at least one –OH hydroxyl group is replaced by an –O– alkyl (alkoxy) group
All pairs of atoms in this entity are transitively connected via covalent bonds
An atom type that has atomic number, charge, and neutron number stated (equivalently: protons + mass + charge)
chemical species of an element: Specific form of an element defined as to isotopic composition, electronic or oxidation state, and/or complex or molecular structure https://goldbook.iupac.org/terms/view/CT06859
A macromolecule consisting of a large number of monosaccharides linked glycosidically
Glycans composed of a single type of monosaccharide residue (homopolysaccharide, synonym homoglycan) are named by replacing the ending '-ose' of the sugar by '-an', e.g. mannans, fructans, xylans, arabinans
a polymer with a single type of repeating unit
Isobars are atoms (nuclides) of different chemical elements that have the same number of nucleons.
A reaction that converts a molecule from one isomer to another.
This class is deprecated. Use the reaction_type slot with value 'isomerization' instead.
a named part of a molecule. In some instances moieties may be composed of yet smaller moieties and functional groups
A molecule in which the units are identical. Example: methyl
A material of which a single unit is sized (in at least one dimension) between 1 and 100 nm
A molecule that has no net charge and is not a zwitterion
A molecule in which the units are not identical. TODO: move this higher
The g-block is a hypothetical region in the periodic table of the elements.
A part of a complex mixture that is of uniform composition
A macromolecule composed of one or more polypeptide chains of amino acids that fold into a specific three-dimensional structure and perform biological functions
a chemical compound that has equal amounts of left- and right-handed enantiomers of a chiral molecule. An example is Thalidomide
an atom that has excess nuclear energy, making it unstable
Formation of aromatic rings containing heteroatoms
Removal of protecting groups to restore original functionalities
Addition of functional groups to unsaturated bonds or reactive centers
Introduction of protecting groups to temporarily mask reactive functionalities
Separation of enantiomers or other stereoisomers
Cleavage of cyclic structures to form linear products
A molecule characterized by availability in small-molecule databases
polymeric arrays of monomeric units that are connected by reversible and highly directional secondary interactions–that is, non-covalent bonds
A molecule that has both a positive and negative charges but is net neutral
An individuated atom in the context of a chemical structure.
Relation between a molecule and the atoms it contains. Note that this is a shortcut relation: for granular representations go via atom occurrences
Relationship between a complex mixture and its parts
The negative logarithm of the acid dissociation constant (Ka) for ionizable groups in a molecule. Multiple pKa values may exist for molecules with multiple ionizable groups.
For molecules with multiple ionizable groups, this field can contain multiple values
Lower pKa values indicate stronger acids
Standard conditions: aqueous solution at 25°C
A hashed representation of a RInChi string
a relationship that holds between two forms of the 'same' molecule with identical chemical formulas but different bonds
Applies to entities that have a charge state, which may be positive, negative, or neutral
a chemical compound consisting of an ionic assembly of cations and anions.
in SIO falls under molecular complex? Also in biolink
Abstract grouping for slots that related chemical entities via a connectivity relationships
Instances of this class represent generic concepts that can be used to group more specific concepts, or to classify entities
A macroscopic polyatomic entity that consists of multiple chemical entities where the stoichiometry is not specified and the spatial arrangement of the ingredients is not defined. Examples include coal, tea tree oil, toothpaste, organometallic compounds, heterogeneous metals
although the stoichiometry is not known rough percentage parts can be provided
A molecular complex is a chemical complex composed of at least one weakly interacting molecule.[SIO] Examples: chromosome, double-standed DNA, protein-containing macromolecular complex
In SIO, molecular complex is an only child of chemical complex, which is under chemical substance. chemical complex is defined as A chemical complex is a chemical substance composed of a weakly connected molecules and ions in a known stoichiometry.
In bioptop, molecule complex is a sibling of structured biological entity under poly molecular composite entity
a geometric point in a molecule in which the interchanging of two substituents creates a stereoisomer.
Applies to entities that are uncharged, i.e. have an elemental charge of zero
relationship that holds between two allotropes, where both allotropes are allotropes of the same element
the measure of bond strength in a chemical bond.
the average distance between nuclei of two bonded atoms in a molecule
the average distance between nuclei of two bonded atoms in a molecule. It is a transferable property of a bond between atoms of fixed types, relatively independent of the rest of the molecule.
the number of electron pairs (bonds) between a pair of atoms
a relationship that holds between two forms of a parent molecule with identical chemical formulas but distinct arrangements of atoms in space
The number of atoms bonded to the atom of interest. [https://doi.org/10.1021%2Fed083p791]
One of l->r, r->l, bidirectional, neutral
A chemical formula where numbers denote relative proportion of atoms. E.g. CH2O for glucose
Example: R-thalidomide is the enantiomer form of 2-(2,6-dioxopiperidin-3-yl)-1H-isoindole-1,3(2H)-dione
The charge remaining on an atom when all ligands are removed homolytically. [https://doi.org/10.1021%2Fed083p791]
The pattern in which the atoms are bonded; e.g. hexagonal lattice, sheets, etc
Relation between a molecule and the groups it contains
Location of a MixFile representing a chemical mixture
The main layer consists of chemical formula, atom connections, and hydrogen atoms. Example: CH3O/c1-2/h1H3/q-1
The first part of the inchi_string, after 'InChI='
An organic molecule is a molecule composed of organic atoms (at least carbon, hydrogen, and optionally oxygen, phosphorus, nitrogen, sulfur) [SIO]
A SMILES string that distinguishes between isomeric forms. E.g. [13C] for carbon-13
relationship that holds between two isotopes, always holds if the isotopes have the same atomic number and a different neutron number.
The sum of the relative atomic masses of the constituent atoms of a molecule.
number of nucleons in an atom. proton number plus neutron number.
The charge remaining on an atom when all ligands are removed heterolytically in their closed form, with the electrons being transferred to the more electronegative partner; homonuclear bonds do not contribute to the oxidation number. [https://doi.org/10.1021%2Fed083p791]
Ionic strength of solution in mol/L at which pKa was measured. Default is 0.0 M if not specified.
Salt concentration affects pKa through electrostatic shielding of charges
Standard ionic strength is 0.0 M (zero ionic strength corresponding to distilled water)
Pressure in atmospheres at which pKa was measured. Default is 1 atm if not specified.
Generally minor effect under standard laboratory conditions
Solvent system for pKa measurement. Default is water (H₂O) if not specified.
pKa values in non-aqueous solvents can be dramatically different due to polarity effects
Temperature in Celsius at which pKa was measured. Default is 25°C if not specified.
pKa values can shift significantly with temperature following the van't Hoff equation
the overall speed of a reaction, typically measured in concentration change per unit time
a proportionality constant that relates the reaction rate to reactant concentrations.
Classification of the chemical reaction based on mechanistic and functional categories
a molecular pattern matching language, related to the popular SMILES molecular language, that can be used to specify sub-structural patterns in molecules.
the number of electrons that an atom uses in bonding [https://doi.org/10.1021%2Fed083p791]
example: In in ammonia, nitrogen has a valence of 3, each each hydrogen has a valency of 1
example: In methane, carbon has a valence of 4, and each hydrogen has a valency of 1
forumla: number of bonds + formal charge
forumla: number of electrons in valence shell of free atom – number of non-bonding electrons on atom in molecule
todo: determine if this is in CHEBI and how to map
The maximum amount of a substance that can dissolve in water at 25°C, expressed in grams per liter (g/L).
This property represents the maximum equilibrium solubility in pure water
Conversion of one functional group to another without changing the carbon skeleton
A molecule consisting of atoms of the same element
This mixin is applied on an entity (atom or molecule) that is negatively charged
an atom type in which only charge state is specified, designated by the element followed by charge
This mixin is applied on an entity (atom or molecule) that is positively charged
A polyatomic entity that consists of two or more parts that are weakly bound, may be of known or unknown stoichiometry
this is mass-number neutral, so there can be no mass associated with a monatomic ion instance
A macromolecule composed of repeating subunits. Examples: cellulose
A molecule that has a net charge. For example, nitrate is a molecular and ionic species; its formula is (NO3-).
Instances of this link a reaction to a chemical entity participant
a chain of connected monomers in a linear polymer - for example, a sub-region of an amino acid or nucleotide sequence.
- includes an interval corresponding to the whole molecule as an edge case
A chemical entity below the granularity of an atom.
connects an acid to any of the the base anions. E.g. citric acid acid form of citrate(1-),citrate(2-),citrate(3-)
a relationship that holds between two forms of the 'same' molecule with identical chemical formulas but different bonding patterns
Applies to entities that are charged, either positive or negative
Instances of this class represent generic chemical concepts that can be used to group more specific concepts, or to classify entities. For example "amino acid" is a grouping for "serine", "leucine" etc; ester is a grouping for nitroglycerin; alkane is a grouping for pentane, butane, methane, etc
A substance composed of repeated chemical units that has a specific arrangement of atoms or molecules.
this is intentionally placed outside the chemical entity hierarchy as the concept encompasses more than the chemical structure.
an atomic species characterized by the specific constitution of its nucleus
An atom type that only has a subset of properties (has atomic number, charge, and neutron number) stated
A polyatomic entity that consists of two or more parts that are weakly bound, and of known stoichiometry
Reactions that break existing bonds to form fragments or rearrange structures
Relation between a molecule and the molecules it is made from.
one of two stereoisomers of a chiral molecule that are mirror images. Example: R-thalidomide
key= (enantiomer form of, absolute configuration)
key= (enantiomer form of, inchi tetrahedral stereochemical sublayer)
A discrete chemical structure, material structure, or subatomic particle type
Any chemical entity consisting of more than one atom.
A block of the periodic table is a set of elements unified by the orbitals their valence electrons or vacancies lie in
Holds between C and P if C owl:subClassOf P. Note that in this model, most classes are metaclasses (see 'owl class'), where these metaclasses may represent *groupings* or specific countable elements or species. We provide two different sub-properties of subclass of for two cases: (1) subtype_of, which connects grouping classes (e.g. alkane is_a hydrocarbon; alpha-amino-acid is_a amino-acid), (2) classified_by, which connects a specific element to a grouping class (e.g. methane is_a hydrocarbon; iron is_a metal; serine is_a amino-acid)
short symbol for chemical entity, e.g. K, C-16
A discrete, specific named entity in the domain of chemistry.
Links different variants of the same chemical in different protonation states, where the target of this link is the (predicited) to be most common protonation state for this chemical at a pH of 7.3. This link may point to it's source. Connects an acid to the form that is stable at physiological pH (7.3). E.g. citric acid has physiological base citrate(3-)
A string encoding of a molecular graph, no chiral or isotopic information. There are usually a large number of valid SMILES which represent a given structure. For example, CCO, OCC and C(O)C all specify the structure of ethanol.
a problematic set of structures to describe using SMILES notation is those which cannot be easily described using molecular graphs (see “Limitations of molecular graph representations” section), such as organometallic compounds and ionic salts.
An occurrence of an atom in the context of a particular molecule. For example, one of two occurrences of oxygen in nitrate
generic form of an atom, with unspecified neutron or charge
A proper part of a molecule that is larger than an atom
Reactions that create new bonds between atoms or groups
connects the base form of an acid to an acid. Also connects the different charge states of the base. Example: the different charge states of lactate (CHEBI:24996) conjugate base of lactic acid (CHEBI:28358)
sometimes chebi hops over a state skipping an intermediate
A large molecule, such as a polymer, lipid, or macrocycle
A molecule that has a charge state specified
A grouping class that classifies molecules. Example: carbohydrate, monosaccharide, amino acid, polyacrylamide
Molecular grouping classes are typically defined by elemental composition and structure as well as chemical properties
Unlike an actual molecule, a molecule grouping class will not have an inchi or properties such as mass
The part of an InChI string that represents the chemical formula, occurring after the version string. E.g. C6H12O6 for glucose
Coordination Complexes: In coordination chemistry, dots can separate the metal complex from its counterions or ligands that are not directly bonded to the metal center. For example, "[Co(NH₃)₆]Cl₃" indicates a complex of cobalt with six ammonia ligands, and the three chloride ions are counterions. If written as "[Co(NH₃)₆]·3Cl", it would similarly denote the presence of three chloride ions associated with the complex, though this notation is less common
Molecular Assemblies: For certain supramolecular structures or assemblies, dots might be used to indicate a non-covalent association of components. This usage is less common and more context-dependent
Salt Formulations: Dots can also be used to denote the proportions in which different components are combined to form a salt. For instance, "CaCl₂·2AgNO₃" would suggest a complex formed from one unit of calcium chloride and two units of silver nitrate, though this particular example is more illustrative than practical.
in the case of hydrates, the dot separates the formula of the compound from the water molecules. For example, CuSO₄·5H₂O represents copper(II) sulfate pentahydrate, indicating that there are five water molecules associated with each copper(II) sulfate unit in the crystal.
Describes how many hydrogen atoms are connected to each of the other atoms.
inchi stereochemical double bond sublayer
A relationship between two entities of the same type
The atoms in the chemical formula (except for hydrogens) are numbered in sequence; this sublayer describes which atoms are connected by bonds to which other ones.
inchi tetrahedral stereochemical sublayer
A generic grouping for molecular formulae and empirical formulae
A chemical entity consisting of exactly one atomic nucleus and the electron(s) orbiting it.
{'chemical species of an element': 'Specific form of an element defined as to isotopic composition, electronic or oxidation state, and/or complex or molecular structure https://goldbook.iupac.org/terms/view/CT06859'}
instances of this class mixin are OWL Classes
A specific subtype of an atom with a specified neutron number
Wikidata has isotope as a subclass of nuclide, but nuclide has no instances that are not isotope instances.
A subtype_of relationship holds between C and P if C is a more specialized form of P. Here C and P denotes instances of OWL classes, where C and P both function as grouping class
Classification of chemical reactions based on mechanistic and functional categories
number of protons minus number of electrons
name of chemical entity. E.g. nickel, carbon-16
A discrete structure that is one or more atoms that can be described by a chemical formula.
Does not encompass chemical grouping classes, such as "amino acid". Use the class ChemicalGrouping for this.
In common chemical usage generic and specific chemical names (such as radical or hydroxide ion) or chemical formulae refer either to a chemical species or to a molecular entity[https://goldbook.iupac.org/terms/view/CT01038]
A chemical entity that consists of two or more atoms where all atoms are connected via covalent bonds.
Chemical Entities Mixtures and Reactions Ontological Framework
A data model for managing information about chemical entities, ranging from atoms through molecules to complex mixtures. Aspects of this have been cribbed from various sources including CHEBI, SIO, Wikipedia/Wikidata, the NCATS Translator Chemical Working Group, but all mistakes are my own. For full context/motivation see the [GitHub repo](https://github.com/chemkg/chemrof).