Advanced Synthetic
Laboratory (333):
Course Manual
Dr. Chad L. Landrie
Spring 2012
University of Illinois at Chicago
ii
iii
Table of Contents
TABLE OF CONTENTS.................................................................................................. III!
A. SYLLABUS FOR ADVANCED SYNTHETIC LABORATORY (CHEM 333)............... 1!
A.1. INSTRUCTOR CONTACT INFORMATION ................................................................................................ 1!
A.2. OFFICE HOURS ................................................................................................................................. 1!
A.3. REQUIRED TEXTBOOK ....................................................................................................................... 1!
A.4. PREREQUISITES ................................................................................................................................ 1!
A.5. COURSE DESCRIPTION AND OBJECTIVES ............................................................................................ 1!
Project One Overview ..................................................................................................................... 2!
Project Two Overview ..................................................................................................................... 4!
Project Three Overview................................................................................................................... 4!
Project Four Overview..................................................................................................................... 5!
A.6. CLASS PREPAREDNESS, TAS, LECTURE AND CLASS STRUCTURE......................................................... 6!
A.7. WEBSITE .......................................................................................................................................... 6!
A.8. ASSESSMENT AND ATTENDANCE ........................................................................................................ 7!
A.9. GRADING.......................................................................................................................................... 7!
A.10. COURSE CURVE ............................................................................................................................. 7!
A.11. DISABILITY STATEMENT ................................................................................................................... 8!
A.12. RELIGIOUS HOLIDAYS STATEMENT ................................................................................................... 8!
A.13. POLICIES ........................................................................................................................................ 9!
A.14. COURSE SCHEDULE ...................................................................................................................... 10!
B. WRITING A LABORATORY REPORT ..................................................................... 14!
C. SAMPLE EXPERIMENTAL PROCEDURE............................................................... 16!
D. LABORATORY REPORT GRADING RUBRIC......................................................... 17!
E. KEEPING A LABORATORY NOTEBOOK ............................................................... 18!
E.1. INTRODUCTION ............................................................................................................................... 18!
E.2. ORGANIZATION OF LAB NOTEBOOK ENTRIES .................................................................................... 18!
General Practices.......................................................................................................................... 18!
Pre-lab........................................................................................................................................... 18!
In-lab ............................................................................................................................................. 19!
Post-lab ......................................................................................................................................... 19!
E.3. SAMPLE LABORATORY NOTEBOOK ENTRY ........................................................................................ 21!
F. LABORATORY NOTEBOOK GRADING RUBRIC ................................................... 24!
G. MATTSON GENESIS II INFRARED SPECTROMETER OPERATING
INSTRUCTIONS ....................................................................................................... 25!
Obtaining an IR Spectra................................................................................................................ 25!
Spectral Manipulation ................................................................................................................... 25!
Shutting Down the IR Spectrometer ............................................................................................. 25!
H. USING THE GLADIATR ATTENUATED TOTAL REFLECTANCE (ATR) FT-IR
ACCESSORY ........................................................................................................... 26!
H.1. INTRODUCTION TO ATTENUATED TOTAL REFLECTANCE ..................................................................... 26!
H.2. INSTRUCTIONS FOR SOLID SAMPLING ............................................................................................... 27!
H.3. INSTRUCTIONS FOR LIQUID/OIL SAMPLING ........................................................................................ 28!
H.4. CLEANING THE ATR CRYSTAL AND PRESSURE-TIP ........................................................................... 29!
I. PREPARATION OF A KBR PELLET FOR SOLID SAMPLES IN TRANSMISSION
INFRARED SPECTROSCOPY................................................................................. 30!
J. GOW-MAC 350/400 GAS CHROMATOGRAPH & VERNIER LABPRO™ ADC
OPERATING INSTRUCTIONS................................................................................. 31!
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K. INFRARED SPECTROSCOPY PRIMER .................................................................. 32!
Functional Groups......................................................................................................................... 32!
Valency ......................................................................................................................................... 33!
Infrared Spectroscopy ................................................................................................................... 34!
Examples of Infrared Spectra: Characteristic Vibrational Frequencies......................................... 37!
L. INTRODUCTORY LAB: SEPARATION, PURIFICATION AND
CHARACTERIZATION OF FLUORENE AND FLUORENONE ............................... 39!
Objective ....................................................................................................................................... 39!
Tasks............................................................................................................................................. 39!
Column Chromatography procedure............................................................................................. 39!
Recrystallization Procedure .......................................................................................................... 41!
1
A. Syllabus for Advanced Synthetic Laboratory
(CHEM 333)
A.1. Instructor Contact Information
Dr. Chad L. Landrie
Office Room: 2206A SEL
Office Phone: (312) 996-3178
Email: clandr1@uic.edu
Website: http://www.chadlandrie.com
A.2. Office Hours
Regularly scheduled office hours will be held Monday & Wednesday, 3-5 pm. Students
who cannot attend during this time may send me an email to request an appointment.
Although I will guarantee my availability during the above hours, I am also usually
available at other times, such as during your laboratory time, for walk-ins.
A.3. Required Textbook
Gilbert, J.C., Martin, S.F. Experimental Organic Chemistry: A Miniscale and
Macroscale Approach, 5th ed.; Brook/Cole: Pacific Grove, CA, 2011.
A.4. Prerequisites
CHEM 233. CHEM 232. CHEM 234 or concurrent enrollment.
A.5. Course Description and Objectives
CHEM 333 is divided into two parts. Part I consists of three laboratory projects—each
spanning several weeks—and focuses on the synthesis of organic molecules with an
emphasis on those compounds that are significant to biology, medicine and
pharmacology. Unlike the chemistry in CHEM 233, most syntheses in this course
involve several steps with molecules that have more than one functional group.
Occasionally, this requires protecting groups to prevent the reaction of undesired
functional moieties and ensure only the desired functional group transformation is
taking place. The techniques for isolation, purification and characterization of these
molecules are founded upon the skills acquired in CHEM 233 or a similar Organic
Laboratory I course. Melting point determination, infrared spectroscopy, Raman
spectroscopy, nuclear magnetic resonance spectroscopy and gas chromatography are
used for molecular characterization and analysis of purity. Part II—comprising the final
project—engages students in authentic research developed by the Center for Authentic
Science Practice in Education (CASPiE). The research goals for this semester are aimed
at designing and undertaking the synthesis of triazoles, which may then be evaluated for
their anti-viral properties. Students will construct a known triazole through a [2+3]
cycloaddition of an azide with an alkyne. After evaluating a series of triazoles for their
potential as drug candidates, they will then undertake independent syntheses of new
triazoles modeled after their previous experiments.
2
Project One Overview
Benzocaine: The semester begins with the conversion of carboxylic acids to reactive
acyl derivatives that participate in nucleophilic acyl substituion reactions. This process
is used to construct two common anesthetics, benzocaine (2) and lidocaine (xx), as well
as the commercial insect repellent N,N-diethyl-m-toluamide (DEET) (7). First, paminobenzoic acid (PABA) (1) is esterified using the method of Emil Fischer to form the
anesthetic benzocaine (Figure A.5.1). Structural characterization is achieved through 1HNMR, melting point determination and confirmation of the ester’s infrared stretching
frequency.
O
O
OH
H2SO4
EtOH
H2N
p-aminobenzoic acid (1)
OEt
H2N
Benzocaine (2)
Figure A.5.1
Derivatization of carboxylic acids can be achieved by the synthesis of a more reactive
carbonyl functional group such as an acid chloride followed by nucleophilic acyl
substitution (Figure A.5.2, path a then c); the carboxylic acid derivatives are arranged in
order of decreasing reactivity. The basic principle is that a more reactive derivative can
be used to form a less reactive derivative. In the case of esters, however, Fischer
esterification proves to be a more direct route and operates through a different
mechanism (Figure A.5.2, path a). Many methods for the synthesis of amides are known.
In one of the most common, as seen in the synthesis of DEET (7) (Figure A.5.4), the
amide can easily be constructed by forming the acid chloride (Figure A.5.2, path a)
followed by the addition of an amine (Figure A.5.2, path e).
path a = thionyl chloride (SOCl2)
path b = Fischer (H3O+ / HOR')
Other Mechanisms
O
R
Cl
acid chloride
O
O
O
R
O
R'
anhydride
R
SR'
thioester
O
O
R
OR'
ester
NR'2
R
amide
O
R
OH
carboxylic acid
descreasing reactivity toward nucleophillic addition/elimination
Nucleophillic Acyl
Substitution
path e = add amine (NR'3)
path c = add alcohol (HOR')
path d = add hydroxide (OH-)
"saponification"
Figure A.5.2
PABA (1) itself is a building block used by bacteria to synthesize Vitamin B9 also known
as folic acid. Sulfa drugs take advantage of this mechanism by competing with PABA
(1) for the active site in the enzyme, which synthesizes folic acid from PABA (1).
Without the ability to synthesize folic acid, the bacteria die. Until recently it was also
used as a UV blocker in sunscreen until it was discovered to increase DNA malformation
in skin cells and thus increase consumer’s risk of developing skin cancer. Esterification
3
of PABA (1), however, dramatically changes its function. Benzocaine (2) is widely used
in cosmetics, particularly shaving gels to reduce dermal pain and discomfort. It is
structurally related to other anesthetics and analgesics such as piperocaine (3),
novacaine (4) and cocaine (5) (Figure A.5.3).
NH2
CO2CH3
N
EtO
O
Benzocaine (2)
O
CH3
N
O
H3C
O
O
Piperocaine (3)
N
O
O
Novocaine (Procaine) (4)
Cocaine (5)
Figure A.5.3
N,N-Diethyl-m-toluamide (DEET): Second, the commercial insect repellent DEET (7)
is prepared (Figure A.5.4), which is the active ingredient in the commercial repellant
“OFF” and currently the most effective. DEET (7) was developed by the United States
Army and is thought to bind to CO2 receptors in insects such as mosquitos and ticks,
which are necessary to locate hosts. DEET (7) is synthesized by the derivitization of mtoluic acid (6) into its acid chloride by thionyl chloride (SOCl2) (Figure A.5.2, path a).
Nucleophillic acyl substitution of the highly reactive acid chloride with diethyl amine
(Figure A.5.2, e) then completes the synthesis of 7.
O
O
OH
1. SOCl2
N
Et
2. Et2NH
CH3
m-toluic acid (6)
Et
CH3
N,N-Diethyl-m-toluamide (7)
(DEET)
Figure A.5.4
Lidocaine Synthesis: Third, students will embark on the total synthesis of the
anesthetic and antiarrythmic drug, Lidocaine (9) (Figure A.5.5). Lidocaine (9)
effectively blocks sodium channels, preventing nerve signal transduction necessary for
pain perception and muscle contraction. Lidocaine (9) is similar in structure to the
previously mentioned analgesics, with the exception of an amino-amide rather than an
amino-ester motif. This small change causes a more rapid onset and longer duration of
anesthesia, most likely due to a stronger binding affinity to the sodium channels. The
synthesis is completed in three steps using infrared spectroscopy and 1H-NMR
spectroscopy to confirm functional group transformations. A key component of
isolation and purification in this synthesis is the preparation of salts of the resulting
amines, which allows selective recrystallization as well as acid extractions. Also, the
chemoselectivity of acid chlorides compared to alkyl chlorides is highlighted in the key
step; 2,6-dimethylaniline is preferentially acylated by α-chloroacetylchloride.
4
CH3
NO2
1. SnCl2, HCl/AcOH
2. ClCH2COCl, AcOH/NaOAc
CH3
3. Et2NH, toluene
CH3
H
N
O
CH3
2-nitro-m-xylene (8)
N
Et
Et
Lidocaine (9)
Figure A.5.5
Project Two Overview
Preparation of Benzanilides:
Students will use the techniques learned in project one to develop their own syntheses of
a variety of 4’-substituted benzanilides (10) from easily obtainable starting materials
(Figure A.5.6). Additionally, chemical databases and search engines such as SciFinder,
Beilstein and Web of Science, will be employed to find related literature procedures,
background information and spectral properties of the target compounds. Final
products will be characterized by mp, IR and NMR.
Hammett Plot: The N-H 1H-NMR chemical shift (δN-H) will be recorded for each
synthesized benzanilide (10); the data will be compiled as a class and a Hammett plot
constructed using standard substituent constants (σ) for each 4’-substituent. Students
will use this data to determine whether a linear free energy relationship (LFER) exists
between 4’-substituents and the δN-H. Substituents that display both inductive effects
and resonance effects will be examined.
Additionally, the effects of sample
concentration, solvent composition and temperature may be varied in order to
determine the effect each factor has on the relative sensitivity (ρ) of the δN-H to electronperturbing capabilities of the substituents.
R
O
N
H
O
OH
1
H2N
+
H-NMR chemical shift?
R
10
11
12
Figure A.5.6
Project Three Overview
Students will prepare N-cinnamyl-m-nitroaniline (16) by reductive amination with
cinnamaldehyde (13) and m-nitroaniline (14); the final product will again by
characterized by mp, IR and NMR (Figure A.5.7). A salient task of this synthesis will
require students to scale-up a standard literature or textbook preparation in order to
obtain multigram quantities of 16. Pedagogically, the synthesis highlights the
chemoselectivity of NaBH4 reduction for the imine over the alkene functional group.
Students will then use the N-cinnamyl-m-nitroaniline (16) they obtained to evaluate
two transfer hydrogenation methods for the reduction of the remaining alkene moiety.
This method is particularly appealing for the undergraduate laboratories since it
precludes the use of H2 gas required in typical catalytic hydrogenations. Since a number
of transfer hydrogenation methods exist, each student will decide on their own method.
5
They will use chemical databases such as SciFinder and Beilstein to develop
experimental procedures based upon recent literature precedents.
H
H
cyclohexane
O
N
+
H2N
cinnamaldehyde (13)
NO2
+
H2O
NO2
N-Cinnamylidene-m-nitroaniline (15)
m-nitroaniline (14)
H H
a. NaBH4, MeOH
N
H
b. H2O
NO2
transfer
hydrogenation
method
N-cinnamyl-m-nitroaniline (16)
N
H
NO2
(3-nitrophenyl)-(3-phenylpropyl)-amine (17)
Figure A.5.7
Project Four Overview
Finally, students will participate in a laboratory module developed by the Center for
Authentic Science Practice in Education (CASPiE). CASPiE modules engage students in
authentic research aimed at answering specific questions posed by faculty members
whose research the results will support. Unlike traditional “cookbook” experiments, the
results of the research are unknown. The overall goal of the project this semester is to
contribute to a growing library of triazoles, such as 20, which have been shown to
exhibit antiviral properties (Figure A.5.8). Students will first undertake the synthesis of
the known triazole 20 through a Cu-mediated coupling reaction between azide 18 and
alkyne 19. Both starting materials must also be constructed. Based on available starting
materials in the lab, each student will then choose four potential drug targets (triazoles),
which have not been synthesized before. Each will be evaluated for oral bioavailability
using Lipinski’s Rule of Five. After selecting the best drug candidate from their pool,
each student will undertake the synthesis of the target triazole based upon their
previous synthesis of 20. The products will be characterized by IR and 1H-NMR as well
as mass spectrometry. The partition coefficient in t-BuOH/water (logP) will also be
measured using UV-spectroscopy. These results, with the triazole samples, will then be
submitted for evaluation as antiviral compounds. If we’re lucky, one of the triazoles
synthesized this semester may prove to exhibit exceptional antiviral activity.
O
N
N
N
O
CH3
+
sodium ascorbate
CuSO4•5H2O
O
N N
N
O
CH3
O
18
19
20
Figure A.5.8
O
6
A.6. Class Preparedness, TAs, Lecture and Class Structure
A primary requirement for success in this course is student preparation. Because most
of the work will be completed individually, each student must study and understand the
required readings and techniques prior to completing each experiment. Poor planning
often results in greater experiment times which may prevent the completion of the
laboratory by the class end. The topics for review for each experiment, as well as the
textbook page numbers where they can be found, will be announced during the Friday
lecture immediately proceeding the first lab of the project. Homework problems—that
are graded as part of the project report—lab report topic suggestions and procedural
notes will also be presented during lecture.
The experiments undertaken this semester—while important and representative of
functional group transformations actually performed by organic chemists—only scratch
the surface of synthetic organic chemistry as a whole. The goal of this course then is not
to provide the student with a large repertoire of organic reactions which they can
perform, but rather to teach the student how to approach an organic transformation and
apply that to areas including methodology and natural product synthesis. Wherever
possible, the experiments have been designed around discovery and authentic studentderived procedures. The lecture component of the course then will present the skills
and tools needed to achieve these goals including searching scientific literature, scale-up
and work-up of organic reactions, purification, molecular characterization as well as
data analysis and collection.
Teaching assistants—relying on their extensive organic chemistry experience—will train
students in a variety of advanced organic laboratory techniques including column
chromatography, infrared spectroscopy, recrystallization, adding reagents under inert
atmospheres, etc. Where students are asked to develop original experimental
conditions, TAs will be a particular valuable source of advice. Ultimately, however, the
experiment belongs to the student undertaking the task; TAs will not provide step-bystep instructions during the laboratory. Finally, although students will prepare samples
for NMR spectroscopy, the TA will acquire the spectra for their students.
A.7. Website
The URL for the course website is www.chadlandrie.com. The site will be under
continual construction this semester. Some of the current content includes course
descriptions, instructor profiles, TA information, a description of the laboratory
facilities, lecture notes and shared files available for download including rubrics, sample
exams and manuals. A salient feature of the website will hopefully be the blog complete
with comment capability. While the blog will function primarily as an announcement
board, I also expect it to grow into a platform for initiating interesting discussions in
chemistry.
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A.8. Assessment and Attendance
The course will be graded according to individual performance on each of the following
assessment items:
• 4 project reports on each of the 4 projects undertaken in part one of the course.
Theses reports are graded by the instructor according to a rubric written by the
instructor. This rubric is distributed to the students at the beginning of the
course.
• 4 homework sets on each of the 4 projects.
• 1 midterm exam covering the theory and techniques behind the syntheses
performed. The exam is written and graded by the instructor of the course.
• 1 laboratory notebook. The laboratory notebook is graded by the instructor
according to a rubric, which can be found on the following pages. This rubric, as
well as supplementary information on maintaining a laboratory notebook, is
distributed at the beginning of the term.
• The final exam is comprehensive and covers both the chemical theory behind
each synthesis as well as practical laboratory techniques.
• Attendance is required for all laboratories and lectures. Students will be allowed
3 absences total for both the laboratory and lecture component of the course.
These should be reserved for emergencies such as illness and family leave. If a
lab period is missed, the student is responsible for making-up missed work on
their own time and should consult with the instructor to arrange additional time
to work in the lab. Each absence in excess of three will result in a 16 point
deduction (2%) from the final score.
Table A.8.1: Summary of Point Distribution.
Item
Points
Project Reports
Homework (1 set each project)
Laboratory Notebook
Midterm Exam
Final Exam
CASPiE Powerpoint Presentation
Course Total
50
25
100
100
200
100
No.
x
x
x
x
x
x
4
4
1
1
1
1
=
=
=
=
=
=
Total
Points
200
100
100
100
200
100
800
A.9. Grading
Project reports and homework will be graded by the teaching assistants according to a
rubric and answer keys written by the instructor. Exams, notebooks and final projects
will all be graded by the instructor of the course according to pre-established rubrics or
grading guidelines.
A.10. Course Curve
This course will be curved at the end of the semester based on the total number of points
earned. A curve simply implies that the instructor will determine the minimum point
values required for each letter grade at the end of the semester rather then setting these
limits a priori. Approximate curves will also be announced following each exam
8
although the actual point value is entered into the grade book not a letter grade. A curve
does not imply that your grade will be raised or lowered. These limits vary slightly each
semester since variations in exam difficulty, teaching quality and grading styles cannot
be avoided. Because of the small number of students in this course—and also because
students proficient in organic chemistry are most likely to take this course—there is no
pre-established curve; it is quite possible for every student to earn an A, although that
outcome is certainly not guaranteed.
A.11. Disability Statement
Students with disabilities must inform the instructor of the need for accommodations.
Those who require accommodations for access and participation in this course must be
registered with the Disability Resource Center. Please contact ODS at 312/413-2183
(voice) or 312/413-0123 (TTY).
A.12. Religious Holidays Statement
The faculty of the University of Illinois at Chicago shall make every effort to avoid
scheduling examinations or requiring that student projects be turned in or completed on
religious holidays. Students who wish to observe their religious holidays shall notify the
faculty member, by the tenth day of the term, of the date when they will be absent unless
the religious holiday is observed on or before the tenth day. In such cases, the student
shall notify the faculty member at least five days in advance of the date when he/she will
be absent. The faculty member shall make every reasonable effort to honor the request,
not penalize the student for missing the class, and if an examination or project is due
during the absence, give the student an exam or assignment equivalent to the one
completed by those students in attendance.
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A.13. Policies
a. Goggles:
It is prohibited to work in the laboratory without approved (must seal completely around eyes)
safety goggles according to state law. First, second and third time offenses will result in the loss
of 10 points, the lowering of the final score by one letter grade and dismissal from the course with
a grade of F respectively. Students who forget their goggles will not be allowed to participate in
the lab.
b. Attendance:
Attendance is required for all laboratories and lectures. Students will be allowed 3 absences total
for both the laboratory and lecture component of the course. These should be reserved for
emergencies such as illness and family leave. If a lab period is missed, the student is responsible
for making-up missed work on their own time and should consult with the instructor to arrange
additional time to work in the lab. Each absence in excess of three will result in a 12 point
deduction (2%) from the final score.
c. Lab Reports: Lab Reports are due during lecture the week following the last day of the scheduled project.
Students will not be granted additional time for project or reports except in extenuating
circumstances.
d. Results:
Each student must show their results to their TA before leaving the laboratory. Your TA may
instruct you to obtain additional data depending on the quality of your results. Failure to gain TA
approval will result in zero for the data acquisition/presentation section of your lab report.
e. Class End:
The class period does not end when you finish your experiment, but when your TA dismisses you
from the class. Often times it is necessary to reconvene the entire class after the experiment to
discuss results and other relevant items and also to ensure that everybody participates in the cleanup of the lab space. Students leaving the lab prior to the TA’s approval will receive a five-point
deduction on that week’s lab report.
f. Exams:
There are no provisions for making up an exam without my prior approval.
g. Safety:
All students must be diligent in keeping the laboratory space clean, organized and safe. Severe
safety violations will result in a deduction of 20 points per violation and possible removal from the
class with a grade of F.
h. Food:
No food or drinks are allowed anywhere in the lab space. 20 points will be deducted per violation.
i. Hygiene:
All students are responsible for keeping the lab spaces clean and organized. Examples include
cleaning off balances, balance tables, wiping down benches, sweeping up excess powders and
glass from the floors, cleaning up spilled water from the floors, cleaning mortars and pestles when
finished, cleaning IR castors, disposing of waste properly, etc. If a lab space is found to be
unclean or unorganized by the instructor or a TA, each student from the previous section will
receive a five-point deduction from their final score.
j. Grades:
Students are responsible for keeping all graded lab reports and exams until final grades have been
entered. Students are also responsible for periodically checking their point totals with the records
of their TA’s to ensure no mistakes have been made. No grades will be changed after the
completion of the course because of grading, recording or addition errors.
k. Incomplete:
Incompletes will not be given for students who have taken the final exam. Also, incompletes will
only be granted for students showing proof of extenuating circumstances such as extended illness.
Incompletes will not be given for students who are simply dissatisfied with their final grade.
l. Tardiness:
Students who are more than 15 minutes late will not be allowed to participate in that laboratory.
n. Waste:
All chemical waste must be disposed of in the appropriate labeled waste bottles. If a waste bottle
is full or unavailable, notify your teaching assistant and one will be provided for you.
A.14. Course Schedule
Wk.
Lab
M
1
W
Laboratory Activities
☞ Introduction & Check-in
☞ Begin Intro Lab (Column Chromatography only)
☞ Finish Intro Lab (Recrystallization and IR)
Tentative
Lecture Topics
• Lecutre 1
• nucleophlic acyl subst.
• carboxylic acid deriv.
• reaction tables
• benzocaine synth.
• Fischer esterification
Benzocaine: 651-661
M
2
Project 1: Preparation of Benzocaine, Lidocaine and DEET
through Fischer Esterification and Nucleophilic
• Lecture 2
• Infrared spectroscopy
Acyl Substitution of Carboxylic Acids.
☞ Benzocaine: Synthesis
W
☞ Benzocaine: Recrystallization, IR and mp
☞ Benzocaine: Prepare sample for NMR (give toTA)
M
☞ DEET: Synthesis
W
☞ DEET: Column Chromatography, IR and mp
☞ DEET: Prepare sample for NMR (give to TA).
M
☞ Lidocaine: A. Preparation of 2,6-Dimethylaniline
☞ Lidocaine: Obtain IR of crude product.
W
☞ Lidocaine: B. Preparation of 1-chloro-2,6dimethylacetanilide
☞ Lidocaine: Recrystallize crude product
☞ Lidocaine: Obtain IR & mp of recrystallized product
3
4
5
M
☞ Lidocaine:
☞ Lidocaine:
☞ Lidocaine:
☞ Lidocaine:
C. Preparation of Lidocaine
Recrystallize crude product
Obtain IR & mp of recrystallized product
Prepare sampe for NMR (give to TA)
• Raman spectroscopy
• Characterization of
organic molecules
DEET: 664-670
IR: 236-257
• Lecture 3
• NMR spectroscopy
1H-NMR: 257-283
• Lecture 4
• NMR cont.
• Complex coupling
• Practice Problems
• Distribute Literature on
Hammet equation
Lidocaine: 685-686, 729-747
• Lecture 5
• Linear Free Energy
Relationships (LFERs)
• Hammett Equation
• Preparation of
benzanilide derivatives
Read literature distributed on
Hammet Equation
11
5
M
☞ Lidocaine:
☞ Lidocaine:
☞ Lidocaine:
☞ Lidocaine:
C. Preparation of Lidocaine
Recrystallize crude product
Obtain IR & mp of recrystallized product
Prepare sampe for NMR (give to TA)
W
Project 2: Independent Preparation of 4’-Substituted
Benzanilides. Demonstration of LFER by Construction of a
Hammett plot of the Amide Proton Chemical Shift.
☞ Benzanilides: Present proposed synthesis for review
☞ Benzanilides: Begin synthesis of benzanilide I
M
☞ Benzanilides: Finish synthesis of assigned benzanilide I
☞ Benzanilides: Purification, IR, NMR
W
☞ Benzanilides: Synthesis of assigned benzanilide II
M
☞ Benzanilides: Finish synthesis of benzanilide II
☞ Benzanilides: Obtain IRs & prepare NMR samples (to TA)
☞ Obtain NH δ from all groups and construct Hammett Plot
6
Project 3: Evaluation of Solution-Phase Methods for the
Reduction of N-Cinnamylidene-m-nitroaniline Prepared by
Reductive Amination.
7
W
☞ [R] Amination: Scaled-up synthesis and work-up
☞ [R] Amination: Gather materials, research & prepare for [R]
☞ [R] Amination: Submit proposed [R] procedures for review
☞ [R] Amination: Recrystallize crude product
☞ [R] Amination: Obtain mp & IR
☞ [R] Amination: Prepare NMR sample (give to TA)
M
8
• Lecture 5
• Linear Free Energy
Relationships (LFERs)
• Hammett Equation
• Preparation of
benzanilide derivatives
Read literature distributed on
Hammet Equation
• Lecture 6
• Deviations from linear
Hammett plot
• modified sigma values
Read literature distributed on
benzanilide preparation
• Lecture 7
• Reductive Amination
• Transfer hydrogenation
• Azeotropic distillation
Reduction: 551-554
Imine Red.: 559-568
• Lecutre 8
• Introduction to CASPiE
• Antiviral drug
development
• Lipinski rule of 5
• LogP
• Triazoles as drugs
• Click chemistry
• CuAAC
CASPiE Manual: 1-25
W
☞ Reduction: Reduce N-cinnamylidene-m-nitroaniline
M
☞ Reduction: Isolate and purify crude product
☞ Reduction: Prepare NMR sample (give to TA)
9
W
Project 4: CASPiE: Anti-Viral Drug Development
☞ Laboratory 1: Nucleophilic Substitution of Propargyl Bromide
by a Phenoxide with an Introduction to Thin-Layer
Chromatography (TLC)
Midterm Exam (Covers
projects 1-3)
CASPiE Manual: 26-end
Read literature distributed on
“click” chemistry.
12
M
☞ Obtain IR of product
☞ If necessary, purify alkyne by column chromatography
☞ Submit sample for 1H-NMR & MS
W
☞ Laboratory 2: Reaction of an Alkyne Product from
Laboratory 1 with Alkyl Azide by a [2+3] Cycloaddition Reaction
with an Introduction to IR Spectroscopy
M,W
Spring Break, No Classes
10
XX
M
☞ Obtain all IRs using the ATR accessory (no KBr pellets)
☞ If necessary, purify triazole by recrystallization or column
☞ Obtain IR of product
☞ Submit sample for 1H-NMR & MS
W
☞ Laboratory 3: Drug and Synthesis Design (Design one)
☞ Measure log P
☞ Gather materials for syntheses
M
☞ Laboratory 4-6: Independent research
☞ Synthesis of proposed alkyne
11
12
W
☞ Purify alkyne if necessary
☞ Obtain IR of alkyne (confirm reaction)
☞ Submit sample for 1H-NMR & MS
M
☞ Laboratory 4-6: Independent research
☞ Synthesis of proposed triazole from alkyne
W
☞ Purify triazole if necessary
☞ Obtain IR of triazole (confirm reaction)
☞ Submit sample for 1H-NMR
☞ Prepare sample for GC-Mass Spec (consult TA)
M
☞ Perform log P analysis on triazole
☞ Fill out online submission form for triazole (can also be done
later)
13
14
15
W
☞ Finish chemistry
M
☞ Finish chemistry
• Lecture 9
• Pharmacokinetics
• Designing your drug
• Molinspiration site
• Microwave reactor
conditions
Spring Break, No Lecture
• Lecture 10
• MW dielectric heating
• loss tangent
• thermal MW effects
• specific MW effect
• Discuss/analyze
results
• Plan presentations
• CASPiE Presentations
• CASPiE Presentations
• CASPiE Presentations
13
W
16
☞ Check out and cleanup
Final Exam; Day, Time and Location TBA
14
B. Writing a Laboratory Report
There are four laboratory reports, one at the end of each project. These reports are your
opportunity to put all of your theoretical research, experimental work and collected data
together in a cohesive and organized description of the project. Each report should be
divided into the following sections:
•
•
•
•
Methods
Experimental Procedures
Data Acquisition/Presentation
Conclusion
The methods section presents a thorough, yet concise explanation of the relative
chemical theory behind the project including the importance of the synthetic target (i.e.
biological significance). Following this background information, the synthesis itself
should be presented and explained beginning with the first reaction. For each synthetic
step a brief discussion of the mechanisms involved in functional group transformations
should be included. This is not the place to describe the experimental procedures, but
rather to state what reactions were done, how they were performed and what challenges
may have been encountered. One of the most important components of every section is
a diagram. Diagrams should clearly summarize what you are stating in the body of the
text. In summary, the methods section should contain the following:
•
•
•
•
•
Statement of the project goals
Chemical Theory background
Synthetic Target Background
Description of your Synthesis including mechanisms and yields
Challenges, successes, failures and explanations
Next the experimental procedures are written, one for each synthetic step. An
experimental procedure is precise, direct and detailed. A reader should be able to repeat
your experiment following your experimental procedure exactly.
Little to no
explanation for the steps undertaken is provided. This is reserved for the discussion.
You can find an example of how to write an experimental procedure in this manual.
Your data is presented not just as a stack of spectra and tables at the back of the report.
Rather, your data should be organized according to each synthetic step. Data tables and
spectra should be appropriately labeled with titles and figure numbers so that you can
reference these in your descriptions in the conclusion. Spectra can be made more clear
by neatly drawing the structure it represents. A brief paragraph preceding this data
describes how the data was acquired and on what instruments. In summary, the Data
section should contain the following:
•
•
•
Brief description of instrumentation used and acquisition methods
Organized spectra and tables with titles and structures
Calculations
15
Finally, the conclusion should restate the goals of the project and whether these goals
were successfully achieved. Use your data to summarize each synthetic step and as
evidence to support the functional group transformations you observed.
Your Lab report will be graded by the instructor according to the following rubric. Use
this rubric also as your guide to writing your reports.
16
C. Sample Experimental Procedure
An experimental procedure is precise, direct and detailed. A reader should be able to
repeat your experiment following your experimental procedure exactly. Little to no
explanation is provided. This is reserved for the discussion. Notice below that
quantities are written within parentheses. This helps the procedure to flow smoothly
without frequently interrupting every sentence with a dependant clause involving a
number. Also, experimental procedures are written in the past tense and in the thirdperson. Finally, structural data is included at the end of the procedure in the format
demonstrated below. Most often your structural data will consist of retention factors,
melting points and IR frequencies. Some experimental procedures in organic chemistry
are further illustrated with the name of the product of the reaction and a reaction
scheme. You will follow this format as well when writing your experimental procedures
for your lab reports. If you do not have access to ChemDraw which enables your to
name and draw the structures below, you may draw these reaction schemes by hand.
Please check ChemDraw’s website though. They frequently allow students to obtain a
one semester trial version. Finally, further examples of experimental procedures may be
found in the scientific literature. Journal of the American Chemical Society(JACS) and
Journal of Organic Chemistry (JOC) are good examples.
4-(2,4-Dimethoxy-phenyl)-4-oxo-butyric acid.
OCH3
OCH3O
+O
H3CO
O
O
AlCl3, ClCH2CH2Cl
r.t., 12 h, 31%
OH
H3CO
O
Figure C.1
To a solution of AlCl3 (6.63 g, 49.2 mmol) in 1,2-dichloroethane (200 mL) at 0 °C was added succinic anhydride
(3.90 g, 37.8 mmol) under N2. 1,3-dimethoxy benzene (5.0 mL, 37.8 mmol) was added via syringe, the reaction
mixture stirred at 0 °C for 1 h then allowed to warm to r.t. and stirred an additional 12 h. The reaction mixture was
poured into ice, the aqueous and organic layers separated and the aqueous layer extracted with Et2O (3 x 50 mL).
The combined organic extracts were dried (Na2SO4), filtered and concentrated in vacuo then recrystallized (MeOH)
to provide 4-(2,4-Dimethoxy-phenyl)-4-oxo-butyric acid (2.85 g, 31%) as a yellow oil: Rf 0.10 (1:1,
EtOAc/hexanes); 1H-NMR (400 MHz, CDCl3) δ 7.89 (d, J = 8.8 Hz, 1 H), 6.54 (dd, J = 8.3, 2.3 Hz, 1 H), 6.46 (d, J
= 2.3 Hz, 1 H), 3.90 (s, 3 H), 3.86 (s, 3 H), 3.30 (t, J = 6.6 Hz, 2 H), 2.73 (t, J = 6.6 Hz, 2 H); 13C NMR (100 MHz,
CDCl3) δ 197.8, 178.7, 165.0, 161.5, 133.2, 120.2, 105.5, 98.5, 55.8, 55.7, 38.7, 28.9; FTIR (film) υmax 3437, 1707,
1655, 1606, 1420, 1122 cm-1.
17
D. Laboratory Report Grading Rubric
Student Name:______________________________ Lab Title:__________________________
Good
Fair
Poor
10-9 pts: The lab report
contains
few
to
no
grammatical errors. and is
concise and clear. The report
is also structured into logical
well-organized paragraphs for
each section. The report is
divided into the required
sections and is typed.
8-7 pts: Minor grammatical
errors persist throughout the
report and there is some loss
of writing clarity and
organization, but overall the
report is well written and
divided into the required
sections and typed.
3-0 pts: The report
contains
random
thoughts and sentences
with little thought or
organization.
Grammatical errors are
abundant and detract
from the flow of the
writing.
10-9 pts: The introduction
begins with a statement of the
purpose of the lab undertaken
and then presents a thorough,
yet concise, introduction to
the chemical theory behind
the lab including a brief
discussion on mechanisms,
analytical techniques, etc. At
least one diagrams support
the written word. Succinctly
presents conclusions and
overall findings of the lab.
10-9 pts: Procedural details
are written according to the
examples provided with the
correct format including
product name and reaction
diagram. Math (mols, equivs,
etc) is correct. Procedure is
original and authentic.
8-7 pts: The report begins
with a statement of purpose.
The introduction may miss
some of the relevant
chemical theory/diagrams or
have a small amount of
theory incorrect, but overall
demonstrates
proficient
knowledge
about
the
background material. Final
conclusions and overall
findings are adequately
presented.
8-7
pts:
Minor,
but
significant errors in the
format or calculations exist,
but all required components
are
present
including,
diagram, quantities, and
stoichiometry.
The
procedure is original and
authentic.
6-4 pts: The report has
obviously
not
been
proofread for mistakes
and contains gross errors
that detract from the
clarity of the report.
Paragraphs are loosely
strung together with
weak
logical
order
although the report may
still be divided into the
required sections.
6-4 pts: Report may be
missing a statement of
purpose.
Chemical
theory background is
minimal,
contains
substantive errors, or
lacks application of the
theory to the current lab
undertaken.
Final
conclusions and overall
findings may be missing,
unclear, or lacking detail.
6-4 pt: The experimental
procedure
contains
several errors and/or
resembles almost exactly
the procedure provided
by the text with no
thought behind the actual
procedure followed. One
to two components may
be missing.
3-0 pts: Two or more
required components are
missing. The procedure
is unclear or mimics the
text.
The procedure
lacks
or
presents
incorrect details such as
mols, equiv, conc, etc.
Details may be missing.
Procedure may be a list.
Data
Acquisition
10-9 pts: All data including
IR, GC, and NMR spectra is
provided when available with
appropriate titles. Data tables
are present when appropriate
and a brief paragraph or two
describes the acquisition
method(s) and highlights
relevant
data.
Calculations/Equations
are
shown and explained.
8-7 pts: All data and
calculations
are
shown
accurately.
Minor errors
exist
in
titles,
table
presentation
or
the
description of acquisition
method(s). Calculations are
shown and are correct as
well as important equations.
6-4 pt: Some data
spectra,
tables,
calculations or equations
are missing or grossly
incorrect. If all data is
present, there is no
description
of
the
acquisition method and
the relevant data.
3-0 pts: Data section is
incomplete. There are
little to no spectra,
tables or calculations
and no description of
the acquisition method.
10-9 pts: The conclusion
accurately
restates
the
purpose of the lab and
concisely indicates whether
the purpose and goals were
achieved. The data collected
is explained and used to
verify
and
prove
the
concluded
outcome.
Insightful explanations are
offered
for
unexpected
results/procedures.
8-7
pts:
The
author
accurately
restates
the
purpose of the lab. Data is
used to solidly verify and
prove conclusions, but with
some minor errors in theory
and analysis. Explanations
for unexpected results are
offered.
6-4 pt: The purpose and
conclusions of the lab
may or may not be
correct, but the author of
the report makes gross
errors in analyzing the
data to arrive at any of
these conclusions
3-0 pts: Little to no
connections between the
data acquired and the
conclusions of the lab
are presented.
Data
explained contains little
thought and depth.
Experimental
Procedures
Methods and
Background
Grammar
Style & Organ.
Excellent
Conclusion
Performa
nce
Element
 Lab Number
3-0
pts:
The
introduction does not
connect the principles of
the laboratory with the
chemical theory. Very
small
amounts
of
material are presented
and show very little
original thought.
Total Score (50 pts) 
Earned
Points
18
E. Keeping a Laboratory Notebook
E.1. Introduction
Lab notebooks are important records of everything a scientist has done in the research
laboratory, whether at a university or a company. Lab notebooks can be used to prove
authorship of an invention or to combat accusations of scientific misconduct.
Your lab notebook will assist others who may read your lab notebook at a later time to
understand your work. A well-maintained lab notebook will be very helpful to you as
you analyze your data, decide upon further experiments to carry out, and prepare
written summaries of your work. These summaries could range from a lab report to a
journal article for publication. The more detailed your lab notebook is, the less likely
your experiments will have to be repeated due to uncertainty about what you did before.
Remember that the data you collect could contribute to a scientific paper.
E.2. Organization of Lab Notebook Entries
General Practices
Record your name and contact information on the inside cover of your lab notebook.
Reserve the first five pages of your lab notebook for a Table of Contents. Write your
name and the date on the top of every page of your lab notebook, and write the title of
the week’s lab on the first page for each entry that you hand in. Use every page. If you
make a mistake, draw a line through it. Write with a pen. If you create any graphs of
your data, print out two small copies of each graph and glue or tape them on the original
and the carbon copy page in your book.
Each week’s work should be outlined as follows:
Pre-lab
• Title - describes the nature of the experiment
•
Introduction - a brief (~ 1 paragraph) summary, in your own words, describing the
experiments you will be doing and why they are important to your research.
•
Methods and Calculations - include a table of reagents you will use in the lab. List the
chemicals, their formula, structure, molecular weight, and their physical state during
the experiment. Make a note of any safety hazards identified in the lab’s written
materials or the MSDS for each reagent. If it will be useful to know a reagent’s
melting point, boiling point, and/or density, include that information. Information
about reagents can be found in any chemicals catalog, the CRC, Merck Index, or at
chemfinder.com.
Describe any methods you will be using. (You will go into more detail in your postlab.) Include any reaction equations and mechanisms (when available). Make sure
you draw structures.
19
Carry out any calculations that can be done ahead of time, such as the amount of
reagents needed to make solutions, any conversions (mass to moles, etc.), and
theoretical yield. Also, outline examples of calculations you will do during the
experiment.
•
Outline of the Experiment: make a numbered list of the steps you will be performing
in lab. Take all the information that was given to you and boil it down to clear and
concise directions in your own words. This should make it easier for you to perform
your experiment because you won’t be sifting through excess information. Make it
easy to follow and understand; it will only help you get done faster! The best
outlines allow a person to complete the experiment without referring to the lab
manual.
In-lab
• All lab notebook entries from the lab period need to be legible and wellorganized. Also, they must include the procedure followed, observations, and
experimental data. Choose a format that works for you. One suggested format is
to divide the page in half vertically, using the left side for the procedure and the
right for data and observations.
•
No matter the format you choose for your in-lab notes, the procedure should be a
numbered list of what you actually do in lab. It should include detailed
descriptions of each step, so it will probably be longer than your outline from the
pre-lab. The steps do not necessarily have to be in the same order. For example,
if your group will be dividing up tasks, repeating steps, or moving on to another
part while waiting for a reaction to finish, your steps will be in a different order.
•
In the space for data & observations, write down everything you observe. Make
sure you use all your senses (except taste). Make notes about what your reagents
look like, what happens after you mix them, any temperature changes, etc. This is
also the place to write down your actual measurements. When your procedure
says, “weigh out 10g,” the data should list the actual mass measured (for example,
10.082g).
Post-lab
• Summarize your work in the lab, including a discussion of problems and
successes. Explain the mechanisms of any reactions that occurred. Demonstrate
that you understand what you were doing in the lab and weren’t just following
directions.
•
Analyze the data you collected, including all calculations. Discuss your results,
but also go further. There are many times when research doesn’t give the
expected result. If your procedure didn’t result in the product or data you were
expecting, it is important to understand why. (There could be many possibilities,
so don’t limit yourself to just one.) As long as you can explain your results, your
experiment is considered a success.
20
•
Lastly, explain what you’re going to do with your product(s), information, and
results in the next lab. How will the procedure and results from today allow you
to move forward with your overall experiment?
21
E.3. Sample Laboratory Notebook Entry
22
23
24
6
F. Laboratory Notebook Grading Rubric
Student Name:
Caclculations
Observations
Procedures
Postlab
Mechanisms
& Structures
Reaction
Tables
Organization
Table of
Contents
Performance
Element
TA Name/Section:
Excellent
Good
Fair
Poor
10-9pts: A table of contents is
present and orderly with page
numbers, a summary diagram and a
title for each entry. Page numbers
for subsection are also included.
8-6pts: The TOC lists all
entries and subsections, but
may
be
unorganized,
messy or missing some
diagrams.
5-4pt: Titles, diagrams
and/or page numbers are
missing for several entries
or entries are missing
entirely.
3-0pts: The index
is unclear, messy
and missing the
majority of the
required
components.
20-16pts: Each experiment is
clearly divided into the Prelab, InLab, and Post-lab sections with
their respective subsections as
described in the course manual.
Each Prelab contains TA signature.
15-11pts:
3
5
experiments are NOT
divided into the correct
sections or are unclearly
divided or poorly written.
10-6pts: 6 - 8 experiments
are not divided into the
correct sections or are
unclearly divided or poorly
written.
20pts: A reaction table is present
and calculated correctly for all
experiments using the starting
material values given in the manual
or textbook.
15-11pts: 3 – 5 reaction
tables
are
missing,
calculated incorrectly or
missing data.
10-6pts: 6 – 8 reaction
tables
are
missing,
calculated incorrectly or
missing data.
5-0pts: More than
8
of
the
experiments
are
not divided into
the
correct
sections and are
unclearly divided
or poorly written.
5-0pts: More than
8 reaction tables
are
missing,
calculated
incorrectly,
or
missing data.
20pts: Arrow pushing mechanisms
are drawn in the postlab for each
experiment where appropriate.
Alternatively,
the
chemical
structure of each component used
during the lab is illustrated.
15-11pts: 3 – 5 needed
mechanisms are missing or
incorrect.
10-6pt: 6 - 10 needed
mechanisms are missing or
incorrect.
5-0pts: More than
10
mechanisms
are missing or
incorrect.
10-9pts: The Prelab and Inlab
procedures are detailed and correct
for each experiment.
Inlab
procedure
is
authentic
and
accurately reports experimental
details as well as procedural details
related to data collection such as
mp, bp, GC, IR, etc.
10-9pts: Observations are noted
for each experiment with details
including TLC, color changes,
precipitation, etc. Also, charts and
graphs
are
recorded
where
necessary.
Data such as IR
frequencies, GC peak ratios, bps
and mps are also recorded.
10-9pts:
Calculations such as
percent yield, Rfs, & GC peak
ratios are present, correct and
clearly labeled for each experiment.
The calculation is performed
correctly and clearly demonstrated
by showing ALL work.
8-6pts:
Overall,
procedures lack some
detail and thought, but are
generally well written.
Data
is
collected
accurately.
5-4pt: Several procedural
steps may be missing or
lacking detail. Some Inlab
procedures may mimic
textbook procedures.
3-0pts:
The
majority
of
procedures either
copy the textbook
exactly or lack
enough detail to be
useful.
8-6pts:
Some relevant
details are missing, but
observations are generally
thorough
and
clearly
written.
5-4pts: Observations lack
several details and/or are
unclearly written.
3-0pts: Few to no
observations are
recorded.
8-6pts:
3 – 5 needed
calculations are missing or
incorrect.
5-4pts:
6-10 needed
calculations are missing or
incorrect.
3-0pts: More than
10 calculations are
missing
or
incorrect.
Total Score (100 pts) 
Earned
Points
25
G. Mattson Genesis II Infrared Spectrometer
Operating Instructions
IR Measures the Energy Absorbed by Molecular Bonds
Whose Dipoles Change Due to Stretching and Bending
δ+
δ−
δ+
δ−
δ+
δ−
δ−
δ−
δ+
N-H O-H
3400
δ−
δ+
δ+
C(sp)-H
C(sp2)-H
C(sp3)-H
3000
CO2
(2380)
2600
C
N
C C
2200
C
1800
O
C
C
C
fingerprint
region
C O
N
1400
1000
-1
wavenumber (cm )
Obtaining an IR Spectra
1.
2.
Uncover the IR spectrometer.
Turn the IR power ON. The power switch is located in the rear left corner of the IR. Check that the power
is on by visualizing the green LED light on the front lower corner.
3. Turn on the computer.
4. Open the application, WinFirst Lite.
5. If control panel is not already open, click on TOOLS then CONTROL PANEL.
6. In the control panel box click on METHOD SETUP. Set the number of scans for the background and the
sample and click OK.
7. Place the appropriate background in the IR spectrometer. This will be air for KBr pellets.
8. Click on BACKGROUND then SCAN in the control panel.
9. Observe a proper emisivity curve for you background. DO NOT close this window.
10. Maximize the now minimized control panel.
11. Place your sample in the IR spectrometer.
12. Click SAMPLE then SCAN in the control panel. Your IR spectra should appear after scanning is complete.
Spectral Manipulation
1.
2.
3.
4.
5.
Click on MATH then BASELINE. With the mouse, left click 5-10 points on the baseline and then click
OK. This process may be repeated.
Click on MATH then PEAKS. With the mouse, left click at a vertical position above and to the left of the
peaks you wish to select. Drag your mouse across the peaks to a vertical position above and to the right of
the peaks you wish to select. Click OK. This process may be repeated.
Click on DISPLAY then TITLE. Type an appropriate title and click OK.
Click on File, PLOT, PLOT again, then DONE. DO NOT save your file.
Close your spectral window for the next student. It is not necessary for every student to obtain a
background.
Shutting Down the IR Spectrometer
1.
2.
3.
Leave IR ON at all times.
Leave the computer ON at all times.
Cover the IR.
26
H. Using the GLADiATR Attenuated Total
Reflectance (ATR) FT-IR Accessory
H.1. Introduction to Attenuated Total Reflectance
solid or liquid sample
effanescent wave
(0.5 - 5 µm)
total reflection
high refractive index crystal
(e.g. ZnSe, Ge, Diamond)
attenuated
infrared beam
to detector
infrared beam
from source
Figure H.1
The ATR accessory intercepts the infrared
beam of a typical transmission FT-IR spectrometer.
As shown in the figure above, the infrared beam is
directed through a series of mirrors (not shown) into
an optically dense crystal with a high refractive index
(Figure H.1). By adjusting the angle of incidence
between the IR beam and the crystal, the IR beam
can be made to totally reflect within the crystal and
thus exits the opposite end toward the detector. As a
result of this total reflection, an effanescent wave
(decays exponentially with distance) is produced,
which extends partially into a sample that is in direct
contact with the crystal surface. The energy of the
evanescent wave is attenuated (magnitude decreased)
by absorption of the characteristic vibrational
frequencies of the sample. The attenuated wave then
returns to the path of the IR beam and continues to
the detector. Depending on the crystal length and the
angle of incidence, several reflections (typically 9-17)
within the crystal are possible. The diagram above
depicts a single reflection apparatus, which is the
configuration of the ATR accessory in the laboratory.
Crystals are typically made of zinc selenide
(ZnSe), germanium (Ge) or diamond.
While
diamond is the most expensive, it best resists
scratching and tolerates a wide pH range as well as
strong oxidants and reductants.
Diamond was
chosen as the ATR crystal for this laboratory because
of its robustness, long-term cost effectiveness and
useful range (~30,000-2 cm-1).
There are several advantages to ATRspectroscopy as opposed to traditional transmission
spectroscopy.
Most importantly,
sampling is
significantly faster since there is little to no sample
preparation required. This is paramount for large
laboratory settings and is the primary reason the ATR
accessory was added. Additional advantages include:
improved
sample-to-sample
reproducibility,
minimized spectral variation and higher quality
spectral databases for more precise material
verification and identification.
Despite the drastically reduced sampling
time, ATR spectroscopy does present some
challenges.
The spectrum obtained from ATR
spectroscopy is not identical to a spectrum obtained
through transmission techniques. ATR causes shifts
in band intensities as well as small, but significant
shifts in absolute frequency. The intensities of
spectral features are dependent on the penetration
depth of the evanescent wave, as well as the
wavelength of IR radiation. This is especially true at
shorter wavelengths (higher wavenumbers) where
the penetration depth of the evanescent wave is the
smallest. Consequently, typical signals from 40002800 cm-1 (e.g. C-H, N-H & O-H vibrations) may be
missed if there are not a sufficient number of scans,
proper sample-to-crystal contact is not achieved or
tuning and alignment are inadequate. The most
serious artifact of ATR, however, is the absolute shift
in frequency since this may make interpretation and
spectral comparisons ambiguous.
If an ATR
spectrum representative of a transmission spectrum
is desired, the ATR spectrum must be processed with
ATR correction software. Currently, there is no such
correction software for the laboratory IR instrument,
so care must be taken when comparing ATR spectra
to transmission spectra.
Additionally, diamond crystals also have a
strong phonon absorption band between 2300 and
1800 cm-1. While this is normal, and should subtract
well if a proper background scan is conducted, the
signal-to-noise ratio in this region, which is typical of
alkynes and nitriles, may be reduced.
Finally, for successful spectral acquisition,
the sample must closely contact the crystal surface
since the evanescent wave only propagates 0.5-5 µm
beyond the surface of the crystal. The following
sections describe the sampling procedures and
configurations for solids and liquids, which will
maximize the sample-crystal contact and thus the
spectral quality.
27
H.2. Instructions for Solid Sampling
Transmission IR spectroscopy requires that infrared light be able to pass through (transmit) the
sample. This, of course, is not possible in the case of opaque solids. Therefore, they must be prepared
by one of three methods, which will allow the transmission of infrared radiation: dissolution in a solvent,
dispersion in mineral oil (nujol mull) or suspension in a compressed, transparent KBr disc. Each of these
techniques has inherent disadvantages. Potassium bromide discs are particularly challenging since a
number of conditions must be precisely met to obtain a transparent disc. In the event that the ATR
accessory is not available, a full-description of and instructions for the KBr method can be found on the
following pages.
ATR-IR spectroscopy, which does not require that infrared radiation transmit completely through
the samples, eliminates most of the above difficulties. Since the effanescent wave only propagates 0.5-5
µm beyond the surface of the crystal into the sample, the only requirement is that the sample make
intimate contact with the crystal. This is achieved by pressing the solid onto the crystal with a highpressure clamp, which is preset to 40 pounds of force. Powders and soft pliable films can typically be
used without any additional preparation. Crystalline solids should be ground in an agate mortar and
pestle before application. Irregularly shaped solids and granular, large bead solids may require a swiveltip and concave tip attachment, respectively. Contact your instructor if either of these attachments is
deemed necessary. Follow the instructions below for spectrum acquisition of a solid sample.
1.
If the pressure clamp is in the down position, press the black knob on the top of the arm and gently
tilt the arm backward until it locks into position. Ensure that the crystal surface and tip are clean. If
necessary, follow the cleaning procedure on the following page.
2. Run a background scan with a minimum of 64 scans by following the general IR instructions on the
previous pages. Consult your TA to determine if more scans are required. Alternatively, consult your
TA to load the pre-run background for the number of scans you require.
3. Place a small amount of solid powder (grind in a mortar and pestle if necessary) directly onto the
surface of the crystal. Thick layers of solid should be avoided for optimal spectra.
4. Lower the pressure clamp. Then, lower the pressure tip onto the solid sample by turning the dial
clockwise until the clutch slips (clicks).
5. Scan your sample according to the general IR instructions on the previous pages. Be sure to use the
same number of sample scans that were used for the background. (Minimum 64 scans.)
6. After scanning, turn the pressure dial counterclockwise until the pressure tip clears the sample. Raise
the pressure clamp by following step one.
1
2
3
4
5
6
28
H.3. Instructions for Liquid/Oil Sampling
In transmission IR spectroscopy, liquids and oils are typically applied as thin films onto transparent NaCl
discs or onto PTFE (polytetrafluoroethylene, Teflon®) cards. While these techniques are fairly easy to
perform, replacing NaCl discs and purchasing disposable PTFE cards is costly for large laboratory classes.
ATR-IR spectroscopy, in contrast, does not require any consumable materials. The liquid or oil is applied
directly onto the crystal. Because the contact between the crystal and a liquid is inherently close, the high
pressure clamp is not needed. Rather, a liquids-retainer is placed over the crystal; evaporation is further
prevented by using a volatiles-cover. For non-volatile liquids and oils, neither the retainer or cover is
necessary. Follow the instructions below for spectrum acquisition of a liquid sample.
1. The pressure clamp is not needed for liquid sampling. If the pressure clamp is in the down position,
press the black knob on the top of the arm and gently tilt the arm backward until it locks into position.
Ensure that the crystal surface is clean. If necessary, follow the cleaning procedure on the following
page.
2. Run a background scan with a minimum of 32 scans by following the general IR instructions on the
previous pages. Consult your TA to determine if more scans are required. Alternatively, consult your
TA to load the pre-run background for the number of scans you require.
For non-volatile liquids and oils:
3. Apply one drop of liquid/oil directly onto crystal surface. The liquids-retainer and volatiles cover are
not needed. Proceed to step 7.
For volatile liquids:
4. Place the liquids retainer onto the crystal plate with the Teflon gasket facing toward the crystal.
Ensure that the crystal is visible through the opening in the liquids retainer.
5. Apply 2-3 drops of the liquid sample onto the crystal through the opening in the liquids retainer.
6. Place the volatiles cover over the opening of the liquids retainer
7. Scan your sample according to the general IR instructions on the previous pages. Be sure to use the
same number of sample scans that were used for the background.
8. When finished, remove the volatiles cover and the liquids retainer. Clean the volatiles cover, liquid
retainer and the crystal surface according to the directions on the following pages.
1
2
4
5
6
7
29
H.4. Cleaning the ATR Crystal and Pressure-Tip
Cleaning the pressure tip and crystal surface after every sample acquisition is important to protect the
surface of the crystal, to prevent corrosion of the steel plate, to ensure proper chemical hygiene and safety,
and to prevent cross-contamination, which could lead to misleading results. Zinc selenide (ZnSe) and
germanium (Ge) crystals are easily scratched with abrasive products such as Kleenex, Kimwipes, paper
towels and most paper products. While diamond is resistant to scratching, it is good practice to clean
every crystal with the mildest products possible. This is particularly true where crystals are frequently
interchanged, which may be the case in the teaching laboratory. Therefore, never use paper products to
clean the ATR crystal. Only use soft cotton products, such as Q-tips, and a mild solvent such as ethanol or
isopropanol. For stubborn samples, acetone or dimethylformamide may be used. Follow the instructions
below for proper cleaning of the crystal surface, liquids retainer, volatiles cover and pressure tip.
Liquids Retainer and Volatiles Cover
Clean the liquids retainer and volatiles cover with a Q-tip. First, absorb the excess liquid from each piece
with a dry Q-tip. Then, place a couple of drops of isopropanol onto the clean end of the Q-tip and wipe
away the remaining residue. Repeat with a new Q-tip if necessary.
Crystal Surface (Liquid Samples)
1. Wipe away the excess liquid or oil from the surface of the crystal and metal plate with a dry Q-tip.
2. Saturate the end of a clean Q-tip and wipe away the remaining residue from the crystal surface and
metal plate. Repeat with a new Q-tip if necessary.
Crystal Surface (Solid Samples)
3. Place 2-3 drops of isopropanol onto a Q-tip and remove excess solid with a dabbing motion.
4. Saturated the clean end of the Q-tip with isopropanol and wipe away remaining residue from the
crystal surface and the metal plate. Repeat with a new Q-tip if necessary.
Pressure Tip
5. Place 2-3 drops of isopropanol onto a Q-tip and wipe residue off of the pressure tip.
1
2
3
4
5
6
30
I. Preparation of a KBr Pellet for Solid Samples
in Transmission Infrared Spectroscopy
1
2
3
4
5
6
7
8
9
1. Obtain a die set (1 nut, 2 bolts) from the stockroom. You will need to leave your UIC ID as a deposit. Do not loan your die
set to others since you will be held responsible for its return. Also, obtain a bottle of KBr and a small mortar and pestle from
the oven in room 3223 SEL.
2. Place 2-3 spatula measures (depending on size) of KBr into the mortar. This should be approximately 100 mg.
3. Add 1 very small spatula tip of your solid sample to the KBr. This should be approximately 1-2 mg. Generally, the ratio of
KBr to sample should be 100:1. Excess sample will prevent the mixture from turning transparent when compressed. Grind
the mixture with the pestle. Ensure that the KBr and your sample are homogenous.
4. By hand, screw one bolt into the nut fully.
5. Add approximately 2-4 small spatula tips of the mixture to the open end of the nut so that the face of the bolt is covered
completely. Excess mixture will cause the pellet to be opaque; too little and the pellet will not adhere to the interior surface
of the nut.
6. By hand, screw the remaining bolt into the nut as far as it will go; then, finish tightening with the wrench located in 3223
SEL. Tighten the bolt as much as possible with one hand; wait 15 seconds. Only tighten the last bolt.
7. Remove both bolts gently—first with the wrench, then by hand. Hold the nut up to the light and check that the KBr pellet is
secured and is transparent, particularly through the center.
8. Obtain a background scan of air only (8 scans). Then place the nut onto the holder in the infrared spectrometer. The holder
may need to be inserted into the front slot of the sample compartment if it has been removed. Scan your sample (minimum
16 scans, ideal 64 scans). More scans may be needed if your pellet is slightly opaque and/or your sample is very dilute.
9. Empty the unused mixture into a waste bottle and wash any remaining residue into the waste bottle with acetone only. Do not
use water. Return the mortar, pestle and KBr bottle to the oven. KBr bottles should be placed on the top shelf only to prevent
the bottle from melting.
J. GOW-MAC 350/400 Gas Chromatograph &
Vernier LabPro™ ADC Operating Instructions
Obtain a Gas Chromatograph
1. Turn the GC power ON.
2. Turn the TCD (Thermal Conductivity Detector) power ON if it is not on already.
3. Open the MAIN helium tank valve. Check to make sure the tank is not empty and that the initial
pressure is 15-20 psi.
4. Plug the power cord into the LAB PRO analog to digital converter (ADC). This is the green
rectangular box in front of the GC.
5. Turn on the computer.
6. Open the Logger Pro 3 application. There is a shortcut on the desktop.
7. Click OK in the first dialog box that appears.
8. Click on FILE then OPEN.
9. Open the appropriate file for the experiment you are running. The correct path to your files are
C:/HP Pavillion  PROGRAM FILES  VERNIER SOFTWARE  LOGGER PRO 3 
EXPERIMENTS  CHEM 233 or CHEM 235. The EXPERIMENTS folder will most likely be
your starting folder after clicking OPEN.
10. Adjust the GC settings according to the specifications in the blue box on the screen including
attenuation, carrier gas pressure, column temperature, detector temperature and injection port
temperature. (Note: Allow at least 60 minutes for the column temperature to equilibrate.)
11. Follow the instructions in the pink box for obtaining your gas chromatograph.
12. Click on FILE then PRINT GRAPH. Enter your name in the dialog box that appears and click on
OK. DO NOT save your file.
13. The next student will click on COLLECT, then on ERASE AND CONTINUE in the dialog box.
Shutting Down the GC
1. Turn the GC detector power OFF.
2. Turn the GC main power OFF.
3. Close the MAIN helium tank valve.
4. Unplug the LAB PRO ADC power cord. DO NOT unplug from the wall.
5. Close the Logger Pro 3 application. Do not save any file.
6. Shut down the computer.
K. Infrared Spectroscopy Primer
Infrared spectroscopic methods and theory are taught in Organic Laboratory I (CHEM
233). This primer is provided in the CHEM 333 manual only as review.
Functional Groups
A functional group is a defined combination of atoms with specific bond types and
constitution (bonding order) within a molecule that accounts for the physical properties
as well as the chemical reactivity of that molecule. Draw an example, either specific or
general, of each functional group below.
Alkane
Alkene
Alkyne
Nitrile
Alcohol
Amine
Ether
Carboxylic Acid
Ester
Amide
Ketone
Aldehyde
(C-H, 2850-2760 cm-1)
(C=O, 1725-1705 cm-1)
Haloalkane
Nitroalkane
O
C
H3C
H
33
Valency
Valent electrons are those in the outermost atomic orbitals. These are the electrons
responsible for forming chemical bonds. Therefore, valency is another way to say
bonding. For example, a tetravalent carbon atom has four bonds, while a trivalent
carbon atom has three bonds. Most of the bonds encountered in this course are
covalent, meaning, the valent electrons are shared (co-) between the two atoms they are
holding together. This sharing is not always equal, however, resulting in slight
separation of charge between the atoms. More electronegative atoms pull the electrons
in the bond closer, resulting in partial negative charge. The less electronegative atom
then is partially positively charged. Greater differences in electronegativity between the
two atoms in the bond cause greater separation of charge between them, otherwise
known as a dipole. Using the diagram below as a guide, draw a dipole arrow for every
bond drawn in the following molecules.
covalent 2
electron bond
more
electronegative
atom
less
electronegative
atom
dipole arrow
δ
δ
(partially negatively charged)
(partially positively charged)
O
H
H
H
O
C
O
H
H
C
H
C
H
C
O
H
O
H
C
H
H
H
1. Using a periodic table, rank the two sets of atoms in order of increasing
electronegativity (1 = least electronegative, 6 = most electronegative).
H O B C F N
C Si O Cl F H
2. What is the trend in electronegativity moving left to right across the periodic table?
Why?
3. What is the trend in electronegativity moving top to bottom in the periodic table?
Why?
34
Infrared Spectroscopy
Simply put, infrared spectroscopy measures the bond’s dipole (a.k.a dipole moment, m)
when it stretches or bends (see figure below). Yes, bonds are stretching and bending
constantly. Sometimes these actions are generally called vibrations. The energy
associated with each stretch and bend can be described either in terms of frequency (ν)
or wavelength (λ). Remember that E=hν and c=νλ. Bonds with no dipole moment are
not IR active. All of the frequencies of molecular stretching and bending occur in the
infrared region of the electromagnetic spectrum, hence the name. The frequency
associated with stretching or bending depends upon the strength of the bond and the
mass of the atoms at either end of that bond, analogous to a spring. This unique
property of bonds allows us to identify functional groups using infrared spectroscopy
based on the frequencies of infrared light absorbed by an organic compound. Organic
chemists generally measure the frequency of bond stretching and bending in reciprocal
centimeters (1/cm or cm-1) also known as wavenumbers. Higher wavenumbers
correspond to lower wavelengths, higher frequencies and thus higher energies. Using
the tables of IR frequencies beginning on page 247 in your textbook, fill in the
approximate median frequency for each bond type below.
IR Measures the Energy Absorbed by Molecular Bonds
Whose Dipoles Change Due to Stretching and Bending
δ+
δ−
δ+
Bond Type
C C
single bond
C C
double bond
C
δ−
δ+
δ−
δ−
δ−
C
δ+
triple bond
δ+
Bond Strength
(kcal/mol)
81
δ−
δ+
Median Wavenumber
(cm-1)
1300-625
“fingerprint region”
145
198
4. From the table above, what general conclusion can you draw about the frequency of
vibration and bond strength?
5. The strength of a C—H bond is 98 kcal/mol. Based on this information and the table
above, predict the approximate IR frequency for a C—H bond and write this below.
35
36
6. Look up the actual frequency of a C—H vibration in an alkane. Explain the drastic
difference compared to your approximation above. Can you make IR frequency
conclusions based solely on bond strength? What other property must be
considered?
7. The ketone IR frequencies of cyclohexanone and cyclohex-2-enone are indicated
below. Use resonance structures to help explain why the IR frequency in cyclohex-2enone is lower than cyclohexanone.
IR = 1714 cm-1
IR = 1687 cm-1
O
C
O
C
Cyclohexanone
Cyclohex-2-enone
8. Alcohols, carboxylic acids and water exhibit a very broad O—H peak between 32002600 cm-1. Broad peaks are typically associated with intermolecular interactions
resulting in multiple bonding scenarios. What intermolecular interaction between
the molecules of these three compounds might explain their broad peaks?
9. Symmetrical alkynes, such as the one shown below, do not show an IR absorption for
the carbon-carbon triple bond. Why?
C C
10. Wavenumbers are defined as 1/l(cm). Using this equation, convert a wavelength of
5000 nm into wavenumbers (cm-1).
11. Microns—also known as micrometers (µm)—is another common unit used by
chemists to measure infrared energy. A helpful equation for quickly converting
between wavenumbers and microns is as follows: wavenumbers(cm-1) =
10,000/microns(µm). Using this equation, convert a wavelength of 6 microns (µm)
into wavenumbers (cm-1).
37
Examples of Infrared Spectra: Characteristic Vibrational Frequencies
12. Circle the appropriate infrared peak in the spectra for each bond motion highlighted
in red (bold). The first structure has been completed for you as an example.
Structure
Infrared Spectra
100
1
3
80
1
H
H H
C
C
C
H2
H
3
H
C
H
2
CH3
C
H H
60
40
H
2
20
hexane
4000
3500
3000
2500
2000
Wavenumbers
1500
1000
500
3500
3000
2500
2000
Wavenumbers
1500
1000
500
3500
3000
2500
2000
Wavenumbers
1500
1000
500
100
H
H H
C
H
H
C
H3C
C
C
H
5
H
C
H
H
4
80
60
40
20
1-hexene
4000
6
H
C
H3C
C
7
1-hexyne
100
80
9
H
N
C
O
8
3-hydroxy-propionitrile
60
40
20
4000
38
100
H
H
H
H
C
O
80
C
H
60
H
C
9
5
4
40
prop-2-en-1-ol
(allyl alcohol)
20
4000
3500
3000
2500
2000
Wavenumbers
1500
1000
500
3500
3000
2500
2000
Wavenumbers
1500
1000
500
3500
3000
2500
2000
Wavenumbers
1500
1000
500
3500
3000
2500
2000
Wavenumbers
1500
1000
500
100
O
10
80
C
C
Bu
O
60
4
C
H
N
H
40
11
20
2-amino-benzoic acid butyl ester
4000
100
O
10
80
C
H
O
C
C
5
H
60
9
40
H
4
20
cyclohex-2-enecarboxylic acid
4000
100
O
H
C
H
hept-2-enal
80
60
C
C
4
10
H
12
40
20
4000
L. Introductory Lab: Separation, Purification and
Characterization of Fluorene and Fluorenone
O
Fluorene
Fluorenone
Figure L.1
Objective
The objective of this lab is to review the techniques of column chromatography, thin layer
chromatography, recrystallization, IR spectroscopy and melting points that were presented in
CHEM 233 to prepare the CHEM 333 student (that's you!) for the independent use of each of
these techniques in their synthetic projects.
Tasks
Separate a 1:1 mixture of fluorenone and fluorene by column chromatography and thin layer
chromatography. Recrystallize the isolated compounds and obtain an IR (ATR spectrum) and a
melting point for each. Work in groups of 3-4.
Column Chromatography procedure
Column chromatography is a useful method for separating two or more compounds from a
mixture. You may remember performing a micro column chromatographic separation of dyes
using a pipette in CHEM 233. Now its time scale things up to a useful level and practice this
technique so that it will be useful for you in your synthetic projects. The example below is just
that, an example. Column chromatography is more of an art than a science, but serves a useful
purpose in purifying organic compounds. Don’t be afraid to experiment with your technique.
The theory is the same as what was presented in CHEM 233 and can be reviewed in your
textbook and in the CHEM 233 course manual.
1. Choose an appropriate solvent system for your separation.
a. Dissolve approximately 10 mg (very small spatula-tip full) of a 1:1 mixture of fluorenone
and fluorene in ethyl acetate.
b. Run a TLC of the above mixture (Do you remember this from CHEM 233? If not, ask
your TA for help.) Using a binary mixture of ethyl acetate (polar) and hexanes
(nonpolar), determine by trial and error what ratio of ethyl acetate provides an Rf of 0.10.2 for the most polar compound. This will be your solvent system for your column.
Don’t waste solvent; only make 10-15 mL of your trial solutions. Visualize your TLCs by
UV and stain. Ask your TA for instructions on TLC visualization and staining.
c. Prepare approximately 250 mL of this solvent. You may prepare more later if you need.
2. Assemble your column.
a. Place a loosely packed wad of cotton or glass wool at the bottom of the column.
b. Add enough sand to give a level base layer of approximately 1 cm.
c. Add silica gel to a clean beaker. You should use approximately 50 times the mass of
your intended sample to be separated.
40
d. Add enough of the solvent from step 1 to completely cover the silica gel. Swirl this
mixture to obtain a slurry and quickly add this to the column. Use more solvent if
needed. Rinse sides of column and drain excess solvent until the solvent level reaches
the level of silica gel (baseline).
3. Load sample onto column.
a. Dissolve 2.0 g of a 1:1 mixture of fluorene/fluorenone in a minimum amount of your
solvent system. Add a couple drops of ethyl acetate if all the product does not dissolve.
b. Add this mixture gently to the silica layer with a pipette.
c. Rinse sample flask with a small amount of solvent mixture and add this to the silica
layer.
d. Drain column until all of this liquid reaches top of silica layer.
4. Elute Column
a. Continue to elute your column with your solvent system.
b. Collect eluant in 5-10 mL test tubes. You should be able to see the fluorenone moving
through the column; it is yellow. Fluorene, however, is colorless in solution and should
elute first since it is the least polar.
c. Analyze each test tube (several at a time preferably) to determine which contain
fluorenone and which contain fluorene.
5. Isolate Fractions
a. Combine those fractions (test tubes) that contain fluorenone into a round bottom flask of
approximately twice the volume you intend to add to it.
b. Rotovap away the solvent to obtain your solid.
c. Repeat this procedure for the fluorene fractions.
6. Recrystallize each of your solids (fluorene and fluorenone) separately according to the
procedure on the following pages.
41
Recrystallization Procedure
Every recrystallization is unique. Most of the time, more than one attempt is required to
determine the precise conditions necessary. Practice does make perfect in this case. In this
course you should attempt to recrystallize every compound you isolate to obtain high levels of
purity. This will not only provide you with better IRs and more accurate melting points, but
because your syntheses involve several steps, impure intermediates will often complicate the
subsequent reactions. The requirements and process for recystallilzation are summarized in the
figure below (Figure L.2).
Figure L.2
The procedure below utilizes a mixture of a polar (ethyl acetate) and a nonpolar (hexane)
solvent. You will start by adding the nonpolar solvent first and then adding the polar solvent at
reflux until your entire sample dissolves. This method will work well for you most of the time in
this course, as will these solvents. The reverse procedure, however, is also common in organic
chemistry, but a bit more tedious. In that case, your sample is dissolved in a small amount of the
polar solvent and then the nonpolar solvent is added at reflux until just before the point where
your sample would precipitate out of solution. For a more comprehensive review of
recrystallization techniques and methods, consult your textbook and the CHEM 233 course
manual.
1. Add the solid fluorenone obtained from your column chromatographic separation to
an appropriately sized round bottom or Erlenmeyer flask.
2. Add approximately 20 times your sample mass of hexanes. You should have about
1.0 g, so 20 mL should work.
3. Heat the mixture to a gentle reflux on a hotplate or with a heat gun while swirling.
Don’t heat too fast or too high; you’ll just boil away all the hexanes.
4. Now begin adding ethyl acetate dropwise with a pipette until your sample completely
dissolves. Be patient; your sample won’t dissolve the instant you add ethyl acetate.
42
Adding too much of the polar solvent will prevent your sample from crystallizing out
of solution. You want to add the minimum amount.
5. Remove the flask from the heat source and let the solution cool to room temperature.
At this stage you could also perform a hot filtration to remove insoluble impurities,
but since you ran a column previously, you can assume there are no insolubles. Also,
do not agitate your solution; keep it nice and still. Agitation disrupts crystal growth
causing the crystal size to be smaller. Smaller crystals have larger surface area to
volume ratios. Larger surface areas can adsorb more soluble impurities.
6. If at room temperature no crystals have formed, scratch the inner surface of the vessel
at the solvent line.
7. Place your solution in an ice bath.
8. Suction filter your crystals. Wash them with small amounts of hexanes.
9. Obtain both an IR (by KBr pellet) and a melting point of your sample.
10. Compare this data with literature.
11. Repeat for fluorene. Because fluorene is relatively non-polar, you may be able to
recrystallize from hexanes alone without the addition of ethyl acetate.