Embed Size (px)
Citation preview
CH352: Chemistry Major Lab II
Orientation MeetingMarch 8 and 10, 2018
Prof. Sunkyu Han
Overview of CH352: Chemistry Major Lab II, a.k.a Organic Chemistry Lab
softwares
journals searches
science ethics
paper manuscripts
lab notebook
term papers
results PPTsenior coworker
TA
safety
Laboratory Course
Research Laboratory
Harran admitted no wrongdoing in what is thought to be the first criminal case arising in an academic lab accident. The charges will be dropped if he successfully fulfills the terms of the agreement. –June 2014-
Course Description
This organic chemistry laboratory course is intended to provide students majoring inchemistry with fundamental and essential experimental skills and concepts inorganic chemistry.
Understanding the mechanism of the reaction. Drawing organic structures using a computer. Searching organic chemistry literatures. Writing a scientific report.
Recognizing potential safety hazards. Conducting experiments safely and
efficiently. Prelab Report
Result PPT
Midterm &Final papers
Safety Rule
Introduction to the Fume Hood
Introduction to the Fume Hood
1. Wear approved eye protection at all times while in the laboratory.
2. Wear shoes at all times. No open toe shoes are allowed in the lab.
3. Eating, drinking, and smoking are strictly prohibited in the laboratory at all times
4. Know where to find and how to use all safety and first-aid equipment.
5. Consider all chemicals to be hazardous unless your are instructed otherwise. Dispose of chemicals as directed by your TA.
6. If chemical come into contact with your skin or eyes, wash immediately with copious amounts of water and then consult your laboratory instructor.
7. Never taste anything. Never directly smell the source of any vapor or gas.
8. Perform in the fume exhaust hood any reactions involving skin-irritating or dangerous chemicals, or unpleasant odors.
9. Never point a test tube that you are heating at yourself or your neighbor-it may erupt like a geyser.
10. Do not perform an unauthorized experiments.
Laboratory Safety
11. Clean up all broken glassware immediately.
12. Always pour acids to water, not water into acid, because the heat of solution will cause the water to boil and the acid to spatter.
13. Avoid rubbing your eyes unless you know that your hands are clean.
14. NOTIFY THE INSTRUCTOR IMMEDIATELY IN CASE OF AN ACCIDENT.
15. Many common reagents-for example, alcohols, acetone, and especially ether-are highly flammable. Do not use them anywhere near open flame.
16.Observe all special precautions mentioned in experiments.
17. Learn the location and operation of fire-protection devices.
18. Whenever possible, use hot plates in place of Bunsen burners.
Laboratory Safety
http://msds.ohsah.bc.ca/
MSDS (Material Safety Data Sheets)
OHSAH MSDS Database
Unique site focused on healthcare agencies such as hospitals and doctor's offices. All sheets are less than 3 years old and are WHMIS compliant PDF files. Handy popups in results with additional info. Search by product and/or manufacturer. Site has a handy MSDS request form for items not currently in the database (for those within the BC healthcare system only).
Sigma, Aldrich, Fluka, Supelco, RdH-Lab
Search for the product and then click on the SDS link to display GHS-compliant sheet in PDF format. Versions are available in 50 languages.
http://www.sigmaaldrich.com/korea.html
Category 1 is always the greatest level of hazard (that is, it is the most hazardous within that class). If Category 1 is further divided, Category 1A within the same hazard class is a greater hazard than category 1B.
Category 2 within the same hazard class is more hazardous than category 3, and so on.
OHSAH MSDS Database
MSDS (Material Safety Data Sheets)
http://www.sigmaaldrich.com/korea.html
Course Prerequisites
Organic Chemistry I (CH221) and II (CH223)
Class Details
Wed (Class A) 13:00-19:00.Fri (Class B) 13:00-19:00.
Schedule
Venue (Class A, Wednesday, Goong-ri Laboratory Building, #502)
화학과 20160047 권성연
화학과 20160108 김서진
화학과 20160176 김창하
화학과 20160257 박인영
화학과 20160557 임현재
화학과 20160571 전지원
화학과 20160699 허성
화학과 20160783 주형건
화학과 20160862 Meredov, Myrat
화학과 20170371 안영균
화학과 20170566 전성민
화학과 20170728 허성록
Class Details
Venue (Class B, Friday, Goong-ri Laboratory Building, #502)
Venue (Class B, Friday, Goong-ri Laboratory Building, #506)
화학과 20130638 진승욱화학과 20130816 AMANZHOLOV, AZ화학과 20140023 구본승화학과 20150205 김준하
생명화학공학과 20150311 박상빈화학과 20150376 배재윤화학과 20160007 강보라화학과 20160116 김성주화학과 20160149 김재훈화학과 20160162 김준형화학과 20160168 김지후화학과 20160202 김효수화학과 20160210 노유진화학과 20160222 문민준화학과 20160236 박도훈화학과 20160311 손미나
화학과 20160356 안지송화학과 20160431 이경목화학과 20160483 이아진화학과 20160531 이채우화학과 20160599 정재우화학과 20160616 정현태화학과 20160619 조기영화학과 20160679 최훈철
화학과 20160861 Mametov, Dooronbek
신소재공학과 20170050 권형신화학과 20170079 김도영
전기및전자공학부 20170114 김선규화학과 20170175 김진우화학과 20170380 양수정화학과 20170512 이중원
울산과학기술원 20186130 윤여정
Introduction to the TA Team
Class A (Wednesday, #502)
Inwon KimSungwoo Hong Research GroupMy research is development of new photoredox catalyst and new reaction method via photocatalysis.
Yonghoon MoonSungwoo Hong Research GroupMy Goal is developing reaction methods which are more efficient and have milder condition. Now I'm studing visible-light-photoredox chemistry which use visible light as fuel of reactions.
I. Kim, M. Min, D. Kang, K. Kim, S. Hong* Org. Lett. 2017, 19, 1394.
NOEt
R
H
H
1 mol%
N O
PO
PhPh
MeO
N
PROR
RH NR2
O
NR
O
NR2PO
RR
H
C4 selectivephosphonation
C2 selectivecarbamoylation
QuinolinonePhotocatalyst
up to > 50:1(para : ortho)
up to 22:1(ortho : para)
“안전한 전공 실험이 되도록 노력하겠습니다.”
Moon, Y.; Jang, E.; Choi, S.; Hong, S. Org. Lett. 2018, 20, 240.Moon, Y.; Moon, Y.; Choi, H.; Hong, S. Green Chem. 2017, 19, 1005.
“Safty First! & Chem is try!”
ONR
NH
OR
R
OHNR
PC
(E)or
quinolinones or
phenanthridinones
blue LED
Introduction to the TA Team
Class A (Friday, #502 )
Youseob LeeHyunwoo Kim research groupResearch interest: Chemoselective conversion of epoxy amine using aluminum complex.
HN
OCO2 N
OO
OHHN
OO
O
O
N
OOAl
CO2
RR
R
Al complex
Hyeonggeun LimSunkyu Han research groupResearch interest: Total synthesis of complex iboga alkaloids
6 differenct natural products
Manuscript under preparation
Introduction to the TA Team
Class B (Friday, #506 )
Taeil ShinHyunwoo Kim research groupResearch interest: Ligand design and synthesis for Rh(I)-catalyzed Hydroformylation, Organic synthesis using nanoparticles
Wonkoo YoonInsung Choi research groupResearch interest: Cell encapsulation and surface reaction discovery
T. Shin, Y. Jung, K. Kim, H. Byun, S. Cho*, H. Kim*, and H. Song*; ChemCommun. 2017,53, 384
“한 학기동안 유익한 시간이 될 수 있도록 노력하겠습니다”
Modulation of Heterotypic and Homotypic Cell-Cell Interactions via Zwitterionic Lipid Masks. Youn, W. et al. Adv. Healthcare Mater. 2017, 6(15), 1700063.Cytoprotective Encapsulation of Individual Jurkat T Cells within Durable TiO2 Shells for T Cell Therapy. Youn, W. et al. Angew. Chem. Int. Ed. 2017, 56(36), 10702-10706.
“앞으로한학기동안안전하게, 재미있게실험하고부담갖지말고조교들과도잘지냈으면좋겠습니다.”
Head TA
Youseob LeeHyunwoo Kim Laboratory
Chief TA: Youseob Lee ([email protected]):All questions and claims will be accepted ONLY bythe Head TA
Grading Policy
25%: Pre-lab reports (hand-writing) 30%: Experiments and Results (Experiments
and Results PPT files) 20%: Mid-term paper 25%: Final paper
Prelab Report
Download the lab manual from the website. Read the manual and answer thepre-lab questions.
Refer to references for answers to the pre-lab reports. Hand-writing only (typing is not acceptable). Use your pre-lab report during the lab and SUBMIT to your TA when you leave
the lab. Your TA will inspect the cleanness of your hood, bench, and glasswares. Only
after the approval of your TA, your pre-lab report will be accepted. Pre-labreports that are not properly submitted won’t be graded and will not get credit.
General Information about Prelab Report
Grading Policy
A: >80% reasonable answersB: >60% reasonable answersC: >40% reasonable answersD: <40% reasonable answers
Feedback
Feedback of the letter grade will be given within a week by the TA.However, prelab note won’t be returned.
Nicknames -> Email or posting of the letter grades -> In class consulting
Experiments and Results PPT Files
Follow the instructions of the manual.
Adhere to the safety rules.
During the course of experiments, take notes of experimental set up, observations,
data etc.
You may take photo of experimental set ups and result.
After finishing the labwork, generate a PPT file (maximum 5 pages) that contains
the experimental data.
Submission of a text light, scheme (Chemdraw, see below on how to install it) and
photo heavy PPT file is encouraged. That will make your life easier.
Submit your ppt file using turnitin before the next lab starts. In case of “Converting
Aniline to Brominated Acetanilide: A Multistep Synthesis” experiment turn it in by
6/8 10 pm.
Purpose of the Results PPT file
Emulation of the actual lab note used in the organic laboratory
Contents of Results PPT file
1. Reaction (use Chemdraw).
Starting materialreagent
conditionsproducts (or results)
%yield
2. SM and reagents details.
reagents source mmol equiv. MW M (mg) V (µL)
Source: for commercially available starting material: vendor (제조 회
사), compound purity (ex 99%), density, etc..
Contents of Results PPT file
3. Detailed experimental procedure
In a chronological order, with specific time written.
Make sure to delineate the order of the addition of each reagents.
Mark reaction temperature, color changes….
Include the time TLC checking was conducted. Also, include the TLC
eluent conditions..
Work-up procedure.
Crude yield.
Contents of Results PPT file
4. Purification and isolation of products
- For Flash column chromatography
Diameter of the column, height of the silica packing..
Actual eluent system. .
Collected fractions.
Isolation yield.
NMR taken?
Product structure
Contents of Results PPT file
4. Purification and isolation of products
- Recrystallization (distillation) 자세한 조건 (사용한 용매 양, 온도 등 자세
한 procedure)을 적음
Isolation yields.
Products structure.
NMR taken?.
5. TLC copy:Take pictures of key TLC plates generated during the experiment. (TAs:make sure to give credits to students who included appropriate TLC platespicture in the results PPT file.
Contents of Results PPT file
4. Spectral Analysis
5. Post laboratory discussionKeep it concise.Text light, chemical structure heavy discussion.
NMR, etc.
Bench-Top NMR Spectroscopy
Follow TA’s instruction.
Exp4. Solid-Solid reaction of reductive amination
Molecular name
Molar weight [g/mol]
n [mmol]
mass [g]
density [g/ml]
volume [ml]
equivalent [eq]
o-Vanilin
0.76
152.15
5.0
-
-
1
OCH3
OH
O
H
H3C
NH2
OCH3
OH
N
CH3
OH
O
O
O ON
CH3OHOCH3
O
+ rt NaBH4
Ethanol, rtH2O N
H
CH3OHOCH3
+ +
p-Toluidine
0.535
107.16
5.0
-
-
1
Imine
1.20/1.21
241.29
5.0/5.0
-
-
1.0/1
Yield : 100%
Sodiumborohydride
0.1
37.83
2.6
-
-
0.53
Ethanol
-
46.07
-
-
15
(0.33M)
Amine
-/1.22
243.30
-/5.0
-
-
-/1.0
Acetic acid
2.10
60.05
35.0
1.05
2
7.0
Acetic anhydride
2.16
102.09
21.2
1.08
2
4.2
Product
1.36/1.43
285.34
5.0/5.0
-
-
0.95/1
Yield : 95%
80oC
Bright OrangePale yellow White Yellow White
Meting point [oC] 40-42 41-46
1:26pm reaction preparation1:32pm reaction start
- color : bright orange1:40pm add 10ml ethanol
- slightly dissolved1:47pm add sodium borohydride
- bubble(H2)- color : clear orange- all dissolved
2:00pm add 2ml acetic acid2:04pm add 2ml acetic anhydride2:06pm heating2:24pm add 75ml water
- white solid precipitation2:35pm ice bath2:40pm vacuum filter
- white solid3:00pm NMR sampling
Exp4. Solid-Solid reaction of reductive amination1:26pm reaction preparation
p-Toluidine
o-Vanilin
1:32pm reaction start
OCH3
OH
O
H
H3C
NH2
Pale yellow
White
OCH3
OH
N
CH3
Imine
40-42oC
41-46oC
Low melting point => Impurity => Lowering of melting point => Melting, direct reaction- Ecofriendly, no solvent
- Fast reaction
Bright orange
1:40pm add 10ml ethanol
Slightly dissolved
1:47pm add sodium borohydride (reductive amination)
H2 bubble clear orange solution All reactants are dissolved
NH
CH3OHOCH3
Exp4. Solid-Solid reaction of reductive amination
2:06pm heating (15min)2:00pm add 2ml acetic acid+ add 2ml acetic anhydride
2:24pm add 75ml water 2:35pm ice bath 2:40pm vacuum filter
80oC
NH
CH3OHOCH3
O
O O
O
O O
N
CH3OHOCH3
ONH
CH3OHOCH3
Amide formation
More clear solution
Clear solution
Strongly stirring White precipitation Crystallization
Solubility
Ethanol >> Water
N
CH3OHOCH3
O
Washing by waterAir dry
White solid1.36g (Yield : 95%)
Bench Top NMR (CDCl3)
High resolution NMR (CDCl3)
Exp4. Solid-Solid reaction of reductive amination
Reference1H-NMR (300MHz, CDCl3, δ): 1.85 (s, 3H), 2.37 (s, 3H), 3.88 (s, 3H), 4.76 (s, 2H), 6.33 (dd,1H, J=7.5, 1.8 Hz), 6.63 (t, 1H, J=8.1Hz), 6.81 (dd, 1H, J=7.8, 1.8), 6.88 (d, 2H, J=8.7Hz), 7.15(d, 2H, J=7.8Hz).Journal of Chemical Education 2006, 83, 6, 929-930
CDCl3
1(3H)2(3H)3(3H)
4(2H)
a b
N
CH3OHOCH3
O1(3H)
2(3H)3(3H) -OH peak broad
4(2H)a(2H)
b(2H)c(1H)
d(1H)
e(1H)
d ec
-OH peak broad
Post-Laboratory Question
OCH3
OH
N
CH3
OCH3
OH
H
O
H2N
CH3+
OCH3
OH
NH2O
H
CH3
OCH3
OH
NHHO
H
CH3
H2O
NaBR
HR
R
+
OCH3
OH
N
CH3BR
R RNa
+
A HO
CH3
OH
NH
CH3
O
O O
+
HN
CH3OHO
H3C
O
O
O
N
CH3OHO
H3C
O
BH
H H
O
O+ H
(excess)
BO
OO
HO
O
O
+ 3H2
Exp4. Solid-Solid reaction of reductive amination
<Mechanism>
- role of acetic acid
Grading Policy
A: >80% of relevant data included
B: >60% of relevant data included
C: >40% of relevant data included
D: <40% of relevant data included
Evaluation of Results PPT file
Feedback
Feedback with the letter grade will be given within a week by the TA.
Feedback will be given via the Turnitin system.
Submitting Results PPT file: Use turnitin system
Class ID Password
Wed 17599961
qwer1234Fri #502 (A) 17600131
Fri #506 (B) 17600093
Chemistry Journals
https://apps.webofknowledge.com/WOS_GeneralSearch_input.do?product=WOS&search_mode=GeneralSearch&SID=4Bs5gAdAzm3FiNtvp1d&preferencesSaved=
Web of Science
Chemistry Journals
https://apps.webofknowledge.com/WOS_GeneralSearch_input.do?product=WOS&search_mode=GeneralSearch&SID=4Bs5gAdAzm3FiNtvp1d&preferencesSaved=
Web of Science
From my personal perspective (Publishing a communication):
1. Science
2. Nature
3. Nature Chemistry
4. Journal of the American Chemical Society (JACS)
5. Angewandte Chemie International Edition (ACIE)
6. Chemical Science
7. Organic Letters
8. Chemical Commumications
9. Journal of Organic Chemistry
10. Organic Chemistry Frontiers
11. Asian Journal of Organic Chemistry
Searching the Chemistry Journals
Task: Search the following paper:
An Accelerated Intermolecular Rauhut–Currier Reaction Enables the Total Synthesis of (−)-Flueggenine C
JACS 2017, 139, 6302.
Journal nameYear published
Volume numberPage number
Introduction to Scifinder
What is ‘SciFinder’ ?
SciFinder, produced by Chemical Abstracts Service (CAS), is the most comprehensive database for the chemical literature, indexing journal articles and patent records (and other document types), as well as chemical substances and reactions. You can search by topic, author, and substances by name or CAS Registry Number, OR use the editor to draw chemical structures, substructures, or reactions.It's a core research tool for chemistry, biochemistry, chemical engineering, materials science, nanotechnology, physics, environmental science and other science and engineering disciplines. Depending on your research, SciFinder's is complementary to other databases like Reaxys, Web of Science, PubMed,Compendex and INSPEC.
How to use Scifinder
https://www.cas.org/training/scifinderScifinder user tutorial SciFinder (http://scifinder.cas.org)
Introduction to Scifinder
Introduction to Scifinder
Introduction to Scifinder
- ID/PW Registration: http://bit.ly/yghci8* Registration should be done in campus using KAIST domail.
Use your institution email address.
- Registration completion: Click the "registration complete link"
Introduction to Chemdraw
ChemDraw is a molecule editor first developed in 1985 by David A. Evans and Stewart Rubenstein (later by the cheminformatics company CambridgeSoft). The company was sold to PerkinElmer in the year 2011. ChemDraw, along with Chem3D and ChemFinder, is part of the ChemOffice suite of programs and is available for Macintosh and Microsoft Windows.
-Wikipedia-
Introduction to Chemdraw
https://www.youtube.com/watch?v=Ry_hj6k7Ges
How to Download and Install Chemdraw Software
Go to
http://www.cambridgesoft.com
and create an ID and sign-in.
Go to
http://sitelicense.cambridgesoft.com/sitelicense.cfm?sid=2207
Log-in using your KAIST email and obtain the Serial Number via email.
Serial number can be obtained only once by the KAIST email account. Be
careful about the privacy of your account.
Chemdraw demo.
Midterm (in Korean) and Final (in English) Papers (25% each)
1. Topic (experimental theme) of your midterm/final paper will be randomly announced on 4/10 (midterm paper) and 6/4 (final
paper).
2. Online submission: www.turnitin.com
3. Create your account. Enter Class ID and Password (Provided by TA)
4. Use ACS style template from
http://pubs.acs.org/page/jacsat/submission/jacsat_templates.html
http://pubs.acs.org/paragonplus/submission/templates/acsPageWide-MSW2010.dotx
5. Enter your name in Korean (한글로 이름과 성 입력). English for foreign students.
6. Submission due: 04/23 10 pm (midterm paper), 6/18 10 pm (final paper)
7. For chemical drawing, use ChemBioDraw software.
8. Reports should contain general contents: introduction, data & results, actual experimental procedures, discussion, and
references.
9. Post-lab questions should be included in the paper.
10. Plagiarism results in zero for all reports involved (Determined by Chief TA and Professor, turnitin platform are very good at
detecting similarity between reports. Copy and paste of published paper will also be detected in the turnitin platform. So don’t do
that!).
11. Late submission is not allowed in Turnitin website. You should send your lab report to Chief TA. The maximum score for
the late report is B+.
Evaluation Criteria of the Midterm and Final Papers
The more it looks like a real JACS paper in terms of organization, referencing, scheme preparation, logic in writing etc. the higher the grade. Read many papers and emulate them.
Title: Succinct and clear title (5)Abstract: (15)Introduction: with background information, referencing (20)Results: Data presentation, chemdraw (25)Discussion: Data interpretation, chemdraw (25)Conclusion: (10)
A >80B >60C >40D <40
Submit a word file to turnitin.com.
Scientific Ethics
○ Plagiarism of previous reports. ○ Data Manipulation
Turnitin system detect the similarity of your report by comparing it with previously written report or published contents.
Thank you for your attention
People should continue to work hard at organic synthesis - it's hard, exacting,
frustrating, but always fascinating. Synthesis can create whole new world.
-Samuel Danishefsky-
Thank you for your attention.
