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Chapter 24

Chapter 24. Computational Chemistry Research. Contents. Choosing a Research Problem Applying for a research account Choosing a Model Chemistry The Computational Chemistry Notebook Presenting Results Sample Project Titles. Choosing a Research Problem. Challenge:

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Chapter 24

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  1. Chapter 24 Computational Chemistry Research

  2. Contents • Choosing a Research Problem • Applying for a research account • Choosing a Model Chemistry • The Computational Chemistry Notebook • Presenting Results • Sample Project Titles

  3. 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

  4. 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

  5. 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.

  6. Research Guiding Questions • How much time do you have?

  7. Research Time Chart

  8. 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

  9. 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 Applying for a research account

  10. 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 Choosing a Model Chemistry

  11. The Computational Chemistry Notebook • Parts • Page number • Date • Title of project • Drawing of project • References to the literature • Program(s) used in calculations • Computational approach • Procedure • Calculation type • File name(s) • Basic data results • Data • Summary

  12. Presenting Results • Three methods: • Poster • Lab Abstract • Journal-type article • Upcoming • Student Journal of Computational Chemistry

  13. Poster • Standard format at scientific professional meetings • Can use standard tri-fold cardboard display • PowerPoint formatted - ~$150 at Kinkos for printing

  14. Lab Abstract • Contains the basic parts of the research • Purpose • Computational approach • Example data • Sample results • Conclusion(s) • Typically 250-350 words

  15. Length: 3-10 pages Contents Title Author(s) Institution Keywords Abstract Introduction Computational Approach Results and Discussion Conclusion(s) Acknowledgement References Journal-type article

  16. 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 Sample Project Titles

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