1Computational Chemistry for Chemistry Educators - Gotwals/Sendlinger Copyright© 2007 All Rights Reserved Chapter 24 Computational 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

4Computational Chemistry for Chemistry Educators - Gotwals/Sendlinger Copyright© 2007 All Rights Reserved 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

5Computational Chemistry for Chemistry Educators - Gotwals/Sendlinger Copyright© 2007 All Rights Reserved 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.

6Computational Chemistry for Chemistry Educators - Gotwals/Sendlinger Copyright© 2007 All Rights Reserved Research Guiding Questions How much time do you have?

7Computational Chemistry for Chemistry Educators - Gotwals/Sendlinger Copyright© 2007 All Rights Reserved Research Time Chart

8Computational Chemistry for Chemistry Educators - Gotwals/Sendlinger Copyright© 2007 All Rights Reserved 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

9Computational Chemistry for Chemistry Educators - Gotwals/Sendlinger Copyright© 2007 All Rights Reserved 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 ( words) –Software Requirements –Per job time limit –Total CPU time –Name of teacher/mentor

10Computational Chemistry for Chemistry Educators - Gotwals/Sendlinger Copyright© 2007 All Rights Reserved 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 Parts 1.Page number 2.Date 3.Title of project 4.Drawing of project 5.References to the literature 6.Program(s) used in calculations 7.Computational approach 8.Procedure 9.Calculation type 10.File name(s) 11.Basic data results 12.Data 13.Summary

12Computational Chemistry for Chemistry Educators - Gotwals/Sendlinger Copyright© 2007 All Rights Reserved Presenting Results Three methods: –Poster –Lab Abstract –Journal-type article Upcoming –Student Journal of Computational Chemistry

13Computational Chemistry for Chemistry Educators - Gotwals/Sendlinger Copyright© 2007 All Rights Reserved Poster Standard format at scientific professional meetings Can use standard tri-fold cardboard display PowerPoint formatted - ~$150 at Kinkos for printing

14Computational Chemistry for Chemistry Educators - Gotwals/Sendlinger Copyright© 2007 All Rights Reserved Lab Abstract Contains the basic parts of the research –Purpose –Computational approach –Example data –Sample results –Conclusion(s) Typically words

15Computational Chemistry for Chemistry Educators - Gotwals/Sendlinger Copyright© 2007 All Rights Reserved 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