Undergraduate Research at UA in the Dixon Group in Chemistry

1. Undergraduate Research at UA in the Dixon Group in Chemistry David Dixon Robert Ramsay Chair Chemistry 205-348-8441 dadixon@bama.ua.edu Hydrogen Storage Grand Challenge, Solicitation No. DE-PS36-03GO93013 Robert Ramsay Chair Fund

2. Mostly CBHP students – strong math and computing backgrounds • Many Honors Chemistry CH-117 • Use computational chemistry to solve real problems • No actual research cost due to presence of computational resources in the Dixon group, at UA, and at Alabama Supercomputing Center including desktop computers, servers, massively parallel computers, and software. • Usually assign student to individual project that meets group research interest and the student’s interest. If the student wants an individual project, arrange for that. • Usually try to get students involved as 2nd semester freshman or 1st semester sophomores. Try to get students into REU program during the summer if funds available. • Pick projects based on students length of stay. • Assign student to graduate student or postdoctoral mentor. • Encourage peer-to-peer mentoring

3. Try to visit with students in the lab on a regular basis • Focus on letting students learn how to do research by allowing failure. Acceptable due to low cost of computer cycles. • Work with students for publications. Focus on real publications not student ones. • Work with students on awards. • Pick projects students can do. If a project requires students to come in and work every day for a week for 5 to 6 hours a day to get it going, it will not succeed. Example molecular dynamics of biomolecules. Too hard to get calculations initiated. • Have excellent GUIs and software. • Provide students with place to work not only on research. • Try not to overlap projects. • Give student independent project. • Either use CBHP or Departmental effort for formal research training – literature searching, equipment use, writing. • Research presentations – CBHP, REU, Department, UA Research Day

4. Science Drivers: Science across Scales in Space & Time • Catalysis: Computational catalysis – transition metal oxides, homogeneous catalysts, metal clusters, site isolated catalysts • Nanoscience: TiO2 clusters for sensors and photocatalysts; Shape memory alloys (Nitinol) (NASA) • Energy: H2 storage in chemical systems – organic & inorganic • Energy: Advanced Fuel Cycle Initiative – Metal oxide clusters in solution for new fuels and environmental cleanup • Energy: New sources of energy (solar) • Geochemistry: Geological CO2 sequestration • The Environment: Atmosphere, Clean Water, Subsurface & Cleanup • Biochemistry: Peptide and amino acid negative ion chemistry • Computational main group chemistry – fluorine chemistry, acids and bases, other elements • Computational thermodynamics and kinetics – high accuracy, solvation effects. • Chemical End Station: RC3 & software development

5. Computing Hardware Resources

6. Computing Software Resources • Other computational chemistry programs • For quantum chemistry: ACES3, CFour, Columbus, Dalton, GAMESS, Molcas, MPQC, PSI3, etc. • For molecular dynamics: CPMD, Espresso, NAMD, Tinker, ZORI, etc. • Khimera – interface to Gaussian to do kinetics modeling • Software for program development • Intel C/C++/Fortran compilers, MKL/IPP/TBB libraries; • PGI C/C++/Fortran compilers, ACML libraries

7. Ampac / Agui from Semichem • Ampac for fast semi-empirical calculations • Fast and reliable • Many methods: AM1, MNDO, MINDO3, PM3, MNDO/d, RM1, PM6, SAM1, MNDOC • Geometry optimization, frequencies, transition state, IRC, solvation, etc. • Agui for molecular visualization • Support most features of Gaussian 09 including periodic systems, ONIOM, etc. • Support many file formats including Mol, Mol2, SDF, PDB, CIF • Support many platforms: Windows, Linux, Mac OS X, etc. Manage Molecular Orbitals 3D Reaction Surface Plot Surface Adsorption