chem 3372: organic chemistry summer ii 2017, m–f 3:30 …faculty.smu.edu/alippert/chapter...

Chem 3372: Organic Chemistry

Summer II 2017, M–F 3:30 pm–5:20 pm Fondren Sci Bldg 133

Instructor: Professor Alexander R. Lippert, PhD Office: 141 FOSC Email: [email protected] (please include “CHEM 3372” in the subject line) Telephone: 214-768-2482 Office hours: TBD TA: TBD TA Office Hours: TBD Website: http://faculty.smu.edu/alippert/CHEM3371.html Textbook: Organic Chemistry, 4th Edition, by Janice Gorzynski Smith Organic chemistry focuses on the composition, properties, and behavior of compounds that contain the element carbon, spanning from biological molecules to drugs to materials. This course is the second in a two-semester series to introduce students to the principles, concepts, and practice of organic chemistry. Learning Outcomes: Students will be able to identify and draw complex organic molecules. Students will be able to predict the reactivity of basic organic molecules. Students will be able to formulate basic synthetic schemes. Students will be able to solve basic organic structures from spectral data. Assignments and Grades: Homework 10% Exam I 20% Exam II 20% Exam III 20% Final 30% Connect Homework Assignments: Homework assignments will be found on the faculty website and the problems with a (*) will be graded for completion. Assignments should be completed and submitted online before 11:59 pm on the due date. Exams and Finals: Exams and finals will be given during class and will be cumulative. Office Hours: Office hours will be held after class and will involve extra practice problems as well as answering one-on-one questions.

Class Schedule: Thurs July 6 Chap 15 Mass Spec and IR

Fri July 7 Chap 13 Radical Reactions Mon July 10 Chap 14 NMR Tues July 11 Chap 16 Conjugation, Resonance,

and Dienes Wed July 12 Chap 17 Benzene and Aromatic

Compounds Thurs July 13 Exam 1 Fri July 14 Chap 18 Reactions of Aromatic

Compounds Mon July 17 Chap 18 Reactions of Aromatic

Compounds Tues July 18 Chap 19 Carboxylic Acids Wed July 19 Chap 20 Intro to Carbonyl Chemistry Thurs July 20 Chap 20 Intro to Organometallic

Chemistry Fri July 21 Chap 21 Aldehydes and Ketones Mon July 24 Exam II Tues July 25 Chap 21 Aldehydes and Ketones Wed July 26 Chap 22 Carboxylic Acid Derivatives Thurs July 27 Chap 23 Enols and Enolates Fri July 28 Chap 24 Carbonyl Condensation

Reactions Mon July 31 Exam III Tues August 1 Chap 25 Amines Wed August 2 Chap 26 Cross Coupling Reactions Thurs August 3 Chap 27 Pericyclic Reactions Fri August 4 Final *Schedule is tentative and subject to change at the instructor’s discretion.

Class Schedule: Thurs July 6 Chap 13 Mass Spec and IR Fri July 7 Chap 14 NMR Mon July 10 Chap 15 Radical Reactions Tues July 11 Chap 16 Conjugation, Resonance,

and Dienes Wed July 12 Chap 17 Benzene and Aromatic

Compounds Thurs July 13 Exam 1 Fri July 14 Chap 18 Reactions of Aromatic

Compounds Mon July 17 Chap 18 Reactions of Aromatic

Compounds Tues July 18 Chap 19 Carboxylic Acids Wed July 19 Chap 20 Intro to Carbonyl Chemistry Thurs July 20 Chap 20 Intro to Organometallic

Chemistry Fri July 21 Chap 21 Aldehydes and Ketones Mon July 24 Exam II Tues July 25 Chap 21 Aldehydes and Ketones Wed July 26 Chap 22 Carboxylic Acid Derivatives Thurs July 27 Chap 23 Enols and Enolates Fri July 28 Chap 24 Carbonyl Condensation

Reactions Mon July 31 Exam III Tues August 1 Chap 25 Amines Wed August 2 Chap 26 Cross Coupling Reactions Thurs August 3 Chap 27 Pericyclic Reactions Fri August 4 Final *Schedule is tentative and subject to change at the instructor’s discretion.

Disability Accommodations: Students needing academic accommodations for a disability must first be registered with Disability Accommodations & Success Strategies (DASS) to verify the disability and to establish eligibility for accommodations. Students may call 214-768-1470 or visit http://www.smu.edu/alec/dass.asp to begin the process. Once registered, students should then schedule an appointment with the professor to make appropriate arrangements. (University Policy No. 2.4.) Excused Medical Absences: Verification of medical illness and request for an excused absence from class will be handled in one of two ways. A physician or staff member from health/counseling and testing will provide either (1) a hand written note on a Health Center prescription form or 2) a signed letter written on Health Center stationery. Excused medical absences shall have specific dates of time periods indicated. Encounter Forms and Walk-Out Statements verify a student's visit to the Health Center BUT DO NOT INDICATE AN EXCUSED MEDICAL ABSENCE.

Religious Observance: Religiously observant students wishing to be absent on holidays that require missing class should notify their professors in writing at the beginning of the semester, and should discuss with them, in advance, acceptable ways of making up any work missed because of the absence. (University Policy No. 1.9.)

Excused Absences for University Extracurricular Activities: Students participating in an officially sanctioned, scheduled University extracurricular activity should be given the opportunity to make up class assignments or other graded assignments missed as a result of their participation. It is the responsibility of the student to make arrangements with the instructor prior to any missed scheduled examination or other missed assignment for making up the work. (University Undergraduate Catalogue)

Study Tips:

1. Review 1st semester2. Come to office hours (practice, practice)3. Make a list of reactions (refer during syntheses)

Introduction-In O-Chem II, we will really learn how to make molecules.

O

OO

NH2

NH

O

tamiflu(flu)

OOH

HO

OH O

OH

NH2

O

H H N

OH

tetracycline(antibacterial)

N

OOHO

HS

captopril(heart failure)


O

OO

NH2

NH

O

tamiflu(flu)

OOH

HO

OH O

OH

NH2

O

H H N

OH

tetracycline(antibacterial)

N

OOHO

HS

captopril(heart failure)

NN

O

NH

H

lysergic acid diethylamide

NH2H3CO

H3COOCH3

mescaline

HN

O

OMDMA


NN

O

NH

HNHO

O

NH

H

Chapter 22

N

NH

HO

Chapter 21

O

NH

Chapter 23-24

NH

Chapter 18 O

Cl

Chapters 13–14: SpectroscopyInteractions between light, energy, and matter allow us to "see" molecules.

• Mass spectroscopy – electron beams, electric field (Ch 13 pt 1)• IR Spectroscopy – infrared light (Ch 13, pt 2)• NMR Spectroscopy – radio waves and magnetic fields (Ch 14)

13.1 Mass SpectrometryA. General Features

• electron beam ionizes and fragments molecules• fragments separated by M/Z ratio• M+• is called the molecular ion or parent ion

13.1 Mass SpectrometryA. General Features • M+• (molecular ion) breaks into fragments (fragmentation)

• X-axis: mass-to-charge (m/z) ratio• Y-axis: relative abundance• tallest peak is called base peak (relative abundance = 100)• base peak is not always the molecular ion• M+1 peak due to 13C

(13CH4)+•


Example: Hexane

Which peak is the molecular ion?Which peak is the base peak?

A.

B.C.


Example: Hexane

Which peak is the molecular ion? m/z = 86Which peak is the base peak? m/z = 57

13.1 Mass SpectrometryB. Analyzing Unknowns by Molecular Ion

13.1 Mass SpectrometryB. Analyzing Unknowns by Molecular IonGeneral Guidelines:

• Divide molecular ion by 12 = max # Carbons (remainder = #H)• Replace12H for 1C• Replace 1O for CH4• Nitrogen: odd #N gives odd molecular ion, even #N gives even molecular ion• Try drawing the structure to see if it makes sense

Example: Propose possible molecular formulas for m/z = 86.

13.2 Alkyl Halides and the M + 2 Peak

Chlorine and Bromine have two stable isotopes (giving characteristic fingerprints!):• 35Cl and 37Cl in a 3:1 ratio• 79Br and 81Br in a 1:1 ratio

C3H735Cl m/z = 78 C3H737Cl m/z = 80

C3H779Br m/z = 122 C3H781Br m/z = 124

13.3 Fragmentation

• Electron beam removes 1 e– to form an unstable radical cation

• Bond cleavage forms more stable (substituted) cation

• Loss of CH3 (–15)

• Loss of CH2 (–14)

• only charged fragments show up on MS

A. General Features of Fragmentation

13.3 Fragmentation

Example 2,3-dimethyl pentane shows fragments at m/z =85 and 71. Propose structures for these fragments. (on board)

A. General Features of Fragmentation

13.3 Fragmentation ***B. Fragmentation Patterns of Some Common Functional Groups

Aldehydes/Ketones (acylium ion formation by a-cleavage):

Alcohols (a-cleavage):

Alcohols (dehydration):

13.4 Other Types of Mass SpectrometryA. High Resolution Mass Spectrometry (HRMS)

• Accurate to 4 decimal places• Many molecules have similar molecular weight, but can be differentiated with HRMS

13.4 Other Types of Mass SpectrometryC. Electrospray Ionization Mass Spectrometry (ESI-MS)

• ESI is very gentle ionization method• Useful for higher molecular weight molecules like peptides and proteins• Multiple ionization states (Z) often seen

13.4 MS Sample Problems (13.24a, 13.26a, 13.30a)

13.5 Electromagnetic Radiation

• Wavelength (l) – distance from peak to peak (m)• Frequency (n) – number of waves per time (Hz = s–1)• Speed of light (c) = 3.0 x 108 m s–1

• Planck's constant (h) = 6.63 x 10–34 J s• higher l = lower E• higher n = higher E

A. Light and Energy

c = lnE = hn = hc/l

13.5 Electromagnetic Radiation

• Wavelength (l) – distance from peak to peak (m)• Frequency (n) – number of waves per time (s–1)• Speed of light (c) = 3.0 x 108 ms–1

• Planck's constant (h) = 6.63 x 10–34 Js• higher l = lower E• higher n = higher E

B. Interaction of Light and Matter

c = lnE = hn = hc/l

13.6 Infrared Spectroscopy

• Infrared radiation: l = 2.5 – 25 µmn = 1.2 x 1014 – 1.2 x 1015 Hz (hard to report)Wavenumber (n) = 1/ l = 4000 – 400 cm–1 (easy to report)

• Energy increases as wavenumber increases

• Absorption of IR light causeschanges in bond vibrations

• Different bonds vibrate at different frequencies (wave numbers)

• IR spectroscopy can differentiatebonds and functional groups

A. Background

~

13.6 Infrared SpectroscopyB. Characteristics of IR Spectrum

• IR spectrometer scans through the IR spectrum and reports on light absorption • Energy increases as wavenumber increases• Each peak corresponds to a specific bond

• X-axis: wavenumber• Y-axis: Transmittance• Two main regions:Functional Group (> 1500 cm–1)Fingerprint (<1500 cm–1) OH

13.6 Infrared SpectroscopyB. Characteristics of IR Spectrum• Similar molecules may have similar Functional Group regions but unique Fingerprint regions

13.7 IR AbsorptionsA. Where Particular Bonds Absorb in the IR1. Bond strength: stronger bonds vibrate at higher energy and higher n2. Atom mass: bonds with lighter atoms vibrate at higher energy and higher n

~~

13.7 IR AbsorptionsA. Where Particular Bonds Absorb in the IR

~~

13.7B IR Absorptions in Hydrocarbons

• Csp3–H 3000–2850 cm–1

• Csp2–H 3150–3000 cm–1

• Csp3–H 3000–2850 cm–1

• 1650 cm–1C C

• Csp –H 3300 cm–1

• Csp3–H 3000–2850 cm–1

• 2250 cm–1C C

13.7C IR Absorptions in Oxygen Compounds• O–H 3600–3200 cm–1

• ~1700 cm–1

• precise value can differentiatespecific carbonyls

• no distinctive functional group peaks

O

O

OH

C O

13.7D IR Absorptions in Nitrogen Compounds

• N–H (2 peaks) 3200, 3400 cm–1

• 1660 cm–1

• 2250 cm–1

NH2

N

H2N

O

• N–H (2 peaks) 3300, 3400 cm–1

C O

C N

13.7E Examples OH

O

a.

b.

OH

O

c.

d.

13.7E Examples

N

a.

b.

c.

d.

OH N

13.7E Examplesa.

b.

c.

d.

OH

O

O

O

O

13.8 MS and IR to Determine an Unknown

chem 3372: organic chemistry summer ii 2017, m–f 3:30 …faculty.smu.edu/alippert/chapter...

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