exp50_SPrev60_9_07 - Experiment 50 Chemistry Laboratory...

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Experiment 50 Chemistry 541/2 Physical Chemistry Laboratory Computational Approaches to Molecular Structure (revised 9/ 07) Introduction Computational chemistry is finding increased application in all branches of chemistry. This experiment will introduce you to some of the methods used in computational chemistry to study molecules. You will learn how to use the program Spartan which is a working compendium of the ab initio efforts of several generations of scientists. This program performs calculations (molecular geometry optimizations and vibrational analysis) from first principles ( ab initio ) which are widely available for use on
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2 desktop PCs. Spartan includes a simple user-friendly graphical interface (GUI) for visualizing the input and output. Why do chemistry on a computer? Paraphrasing Mike Colvin of Sandia National Lab: It is now generally possible to obtain molecular structures (with ~1% accuracy), reaction enthalpies (~1 kcal/mol), dipole moments and infrared intensities, vibrational frequencies (~5%), reaction free energies (~2 kcal/mol), relative acid constants (~2 pK a units), and reaction rates (for certain types of reactions) without doing any laboratory experiments, i.e. at reduced cost. There is also increased safety and faster turnaround when toxic or explosive compounds are involved. There is the prospect of an improved understanding especially when we have both an experimental and theoretical perspective on a problem. There is a caveat, however. "Computational Chemistry is far from a black box - Care must be taken in choice of method and interpretation of results." We will start by going through exercises that teach you how to use the software and finish with a computational experiment on intermolecular interactions. The procedure involves the following steps: 1) learning to use Spartan with the H 2 molecule, 2) determination of the potential energy curve for the H 2 molecule using single point calculations at different bond distances with different levels of theory, 3) development of skills for the input of simple molecules, measurements on the structure of molecules, optimizations of structure, and vibrational properties of a simple polyatomic molecule, like H 2 O, CH 4 , or CH 3 OH, 4) calculations to determine the H of the reaction of N 2 (g) + O 2 (g) 2 NO(g), and 5) calculations of the dipole moments of a number of complexes of molecules interacting with a water molecule. Before you start. .. All data is initially stored on the hard drive, however at the end of the day, you must transfer your files or data to an independent location. Either bring a 3.5" floppy disk memory stick for USB port, or transfer your files over the chemistry network to another PC. Do not assume that files left on the PC hard drive will still be available the next time you return to the PC. There is extensive documentation for Spartan (via the help menu) on the computers in MP 2047 and MP 0008, as well as tutorial manuals in both rooms. You may try to familiarize yourself with this program before coming to lab as you have access to the software independent of lab time.
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exp50_SPrev60_9_07 - Experiment 50 Chemistry Laboratory...

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