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Dr. Ron Rusay Diablo Valley College

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.

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Dr. Ron Rusay Diablo Valley College

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  1. Nanotechnology: a chemist’s constructivist viewMathematical 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.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

  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/ • National, Regional, Local Initiatives eg. • US: http://www.nano.gov/ • UK: http://www.nano.org.uk/ • Molecular Foundry (LBL): http://www.foundry.lbl.gov/ • Nano High School: 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: Models of Atoms & Molecules • Rutherford (1913-1917) • Atoms, molecules, and nucleii

  8. ~ 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

  9. 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

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

  11. 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.

  12. Larger Molecules http://info.bio.cmu.edu/courses/03231/ProtStruc/ProtStruc.htm B-DNA: Size, Shape & Self Assembly 46 Å 12 base sequence (1953-2003) http://molvis.sdsc.edu/pdb/dna_b_form.pdb

  13. 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.

  14. PROTEIN DATA BANK 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/

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

  16. Protein Shape: Forces, Bonds, Self Assembly, Folding Ion-dipole (Dissolving) 40-600kJ/mol 10-40kJ/mol 150-1000kJ/mol 0.05-40kJ/mol 700-4,000kJ/mol

  17. 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

  18. 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

  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- S-(+)- caraway R-(-)- spearmint http://ep.llnl.gov/msds/orgchem/Chem226/Smell-Stereochem.html

  24. Enzyme interaction: neurotransmission The interaction of a globular protein, 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. Another Way to Inhibit Enzymes The Importance of Shape Statins: Inhbiting cholesterol biosynthesis

  29. Hemoglobin and Oxygen Transport An allosteric effect & sickle cell anemia http://ep.llnl.gov/msds/Columbia/slide8-3.html Oxygen BPG

  30. H2C CH CH3 H3C CH CH2 N N Fe 2+ N N H3C CH3 HO2CCH2CH2 CH2CH2CO2H Heme • Heme is the coenzyme that binds oxygen in hemoglobin (transport) and myoglobin (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”.

  31. C-terminus N-terminus Myoglobin Heme

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

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

  34. 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

  35. 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

  36. 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

  37. 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

  38. ColloidsHydro- philes & phobes

  39. Colloids Hydrophilic and Hydrophobic

  40. Colloids

  41. 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 

  42. 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

  43. 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

  44. Web MO Visual Output 0.143 nm Color coded electron density distribution: blue-lowest, red highest, green balanced

  45. Examples of Planned Web MO Projects • 1) S-(+)- caraway R-(-)- spearmint • 2) Ambrox-Ambergris • http://ep.llnl.gov/msds/orgchem/Chem226/Mol-Modl-II.html#ambergris

  46. Examples of Planned Web MO Projects • 3) d- and l- tartaric acid

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

  48. 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)

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

  50. 32 -37mV 24 rotations per second 16 ((( ) ( ))) 8 0 0 50 100 150 200 250 300 350 400 450 V = 20 mV 200 1 current (pA) 150 100 50 2,3 0 100 1.72 seconds 253 pA 10 Log(Hops/s) 1 0.1 0 -50 -100 -150 -200 -250 -300 Tip Bias (mV) Measuring the excitation rate Pd Pd 3 2 2 x 1 Pd Pd Pd Pd Center of molecule Tip fixed at position 1: Current (pA) M. Salmeron (LBL)

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