How to draw coordination compounds

Reaxys Training Center - Tutorial

April 19, 2023 Slide 2

Tutorial

In this tutorial you learn how to

• draw a coordination compound

April 19, 2023 Slide 3

Organometallic compounds in Reaxys

In Reaxys most of the inorganic and organometallic compounds are available with structures.

Coordination compounds are drawn with a ‘normal’ (single) bond from the central metal atom to the coordinating atom of the ligand, e.g.

Halogenides

Hydroxides

Cyanides

Thiocyanates

Isothiocyanates

Carbonyls

April 19, 2023 Slide 4

Drawing organometallic compounds

Coordination compounds with pi-ligands are drawn according to their bond characteristics, e.g. 5-cyclopentadienyl with 5 bonds from the central metal atom to each carbon atom of the ring.

pi-Bonds have to be drawn as undefined (“single or double”)

Cyclopentadienyl: Draw all ring bonds as “single or double”

Draw single bonds from the metal to each ring atom

AllylDraw all C-C bonds as “single or double”Draw a single bond from the metal to each carbon

OlefinsDraw a regular single bond between the carbon and the metal

April 19, 2023 Slide 5

Task: Draw the coordination compound Bis(diphenylphosphin)ferrocene

Draw the structure below using the structure editor Marvin Sketch

Note:

pi-Bonds have to be specified with Bond Type = “Single or double”

Double click here to draw a structure

April 19, 2023 Slide 7

Draw the above structure:

1. Click the MORE button, click on the Fe-symbol, click the drawing canvas to set the Fe atom.

2. Draw two 5-rings using the template.3. Draw the ring-metal-bonds using

the single bond-drawing tool.

If the ring-metal-bonds are difficult to draw enlarge the rings or move the Fe atom

1

23

April 19, 2023 Slide 8

Change all ring-bonds to “Single or Double”

1: Use the Shift key from the keyboard plus the Selection tool (1) to mark all 5-ring-bonds. Atoms and bonds show green highlighting.2. Click Object >Bond > Type > Single or Double

1

2

April 19, 2023 Slide 9

All 5-ring-bonds are now set as “single or double”

Draw the diphenyl-phosphin-substituents using the atom (1) and bond-tool (2) and the phenyl-template (3)

1

2

3

Transfer query to query menu

4

April 19, 2023 Slide 11

Tutorial

In this tutorial you learned how to

• draw a coordination compound using MarvinSketch as your structure editor.