XyM Notation for Electronic Communication of Organic Chemical Structures

Abstract

The XyM notation system is proposed as a linear notation for the electronic communication of structural formulas. Each XyM notation consists of a skeleton with such arguments as SUBSLIST, ATOMLIST, and BONDLIST. The arguments are designed to be capable of carrying out substitution derivation for placing large substituents, atom derivation for spiro fusion, and bond derivation for ring fusion. Additional arguments, SKBONDLIST and OMITLIST, are discussed for stereochemical and ring-opening information. The XyM notation system is implemented as a LaTeX2e application.

Sphericity Governs Both Stereochemistry in a Molecule and Stereoisomerism Among Molecules

“…These methods are collectively called the USCI approach , because they start from USCIs obtained by the subduction of CRs. I have shown the versatility of the USCI methods by applying them to systematic enumerations of a variety of chemical objects: highly symmetric cage‐shaped molecules,43 adamantane isomers,44 compounds derived from D 3 h skeletons,45 dodecahedrane derivatives,46 soccerane derivatives,47 nonrigid molecues,48,49 octahedral complexes,50 benzene derivatives,51 digraphs,39 polyhedrons,52 C 60 adducts,53 and superphanes 54…”

WWW (World Wide Web) Communication and Publishing of Structural Formulas by XyMML (XyM Markup Language)

“…The values in the respective tags represent the following meanings: the letter 1 in the tag <substid> represents a locant number; the letter S in the tag <bondmod> and the letter A in the tag <bndsbmod> are combined to give a bond modifier 'SA', which indicates that the bond to be drawn is a single -bond [6,14]; and the substituent NO 2 is placed in the <substval> tag.…”

“…We have proposed the XyM Notation [5] as a new representation for communicating chemical structural formulas [6]. We have developed the XyMTeX system [7,8,9] as an implementation of the XyM Notation.…”

Systematic Enumeration and Symmetries of Cubane Derivatives

“…From a quantitative point of view, Fujita's USCI approach supports four methods of symmetry‐itemized enumeration of chemical compounds,24 i.e., the fixed‐point‐matrix (FPM) method,27,30 the partial‐cycle‐index (PCI) method,31 the elementary‐superposition (ES) method,32,33 and the partial‐superposition (PS) method 33. These methods have been applied to symmetry‐itemized enumerations starting from various skeletons, e.g., cage‐shaped skeletons,34 adamantane isomers,35 non‐rigid tetrahedral molecules,36 D 3h skeletons,37 D 2d skeletons,32 a dodecahedrane skeleton of I h symmetry,38 a fullerene skeleton of I h symmetry,31 imaginary transition structures for counting organic reactions,39 flexible six‐membered skeletons,40 a benzene skeleton of D 6h symmetry,41 ferrocene derivatives,42 a dumbbell skeleton of D ∞h symmetry,43 and an octahedral skeleton of O h symmetry 44,45…”