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Computer models of CB[5], CB[6], and CB[7]. Top row is the view into the cavity and the bottom is the side view. In host–guest chemistry, cucurbiturils are macrocyclic molecules made of glycoluril (=C 4 H 2 N 4 O 2 =) monomers linked by methylene bridges (−CH 2 −).
The finite group notation used is: Z n: cyclic group of order n, D n: dihedral group isomorphic to the symmetry group of an n–sided regular polygon, S n: symmetric group on n letters, and A n: alternating group on n letters. The character tables then follow for all groups.
The Simplified Molecular Input Line Entry System (SMILES) 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 Hill system (or Hill notation) is a system of writing empirical chemical formulae, molecular chemical formulae and components of a condensed formula such that the number of carbon atoms in a molecule is indicated first, the number of hydrogen atoms next, and then the number of all other chemical elements subsequently, in alphabetical order ...
The Leatherface program [11] is a general purpose molecule editor which allows automated modification of a number of substructural features of molecules in databases, including protonation state, hydrogen count, formal charge, isotopic weight and bond order. The molecular editing rules used by Leatherface are defined in SMARTS.
Chiral molecules can differ in their chemical properties, but are identical in their physical properties, which can make distinguishing enantiomers challenging. Absolute configurations for a chiral molecule (in pure form) are most often obtained by X-ray crystallography , although with some important limitations.
The SYBYL line notation or SLN is a specification for unambiguously describing the structure of chemical molecules using short ASCII strings. SLN differs from SMILES in several significant ways. SLN can specify molecules, molecular queries, and reactions in a single line notation whereas SMILES handles these through language extensions.
The hierarchical editing language for macromolecules (HELM) is a method of describing complex biological molecules. It is a notation that is machine readable to render the composition and structure of peptides, proteins, oligonucleotides, and related small molecule linkers. [1]