CAS RN

To automate functions on chemical data, the data structure needs to be systematically defined and consistently applied.

NOTATIONSLine notations represent structures as a linear stringof alphanumeric symbols. Their compactness was anadvantage in the early days of cheminformatics whenstorage space was at a premium, and even nowa-days, it can be faster to enter a structure as a no-tation instead of using a chemical structure drawingprogram. Several notations20–22were proposed in the1950s and 1960s, but only one, the Wiswesser Line-Formula Notation (WLN; see Figure 1)23–28becamewidely used,29–47despite the fact that the Dyson no-tation was formally adopted by IUPAC.20,21WLNstarted to fall out of use in the early 1980s.

To the practicing chemist, the language ofchemistry is the two-dimensional (2D) structure dia-gram and most chemical information systems featuregraphical input and output of chemical structures; themachine-held representation need not be meaningfulto the synthetic chemist. In the ideal (unique) repre-sentation there is only one ‘code’ for a given struc-ture and any one code can be interpreted to give onlyone structure. A unique representation is essential forchemical registration systems in which the novelty ofa structure is determined before it is recorded in adatabase. Some representations, for example, molec-ular formulas, are not unique; one molecular for-mula will generate more than one full structure. Somenonunique representations (e.g., molecular formulasand fragment codes) do, however, play a part in cer-tain chemical information systems, even though theydo not represent the full topology of a structure

Efforts have been madeto establish an agreed standard format but theyhave not been generally unsuccessful.

Hydrogenatoms are not necessarily included explicitly in aconnection table: they may be implicit.

TheMolecular Structure Encoding System, MOSES, fromMolecular Networks (Erlangen, Germany) is a laterdevelopment from Gasteiger’s team.

Of course, chemical structuresand topological graphs are not entirely equivalent: aconnection table is akin to a description of a singlevalence bond structure and does not take account,for example, of delocalized bonds.

It is termed redundant because each connection isdescribed twice. The redundancy is removed whena unique version of the table is stored.

WIREs Computational Molecular Science Representation of chemical structuresFIGURE 3|A redundant connection table

Of course, chemical structuresand topological graphs are not entirely equivalent: aconnection table is akin to a description of a singlevalence bond structure and does not take account,for example, of delocalized bonds.Alternative approaches have been suggested.

The Morgan algorithm identifies atoms basedon an extended connectivity value. The atom withthe highest value becomes the first atom in the name,and its neighbors are then listed in descending or-der. Ties are resolved based on additional parame-ters, for example, bond order and atomic number.The original Morgan algorithm did not handle stere-ochemistry; the stereochemically unique naming algo-rithm [stereochemical extension of Morgan algorithm(SEMA)] was developed to handle stereoisomers

Another notation, called rep-resentation of structure diagram arranged linearly(ROSDAL),52,53was written to transfer structuresquickly in a compact form over a network to enablesearching of the Beilstein database online.54ROSDALis still supported by InfoChem, and by Elsevier (Am-sterdam, The Netherlands) in Reaxys (vide infra) andthe Beilstein CrossFire structure editor.

Morgan algorithm initially developed by Gluckat DuPont (Wilmington, DE, USA) and adapted byCAS.55

The chemical formula is straightforward enough, but the connectivity and hydrogen sections require some explanation. The connectivity layer describes chains and branches –for example in the above Propene example, atom 1 is bonded to atom 3, which is bonded to atom 2. In the final example, we have branching, as represented by paren

the full stop (“.”) which overrides the implicit single bond between adjacent atoms we can make some exotic variants on SMILES:C1C.CC1ButaneC1CC1.C2CC2Cyclohexane

An InChI Keycan also be generated for a compound. This is completely separate from the InChI linear notation, and is used to provide an identifier for a compound that is particularly suitable for use in Web search engine

Systematic name

n InChI Keycan also be generated for a compound. This is completely separate from the InChI linear notation, and is used to provide an identifier for a compound that is particularly suitable for use in Web search engines. It is an ASCII character string based on a hashing of the InChI linear notation, but is of fixed length and uses only characters not normally conside

Fortunately, this can be done with the Morgan Algorithm18.In this algorithm, each atom is given a "connectivity value" reflecting how many atoms it is connecte

All InChIs currently are prefixed with “INCHI=”. Following this, a designator of “1/” or “1S/” indicates whether the InChI is non-standard or standard (i.e. with fixed standardized options in the software)

We would need to add an additional field to the atom and/or bond table to handle chirality (SCT VI, VII). We could do so either in a chemically sophisticated way, annotating the atom property, in a chemically-naive translation of a diagram feature, annotating the bond configuration, or both.

Our atom table will consist of two fields: one an index number identifying the atom we’re talking about, one indicating atom type (i.e. C, H, O, N, etc.). Our bond table will consist of three fields: two indicating the two atoms that the bond connects, and one indicating the bond order (1=single, 2=double, 3=triple).

As an example, take isopropyl alcohol. SCT I is a connection table representing this compound – or, more specifically, representing this structural formula. Connection tables are not necessarily unique We could draw up other tables of atoms and bonds that represent this compound as well: for example, SCT II and SCT III

As a starting point, this section will introduce a simplified form of connection table, which we’ll call an “SCT”. This SCT does not correspond directly to any existing file format (at least as far as we know!). Rather, it is a convenient model that we will use just for the purpose of this demonstration.

The MOL file format uses the number 4 to indicate bonds that are explicitly labeled as aromatic (MOL V). This has the advantage of differentiating aromatic bonds from single and double bonds without requiring the chemist to write a script to identify and label the alternating single and double bonds of a Kekulé structure. However, some software may not be built to handle this convention. (You might even run into cases in which it’s interpreted as a quadruple bond!)

ted to share with you all my project that I am working on here at Centre. During my ti

uick searchin Reaxysallows you to combine structure and text searches. Try doing the searc

Issues with Intelligent Search Engines

SearchforpropertiesusingtheSearchpropertiesfieldandDrag&Drop

that is, a string of 0’s and 1’s).  The position of each number in this string corresponds to a particular fragment.  If the molecule has a particular fragment,

Molecular similarity methods can be broadly classified into two-dimensional (2-D) and three-dimensional (3-D) similarity methods.  Typically, 2-D similarity methods use so-called molecular fingerprints, which encode structural information of a molecule into a binary string (that is, a string of 0’s and 1’s).  The position of each number in this string corresponds to a particular fragment.  If the molecule has a particular fragment, t

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