1 / 28

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?

tommy
Download Presentation

Molecular Structure: Introduction and Review Lecture Supplement page 3

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  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

More Related