Representation of Molecular Configurations by CAST Coding Method

Abstract

A configurational CAST (CAnonical representation of STereochemistry) coding method, which represents relative and absolute configuration, is described. The configurational CAST codes are constructed by canonical rotation of the dihedral angles of the input structure before the CAST codes are assigned. Using the configurational CAST, configurational differences can be distinguished independently of conformational differences. Representation of enantiomers is also achieved by a mirror image conversion method. The CAST representation shows the distinctive characteristics of several diastereomers and conformers that were examined. The method clearly represents the differences in configurations. Applications to organic molecules having complex stereochemistry are also demonstrated.

“Found in Translation”: predicting outcomes of complex organic chemistry reactions using neural sequence-to-sequence models

“… 3 – 6 In this specific context, candidate products are generated from the templates and then are ranked according to their likelihood. Satoh and Funatsu 3 , 4 used various hard-coded criterion to perform the ranking whereas more recent approaches 5 , 6 used a deep neural network. However, these types of approaches are fundamentally dependent on the rule-based system component and thus inherit some of its major limitations.…”

Extended CAST Coding Method for Exact Search of Stereochemical Structures

“…The relationships between codes in the molecular tree are translated to linear notations using some separator codes, a semi-colon, a comma, and an asterisk as mentioned above, according to the CAST coding rule. 7,8 In Figure 3, the notations that related to R and S-configurations are bold-and double-underlined, respectively. In the notations from C1, the absolute configurational difference for C3 and C4 are represented, and in the notations from C4, the differences for C2 are represented.…”

“…If any rotational operation is not performed, the dihedral angle defined by B-A-B-C is the same as that defined by C-B-A-B. However, the dihedral angle is rotated to make the basic configurational CAST notations according to the canonical rearrangement rules as described in a previous paper, 8 thus, both notations started from C and B are needed.…”

“…Some coding methods for three-dimensional chemical structures have been developed and used for structural representation in some chemical software, however, an essential problem of exact search of structures considering configurational and conformational structural environments has been remained. [1][2][3][4][5][6] We reported CAST (CAnonical-representation of STereochemistry) coding method in the previous paper 7,8 . The basic CAST gives canonical codes based on the dihedral angles.…”

Handling of Highly Symmetric Molecules for Chemical Structure Elucidation in a CAST/CNMR System

“…We have been developing CAST/CNMR, a data-centric system for chemical structure analysis based on NMR data [1][2][3][4][5][6][7]. CAST/CNMR consists of two modules for prediction These classical topics in chemoinformatics have been intensively studied in the last couple of decades [8][9][10][11][12][13][14][15][16][17][18][19][20].…”