7.1: Pre-Lab Assignment
- Page ID
- 371809
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\(\newcommand{\avec}{\mathbf a}\) \(\newcommand{\bvec}{\mathbf b}\) \(\newcommand{\cvec}{\mathbf c}\) \(\newcommand{\dvec}{\mathbf d}\) \(\newcommand{\dtil}{\widetilde{\mathbf d}}\) \(\newcommand{\evec}{\mathbf e}\) \(\newcommand{\fvec}{\mathbf f}\) \(\newcommand{\nvec}{\mathbf n}\) \(\newcommand{\pvec}{\mathbf p}\) \(\newcommand{\qvec}{\mathbf q}\) \(\newcommand{\svec}{\mathbf s}\) \(\newcommand{\tvec}{\mathbf t}\) \(\newcommand{\uvec}{\mathbf u}\) \(\newcommand{\vvec}{\mathbf v}\) \(\newcommand{\wvec}{\mathbf w}\) \(\newcommand{\xvec}{\mathbf x}\) \(\newcommand{\yvec}{\mathbf y}\) \(\newcommand{\zvec}{\mathbf z}\) \(\newcommand{\rvec}{\mathbf r}\) \(\newcommand{\mvec}{\mathbf m}\) \(\newcommand{\zerovec}{\mathbf 0}\) \(\newcommand{\onevec}{\mathbf 1}\) \(\newcommand{\real}{\mathbb R}\) \(\newcommand{\twovec}[2]{\left[\begin{array}{r}#1 \\ #2 \end{array}\right]}\) \(\newcommand{\ctwovec}[2]{\left[\begin{array}{c}#1 \\ #2 \end{array}\right]}\) \(\newcommand{\threevec}[3]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \end{array}\right]}\) \(\newcommand{\cthreevec}[3]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \end{array}\right]}\) \(\newcommand{\fourvec}[4]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \\ #4 \end{array}\right]}\) \(\newcommand{\cfourvec}[4]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \\ #4 \end{array}\right]}\) \(\newcommand{\fivevec}[5]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \\ #4 \\ #5 \\ \end{array}\right]}\) \(\newcommand{\cfivevec}[5]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \\ #4 \\ #5 \\ \end{array}\right]}\) \(\newcommand{\mattwo}[4]{\left[\begin{array}{rr}#1 \amp #2 \\ #3 \amp #4 \\ \end{array}\right]}\) \(\newcommand{\laspan}[1]{\text{Span}\{#1\}}\) \(\newcommand{\bcal}{\cal B}\) \(\newcommand{\ccal}{\cal C}\) \(\newcommand{\scal}{\cal S}\) \(\newcommand{\wcal}{\cal W}\) \(\newcommand{\ecal}{\cal E}\) \(\newcommand{\coords}[2]{\left\{#1\right\}_{#2}}\) \(\newcommand{\gray}[1]{\color{gray}{#1}}\) \(\newcommand{\lgray}[1]{\color{lightgray}{#1}}\) \(\newcommand{\rank}{\operatorname{rank}}\) \(\newcommand{\row}{\text{Row}}\) \(\newcommand{\col}{\text{Col}}\) \(\renewcommand{\row}{\text{Row}}\) \(\newcommand{\nul}{\text{Nul}}\) \(\newcommand{\var}{\text{Var}}\) \(\newcommand{\corr}{\text{corr}}\) \(\newcommand{\len}[1]{\left|#1\right|}\) \(\newcommand{\bbar}{\overline{\bvec}}\) \(\newcommand{\bhat}{\widehat{\bvec}}\) \(\newcommand{\bperp}{\bvec^\perp}\) \(\newcommand{\xhat}{\widehat{\xvec}}\) \(\newcommand{\vhat}{\widehat{\vvec}}\) \(\newcommand{\uhat}{\widehat{\uvec}}\) \(\newcommand{\what}{\widehat{\wvec}}\) \(\newcommand{\Sighat}{\widehat{\Sigma}}\) \(\newcommand{\lt}{<}\) \(\newcommand{\gt}{>}\) \(\newcommand{\amp}{&}\) \(\definecolor{fillinmathshade}{gray}{0.9}\)Pre-Lab Assignment
This module is an introduction to computational chemistry and molecular electronic structure calculations using Spartan software. These computational exercises circle back around to some of the "wet lab" modules you completed earlier in the semester.
To help you prepare for this final experiment we ask that you do the following:
- Read the introduction to the lab, and the chapters in your textbook on quantum mechanics and electronic structure theory for molecules.
- Briefly read the Guidelines for Using Spartan® Software and look over some of the helpful materials found on your Sakai site.
Additional pre-lab assignment for Chem310L Independent Project
For CHEM 310L students, the Spartan exercises will be followed by an independent project in which you can choose to do a computational study.
We ask that you begin to think about your independent project, and we want you to do something you are really interested in! In 310L, you can choose a topic for your independent project, and choose whether you would like to dive into more computational work, or explore other applications of physical chemistry in the peer-reviewed literature. You should begin searching the literature (eg using Web of Science or looking at the Table of Contents for leading Physical Chemistry journals) for physical chemistry topics that interest you. Alternatively, you can think about simple chemical phenomena or reactions that you are interested in and that you can model using Spartan. Come to the laboratory session prepared with a brief written proposal (1 paragraph) on at least two ideas for what you might do for your independent project and be prepared to discuss it with your instructors.
Introduction
Computers and computational methods have become major tools of chemical research. This comes from the availability of powerful workstations and software packages at affordable prices, the development and implementation of accurate and efficient computational theory, and the insight and user-friendly interface provided by scientific visualization.
In this laboratory exercise, you will use the Spartan® software to explore the calculations of properties of isolated molecules based on a whole range of modeling methods, from empirical molecular mechanics to accurate ab initio quantum mechanical methods. You will carefully study the accuracy of each method by comparison with experimental results and with other computational methods. Understanding the limitations of modeling methods is as important as knowing their availability and accuracy. We will learn how such techniques can be used to help solve chemical problems.
There are two parts to the Spartan Exercise:
- The first part of the exercise is designed to relate to the previous "wet lab" modules of this course.
- The second part focuses on using computational methods to gain knowledge that is difficult to get from experimental methods; that is to study frontier molecular orbitals and transition state structure in chemical reactions.
This lab is split into 5 separate exercises designed to illustrate the various capabilities of Spartan. The requirements for your lab notebook are stated within each exercise instead of at the end of the chapter. It is recommended that you follow along with the ELN template while completing this lab to ensure that all data is properly recorded.
Independent Project
This is for Chemistry 310L students only (301L students don't need to do this). After completing the Spartan excecises, you will porpose and complete an independent project - for this project, you are welcome to model your own favorite molecules or reactions. You will need to design this part of the project before you come to the laboratory and learn to ask the right questions with the proper tools. This is an opportunity to explore something that is interesting to you.