Fundamentals of Medicinal and Pharmaceutical Chemistry PDF

Fundamentals of Medicinal and Pharmaceutical Chemistry FUNCHEM.9 Coordination Chemistry Professor Celine Marmion DAT E : 1 4 t h O c t o b e r 2 0 2 4 Learning outcomes At the end of this lecture, the learner will be able to Define ‘dative or coordinate bonds’. Define ‘Lewis acids and...

Fundamentals of Medicinal and Pharmaceutical Chemistry FUNCHEM.9 Coordination Chemistry Professor Celine Marmion DAT E : 1 4 t h O c t o b e r 2 0 2 4 Learning outcomes At the end of this lecture, the learner will be able to Define ‘dative or coordinate bonds’. Define ‘Lewis acids and bases’, ‘Arrhenius acids and bases’, ‘Bronsted-Lowry acids and bases’. Define ‘coordination compounds’. Recall examples of Lewis acids and bases. Define ‘ligand’ and ‘metal complex’. Determine ‘coordination number’ and ‘oxidation number’ of a metal ion in a metal complex formula or structure. Identify or predict geometry around a metal ion in various complexes. Define ‘ligand denticity’. Recall and identify examples of monodentate and bidentate ligands. FUNCHEM.9 Coordination Chemistry 2  General Chemistry - The Essential Concepts by Chang and Goldsby 7e Recommended  Chapter 20  Chapter 10, Section 10.1 on reading molecular geometry FUNCHEM.9 Coordination Chemistry 3 Recall: Ionic Bonding In an IONIC bond, electrons are lost or gained, resulting in the formation of IONS in ionic compounds. _ + K F K F The ionic bond is the attraction between the positive K+ ion and the negative F- ion FUNCHEM.9 Coordination Chemistry 4 Recall: Covalent Bonding Cl Cl octet octet The octet is achieved by each atom sharing the electron pair in the middle FUNCHEM.9 Coordination Chemistry 5 What is a dative or coordinate bond? Fe3+(aq) + 6CN-(aq) [Fe(CN)6]3-(aq) Recall the Lewis Dot Structure for CN- (isoelectronic with CO): This lone pair of electrons can be donated to the Fe3+ metal ion to generate a new complex FUNCHEM.9 Coordination Chemistry 6  Fe3+(aq) + 6CN-(aq) [Fe(CN)6]3-(aq) What is the oxidation state CN 3- of the metal? Its coordination number? Its geometry? NC CN Its magnetic properties? NC Fe CN Its biological activity? Each bond is called a dative or coordinate bond CN The substance above is a coordination compound or a coordination complex ion since it has a charge. FUNCHEM.9 Coordination Chemistry 7 What is coordination chemistry and why study it? Coordination chemistry is the study of the interactions between transition metal ions and other molecules and/or ions A coordination compound will generally contain one or more metal ions (usually transition metals) which is surrounded by a small number of small molecules or ions called ligands. FUNCHEM.9 Coordination Chemistry 8 Why study coordination chemistry? Many biomolecules contain transition metals which play a key role in the functions of these biomolecules Vitamin B12 contains Co Metalloenzymes such as matrix metalloproteinases and histone deacetylases contain Zn Hemoglobin, myoglobin contain Fe – responsible for O2 transport and storage Transition metal complexes can also be used as therapeutic agents Pt complexes as anti-cancer agents; Gold complexes as anti-arthritic agents …… FUNCHEM.9 Coordination Chemistry 9 What are transition metals? FUNCHEM.9 Coordination Chemistry 10 Structure of Cisplatin – used to treat various types of cancers e.g. testicular, lung, ovarian Lewis bases Cl NH3 Cl Pt NH3 Coordination Compound Lewis acid or Coordination Complex FUNCHEM.9 Coordination Chemistry 11 What are Lewis acids and Lewis bases? Lewis acid is a species that can accept a pair of electrons i.e. an electron pair acceptor Lewis base is a species that can donate a pair of electrons i.e. an electron pair donor But I thought acids and bases donated H+ and OH- ions in solution? FUNCHEM.9 Coordination Chemistry 12  But I thought acids and bases donated H+ and OH- ions in solution? ‘Arrhenius’ definitions of acids and bases: Arrhenius acid - a substance that ionizes to produce H+ in aqueous solution ca. 1885 - Svante Arrhenius Arrhenius base - a substance that ionizes to produce OH- in aqueous solution FUNCHEM.9 Coordination Chemistry 13 Bronsted-Lowry Acids and Bases! Base Conjugate acid - + H2CO3 + H2O HCO3 + H3O Acid Conjugate base Bronsted-Lowry acid is a proton (H+) donor Bronsted-Lowry base is a proton acceptor FUNCHEM.9 Coordination Chemistry 14 How do Lewis acids and bases combine to give coordination compounds? Let’s go back to our first example Fe3+(aq) + 6CN-(aq) [Fe(CN)6]3-(aq) Lewis acid Lewis bases – - metal ion also called ligands FUNCHEM.9 Coordination Chemistry 15 Recall electronic configurations of the first row transition elements Sc [Ar] 4s23d1 Ti [Ar] 4s23d2 V [Ar] 4s23d3 Cr [Ar] 4s13d5 Mn [Ar] 4s23d5 Fe [Ar] 4s23d6 Co [Ar] 4s23d7 Ni [Ar] 4s23d8 Cu [Ar] 4s13d10 Zn [Ar] 4s23d10 where [Ar] = 1s22s22p63s23p6 FUNCHEM.9 Coordination Chemistry 16  Fe3+(aq) + 6CN-(aq) [Fe(CN)6]3-(aq) Fe [Ar] 4s23d6 Fe3+ has lost 3 electrons Fe3+ [Ar] 3d5 To get a d-block metal ion (1st row) from the neutral atom you remove the 4s electrons first before removing 3d electrons Co Co3+ + 3e- [Ar]3d74s2 [Ar]3d6 Mn Mn4+ + 4e- [ Ar]3d54s2 [Ar]3d3 FUNCHEM.9 Coordination Chemistry 17  Coordination complex or coordination compound Coordination complex or coordination compound NH3 2+ H3N NH3 Fe 2Cl- Cl NH3 H3N NH3 Cl Pt NH3 NH3 Neutral Counter Complex ion ions Neutral FUNCHEM.9 Coordination Chemistry 18 How do Lewis acids and bases combine to give coordination compounds? Let’s go back to our first example Fe3+(aq) + 6CN-(aq) [Fe(CN)6]3-(aq) Crystal Field Theory CN 3- (explained later!) NC CN Fe3+ NC Fe CN CN CN- FUNCHEM.9 Coordination Chemistry 19  NH3 2+ Cl NH3 NH3 Pt H3N Cl NH3 H 3N Fe NH3 2Cl- NH3 Each ligand is classified according to CN = 4 and CN = 6 the number of donor atoms – in this case, Coordination number is the number of each N in NH3 and donor atoms bonded to the central each Cl- donates one metal ion in the complex pair of electrons, hence they are monodentate ligands FUNCHEM.9 Coordination Chemistry 20 Ligand Denticity – classified according to the number of donor atoms – Examples monodentate = 1 bidentate = 2 Tridendate = 3 tetradentate = 4 hexadentate = 6 polydentate = 2 or more donor atoms FUNCHEM.9 Coordination Chemistry 21 Examples of monodentate ligands H2O H2S HS - CH3OH CH3SH F- OH- Examples of bidendate ligands oxalate ion (ox) = C2O42- H2N NH2 ethylenediamine (en) ethylenediamine (en) = NH2CH2CH2NH2 O O N 2,2’-bipyridine (bpy) - - N O O 2,2'-bipyridine oxalate (ox) FUNCHEM.9 Coordination Chemistry 22  H Mn+ H N H N The bidentate ligand 1,2- H diaminoethane or ethylenediamine (en) O O Mn+ O - O O- O oxalate (ox) O O FUNCHEM.9 Coordination Chemistry 23 Oxidation State of the Metal Ion Three en ligands Each en ligand is bidentate and neutral Overall charge on complex ion is = 3+ Oxidation state of metal ion: +3 Co + 3(0) = +3 FUNCHEM.9 Coordination Chemistry 24 Oxidation State of the Metal Ion NH3 2+ H3N NH3 Cl NH3 H 3N Fe NH3 2Cl- Cl Pt NH3 NH3 Each Cl is -1 i.e. Cl- Each NH3 is neutral Each NH3 is neutral Complex ion has a charge of Complex is neutral 2+ Pt + 2 Cl- + 2 NH3 = 0 Fe + 6 NH3 = +2 Pt + 2(-1) + 2(0) = 0 Fe + 6(0) = +2 Pt = +2 Fe = +2 FUNCHEM.9 Coordination Chemistry 25 Geometries in Complex Ions FUNCHEM.9 Coordination Chemistry 26 Geometries Coordination Number: 2 Geometry: Linear Example: [Ag(NH3)2]+ FUNCHEM.9 Coordination Chemistry 27 Common Geometries of Complexes Coordination Number: 4 Geometry: Tetrahedral (most common) Examples: [Zn(NH3)4]2+, [FeCl4]- Geometry: Square planar (characteristic of metal ions with 8 d e-) Example: [Ni(CN)4]2- FUNCHEM.9 Coordination Chemistry 28 Geometry Octahedral If the coordination no is 6 the ligand donor atoms are arranged octahedrally around the metal ion (octahedral complex) For 1st row d-block metal ions, coordination no = 6 (octahedral) is by far the most common FUNCHEM.9 Coordination Chemistry 29 Geometry NH3 2+ Cl NH3 Cl Pt NH3 H3N NH3 H3N Fe NH3 2Cl- Square planar NH3 Octahedral Oxidation State: Coordination Number: Oxidation State: Coordination Number: FUNCHEM.9 Coordination Chemistry 30 Learning outcomes At the end of this lecture, the learner will be able to Define ‘dative or coordinate bonds’. Define ‘Lewis acids and bases’, ‘Arrhenius acids and bases’, ‘Bronsted-Lowry acids and bases’. Define ‘coordination compounds’. Recall examples of Lewis acids and bases. Define ‘ligand’ and ‘metal complex’. Determine ‘coordination number’ and ‘oxidation number’ of a metal ion in a metal complex formula or structure. Identify or predict geometry around a metal ion in various complexes. Define ‘ligand denticity’. Recall and identify examples of monodentate and bidentate ligands. FUNCHEM.9 Coordination Chemistry 31 Thank you F O R M O R E I N F O R M AT I O N P L E A S E C O N TA C T Professor Celine J. Marmion EMAIL: [email protected] 32