NCSSM Online: Introduction to Computational Chemistry
Mr. Robert R. Gotwals (
[email protected]) Fall Semester, 2011 Chemistry Department, NCSSM
[email protected] (919) 416-‐2774 (work) (919) 452-‐8120 (home, emergency only) Course description (courtesy of Professor Hai Lin, Chemistry, University of Denver, Comp Chem 5510). This course provides the essential theoretical background of computational chemistry and the practical skills to perform computations to solve chemical problems. The intended audiences are both students who need a background for studying more advanced computational techniques and students who are doing experiments but also have interests in computations. Students need not memorize specific theoretical details and algorithms, however, by the end of the course, the students should be able to critically assess the applicability of computational methods to specific questions from a chemistry point of view, and successfully apply appropriate computational techniques in their academic and scientific careers. The content includes discussions of molecular mechanics, Hartree-‐Fock theory, semi-‐empirical methods, density functional theory (DFT), basis sets, geometry optimization and transition state searches, and molecular property calculations. In addition, students will learn how to read the professional literature in computational chemistry, with a focus on the Journal of Computational Chemistry and the Journal of Chemical Education. Students will be expected to plan and complete a small research project, with a journal-‐type article and a conference-‐ready poster as the deliverables. The structure of the course is a combination of lecture and lab. All labs are done computationally, and require no traditional chemistry equipment (test tubes, beakers, etc.) Hands-‐on training will be given in the application of computations using available software packages on the North Carolina High School Computational Chemistry Server (http://chemistry.ncssm.edu). Packages include GAMESS (General Atomic and Molecular Electronic Structure System), Gaussian 03, MOPAC (Molecular Orbital PACkage), and Tinker. All four are heavily used in the academic and research communities. You may also buy a computational chemistry software package (Spartan) for $20.00. For most labs you will be required to use the North Carolina High School Computational Chemistry server and/or the SGI Origin (“Zeus”) high performance resource at the Center for Applied Computational Studies (CACS) at East Carolina University. Course Objectives: Fundamentally, the successful student will be able to do three things at the completion of this course: 1. Answer, via multiple-‐choice, short answer, and essay format, these six (6) questions: a. What is the role and purpose of computational chemistry? What does computational chemistry allow us to do that cannot be done using "traditional" (i.e. wet) chemistry? b. What is the fundamental mathematical expression that needs to be solved in doing computational chemistry? What are the terms in this equation, what is their significance, what variations can be used? c. What are the approximations that can be used in doing computational chemistry? What are the pros and cons of the various approximations? How does choice of approximation affect the results, the computing time, etc? d. There are roughly four different "flavors" to computational chemistry: ab initio methods, semi-‐ empirical methods, density functional theory (DFT) and molecular mechanics/molecular dynamics. What are these methods? How do they differ? e. What are the fundamental units of measure used by computational chemists? What are some different ways that these fundamental units might be expressed? f. What are some of the computer codes that one might use to do computational chemistry? What platforms are needed for these codes, what are the strengths and limitations of these codes?
2. 3.
Demonstrate an ability to develop a small-‐scale research question that requires the use of the technologies, techniques, and tools learned in this course. Communicate research methods and findings by preparing a 6-‐12 page journal article, following the format of the Journal of Computational Chemistry.
General weekly schedule (subject to change as needed): there are approximately 16 topics presented in this course. Each “topic week” begins on Wednesday. A typical week follows this schedule. IT IS RECOMMENDED THAT YOU PRINT THIS SCHEDULE AND POST IN A PROMINENT LOCATION: What’s due (by Weekday “In class” activity/ “Homework” 10 pm unless “Office Hours” assignment otherwise indicated) Wednesday Watch podcast (“BobTV”); Podcast and reading notes Podcast and Email most of day read the related chapter (electronic notebook) reading notes until 9 pm in the textbook (MMA) (not collected every week – spot checked!) Required attendance in Do pre-‐lab activities Chapter 8:30– 9:30 pm Thursday evening via (readings, assignments, etc.) homework by 8 MANDATORY videoconference for structured lab pm (BH)
videoconference
Friday/ Saturday Sunday
Conduct structured lab activity, either individually or with group, as determined by instructor; journal reading as assigned Complete the structured lab; complete journal reading as assigned
Monday
Conduct all pre-‐lab activities for the open lab activity; consult with partners (if assigned) and instructor as needed
Tuesday
Conduct computational experiments for open lab activity
Complete all analysis work for structured lab activity; submit Question of the Week (QOTW) Complete structured lab; Do journal reading activity if assigned
Saturday; QOTW (11 pm, BH) Submit all documents for structured lab activity (BH)
Participate in optional office hours videoconference as Submit journal needed; collaborate with lab reading activity partners (as appropriate) on form (if open lab assigned) (BH) Complete all open lab Submit requirements completed lab report by 10 pm (BH)
Email throughout the weekend
8:30 – 9:30 am OPTIONAL videoconference; 8:30 – 9:30 pm OPTIONAL videoconference (office hours); email until 9 pm 8:30– 9:30 pm OPTIONAL videoconference (office hours); email until 9 pm Email most of day until 9 pm
A generalized weekly workload schedule is shown in the table below. This time does not include time spent on email, Facebook, and other related (or should we say non-‐related) activities! The time estimates are probably on the low end, depending on a variety of factors. You may also need to spend time reviewing forgotten chemistry from your introductory course(s). NOTE! The amount of time/total time schedule shown below are considered to be BARE MINIMUMS. Total weekly time commitment is probably closer to 12-‐14 hours/week. Day of the Week What you should be doing Amount of Time Total Time for the week Wednesday Watch podcast (approx. 30 minutes on average), 1.5 hours 1.5 hours reading assignments, chapter and podcast notes Thursday Videoconference; finish 2 hours (1 hour VC, 1 hour 3.5 hours BrainHoney homework HW) Fri/Sat/Sun Work on labs; Question of 3 hours 6.5 hours the week; journal reading, if assigned Monday Finish Tuesday night lab 2 hours 8.5 hours Tuesday Last minute lab work; 1.5 hours 10 hours Topics Schedule (subject to change; see BrainHoney pages for more detailed assignment list). IT IS RECOMMENDED THAT YOU PRINT THIS SCHEDULE AND POST IN A PROMINENT LOCATION. All chapter readings are from “A Student Guide to Computational Chemistry” (Gotwals/Sendlinger) Class Date Topic Chapter Reading 1 Aug 24 Introductions; Course Logistics 2 Aug 31 Introduction to computational science Chapter 1 3 Sept 7 Introduction to computational chemistry Chapter 2 4 Sept 14 Applications in computational chemistry Chapter 11 5 Sept 21 Computational Chemistry Methods Chapter 3 6 Sept 28 Mathematics; Midterm Week; Using HPC Systems in Chapter 6; MIDTERM Computational Chemistry (Residential Weekend I) 7 Oct 5 Molecular Orbital Theory I Chapter 5 8 Oct 12 Molecular Orbital Theory II Chapter 5 9 Oct 19 Basis Sets I Chapter 8 10 Oct 26 Basis Sets II Chapter 8 11 Nov 2 Focus on Gaussian; Research in Computational Chemistry Chapter 19; Chapter 24 (Residential Weekend II) 12 Nov 9 Calculating Molecular Properties Chapter 13 13 Nov 16 Transition States; PROJECT PROPOSALS DUE Chapters 15 14 Nov 30 Spectroscopy Chapter 14 15 Dec 7 Density Functional Theory Chapter 10 16 Dec 16 Project Work Chapter 14 17 Jan 4 Review and project work FINAL EXAM, PROJECT DUE JAN 13
Course Contract: This syllabus is considered a contract between you and the instructor. It includes the "rules" for taking the course, including the instructor's expectations of your performance and behavior during the course. In return, the instructor will honor the specifications of the course as outlined in this syllabus. No changes will be made without a class discussion and agreement. However, the class cannot vote to change the syllabus without the full agreement of the instructor. Course Pre-‐requisites Students participating in this online course should have the following pre-‐requisites: 1. Chemistry: at least one semester of an introductory chemistry course, preferably at the honors level or above 2. Mathematics: solid arithmetic skills, and reasonable algebra skills (Algebra II or above; pre-‐ calculus/calculus preferred) 3. Computer skills: a. Basic computer literacy: typing; use of a word processor; ability to save and print documents; comfort with Web browsers (Firefox preferred; Chrome and Internet Explorer often do not work); comfort with email, including ability to send and open files via email; a good understanding of directory structure (how to manage files, download files, find files, etc.); the ability to download and install software on the machine being used (Mac or PC), or access to a local resource who can help you with installations. NCSSM Online tech support can provide some help, but some problems will need local help. b. Graphics: comfort with some drawing package (i.e. Paint in Windows, Grab on a Mac), ability to capture screen graphics and paste them into electronic documents c. Communications: this course will make heavy use of chat sessions, videoconferencing technologies, and other computer-‐related tools. Students are expected to learn these skills during the course 4. Scholarship skills: an online course requires more self-‐motivation and academic discipline than does a regular classroom course. In an online course, the instructor helps you to learn the material, rather than trying to control your behavior in a classroom. Inability to be self-‐motivating and disciplined in your academics will make this an unsuccessful endeavor! Grade Distribution • Weekly homework 10% • Midterm exam 10% • Electronic notebook 10% • Final project 30% • Labs 25% • Final Exam (proctored) 10% • Class participation 5% (including attendance, QOTW, and participation in discussions) Grading Scale (based on NCSSM residential scales): A+ = 97 A = 93 A-‐ = 89 B+ = 85 B = 81 B-‐ = 77 C+ = 73 C = 69 D= 65 and below There is a 10% per day “late fee” on all assignments. In other words, if an assignment is late, grading starts at an 90%. This is designed to encourage you not to procrastinate and to manage your time effectively and efficiently! On-‐campus activities: During on-‐campus sessions, students will spend considerable time interacting with the computational chemistry server and other computational tools, improving their ability to set up computational “jobs” and otherwise learn how to deal with the technical challenges of doing computational and medicinal calculations. If you MISS these sessions, you may not have the knowledge and skillset to use some of the more advanced computational resources that we make available to you! Communication and Software:
Students will interact with the instructor and fellow students using a wide variety of technologies, including email, videoconferencing, chat rooms, podcasts, shared collaboration tools (such as Google Docs), and other resources. All students will have accounts on the North Carolina High School Computational Chemistry server (http://chemistry.ncssm.edu), a computing platform for doing chemistry housed at and maintained by the North Carolina School of Science and Mathematics. You will also have an account for Gaussian09 at the Center for Applied Computational Studies at East Carolina University. We will make significant use of a software tool at NCSSM entitled Mathematica. Weekly homework will be done on the BrainHoney assignment resource. There are no physical (wet) labs conducted in this course. More to know: • Computers: this is a computational course. As such, there is very little you can do without a computer. If your computer is broken, you have a responsibility to have a plan for accessing a backup computer. All labs are conducted online, so poor Internet connections will make this course difficult if not impossible. Mr. Lee, NCSSM Online technical support, can provide some assistance, but it is fundamentally your responsibility to have the functioning tools needed to do computational chemistry work. • Attendance: there is one MANDATORY videoconference per week, scheduled for Thursdays from 8:30 to 9:30 pm. Given that this is our ONLY formal weekly meeting, attendance is critical. You are limited to three excused absences, two excused and one unexcused, or two unexcused absences. More that this results in a zero for class participation. If you have Internet connection problems at home, I will need an email from a parent verifying that situation (but see note on “Computers” above. IF YOU MISS FOUR (4) OR MORE ELLUMINATE SESSIONS (excused or unexcused), YOU WILL BE DROPPED FROM THE COURSE. If you are approaching four missed sessions, a parent/student/administrator conference will be scheduled. • Office Hours: office hours are posted on the schedule above. Office hours take the form of email communications, online chat sessions, and online videoconferencing sessions. While email might be read after 9 pm, students should not expect an immediate reply to any email sent after that time. Email sent after 9 pm will typically be answered the next day. • Contacting the instructor: the instructor can be contacted via email, during the videoconferencing sessions, and/or during chat sessions or other electronically supported opportunities. My home phone number is listed only for emergencies, not for general or specific questions. It is my preference that my home number only be used by your parent(s) or another adult to report problems with accessing the course materials (i.e., “We have lost power to our house, so our student won’t be ‘in class’ tonight for the videoconference session.”). I prefer email communications to phone calls! • Facebook: there is a Facebook group for this course, and students are strongly encouraged to join this group. This is a good place to ask questions of each other. NOTE! THIS IS A MONITORED SITE! I read all posts to this group. • Electronic Notebook: you are expected to keep an electronic notebook (in Mathematica) of your readings, videoconference notes, relevant comments from email, etc. These notebooks are collected ON DEMAND, and are expected to be up to date at all time! • Textbook: Gotwals, R., and Sendlinger, S. A Student’s Guide to Computational Chemistry), in press, 2007. This book is available electronically via the course Web pages. • Labs: There will typically be a small structured lab in the first part of the week, then a larger open lab during the second part (see schedule above). For the second lab, students will be required to prepare a complete Mathematica lab writeup, including a lab abstract. For all labs, follow the instructions on what is expected as the deliverable. • Homework: Homework typically includes reading assigned textbook chapters and a weekly journal article (usually with a short comprehension quiz and discussion), and answering related questions. • Software: you will need to have a functioning copy of Mathematica (MMA) at all times. MMA will be used for podcast and chapter notes and your electronic lab notebook. • Computational Chemistry Server “queues”: students will be using a variety of shared computational chemistry resources, including the North Carolina High School Computational Chemistry server and the SGI Origin (Zeus) server at East Carolina University. The use of shared computing resources requires an
above average ability to be considerate of other users; not use more of the resource than required to solve the problem; and otherwise be a good steward of some very expensive computing tools. • Journal articles: We will discuss theory and applications of computational techniques to solve chemical problems. This requires the prior reading of journal articles handed out in class. We will occasionally have a short open-‐article quiz on the week’s article. • Final Project: Every student is required to work on a small project within the student’s area of interest due on the date of the final and submit a short journal-‐style report (6 to 12 pages), due on the final day. Students can work in collaborative groups of NO MORE THAN THREE (3). • Comments on Grading: this course requires active participation, and your grade will reflect that. You should anticipate at least ten hours a week (see sample schedule above) of work outside of class. Some weeks may be more, some may be less. • KEY TO SUCCESS: in this and ANY ONLINE COURSE, you must be willing and able to READ. 95% of the course information comes from reading: documents and, most importantly, EMAIL. I send out a LOT of email, and I am assuming that you are reading it. ACADEMIC HONESTY: Individual ownership of your work is important. You will learn more effectively by taking your own notes and struggling with the problems and assignments yourself. Faculty and student tutorials are available to help you but it will be to your advantage to make a serious attempt at the assignment before seeking help. If you are having trouble making progress, seek help as soon as possible. It is important to get notes for any class missed and to make up any work missed as soon as possible. The following will be considered a breach of academic honesty: 1. Giving or receiving help during a test or quiz. 2. Discussing the contents of a test or quiz with members of the class or with other sections of the course that have not taken it. 3. Programming information into your calculator to be used during a test or quiz. 4. Completing assignments to be graded for other students is a violation for both the giver and the recipient of the work. 5. Consulting an online resource (Google, Wikipedia, electronic notes, etc.) when ask not to do so.
