1. Nanotechnology: a chemist’s constructivist view Mathematical Modeling, Technology and Bridging to the Nano-realm in Teaching Undergraduate Chemistry Dr. Ron Rusay Diablo Valley College University of California, Berkeley / Lawrence Livermore National Laboratory

2. Nanotechnology : Perspectives & Perceptions How small is small? The width of a human hair is ~ 50,000 nanometers nanometer = 1 billionth of a meter (1/1,000,000,000 m; i.e., 50,000 x 10 -9 meters) It takes about 200 human hairs lined up side by side to equal 1 cm ….more than 500 per inch.

3. 1/50 of ~ 50,000 nanometers

4. What is considered too large for the nano realm? Powers of 10 (10 x ) http://www.eamesoffice.com/powers_of_ten/powers_of_ten.html http://www.powersof10.com/ http://www.eamesoffice.com/powers_of_ten/powers_of_ten.html http://www.powersof10.com/ Earth = 12,760,000 meters wide (12.76 x 10 6 ), 12.76 million meters Plant Cell = 0.00001276 meters wide (12.76 x 10 -6 ) (12.76 millionths of a meter) (12,760 nanometers!)

5. Nanotechnology: A Brief Chronology Feynman’s miniaturization: prescience and seminal views (1959) http://www.zyvex.com/nanotech/feynman.html Nanotechnology, (Journal’s first issue: 1990) http://www.iop.org/EJ/journal/0957-4484 Curl, Kroto, Smalley: Nobel prize (1996); Fullerene, Nano tubes, http://www.nobel.se/chemistry/laureates/1996/ http://www.nobel.se/chemistry/laureates/1996/ National, Regional, Local Initiatives eg. –US: http://www.nano.gov/ http://www.nano.gov/ –UK: http://www.nano.org.uk/ http://www.nano.org.uk/ –Molecular Foundry (LBL): http://www.foundry.lbl.gov/ http://www.foundry.lbl.gov/ –Nano High School: http://www.lbl.gov/nanohigh/nanoscience_links.html http://www.lbl.gov/nanohigh/nanoscience_links.html

6. “Nanotechnology” Regarded as < 1,000 nanometers ~1/50 the diameter of a human hair. (Basically anything less than a micron (10 -6 m). Chemists typically think in mental views and images of < 1 nanometer.) Can be defined as the science of arranging and re- arranging atoms. (Manufacturing at a molecular level.) Two commonly used terms that broadly describe Nanotechnology: –Positional assembly http://www.zyvex.com/nanotech/CDAarticle.html –Self replication http://www.zyvex.com/nanotech/selfRep.html

7. Nano-scale compared to Atoms & Molecules Rutherford (1913-1917) Atoms, molecules, and nucleii

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

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

10. http://ep.llnl.gov/msds/orgchem/Chem226/Smell-Stereochem.html Larger Size Molecules 8.16 Å (0.816 nm)

11. Larger Molecules http://www.umass.edu/microbio/chime/beta/pe_alpha/atlas/atlas.htm DNA: Size, Shape & Self Assembly 10.85 Å

12. Larger Molecules http://www.umass.edu/microbio/chime/beta/pe_alpha/atlas/atlas.htm B-DNA: Size, Shape & Self Assembly http://molvis.sdsc.edu/pdb/dna_b_form.pdb 46 Å 12 base sequence (1953-2003)

13. Visualizing Molecules http://www.umass.edu/microbio/rasmol/history.htm 46 Å Physical Models & Tools 1958: Kendrew's wire models and the Richards Box 1960's: Physical "Ball and Spoke" Models 1970: Byron's Bender Molecular Sculpture 1990's: Rapid Prototyping Computer Models & Visualization Programs 1960's - 70's: Earliest Computer Representations 1980: TAMS: Teaching Aids for Macromolecular Structure 1980-1990: Evans & Sutherland Computers 1992: David & Jane Richardson's Kinemage 1993: Roger Sayle's RasMol 1996: MDL's Chime 2001 Eric Martz Protein Explorer

14. Even Larger Molecules http://www.umass.edu/microbio/chime/beta/pe_alpha/atlas/atlas.htm DNA: Size, Shape & Self Assembly http://www.rcsb.org/pdb/ PROTEIN DATA BANK

15. Proteins: Size, Shape & Self Assembly http://www.umass.edu/microbio/chime/beta/pe_alpha/atlas/atlas.htm

16. The Ribosome: RNA  Proteins 227 Å Crystal structure of a part of the ribosome at 5.5 Å Resolution. (1GIX): Contains the 30S Ribosome Subunit, three tRNA, and mRNA molecules (2001) Noller, Ramakrishnan, Steitz ~ 50 proteins + 1,000s nucleotides

17. Protein Shape: Forces, Bonds & Self Assembly

18. Globular proteins

19. Interactions: Large proteins (Enzymes) with small molecules (Substrates)

20. Models, Theories & Interactions Molecular Shape & the Sense of Smell http://ep.llnl.gov/msds/orgchem/Chem226/smell-links.html Structure-Odor Relationships Karen J. Rossiter, Chem. Rev., 1996, 96, 3201-3240

21. Three different smell receptors.

22. Modeling and Smell Four different molecules fitting the same smell receptor.

23. Shapes & Interactions: Mirror Images & Smell S-(+)-d- R-(-)-l- http://ep.llnl.gov/msds/orgchem/Chem226/Smell-Stereochem.html S-(+)- carawayR-(-)- spearmint

24. Enzyme interaction: neurotransmission The interaction of a large protein bio-polymer, acetylcholinesterase, with a relatively small molecule, acetylcholine. Richard Short (Cornell University)

25. Acetylcholine, Nerves & Neurotransmission The Neuron: Shapes and Spaces

26. Acetylcholine: OP Pesticides and Nerve gases

27. Trypsin: Hydrolysis Acetylcholinesterase works in a similar way to the digestion proteins.

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

29. Another Way to Inhibit Enzymes The Importance of Shape Statins and cholesterol

30. Hemoglobin and Oxygen Transport An allosteric effect The Importance of Shape BPG

31. Heme N NN N Fe 2+ H3CH3CH3CH3C H3CH3CH3CH3C CH 3 CH 2 CH 2 CO 2 H CH CH 2 H2CH2CH2CH2CCH HO 2 CCH 2 CH 2 Heme is the coenzyme that binds oxygen in hemoglobin (oxygen transport) and myoglobin (oxygen storage in muscles) Molecule surrounding the iron is a type of porphyrin. Important in Photodynamic therapy (PDT) The U.S. would still be a British colony except for porphyria, a medical condition in “blue bloods”.

32. Myoglobin N-terminusC-terminus Heme

33. myosin-actin: muscle Structural proteins collagen: connective tissue

34. Mechanical proteins Pathogens & Cell Invasion Streptococcus pyogenes 96,000 x Vincent A. Fischetti Ph.D., Rockefeller University

35. A Gecko’s toe, setae, spatulae 6000x Magnification http://micro.magnet.fsu.edu/primer/java/electronmicroscopy/magnify1/index.html Geim, Nature Materials (2003) Glue-free Adhesive 100 x 10 6 hairs/cm 2 Full et. al., Nature (2000) 5,000 setae / mm 2 600x frictional force; 10 -7 Newtons per seta

36. The “Lotus Effect” Biomimicry http://www.bfi.org/Trimtab/spring01/biomimicry.htm

37. Bridging to the Nano realm Molecular Modeling: Visualizations & Making Predictions Modeling Methods: Numerical Methods Integral Method Ab Initio Methods Semi-Empirical MO-SCF Methods Approximate MO Methods

38. Molecular Modeling Methods Output Applications Nano machinery Pick up -> carry -> drop at work site Eg. Oxygen transport: hemoglobin Conformational Changes (Adrenalin, Sugar digestion)

39. Web MO NSF Funded Project: Dr. Harry Ungar, Cabrillo College / University of California, Santa Cruz PI Web-based, free, instructional tool MOPAC 7 & GAMESS 2000 Activities and Lessons under development One example of a planned nanotechnology lesson: Pd (1,1,1) and Acetylene

40. 0.143 nm

41. S-(+)- carawayR-(-)- spearmint

42. C C H H Calculated image (Philippe Sautet)   orbital pzpz TIP H O + Imaging: acetylene on Pd(111) at 28 K Molecular Image Tip cruising altitude ~700 pm Δz = 20 pm Surface atomic profile Tip cruising altitude ~500 pm Δz = 2 pm 1 cm (± 1 μm) The STM image is a map of the pi-orbital of distorted acetylene 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 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 M. Salmeron (LBL)

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

44. -37mV 0 8 16 24 32 050100150200250300350400450 current (pA) rotations per second 1.72 seconds V = 20 mV 0 50 100 150 200 1 2,3 Pd 1 23 2 Measuring the excitation rate Tip fixed at position 1: Current (pA) ((( ) ( ))) x Center of molecule M. Salmeron (LBL)

45. Excitation of translations of C 2 H 2 molecules: R = 150 M  R = 94 M  R = 0.55 G  Rotation by electron excitation: R = 10.5 M  Translation by direct contact (orbital overlap):  z ~ +0.8 Å  z ~ -0.2 Å  z ~ - 1 Å Tip zz ((( ) ( ))) Trajectories of molecule pushed by the tip M. Salmeron (LBL)

47. Crystals: A story that bridges large and small: realms of macro and nano scale An example of a collection of teaching-learning tools for undergraduate chemistry courses that can be adapted to teach various STEM topics and concepts Chemistry is the focus of particular lessons that are embedded in the story of NIF ( The National Ignition Facility) Learning activities were developed relative to the context of the research and science behind NIF. Activities provide a diverse collection that support a wide variety of learning and teaching styles Web based, distributed freely

48. Learning Styles http://ep.llnl.gov/msds/Chem120/learning.html

49. Learning Styles - Activities Seeing - Hearing - Doing Various Types: Visualizations: Time lapsed Growth Simulations: Fusion - Fission Truman’s Announcement Numerical and Graphical Problems Debate Interpreting Data

50. 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 Nanostructured Materials (S.G. Louie)

51. 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.

52. Bond lengths and Radii picometer (pm) = 1 x 10 -12 m (1/1,000 nm) Radius