IQmol can help us visually identify the atom numbers corresponding to desired substitution sites by using Display > Atom Labels > Index. For complicated molecules, it would be easier to draw or import the structure in such a program before manual manipulation. This template can be manually constructed by hand from scratch or by editing a Z-matrix from a molecular graphics software such as IQmol. The six halogen atom substitution sites are labelled as a, b, c, d, e and f. (The use of lowercase letters is helpful for a case-sensitive replacement in later steps to avoid ambiguity with atomic symbols.) The example shown in Fig. 2 is a template for the generation of halo-substituted benzenes. The template molecule is defined as a Z-matrix with the substituting atoms in lowercase strings. The first step of the procedure, construction of the template, can be achieved on any text editor. These may be replaced by other software available on the user's platform. Preferred toolkits on Windows platform are Notepad++ for plain-text editing, Wolfram's Mathematica for generation of tuples and duplicate elimination, GNU's sed on Cygwin for substitution into the template file, and IQmol for visualization. In this paper, we demonstrate step-by-step how to generate an exhaustive collection of halo-substituted benzenes. The substitution approach can help us explore structures of different chemical compositions and structures of identical chemical formula (constitutional, configurational and conformational isomers) simultaneously. For simplicity, in this article, we use hydrogen and halogen atoms (F, Cl, Br and I) as substituents. (Cartesian coordinates would not be trivial to manipulate using this template-based substitution method.) As mentioned earlier, templates and substitution sites must be identified manually. We use Z-matrix for convenience as bond lengths, bond angles and torsional angles, which are natural quantities for chemists, can be explicitly laid out. The two representations can easily be interconverted by freely available software. Three dimensional molecular structures are often represented by a Z-matrix or Cartesian coordinates. Z-matrix template-based substitution approach Comparison of this approach to other existing methods and future work are discussed in the last section. The concept and tutorial (template construction, generation of tuples for substitution sites, removal of duplicate tuples and substitution on the template) are described in the next section. Based on these previous reports, this is our first paper devoted to the methodology of generic structure generation using Z-matrix template-based substitution. 1), we successfully applied it to 26 classes of compounds to exhaustively generate over ten thousand 3D structures for further investigation by quantum chemical methods, ,. Inspired by the use of this approach in dichlorodiphenyltrichloroethane (DDT) analogues ( Fig. The Markush structures, represented as templates with defined substitution points, can be enumerated for the combinatorial investigation of compounds. There are ad hoc solutions to overcome these limitations but, alternatively, a new method may be used instead or in combination with the existing methods.Ĭhemists, by their manual intuition and labour, have been able to identify Markush or generic structures that represent a group of compounds with common chemical and/or physical properties. Molecular graph-based methods may also suffer from resonance, unusual bond types or infeasible structures. Most of the existing methods are based on molecular graphs for representation of molecular structures and intrinsically lack crucial spatial information in terms of configuration and conformation of generated structures. However, there are still no consistent one-size-fits-all standard for structural enumeration. Robust and exhaustive processes to generate chemical structures have been described previously in different contexts, ,, ,, ,. Initial structures (Z-matrix or Cartesian coordinate) are important starting points for the in silico investigation of chemical species.
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