cOMPUTATIONAL ChemiCAL LAB –Spring2007

Syllabus for CHEM-421for 1-hour credit

Meeting in the ASC-130, the Asher Computer Lab, on Wednesdays, 2:00 – 5:00

Dept. of Chemistry – GeorgetownCollege

Dr. David Fraley in ASC-211, 863-8771 (Office) and 863-6108 (Home)

Course Description:This lab will utilize powerful, yet convenient, molecular modeling software suites to model the chemical and physical properties of organic, inorganic, and biological molecules. Modern theoretical methods will examine molecular structure, spectra, bonding, and reactivity. Studies of Quantitative Structure Activity Relationships (QSAR) and the molecular dynamics of physical processes will be included. One 3-hour lab per week.

Course Objectives:

  • To learn about the past contributions and future promise of computational chemistry
  • To develop a high degree of skill in carrying out computational chemistry operationsthat are essential for success in a modern chemical laboratory
  • To learn the theoretical basis and practical uses of threetheoretical models (Molecular Mechanics, Semi-Empirical, and ab initio / Hartree-Fock) that are used to perform molecular modeling
  • To demonstrate an ability to carry out graphing operations related to QSAR results
  • To compare spectra acquired in the lab with those generated via computational techniques
  • To enhance the student’s ability to communicate results in a clear, concise, and professional manner

Prerequisite: Organic Chemistry-201

Course Materials and Software:

  • Getting Started with Spartan, Student Edition, 3rd Ed., Wavefunction, Inc. 2004
  • Spartan-02 software is installed in the Asher Computer Lab - 9 licenses are available for student use
  • Spartan-06, Odyssey, and the ACD ChemSketch, NMR Predictor, and Log P are available in Chemistry
  • Screen Saver Lifesaver (for cancer research) is running on the Web and may be readily downloaded
  • Computational Chemistry (Chap. 27) by Warren Hehre in Physical Chemistry by Thomas Engel and Philip Reid, 2006, Pearson/Benjamin Cummings

Requirements of the Course:

  • Attend lab each week
  • Read text assignments and be prepared for lab procedures
  • Take 6-10pre- or post-lab quizzes
  • Do assigned lab work and homework
  • Complete weekly Informal Lab Reports

Laboratory Attendance:

Since technical skill development requires on-task time on the computers, laboratory attendance is mandatory.Your lab will meet weeklyon Wednesday afternoons for 3 hours.

Labs should be completed by the end of the week assigned – generally during the regularly scheduled time slots. In the event an illness or other acceptable excuse makes it impossible to complete the work on this schedule, it should be completed as early as possible the following week. Please talk to Dr. Fraleyas soon as possible, if you intend to miss or have missed a lab… you must be proactively responsible to contact him.

For each lab that is not completed as required, 10 percentage points will be subtracted from your final course grade. This will essentially lower yourcourse average at least one-letter grade. Ouch!

Quizzes and Projects:

For most laboratory periods, we will have a pre-lab quiz and/or possibly a post-lab quiz. Pre-lab quizzes will be short and will be given to ascertain that you have read and studied the assigned experiment and reading assignments before coming to lab. Many computational exercises are available from which we can select appropriate activities that may meet your interests. Students will be performing different, yet similar, exercises during the semester. Your Final Project will highlight a particularly interesting exercise in detail.

Laboratory Preparedness and Effort:

This component of your grade allows the lab instructor (who will have ample opportunity to observe your work) a chance to consider some items that are not fully taken into account in other portions of your grade. Such items as the following will help your instructor assess your ability and development as a laboratory worker:

Promptness Attendance PreparationEffort Attitude Neatness Lab Technique Proactive Initiatives

Cooperativeness TeamworkLab EfficiencySafety… most important!

Please note that this is a subtle, yet very important, aspect of the evaluation of your laboratory experiences. You primarily will be working solo this semester, but occasionally you will be working with a lab partner. This teamwork helps learning, safety, and efficiency in the lab.

Evaluation:

Informal Lab Reports (10-11)20-50 points each typically

Quizzes (6-10)100 points total [The lowest quiz will be dropped.]

Final Project100 points total _

Total Points500-600 depending on the individual lab reports

The adjustment for your Laboratory Preparedness and Effort will then be used to adjust the final average up to + 5% at the discretion of the instructor. Your total number of points will then be normalized to 100 and applied to the following grading scale:

Letter

Points GradeLevel of Academic Accomplishment _

90-100AClearly Excellent Performance at the Distinguished Level

85-89ABVery Good

80-84BReasonably Good Work at the Proficient Level

74-79BCSatisfactory

66-73CAcceptable Performance at the Apprentice Level

55-65DPoor, but Passing at the Novice Level

54FUnacceptable with Failure

Academic Performance:

In this course, the students have diverse backgrounds and different expectations. My expectations include individual accomplishment on the part of every student, so that all of you not only fulfill your capabilities, but also expand your capacity and enrich your life. Of great importance to me is the knowledge you acquire, the skills you cultivate, and the attitude you develop. I expect that by the end of the semester each of you will have enough accomplishment to be at least at an Acceptable level (which is a “C” letter grade). Everything I do is aimed toward helping you achieve this goal.

Although grades are not the ultimate measure of your knowledge, abilities, or potential, they are useful guides to you and to others. Your level of accomplishment will be recognized at the end of the semester by the letter grade you receive for the course. Individual accomplishment is measured against absolute course standards and not necessarily against the relative performance of other students. Please remember that I don't give any grades...each of you earn your own grades (be that an A or a C) for the semester. Study well!

Laboratory Policies

Grading: I do not "Curve" grades such that a preset number of students will get A's, B's, etc. If you earn a 90, you've got an A, no matter how many students that turns out to be. (Wouldn't it be great if everyone earned A’s?) I typically lower the various final grade cut-offs though, depending on how difficult some of the quizzes or tests are, i.e. an 88may become an A and a 78may become a B. I'll never raise these cut-offs – if you earned a B at 80; you've got it. It cannot slide to a C. This procedure thus gives you some grade insurance. Since high standards in performance are expected from the start, individual extra credit work is not available to students to compensate for less than quality work earlier in the semester

Promptness: The lab will begin promptly at 2:00. You are expected to be On Time. However, arriving late is better than not arriving! Since attendance is a modest part of your weekly lab grade, it is to your advantage to be there. Likewise, it’s to your benefit to be prompt in completing your lab work each day and in turning in your lab reports the next week.

Attendance at all labs is required. Excused-absences do sometimes occur:

  • Typical acceptableexcuses: sickness, accidents, death in the family, weddings, and official college trips. (Proof may be required.)
  • Typical unacceptable excuses: conflict with work schedules, vacations, plane reservations, tests in other courses, or social events such as fraternity or sorority activities.

If you have a valid excuse for missing lab, it is your responsibility to let me know why you were absent... please notify me in writing or by email (for my records) as soon as possible. If you know in advance that you will miss a lab or have a valid excused absence, we’ll do our best to find an appropriate time to make it up. All missed work must be completed within 2 weeks, but hopefully will be completed the week it was missed.

A modest bonus will accrue for perfect attendance at all your scheduled labs, while a reduced bonus will accrue for completing any missed labs at another time during the scheduled week.

Communication: Any updates, changes to the lab schedule, or helpful hints to aid your lab preparation, will be communicated to you via email. Please make sure that your College email account is up-to-date.

Academic Misconduct and Cheating: In this course, you are encouraged to study and prepare for labs and for quizzes with other students. However, when taking quizzes or writing-up lab reports that are to be done solo, you are to work alone… plagiarism is a very serious offense. The Georgetown College regulations are very explicit about academic misconduct and cheating and these regulations will be fully enforced. During quizzes, we will apply the Honor Code under which you are to work alone and neither give nor receive help from any source. In addition, you are expected to help enforce this code by reporting incidences of cheating to the instructor. (Please carefully review page 5 for further details.)

Safety is an absolutely critical aspect in any chemical laboratory. Everyone is expected to carefully follow all safety guidelines when we will be in the chemical laboratory. Always be alert!

Office Hours are 10:30-12:00 Mon. and Wed. If possible, please contact me prior to coming by to make sure I will be there. Of course, other times are available by appointment.

Lost and Found: I encourage you to place your name in your books and on your personal belongings, particularly your calculator. If you either lose or find something, please let your instructor know ASAP.

Food and drinks are not permitted in the computer lab, but are fine in the classroom or hall. Tobacco products (cigarettes, snuff, and chewing tobacco) are not permitted in the building. Appropriate clothing, including eye protection, is required when in the chemistry lab. Please use discretion with your cell phones.

Laboratory Schedule for CHEM-421 – Spring 2007

This is atentative guide listing the weeks when we will cover selected lab experiments. The assigned experiment and appropriate readings must be studied prior to the laboratory period. All assigned reading material may be used for quiz questions. There are 15 weeks in the semester.

Wed.Experiments in

DatesComputational Chemistry Essays to Read _

Jan. 17Tutorial on Getting Started withTheoretical Models and Choosing

Spartan-02 a Theoretical Model

Jan. 24Tutorial on Getting Started withTotal Energies and Thermodynamic

Spartan-02 and Kinetic Data

Jan. 31Exercises: Too Few and Too ManyFinding Equilibrium and Transition

Electrons State Geometries
Feb. 7Exercises: Acidity and BasicityAtomic and MolecularOrbitals

Feb. 14Exercises: Molecular ShapesElectron Densities: Sizes and

Shapes of Molecules

Feb. 21Exercises: Biological Molecules andElectrostatic Potential Maps:

using the Peptide Builder Charge Distributions and Maps

Feb. 28Predicting Spectra of Organics:Find published spectra of 4 varied,

NMR, IR, UV-Vis small, biological compounds

March 7Acquiring Spectra on the

Spectrometers in lab

March 14Spring BreakEnjoy the sunshine and win BB games!

March 21Quantitative Structure ActivityQSAR Handout

Relationships (QSAR)

March 28QSAR continued

April 4Substituted Chlorobenzenes Review the ASMS poster on

research for the UK-MS Lab substituted Nitrobenzenes

April 11Substituted Chlorobenzenes

continued

April 18Physical Chemistry exercises Odyssey Tutorial

with Odyssey: Molecules in Motion

April 25Physical Chemistry exercises:

Molecular dynamics simulations

May 2Final Project presentation

March 27 = Last day to drop without a grade and April 12 = Last day to drop WP/WF.

Recommended Free Software to Download:

  • Advanced Chemistry Development Labs offers a very popular and powerful structure drawing tool, ChemSketch. Version 10 is now available from
  • Screen Saver Lifesaver is a distributed computing program from Oxford Univ. It is the biggest computational chemistry project ever undertaken, involving screening 3.5 billion potential anti-cancer compounds against protein targets by using screen saver time on over three million personal computers in over 200 countries. It is available at

General Policy on Non-Chemical Aspects of the Class and Grading

Dr. David Fraley and Dr. John Blackburn

Chemistry Dept. – Georgetown College

Demonstrating mastery of a subject (e.g. with an A, B, or C grade) at any level from introductory to upper division courses includes demonstrating the ability to communicate your knowledge in an acceptable fashion, according to recognized academic standards. This includes grammar, spelling, sentence structure, and phraseology, as well as correct documentation in cases where the work of other persons is involved.

In addition, a premium is placed on being able to state clearly what is meant, such that instructors or others do not have to "read between the lines" or interpret. If you ask for additional credit on written work that has been graded, it will be unacceptable to say, "I meant..." or "that means...." You will be graded on what is actually said, rather than on what you meant to say or what is implied.

In this vein, however, it is also imperative to directly answer the question that is asked, rather than to simply put down all that you know about the subject dealt with in the question. A short, succinct answer, which contains the requested information, is a better answer than one that contains the information buried in a mass of other information, which "might apply" to the case. Thus, answers should be complete, specific, and succinct, in addition to being well constructed according to the recognized rules of English grammar. Additionally, clear, readable handwriting is expected.

* * * * *

Questions frequently arise concerning homework assignments and the propriety of working together in relation to the question "What is cheating?” In the Chemistry classes, which we teach, we believe that working together, even in small groups rather than pairs, is a legitimate and highly beneficial form of study. This is acceptable for problem assignments. It is not considered cheating when people work together on homework problems and turn in similar work, even if one member of the group contributes more than the others.

It is considered cheating if someone simply uses another's work, to which he did not contribute, as his own (i.e. copying someone else's lab report). There may be occasions when take-home assignments are given with the specific instructions that you are to work alone. In these instances, there is to be NO group involvement or discussions with other students other than perhaps "Did you get number 5?" Obviously, you are expected to do your own work on quizzes, tests, and exams, and any attempt to get outside help will be interpreted as cheating. The penalty for cheating will be no less than a zero on the assignment and may include failure in the course and/or suspension from the College.

The Georgetown College Honor Code gives further guidelines for cheating violations.

Please be well aware of its ramifications.

* * * * *

Students are actively encouraged to interact with faculty individually for additional help on material that may be difficult. Feel free to come by their office, or better, to make an appointment for individual help.

When in doubt, please ask!

Helpful Study Hints -- How to Succeed by Trying

Dr. Frank Wiseman has noted the following 3 reasons why the study of Chemistry may be challenging to beginning students:

  • First, students encounter many new ideas and words for the first time and new material does take a certain amount of time to be assimilated by the mind.
  • Second, one is required to think about abstract concepts and about real physical entities (such as atoms and molecules) that cannot be seen or otherwise experienced. Most people develop the ability to think about abstractions sometime between the ages of 15 and 20. Thus, some college students may not have fully developed this ability yet.
  • Third, Chemistry can have the widespread, but erroneous, notion that it is harder to learn than other subjects. This may come from previous conditioning. If a student perceives the sciences as hard, however, the anxiety that results can, in itself, become a barrier.

So what can you do? Generally, for most Chemistry courses diligent students should plan to study 2 hours outside of class for every hour in class to achieve an Acceptable (a “C”) to Proficient (a “B”) level of performance. During this time, consider doing the following:

  • First, carefully read the assignment prior to lecture. This greatly helps most students, but we realize that those who are more visual or aural learners may benefit more by seeing the material first in class.
  • Take good, thorough notes during the lecture, and then review them before the next class while they are fresh... don't wait until the night before the test. Reread and then study or outline the appropriate pages in your textbook. Prepare flash cards for short, frequent drills. Do the sample questions/exercises in the book. Then try even more sample problems.
  • Please note that the text talks about how to approach and solve chemical problems (with an emphasis on a qualitative understanding of concepts before quantitative problems are considered). Next, thoroughly examine the sample exercises and the appropriate problem-solving strategies. Finally, do the exercises at the end of each chapter.
  • Don't forget to review the excellent supplementary resources in the Library or Bookstore. Pay close attention to diagrams, models, and analogies to help understand abstract chemical concepts.
  • Don't cut class because subtle or even key details may be lost if you just review class notes from your friends.
  • Ask questions in class. Seek advice from your instructor. Work with a tutor outside of class. Finally, exercise regularly, get sufficient sleep, follow a nutritious diet, and don't party too much!
  • I strongly encourage you to study with fellow students. One of the hallmarks of excellence of Georgetown College is the quality of its students. Share your talents with others and take advantage of the rich talent surrounding you.

Finally, remember that all of these suggestions are designed to help you develop a positive confidence in your ability to master the material. I am confident that you can succeed in CHEM-421. When in doubt, please come talk to Dr. Fraley.