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Syllabus for CH 339 – Organic Chemistry Laboratory 2 for

Majors

Learning goals:

• To introduce fundamental and advanced reactions in organic chemistry, as well

as several important name reactions

• To introduce organic chemistry concepts, such as catalysis, green chemistry, and

Pd-catalyzed coupling reactions.

• To expose students to fundamental and advanced laboratory techniques

• To show students how to work independently, safely and reliably

• To teach students about good laboratory hygiene, handling of chemicals and safe

working procedures

• To write scientifically sound and logical laboratory reports

• To learn about searches in the literature, and compile reports about chemical

literature

• To learn about multi-step syntheses and conduct a multi-step synthetic route

Dr Alexander H. Sandtorv

Sandtorv@pdx.edu

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Table of contents

Schedule and TAs ......................................................................................................................................... 3 Before Attending the First Lab ..................................................................................................................... 5

Access and Inclusion for Students with Disabilities ................................................................................. 6 Course Grading ............................................................................................................................................. 7

Laboratory Policies ..................................................................................................................................... 10 Laboratory Safety and Safety Protocols ..................................................................................................... 12

Handling Chemicals and Chemical Waste .................................................................................................. 15 Practical Advice .......................................................................................................................................... 18

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Schedule and TAs

Week Week

start Experiments

1 3rd April Diels Alder reaction of a diene found in eucalyptus oil

Oxidation of borneol

2 10th April The Wittig reaction

Acetylation of Ferrocene

3 17th April The Grignard reaction

Fischer esterification

4 24th April Extraction of 3-chlorobenzoic acid, 2-naphthol and acetanilide

The Suzuki cross coupling reaction

5 1st May Lectures concerning the chemistry project

Break

6 8th May Library project

Library project

7 15th May Library project

Experiment 1

8 22nd May Experiment 2

Experiment 3

9 29th May Experiment 4

Experiment 5

10 5th June Finishing up the project

Check out and make-up lab

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Day Time Section CRN TA Email

MW 8.00 a – 11.50 p 011 60706 Joseph Armstrong Joe6@pdx.edu

1.00 p – 4.50 p 016 60708 Austin Shigemoto shigemot@pdx.edu

5.30 p – 9.20 911 60705 Hayden Winter hwinter@pdx.edu

TR 1.00 p – 4.50 p 026 60707 Rory Gallagher Rory3@pdx.edu

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Before Attending the First Lab

Please read the following information carefully.

- Experiments begin on the first day of lab

- Safety goggles are required for all experiments, including the first experiment. The chemistry

stockroom sells the following goggles:

o Pyramex Capstone Goggles: $15

o UVEX V-Maxx Goggles: $8

- A notebook is also required for all experiments. Notebooks can be purchased from the chemistry

stockroom (Composition notebook: $3)

- You are expected to finish all required pre-lab exercises before attending each lab. These are:

o Know the risk and safety precautions associated with all chemicals handled for that

week’s experiment

o Reading the experiment carefully and familiarizing yourself with the lab

o Read and understand the lab slides uploaded in D2L

o Complete a multiple choice quiz online (must be done before the lab starts. The quizzes

are time stamped online).

- If the required pre-lab exercises have not been completed, you are excused from the lab until the

required assignments are completed. You will also receive 0 points for the pre-lab assignment.

- You must bring a hard-copy of the procedure, either a directly printed version or a hand-written

copy.

- Attendance in this lab is mandatory. You must attend all scheduled laboratory sessions. The labs

closing time is strictly enforced, no student is allowed to work overtime.

- If a personal emergency occurs, please contact the professor (sandtorv@pdx.edu) as soon as

possible.

- You are expected to fully read the syllabus and familiarize yourself with all concepts described

herein.

- Repeated phone use is not allowed for non-lab purposes.

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- Organic chemistry labs are not recommended for students who are pregnant, or planning on

becoming pregnant. Please contact Dr. Sandtorv if you have questions or concerns.

Access and Inclusion for Students with Disabilities

PSU values diversity and inclusion; we are committed to fostering mutual respect and full participation

for all students. My goal is to create a learning environment that is equitable, useable, inclusive, and

welcoming. If any aspects of instruction or course design result in barriers to your inclusion or learning,

please notify me. The Disability Resource Center (DRC) provides reasonable accommodations for

students who encounter barriers in the learning environment.

If you have, or think you may have, a disability that may affect your work in this class and feel you need

accommodations, contact the Disability Resource Center to schedule an appointment and initiate a

conversation about reasonable accommodations. The DRC is located in 116 Smith Memorial Student

Union, 503-725-4150, drc@pdx.edu, https://www.pdx.edu/drc.

• If you already have accommodations, please contact me to make sure that I have received a

faculty notification letter and discuss your accommodations.

• Students who need accommodations for tests and quizzes are expected to schedule their tests to

overlap with the time the class is taking the test.

• Please be aware that the accessible tables or chairs in the room should remain available for

students who find that standard classroom seating is not useable.

• For information about emergency preparedness, please go to the Fire and Life Safety webpage

(https://www.pdx.edu/environmental-health-safety/fire-and-life-safety) for information.

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Course Grading

General

The total grade for this course is assigned as follows:

Lab Reports 50% Pre-lab 10%

Lab Technique 40%

There may be curving in this course, but it is to the instructors discretion, so do not count on it.

Grade Points Grade Points

A 100-90 C+ 69-68

A- 91-85 C 67-58

B+ 84-80 C- 57-55

B 79-74 D 55-45

B- 73-70 F <45

Lab reports

Reports must be typed in the format provided in D2L and must be handed in one lab period after the

experiment is completed. Reports must be handed in at the start of the lab period.

The reports will be graded by your TA and returned to you with clear comments and scores. A detailed

grading overview on how to write the report is a provided in D2L. Your TA will also be available to give

you feedback if necessary. The grading of the reports is based on a rubric and meetings between the TA-

pool and the professor.

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Lab Technique

You will be evaluated on your lab technique and performance by your TA. For each lab session, you can

receive a total of 40 technique points, based on four categories worth ten points each:

Is the student able to work in a safe manner? (Safety)

Safety is a number one concern when working in the lab. Safety awareness means handling and disposing

chemicals in a reliable manner, always wearing appropriate safety attire (lab-coat and goggles) and

following instructions from the TA and slides / manual. Unsafe behavior can be: touching face and key-

board with gloves, wearing lab-coat and/or gloves in the hallway, not setting up experiments as described

or handling chemicals in a way that is considered unsafe. Maintaining a neat and safe working space is

also part of safety. You may at any time in the course be asked to answer short quizzes concerning the

hazard statement associated with chemicals used for that lab. The outcome of this quiz will be the safety

grade for that lab.

Is the student able to work independently? (Independence)

We want to encourage students to ask questions and approach the TA if they feel unsure or want to

discuss any facet of the chemistry, but we also wish to encourage students to think critically and make

good and independent decisions on their own. Simple procedural questions that can be answered by

reading the lab journal or adequately preparing should be kept to a minimum. Adequately preparing by

reading the manual, attending the lecture and preparing as needed is expected.

Is the student able to carry out laboratory procedures and apply laboratory techniques in a reliable way?

(Effort)

In this course, we are focused on teaching the students standard laboratory procedures and protocols,

such as extraction, distillation, melting point analyses, and so on. Students that follow instructions and

perform the laboratory procedures in safe, reliable ways will therefore receive points in this category. The

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slides uploaded should provide the necessary background to prepare, along with some time individually

preparing.

Is the student able to write and use a laboratory note book? (Note book)

An important aspect of laboratory work is to make appropriate notes during the experiment. You must

make notes of important observations, and measurements. A full synthesis table is expected for synthesis

experiments, with molecular masses, masses, volumes, densities, moles and other important physical

parameters used during and after the experiment. Your TA may ask to see your notebook at any time.

We wish to highlight that the technique grade is not to give penalties, but to properly award good

behavior and to emphasize proper laboratory practices.

Pre-lab

There are three components to each pre-lab exercise that you are required to complete prior to attending

the lab: reading the lab manual, looking up safety information for relevant chemicals, and answering a

multiple-choice quiz. The quiz is available on D2L. A maximum of 10 points can be rewarded. Your pre-

lab grade is calculated based on the percent score (y) achieved on the quiz

Pre lab grade = y/100 x 10

Library project

The library project will encompass three lab sessions. One of the three sessions will be held at the PSU

library and led by librarian Michael Bowman.

The goal of the project is to compile a representative literature survey concerning two structures that we

later will prepare in the lab through a multi-step synthesis. A detailed description of the project will be

posted on D2L. The project will be worth 270 points (equivalent to three standard laboratory reports)

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Laboratory Policies

What happens if students do not complete their pre-lab assignments?

Students are excused from the lab until the pre-lab has been completed and they receive no points for the

pre-lab assignment.

What happens if students show up late?

If the students are more than 5 minutes late, they lose 20 points from their technical score. If they are

later than 30 minutes, they are excused from the lab. This counts as one missed lab.

What happens if students miss a lab?

Students are only allowed to miss a lab if there is a medical emergency, or an emergency of similar

nature. The student must let the TA and professor know immediately. Make up labs are offered during

check-out. Missing three labs is an automatic no pass.

What happens if the student wants to change labs permanently?

Permanent lab changes are usually not allowed.

What happens if students hand in reports late?

A penalty of 5 points per day is subtracted from the total score of the report. If the report is not handed in

one week after the assignment was due, the student receives a 0 on that report. After two reports not

handed in, the student cannot complete the course.

Please note that lab reports are handed in at the beginning of lab. If the reports are handed during or after

lab, this counts as one day late.

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What happens if students are found to have plagiarized material, either from sources, or from lab-mates

or other individuals?

Copying any material without clearly stating the source of such material is considered plagiarism. This

includes, but is not limited to: the internet, books, written materials, and material written by class-mates,

former students, professors or other teaching staff.

Sections of text that are found to be identical or near-identical with respect to content and information

(but not necessarily word-by-word copies) are also considered plagiarism.

It is the professor’s discretion what penalties will be instated on a case-by-case basis. Point deductions

might be introduced, or in severe cases, expulsion from the course.

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Laboratory Safety and Safety Protocols

General safety

The most important aspect in the laboratory is the safety and well-being of the people that work there.

There are several safety features associated with this lab course:

• Goggles and lab coat should be worn at all times.

• Dress appropriately for laboratory work. You must wear

shoes that cover your entire foot, including the heel. They should fit

up near your ankle; leather is preferred but any non-porous material

is okay. Your clothing must cover your torso and legs down to your

shoes. In addition, you are required to wear a department provided lab

coat while working in the lab. If you show up for lab in inappropriate clothes, you will be asked to

leave and this will count as a missed lab.

• Avoid wearing contact lenses.

• Know the location of the following:

- fire extinguisher - fire blanket

- first aid kit - safety shower

- eyewash fountain - all exits

• No eating or drinking in the lab.

• We generally provide nitrile gloves for handling chemicals. Please note that the protection offered

by these gloves, is minimal and most organic liquids and some solids penetrate the nitrile layer

readily.

• Do not touch keyboards or phones while wearing gloves. Do not touch face with gloves.

• If you find a mercury thermometer in your drawer, please notify your TA. These should be

exchanged for other thermometers immediately.

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Fires

- Most organic chemicals are flammable

- If organic solvents are spilled, soak the solvents up with a paper towel and leave it in the hood to

evaporate. Never dispose of solvents in the waste bin or down the sink.

- Never pour organic solvents around a hot plate in use.

- If a fire occurs, inform your TA immediately.

- If clothing catches on fire, inform your TA immediately. Walk the individual to the safety shower

or roll them in a fire blanket to extinguish the flames.

- For small heat burns hold the burn under cold water for 5-10 minutes. Please report all burns to the

TAs.

Spilled Acids and Bases

- For spills of dilute acids and bases, wash your skin under running water.

- For spills of concentrated acids and bases, immediately wash the contaminated skin under running water

for five minutes. Report the incident to your TA.

- For spills of concentrated acids and bases on clothing, remove the clothing immediately. Report the

incident to your TA.

Chemical splashes in the Eyes

- Immediately wash your eyes at the eyewash station. It is imperative to keep eyes open (sometimes by

force) and let the water run over the eyes for at least 15 minutes. Contact your TA and seek medical

attention.

Inhalation of Organic Fumes:

- If an individual inhales a large amount of organic fumes, report it to the TA.

- The individual should immediately be moved to an area with fresh air.

- If the individual stops breathing, call campus safety (503-725-4404) and 911.

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Cuts

- For small cuts, rinse the affected area under running water and apply a bandage from the first aid kit.

Contact your TA.

- For larger cuts or strong bleeding, contact your TA and call campus safety (503-725-4404) for medical

attention.

- Notify the professor or stockroom personnel if any blood is spilled in the lab so that proper cleanup and

disposal procedures may be followed.

Broken glass

- Do not remove any broken glass from the lab, and do not bring it to the stockroom. Broken glass is

immediately placed in the broken glass waste.

Evacuation

- If evacuation of the lab is necessary, leave through any door that is safe or not obstructed- doors that lead

to other labs may be the best choice.

- Leave the building by the nearest exit and meet your TA on the field next to Hoffmann Hall.

- This would also be the meeting place in the event of an earthquake or other emergency

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Handling Chemicals and Chemical Waste

Handling chemicals

The major safety hazard when working in a chemical laboratory is the handling of chemicals.

- As part of your pre-lab assignment, you should know the risk and safety precautions associated

with all chemicals handled for that week’s experiment.

- Safety information is available by using the chemical’s Safety Data Sheet (SDS). The SDS can

be downloaded from www.msds.com free of charge.

- For a large chemical spill stand under the safety shower and flood the affected area with water.

Remove clothing to minimize contamination with the chemical.

- If any chemicals are spilled, consult your TA immediately.

- If a mercury thermometer breaks, notify your TA immediately. It might be necessary to evacuate

the lab. Do not attempt to clean up on your own

- Chemicals should not be handled on the bench

- Never pick up a bottle by its lid

- For liquids, do not place your own pipet, dropper, or spatulas into the reagent jar. Pour a small

amount into a beaker and measure from that

- Never put any excess reagent back in the reagent jar.

- Never taste a chemical or solution.

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Labels

Chemicals in our laboratories have been marked with the following labels.

(1) Name of chemical

(2) Pictograms depicting the various health and safety hazards associated with the chemical

(3) Health statements

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Handling chemical waste

- All chemical waste must be disposed of in a proper way, and in general, no waste generated in the lab

should go down the sink.

- There are four chemical waste categories, all available in your fume hood. Each experiment has a specific

description of where waste should be placed. Ask your TA if unsure.

• Organic waste

• Halogenated waste (only appropriate for a few experiments)

• Solid waste

• Aqueous waste

- There are also waste bins available outside of the hoods. These include:

• General waste bins (none of the chemicals handled should be placed in this bin)

• Broken glass container

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Practical Advice

During the laboratory course you will become acquainted with organic reactions and purification

techniques. You will also learn about how to be a productive and respectful member of a laboratory. This

primer will help guide you through many of the techniques and “rules” you should learn during your time

in our organic chemistry labs.

- How to clean glassware: Most of the reagents used in your labs will be readily soluble in either a

very polar inorganic solvent (such as water) or a polar organic solvent (such as acetone). An

acetone squirt bottle is in your hood to aid with rinsing glassware. All acetone rinse waste should

go into the organic waste container in your hood. Acetone should never be used out of the fume

hood and should never be poured into the sink. After rinsing with acetone and letting it dry, the

glassware can be washed at the sink with soap and water if necessary.

- Upkeep of hot/stir plate: wipe down surface after it cools with a damp sponge.

- Cleaning a hood at the end of class: wipe down the hood with a moist sponge to remove any solid

residue or sand, then dry the hood with a small paper towel. Spills should be cleaned up using

proper techniques during the lab.

- The uncertainty of spilled materials left out: If you spill something, clean it up. If you do not

know how to clean it up, ask your TA. If you spill a large amount of material, consult your TA.

Here are some basics:

• Acids: Shake spill neutralizer on this spill until liquid is covered and fizzing stops. Pick

this up by brushing onto a piece of paper and put it into the trash. Use a wet paper towel to

pick up any residue.

• Solids: scoop the solid up and put into the solid waste jar. Pick up remaining residue using

a moist paper towel and throw it away in the trash.

- Gloves: Please be aware that nitrile gloves do not provide protection against most organic

solvents. Change gloves every time something has gotten onto the glove, with stress put on

prevention of contamination rather than the gloves providing protection. Wearing the same gloves

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for longer periods of time is not good practice, because many contaminants can diffuse through

the glove over time. Do not touch your face with gloves.

- How to weigh solids: Solid should not be added to a receptacle (weigh boat) that is already on the

scale. The receptacle should be removed from the scale after taring, have solid added to it, then

placed back on the scale for reweighing. Repeat as necessary until desired amount is acquired.

- Proper salt plate cleaning technique: Do not get water on salt plates, they are made of

compressed sodium chloride and will dissolve. After a salt plate is used, the sample should be

wiped from the salt plate using AR acetone (which is acetone of a higher purity) and folded kim-

wipe. Rub the salt plate on/with the acetone moistened kimwipe, then on a dry area of the kim

wipe. Use DCM with extreme caution.

- Use of solvent/acid pumps: Chemical resistant pumps (cost: $600-900) are used in the lab to aid

with dispensing small amounts of liquid reagents. As long as the pump is set to the desired

volume, they accurately dispense even a small amount of liquid.

• These flammable (red) and general (yellow) pumps work by gravity. Pull the plunger up,

then release and watch your solvent being dispensed. The acid (green) pumps work by

pressure. Pull the plunger up, then depress the plunger until it stops.

- Using sodium sulfate to dry a liquid: add sodium sulfate(s) to your liquid in small amounts until

the sodium sulfate is free flowing instead of clumping. You do not need to weight sodium sulfate

out, just scoop a little directly into your container.