Lecture19 Ch19 111405

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Frequency of scores on exam 2 Grade = n(right)/28 x 100

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Photochemistry and biology Photons can be toxic (cause DNA bases to dimerize) Photons can be therapeutic: phototherapy Photons can track thoughts, one molecule at a time (Chapter 25) Photons can image whole bodies and search for disease (Chapter 25)

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The Central Dogma of Chemical Biology Biology is chemistry in action!

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Phototoxicity: Damage to DNA

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DNA: UV photochemistry Photons cause two DNA bases to link: this kills the cells containing the irradiated DNA Two DNA bases lined together

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Singlet molecular oxygen: excited states of ordinary oxygen

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Electronic states of molecular oxygen: two low lying spin paired singlet states The singlet states of O2 can kill cancer cells (and other cells)

Photodynamic therapy using singlet oxygen: 

Photodynamic therapy using singlet oxygen Patient cured!

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Irradiating babies with jaundice causes a photochemical change that causes the jaundice pigment to become water soluble and to be excreted

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Different forms of elemental carbon: from diamond to graphite to buckyballs!

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Discovery of Deuterium Nobel Prize: 1934 Discovery of C60 Nobel Prize: 1996

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Flow diagram for revolutionary science:Extraordinary claims that become accepted and are integrated into “normal science.” The BIG One!

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The first “evidence” for the special stability of C60 An Extraordinary Claim: Carbon can exist in an elemental form that has a structure reminiscent to a soccer ball. Would you have predicted a Nobel Prize?

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The proposal of Buckeyballs turned out to be revolutionary science

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Buckyballs pulled into nanowires: Carbon nanotubes!

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Nanodevices: A carbon nanocar rolling on a gold surface Thanks to Whitney Zoller

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Putting H2 inside a buckyball! Collaborator: Professor Koichi Komatsu (Kyoto University)

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Chapter 19 Coordination Complexes 19.1 The Formation of Coordination Complexes 19.2 Structures of Coordination Complexes 19.3 Crystal-Field Theory and Magnetic Properties 19.4 The Colors of Coordination Complexes 19.5 Coordination Complexes in Biology Chapter 24 From Petroleum to Pharmaceuticals 24.1 Petroleum Refining and the Hydrocarbons 24.2 Functional Groups and Organic Synthesis 24.3 Pesticides and Pharmaceuticals Chapter 25 Synthetic and Biological Polymers 25.1 Making Polymers 25.2 Biopolymers 25.3 Uses for Polymers C1403 Lecture 19 Monday, November 14, 2005 Infrared spectroscopy (IR tutor) Nuclear magnetic resonance spectroscopy

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The d block metal form coordination complexes with molecules and ions

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19.1 Coordination complexes What is the electronic basis of the color of metal complexes?

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Coordination complex: A structure containing a metal (usually a metal ion) bonded (coordinated) to a group of surrounding molecules or ions. Ligand (ligare is Latin, to bind): A ligand is a molecule or ion that is directly bonded to a metal ion in a coordination complex Coordination sphere: A metal and its surrounding ligands Note: religion is derived from Latin: religare, to bind tightly A ligand uses a lone pair of electrons (Lewis base) to bond to the metal ion (Lewis acid)

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Complex ions: Three common structural types Octahedral: Most important Tetrahedral Square planar What determines why a metal takes one of these shapes?

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Lewis acids and bases A Lewis base is a molecule or ion that donates a lone pair of electrons to make a bond A Lewis acid is a molecule of ion that accepts a lone pair of electrons to make a bond Electrons in the highest occupied orbital (HO) of a molecule or anion are the best Lewis bases Molecules or ions with a low lying unoccupied orbital (LU) of a molecule or cation are the best Lewis acids

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Coordination complex: Lewis base (electron pair donor) coordinated to a Lewis acid (electron pair acceptor) Coordination complex: Ligand (electron donor) coordinated to a metal (electron acceptor) The formation of a coordinate complex is a Lewis acid-base reaction The number of ligand bonds to the central metal atom is termed the coordination number

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The basic idea is that the ligand (Lewis base) is providing electron density to the metal (Lewis acid) In terms of MO theory we visualize the coordination as the transfer of electrons from the highest occupied valenece orbital (HO) of the Lewis base to the lowest unoccupied orbital (LU) of the Lewis acid The bond from ligand to metal is covalent (shared pair), but both electrons come from the ligand (coordinate covalent bond)

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Types of Ligands (electron pair donors: Monodentate (one tooth) Ligands Latin: “mono” meaning one and “dens” meaning tooth

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Types of Ligands: Bidentate (two tooth) Ligands Some common bidentate (chelates):

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Types of Ligands: Ethylenediaminetetraacetate ion (EDTA): a polydentate chelating ligand Chelate from Greek chela, “claw” EDTA wraps around the metal ion at all 6 coordination sites producing an exceedingly tight binding to the metal

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The Nobel Prize in Chemistry 1913 "in recognition of his work on the linkage of atoms in molecules by which he has thrown new light on earlier investigations and opened up new fields of research especially in inorganic chemistry" Alfred Werner: the father of the structure of coordination complexes

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Conventions in writing the structure of coordination compounds: Brackets [] are used to indicate all of the atomic composition of the coordinate complex: the central metal atom and the ligands. The symbol for the central metal atom of the complex is first within the brackets Species outside of the [] are not coordinated to the metal but are require to maintain a charge balance A coordination compounds is a neutral species consisting of a coordinate complex and uncoordinated ions that are required to maintain the charge balance

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(2) Brackets [] are used to indicate all of the atomic composition of the coordinate complex: the central metal atom and the ligands. The symbol for the central metal atom of the complex is first within the brackets (3) Species outside of the [] are not coordinated to the metal but are require to maintain a charge balance (1) A coordination compounds is a neutral species consisting of a coordinate complex and uncoordinated ions required to maintain the charge balance

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Ligand substitution reactions For some complex ions, the coordinated ligands may be substituted for other ligands Complexes that undergo very rapid substitution of one ligand for another are termed labile Complexes that undergo very slow substitution of one ligand for another are termed inert [Ni(H2O)6]2+ + 6 NH3  [Ni(NH3)6]2+ + 6 H2O (aqueous)

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Werner’s explanation of coordination complexes Metal ions exhibit two kinds of valence: primary and secondary valences The primary valence is the oxidation number (positive charge) of the metal (usually 2+ or 3+) The secondary valence is the number of atoms that are directly bonded (coordinated) to the metal The secondary valence is also termed the “coordination number” of the metal in a coordination complex

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Exemplar of primary and secondary valence: [Co(NH3)6]Cl3 [Co(NH3)6]3+ What is the atomic composition of the complex? What is the net charge of the complex? [Co(NH3)6]Cl3 How do we know the charge is 3+ on the metal? 3+ is required to balance the three Cl- ions The secondary valence of [Co(NH3)6]Cl3 is The primary valence of [Co(NH3)6]Cl3 is 3 (charge on Co3+) 6 (six ligands)

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19.2 Structures of Coordination Complexes: The ammonia complexes of Co(III) = Co3+ CoCl3.6NH3 CoCl3.5NH3 CoCl3.4NH3 CoCl3.3NH3 In all of these complexes there are no free NH3 molecules (No reaction with acid) How did Werner deduce the structure of coordination complexes?

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Compound 1: CoCl3.6NH3 = [Co(NH3)6]3+(Cl-)3 = [Co(NH3)6](Cl)3 Conclude: 3 free Cl- ions, complex = [Co(NH3)6]3+ Compound 2: CoCl3.5NH3 = [Co(NH3)5Cl]2+(Cl-)2 = [Co(NH3)5Cl](Cl)2 Conclude: 2 free Cl- ions, complex = [Co(NH3)5Cl]2+ Compound 3: CoCl3.4NH3 = [Co(NH3)4Cl2]1+(Cl-) = [Co(NH3)4Cl2](Cl) Conclude: 1 free Cl- ion, complex = [Co(NH3)4Cl2]1+ Compound 4: CoCl3.3NH3 = [Co(NH3)3Cl3] = complex No free Cl- ions, both Cl- and NH3 in sphere “free” Cl- is not in sphere; all NH3 molecules are is in sphere

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CoCl3.6NH3 CoCl3.5NH3 CoCl3.4NH3 Isomers! Coordination complexes: Three dimensional structures

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Coordination complexes: isomers Isomers: same atomic composition, different structures We’ll check out the following types of isomers: Hydrate Linkage Cis-trans Optical (Enantiomers)

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Water in outer sphere (water that is part of solvent) Water in the inner sphere water (water is a ligand in the coordination sphere of the metal) Hydrate isomers:

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Linkage isomers Bonding to metal may occur at the S or the N atom Bonding occurs from N atom to metal Bonding occurs from S atom to metal

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Stereoisomers: geometric isomers (cis and trans)

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CoCl3.3NH3 Cis-trans isomers and beyond Beyond cis and trans isomers: facial & meridian isomers and enantiomers facial (fac) meridian (mer) 3 NH3 ligands in one plane, 3 Cl ligands in a perpendicular plane 3 NH3 and 3 Cl ligands are adjacent (on triangular face)

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Optical isomers: enantiomers Enantiomers are mirror images which are not superimposable Enantiomers do not have a plane of symmetry Any molecule which possesses a plane of symmetry is superimposable on its mirror image Enantiomers rotate polarized light in different directions; therefore, enanotiomers are also termed “optical isomers” Mirror images are either superimposible or they are not

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Enantiomers: non superimposable mirror images A structure is termed chiral if it is not superimposable on its mirror image Two chiral structures: non superimposable mirror images: Enantiomers! Structure Mirror image Of structure

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Two coordination complexes which are enantiomers

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EDTA complexes are optically active No plane of symmetry

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Plane of symmetry Achiral (one structure) Chirality: the absence of a plane of symmetry Enantiomers are possible A molecule possessing a plane of symmetry is achiral and a superimposible on its mirror image Enantiomers are NOT possible Are the following chiral or achiral structures?

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Which are enantiomers (non-superimposable mirror images) and which are identical (superimposable mirror images)?