Vicinal (chemistry)
In chemistry the descriptor vicinal (from Latin vicinus = neighbor), abbreviated vic, describes any two functional groups bonded to two adjacent carbon atoms (i.e., in a 1,2-relationship).
Hypervalent molecule
In chemistry, a hypervalent molecule (the phenomenon is sometimes colloquially known as expanded octet) is a molecule that contains one or more main group elements apparently bearing more than eight e
Bond length
In molecular geometry, bond length or bond distance is defined as the average distance between nuclei of two bonded atoms in a molecule. It is a transferable property of a bond between atoms of fixed
Prismanes
The prismanes are a class of hydrocarbon compounds consisting of prism-like polyhedra of various numbers of sides on the polygonal base. Chemically, it is a series of fused cyclobutane rings (a ladder
Dodecahedral molecular geometry
In chemistry, the dodecahedral molecular geometry describes the shape of compounds where eight atoms or groups of atoms or ligands are arranged around a central atom defining the vertices of a snub di
Trigonal prismatic molecular geometry
In chemistry, the trigonal prismatic molecular geometry describes the shape of compounds where six atoms, groups of atoms, or ligands are arranged around a central atom, defining the vertices of a tri
Nucleic acid secondary structure
Nucleic acid secondary structure is the basepairing interactions within a single nucleic acid polymer or between two polymers. It can be represented as a list of bases which are paired in a nucleic ac
Nucleic acid double helix
In molecular biology, the term double helix refers to the structure formed by double-stranded molecules of nucleic acids such as DNA. The double helical structure of a nucleic acid complex arises as a
Cyclic compound
A cyclic compound (or ring compound) is a term for a compound in the field of chemistry in which one or more series of atoms in the compound is connected to form a ring. Rings may vary in size from th
Prismane
Prismane or 'Ladenburg benzene' is a polycyclic hydrocarbon with the formula C6H6. It is an isomer of benzene, specifically a valence isomer. Prismane is far less stable than benzene. The carbon (and
Isostructural
Isostructural chemical compounds have similar chemical structures. "Isomorphous" when used in the relation to crystal structures is not synonymous: in addition to the same atomic connectivity that cha
Pentagonal pyramidal molecular geometry
In chemistry, pentagonal pyramidal molecular geometry describes the shape of compounds where in six atoms or groups of atoms or ligands are arranged around a central atom, at the vertices of a pentago
Pauling's rules
Pauling's rules are five rules published by Linus Pauling in 1929 for predicting and rationalizing the crystal structures of ionic compounds.
T-shaped molecular geometry
In chemistry, T-shaped molecular geometry describes the structures of some molecules where a central atom has three ligands. Ordinarily, three-coordinated compounds adopt trigonal planar or pyramidal
Vibrational circular dichroism
Vibrational circular dichroism (VCD) is a spectroscopic technique which detects differences in attenuation of left and right circularly polarized light passing through a sample. It is the extension of
Bartell mechanism
The Bartell mechanism is a pseudorotational mechanism similar to the Berry mechanism. It occurs only in molecules with a pentagonal bipyramidal molecular geometry, such as IF7. This mechanism was firs
Tetrahedral molecular geometry
In a tetrahedral molecular geometry, a central atom is located at the center with four substituents that are located at the corners of a tetrahedron. The bond angles are cos−1(−1⁄3) = 109.4712206...°
Octafluorocubane
Octafluorocubane or perfluorocubane is an organofluorine compound with the formula C8F8, consisting of eight carbon atoms joined into a cube, with a fluorine on each corner. It is a colorless sublimab
Chicken wire (chemistry)
In chemistry the term chicken wire is used in different contexts. Most of them relate to the similarity of the regular hexagonal (honeycomb-like) patterns found in certain chemical compounds to the me
Corey-Pauling rules
In biochemistry, the Corey-Pauling rules are a set of three basic statements that govern the secondary nature of proteins, in particular, the CO-NH peptide link. They were originally proposed by Rober
Orbital overlap
In chemical bonds, an orbital overlap is the concentration of orbitals on adjacent atoms in the same regions of space. Orbital overlap can lead to bond formation. Linus Pauling explained the importanc
Topology (chemistry)
In chemistry, topology provides a way of describing and predicting the molecular structure within the constraints of three-dimensional (3-D) space. Given the determinants of chemical bonding and the c
Tricapped trigonal prismatic molecular geometry
In chemistry, the tricapped trigonal prismatic molecular geometry describes the shape of compounds where nine atoms, groups of atoms, or ligands are arranged around a central atom, defining the vertic
RNA CoSSMos
The RNA Characterization of Secondary Structure Motifs database (RNA CoSSMos) is a repository of three-dimensional nucleic acid PDB structures containing secondary structure motifs ( loops, hairpin lo
Trigonal pyramidal molecular geometry
In chemistry, a trigonal pyramid is a molecular geometry with one atom at the apex and three atoms at the corners of a trigonal base, resembling a tetrahedron (not to be confused with the tetrahedral
Cubane
Cubane (C8H8) is a synthetic hydrocarbon compound that consists of eight carbon atoms arranged at the corners of a cube, with one hydrogen atom attached to each carbon atom. A solid crystalline substa
Circuit topology
The circuit topology of a folded linear polymer refers to the arrangement of its intra-molecular contacts. Examples of linear polymers with intra-molecular contacts are nucleic acids and proteins. Pro
Ring (chemistry)
In chemistry, a ring is an ambiguous term referring either to a simple cycle of atoms and bonds in a molecule or to a connected set of atoms and bonds in which every atom and bond is a member of a cyc
MDL Chime
MDL Chime was a free plugin used by web browsers to display the three-dimensional structures of molecules. and was based on the RasMol code. Chime was used by a wide range of biochemistry web sites fo
Pentagonal planar molecular geometry
In chemistry, the pentagonal planar molecular geometry describes the shape of compounds where five atoms, groups of atoms, or ligands are arranged around a central atom, defining the vertices of a pen
Ray–Dutt twist
The Ray–Dutt twist is a mechanism proposed for the racemization of octahedral complexes containing three bidentate chelate rings. Such complexes typically adopt an octahedral molecular geometry in the
Triangular bipyramid
In geometry, the triangular bipyramid (or dipyramid) is a type of hexahedron, being the first in the infinite set of face-transitive bipyramids. It is the dual of the triangular prism with 6 isosceles
Coordination number
In chemistry, crystallography, and materials science, the coordination number, also called ligancy, of a central atom in a molecule or crystal is the number of atoms, molecules or ions bonded to it. T
Hypercubane
Hypercubane is a hypothetical polycyclic hydrocarbon with the chemical formula C40H24. It is a molecular analog of the four-dimensional hypercube or tesseract. Hypercubane possesses an unconventional
Open-chain compound
In chemistry, an open-chain compound (also spelled as open chain compound) or acyclic compound (Greek prefix "α", without and "κύκλος", cycle) is a compound with a linear structure, rather than a cycl
DiProDB
DiProDB is a database designed to collect and analyse thermodynamic, structural and other dinucleotide properties.
VSEPR theory
Valence shell electron pair repulsion (VSEPR) theory (/ˈvɛspər, vəˈsɛpər/ VESP-ər, və-SEP-ər), is a model used in chemistry to predict the geometry of individual molecules from the number of electron
Capped octahedral molecular geometry
In chemistry, the capped octahedral molecular geometry describes the shape of compounds where seven atoms or groups of atoms or ligands are arranged around a central atom defining the vertices of a gy
Linear molecular geometry
In chemistry, the linear molecular geometry describes the geometry around a central atom bonded to two other atoms (or ligands) placed at a bond angle of 180°. Linear organic molecules, such as acetyl
Berry mechanism
The Berry mechanism, or Berry pseudorotation mechanism, is a type of vibration causing molecules of certain geometries to isomerize by exchanging the two axial ligands (see Figure at right) for two of
Trigonal bipyramidal molecular geometry
In chemistry, a trigonal bipyramid formation is a molecular geometry with one atom at the center and 5 more atoms at the corners of a triangular bipyramid. This is one geometry for which the bond angl
Diatomic molecule
Diatomic molecules (from Greek di- 'two') are molecules composed of only two atoms, of the same or different chemical elements. If a diatomic molecule consists of two atoms of the same element, such a
Bent molecular geometry
In chemistry, molecules with a non-collinear arrangement of two adjacent bonds have bent molecular geometry, also known as angular or V-shaped. Certain atoms, such as oxygen, will almost always set th
Trigonal planar molecular geometry
In chemistry, trigonal planar is a molecular geometry model with one atom at the center and three atoms at the corners of an equilateral triangle, called peripheral atoms, all in one plane. In an idea
Jacobi coordinates
In the theory of many-particle systems, Jacobi coordinates often are used to simplify the mathematical formulation. These coordinates are particularly common in treating polyatomic molecules and chemi
Molecular models of DNA
Molecular models of DNA structures are representations of the molecular geometry and topology of deoxyribonucleic acid (DNA) molecules using one of several means, with the aim of simplifying and prese
Capped square antiprismatic molecular geometry
In chemistry, the capped square antiprismatic molecular geometry describes the shape of compounds where nine atoms, groups of atoms, or ligands are arranged around a central atom, defining the vertice
Bent's rule
In chemistry, Bent's rule describes and explains the relationship between the orbital hybridization of central atoms in molecules and the electronegativities of substituents. The rule was stated by He
Ring flip
In organic chemistry, a ring flip (also known as a ring inversion or ring reversal) is the interconversion of cyclic conformers that have equivalent ring shapes (e.g., from a chair conformer to anothe
Bicyclic molecule
In chemistry, a bicyclic molecule (from bi 'two', and cycle 'ring') is a molecule that features two joined rings. Bicyclic structures occur widely, for example in many biologically important molecules
Pentagonal bipyramidal molecular geometry
In chemistry, a pentagonal bipyramid is a molecular geometry with one atom at the centre with seven ligands at the corners of a pentagonal bipyramid. A perfect pentagonal bipyramid belongs to the mole
Journal of Molecular Structure
Journal of Molecular Structure is a scientific journal published by Elsevier ScienceDirect since 1968. Its articles discuss molecular structure in chemistry. After the 2022 Russian invasion of Ukraine
Non-B database
Non-B DB is a database integrating annotations and analysis of non-B DNA-forming sequence motifs. The database provides alternative DNA structure predictions including Z-DNA motifs, quadruplex-forming
LCP theory
In chemistry, ligand close packing theory (LCP theory), sometimes called the ligand close packing model describes how ligand – ligand repulsions affect the geometry around a central atom. It has been
Bicapped trigonal prismatic molecular geometry
In chemistry, the bicapped trigonal prismatic molecular geometry describes the shape of compounds where eight atoms or groups of atoms or ligands are arranged around a central atom defining the vertic
Seesaw molecular geometry
Disphenoidal or seesaw (also known as sawhorse) is a type of molecular geometry where there are four bonds to a central atom with overall C2v molecular symmetry. The name "seesaw" comes from the obser
Square planar molecular geometry
The square planar molecular geometry in chemistry describes the stereochemistry (spatial arrangement of atoms) that is adopted by certain chemical compounds. As the name suggests, molecules of this ge
Octahedral molecular geometry
In chemistry, octahedral molecular geometry, also called square bipyramidal, describes the shape of compounds with six atoms or groups of atoms or ligands symmetrically arranged around a central atom,
Bailar twist
The Bailar twist is a mechanism proposed for the racemization of octahedral complexes containing three bidentate chelate rings. Such complexes typically adopt an octahedral molecular geometry, in whic
Polyhedral symbol
The polyhedral symbol is sometimes used in coordination chemistry to indicate the approximate geometry of the coordinating atoms around the central atom. One or more italicised letters indicate the ge
Square antiprismatic molecular geometry
In chemistry, the square antiprismatic molecular geometry describes the shape of compounds where eight atoms, groups of atoms, or ligands are arranged around a central atom, defining the vertices of a
Cubane-type cluster
A cubane-type cluster is an arrangement of atoms in a molecular structure that forms a cube. In the idealized case, the eight vertices are symmetry equivalent and the species has Oh symmetry. Such a s
Molecular geometry
Molecular geometry is the three-dimensional arrangement of the atoms that constitute a molecule. It includes the general shape of the molecule as well as bond lengths, bond angles, torsional angles an
Capped trigonal prismatic molecular geometry
In chemistry, the capped trigonal prismatic molecular geometry describes the shape of compounds where seven atoms or groups of atoms or ligands are arranged around a central atom defining the vertices
Square pyramidal molecular geometry
In molecular geometry, square pyramidal geometry describes the shape of certain compounds with the formula ML5 where L is a ligand. If the ligand atoms were connected, the resulting shape would be tha
Orbital hybridisation
In chemistry, orbital hybridisation (or hybridization) is the concept of mixing atomic orbitals to form new hybrid orbitals (with different energies, shapes, etc., than the component atomic orbitals)