Chem 312-01 Instrumental Methods of Chemical Analysis

Spring 2010

Lecture:          MWF 11:00 – 11:50 a.m., Clement 210

Laboratory:   W 1:15 p.m., Clement 317/Clement 122



Instructor:        Prof. David E. Henderson                                   Phone:            297-2514

Office:               Clement 129                       E-mail:

Office Hours:   M    1:30 – 3:30 p.m.

                            Tu  10:00 a.m. – 12:00 p.m.

                            (or by appointment)

Laboratory T.A.’s:  None



Required Text


Additional Required Materials:

·       Laboratory Manual and Lecture Handouts $5.00  - These will be distributed over the course of the semester. Please pay Robin Kelly when you pick up the first installment.

·       Laboratory notebook, spiral bound, carbonless copy, 100 pages (50 sets) – available in bookstore at a cost of approximately $15. You may use pages in an old notebook.

·       Laboratory safety glasses -- available in Chemistry Office (CT 208) at a cost of $5.00


Class Format:


Laboratory: (see detailed description and policies in the Laboratory Manual)



All laboratory experiments must be completed during the week in which they are scheduled in order to pass this course.  There are no make-up laboratory sessions.



·       Exams and quizzes(Midterm and Final)                          45%

·       Laboratory                                                                             25%

Includes formal lab reports, pre-lab

quizzes, & lab notebook

·       Project Lab                                                                            15%

Includes Annotated Bibliography, proposal,

time spent on project, quality of results

report and poster session.

·       Chemical Literacy Game                                                    7.5%

Includes annotated bibliography, presentation and discussion

of current literature and bonus for winning investments

·       Problem Seminars and class participation                                   7.5%


Chemical Literacy Game


Four classes will be devoted to the Chemical Literacy Game. In this game, students will read current literature and research the state of the art of chemical instrumentation on specific topics. In each topic, four students will present a current article to the class along with supporting information about the potential of this application to have an impact on the instrument business. At the end of each game session, students will decide how much of their resources to invest in each student’s projects. The goal is to convince the class to invest in your applications and accumulate investment money.

A separate handout provides more detail on this part of the course.




Examination Schedule

Three examinations are scheduled for this semester; two will be given during regular class time, and the third will be given during the final exam period.    Please review policy on missed exams below.

                                    1st examination:       Wednesday, February 27, 2008 (during class)

                                    2nd examination:      Friday, April 4, 2008 (during class)

                                    3rd examination:       Thursday, May 8, 2008 at 12:00 noon (during



Use of Moodle and E-mail

Moodle and e-mail will be used extensively in Chem 312.  All students are required to have an active e-mail account.  Students will be expected to consult the Chem312 Moodle site on a routine basis for assignments, announcements, schedule changes, lecture materials, posted supplementary course materials and external links.




            Each chapter includes a number of problems at the end which allow you to review the material and assess your learning. The problems which are deemed most important are listed with the reading assignments for the chapter. The answers to the most problems are at the end of the text. Problems will not be collected for grading, but a class period will be designated to address each problem assignment. This problem seminar will be used to have students work some problems on the board. Answers to problems will be posted prior to each exam.


            Problem seminars will begin by asking students to indicate problems they had difficulty with. The professor may also add to this list. These problems will be worked on the board. Students will be asked at random to work problems from the list. When a student works a problem more or less correctly on the board, they will receive one Problem Seminar participation credit. Students who attempt a problem but fail to work it correctly will receive ˝ credit.  Student who will not attempt the problem may pass. However, seminar credits will count constitute a portion of the grade and it is expected that every student will receive at least four credits. Attendance will be taken on all Problem Seminar days and will also count toward participation.







You are expected to attend class and laboratory sessions. Attendance will be taken at all problem seminars and literacy game sessions and absences will result in a reduced participation grade.  Except in extreme circumstances (and then only when a request for rescheduling is submitted and accepted prior to the exam), rescheduling of an examination will NOT be permitted. Unexcused absences from an examination will result in a grade of zero (F) for that examination.   Please be aware that laboratory experiments must be completed during the week in which they are scheduled in order to pass this course.  There are no make-up laboratory sessions.  Laboratory reports submitted after the assigned due date and time will receive one letter grade deduction per day late unless a request for an extension is approved prior to the due date. Requests may be submitted by email and should include a proposed date when you can submit the work. Requests are not deemed accepted until you receive a reply.






Various aspects of this course will require you to work in pairs or groups (i.e., laboratory experiments, projects, literature reviews).  While it is expected (and encouraged) that you will work together to evaluate/interpret results or critically assess the literature, individual laboratory reports and writing worksheets reflecting your OWN writing must be submitted in all cases.   Likewise, students are encouraged to work collaboratively to solve assigned homework problems. Students are expected to uphold intellectual honesty standards in accordance with the Trinity College Student Integrity Contract.  Please see the appropriate sections in the Trinity College Student Handbook 2007-2008 and the handout entitled Academic Honesty, Plagiarism, and Collaborative Work posted on Moodle.  Any breach of this position will be subject to the severest penalties. All lab reports will be submitted electronically and may be compared with reports from previous years.





Laboratory Notebooks: Possibly the most important tool of a scientist is the laboratory notebook. Recent experience has found students do a poor job of keeping a notebook, so this will be treated as a priority in this course. Prior to the laboratory session, outline the experimental procedure to be performed in your duplicate-page laboratory notebook.  Include the title of the experiment and the type of instrumentation which will be employed and a summary of the experimental steps which you will carry out.  Once in the laboratory, record all experimental details in the laboratory notebook (e.g., sources of chemicals, details of reagent/solution preparation, instrument manufacturer and model, instrument parameters, experimental data, etc.).  Be sure to record all information necessary to prepare a research article in Analytical Chemistry format (see Instructions for Authors--Research Article Guidelines, attached).  The duplicate pages will constitute the experimental section of the laboratory report and will be handed in at the end of each laboratory session. Nothing not recorded before the end of the lab counts as part of the notebook.  (originals retained in notebook by student); Consequently, please ensure that notebook information is clearly labeled, sufficiently detailed, and legible.  Initial and date each page of the laboratory notebook. Because most experiments involve storing data on computers, it is critical that the file names used be accurately recorded. Failure to do this will be severely penalized.


               Laboratory Reports:  Laboratory reports will focus on analysis of data and your discussion of the significance of the results. None of the 8 rotation experiments will include anything except data, results and discussion, and conclusions. Reports will be typed (double spaced) with all figures and tables referenced in the text and properly numbered. Any figures or data which are not labeled with a figure number and caption and which are not explicitly referred to in the text of the laboratory report will be disregarded during grading.  The lab report is not a catchall of every page of paper generated in the lab. Be sure to adequately address any discussion points/questions included in the laboratory manual write-up. These may not be all in one place, so you will need to go through the experiment to look for them.  Adequate attention must be given to clarity of presentation and cogency of discussion.  Lab reports are due after the class discussion of the relevant chapters in the text. Specific due dates are listed in the Schedule. While you will perform the laboratory experiments in pairs or groups and it is expected that you will work together to evaluate/interpret results, individual laboratory reports reflecting your own writing will be submitted.   


All lab reports will be submitted electronically.





  The Project lab is done by groups. Students will be assigned to project groups by a random drawing.  Students who have project ideas may bring them to the attention of the faculty during the first week of class for possible inclusion in the list. The process of completing the project is broken into parts, each with its own deadline listed in the detailed syllabus.


Annotated Bibliography – Do a thorough literature search on the problem and compile a list of relevant literature. You will be given access to STN Easy for Chemical Abstracts searching. Obtain electronic copies of all articles you need to develop a proposal and report. (Most articles will be acquired electronically, but if you need to photocopy material, use the Digital Sender in the library to convert it to a .pdf file. Be aware that it can take up to 2 weeks to get articles through interlibrary loan. Read the articles and write a brief summary of the relevant parts of each article. The summary should evaluate the relevance of the article and what parts of it may be useful to the specific question. These summaries are not just abstracts but should connect the article specifically to the project. Load all articles and your summary to the Digital Drop Box on Moodle for your group.


Draft Proposal- The draft proposal consists of two parts, an Introduction and Procedure. The Introduction is a comprehensive review of the relevant literature related to your project and supports the details of the method you propose to use in the Procedure. The Introduction after revision will be the Introduction to your formal report. It should include appropriate references to the literature using ACS standard format. This section should define the problem you plan to solve, the methods reported for solving it in the literature, and the rationale for your choice of a specific method or a blend of several methods. The Procedure will detail the materials and instrumentation you will require for the project and an outline of the experimental approach you will take. This needs to be specific since you will be going into the laboratory to do it. The Draft proposal will be a work in progress and the purpose of handing in a draft is to allow faculty to make constructive suggestions before the final proposal is submitted.


Final Proposal- The Final proposal is a revised form of the Draft. It is expected that this will include a complete list of all chemicals, glassware, columns, special equipment, etc. that you will require. It will be used to order the necessary materials for the project. The procedure should be detailed enough that it is clear exactly what you will do the first day of lab and that you have addressed all deficiencies noted in the draft.


Poster Presentation – The results of all projects will be presented in the form of a poster presentation during Reading Days. This will provide an opportunity for feedback on your data analysis and conclusions which will be reflected in the final report below.


Final Project Report – The final project report is an individual, formal, journal style report using the Analytical Chemistry Instructions for Authors format. The introduction of the proposal, modified as needed by in-lab experiences, will constitute the Introduction to the report. The Procedure section of the proposal, suitably modified to reflect in lab changes, will constitute the Experimental Section. These two sections may be the same for every member of the group if desired. Each report may use the same figures and tables as well. The Discussion section and Conclusions will be written by each individual student. The usual admonitions against plagiarism apply to these sections.


Hints on Group Organization- These projects are Group Activities, and each group will want to divide the labor in an efficient manner. Within each part of the project, work can be broken up and the results pooled. One important key to success is for someone to be in charge and know what everyone is supposed to be doing. It is suggested that each group designate a group leader for each part of the project. The leadership can rotate, either weekly, or change with each new phase of the project. Everyone should have a chance to be the leader. The leader should know what each person’s responsibilities are and insure that the job is being done. The leader can schedule group meetings. The leader is also responsible to see that each group member is doing their fair share of the work and to report any deficiencies to the professor.


































Lecture Topic


Assigned Text Reading


Lab Rotation


Important Due Dates



1/25 – 1/29







Course introduction


Performance Characteristics of Instruments (Figures of Merit); S/N Ratio; Review Calibration Methods: External Standard, Internal Standard, and Standard Addition



Chapter 1

Chapter 5 (pp. 100-113; section 5C-2 on Ensemble Averaging pp 117-119)

Appendix 1 (Reference)



Wed., 1/27

Lab Check-in;

Review of Policies


Chapter 1; Chapter 5 (pp110-113; 117-123)

Review Appendix 1 (Treatment of Analytical Data)--use as reference



2/1 – 2/5



Introduction to Spectrometric Methods


Introduction to Components of Optical Instruments



Chapter 6



Chapter 7


Wed., 2/3

Lab Rotation I

Week 1




Problem seminar for  Jan 28th

Chapter 1:  Problems 10, 11, and 12 d,e

Chapter 5:  Problems 6, 8, 10, 11


2/8 – 2/12


Components of Optical Instruments (continued)


Introduction to Ultraviolet-Visible Molecular Absorption Spectroscopy ( Intro, Beer’s Law, Instrumentation) Quantitative Analysis, and Applications)



Chapter 7 (cont’d)



Chapter 13



Wed., 2/10

Lab Rotation I



Text ReadingChapter 6; begin Chapter 7

Problem Seminar  Feb 4 

Chapter 6: Problems 3, 5, 6, 8, 12, 14, 15, 16, 17, 18, 19  Show all work!



2/15 – 2/19



Ultraviolet-Visible Molecular Absorption Spectroscopy (continued); Applications of Ultraviolet-Visible Molecular Absorption Spectroscopy


Molecular Luminescence Spectroscopy



Chapter 14 (selected sections TBA)



Chapter 15


Wed., 2/16

Lab Rotation I

Week 2





Problem Seminar Monday 2/15)

Chapter 7 Problems 1, 6, 7, 9, 12, 13, 14, 15, 17, 18

Problem Seminar  Friday 2/19

Chapter 13-13  Chapter 14- 2, 5, 8, 10, 






2/22 – 2/26


Infrared Absorption Spectroscopy: Theory  and instrumentation; dispersive vs. FT instruments; qualitative and quantitative applications; internal reflectance methods, photoacoustic spectroscopy, near-IR spectroscopy


Chapter 16

Chapter 17 (selected sections TBA)


Read J. Chem Ed. articles in IR lab folder on Moodle

Perkins, W.D. Fourier Transform Infrared Spectroscopy: Part I. Instrumentation.  J.Chem. Educ. 63 (1) A5-A10 (1986).

Perkins, W.D. Fourier Transform Infrared Spectroscopy: Part II. Advantages of FTIR.  J.Chem. Educ. 64(11) A269-A271 (1987). 


Wed., 2/24

Lab Rotation I

Week 3





Problem Seminar Feb 24

Chapter 15- 3, 4, 9, 10



Friday, 2/26


UV Lab Report Due

Literacy Game Part 1 IR-Raman











EXAMINATION 1 – Wednesday, 3/3


Continue IR;

Intro. Raman Spectroscopy



Chapter 16 &17 (cont’d)

Chapter 18





Wed., 3/3


Lab Rotation I

Week 4



Friday, 3/5

RotationI/Fluorescence  Report Due




3/8 – 3/12





Introduction to Atomic Optical Spectroscopy:  Theory and Instrumentation; Atomic Absorption and Atomic FluorescenceTechniques




Chapter 8

Chapter 9


Wed., 3/10

Lab Rotation II

Week 1




Monday, 3/8

Annotated bibliography for project lab due (references with photocopies and summary)

3/10Literature Game IR/Raman


Problem Seminar  Wed 3/12

Chapter 16-3, 7, 9, 13. 17-9. 18-3, 6, 7.


Friday, 3/6

Rotation IR/Raman Report Due



3/9 – 3/13



Atomic Emission Techniques including ICP; Applications



Chapter 10



Wed., 3/12

Lab Rotation II

Week 2





Wednesday, 3/11 Draft of Project Proposal Due (including list of supplies, chemicals)


Friday, 3/13

RotationII/ICP Lab due



3/15 – 3/19


Molecular Mass Spectrometry



Chapter 20


Wed., 3/17

Lab Rotation II

Week 3





Problem Seminar  3/15

Chapter 8-4, 9, 11,  Chapter 9-5, 6, 11, 16, 17, 20

Chapter 10-4, 8, 10, 13


3/17 Literacy Game Part 2-

Atomic Spectroscopy Friday, 3/19

RotationII/GC-MS Lab Due



3/22 – 3/27









Spring Break NO LABS!







3/29 – 4/2






Molecular Mass Spectrometry (continued)

EXAMINATION 2 – Friday, 4/2






Chapter 20 (cont’d)








Wed., 3/31

Lab Rotation II

Week 4






Monday, 3/29

Final Project Proposal due


Problem Seminar


Chapter 20:  11, 13, 17, 19



4/5 – 4/9


Nuclear Magnetic Resonance



Chapter 19


Wed., 4/7




4/7 Literacy Game Part 3 – Mass Spectrometry

Friday, 4/9

RotationII/LC-MS Lab Due



4/12 – 4/16



Electroanalytical Chemistry







Selected sections of Chapters 22 & 25

Review 22 A-C

Study 22E

Study 25A-C3

Review 25 C4

Study 25D-F &H-I


Wed., 4/14


Problem Seminar  Mon

Chapter 19:
3, 6, 7, 9, 17, 19, 20, 21, 27, 30, 42


Friday, 4/16

RotationII/NMR Lab Due




4/19 – 4/23




X-ray and Surface Analysis


Selected sections of Chapters 12 & 21


Wed., 4/21


Friday, 4/23

RotationII/ Electrochem lab due



4/26 – 4/30





Catch-up and review

Last day of class 4/29





Wed., 4/28


Lab Check-out


Mon 4/26

Literacy Game Part 4

- Electrochemistry and Mass Spec



5/3 Last Class



Thursday, 5/6

Poster Presentation of Project Lab at Science Symposium





(during final exam period)













*Assigned readings from Skoog, D.A.; Holler, F.J.; and Crouch, S.R.  Principles of Instrumental Analysis, 6th ed., Thomson Brooks-Cole: Belmont, CA (2007).  Journal articles and handouts will be assigned periodically as additional required reading.  It is expected that assigned reading will be completed prior to class!