1computational chemistry for chemistry educators - gotwals/sendlinger copyright© 2007 all rights...
TRANSCRIPT
1Computational Chemistry for Chemistry Educators - Gotwals/Sendlinger Copyright© 2007 All Rights Reserved
Chapter 24Computational Chemistry
Research
2Computational Chemistry for Chemistry Educators - Gotwals/Sendlinger Copyright© 2007 All Rights Reserved
Contents
• Choosing a Research Problem
• Applying for a research account
• Choosing a Model Chemistry
• The Computational Chemistry Notebook
• Presenting Results• Sample Project Titles
3Computational Chemistry for Chemistry Educators - Gotwals/Sendlinger Copyright© 2007 All Rights Reserved
Choosing a Research Problem
• Challenge:– Choosing a project appropriate to the research situation•Appropriateness defined
– Do-able in the amount of time available– Within the cognitive and experiential abilities of the student researcher
– Within the limits of available resources» Software, job limits, other resources
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Research Guiding Questions
• What area of chemistry is most interesting?– Organic chemistry
• Structures and mechanisms
– Medicinal chemistry• Comparison of energies of lead drugs
– Environmental chemistry• Rates of hydroxyl radical degradation in the atmosphere
– Inorganic chemistry• Exitation states of coordination complexes
– Reaction chemistry• Prediction of kinetics, thermodynamics, transition states
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Research Guiding Questions
• What resources do you have at your disposal?– Software
• Comp chem server cannot do protein folding/docking, crystal structures, etc.
– Job time limits• Computational resources are not unlimited
– Mentors• Are there intellectual resources available, i.e smart people?– University mentors, online mentors, local educators, etc.
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Research Guiding Questions
• How much time do you have?
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Research Time Chart
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Research Guiding Questions
• Is there a particular category of computations that is of most interest?– Structure:
• Geometry optimizations based on model chemistry• Comparison of computational results to experimental results
• Transition state geometries
– Property:• Determination of spectra• Calculation of quantum descriptors (QSPR)
– Activity:• Reaction mechanisms• QSAR-types of problems
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Applying for a research account
• Real world:– Researchers apply for computing time on large machines• How? By submitting a research proposal
• Student researchers:– Also required to submit research proposal
– Done online via online form
• Components:– Paper Title– Paper Abstract (250-300 words)
– Software Requirements
– Per job time limit– Total CPU time– Name of teacher/mentor
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Choosing a Model Chemistry
• Goal– Choose the simplest model chemistry that produces the data needed to answer the research question
• Tradeoff– Computational accuracy vs. compute time (resource stewardship)
• Classroom research projects– Semi-empirical typically adequate• AM1 or PM3
– Smaller basis sets are adequate• STO-3G• 3-21G
• Independent research– 6-31G basis sets for final runs
– Can do prelims with smaller basis set
11Computational Chemistry for Chemistry Educators - Gotwals/Sendlinger Copyright© 2007 All Rights Reserved
The Computational Chemistry Notebook
• Parts1. Page number2. Date3. Title of project4. Drawing of project5. References to the
literature6. Program(s) used in
calculations7. Computational approach8. Procedure9. Calculation type10.File name(s)11.Basic data results12.Data 13.Summary
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Presenting Results
• Three methods:– Poster– Lab Abstract– Journal-type article
• Upcoming– Student Journal of Computational Chemistry
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Poster
• Standard format at scientific professional meetings• Can use standard tri-fold cardboard display• PowerPoint formatted - ~$150 at Kinkos for printing
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Lab Abstract
• Contains the basic parts of the research– Purpose– Computational approach
– Example data– Sample results– Conclusion(s)
• Typically 250-350 words
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Journal-type article
• Length: 3-10 pages
• Contents– Title– Author(s)– Institution– Keywords– Abstract
• Introduction• Computational Approach
• Results and Discussion
• Conclusion(s)• Acknowledgement• References
16Computational Chemistry for Chemistry Educators - Gotwals/Sendlinger Copyright© 2007 All Rights Reserved
Sample Project Titles
• Symmetry in Superconductors• Transition State of a
Creatine Molecule during Dehydration
• The Diels-Alder Reaction• Comparison of Relative
Sweetness to Molecular Properties of Artificial and Natural Sweetners
• Comparative Study: Sarin and VX
• Is there a transition state for the insertion of ethylene into the Ziegler-Natta catalyst?
• Gaussian94 Analysis of C60• Potential Energy Scan of an
Ester using Gaussian94
• GAMESS Animation Study of LiH
• Transition State Study of a Diels-Alder Reaction
• Transition State Study of a Cocaine Molecule
• Basicities of Amines• Comparison of the
Bonding Properties of Serotonin and Lysergic Acid
• Conformational Anaysis Study of n-Butane
• Transitional State Study of ATP