Chemistry 114:   Advanced Organic Chemistry

 

Roy K. Okuda, PhD                                                                   Fall 2006

Office:  Duncan 9A                                                                                lecture: W  1330-1430                                             lab:    MW  1030-1320

Phone: (408)-924-2525                                          email:   okuda@sjsu.edu

Office Hours:  Tu 3:00-4:15pm, W 3:30-4:30pm, F 10:00-11:00am                                                              

 

Prerequisites:   Chem  113B (with a grade of "C" or higher, "C-" not acceptable), Chem 55, Chem 100W is a prerequisite (required to take 114). If you did not take Chem 113B at SJSU, you must get the consent of  the instructor.  You may be asked to provide information on prerequisite courses taken at other institutions (syllabi, coursework, texts, etc). 

 

 

Required Texts:        Silverstein, R.M., Webster, F.X.; Kiemle, D.J. Spectrometric Identification of Organic Compounds, 7th ed.(multicolor cover), 2005.

Pavia, Lampman, Kriz    Introduction to Spectroscopy, 3^rd edition,

2000.

                                    Dodd, Janet S.  The ACS Style Guide (recommended)

 

Other Needs: Lab Notebook (one which allows for duplicate pages)

                                    Ruler (at least 6", preferably transparent)

                                    Calculator

                                    Pencils

 

GENERAL INFORMATION AND EXPECTATIONS

As the title of this course implies, Chem 114 is intended to provide you with experience in more advanced procedures over what you learned in Chem 113A and 113B.  It is particularly designed to give you greater familiarity with the manipulation, synthesis, and analysis of organic compounds, and to give you some exposure to research in this area of chemistry.  As a "Capstone" course in Chemistry, Chem 114 is designed to encourage you to apply your basic knowledge in chemistry to solve experimental problems and to design solutions.  In some cases, you will be given only general instructions, and you will have to decide how to proceed.  In other cases, you may have to troubleshoot a challenging reaction or lab procedure with little input from the instructor.  In addition, oral and written communication skills will be stressed in Chem 114.

 

Briefly, this course will involve 2 Sections.  Section 1 will consist of two unknowns (one will be pure, and the other a binary mixture), and you will be expected to identify the individual components (after separation, if necessary) using spectroscopic techniques.  This section is also intended to give you a chance to re-familiarize yourself with the lab equipment and bench techniques, as well as with spectroscopy.    Section 2 will be more "free form" and will entail a short-term "Mini-project."    You will research a topic of interest to you, and develop a protocol to perform the project in class.  At the end of the semester, you will present the results of this project orally during one of the last lab meetings. The presentations will be done in the format of an American Chemical Society "symposium" and you will give your talk using PowerPoint.   Both sections also include progress reports (written or oral) and a written formal report.

 

Since this is the third semester of organic labs, you will be expected to have a good understanding of the following forms of spectroscopy that we covered in Chem 113A and 113B:  1H and 13C NMR, COSY 2D NMR, IR, and mass spectrometry.   You should immediately begin to review the appropriate sections of your textbooks, since you will use these methods in lab from the very start of the semester.   Although we will be reviewing these techniques in the Wed 1:30pm lectures during the next 15 weeks, it is to your benefit to have a working knowledge now.  You should note that the scheduled lecture on Wednesday will only give a brief overview of each spectroscopic method, and will not emphasize problem solving using that method. You will be expected to work problems on your own, including from the textbooks, problem sets  online resources. An optional problem solving session, scheduled as "Chem 190, Section 1 (1 credit)" will be held every Monday at 1:30pm    However, since much of the emphasis on this course will be on structure proof or confirmation (read: a lot of this on the quizzes and final), these sessions are highly recommended.

 

 

 

 

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It is also assumed that you are familiar with other basic laboratory techniques, such as extraction, distillation, GC, TLC and column chromatography, reflux, recrystallization and other techniques which were covered in Chem 113A and 113B. You may wish to re-acquaint yourself with the appropriate section in your Chem 113A lab book or any organic chemistry laboratory textbook, or the SJSU Chem 113A website, which has photos and videos of nearly every method we will use. http://www.chemistry.sjsu.edu/straus/visioche.htm    If you have little or no actual experience with these techniques, you should not take Chem 114, but should take either Chem 113A or 113B, depending on your prior experience.  Other techniques and instruments will be introduced during this course.

                                                                                   

GRADING

The grades for this course will assigned as "plus/minus" and will be based on the following categories:

                        Experiment formal reports                   2  x  40pts each    =     80pts

                        Quizzes (drop 1)                                 5  x  10pts each    =     50pts

                        Final exam                                                                        =     50pts

                        Oral presentation                                                              =     20pts

                                                                                                                      200pts

 

In detail:   Each of the two experiments will be worth 40 points.  Of this, 10pts will be assigned to the progress report, and 30pts for the formal report (including the lab notebook, product, and spectral assignments).  Details of the format for the progress and formal lab reports will be provided.

A total of 6 quizzes will be given during the semester.  Five of these quiz scores will be counted to your grade.  You may either: A) take all 6, with the lowest grade may be dropped, or B) take any 5 quizzes, and all 5 will count toward your grade.  In general, makeup quizzes will not be granted except in extraordinary circumstances (i.e. debilitating medical emergencies).  Note that the SIXTH quiz (Dec 6) will be worth "double points" (20pts) and will involve advanced spectroscopic methods for structure analysis (if you take this quiz, it is possible to have >50pts for the quizzes). 

 

 

The final exam will be comprehensive, and will include elements of the lab experiments and the spectroscopy lectures.

The oral presentation, as mentioned, will be done during the end of this semester (Nov 29 and Dec 4).  Each student will present a 20 minute synopsis of the project s/he had chosen for the second experiment. Your presentations will be given in the style of "short-talks" such as may be seen in an ACS symposium.

 

Except in unusual circumstances, any missed deadline for a report will be assessed a penalty of up to 1 point per day past the date.   Late reports for Experiment 1 will be accepted only up until graded reports are returned to the class.  The formal report for Experiment 2 must be received by the date shown on your schedule (2pts/day will be deducted for late reports;  no reports accepted once final grades are sent to the Registrar).  Use the attached schedule to plan your time accordingly, and preparation for the lab will help you immensely.  All formal reports are mandatory:  for each formal report not turned in, 10 points will be deducted from the total points accumulated for the semester.

 

Note that the final 114 grade is based on a conglomerate of the individual graded items (each item is not assigned a "grade").   So, if you have a somewhat low point total on one item, you can make it up with a better point total of another graded item. The course grades are given on a "+/-" system, and the instructor may modify the point total up to 10% higher or lower based on a student's performance in the lab (such as preparation and efficient use of time, attendance, general lab skills, etc.).  Historically, course grades have typically been based on 90% A range, 80% B range, 70% C range, etc.   These may be modified for the actual course grade, but usually are not far out of these ranges.  A "bell curve" is not used to determine grades. 

 

NOTEBOOK  (also see attached guide)

 The following points also apply:

1.  Use a notebook which has duplicate pages (e.g. National brand #43-649).  Either carbon or "carbonless" styles are fine.  If you have a partially-used notebook from 113B, you may continue to use it for 114. 

2.  Reserve the first 2-3 pages for a Table of Contents.

3. All entries must be in ink (absolutely no pencil!), and any changes should simply be crossed out (never erase or use            "white-out")

 

 

 

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NOTEBOOK  (continued)

 

4. Enter your observations, measurements, and analysis as they occur - don't rely on scraps of paper for transfer    later. 

5. Before you begin any experimental procedure, you should enter your introduction, a flow scheme, and mechanism          (if appropriate) for that day's work.

6. Criteria for grading will include organization, legibility, and completeness.  Please note that the notebook does not       have to be absolutely neat, the main point is that it can be understood by someone else.

7.  At the end of each experiment, be sure to include a brief summary of your results and discussion.

 

PROGRESS REPORT

A 2 to 3-page progress report (or project proposal for the Mini-project) will be due for each experiment on the dates shown on the schedule.  This report is meant to help you organize your thoughts on the experiment up to that point, and to ensure that you are heading in the right direction. Time permitting, we may also have everyone provide an oral version of their progress report.

                                                                                   

FORMAL REPORT

At the conclusion of each experiment, a typewritten formal report is due (see schedule).  The body of this report should be organized according to the format of a Journal of Organic Chemistry (JOC) "Note."  Please note that this report should be an expanded version of your lab notebook, not simply a re-statement of your entries.  Emphasis will be placed on organization, grammar and spelling, and thoroughness (i.e. the ability of the reader to understand what you did and what results you obtained).   These reports will be graded with comments (if time allows) and returned to you. 

 

The full formal report is really a package of items, and includes:       

                                    A)        A printed copy of the written formal report (in JOC Note Style)     

                                    B)        The duplicate pages from your notebook

                                    C)        All spectra (e.g. GC, IR, MS, NMR) with assignments written on them

D)            The products (if requested)

E)             Copies of any references used in your report (other than class textbooks)

F)             An electronic version submitted to turnitin.com  

All of these items must be submitted by the due date and time to be considered for full credit. 

 

Chemical Safety (CHEM 120S)

Chemistry 120S (Chemical Safety) is a required course for all chemistry majors and minors, and a prerequisite for all students involved in Chemistry 180 or 298 research courses.

 

SAFETY

            Before you will be allowed to work in the laboratory, all students in Chem 114 must:

            1.  read the "SJSU Dept. of Chemistry Safety Rules and Regulations for Upper Division and                Research Laboratories", and sign and turn in the slip at the end of the document,

                        indicating you have read and understand the rules and regulations.

            2.  attend the safety lecture (first lab meeting), and

            3.  view the Safety film:  if you have not already viewed a safety film at SJSU, you must attend one of the scheduled screenings and turn in to the instructor the form signed by both you and the proctor that you attended the showing of the film. If you viewed a safety film in 113A or 113B, you can turn in a signed viewing form.

 

All of the above conditions are mandatory, and must be completed before you will be allowed to work in the lab!

 

            In addition to the points covered above, these are especially worth emphasizing:

            1.  ALWAYS WEAR SAFETY GOGGLES IN THE LAB!!!  (over your eyes, not on your forehead!)

            2.  Be aware that we will be using some flammable solvents, do not have any flames when you (or someone else in the room) are handling these

            3.  Similarly, treat all acids, bases, and reagents as potential hazards.  Avoid skin contact with all of these, and treat any contact immediately.  If you have a spill, never leave it unattended (let the instructor know).

            4.  Glassware breaks.  Use caution in any experimental procedure, and exchange any chipped or cracked glassware  Also, dispose of all glassware in the special bins, not in the trash cans!

            5.  The texts have sidebars or highlighted sections outlining special safety precautions - always enter these into your procedure section in your notebook (another reason to read ahead!)

            6.  You are absolutely required to follow any instructions provided by the instructor related to procedures and/or safety.  Failure to do so will result in your immediate disenrollment from this class.

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7.  If you are not sure, ask!!

 

 

SAFETY (continued)

In addition, for safety reasons, before you start an experiment, you are expected to fully understand the procedures and hazards involved, and follow the instructors directions.   Familiarize yourself with the safety section of the SJSU Catalog under the Chemistry Department (p. 121 of the 2006/2008 edition).  Note in particular:  "Failure to comply with proper procedures and prescribed safety concerns shall subject the student to disciplinary action.  1)  Any student who engages in unauthorized experimentation, or who seriously disregards safety, thereby endangering self or others shall be withdrawn immediately from the class with a grade of "F".  2)  Any student who shows persistent disregard for safety may have his/her grade lowered, and may risk being withdrawn with a final grade of "F". "

 

 

 

With preparation and organization, it will be possible to complete all of your lab work during the scheduled lab period.  Except in unusual cases, no lab work will be permitted outside of the scheduled lab times. Usually, the only situation where this may be allowed is in cases of illness where more than a few periods are missed and for which you provide verification by your doctor.  However, if you miss more than a few lab periods during the semester, it may be difficult to complete the course, since there is no other section of Chem 114 where you can perform makeup work (making up lab work in  different lab courses is usually not allowed).  In any case, under NO circumstances are you to perform any laboratory work for 114 outside of the scheduled lab time.  Any student found performing unauthorized lab work for 114 may be disenrolled from the class.

 

Equipment

            You will be assigned an individual locker of equipment for your use during this course.  You will be checked into your locker during the first lab period by the instructor, and sign an acknowledgement that you have all of your equipment.  You are responsible for keeping track of all of the contents of your drawer.  If you lose or break any item, you will be assessed a breakage fee at the end of the semester, so be careful with your equipment.  It is possible to complete this course with a relatively small bill for expendable items:  it is also possible to end up with a >$100 bill.  At the end of each lab period, make sure you have collected all your locker items before leaving. 

            When you check in, you will be given a coded check out pad from the storeroom.  You may use this pad to check out additional equipment from the storeroom which may be required for a particular experiment.  Note that certain equipment items checked out must be returned the same day to avoid a late fee.  Remember, the code on your pad is assigned to you only, don't lose it, or someone else can check out items which will be charged to you.

            At the end of the semester, you must clean out your locker, replace all broken equipment or glassware, and have the instructor sign the check-out form.  If this process is not completed fully, you may be charged a fee to clean and refurbish your locker.  (also, if you drop the class, you must checkout before December 6 to avoid this fee)

 

Office:  

My office is in Duncan Hall room 9A (enter through Duncan 9; Room 9A is to the left of the door).  In addition to office hours, questions are also welcome by email:    okuda@sjsu.edu   If you send me an email, ALWAYS put “114” in the subject line, since I receive well over 100 spam messages a day.

 

Final Grades:

Grades will not be posted or sent by email due to personal security issues.  If you would like your final course grade, provide me with a stamped and addressed envelope during the final exam.   All reports and exams will be discarded (shredded) if not picked up or viewed one year after the semester ends. 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

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Academic Integrity

            No form of cheating, copying, or other unfair advantage will be tolerated, and will be dealt with severely.  A first infraction will result in 0 (zero) points for that experiment or exam.  A second will result in an automatic grade of "F" for the course.  The underlying principle will be fairness to all students in the course.  In particular, copying or plagiarism (the excessive use of someone else's words, even if acknowledged, see the section from the Academic Senate below)  is considered a serious offense, especially with regard to the formal lab reports. Note that simply "re-ordering" words from another source does not constitute an original paper.  You must use your own words and analysis in these reports

Additionally, when you work on and turn in a report, it is expected that the work is your own only. While you may get general advice from your classmates and faculty members, you may not ask others to analyze your data for you.   This includes faculty members at SJSU or other colleges/universities, trained professionals in the field, or any commercial services.

The "SJSU Policy on Academic Dishonesty" will be used as the guideline should any problems arise. The policy on academic integrity can be found at:   http://www2.sjsu.edu/senate/S04-12.htm

 

From the Office of Judicial Affairs:  "Your own commitment to learning, as evidenced by your enrollment at San Jose State University, and the University's Academic Integrity Policy requires you to be honest in all your academic course work.  Faculty are required to report all infractions to the Office of Judicial Affairs."

 

 

Emergencies and Building Evacuations

 If you hear a continuously sounding alarm, or are told to evacuate the building by an Emergency Coordinator, walk quickly to the nearest exit (out the door and turn left to exit the Science Building).  Take your personal belongings as you may not be allowed to return.  Follow the instructions of the Emergency Coordinators.  Be quiet so you can hear instructions.  Once outside, move away from the building.  Do not return to the building unless the Police or the Emergency Coordinator announce that this is permissible.

 

Disabled Students

Any student with a pre-existing disability requiring an accomodation (as documented by the Disability Resource Center) should make this need known to the instructor during the first two weeks of classes.  Every effort will be made to accommodate your needs.

 

A Comment on Attendance and Preparation:

Chemistry 114 is a course which is less ‘structured” than other lab courses.   However, there are deadlines, and doing well in the course will be directly reflected in the time and effort you put in to your experiments while in Science 139.  The available lab time is limited, so you should be present and use each lab period efficiently by preparing for your days’ work before coming to lab.