Chemical Structure Search Quiz

Structure Searching and Substructure Screening Methods

• The canonical SMILES algorithm produces a canonical ordering of atoms in a graph, similar to the Morgan algorithm.
• Formats like canonical InChI representation and Chemical Markup Language are designed for general utility.
• Structure searching converts the structure into a representation and generates a hash key to retrieve information from a database.
• Substructure searching identifies molecules containing a specified substructure, such as a functional group.
• Graph theoretic methods are used for substructure isomorphism screening to rapidly eliminate non-matching molecules from the database.
• Bitstrings are used to represent the query substructure and database molecules for screening.
• Screening methods use a structural key, hashed fingerprint, and predefined fragment dictionary for substructure screening.
• Hashed fingerprint does not require a predefined fragment dictionary and is applicable to any molecular structure.
• The Ullmann algorithm uses adjacency matrices to represent molecular graphs for subgraph isomorphism.
• Modern substructure search methods enable complex queries, such as specifying atoms as part of a group or excluding specific atoms.
• MDL connection table and SMARTS are used to specify substructure-related information.
• Identifying the Smallest Set of Smallest Rings (SSSR) helps in classifying ring systems in complex molecules.

Computer Representations of Chemical Structures

• Chemical structures are stored in a computer as molecular graphs, which consist of nodes (atoms) connected by edges (bonds).
• Nodes in a molecular graph correspond to atoms and edges to bonds, with associated properties like atom type and bond order.
• Subgraphs are subsets of nodes and edges of a graph, for instance, the graph of Benzene is a subgraph of Aspirin.
• A tree is a special type of graph with a single path connecting each pair of vertices and is used to represent acyclic molecules.
• Isomorphic graphs have the same number of nodes and edges and can be established by mapping one graph to the other.
• Connection tables are used to communicate the molecular graph to and from the computer, and the simplest type consists of atomic numbers and bond pairs.
• Linear notations like SMILES are more compact than connection tables and are useful for storing and transmitting large numbers of molecules.
• SMILES notation represents atoms by their atomic symbol and uses uppercase for aliphatic atoms and lowercase for aromatic atoms.
• Stereochemistry and geometrical isomerism are indicated in SMILES using specific symbols and notations.
• A canonical representation is a unique ordering of atoms for a given molecular graph, and the Morgan algorithm is a widely used method for this.
• The Morgan algorithm involves iterative calculation of connectivity values of atoms to enable differentiation and establish a unique order.
• The CANGEN algorithm has been developed to generate a unique SMILES string for each molecule.