Undergraduate Research at UA in the Dixon Group in Chemistry David Dixon Robert Ramsay Chair

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