Chemistry 116  Fall 2013

1. Chemistry 116  Fall 2013 • Martin Larter • Office 30-220 • Phone 644-7346 • martin.larter@gcccd.edu • www.grossmont.edu/martinlarter/

2. Class Schedule • Lecture • Monday and Wednesday 5: 30 PM – 6:45 PM • Bldg. 30, Room 242 • Lab • Monday ( Sec:2515) and Wednesday (2516) 7:00 PM - 10:00 PM • Bldg. 30, Room 222

3. Fall 2013 Schedule

4. Websites • All Course documents will be on either my web page • www.grossmont.edu/martinlarter • Or blackboard http://bb.gcccd.net/

5. SCOPE OF COURSE • This course is designed to continue the formal chemical education of nursing students and allied health students who do not require a full year of organic chemistry for their pre-professional preparation. • Plan to spend two hours per lecture hour and one hour per lab hour per week for studying, minimum

6. Prerequisite • A "C" or "CR" grade or higher in CHEM 115 or equivalent.

7. Text • Text: Bettelheim,’ Brown and March, 7th edition. Introduction to Organic and Biochemistry • Lab Book: Chem 116 Lab manual • Homework: OWL assignments (online homework), http://www.cengage.com/owl/

8. Additional Materials • Notebook: spiral or loose leaf for homework • Safety Glasses: Z-87 Safety goggles (purchased in bookstore), • Ink Pen: Fine Tip Black Sharpie pen, a blue or black ink pen • Combination Lock: preferred V69 series (purchase from hardware store or bookstore) • Covered Shoes

9. COURSE OBJECTIVES The general objectives of the course are: • To extend the elementary patterns of thought initiated in the introduction • To chemistry to the study of organic and biochemistry; • Learned to recognize the common organic functional groups and be able to apply the IUPAC rules for organic nomenclature • Describe the major chemical, physical properties and reactions of the major classes of organic compounds. • Become acquainted with how the stereochemistry of a molecule affects its reactions and properties • Recognize and describe the structural features and characteristics of the four major classes of biochemical (carbohydrates, lipids, proteins an nucleic acids.) • Understand the major metabolic pathways of carbohydrate and lipid catabolism and protein anabolism.

10. Grading Points • Exams (4) 400 • Given in lecture • Laboratory Assignments 200 • Quizzes 100 • Given in lab, cover lecture and lab material • Homework 100 • Poster Project 100 • Final Exam 100 • Cumulative final • Total 1000

11. Grading Scale • Must pass both lab and lecture to pass course!

12. Make-up Policy • Quizzes - No make up allowed. • Exams - Must be make up within 1 week of original test date. (With a reasonable, verifiable excuse).

13. Late Work • Labs - lose 20% per week late. No labs accepted more than 2 weeks late.

14. Supervised Tutoring Referral • Students are referred to enroll in the following supervised tutoring courses if the service indicated will assist them in achieving or reinforcing the learning objectives of this course: IDS 198, Supervised Tutoring to receive tutoring in general computer applications in the Tech Mall; English 198W, Supervised Tutoring for assistance in the English Writing Center (Room 70-119); and/or IDS 198T, Supervised Tutoring to receive one-on-one tutoring in academic subjects in the Tutoring Center (Room 70-229, 644-7387).

15. Attendance • Regular attendance is mandatory - you may be dropped if you miss more than 6 hours of class (1 week). • You will not be dropped if you have not checked out of the laboratory! This means you may receive an F!!!!

16. Academic Integrity Policy • All work must be your own! • See college catalog for more information, as well as the Grossmont Chemistry Departments Academic integrity Policy.

17. Disabled Students • Students with disabilities who may need accommodations in this class are encouraged to notify the instructor and contact Disabled Student Programs & Services (DSPS) early in the semester so that reasonable accommodations may be implemented as soon as possible. Students may contact DSP&S in person in Room 110 or by telephone at (619) 644-7112 or (619) 644-7119 (TTY for deaf).

18. Additional Information: • The maximum number of times a student may enroll in the same credit course is three times. • A student, through a combination of substandard grades (D or F) and withdrawals on their student record, may only take a class three times. • If a student, through a combination of substandard grades (D or F) and withdrawals, wishes to take a class for the fourth time, they must submit a petition to the Admissions and Records Office. Petitions will only be approved based on extenuating circumstances. • Military Withdrawals do not count in terms of repetition restrictions, nor do withdrawals that occur due to fire, flood

19. Chemistry Tutoring • Peer tutoring will be available in the Science Learning Center (30-252). • Please note this tutoring is to ask specific questions on homework or labs • It is not to get the material lectured on or re-lectured on. • Bring chemistry notes for tutoring in SLC so that the tutors have an idea of what has been covered and at what level. • Chemistry tutoring is also available on the second floor of the library. • 2 hrs. free tutoring per week/ per class up to 5 hours of tutoring a week • You can also come to the instructor’s office hour to get help on your chemistry.

20. Studying Chemistry • Be curious • Learn vocabulary (and nomenclature) • Keep current in the class. Don’t wait for a test • Form a study group • Do problems again and again!!

21. Chapter 1 Organic Chemistry

22. Organic Chemistry • Organic chemistry: the study of the compounds of carbon • organic compounds are made up of carbon and only a few other elements • chief among these are hydrogen, oxygen, and nitrogen • also present are sulfur, phosphorus, and halogens (fluorine, chlorine, bromine, or iodine)

23. Organic Chemistry • Why is organic chemistry a separate discipline within chemistry? • historical: scientists at one time believed that a “vital force” present in living organisms was necessary to produce an organic compound • the experiment of Wöhler in 1828 was the first in a series of experiments that led to the demise of the vital force theory

24. Organic Chemistry • The sheer number of organic compounds • chemists have discovered or made over 10 million organic compounds and an estimated 100,000 new ones are discovered or made each year • by comparison, chemists have discovered or made an estimated 1.7 million inorganic compounds • thus, approximately 85% of all known compounds are organic • The link to biochemistry • carbohydrates, lipids, proteins, enzymes, nucleic acids, hormones, vitamins, and almost all other chemicals in living systems are organic compounds

26. Organic Chemistry • a comparison of organic and inorganic compounds

27. Where do we obtain organic compounds? • Isolation from nature • Living organisms are “chemical factories” (biosynthesis) • Natural gas, petroleum and coal • Synthesis in the laboratory • There are few natural organic compounds that chemists can’t synthesize in a laboratory • Organic chemists also synthesize compounds that are not found in nature (the majority of the > 10 million known organic compounds are not found in nature)

28. Molecular Polarity • Recall that a covalent bond can either be polar (if electronegativity difference ≥ 0.5) or nonpolar Examples: C-H is nonpolar, C-O is polar • However, molecular polarity is primarily based on shape: - Symmetrical molecules are nonpolar - Nonsymmetrical molecules are polar if: - there is at least one lone pair on central atom - or, there is at least one polar bond Examples: CCl4 is nonpolar, CHCl3 is polar

30. Intermolecular Forces • Forces holding one molecule to another in a substance. • Electrostatic in nature, they arise from the interaction between positively and negatively charged species. (They are the sum of both attractive and repulsive components) • The attractions between molecules are not nearly as strong as the intramolecular attractions that hold compounds together. • They are, however, strong enough to control physical properties such as boiling and melting points, vapor pressures, and viscosities. • These intermolecular forces as a group are referred to as van der Waals forces.

31. Dispersion Forces Nonpolar interactions • Dispersion forces, or London forces, are the result of a temporary dipole. • Electrons are constantly shifting and a region may become temporarily electron poor and slightly positive while another region becomes slightly negative. • This creates a temporary dipole and two molecules with temporary dipoles are attracted to each other.

32. London Dispersion Forces These forces are present in all molecules, whether they are polar or nonpolar. Dispersion forces, or London forces, are the result of a temporary dipole. Dispersion forces are the weakest intermolecular force The tendency of an electron cloud to distort in this way is called polarizability. London dispersion forces, or dispersion forces, are attractions between an instantaneous dipole and an induced dipole.

33. Dipole-dipole interactions Polar molecules have a permanent dipole. The oppositely charged ends of polar molecules are attracted to each other, this is the dipole force. Dipole forces are stronger than dispersion forces. The strength of a dipole force is typically 10% of a covalent bond’s strength. These forces are only important when the molecules are close to each other.

34. Hydrogen Bonds are a special type of dipole attraction. The stronger of the three Hydrogen bonds are present when a molecule has an N-H, O-H, or F-H bond. Hydrogen bonding arises in part from the high electronegativity of nitrogen, oxygen, and fluorine.

35. Hydrogen bonding arises in part from the high electronegativity of nitrogen, oxygen, and fluorine. When hydrogen is bonded to one of those very electronegative elements, the hydrogen nucleus is exposed. (hydrogen nucleus becomes deshielded). The exposed proton acts as a very strong center of positive charge, creating a large bond dipole, attracting all the electron clouds from neighboring molecules (negative dipoles). Hydrogen Bonds

36. Organic Structure Representations of organic compounds: • structural formula: shows the atoms present in a molecule as well as the bonds that connect them • other representations: condensed formulas, line-angle formulas, perspective (3-D) formulas • VSEPR theory: The various areas of electron density around a nucleus spread out so that each is as far away as possible from the others Areas of electron density = bonds to atoms and lone pairs of electrons (double and triple bonds count as 1 area of electron density) • We can use VSEPR theory to predict bond angles -the most common bond angles are 109.5°, 120°, and 180°

37. Organic Structure • Among neutral (uncharged) organic compounds • carbon: four covalent bonds and no unshared pairs of electrons • hydrogen: one covalent bond and no unshared pairs of electrons • nitrogen: three covalent bonds and one unshared pair of electrons • oxygen: two covalent bonds and two unshared pairs of electrons • a halogen: one covalent bond and three unshared pairs of electrons

38. Functional Groups • Functional group: a part of an organic molecule that undergoes chemical reaction • Functional groups are important because • they undergo the same types of chemical reactions no matter in which molecule they are found • to a large measure they determine the chemical and physical properties of a molecule • they are the units by which we divide organic compounds into families • they provide the basis on which we derive names for organic compounds

39. Functional Groups • Five important functional groups

40. Alcohols • Alcohol: contains an OH (hydroxyl) group bonded to a tetrahedral carbon atom • may be primary (1°), secondary (2°), or tertiary (3°)

41. Amines • Amine: a compound containing an amino group • the amino group may be primary (1°), secondary (2°), or tertiary (3°)

42. Aldehydes and Ketones • Both contain a C=O (carbonyl) group • aldehyde: contains a carbonyl group bonded to a hydrogen; in formaldehyde, the simplest aldehyde, the carbonyl group is bonded to two hydrogens • ketone: contains a carbonyl group bonded to two carbon atoms

43. Carboxylic Acids • Carboxylic acid: a compound containinga -COOH (carboxyl: carbonyl + hydroxyl) group • in a condensed structural formula, a carboxyl group may also be written -CO2H.

44. Chapter 1 Organic Chemistry