Dr. Ron Rusay Diablo Valley College

1. Mathematical Modeling, Technology and Bridging to the Nano-realm in Teaching Undergraduate Chemistry http://ep.llnl.gov/msds/AIT-presentation.htmEnhanced Version:http://ep.llnl.gov/msds/AIT-symposium.htm Dr. Ron Rusay Diablo Valley College University of California, Berkeley / Lawrence Livermore National Laboratory AIT-CUWorkshop on Nano, Continuum, Material and Computational Mechanics

2. What is considered too large for the nano realm?Powers of 10 (10 x)http://www.eamesoffice.com/powers_of_ten/powers_of_ten.htmlhttp://www.powersof10.com/ Plant Cell = 0.00001276 meters wide (12.76 x 10 -6) (12.76 millionths of a meter) (12,760 nanometers!) Earth = 12,760,000 meters wide (12.76 x 10 6), 12.76 million meters Nano scale is regarded as < 1,000 nanometers ~1/50 the diameter of a human hair (anything less than a micron (10-6 m). Chemists typically think in views and images of < 1 nanometer.)

3. ~ 0.1 nm Anders Jöns Ångström (1814-1874) 1 Å = 10 picometers = 0.1 nanometers = 10-4 microns = 10-8 centimeters Nucleus = 1/10,000 of the atom • 1 nm = 10 Å • An atom vs. a nucleus • ~10,000 x larger

4. DNA: Picture 51 http://info.bio.cmu.edu/courses/03231/ProtStruc/ProtStruc.htm B-DNA: The advent of modeling 46 Å 12 base sequence (1953-2003) http://molvis.sdsc.edu/pdb/dna_b_form.pdb

5. DNA: Size, Shape & Self Assembly http://www.umass.edu/microbio/chime/beta/pe_alpha/atlas/atlas.htm Views & Algorithms 10.85 Å 10.85 Å Several formats are commonly used but all rely on plotting atoms in 3 dimensional space; .pdb is one of the most popular.

6. http://www.rcsb.org/pdb/ PROTEIN DATA BANK • What are PDB files? http://chemistry.Gsu.EDU/glactone/PDB/pdb.html • The PDB format (Protein Data Bank), from the Research Collaboratory for Structural Bioinformatics) is a standard file format for the XYZ coordinates of atoms in a molecule. • A few lines from a PDB file for a DNA base pair structure • AUTHOR GENERATED BY GLACTONE • SEQRES 1 A 1 G • SEQRES 1 B 1 C • ATOM 1 P G A 1 -6.620 6.196 2.089 • ATOM 2 OXT G A 1 -6.904 7.627 1.869 • ATOM 3 O2P G A 1 -7.438 5.244 1.299 • ATOM 4 O5' G A 1 -5.074 5.900 1.839 • ATOM 5 C5' G A 1 -4.102 6.424 2.779 • ATOM 6 C4' G A 1 -2.830 6.792 2.049 • ATOM 7 O4' G A 1 -2.044 5.576 1.839 • ATOM 8 C3' G A 1 -2.997 7.378 0.649 • The last three columns are the XYZ coordinates of the atoms.PDB format can be applied to any molecule, very small to very large. It includess enormous on-line libraries of molecules.

7. Proteins: Size, Shape & Self Assembly http://www.stark.kent.edu/~cearley/PChem/protein/protein.htm

8. Globular proteins:A larger number of atoms rolled into relative small volumes Protein sizes are most often referred to by their molecular masses (daltons; 1 amu = 1 dalton), not by their dimensions because of their globular nature. RNA polymerase II-transcription factor J. Biol. Chem., Vol. 274, Issue 11, 6813-6816, 1999 The yellow dashed line is ~ 110-Å

9. Enzyme interaction: neurotransmission The interaction of a globular protein, acetylcholinesterase, with a relatively small molecule, acetylcholine. Richard Short (Cornell University)

10. Some Examples of Structural Proteinshttp://info.bio.cmu.edu/courses/03231/ProtStruc/ProtStruc.htmcollagen: connective tissue myosin-actin: muscle Michael Ferenczi

11. Mechanical proteinsPathogens & Cell Invasionhttp://ep.llnl.gov/msds/Staph-infection/infection.html Streptococcus pyogenes 96,000 x Vincent A. Fischetti Ph.D., Rockefeller University

12. Human’s total ~ 100 x 10 6 immunoproteins Immunoglobin Antibodies Prolific Immunoproteins Combinatorial syntheses from libraries of 250, 10, and 6 possible contributors Human Genome ~30,000 proteins

13. Gecko & it’s toe, setae, spatulae6000x Magnification Full et. al., Nature (2000) 5,000 setae / mm2 600x frictional force; 10-7 Newtons per seta http://micro.magnet.fsu.edu/primer/java/electronmicroscopy/magnify1/index.html Geim, Nature Materials (2003) Glue-free Adhesive 100 x 10 6 hairs/cm2 Yurdumakan, Chem Comm (2005) 200X Gecko’s Force

14. The “Lotus Effect” Biomimicryhttp://www.bfi.org/Trimtab/spring01/biomimicry.htm • Lotus petals have micrometer-scale roughness, resulting in water contact angles up to 170° • See the Left image in the illustration on the right. Wax

15. The “Lotus Effect” Biomimicryhttp://www.sciencemag.org/cgi/content/full/299/5611/1377/DC1 • Isotactic polypropylene (i-PP) melted between two glass slides and subsequent crystallization provided a smooth surface. Atomic force microscopy tests indicated that the surface had root mean square (rms) roughness of 10 nm. • A) The water drop on the resulting surface had a contact angle of 104° ± 2 • B) the water drop on a superhydrophobic i-PP coating surface has a contact angle of 160°. Science, 299, (2003), pp. 1377-1380, H. Yldrm Erbil, A. Levent Demirel, Yonca Avc, Olcay Mert

16. Bridging to the Nano realmMolecular Modeling: Visualizations & Predictions Modeling Methods: • Numerical Methods • Integral Method • Ab Initio Methods • Semi-Empirical MO-SCF Methods • Approximate MO Methods 

17. Web MOhttp://c4.cabrillo.cc.ca.us/projects/webmo/index.htmllogin: dvc1password:chem • Web MO Project: undergraduate molecular modeling college consortium • Web-based, free, instructional service • Uses MOPAC 7 & GAMESS 2000, others to be added • Modeling tools, activities and lessons are under construction

18. Web MOhttp://c4.cabrillo.cc.ca.us/projects/webmo/index.htmllogin: dvc1password:chem • Output: • Dipole moment • Bond Orders • Partial Charges • Vibrational Modes • Molecular Orbitals • Ultraviolet-Visible-Infrared Graphics • NMR Chemical Shifts

19. Molecular Size, Shape & PropertiesOzone and Water 0.1278 nm • Resultant Molecular Dipoles > 0 • Solubility: Polar molecules that dissolve or are dissolved in like molecules • The Lotus flower • Water & dirt repellancy

20. H C C H Example of a Web MO Project Modeling & Energy Calculations of Acetylene Lawrence Berkeley Laboratory (LBL)

21. H C C H TIP pz H + O porbital 1 cm (± 1 μm) Imaging: acetylene on Pd(111) at 28 K Molecular Image Tip cruising altitude ~700 pm Δz = 20 pm Why don’t we see the Pd atoms? Because the tip needs to be very close to image the Pd atoms and would knock the molecule away Surface atomic profile Tip cruising altitude ~500 pm Δz = 2 pm Calculated image (Philippe Sautet) If the tip was made as big as an airplane, it would be flying at 1 cm from the surface and waving up an down by 1 micrometer The STM image is a map of the pi-orbital of distorted acetylene M. Salmeron (LBL)

22. Tip e- ((( ) ( ))) Excitation of frustrated rotational modes in acetylene molecules on Pd(111) at T = 30 K M. Salmeron (LBL)

23. http://www.foundry.lbl.gov/ • Inorganic Nanostructures(A.P. Alivisatos) • Nanofabrication(J. Bokor) • Organic Polymer/Biopolymer Synthesis(J.M.J. Frechet) • Biological Nanostructures(C.R. Bertozzi) • Imaging and Manipulation(M.B. Salmeron) • Theory of NanostructuredMaterials(S.G. Louie)

24. Invited speakers: • Pat Dehmer, Office of Basic Energy Sciences • Paul Alivisatos, Director, Molecular Foundry • Grant Willson, University of Texas at Austin • Roberto Car, Princeton University • Vicki Colvin, Rice University • Mike Roukes, California Institute of Technology • Mike Garner, Intel (invited) ___________________________ • Capabilities of the Foundry facilities and affiliated laboratories • Types of projects that could be pursued in the facilities and affiliated laboratories • Procedures for writing and review of proposals • Logistics of working at the Foundry A special session exploring the application of single molecule characterization and manipulation techniques Sessions dedicated to issues related for the call for proposals for research in the two-year ramp-up period while the Foundry building is under construction.

25. Crystals for the ClassroomBridging the realms of the macro and atomic/nano scalehttp://crystals.llnl.gov • A modular collection of teaching-learning tools for undergraduate chemistry courses that can be adapted to teach various Science, Technology, Engineering and mathematics (STEM) topics and concepts

26. Crystals for the ClassroomBridging the realms of the macro and atomic/nano scalehttp://crystals.llnl.gov • Chemistry lessons are embedded in the story of NIF ( The National Ignition Facility) http://crystals.llnl.gov/nif-kdp-frameset.html • Learning activities were developed relative to the context of the research and science behind NIF.

27. Crystals for the ClassroomBridging the realms of the macro and atomic/nano scalehttp://crystals.llnl.gov • Web based, distributed freely • Activities provide a diverse collection that support a wide variety of learning and teaching styles: http://ep.llnl.gov/msds/Chem120/learning.html

28. Instructor - StudentActivities, Exercises & Resourceshttp://crystals.llnl.gov • Seeing - Hearing - Doing • Powerpoint Presentations • Visualizations: Time lapsed Growth

29. Instructor - StudentActivities, Exercises & Resourceshttp://crystals.llnl.gov • Seeing - Hearing - Doing • Powerpoint Presentations • Visualizations: Time lapsed Growth • Simulations: Fusion - Fission

30. Instructor - StudentActivities, Exercises & Resourceshttp://crystals.llnl.gov • Seeing - Hearing - Doing • Powerpoint Presentations • Visualizations: Time lapsed Growth • Simulations: Fusion - Fission • President Truman’s Announcement • Numerical and Graphical Problems • Student Worksheets • Glossary • Debate on Nuclear Energy • Writing Exercises • Interpreting Research Data • Experimentation

31. Acknowledgements