1. Overview of Coordination Chemistry and Its Importance to Biology
Roat-Malone Ch. 1 (P )
Prof. Arthur D. Tinoco
University of Puerto Rico, Rio Piedras Campus
Chemistry 8990(013)
Spring 2014

2. 1. Defining the Essentiality of an Element
Identification of essential elements was first performed by Klaus Schwarz (1970s). Essentiality defined as:
A physiological deficiency appears when an element is removed from the diet.
For elements like titanium, this definition is tricky because of their high abundance (ubiquity) it is hard to effectively remove them from food.
The deficiency is relieved by the addition of that element to the diet.
A specific biological function is associated with the element.

3. 2. Essential Elements follow a Dose-response curve
What does response mean here?

4. 2. Essential Elements follow a Dose-response curve
At lowest dosages, the organism does not survive.
In the deficiency regions, the organism exists but with less than optimal function.
The body must mobilize its stored supply to compensate for any deficiency.
At dosages higher than optimal, the body may experience toxic effects.
The body does have mechanisms to deplete higher than needed levels.
Very high dosages can be fatal.

5. 2. Essential Elements follow a Dose-response curve
Small molecule and biomolecular interactions enable not just the intake, uptake, and transport of essential elements, but also maintenance of the optimal level of the elements (homeostasis).
For metals, coordination chemistry is at the root of these processes.

6. Coordination Chemistry Supplement

7. 1. Nomenclature Rules
For charged molecules, the cation comes first followed by the anion.
The following rules apply to both neutral and charged molecules:
B. The elemental formulation has the inner coordination sphere in brackets.
[Pt(NH3)4]Cl2
When writing the name, the ligands within the coordination sphere are written before the metal.
tetraammineplatinum(II) chloride
C. Ligand names (refer to handout).
Monodentate: Ligands with one point of attachment
Chelates (Bidentate…multidentate): Ligands with two or more points of attachment

8. 1. Nomenclature Rules
D. The number of ligands of each kind is indicated by prefixes using the following table. A B
Use prefixes in column A for simple cases.
Use prefixes in column B for ligands with names that already use prefixes from column A.
[Co(en)2Cl2]+
Dichlorobis(ethylenediamine)cobalt(III)

9. 1. Nomenclature Rules
E. Ligands are written in alphabetical order-according to the ligand name, not the prefix.
F. Anionic ligands are given an o suffix.
Neutral ligands retain their usual name
Coordinated water is called aqua
Coordinated ammonia is called ammine

10. 1. Nomenclature Rules
G. Designate the metal oxidation state after the metal.
[PtClBr(NH3)(H2O)]
Ammineaquabromochloroplatinum(II)
[Pt(NH3)4]2+
Tetraammineplatinum(II)
If the molecule is negatively charged, the suffix –ate is added to the name
[Pt(NH3)Cl3]-
Amminetrichloroplatinate(II)

11. 1. Nomenclature Rules
Special names for metals when in a negatively charged molecule:
Copper (Cu): Cuprate
Iron (Fe): ferrate
Silver (Ag): argentate
Lead (Pb): Plumbate
Tin(Sn): Stannate
Gold(Au): Aurate

12. 1. Nomenclature Rules
H. Prefixes designate adjacent (cis-) and opposite (trans-) geometric locations
cis-diamminedichloroplatinum(II) is an anticancer agent.
The trans isomer is not.

13. 1. Nomenclature Rules
I. Bridging ligands between two metal ions have the prefix μ
μ-amido-μ-hydroxobis(tetraaminecobalt)(IV)

14. 2. Isomerism
Ligand
isomers

15. 2. Isomerism Conformational Isomers Geometric Isomers cis-trans
fac-mer

16. A. Constitutional Isomers
Linkage (Ambidentate) Isomers
A ligand can bind in more than one way
[Co(NH3)5NO2]2+
Co-NO Nitro isomer; yellow compound
Co-ONO Nitrito isomer; red compound
The binding at different atoms can be due to the hard/soft-ness of the metal ions
SCN-
Hard metal ions bind to the N
Soft metal ions bind to the S
Solvent can influence the point of attachment
For SCN- : M-S bonds favored in solvents of high dipole moment
M-N bonds favored in solvents of low dipole moment

17. A. Constitutional Isomers
Ligand Isomers
III. Ionization Isomers
Difference in which ion is included as a ligand and which is present to balance the overall charge
[Co(NH3)5Br]SO4 vs [Co(NH3)5SO4]Br
IV. Solvate (Hydrate) Isomers
The solvent can play the role of ligand or as an additional crystal occupant
[CrCl(H2O)5]Cl2· H2O vs [Cr(H2O)6]Cl3

18. A. Constitutional Isomers
V. Coordination Isomers
Same metal
Formulation- Pt(NH3)2Cl2
[Pt(NH3)2Cl2]
[Pt(NH3)3Cl][Pt(NH3)Cl3]
[Pt(NH3)4][PtCl4]
Same metal but different oxidation states
[Pt(NH3)4][PtCl6]
[Pt(NH3)4Cl2][PtCl4]
Different Metals
[Co(NH3)6][Cr(CN)6]
[Co(CN)6][Cr(NH3)6]

19. B. Stereoisomers Square planar complex
Enantiomers
Optical isomers (chiral)
Non-superimposable mirror image
Square planar complex
If it were tetrahedral, it would not be chiral.

20. B. Stereoisomers II. Diastereomers Geometric isomers
4-coordinate complexes
Cis and trans isomers of square-planar complexes (cis/transplatin)
Chelate rings can enforce a cis structure if the chelating ligand is too small to span the trans positions

21. B. Stereoisomers II. Diastereomers Geometric isomers
6-coordinate complexes
Facial(fac) arrangement of ligands
Meridional(mer) arrangement of ligands
Two sets of ligands segregated to two different faces.
Two sets of ligands segregated into two perpendicular planes.

22. B. Stereoisomers II. Diastereomers Geometric isomers
6-coordinate complexes
Different arrangements of chelating ring

23. B. Stereoisomers Conformational isomers
Because many chelate rings are not planar, they can have different conformations in different molecules, even in otherwise identical molecules.

24. B. Stereoisomers
Conformational isomers
Ligands as propellers

25. B. Stereoisomers Conformational isomers
Ligand symmetry can be changed by coordination. Coordination may make ligands chiral as exhibited by the four-coordinate nitrogens.

26. C. Separation of Isomers
Fractional crystallization can separate geometric isomers.
a. Strategy assumes isomers have different solubilities in a specific solvent mixture and will not co-crystallize.
b. Ionic compounds are least soluble when the positive and negative ions have the same size and magnitude of charge.
Large cations will crystallize best with large anions of the same charge.
Chiral isomers can be separated using
a. Chiral counterions for crystallization
b. Chiral magnets

27. C. Identification of Isomers
X-ray crystallography
Spectroscopic methods
In general, crystals of different handedness rotate light differently.
a. Optical rotatory dispersion (ORD): Caused by a difference in the refractive indices of the right and left circularly polarized light resulting from plane- polarized light passing through a chiral substance.
b. Circular dichroism (CD): Caused by a difference in the absorption of right-and left-circularly polarized light.

28. 3. Atomic Orbitals px pz py
dx2-y2
dxz
dz2
dyz
dxy