Investigating metal-carbon bonding

•	Examine the structures of the first 4 entries in the file (these include csd refcodes: VADRAU, IGODIR, TODDUL, OKUSES).

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You will notice that each of these structures contains at least one metal-carbon bonding interaction. Each may be selected by clicking on the identifier (such as VADRAU) from the Structure Navigator on the right hand side of the main Mercury window. Bonds between metal and carbon atoms are referred to as organometallic bonds. A ligand that contains a carbon atom which bonds to a metal is an organometallic ligand.

 

To manipulate structures in Mercury

 

1. Structures can be rotated by moving the cursor in the display area while keeping the left-hand mouse button pressed down.

 

2. To zoom in and out move the cursor up and down in the display area while keeping the right-hand mouse button pressed down.

 

3. To translate structures hold down the middle mouse button while moving the cursor in the display area (three-button mouse only). Alternatively, move the cursor in the display area while keeping both the left-hand mouse button and the keyboard Ctrl key pressed down.

 

4. At any stage the display area can be returned to the default view by hitting the Reset button at the bottom of the window.

 

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Change the display style from wireframe to spacefill. In spacefill, atoms are displayed as standard van der Waals radii. Generally when these radii overlap significantly, a bond between the two atoms is present. Mercury will automatically connect bonding atoms, based on a predetermined set of maximum bonding distances. Notice that in these five examples, each carbon atom bonded to a metal is from a separate ligand.

 

To change the display style:

 

Set the required style in the tool-bar Style box, located near the top of the main Mercury window. Al­ternatively, right-click in the display-area background, pick Styles from the pull-down menu, and se­lect the required style (Wireframe, Capped sticks, Ball and stick, Spacefill, Ellipsoid).

 

•	Inspect the structure of OKUSES closely. Which atoms are in van der Waals contact with the magnesium ion? Notice that the allyl ligand bonds to the magnesium ion with only one carbon atom.

•	Next, inspect the structure of ALPHPD01 closely. Again, identify which atoms are in van der Waals contact with the palladium ion. Notice that the allyl ligand has all three carbon atoms sufficiently close to the palladium ion to consider them all to be bonding to the palladium ion.

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Clearly there is a difference in the way the allyl ligand is bonding to the different ions in the OKUSES and ALPHPD01 complexes. The nature of the bonding is not important to this exercise. All examples in this exercise utilize structural data from molecules which have been synthesized, crystallized and characterized by single crystal X-ray crystallography.

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Now let's focus upon nomenclature. The number of contiguous ligand atoms bonding to a singular metal atom is defined as hapticity and is denoted using the Greek symbol η, eta, followed by a superscript indicating the number. The allyl ligand in OKUSES is attached to the metal by one carbon atom, so it is designated η1-allyl. The allyl ligand in ALPHPD01 is attached to the metal by three contiguous carbon atoms, so it is designated η3-allyl.

•	The allyl ligand may be described with the following Lewis structure.

 

•	When the allyl ligand bonds to a metal with only one of its carbon atoms, the bonding is η1-allyl:

 

•	The allyl anion may be represented by two resonance structures:

 

•	The allyl anion has a delocalized pi system and may also be represented as follows:

 

•	A metal may interact with this delocatized pi system so as to have bonding interactions with all three allyl carbon atoms, that is the bonding is η3-allyl

 

•	Closely examine the orientation of the η3-allyl ligand with respect to the metal in structure ALPHPD01. Notice that the allyl carbon and hydrogen atoms are essentially coplanar; however, the metal does not reside in this plane.

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With refcode ALPHPD01 selected in the Structure Navigator, click the More Info button followed by Structure Information from the resulting menu. Notice that the compound name is (η3-allyl)chlorotriphenylphosphinepalladium. The hapticity of the allyl ligand has been clearly denoted. While keeping the information window opened, select OKUSES in the Structure Navigator. Notice the compound name is cis-allylbromobis(dimethoxyethane)magnesium. In cases where the ligand binds η1 to the metal, the η1 binding mode is assumed and need not be noted. This is particularly true in cases where there is only one atom likely to bond to the metal. See for example the names for VADRAU and IGODIR.

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WARNING: Although formally the lack of a hapticity notation implies the ligand bonds η1, very often chemists neglect to indicate hapticity, even when it is other than η1. Such omission often occurs when a ligand is bonding with its most commonly observed hapticity. Be sure to consider the chemistry when assigning hapticity to ambiguously named compounds.