Building Metal Complexes#

This tutorial demonstrates how to efficiently build coordination compounds and organometallic complexes using the Template Tool. We’ll progress from a simple complex to more sophisticated structures.

The Template Tool streamlines construction of metal complexes by providing pre-defined coordination geometries (octahedral, tetrahedral, square planar, etc.), a library of common ligands, and keyboard shortcuts for rapid building.

Activate the Template Tool with Ctrl+3 or by clicking its icon in the toolbar.

Part 1: A Simple Octahedral Complex#

We’ll start by building [Co(NH₃)₆]³⁺, a classic Werner complex.

Set up the metal center

In the Centers tab, you can either use the options panel or some keyboard shortcuts:

Type Co to select cobalt, or pick it from the popup menu
Press + three times to set the formal charge to +3
Press 6 to select octahedral geometry

Click in empty space to place the cobalt center. Six hydrogen atoms will appear at the coordination sites.

Add ammine ligands

Switch to the Ligands tab by pressing → or ] or clicking the tab:

Type n to select ammine (NH₃)

Click on each of the six hydrogens. Each click replaces a hydrogen with an ammine ligand.

Other ligands can also be selected by keyboard shortcuts.

You now have a complete hexaamminecobalt(III) complex with idealized octahedral geometry.

Tip

For other simple complexes, change the element and ligand:

[Fe(CN)₆]⁴⁻: Use Fe and type cn for cyano
[Ni(CO)₄]: Use Ni, tetrahedral (4), and type co for carbonyl

Part 2: Mixed-Ligand Complex with Different Geometries#

Now we’ll build [Ni(en)(NH₃)₂]²⁺, which combines a bidentate ethylenediamine with two monodentate ammine ligands. We’ll also explore how the same ligand set can adopt different geometries.

Building the Square Planar Isomer#

Create a square planar nickel center

In the Centers tab:

Type Ni to select nickel
Press ++ for +2 charge
Press 44 for square planar geometry

Click to place the center.

Add ethylenediamine

In the Ligands tab, type en to select ethylenediamine. Click on two adjacent hydrogen atoms (cis positions). The bidentate ligand bridges both sites, forming a five-membered chelate ring.

Add two ammine ligands

Type n for ammine, then click on each of the two remaining hydrogens.

Building the Tetrahedral Isomer#

Start fresh (File → New) and repeat with one change:

Press 4 (not 44) for tetrahedral geometry

Add the same ligands: ethylenediamine (en) to two adjacent hydrogens, then ammine (n) to the remaining two.

Note

Square planar and tetrahedral geometries are both common for d⁸ metals like Ni(II), Pd(II), and Pt(II). The preferred geometry depends on ligand field strength and steric factors. You can run quantum chemical calculations to compare the relative energies of the isomers.

Part 3: Organometallic Catalysts with Haptic Ligands#

Finally, we’ll build a Ziegler-Natta type catalyst precursor: zirconocene dichloride (Cp₂ZrCl₂). This demonstrates haptic ligand attachment and mixed ligand types.

Zirconocene dichloride has a zirconium(IV) center with two η⁵-cyclopentadienyl (Cp) rings and two chloride ligands. The Cp rings bond through all five carbon atoms (haptic bonding), creating a bent metallocene structure.

Create the zirconium center

We need a 4-coordinate geometry, treating each Cp as occupying one site:

Type Zr to select zirconium
Press + four times for +4 formal charge
Press 4 for tetrahedral geometry

Place the center.

Add the cyclopentadienyl rings

In the Ligands tab, type cp (or e5) to select η⁵-cyclopentadienyl.

Click on one hydrogen. The entire Cp ring attaches, with all five carbons oriented toward the metal. Click on an adjacent hydrogen to add the second Cp ring.

Add the chloride ligands

The Template Tool’s ligand library focuses on organic ligands. For chlorides, switch to the Draw Tool (Ctrl+2), select chlorine from the element selector, and click on each remaining hydrogen to replace it with Cl.

You could also type e2 to select η²-ethylene to insert in one site.

Tip

Try building related catalysts:

Titanocene dichloride: Use Ti instead of Zr
Half-sandwich complexes: Use only one Cp ring with other ligands
η⁶-arene complexes: Use e6 for benzene coordination

The ligand library also has other haptic coordination modes, such as a distorted η³-cyclopentadienyl for fluxional behavior.

Summary#

Complex Type	Key Steps
Simple octahedral	Element → charge → `6` → place → add 6 monodentate ligands
Mixed-ligand	Element → charge → geometry → bidentate first → fill remaining sites
Geometry comparison	`4` for tetrahedral, `44` for square planar
Haptic complexes	Use `cp`, `e5`, `e6` → each haptic ligand counts as one site