Topological Analysis and Network Operations

Implementation

Since the new changes have been introduced into the topological analysis (2003.11), the construction of both homogeneous and heterogeneous networks can be performed by the selection of single node in the "NetNode definition" dialog shown below or on the Generation step in the 'Generation Options' dialog. The construction of such topological networks works only if one uniatomic node exists in the the net. In case of more complex networks use the "specific atom" section of the "Net Node Definition" dialog. The definition of the single uniatomic node allows the automatic identification of the other multiatomic nodes. Sometimes the software needs to consider some auxiliary atoms as nodes, but after all it does not include them in resulting vertex symbol. An example of that is a network with multidentate ligands and two types of homogeneous metal centres - multicoordinate and bicoordinate. To identify ligands the software needs to know about both metal centres as they identify the ligands (something between two or more metal centres is the ligand). However, the bidentate "nodes" will be excluded from the resulting symbol, giving correct ring sizes. Further limitations of the software are described in the introduction.

Construction of homogeneous and heterogeneous topological networks with single uniatomic node can be done by the selection of the network node in 'Generation Options' dialog box. Simply select the chemical element, which will play the role of topological node and generate the extended structure. After end of the generation process, the network bonds becomes accessible via the corresponding command of main toolbar. The construction of the topological networks can be done after structure generation and is discussed below.

More complicated heterogeneous topological networks (consisting of nodes of different types) can be constructed using 'Topological Analysis' command of the main menu. The command launches 'Net Node definition' dialog box, which allows the definition of multiple network nodes. The networks with only one type of uniatomic node can be transformed into their topological equivalents by the selection of the node type of that uniatomic node.

Homogeneous and heterogeneous networks with only one uniatomic node networks can be constructed using this dialog by selecting the 'Atom Type' option or by adding one specific atom to the list.

Multiple nodes can be different metal centres, different ligands etc. The ligand node can be defined by any of it's atoms directly not connected to any other node, and the ligands should be separated by uniatomic nodes to make the analysis correct. Use 'Add' button, which shows 'Add Net Node' dialog, to add new node to the list. The selected atoms should be separated at least by one non-nodal atom. A 'dummy' atom can be placed in the centre of a ligand and used in topological analysis to create a more symmetrical network. This can be achieved by checking corresponding checkbox and ligand atoms.

'Hetero-Net' - if the checkbox is checked, then bonds between the same nodes are automatically removed.

Some notes about constructing complex topological networks see at Bonds List.

View of the 'Net Node Definition' dialog

	This is an auxiliary dialog for 'Net Node Definition' dialog. The dialog allows selection of networks nodes. If 'atom type' selected and structure contains more then one element of such type in the asymmetric unit, then all of those atoms will be placed to the list of nodes. Otherwise only specific atom (identified by its label) will be inserted.
View of the 'Add Net Node' dialog

Notes:
An "edge effect" appears when the asymmetric unit contains parts of ligands. It appears like strange topological bonds existing at the edges of net.. However these bonds can be removed from the network using 'Extract from net' command of the Bonds List window.