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Molecular Structure: Introduction and Review Lecture Supplement page 3

Molecular Structure: Introduction and Review Lecture Supplement page 3. Taxol: An anticancer drug. Example: Cholesterol. Basic Questions. Organic chemistry: What is it? The study of molecules containing carbon Why all this fuss about carbon?

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Molecular Structure: Introduction and Review Lecture Supplement page 3

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  1. Molecular Structure:Introduction and ReviewLecture Supplement page 3 Taxol: An anticancer drug

  2. Example: Cholesterol Basic Questions • Organic chemistry: What is it? • The study of molecules containing carbon • Why all this fuss about carbon? • Millions of molecules known from small set of elements (northeast corner of periodic table) • Carbon is unique in its ability to form stable rings and chains • Carbon compounds basis for life (as we know it)

  3. Basic Questions Why should I study organic chemistry? • Broadly applicable to other fields: Biochemistry, pharmaceuticals, biology, etc. • Skills learned useful elsewhere: Information organization, critical/analytical thinking, etc. • How often should I study organic chemistry? • Monday, Tuesday, Wednesday, Thursday, Friday, Saturday, Sunday…

  4. Basic Questions In Chemistry 14C we expand our knowledge of organic molecular structure by exploring… • Selected topics in structural theory: Resonance, conjugation, aromaticity, stereochemistry, etc. • Laboratory determination of structure: Spectroscopy • Structure controls properties: Physical, chemical, biological • Reaction chemistry (substance  substance) covered in Chemistry 14D

  5. Basic Questions • What is molecular structure? • Molecular structure = electron distribution (in bonds, in molecule) and positions of atoms in space. • Example: Water H-O-H bond angle 104.5o d+ d- O-H bond length 0.96 Å

  6. Molecular RepresentationsHow do we draw molecules? The Rules •  is a covalent bond (electron pair shared by two atoms) • : is a lone (nonbonded) electron pair • Carbons do not always have to be drawn • Hydrogens can be omitted only if carbon not written as C • All other atoms must always be shown • Lone pairs do not always have to be shown • Formal charges must always be shown (unless FC = 0) • Three-dimensional geometry does not always have to be shown CH3NH2 bond projects outward towards viewer bond recedes away from viewer

  7. Molecular Representations • Applying the rules: Taxol, an anticancer drug • Carbons do not always have to be drawn • Hydrogens can be omitted only if carbon not written as C • All other atoms must always be shown • Lone pairs do not always have to be shown

  8. Molecular RepresentationsYour molecular model kit Molecular model kit Benzene a-D-Glucopyranose • Models useful to visualize, manipulate structures in three dimensions • Compare molecular models of molecules in this review versus their “paper” structures • Bring models to discussion sections • Models can be used on exams • Models are a good habit and can be a fun toy! • “How to use your model kit” tutorial is available on Prof. Hardinger’s course website

  9. Molecular Representations Do I have to memorize these structures? • More often you see it, more important it is • More important it is, greater chance you might need to know its structure • Common: Methane, glucose Uncommon: Taxol • Pure memorization (the “m word”) rarely needed

  10. 2-chlorobutane   3-methylcyclohexanol Molecular Representations What do I have to know about nomenclature? • Naming of simple molecules • Drawing structure of simple molecules from name • Examples:

  11. The Electron Count CountsReview Lewis structure tutorial at course web site Valence shell electron count • H full shell = two electrons (same as He) • 2nd row elements (CNOF): Eight electrons and four bonds maximum • The "octet rule" Pentavalent carbon very bad • 3rd row elements easily violate “octet rule” P often has 10 electrons S often has 12 electrons

  12. The Electron Count Counts Formal Charge Definition: The charge on an atom in a Lewis structure if the bonding was perfectly covalent and the atom has exactly a half-share of the bonding electrons. (The difference between the number of electrons “owned” by a covalently bonded atom versus the same atom without any bonds, i.e., a free atom of the same element.) • Significance • Indicates electron excess or deficiency • Desire to gain or lose electrons • Electrostatic interaction between regions of charge • Determination of formal charge • Review tutorial at course web site

  13. The Electron Count Counts • Formal Charge Self-Test • Verify the formal charges in the following molecule: NAD Coenzyme in biological oxidation reactions

  14. The Electron Count Counts • Formal Charge Self-Test • Verify the formal charges in the following molecule: +1 -1 -1 NAD Coenzyme in biological oxidation reactions All other atoms in this molecule have formal charge of zero

  15. Electrons in Bonds • Electron distribution can be… …even (covalent bond) …uneven (polar covalent bond or ionic bond) Electronegativity (EN): Power of an atom to attract electrons to itself High EN = strong electron attraction Low EN = weak electron attraction

  16. EN decreases EN decreases EN decreases Electrons in BondsPauling EN values for elements important to Chemistry 14C EN  with  distance from fluorine • Must I memorize electronegativity values? • Not necessary…just do lots of problems. Learn them by frequent use.

  17. Polar Covalent BondsUneven electron distribution leads to partial charges d+ XY d- EN (X) < EN (Y) • Result: Bond dipole or polar covalent bond • Magnitude of bond dipole influenced by... •  EN difference  bond dipole •  bond length  bond dipole • Example: CH DEN = 0.4 but has low polarity due to short bond length

  18. Adenine Thymine Polar Covalent BondsUneven electron distribution leads to partial charges Consequences of bond polarity • Electrostatic interaction with other ions or molecules Influences chemical, physical, and biological properties Example: Polar H-N bond  hydrogen bonding  DNA base pairing

  19. Functional Groups Functional group (FG): A characteristically bonded group of atoms that determines molecular properties regardless of what molecule contains it. FG Table: Thinkbook Appendix A Why study FG? Similar functional groups  similar properties • Expected skills: • Identify FG within molecules • Draw molecules with particular FG

  20. Identify the Functional Groups in Taxol

  21. e- cloud repulsion bond angle Atomic Positions and Molecular Geometry Atoms = balls of electrons ...have mutual repulsion ...move as far apart as possible •  repulsion causes  bond angle • Larger electron cloud = stronger repulsion • Approx. electron cloud size: H, F < lone pair, Cl, Br, I < group of atoms (CH3, OH, etc.)

  22. The relationship between Lewis Structures, Valence Shell Electron Pair Repulsion Theory (VSEPR) and Hybridization Molecular Formula ↓Propose a good Lewis Structure (fulfill octet rule, minimize formal charges) ↓Use VSEPR to “space out” groups as far away from each other as possible (this final geometry is referred to in the chart below as the “electron arrangement”)↓Choose the hybridization scheme that gives the desired geometry • Discuss handout on hybridization

  23. Atomic Positions and Molecular Geometry Methane • Four electron clouds around central atom  tetrahedral shape • Equal repulsion by all H  equal H-C-H angles (109.5o) 109.5o Water • Four electron clouds around central atom  tetrahedral shape • Lone pair/lone pair repulsion > H/H repulsion  H-O-H angle < 109.5o 104.5o

  24. Bonds, Molecular Geometry, and Orbitals Covalent bonds formed by overlap of orbitals • Orbital: Mathematical equation that describes a volume of space in which there is a certain probability of finding an electron of a certain energy. • Orbitals can be drawn, but have no physical reality. • Bond example: Two H 1s orbitals (spheres) overlap to form H-H bond: + Hydrogen atoms Hydrogen molecule

  25. + Bonds, Molecular Geometry, and Orbitals What orbitals are used for organic molecules? Example: Methane (CH4) H (1s) + C (2s, 2px, 2py, 2pz)  C-H bonds orthogonal H-C-H bond angle 90o H 1s + C 2px + C 2pz wrong H-C-H bond angle! Therefore this orbital combination incorrect Verify with your model kit

  26. Bonds, Molecular Geometry, and Orbitals Solution (Linus Pauling, 1931) • Use mathematical combinations of s, px, py, and pz orbitals to form correct number of bonds with correct geometry • Combinations = hybrid orbitals • Hybridization scheme for atom with four electron groups • Electron group = bond or lone pair • CH4 geometry = tetrahedral; need four bonds and four hybrid orbitals • Orbital conservation: Four hybrid orbitals come from four atomic orbitals • s + px + py + pzsp3 + sp3 + sp3 + sp3 • C sp3 + H 1s C-H bond

  27. Molecular Conformations Acyclic molecules: Eclipsed Staggered Cyclic molecules: Axial Equatorial Additional material available on course web site

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