Topology (chemistry)
Encyclopedia
In chemistry
, topology provides a convenient way of describing and predicting the molecular structure
within the constraints of three-dimensional (3-D) space. Given the determinants of chemical bond
ing and the chemical properties
of the atom
s, topology provides a model for explaining how the atoms ethereal wave functions must fit together. Molecular topology is a part of mathematical chemistry
dealing with the algebraic description of chemical compounds so allowing a unique and easy characterization of them.
Topology is insensitive to the details of a scalar field
, and can often be determined using simplified calculations. Scalar fields such as electron density
, Madelung
field, covalent field and the electrostatic potential can be used to model topology.
Each scalar field has its own distinctive topology and each provides different information about the nature of chemical bonding and structure. The analysis of these topologies, when combined with simple electrostatic theory and a few empirical observations, leads to a quantitative model of localized chemical bonding. In the process, the analysis provides insights into the nature of chemical bonding.
Applied topology explains how large molecules reach their final shapes and how biological molecules achieve their activity.
(TIs). Topological indices are used in the development of quantitative structure-activity relationship
s (QSARs) in which the biological activity or other properties of molecules are correlated with their chemical structure.
Chemistry
Chemistry is the science of matter, especially its chemical reactions, but also its composition, structure and properties. Chemistry is concerned with atoms and their interactions with other atoms, and particularly with the properties of chemical bonds....
, topology provides a convenient way of describing and predicting the molecular structure
Molecular structure
The molecular structure of a substance is described by the combination of nuclei and electrons that comprise its constitute molecules. This includes the molecular geometry , the electronic properties of the...
within the constraints of three-dimensional (3-D) space. Given the determinants of chemical bond
Chemical bond
A chemical bond is an attraction between atoms that allows the formation of chemical substances that contain two or more atoms. The bond is caused by the electromagnetic force attraction between opposite charges, either between electrons and nuclei, or as the result of a dipole attraction...
ing and the chemical properties
Chemical property
A chemical property is any of a material's properties that becomes evident during a chemical reaction; that is, any quality that can be established only by changing a substance's chemical identity...
of the atom
Atom
The atom is a basic unit of matter that consists of a dense central nucleus surrounded by a cloud of negatively charged electrons. The atomic nucleus contains a mix of positively charged protons and electrically neutral neutrons...
s, topology provides a model for explaining how the atoms ethereal wave functions must fit together. Molecular topology is a part of mathematical chemistry
Mathematical chemistry
Mathematical chemistry is the area of research engaged in novel applications of mathematics to chemistry; it concerns itself principally with the mathematical modeling of chemical phenomena...
dealing with the algebraic description of chemical compounds so allowing a unique and easy characterization of them.
Topology is insensitive to the details of a scalar field
Scalar field
In mathematics and physics, a scalar field associates a scalar value to every point in a space. The scalar may either be a mathematical number, or a physical quantity. Scalar fields are required to be coordinate-independent, meaning that any two observers using the same units will agree on the...
, and can often be determined using simplified calculations. Scalar fields such as electron density
Electron density
Electron density is the measure of the probability of an electron being present at a specific location.In molecules, regions of electron density are usually found around the atom, and its bonds...
, Madelung
Madelung
Madelung may refer to:* Erwin Madelung German physicist** Madelung constant chemical energy of an ion in a crystal* Georg Hans Madelung German aeronautical engineer* Otto Wilhelm Madelung German surgeon...
field, covalent field and the electrostatic potential can be used to model topology.
Each scalar field has its own distinctive topology and each provides different information about the nature of chemical bonding and structure. The analysis of these topologies, when combined with simple electrostatic theory and a few empirical observations, leads to a quantitative model of localized chemical bonding. In the process, the analysis provides insights into the nature of chemical bonding.
Applied topology explains how large molecules reach their final shapes and how biological molecules achieve their activity.
Topological indices
It is possible to set up equations correlating direct quantitative structure activity relationships with experimental properties, usually referred to as topological indicesTopological index
In the fields of chemical graph theory, molecular topology, and mathematical chemistry, a topological index also known as a connectivity index is a type of a molecular descriptor that is calculated based on the molecular graph of a chemical compound. Topological indices are numerical parameters...
(TIs). Topological indices are used in the development of quantitative structure-activity relationship
Quantitative structure-activity relationship
Quantitative structure–activity relationship or QSPR is the process by which chemical structure is quantitatively correlated with a well defined process, such as biological activity or chemical reactivity.For example, biological activity can be expressed quantitatively as the concentration of a...
s (QSARs) in which the biological activity or other properties of molecules are correlated with their chemical structure.