CHM 4111/5111 Syllabus 1

CHM 4111/5111 Advanced Physical Chemistry Spring 2017 Dr. Roberto Peverati Olin Physical Sciences, Room 324 rpeverati@fit.edu, Office Hours: see below http://my.fit.edu/~rpeverati/teaching (321) 674-7735

Purpose of the course: The primary purpose of this course is to broaden your exposure to the field of physical chemistry. The junior-year sequence of courses covers three basic areas of physical chemistry: thermodynamics, chemical kinetics, and quantum mechanics. CHM 4111/5111 expands the latter area into a more in-depth analysis of computational chemistry (molecular modeling) and statistical mechanics. The secondary purpose of this course is to provide a practical knowledge on how modern physical chemistry depends on computers to conduct research, and to give a practical overview on how computational tools are used in physical chemistry. This course will achieve these goals by simulating a real research activity in a modern physical chemistry lab and your final evaluation will depend on the research that you will conduct. TL;DR: The real purpose of this course is to give you the capabilities to apply advanced physical chemistry tools (i.e. computational chemistry and statistical mechanics) to problems in chemical research. Books and other materials: There is NO required text for this class, however, most of the materials will be taken from the following three books:

1. A.Szabo and N. Ostlund, “Modern Quantum chemistry” (for the theory portion) 2. C. Cramer, “Essentials of Computational Chemistry”, 2nd ed. (for the computational portion) 3. T. Engel & P. Reid, "Thermodynamics, Statistical Thermodynamics & Kinetics", 3rd ed. (for the

statistical mechanics portion). Other study materials will be provided by Dr. Peverati when necessary and a list of books specific for each topic covered in class is available upon request. You are NOT required to purchase any of these books, but there is a high chance that you already own the Engel book because of P-Chem1 and/or P-Chem2, while the Szabo-Ostlund book currently cost $14 on Amazon, and it’s so inexpensive that it’s a highly suggested purchase for every student that is seriously interested in computational chemistry. Cramer’s book is more expensive (currently at around 58$), but it’s definitely not indispensable for the class in any form and can be compensated with online materials and other sources (see below). Since this course simulate life in a real research environment, the students are encouraged to “smartly” and independently use every online source available (i.e., Literature articles, online lectures – e.g. MIT, UC Berkeley, iTunes U —, online tutorials – e.g. Gaussian, Inc. website –, Wikipedia articles, Google searches, blogs, forums, etc). TL;DR: Google is your friend!

Purpose of this (slightly unconventional) syllabus: This course is radically changed for the Spring 2017 and it will have a very different structure than what you might be used to, especially here at FIT. Therefore, you MUST read this document really carefully, and if you have questions or concerns, report them immediately to Dr. Peverati. TL;DR: Read below. No really, read it! If you don’t really want to read it, at least read the TL;DRs!!!

CHM 4111/5111 Syllabus 2

Structure of the course: Each week, the first two lectures (M,W) will cover the theoretical concepts, while the third lecture (F) will include either a practical training on the computer, a Q&A session on the topics that have been covered in the previous two lectures, or both. During this lecture, you will learn how to apply the theoretical concepts to perform calculations on a real research machine. For this reason, an individual account on the Blueshark supercomputer (http://it.fit.edu/computing/hpc_blueshark.php) is required for each student, and will be set up at the beginning of the course. Because of the uniqueness of the material taught and the format of the course, presence at class is mandatory. If you cannot attend a class, contact Dr. Peverati as soon as possible (see the bottom of this document on how to do that properly). Owning a personal computer (or laptop) is not required, but it might be very helpful, since it will allow you to work on the research project on your own (free) time. You will be able to access Blueshark through a ssh connection, therefore any computer with an internet access will work. Linux, Mac and Chromium machines have a Unix terminal and ssh installed by default and will require very little modifications (including the inexpensive Raspberry Pi, whose OS, Raspbian, is a lightweight Linux distribution with terminal and ssh, although it might be hard to use a word processor or a keynote program on it, but feel free to use it if you like, you can even rent one at FIT library). Windows machine will need a Unix terminal access and ssh installed on them (i.e., Cygwin), but read, memorize and put to good practice the previous TL;DR, since Dr. Peverati is a Mac users since the old days and he has never used a Windows machine or seen one up-close, nor he is particularly eager to do so. ssh client are also available for iPhone/iPad and android devices. Some computers will be available to the students in the computational chemistry lab in room OPS-205, however these machines are slightly outdated (very outdated, I should say, but that’s not very politically correct, so let’s keep the slightly in there) and their usage is suggested only as a last resource for students that don’t have any access to any other computer. If you are a computer geek and want to use your own computer instead of Blueshark to perform calculations, you can do that, but it will take a big effort and a lot of frustration to compile every program, so it is encouraged but not recommended (whatever that means). TL;DR1: If I have NO interest in computers, and NO interest in learning how to use them professionally for chemical research, then I should NOT take this course. TL;DR2: If I DO like computers and I’m interested in chemistry, I think this is going to be the best course at FIT and I can potentially lose a lot of time on it!

Outline: Because of the new format and teaching methodology, and since this is a new approach for CHM4111/5111 (and surely a unique approach in the Chemistry Department and potentially in the entire University), the outline below incudes the topics that will be covered in class in a reasonable time order, but without a lecture date or a book reference and the schedule will be subject to (hopefully slight) changes and corrections throughout the semester. Each topic will take 1 week, but since there will be 10 main topics and about 15 weeks of lectures, some important topics will be expanded along two weeks.

1. Intro to Theory, Computation and Modeling and using computers in science 2. Molecular Mechanics and Force Fields 3. Molecular Orbital (MO) Theory 4. Semiempirical MO 5. ab-initio MO: Hartree–Fock 6. Correlation Methods 7. Density Functional Theory (DFT) 8. Charge-Distribution, Spectroscopy and Solvents 9. Statistical mechanics 10. Calculation of Thermodynamic Properties

TL;DR: A bunch of stuff I’ve never heard about (let’s hope there’s something interesting in there)!

CHM 4111/5111 Syllabus 3

The reason why you are actually reading this (a.k.a. “The Exam”): The final grade will be given according to two essential skills that you will require to perform research in (physical) chemistry: writing and presenting. The exam will be composed of a final report that must be written as a research article. And since public speaking is the second most important tool in research, you will give a research seminar of 20 minutes (15 minutes plus questions) to the class to complete the examination. The topic of the research article and the research seminar will be chosen at the beginning of the course, and the results that must be reported will be collected throughout the semester. The final grade will depend 50% on the report and 50% on the seminar and it will not depend on the quality of the results, nor the hardness of the project, although they might both have an effect on it (i.e., it is much easier to have a very good paper on a very hard, although more time-consuming, topic, while it is much easier to give a seminar on a simpler topic. Middle ground is your friend here!). That also doesn’t mean that I can “fake” a result! It is very easy for an expert (a.k.a. Dr. Peverati) to spot data that don’t fit, and this will result in failing the class altogether (i.e., if I have trouble obtaining a result with some particular method/program, it is better to explain why I’m having such troubles and why I’m not presenting the result, rather than faking it! This is a research simulation, therefore it is perfectly normal to have problems obtaining some data, it’s just a matter of understanding why and explain it. Nothing is ever perfect, so it’s OK to have some holes in my tables, but I should not be lazy and I must still try as hard as possible to get all the results in there by the end of the semester!) TL;DR: Do the calculations throughout the semester, collect the results (don’t fake them!), write a paper, presentation, done. When and how to reach Dr. Peverati: Dr. Peverati’s office hours are not listed above because, if the door at OPS-324 is open, he is available for explanations and clarifications, but only after the student has exhausted every possible online source before visiting, and found no reasonable answers (i.e., questions that can be answered with a simple Google or Wikipedia search will not be answered. You are a Graduate Student – or will be one soon – in the third millennium: act like one!) The highest chance that the door is open will be every day between 11AM and 4PM. The e-mail address above is also a great way to find Dr. Peverati, just don’t assume that if you write to him at 2AM he will reply immediately (although it might happen, from time to time). Same rules apply for e-mail inquiries, therefore use your favorite search engine before sending an e-mail and don’t be surprised to receive a Google link or a Wikipedia screenshot as an answer to a simple question. Is Dr. Peverati going to use Canvas? Mostly no. This course has to be managed as two separate courses on Canvas (4111 and 5111) and this will likely mean confusion and chaos. Also, the utility of Canvas for this course is very minimal, since there are a limited number of students, no midterms and there is no material that need to be distributed in a formal environment. Dr. Peverati’s website, linked above, will contain more useful information than Canvas and will be updated more frequently, so you should use that and his direct e-mail address in case you need to contact him, in place of Canvas. There is also an office phone number, but who’s using phones anymore? TL;DR: Almost any time in his office or anytime via e-mail, but he seems allergic to stupid questions… What if I find out that I like this stuff? Dr. Peverati is looking for students to join his research group and he has several research projects that can go from a short semester of undergraduate research to a full Ph.D. thesis. I should probably talk to him and find out more about them!