Overview of Coordination Chemistry and Its Importance to Biology Roat-Malone Ch. 1 (P. 1 -22) Prof. Arthur D. Tinoco University of Puerto Rico, Rio Piedras Campus Chemistry 8990(013) Spring 2014

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.

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

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.

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.

Coordination Chemistry Supplement

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

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)

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

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)

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

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.

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

2. Isomerism Ligand isomers

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

A. Constitutional Isomers Linkage (Ambidentate) Isomers A ligand can bind in more than one way [Co(NH3)5NO2]2+ Co-NO2 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

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

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] +2 +4 [Pt(NH3)4Cl2][PtCl4] +4 +2 Different Metals [Co(NH3)6][Cr(CN)6] [Co(CN)6][Cr(NH3)6]

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.

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

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.

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

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

B. Stereoisomers Conformational isomers Ligands as propellers

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

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

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.

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