Building Coordination Complexes
To build coordination complexes, you can use the metal fragments and metal ligands in the 3D Builder panel, which you open with Edit → 3D Builder, or click the Build button on the toolbar.
To display the fragments for building, click Add Fragments, then click More (...) in the panel that is displayed. The Fragments panel opens.
To start building a complex, clear the Workspace, chooseMetal Centers from the Fragments option menu, and choose a metal center. The centers available have from one to sixteen ligands. The metal center is placed with hydrogens as the default ligands, and a generic metal. To set the metal, right-click on the metal and choose Set Element,click the more button, and select the metal in the periodic table that is displayed. You can also use the Set Element button in the 3D Builder panel.
The ligand set contains common monodentate ligands (CO, CN, NO, H2O, NH3, and PH3), and a set of η-coordinated ligands (ethylene, acetylene, allyl, butadiene, cyclopentadiene, and benzene). To use these ligands, choose Metal ligands from the Fragments option menu. You can switch bonding styles for η-coordinated ligands from multiple zero-order bonds to a centroid bond: to do this, click the Tasks button and browse to Materials → Tools → Toggle Eta Bond Style.
To add a ligand, click on one of the coordination sites (hydrogens), and choose a ligand from the available set. You can also add other organic fragments, and these will be treated as covalently bonded to the metal.
If you want to build a complex with bidentate ligands, you can start with one of the complex builder panels from the Materials Science suite, listed below, then edit the resulting complex. You can replace the metal center in an existing complex by clicking on the metal atom and choosing one of the metal centers. The existing ligands remain in place and occupy coordination sites of the new center type. Another option is to build with monodentate ligands, then edit two ligands to join them into a bidentate ligand.
To build a porphyrin or phthalocyanine system, choose Rings from the Fragments option menu,and select the appropriate ring system to place the ring in the Workspace.
The Materials Science suite has several tools for building complexes in octahedral, tetrahedral, or square planar geometry, which are listed below.