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

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

Chapter 24Computational 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:– 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


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



• 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.



• How much time do you have?


Research Time Chart



• 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


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


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


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


Presenting Results

• Three methods:– Poster– Lab Abstract– Journal-type article

• Upcoming– Student Journal of Computational Chemistry


Poster

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


Lab Abstract

• Contains the basic parts of the research– Purpose– Computational approach

– Example data– Sample results– Conclusion(s)

• Typically 250-350 words


Journal-type article

• Length: 3-10 pages

• Contents– Title– Author(s)– Institution– Keywords– Abstract

• Introduction• Computational Approach

• Results and Discussion

• Conclusion(s)• Acknowledgement• References


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

Documents

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