1. 1Fall, 2009 CHEM305 Organic Chemistry I Introduction Dr. Ralph C. Gatrone Department of Chemistry and Physics Virginia State University Fall, 2009

2. 2 Objectives Discuss syllabus Discuss syllabus Discuss course requirements Discuss course requirements Review general chemistry Review general chemistry

3. Fall, 20093 Organic Chemistry I CHEM305-01-081 Office Hours Office Hours –T: 2:00 – 5:00 and W: 9:00 – 12:00 –by appointment (524-5762) Office: HM239Nb Office: HM239Nb Email: rgatrone@vsu.edu Email: rgatrone@vsu.edurgatrone@vsu.edu I only respond to an email address that ends in @vsu.edu I only respond to an email address that ends in @vsu.edu

4. Fall, 20094 Organic Chemistry 1 Course Description Survey of compounds composed of carbon Survey of compounds composed of carbon Nomenclature Nomenclature Structure Structure Physical properties Physical properties Reactions Reactions Mechanisms Mechanisms

5. Fall, 20095 Course Emphasis Organic reactions Organic reactions Molecular orbital theory Molecular orbital theory Organic Mechanisms Organic Mechanisms Molecules of biological importance Molecules of biological importance Critical thinking skills Critical thinking skills Skills necessary to do well on Skills necessary to do well on MCAT, PCAT, OAT, DAT, others MCAT, PCAT, OAT, DAT, others

6. Fall, 20096 Roles My role My role Professor Professor Guide Guide Your Role Your Role Student Student Understand the material! Understand the material!

7. Fall, 20097 The Teacher versus the Professor A teacher conveys information to provide a student with certain skills and a knowledge base. A teacher conveys information to provide a student with certain skills and a knowledge base. A professor professes the truth about their area of expertise while providing the student with the skills to accept or refute that truth. A professor professes the truth about their area of expertise while providing the student with the skills to accept or refute that truth. Ideally the professor imparts a sense of wonder such that the student will push the limits of our understanding. Ideally the professor imparts a sense of wonder such that the student will push the limits of our understanding. The student develops the necessary skills and knowledge base to succeed. The student develops the necessary skills and knowledge base to succeed.

8. Fall, 20098 Requirements and Prerequisites Course Materials Course Materials Text: Organic Chemistry A Biological Approach, John McMurry Text: Organic Chemistry A Biological Approach, John McMurry You must purchase the book. You must purchase the book. A study guide is available. It is not required. A study guide is available. It is not required. Prerequisites Prerequisites CHEM101 or 111, 102 or 112 CHEM101 or 111, 102 or 112 Associated Laboratories Associated Laboratories Foundation from General Chemistry Foundation from General Chemistry Quantum mechanics Quantum mechanics Solution chemistry Solution chemistry Acid Base Chemistry Acid Base Chemistry Kinetics Kinetics Thermodynamics Thermodynamics

9. Fall, 20099 Prerequisites are critical You must have passed these courses You must have passed these courses If you have not passed these courses If you have not passed these courses You must drop the course immediately You must drop the course immediately If not sooner! If not sooner!

10. Fall, 200910 Homework Every problem in the Text is recommended. Every problem in the Text is recommended. However, However, –They will not be graded. –They will not be collected. –They will not be discussed in class. –They are available to you to determine if you understand the material. –If you choose not to do the problems it is nearly a guarantee that you will not pass this class.

11. Fall, 200911 Evaluation Test 1: Chapters 1 – 6 100pts Test 1: Chapters 1 – 6 100pts Test 2: Chapters 1 – 7 100pts Test 2: Chapters 1 – 7 100pts Test 3: Chapters 1 – 10 100 pts Test 3: Chapters 1 – 10 100 pts Final Exam Chapters 1 – 10200pts Final Exam Chapters 1 – 10200pts Total Possible 500pts Total Possible 500pts

12. Fall, 200912 Evaluation – Grade Calculation Final Grades will be computed: Final Grades will be computed: –Earned PointsFinal Grade >450A 400 – 449B 325 – 399C 250 – 324D <249F

13. Fall, 200913 Extra Credit No extra credit will be given. No extra credit will be given. If you follow my instructions If you follow my instructions You will not need it. You will not need it. If you do not follow these instructions If you do not follow these instructions It will not help. It will not help.

14. Fall, 200914 Special Consideration Grades are earned. Grades are earned. Grades are not awarded Grades are not awarded Grades cannot be negotiated. Grades cannot be negotiated. Grades cannot be influenced by factors such as: Grades cannot be influenced by factors such as: I like you I like you You like me (rare circumstance) You like me (rare circumstance) I feel sorry for you I feel sorry for you You are a nice person in good standing with the university. You are a nice person in good standing with the university. You will lose a scholarship You will lose a scholarship You will forfeit some tuition reimbursement You will forfeit some tuition reimbursement A previously excellent GPA will be ruined A previously excellent GPA will be ruined You will be sent back to a repressive country You will be sent back to a repressive country You will not graduate on time! You will not graduate on time!

15. Fall, 200915 Attendance Assumption: you are adult students Assumption: you are adult students Attendance in lecture is expected Attendance in lecture is expected Do not ask me to re-lecture material you missed. Do not ask me to re-lecture material you missed. Regardless of your excuse for missing class you made a choice not to attend and you are responsible for the material you missed. Regardless of your excuse for missing class you made a choice not to attend and you are responsible for the material you missed. Attendance at examinations is required. Attendance at examinations is required. A missed examination will receive a zero. A missed examination will receive a zero. No excuse will be accepted. No excuse will be accepted. A missed final exam will receive a zero. A missed final exam will receive a zero.

16. Fall, 200916 A Word on Examinations Examinations will consist of several short answer questions. Examinations will consist of several short answer questions. The final examination will contain 100 multiple choice questions. The final examination will contain 100 multiple choice questions. These will be similar to the questions encountered on the MCAT, DAT, PCAT, etc. These will be similar to the questions encountered on the MCAT, DAT, PCAT, etc.

17. Fall, 200917 A Word on the Final Exam The final exam is scheduled by the university. The final exam is scheduled by the university. This schedule minimizes conflicts between rooms and courses. This schedule minimizes conflicts between rooms and courses. If the scheduled date and time happens to be inconvenient for you, please withdraw from the course today. If the scheduled date and time happens to be inconvenient for you, please withdraw from the course today. There is no excuse that I will accept that would permit you take the exam early. There is no excuse that I will accept that would permit you take the exam early.

18. Fall, 200918 Communication in Class Turn your cell phone off. Turn your cell phone off. Turn your desire to communicate with anyone but me off. Turn your desire to communicate with anyone but me off. An offending cell phone (includes text messaging) will result in the cancelation of that day’s lecture. An offending cell phone (includes text messaging) will result in the cancelation of that day’s lecture. If a class is cancelled because of an offensive cell phone the class will be held responsible for the material not covered me by in that class. If a class is cancelled because of an offensive cell phone the class will be held responsible for the material not covered me by in that class.

19. Fall, 200919 Expectations - Students A professional student is expected to A professional student is expected to attend class attend class purchase course materials purchase course materials study study do the homework do the homework be prepared for class be prepared for class be prepared for tests be prepared for tests do well do well

20. Fall, 200920 Expectations - Faculty I am expected to I am expected to attend class attend class prepare lecture materials prepare lecture materials present lecture materials present lecture materials prepare and grade tests prepare and grade tests be available for outside consultation be available for outside consultation keep accurate records keep accurate records

21. Fall, 200921 Important Note I am not expected to I am not expected to Provide extra credit Provide extra credit Negotiate grades Negotiate grades

22. Fall, 200922 Doing Well Read the chapter before lecture Read the chapter before lecture Attend lecture Attend lecture Take notes Take notes Do not rely on copies of Power Points Do not rely on copies of Power Points Re-read the chapter after lecture Re-read the chapter after lecture Review lecture notes daily Review lecture notes daily Rewriting the lecture notes is strongly suggested Rewriting the lecture notes is strongly suggested Keep, maintain, and study note cards Keep, maintain, and study note cards Do homework problems. Do homework problems. Form a study group Form a study group Learn the functional groups Learn the functional groups

23. Fall, 200923 The Functional Groups Families of Organic Compounds Families of Organic Compounds Millions of compounds Millions of compounds Thousands discovered every year Thousands discovered every year Task of knowing the chemistry would be overwhelming Task of knowing the chemistry would be overwhelming However, compounds can be grouped into families However, compounds can be grouped into families Based upon common structural features Based upon common structural features Suggests common reactivity Suggests common reactivity You must know the Table of Functional Groups provide by me. Others will come along during the semester You must know the Table of Functional Groups provide by me. Others will come along during the semester This course is a survey the chemistry and properties of organic compounds This course is a survey the chemistry and properties of organic compounds It is taught as a tour of the functional groups It is taught as a tour of the functional groups

24. Fall, 200924 Functional Groups

25. Fall, 200925 Functional Groups

26. Fall, 200926 Wow! That’s a lot of stuff to learn and you expect me to know it. That’s a lot of stuff to learn and you expect me to know it. Do you believe that this is the only course I am taking? Do you believe that this is the only course I am taking? This is an important question which we must answer! This is an important question which we must answer! You may not like the answer. You may not like the answer.

27. Fall, 200927 Is this the only course I am taking? YES YES Time invested = Desired grade Time invested = Desired grade Average professional – 60 hours/week Average professional – 60 hours/week Professional student Professional student ~18 hours/week in class ~18 hours/week in class 60 – 18 = 42 60 – 18 = 42 42hours/6 days = 7 hours per day 42hours/6 days = 7 hours per day Or approximately 2 hours/class Or approximately 2 hours/class Time invested = Desired grade Time invested = Desired grade

28. Fall, 200928 Why? Your Role: Your Role: The job of understanding the material is yours. The job of understanding the material is yours. My Role: My Role: Guide Guide I’ve been here. I’ve been here. I’ve done it. I’ve done it. I have the t-shirt (at least a C and a B in Organic I and II) I have the t-shirt (at least a C and a B in Organic I and II) Best advice I can give you! Best advice I can give you! If you choose to study organic chemistry like other courses you have taken you might do well, but the odds are against it. If you choose to study organic chemistry like other courses you have taken you might do well, but the odds are against it.

29. Fall, 200929 Major Complaint I can’t possibly learn this stuff. I can’t possibly learn this stuff. I can’t learn all of those functional groups. I can’t learn all of those functional groups. Why? Again you aren’t going to like the answer. Why? Again you aren’t going to like the answer. You don’t study enough. You don’t study enough. Average of 42 hours per week beyond your class is expected Average of 42 hours per week beyond your class is expected To obtain a C - the average grade To obtain a C - the average grade

30. Comment I have never met a student who could not learn organic chemistry. I have never met a student who could not learn organic chemistry. Some students might make 3 or more attempts to learn the material. Some students might make 3 or more attempts to learn the material. The number of attempts required is dependent upon you. The number of attempts required is dependent upon you. Fall, 200930

31. Why don’t students learn? Fear Fear Wrong attributes Wrong attributes Lack of confidence Lack of confidence Too much confidence Too much confidence Failure to follow through Failure to follow through Paralysis due to personal/family problems Paralysis due to personal/family problems Failure to imitate best practices Failure to imitate best practices Lack of balance of social and academic life Lack of balance of social and academic life Failure to appreciate delayed gratification. Failure to appreciate delayed gratification. Fall, 200931

32. Guide’s Role Fall, 200932 You Your Goals

33. Study Sessions Study sessions will be held Study sessions will be held Tuesday and Thursday Tuesday and Thursday 7 – 8 AM 7 – 8 AM They are not mandatory They are not mandatory The first one will be held next Tuesday. The first one will be held next Tuesday. The last one the first time I enter the room and no one is here. The last one the first time I enter the room and no one is here. Fall, 200933

34. Important Goals of Organic Chemistry Prepare you for MCAT, DAT, OAT, etc. Prepare you for MCAT, DAT, OAT, etc. Assist in your transition from a student to a scholar. Assist in your transition from a student to a scholar. This is done by This is done by –Mastery of content –Application of theoretical constructs –Developing skills to critique, analyze, research, discuss, write, and present. Fall, 200934

35. Fall, 200935 What is the minimum I need to do to get out of here? Depends, what grade do you want? Depends, what grade do you want? W, F, or D W, F, or D –Attend class irregularly –Study just before each test –Rely upon your memory C, B, or A C, B, or A –Never miss class –Read the chapter before and after class –Review lecture notes daily –Study 2 hours per day, 6 days per week –Make and use note cards –Do all assigned homework problems –See me for assistance early and often

36. Fall, 200936 Why Study Organic Chemistry? Required for Major Required for Major I will never need it. I will never need it. Required for Major Required for Major I might need it someday. I might need it someday. Elective Elective I will certainly never need it. I will certainly never need it. Best course on campus. Best course on campus. Best instructor on campus Best instructor on campus Only class available at this forsaken time Only class available at this forsaken time Need to lower my GPA. Need to lower my GPA.

37. Who studies Organic Chemistry? Chemistry Chemistry Biology Biology Pre-medicine Pre-medicine Pre-dentistry Pre-dentistry Pre-pharmacy Pre-pharmacy Animal Science Animal Science Pre-veterinarian Pre-veterinarian Nutrition Nutrition Other programs not offered at VSU also require organic chemistry. Other programs not offered at VSU also require organic chemistry. Fall, 200937

38. A Common Thread Sciences Sciences Scientists do science Scientists do science Scientists do NOT do sloppy work Scientists do NOT do sloppy work Sloppy scientists fulfill Darwin’s principles! Sloppy scientists fulfill Darwin’s principles! Fall, 200938

39. Fall, 200939 Some More Important Questions Is drop/add over? Is drop/add over? Are there any other instructors available? Are there any other instructors available? When is the last day to withdraw? When is the last day to withdraw? What is the minimum I need to pass? What is the minimum I need to pass? What is organic chemistry? What is organic chemistry? Before we start, let’s review some general chemistry concepts that are important for us because organic chemistry depends upon a fundamental understanding of general chemistry Before we start, let’s review some general chemistry concepts that are important for us because organic chemistry depends upon a fundamental understanding of general chemistry

40. Fall, 200940 Important Note If you decide to withdraw from the lecture If you decide to withdraw from the lecture at any point in the semester, at any point in the semester, You must withdraw from the laboratory! You must withdraw from the laboratory! Let’s review General Chemistry! Let’s review General Chemistry!

41. Fall, 200941 Review of General Chemistry To be here you met the pre-requisites. To be here you met the pre-requisites. You have taken General Chemistry I and II. You have taken General Chemistry I and II. You have learned the following You have learned the following The Periodic Table The Periodic Table Structure of the atom and electron configuration Structure of the atom and electron configuration Lewis dot structures and bonding Lewis dot structures and bonding Basic chemical nomenclature Basic chemical nomenclature Stoichiometry Stoichiometry Energy and chemical reactions Energy and chemical reactions Chemical equilibrium, acids, bases Chemical equilibrium, acids, bases Thermodynamics and basic kinetics Thermodynamics and basic kinetics Assumption for Organic Chemistry I Assumption for Organic Chemistry I You received an A in General Chemistry I and II. You received an A in General Chemistry I and II.

42. Fall, 200942 Review of General Chemistry Nucleus Nucleus Orbitals Orbitals Electronic Configuration Electronic Configuration Chemical Bonding Chemical Bonding Ionic and Covalent Ionic and Covalent Hybridization of Carbon’s Orbitals Hybridization of Carbon’s Orbitals sp 3, sp 2, and sp hybridization sp 3, sp 2, and sp hybridization Molecular Orbital Theory Molecular Orbital Theory Formation of C-C sigma and pi bonds Formation of C-C sigma and pi bonds

43. Fall, 200943 Review of General Chemistry Electronegativity Electronegativity F is the most electronegative atom F is the most electronegative atom Electronegativity decreases down group Electronegativity decreases down group Electronegativity decreases right to left Electronegativity decreases right to left Polar covalent bonding Polar covalent bonding Dipole moments Dipole moments Formal Charge Formal Charge

44. Fall, 200944 Review of General Chemistry Review Resonance Review Resonance Consider two structures Consider two structures Acetate ion and Benzene Acetate ion and Benzene

45. Fall, 200945 Acetate Ion Two line structures are possible Two line structures are possible C=O and C-O bonds C=O and C-O bonds However, both C-O bonds are 127pm However, both C-O bonds are 127pm C=O is 120pm and C-O is 135pm C=O is 120pm and C-O is 135pm

46. Fall, 200946 Benzene Two possible line structures Two possible line structures Neither is correct Neither is correct C-C bonds in benzene are all 139pm C-C bonds in benzene are all 139pm C-C bond is 154pm and C=C is 134pm C-C bond is 154pm and C=C is 134pm Problem encountered Problem encountered Drawing these molecules Drawing these molecules True structure can’t be drawn True structure can’t be drawn

47. Fall, 200947 Drawing these Structures We cannot draw the true structure We cannot draw the true structure Therefore, we invoke idea – Therefore, we invoke idea – resonance resonance Individual structures are resonance hybrids of true structure Individual structures are resonance hybrids of true structure We cannot draw the true structure We cannot draw the true structure

48. Fall, 200948 Resonance Structures

49. Fall, 200949 Resonance Guidelines Individual resonance forms are not real Individual resonance forms are not real Resonance forms differ only in placement of electrons (pi or non-bonding) Resonance forms differ only in placement of electrons (pi or non-bonding) Resonance forms do not have to be equivalent Resonance forms do not have to be equivalent Resonance forms obey valence rules Resonance forms obey valence rules Hybrid is more stable than resonance forms Hybrid is more stable than resonance forms

50. Fall, 200950 Review of Acids and Bases Two Definitions of Acids and Bases Two Definitions of Acids and Bases Bronsted-Lowry Bronsted-Lowry Lewis Lewis

51. Fall, 200951 Bronsted – Lowry Acid donates a proton Acid donates a proton Base accepts a proton Base accepts a proton Consider following reaction: Consider following reaction:

52. Fall, 200952 In dilute solution [HOH] = 55.5M, nearly constant [HOH] = 55.5M, nearly constant Therefore, define the acidity constant Therefore, define the acidity constant

53. Fall, 200953 Acid Strength Strong acids – equilibrium is to the right K a is large Weak acids – equilibrium is to the left Ka is small Range of values is 10 15 (strongest) to 10 -60 (weakest)

54. Fall, 200954 pKa Values pKa = -logKa pKa = -logKa Values range -7 (strongest) to 60 (weakest) Values range -7 (strongest) to 60 (weakest) As strength of acid increases As strength of acid increases Strength of base decreases Strength of base decreases HCl pka = -7 (a strong acid) HCl pka = -7 (a strong acid) Conjugate base: Cl - is very weak Conjugate base: Cl - is very weak H-CH 3 H-CH 3 pKa = 60 (a weak acid) Conjugate base CH 3 - is very strong

55. Fall, 200955 A Few pKa Values (learn this list as we will add to it) EtOH16 EtOH16 HOH15.7 HOH15.7 HCN9.3 HCN9.3 HOAc4.8 HOAc4.8 Phosphoric Acid2.2 Phosphoric Acid2.2 Nitric Acid-1.3 Nitric Acid-1.3 HCl-7 HCl-7

56. Fall, 200956 pKa Values Learn values given in Table 2.3 (p 52) Learn values given in Table 2.3 (p 52) Use these values to predict acid base reactions Use these values to predict acid base reactions Consider the following: Consider the following: Which is the stronger acid? pKa of HOAc = 4.76 pKa of HOH = 15.7 (conjugate acid of NaOH) HOAc = stronger acid than HOH, HO - = stronger base than AcO - Reaction proceeds to the right.

57. Fall, 200957 Lewis Acids and Bases Lewis Acids – accept an electron pair Lewis Acids – accept an electron pair Lewis Bases – donate an electron pair Lewis Bases – donate an electron pair The electron pair ends up shared by the acid-base as a covalent bond The electron pair ends up shared by the acid-base as a covalent bond

58. Fall, 200958 Lewis Acids The Lewis definition of acidity includes metal cations The Lewis definition of acidity includes metal cations such as Mg 2+ such as Mg 2+ Neutral Group 3A compounds Neutral Group 3A compounds such as BF 3 and AlCl 3 such as BF 3 and AlCl 3 Neutral transition-metal compounds Neutral transition-metal compounds such as TiCl 4, FeCl 3, ZnCl 2, and SnCl 4 such as TiCl 4, FeCl 3, ZnCl 2, and SnCl 4 The combination of a Lewis acid and a Lewis base can shown with a curved arrow from base to acid The combination of a Lewis acid and a Lewis base can shown with a curved arrow from base to acid

59. Fall, 200959 Lewis Bases Donate an electron pair Donate an electron pair Molecules must contain an electron pair Molecules must contain an electron pair

60. Fall, 200960 Lewis Acids and Bases H + is a Lewis acid H + is a Lewis acid Accepts electron pair from water Accepts electron pair from water Hydronium ion (H 3 O + ) Hydronium ion (H 3 O + ) Water is a Lewis base Water is a Lewis base Donates electron pair to the proton Donates electron pair to the proton

61. Fall, 200961 Illustration of Curved Arrows in Following Lewis Acid-Base Reactions

62. Fall, 200962 Review of General Chemistry Our review of general chemistry is done. Our review of general chemistry is done. We have also covered Chapters 1 and 2 in We have also covered Chapters 1 and 2 in Organic Chemistry: A Biological Approach by John McMurry Organic Chemistry: A Biological Approach by John McMurry Now, we can ask Now, we can ask What is organic chemistry? What is organic chemistry? Why am I studying this course? Why am I studying this course?

63. Fall, 200963 Organic Chemistry is the study of the chemistry of compounds that contain carbon. is the study of the chemistry of compounds that contain carbon. Carbon is a unique element in the Periodic Table in that Carbon is a unique element in the Periodic Table in that (1) it likes to bond to itself and (1) it likes to bond to itself and (2) The number of carbon atoms that can be bonded in a chain appear to be limitless. (2) The number of carbon atoms that can be bonded in a chain appear to be limitless.

64. Fall, 200964 Organic Chemistry and Biology Biological revolution Biological revolution Biotechnological advances Biotechnological advances –Unprecedented scale –Foundation is organic chemistry All organic molecules contain Carbon All organic molecules contain Carbon 99% of 26 million molecules contain C 99% of 26 million molecules contain C Possible because of Carbon’s electronic structure Possible because of Carbon’s electronic structure

65. Fall, 200965 Questions to consider in CHEM305 Why do organic molecules have certain properties? Why do organic molecules have certain properties? Why do certain reactions occur? Why do certain reactions occur? Why do other reactions not occur? Why do other reactions not occur? What drives these processes? What drives these processes? Can we predict the presence or absence of certain properties? Can we predict the presence or absence of certain properties? Can we make new materials with other desired properties? Can we make new materials with other desired properties?

66. Fall, 200966 Biological Organic Chemistry Know what and why something happened Know what and why something happened Molecular level Molecular level Understanding is based on foundation Understanding is based on foundation Bonding Bonding Bond polarity Bond polarity Acid base behavior Acid base behavior Hydrogen bonding Hydrogen bonding Organic chemistry depends upon a fundamental understanding of general chemistry Organic chemistry depends upon a fundamental understanding of general chemistry