Course Syllabus

[This is just the text version of the PDF file I put up]

Chemistry 482: Computational Chemistry Laboratory

Course Syllabus

 

Instructor: Prof. Kevin Kubarych
Office: 4813 Chemistry

Office hour: Fridays at 10 am (no appointment necessary)

kubarych@umich.edu

 

Lab Location: Science Learning Center (Chemistry building)

GSIs: (section scheduling subject to change)

Aaron White	amwhi@umich.edu	Tues., 2-5 pm	Chem 4828
Peter Eckert	zpeckert@umich.edu	Wed., 2-5 pm	Chem 4828

 

Textbook: 

A. R. Leach, Molecular Modeling: Principles and Applications (either 1st or 2nd edition)

Lab Notebook: 

Bound laboratory notebook as you would use in any chemistry laboratory course.

 

Class Schedule:

Section 100: Lecture/discussion, Tues. 1:00-2:00 pm (1650) Lab, 2:00-5:00 pm (SLC)

Section 200: Lecture/discussion, Wed. 1:00-2:00 pm (1636) Lab, 2:00-5:00 pm (SLC)

 

Please note that this syllabus is not final, and some aspects may evolve in the first couple weeks of the course.

1. Introduction

1.1 Overview

Chem 462 is a laboratory course in the methods of computational chemistry. This course will consist of computer-based laboratories in four general theme areas: Monte Carlo simulations, molecular mechanics, molecular dynamics, and quantum chemistry. Aspects of these themes are ubiquitous in contemporary chemical research, regardless of the specific sub-discipline. Each laboratory will introduce a computational method commonly used in chemistry and use it to explore a chemical system. You are encouraged to work together on the laboratories in groups of two (one group of three if required is acceptable). However, each of you must work on all aspects of the laboratory. We ask you not to use the ”divide and conquer” approach, since that generally leaves students with only a partial level of participation and competence. The laboratories are designed so that it should be possible to finish each one during the time allotted over the number of weeks specified. However, due to the changes being made this term, it’s possible we will need to be flexible.
One of the course aims is to provide a fundamental understanding of the capabilities of the different computational tools. Therefore, it is essential to avoid the use of the software in solving the different modules as “black boxes”. The assignments are designed to achieve that goal. 

1.2 Computers are Not Just for Twitter

This is a 1-credit course, and as such it should not have the workload of a full, 3 credit laboratory course. You have 4 contact hours per week, and we will be diminishing the amount of turned-in work you will be required to do. In the past, of the four theme areas, you were required to submit two written reports and present two oral presentations. We are going to change that to a new format. The details of the reports will be given below. 

A key innovation in this year’s version of Chem 462 is significant, but I want to present some context before describing the changes. When I entered college in 1992, the computer I took with me was one of the first color Apple Macintoshes. It had a 16 MHz processor, 4 MB of memory, a 40 MB hard drive, a 13” monitor (640x480 resolution), no ethernet (or wireless), and could only connect to the university’s “mainframe” server using a telephone modem. I had no cellphone, and my email address was ST000123@brown.edu. I had no choice was my username was (within a year that changed, but still...). Only in my junior year did I even see a web browser, and I think it was my senior year (1995) when I first installed Netscape Navigator on my Mac. This is what webpages looked like back then:

 

Besides trying to seem really old, why am I telling you all of this? The reason is that despite the relative stone age tools I had, my programming ability then was superior to most of the undergraduates I have met here in my 10 years at UM. I don’t say this to brag or to whine, but to simply point out something I have noticed: our teaching and curriculum has ignored the largest technological advance in the modern era. We seem to have relied on software to take advantage of the technology, rather than help students develop their own software. Worse, the software has not improved as much as you would think. Here is what Microsoft Word 1.0 looked like:

 

Pretty much what you see today, right? 

Roughly the same year Microsoft launched Word 1.0 (1983 for PCs and 1985 for Mac), MathWorks released MATLAB, a computer programming language geared to engineers. Today MATLAB is a ubiquitous computational tool in all areas of science, technology, social science, industry, finance, and other fields. 

In 2008, this country and the world at large suffered a massive economic shock that is still being felt today. At the 2009 graduation ceremony at the University of Chicago, University announced that the employment of graduating seniors was the lowest level ever recorded in the University’s history. The number probably got worse before it got better (see: https://nces.ed.gov/fastfacts/display.asp?id=561). One area of the economy where the employment crash was less severe was in areas that rely on technology. Knowing how to program a computer, even to do the most basic task, can be a major insurance policy, while at the same time it can provide a liberating and empowering toolset that complements all of your other skills. Here is an article you can read from last year: The One App You Need to Mention on Your Resume If You Want a Job at Google. Whether or not you want a job at Google, I think this article nicely illustrates why knowing a language like MATLAB can be so empowering. 

There is another very attractive reason to learn MATLAB. There are free, open source version programs that reproduce much of what you can accomplish in the full commercial software. The one I have used and have checked most of the programs for this course is called FreeMat. Not everything works in FreeMat, but most of the basic components do. 

So that is the main change: I have ported all of the programs from MathCad to MATLAB. But that’s not all. I know that many of you will not become professional chemists, but I expect that many of you will have jobs in some sort of technical field. Even if you end up in a health field, you are likely to interact with computer models, rely on statistical conclusions, and otherwise engage in information technology. If all you know is Excel, you are not participating in the modern era of computing. So we are going to actually learn some basics of computer programming, using MATLAB as the vehicle. It is simple enough to get started virtually instantly, and the possibilities are unlimited. If you already know MATLAB, you will be ahead and may find it repetitive (please contact me to discuss). If you know another language such as python, PERL, or Ruby, or even a conventional language like Java, C, C++, C#, etc. you will have no trouble learning MATLAB quickly. You might become frustrated when you have to use those languages to do things MATLAB can do much easier, but that is the only real risk. Also, just as it is incredibly valuable to be able to speak more than one human language, it can be very enlightening and productive to know more than one computer language as well!

I am writing a simple, bare bones “textbook” for the programming aspects of the course, and it will be developed and evolve as we go through the course this term. I will continue to update that resource in subsequent terms teaching this course. Look for the text in the Resources section of the Canvas site.

 

1.3 Themes

There will be four themes, with the following breakdown of how time will be spent on them throughout the term:

 

 

Theme	Number of Sessions	Likely Dates (100 section)
Monte Carlo	2-3	Sept. 8 - Sept. 15
Molecular Mechanics	3-4	Sept. 22 - Oct. 6
Molecular Dynamics	4	Oct. 13 - Nov. 3
Quantum Chemistry and Reactivity	5	Nov. 10 - Dec. 8

2. Grading Policy

1. Each student will hand in one full written lab report, and each group will present one full oral report. These will be either the third theme (molecular dynamics) or the fourth theme (quantum chemistry). 
2. For the other two themes—Monte Carlo and molecular mechanics—only brief log reports will be submitted. We will describe a log report during the course, but basically, they will consist of screen captures of the main results.
3. All writing submitted for grading (reports, proposals and reviews) must be in your own words and must not be shared. Plagiarism will be taken seriously and will result in a failing grade for the report. Just please don’t do it!

 

Number and Category	Point Breakdown	Total Category Points
Lab reports
Written Report	100	100
Oral Report	100	100
Log Reports (10)	20	200
GSI points	50	50
	Course total	450

 

2.1 Pre-lab Preparation

Please read through the narrative describing the week’s theme before arriving class. It won’t take long and you will be able to go through the projects much faster if you are even a little bit prepared.

2.2 Laboratory Notebooks

Each student is required to maintain a laboratory notebook, preferably with page duplication via carbon paper. The purpose of a scientific lab notebook is twofold: (1) to record and organize data and observations; (2) to record the procedure and events during the experiment in enough detail so that you will remember what happened and how to repeat the experiment if necessary. Please write down everything you did, not just what worked. That record will help you avoid repeating your mistakes. Your notebook must be kept up-to-date; the GSIs will check and may deduct lab points if it is not. A carbon copy (or photocopies) of the appropriate lab notebook pages must be submitted with your written report. 

It can get a little disorganized running computer programs, and sometimes you might forget what you have done, so please try to save yourself some time and plan your computer experiments, and not what you see.

3. Laboratory Reports

3.1 Introduction

We will schedule the course so that half of the groups submit a written report and half will do orals. That way we should avoid a huge crunch in grading the reports. 

For those submitting written reports on Theme 3 (Molecular Dynamics), the report will be due one week after the last session working on that theme. For the Quantum Mechanics and Reactivity theme, the report will be due on the last day of class (December 14) anytime during the day. Reports may be submitted either on paper or through the dropbox in Canvas (or whatever it’s called). 

A strict style of scientific writing will be emphasized in this course. The reports must follow the format of research articles in Analytical Chemistry or the Journal of Physical Chemistry. “Instructions to Authors” for these journals will be discussed in a Friday lab meeting. Sections of old lab reports, including good and not so good ones, will also be discussed to provide a ‘calibration’ for what is expected. This aspect of the course is designed to prepare you for a professional career involving chemistry. Effectively communicating scientific information is a vital and valuable skill, and can mean the difference between a mediocre and a successful career. Refer to the journals to access more information about manuscript style and format. Use journal articles as templates for the style and content of written reports. Note that in recent years many journals have updated their page layout, but the general format of papers is the same.

Analytical Chemistry home page: http://pubs.acs.org/journals/ancham/index.html 

Journal of Physical Chemistry: http://pubs.acs.org/journals/jpcafh/index.html

3.2 General Guidelines

All text should be typed, double-spaced on one side of the paper (8.5 x 11 in.). For readability 1 inch margins and 12-point font should be used. The recommended length is 6 to 8 pages including figures, tables and references; 10 pages is the maximum length that will be accepted (excluding lab notebook pages). For specific style issues refer to The ACS Style Guide, e.g., unit abbreviations, appropriate use of acronyms, journal abbreviations, reference citations.

The ACS Style Guide, Dodd, J.S. Ed.; American Chemical Society: Washington, DC, 1986.

Scientific writing is a formal style of writing. Do not write in the first person and always write in complete sentences, without contractions and other colloquialisms. Style, organization and information content will be used as grading criteria.

3.3 Abstract

On the cover page, there should be an abstract summarizing the computational findings and conclusions.

• An abstract, or summary, is published together with a research article, giving the reader a "preview" of what's to come. They allow other scientists to quickly scan the large scientific literature, and decide which articles they want to read in depth. 
• Your abstract should be one paragraph (100 to 250 words) that summarizes the purpose, methods, results and conclusions of the paper. 
• It is not easy to include all this information in just a few words. Start by writing a summary that includes whatever you think is important, and then gradually prune it down to size by removing unnecessary words, while still retaining the necessary concepts. 
• Do not use abbreviations or citations in the abstract. It should be able to stand alone without any footnotes. 

3.4 Introduction

The introduction should contain a brief description of the theory or background. It should also contain a statement concerning the purpose of the experiment (why this experiment is important). 

3.5 Computational Methods

Describe how the calculations were performed. This section should contain all the pertinent information for a senior chemistry student to redo the calculations. You may not want to specify all of the parameters that you could set in the calculations, but you should try to summarize the chemical significance or meaning of the parameters, including any algorithms you have employes.

3.6 Results and Discussion

This section is the single most important of the written report: almost half the total points will come from this section. The important computational data should be described clearly. Enough detail about how the data was analyzed should be given so that a colleague, senior chemistry major, could reproduce your results. The results may be presented in tables or figures; however, many simple findings can be presented directly in the text with no need for tables or figures (note: figures required in the lab manual must be included). The discussion should be concise and deal with the interpretation of the results. In most cases, combining results and discussion into one section will give a more clear and concise presentation. The issues/questions raised in the lab manual should be covered in your discussion section. It may also be helpful to compare your findings to other values reported in the literature, if possible. Figures and tables may be either embedded in the text or on a separate page soon after the first mention of the figure/table in the text body. All figures should be numbered consecutively in the order referenced in the text, e.g. Figure 1. Tables should also be consecutively numbered in order of reference, e.g. Table 1. Tables and figures should have a caption (single- spaced) on the same page (see Note) that contains the figure or table number, a brief description and details not included in the text. Legends may be included in the caption or on the figure (see above Note). Both figures and tables should be clearly labeled with the appropriate units. Ask an instructor if you have questions regarding the preparation of figures or tables.

3.7 Conclusions

This is the last section the reader will see. It should briefly recapitulate the main points and significance. Indicate the impact of the proposed research. This should not be a re-statement of the results and discussion. If you are feeling particularly inspired, you might suggest future avenues of research that can be pursued thanks to your contribution.

3.8 References

In-text citations should be superscripted. The citations should be numbered in consecutive order as mentioned in the text, and should include peer-reviewed sources (wikipedia is not an acceptable reference, but you will often find it to be a very helpful starting point). The complete bibliography should be placed on a separate page, at the end of the text and prior to any (optional) appendices.

Use CAS Source Index abbreviations for journal names, and include publication year, volume, and page number (inclusive pagination is recommended). Please use the format given in the following examples.

1. Koile, R.C.; Johnson, D.C. Anal. Chem. 1979, 51, 741–744. 
2. Willard, H.H.; Merrit, L.L., Jr.; Dean, J.A.; Settle, F.A., Jr. Instrumental Methods of
   Analysis, 6th ed.; Van Nostrand: New York, 1981; Chapter 2, pp. 25–37. 
3. Chem. 483 Lab Manual (Winter, 2013) p. 14. 

4. Oral Reports

It is often the case the scientific findings are communicated orally during presentations at scientific meetings. Besides these formal settings, we often talk about our results with colleagues and other researchers at other institutions. From the perspective of an advanced undergraduate, you may find yourself in situations where you need to present your own research projects, for example, on interviews for graduate or medical schools. Even if you just want to do a better job of telling your parents what you are doing in the lab, the importance of communications skills cannot be overestimated. Our aim here is to give you a comfortable space to learn how to present your results, and it gives us a chance to engage you in some discussion, which is generally not possible with written reports.

4.1 The Slides

We typically present our findings using presentations that involve slides. The software you use is not the important part (most people use PowerPoint or Keynote), what counts is what you put on the slides. You have probably seen enough lectures and research presentations to know what a talk looks like, but in case you don’t try to attend at least one seminar this semester (more would be much better) to see examples of good and perhaps less good presentations. 

4.2 The Content

We will want you to follow a similar outline as you would for a written report. So the sections will be more or less the same. What you want to avoid is excessive text on the slides. You will usually have a couple images and perhaps one or two equations that you will describe in words as you talk. If you limit your text to about 30 words, you can’t go wrong. 

4.3 The Length

Plan for an overall time of about 20 minutes, with 5-7 minutes for questions (which we will probably ask as you go through the presentation). A good rule of thumb is 1 slide per minute. Probably there will be some slides that last longer, and that is quite normal. Don’t feel pressured about time, but please don’t plan for a 45 minute seminar length! That said, if we end up having an extended discussion, I would look on that as a nice positive outcome.

5. Potential for Honors Conversion

For students in the honors program interested in an Honors Conversion, please contact me and we can discuss a straightforward and hopefully rewarding plan to go beyond the basic lab activities. 

6. Summary of Policies

1. Each week you will work on the laboratory exercises described in the course manual. That manual is being updated, and will become available as you need it. 
2. You will only submit one written report and present on oral report this term. These will be on themes 3 and 4. 
3. Each week you will submit a log report, which will consist of snapshots of your main results and very short notes describing what they are. You can use the log reports to ask questions or describe challenges that you had. I hope it will be possible to use the Modules in Canvas to submit the log reports.
4. Lectures/discussions will take place each week unless otherwise noted. There we will discuss basics of programming as well as introductions to the chemistry topics.
5. We are hoping to plan group office hours where the GSIs and I will be able to help with any problems that haven’t been addressed in class. It will be a bit of a challenge to schedule these, but we will try using a poll early in the term. It will probably take place in a corner conference room in the chemistry building, and we will bring laptops.