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Mechanisms in Inorganic Chemistry

Introduction

• These pages deal with some substitution mechanisms for transition metal complexes.   Each is accessed via one of the four links below, and should appear in a new window.   Each concerns a mechanism which goes via an intermediate

Each page contains a reaction scheme with reaction arrows leading to or from the intermediate.   Clicking on a reaction arrow produces a JSmol (or Jmol) model positioned beneath the reaction scheme
Hand symbols superimposed on the reaction scheme show which models are switched on currently
One or two models side by side are allowed: the left model is for a reaction leading from the starting material to the intermediate, while the right model is for the step going from the intermediate to the product

Clicking on the same arrow again, switches that model off
Clicking the provided Animate button switches the program to animate mode: starting with the leftmost model, a series of animation frames are shown, representing the course of the reaction.   If two models have been selected, then when the left model ends at the intermediate, the right model starts automatically, carrying on from the intermediate to the product
The models may be rotated by dragging over them using the left mouse button.   Shift key and drag left mouse button upwards zooms out.   Shift key and drag left mouse button horizontally rotates about the screen Z axis
When two models are displayed, mouse control is for each one separately
Clicking the Animate button sets both models back to their default orientations and zoom levels, and to the first frames of the animations.   To set up alternative viewpoints or zoom levels for both animations, proceed as follows

• Have both models selected
• Click the Animate button, then immediately click the Pause button on the individual button bar for the Left Model, then click its First frame button
• Adjust the viewpoint or zoom level for each model separately, so that they match, as desired
• On the button bar for the Left Model, click Play
• Providing the program is in Animate mode, the Right Model animation will start when the Left Model finishes, but now with the desired orientation
• If the program is not in Animate mode, but is in its initial First Frame Only mode, then the two models may still be animated using their individual button bars, but there is no automatic follow-on.   This may be a desirable mode of use for exploring details of the animations

Dissociative Substitution Mechanism for Octahedral Complexes

Animation of a S_n1 octahedral substitution

Enantiomers in an animation of a bis-chelate octahedral S_n1 substitution

• Ethylenediamine ligands favour a 90° angle at the metal, stabilising a trigonal bipyramidal 5‑coordinate intermediate rather than a square pyramidal one, since the axial‑equatorial angle in a trigonal bipyramid is 90°
• Only two trigonal bipyramidal molecules [M(en)₂A] are possible, constituting a pair of enantiomers
• The clickable reaction scheme is in enantiomeric upper and lower halves, connected only by trans‑[M(en)₂A₂], which has a centre of symmetry so is not chiral.   All of the other species in the chart are chiral
• Any racemisation reactions must go via trans‑[M(en)₂A₂] as an intermediate
• Two models may be selected only if they are in the same half of the scheme

Associative Substitution Mechanism for Square Planar Complexes

• Associative substitution in a square planar complex goes via a trigonal bipyramidal intermediate in which the entering group is equatorial
• In contrast to main groups systems, in which attacking and leaving groups are in axial positions in 5‑coordinate intermediates, it is one of the equatorial groups which leaves in substitution reactions in transition metal complexes

Animation of Replacement of a Unique Ligand, with the Remaining Positions Occupied by Diethylenetriamine, a Tridentate Ligand

• Diethylenetriamine gives two adjacent 90° angles at the metal in its complexes, making it ideal for the square planar geometry
• In a trigonal bipyramidal intermediate, diethylenetriamine must bridge the two axial positions via one equatorial position
• This leaves the remaining two equatorial positions for the attacking and leaving groups, in agreement with the principle outlined above

Animation of Replacement of a Ligand, with the Remainder Monodentate

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