Fall 2017 http://ww2.chemistry.gatech.edu/~collard/SpecID/fall2017.html https://t-square.gatech.edu/portal (for grades) CHEM 6371 – Spectroscopic Identification of Organic Compounds CHEM 4341 – Applied Spectroscopy Office Topic Reading (4e) M 21-Aug Introduction Intro-1 DC Tu-DC Introduction W 23-Aug Your intro organic Intro-2 DC Elemental analysis, sites of unsaturation 1:1-5+ intro text F 25-Aug textbook and Intro-3 DC Mass spectrometry 1:6;8.7+ intro text M 28-Aug Pavia Chap 1,3 Intro-4 DC Tu-DC Infrared spectroscopy 2:intro -7+ intro text W 30-Aug Intro-5 HW 1 DC 1 H NMR 3:1-9+ intro text F 1-Sep Intro-6 DC 1 H NMR 3:10-17+ intro text M 4-Sep LABOR DAY Tu-DC W 6-Sep Intro-7 DC 1 H NMR and 13 C NMR 3:19;4:14.2A+ intro text F 8-Sep Intro-8 HW 2 DC Problems Q3.1-12 M 11-Sep EXAM1 Tu-DC Fundamental principles, using basic information to solve structures W 13-Sep Mass Spectrometry MS-1 DC MS techniques F 15-Sep Pavia Chap 8 MS-2 DC Fragmentation, Hydrocarbons M 18-Sep MS-3 DC Tu-DC Alcohols, ethers and amines: α-cleavage W 20-Sep MS-4 HW 3 DC C=O compounds F 22-Sep MS-5 DC Halo compounds, reporting MS data M 25-Sep MS-6 HW 4 DC Problems W 27-Sep MS-7 DC Problems F 29-Sep EXAM 2 MS, plus use of basic principles of IR and NMR to solve structures M 2-Oct Infrared IR-1 LG M-LG CH, CC bonds 2:8-11 W 4-Oct Spectroscopy IR-2 LG OH, NH bonds 2:12;14F,15 F 6-Oct Pavia Chap 2 IR-3 HW 5 (MS) DC CO bonds 2:13 M 9-Oct FALL RECESS Tu-DC W 11-Oct IR-4 DC C=O and CN bonds, reporting IR data 2:14,16-21 F 13-Oct IR-5 HW 6 DC Problems Q2.1-11 M 16-Oct EXAM 3 Tu-DC IR, plus use of basic principles of IR and NMR to solve structures W 18-Oct 1 H and 13 C NMR NMR-1 LG NMR theory F 20-Oct Spectroscopy NMR-2 LG 1 H Chemical Shift 6:1-5 M 23-Oct Pavia Chap 4,5,6 NMR-3 LG M-LG 1 H Chemical Shift 6:6-10 W 25-Oct NMR-4 LG 1 H Multiplicity 5:1-6 F 27-Oct NMR-5 LG 1 H Multiplicity, reporting NMR data 5:7-11 M 30-Oct NMR-6 HW 7 LG M-LG 13 C Chemical shift, shift calculations 4:1-4,11-16 W 1-Nov NMR-7 LG Decoupling, NOE, etc 4:5-9; 6.11 F 3-Nov NMR-8 LG Edited spectra, APT, DEPT 4:10; 10.4-5 M 6-Nov NMR-9 LG M-LG Problems 9:intro-21 W 8-Nov NMR-10 HW 8 LG Problems Q9.22-43 F 10-Nov EXAM 4 NMR, and use of MS and IR to solve structures M 13-Nov 2D NMR Adv-1 LG M-LG 2D NMR Theory 10:1,6 W 15-Nov Pavia Chap 10 Adv-2 LG COSY 10:7 F 17-Nov Adv-3 LG NOESY 10.10 M 20-Nov Adv-4 HW 9 LG M-LG HETCOR, HSQC 10.8-9 W 22-Nov THANKSGIVING F 24 Nov BREAK M 27-Nov Adv-5 LG M-LG HMBC W 29-Nov Adv-6 HW 10 LG Problems Q10.1-11 F 1-Dec EXAM 5 Basic and Adv. NMR, MS and IR to solve structures M 4-Dec More problems Problems DC Tu-DC Problems W 8-Dec (8:00-10:50 a.m.) FINAL Comprehensive
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Fall 2017 http://ww2.chemistry.gatech.edu/~collard/SpecID/fall2017.html https://t-square.gatech.edu/portal (for grades)
Office Topic Reading (4e) M 21-Aug Introduction Intro-1 DC Tu-DC Introduction W 23-Aug Your intro organic Intro-2 DC Elemental analysis, sites of unsaturation 1:1-5+ intro text F 25-Aug textbook and Intro-3 DC Mass spectrometry 1:6;8.7+ intro text M 28-Aug Pavia Chap 1,3 Intro-4 DC Tu-DC Infrared spectroscopy 2:intro -7+ intro text W 30-Aug Intro-5 HW 1 DC 1H NMR 3:1-9+ intro text F 1-Sep Intro-6 DC 1H NMR 3:10-17+ intro text M 4-Sep LABOR DAY Tu-DC W 6-Sep Intro-7 DC 1H NMR and 13C NMR 3:19;4:14.2A+ intro text F 8-Sep Intro-8 HW 2 DC Problems Q3.1-12 M 11-Sep EXAM1 Tu-DC Fundamental principles, using basic information to solve structures W 13-Sep Mass Spectrometry MS-1 DC MS techniques F 15-Sep Pavia Chap 8 MS-2 DC Fragmentation, Hydrocarbons M 18-Sep MS-3 DC Tu-DC Alcohols, ethers and amines: α-cleavage W 20-Sep MS-4 HW 3 DC C=O compounds F 22-Sep MS-5 DC Halo compounds, reporting MS data M 25-Sep MS-6 HW 4 DC Problems W 27-Sep MS-7 DC Problems F 29-Sep EXAM 2 MS, plus use of basic principles of IR and NMR to solve structures M 2-Oct Infrared IR-1 LG M-LG CH, CC bonds 2:8-11 W 4-Oct Spectroscopy IR-2 LG OH, NH bonds 2:12;14F,15 F 6-Oct Pavia Chap 2 IR-3 HW 5 (MS) DC CO bonds 2:13 M 9-Oct FALL RECESS Tu-DC W 11-Oct IR-4 DC C=O and CN bonds, reporting IR data 2:14,16-21 F 13-Oct IR-5 HW 6 DC Problems Q2.1-11 M 16-Oct EXAM 3 Tu-DC IR, plus use of basic principles of IR and NMR to solve structures W 18-Oct 1H and 13C NMR NMR-1 LG NMR theory F 20-Oct Spectroscopy NMR-2 LG 1H Chemical Shift 6:1-5 M 23-Oct Pavia Chap 4,5,6 NMR-3 LG M-LG 1H Chemical Shift 6:6-10 W 25-Oct NMR-4 LG 1H Multiplicity 5:1-6 F 27-Oct NMR-5 LG 1H Multiplicity, reporting NMR data 5:7-11 M 30-Oct NMR-6 HW 7 LG M-LG 13C Chemical shift, shift calculations 4:1-4,11-16 W 1-Nov NMR-7 LG Decoupling, NOE, etc 4:5-9; 6.11 F 3-Nov NMR-8 LG Edited spectra, APT, DEPT 4:10; 10.4-5 M 6-Nov NMR-9 LG M-LG Problems 9:intro-21 W 8-Nov NMR-10 HW 8 LG Problems Q9.22-43 F 10-Nov EXAM 4 NMR, and use of MS and IR to solve structures M 13-Nov 2D NMR Adv-1 LG M-LG 2D NMR Theory 10:1,6 W 15-Nov Pavia Chap 10 Adv-2 LG COSY 10:7 F 17-Nov Adv-3 LG NOESY 10.10 M 20-Nov Adv-4 HW 9 LG M-LG HETCOR, HSQC 10.8-9 W 22-Nov THANKSGIVING F 24 Nov BREAK M 27-Nov Adv-5 LG M-LG HMBC W 29-Nov Adv-6 HW 10 LG Problems Q10.1-11 F 1-Dec EXAM 5 Basic and Adv. NMR, MS and IR to solve structures
M 4-Dec More problems Problems DC Tu-DC Problems W 8-Dec (8:00-10:50 a.m.) FINAL Comprehensive
INSTRUCTORS David M. Collard Leslie Gelbaum [email protected][email protected] Tuesday 1:00-2:00 p.m. Monday 3:00 - 4:00 p.m. MoS&E 2100J MS&E 113 Office hours are only for weeks in which the particular instructor is teaching (see schedule); or by appointment Throughout the semester, Ashley Johns ([email protected]) and Bronson Cox ([email protected]) may present solutions to problems in class. They may be consulted regarding these approaches. LECTURES Come prepared to ask and answer questions! MWF, 11:15-12:05 College of Computing (CoC) 17 WORK PROBLEMS Work as many problems as possible, from the notes, from the book, from other sources. REQUIRED TEXTBOOK “Introduction to Spectroscopy” This text is currently in its fifth edition. You may choose to buy a new copy or a used copy, or a used copy of the fourth edition. The syllabus (above) indicates section numbers in the 4e. 4e, Donald L. Pavia, Gary M. Lampman, George S. Kriz, and James A. Vyvyan; Brooks Cole; ISBN-10 / ASIN: 0495114782; ISBN-13 / EAN: 9780495114789. Note: Section numbers and problems in older and international editions vary from those in the 4th edition (U.S.) GRADES Graded Assignments
Topic Exam 1 Fundamental principles and using basic information to solve structures 100 points† Exam 2 IR, plus use basic principles of MS and NMR to solve structures 100 points† Exam 3 MS, plus use of basic principles of IR and NMR to solve structures 100 points† Exam 4 NMR, plus use of MS and IR to solve structures 100 points† Exam 5 Basic and Advanced NMR techn., plus use of MS and IR to solve structures 100 points† Homework Ten HW assignments (score normalized to 100 points) 100 points Final Wed Dec 14 at 8:00 am-10:50 am: Comprehensive 200 points
The lowest score of the five mid-term exams (†) will be dropped. If you miss an exam that score (0) will be dropped. The course grade will be determined based on your score out of 700 points. Typical Grade Cut-offs
A: 85%+ B: 70-84.99 C: 60-69.99 D: 50-59.99
RETURNED WORK AND REGRADES All graded assignments will be returned as soon as possible, usually within a week. If you want any work regraded you must make a written request and return the assignment within one week. Work will not be regraded after this deadline. LECTURE ATTENDANCE It is strongly recommended that you attend all lectures. MATERIAL COVERED, KEEPING UP, WORKING PROBLEMS, STUDENT RESPONSIBILITIES You are responsible for all material presented in lectures and in assigned readings. You are also responsible for announcements made in class or by email. You must check your gatech.edu email account on a regular basis. Note: there are potential problems associated with automatic forwarding of messages from your gatech mail to other email addresses; check your gatech account even if you have it set up to forward email elsewhere. By the end of each section you should have completed all reading associated with that section, and worked all of the end-of-chapter problems and any additional problems which have been distributed. These questions should form the basis for discussion with your peers, and serve as a guide for the types of questions to appear on examinations (some of these questions might even appear on the exams!) Do not submit answers to these problems, they will not be graded. EXAMS: SCHEDULE, MAKE-UPS AND DROPS You must take the exam at the assigned time. All exams are closed to textbooks, class-notes and electronic devices (unless otherwise stated prior to the exam). Tables of NMR, IR, MS data, along with a periodic table, will be provided. The only valid reasons for missing an exam are illness and official GA Tech business. Make-up exams can only be given if advance notification is given or upon presentation of a doctor’s note. All make-up exams must be administered before the exams are returned to the class (typically before the next class). Exams not made-up by this time for any reason will receive a score of zero and will be the drop grade for the class (i.e., it will be the lowest score). WORK PROBLEMS Work as many problems as possible, from the notes, from the book, from other sources. WORKING IN GROUPS Most learning takes place outside of the classroom. Although lectures should provide a framework for learning and put things in perspective, working through the textbook and solving the problems is when you will come to terms with the material. We encourage you to work together on these reading and problem assignments. For most students, it is actually unwise to try to work alone. Although you might study in groups, remember that you are ultimately responsible for your learning. Everybody can benefit from team work. If you are struggling with the material you stand to learn a lot; if you are a “spectroscopy wizard” you also stand to learn from the challenge of presenting your understanding to others - you will learn through teaching. Office hours are available for individual instruction. No new information will be introduced during office hours. Come prepared to ask and answer problems.
COMPETITION AND GRADING Formal education often puts students in competition with each other for good grades. We do not believe that competition for grades, and the exclusion of everything else, is the most effective way to foster student development. Although grades will be assigned based on a numerical score, which judges attainment on exams/homework, we hope that the course is structured such that if you show a desire to learn, put the effort in, and have the intellectual ability, you can get the grade you want. CANCELLATION OF CLASSES If class is cancelled by Georgia Institute of Technology owing to campus closing, the entire schedule for the course will be delayed by one lecture. This will move all exams and the homework due dates back by one lecture. TIME COMMITMENTS We all have extensive demands on our time. For each hour of lecture you should aim to put in at least another two hours of your own time. You will need to spend more time preparing for exams. Some students will require more, some less. SOME STUDY TIPS Work Problems. Understand and Rationalize. Read the text, prepare your own summaries. Study in groups. Keep up to date! Ask Questions!! Work more problems. STUDENT CLASS ACCOMMODATIONS Students with disabilities who require reasonable accommodations to fully participate in course activities or meet course requirements are encouraged to register with ODS-Office of Disability Services at (404)894-2564 or www. http://disabilityservices.gatech.edu Contact the instructors within the first two weeks if you expect to take exams with ODS. Please send reminders one week before each exam. GEORGIA TECH ACADEMIC HONOR CODE Please visit www.honor.gatech.edu For Graded Homework Assignments: You may work with others in developing approaches to solve problems, but submitted work must be in your own handwriting. For Tests: Cheating from another person's exam and use of unauthorized materials are direct violations of the GT Academic Honor Code, and will be dealt with accordingly. For any questions involving these policies, please discuss them with the instructors or consult www.honor.gatech.edu.
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Introduction to Spectroscopy, 4eDonald L. Pavia, Gary M. Lampman, George S. Kriz,
and James A. VyvyanBrooks ColeISBN-10 / ASIN: 0495114782 ISBN-13 / EAN: 9780495114789
The expensive 5th edition
COURSE OUTLINE
17 Aug - 04 Sept Introduction Your undergraduate textbook and P(4,5) Chap 1,3
04 Sept EXAM 1 - Fundamental principles and using basic information to solve
structures
9 - 21 Sept Infrared Spectroscopy P(4,5) Chap 2
21 Sept EXAM 2 - IR, plus use of basic principles of IR and NMR to solve structures
23 Sept -07 Oct Mass Spectrometry P(4) Chap 8; P(5) Chap 3,4
07 - Oct EXAM 3 – MS, plus basic principles of IR and NMR to solve structures
14 Oct - 06 Nov Fundamentals of 1H and 13C NMR Spectrometry P(4) Chap 3-6;P(5) 5-8
06 Nov EXAM 4 NMR, plus use of MS and IR to solve structures
09 Nov - 23 Nov 2D, Advanced and multinuclear NMR P(4) Chap 10; P(5) Chap 9
23 Nov EXAM 5 - Basic and Advanced NMR techn., plus use of MS and IR to solve structures
30 Nov - 04 Dec More problems
W 09 Dec (8:00 – 10:50) FINAL - Comprehensive
2
GRADING
Exam 1 100
Exam 2 100
Exam 3 100 drop lowest score from E1-5
Exam 4 100
Exam 5 100
Homework 100
Final 200
Course grade out of 700 points
AN APPROACH TO DETERMINING
ORGANIC STRUCTURES
Combustion analysis Empirical formula
Mass spectrum Molecular weight
Molecular formula
Sites of unsaturation
Infrared spectrum Functional groups1H NMR13C NMR
MS isotope patternMS exact mass
(pi bonds, rings)
Structural featuresfragments, connectivity
3
REQUIREMENTS FOR PROOF OF STRUCTURE
AND PURITY IN YOUR RESEARCH
New Compounds
IR: assign important peaks1H NMR: assign all peaks13C NMR: assign all peaks, account
for all carbon atoms
Advanced NMR techniques as
necessary
m.p. (range) or b.p. (range?)
Elemental analysis
(combustion analysis 0.4%)
or
High resolution mass spectrum and
chromatographic proof of purity
Previously Reported
Compounds
At a minimum: 1H NMR
m.p range
J. Org. Chem. guidelineshttp://pubs.acs.org/paragonplus/submission/joceah/joceah_authguide.pdf
EMPIRICAL FORMULAS, MOLECULAR
FORMULAS, SITES OF UNSATURATION &
COMBUSTION ANALYSIS
4
MOLECULAR FORMULAS
Simply considering common valancies (C 4; H and Hal 1, O and S 2, N 3), acylic alkanes (linear or branched) have the formula CnH2n+2
Alkenes and cycloalkanes have the formula CnH2n
For each ring or pi bond in a molecule there are two fewer hydrogen atoms than expected for a non-cyclic alkane, so:
Number of pi bonds or rings = (2#C + 2 – #H) / 2
“sites of unsaturation”, “index of hydrogen deficiency” (IHD) or “sum of double bonds and rings” (SODAR)
The same equation is true in the presence of oxygen or sulfur atoms:
For C,H,O,S: SODAR = (2#C + 2 – #H) / 2
Each halogen atom present replaces a hydrogen atom:
SODAR = (2#C + 2 – (#H+#Hal) / 2
5
Each nitrogen atom requires addition of one hydrogen
For C,H,O,N,S, Hal:
Number of pi bonds or rings = (2#C + 2– #H – #Hal + #N) / 2
Alternative formula for SODAR= C-(#H+#Hal)/2+#N/2+1
Problems - How many rings or pi bonds are there in each of the following
compounds?
C6H6
C6H7BrO
C10H22N2
C10H13NO2
C21H35ClS2
6
Some consequences of valency
1. A hydrocarbon, or CHO-containing molecule, will have an even number of
hydrogen atoms. With n carbon atoms there cannot be more than 2n+2
hydrogen atoms.
2. A molecular formula cannot have an odd number of hydrogen atoms unless
there is an odd total number of halogen and nitrogen atoms [“the nitrogen
rule”].
Differentiating pi bonds and rings
C=C and C≡C bonds hydrogenated to C–C
C=N and N=O also subject to hydrogenation
Benzene rings and C=O bonds do not undergo hydrogenation under these conditions.
Compound A, C7H14N2O3, undergoes hydrogenation to give a product with the formula C7H18N2O3. How many rings are there in compound A? How many bonds?
7
COMBUSTION ANALYSIS
CxHyOz + O2 xCO2 + (y/2)H2O
Measure mass of CO2 and H2O formed from a known mass of
compound; data cited as mass% of each element present.
Generally do not measure mass %O.
e.g., C H O
Mass% 54.51 9.09
Mole Ratio
=
=
Empirical formula Molecular Formula
could be…
8
Elemental analyses provided ±0.4 mass%. A combustion analysis (±0.4
mass%) might represent more than one possible empirical formula. Be
careful when rounding.
e.g., C, 91.51% H, 8.44%
C:H ratio 1.000: 1.111
If assume emprical formula then mass % would be
C1H1 C, 92.26 H, 7.74
C10H11 C, 91.55 H, 8.45
C9H10 C, 91.47 H, 8.53
This becomes a significant problem for larger molecules
e.g, C, 79.21 H, 10.65 could be
C30H49NO2 C, 79.07 H, 10.84 (N, 3.07; m = 455.7)
C30H47NO2 C, 79.42 H, 10.44 (N, 3.09 ; m = 453.7)
C29H47NO2 C, 78.86 H, 10.73 (N, 3.17 ; m = 441.7)
C30H47N3 C, 79.58 H, 10.82 (N, 9.60 ; m = 449.7)
C30H48N2O C, 79.59 H, 10.69 (N, 6.19 ; m = 452.7)
For an accurate determination of empirical formula from combustion analysis- 2-5 mg for C,H,N- Sample must be pure, dry- Sample must fully combust
9
TB-III-32ACHEM, Georgia Tech
901 State St.
Atlanta, GA 30306-0400
T. Brooking 9-8-09
X
C,H
C,H
X
B. Moore
1966-06
C 71.23%
H 9.35%
9-10-09 9-11-09
C 68.09%
H 8.64%
N 6.59%
Cl 16.57%
Problems - With the aid of a calculator:
(i) Calculate the elemental composition of:
(a) C21H25NO5
(b) C17H20BrNO4
Use atomic masses to 3 decimal places (C, 12.011, ….)
(ii) Calculate the empirical formula of a compounds that give the following
analyses:
(a) (b)
Formula %mass calculators
fluorine.ch.man.ac.uk/research/analyse.php
www.calctool.org/CALC/chem/molecular/elemental
%mass formula calculators
http://www.chemicalaid.com/tools/empirical.php
[NOTE: be careful with syntax; only gives one possible formula!]