Nanotechnology a chemists constructivist view Mathematical Modeling Technology

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

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 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.

1/50 of ~ 50, 000 nanometers

What is considered too large for the nano realm? Powers of 10 (10 x) http: //www. eamesoffice. com/powers_of_ten. html http: //www. powersof 10. 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!)

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

“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 rearranging 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/self. Rep. html

Nano-scale: Models of Atoms & Molecules • Rutherford (1913 -1917) • Atoms, molecules, and nucleii

~ 0. 1 nm Anders Jöns Ångström (1814 -1874) 1 Å = 10 picometers = 0. 1 nanometers = 10 -4 microns = 10 -8 centimeters • 1 nm = 10 Å • An atom vs. a nucleus ~10, 000 x larger Nucleus = 1/10, 000 of the atom

Molecular Size, Shape & Properties Ozone 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

Larger Size Molecules 8. 16 Å (0. 816 nm) http: //ep. llnl. gov/msds/orgchem/Chem 226/Smell-Stereochem. html

DNA: Size, Shape & Self Assembly http: //www. umass. edu/microbio/chime/beta/pe_alpha/atlas. htm Views & Algorithms 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.

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

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 ATOM 2 OXT G A 1 -6. 904 7. 627 ATOM 3 O 2 P G A 1 -7. 438 5. 244 ATOM 4 O 5' G A 1 -5. 074 5. 900 ATOM 5 C 5' G A 1 -4. 102 6. 424 ATOM 6 C 4' G A 1 -2. 830 6. 792 ATOM 7 O 4' G A 1 -2. 044 5. 576 ATOM 8 C 3' G A 1 -2. 997 7. 378 2. 089 1. 869 1. 299 1. 839 2. 779 2. 049 1. 839 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.

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

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

Protein Shape: Forces, Bonds, Self Assembly, Folding 10 -40 k. J/mol 150 -1000 k. J/mol 700 -4, 000 k. J/mol Ion-dipole (Dissolving) 40 -600 k. J/mol 0. 05 -40 k. J/mol

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

The Ribosome: RNA Proteins 227 Å Crystal structure of a part of the ribosome at 5. 5 Å Resolution. (1 GIX): Contains the 30 S Ribosome Subunit, three t. RNA, and m. RNA molecules (2001) Noller, Ramakrishnan, Steitz ~ 50 proteins + 1, 000 s nucleotides

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

Models, Theories & Interactions Molecular Shape & the Sense of Smell http: //ep. llnl. gov/msds/orgchem/Chem 226/smell-links. html Structure-Odor Relationships Karen J. Rossiter, Chem. Rev. , 1996, 3201 -3240

Three different smell receptors.

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

Shapes & Interactions: Mirror Images & Smell S-(+)-d- S-(+)- caraway R-(-)-l- R-(-)- spearmint http: //ep. llnl. gov/msds/orgchem/Chem 226/Smell-Stereochem. html

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

Acetylcholine, Nerves & Neurotransmission The Neuron: Shapes and Spaces

Acetylcholine: OP Pesticides and Nerve gases

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

Another Way to Inhibit Enzymes The Importance of Shape Statins: Inhbiting cholesterol biosynthesis

Hemoglobin and Oxygen Transport An allosteric effect & sickle cell anemia http: //ep. llnl. gov/msds/Columbia/slide 8 -3. html Oxygen BPG

Heme H 2 C CH H 3 C CH 3 N N Fe 2+ N N HO 2 CCH 2 CH 3 CH 2 CO 2 H • 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”.

Myoglobin C-terminus N-terminus Heme

Some Examples of Structural Proteins http: //info. bio. cmu. edu/courses/03231/Prot. Struc. htm collagen: connective tissue myosin-actin: muscle Michael Ferenczi

Mechanical proteins Pathogens & Cell Invasion http: //ep. llnl. gov/msds/Staph-infection/infection. html Streptococcus pyogenes 96, 000 x Vincent A. Fischetti Ph. D. , Rockefeller University

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

Gecko & it’s toe, setae, spatulae 6000 x Magnification Full et. al. , Nature (2000) 5, 000 setae / mm 2 600 x frictional force; 10 -7 Newtons per seta Geim, Nature Materials (2003) Glue-free Adhesive 100 x 10 6 hairs/cm 2 http: //micro. magnet. fsu. edu/primer/java/electronmicroscopy/magnify 1/index. html

The “Lotus Effect” Biomimicry http: //www. bfi. org/Trimtab/spring 01/biomimicry. htm Wax • Lotus petals have micrometer-scale roughness, resulting in water contact angles up to 170° • See the Left image in the illustration on the right.

The “Lotus Effect” Biomimicry http: //www. sciencemag. org/cgi/content/full/299/5611/1377/DC 1 • • • 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

Colloids Hydro- philes & phobes

Colloids Hydrophilic and Hydrophobic

Colloids

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

Web MO http: //c 4. cabrillo. cc. ca. us/projects/webmo/index. html login: dvc 1 password: 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

Web MO http: //c 4. cabrillo. cc. ca. us/projects/webmo/index. html login: dvc 1 password: chem • Output: – – – – Dipole moment Bond Orders Partial Charges Vibrational Modes Molecular Orbitals Ultraviolet-Visible-Infrared Graphics NMR Chemical Shifts

Web MO Visual Output 0. 143 nm Color coded electron density distribution: blue-lowest, red highest, green balanced

Examples of Planned Web MO Projects • 1) S-(+)- caraway R-(-)- spearmint • 2) Ambrox-Ambergris http: //ep. llnl. gov/msds/orgchem/Chem 226/Mol-Modl-II. html#ambergris

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

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

Imaging: acetylene on Pd(111) at 28 K Molecular Image Tip cruising altitude ~700 pm Δz = 20 pm H C C H 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 TIP pz H + O p orbital 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) 1 cm (± 1 μm)

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

Measuring the excitation rate Pd 3 2 x 1 Pd Pd Pd ((( ) ( 2 Pd Center of molecule Tip fixed at position 1: V = 20 m. V 0 24 16 8 0 100 2, 3 50 100 150 200 250 300 350 400 450 current (p. A) 253 p. A 10 1 0. 1 1. 72 seconds ))) -37 m. V 1 150 50 32 0 Log(Hops/s) Current (p. A) 200 rotations per second Pd 0 -50 -100 -150 -200 Tip Bias (m. V) -250 -300 M. Salmeron (LBL)

Excitation of translations of C 2 H 2 molecules: Rotation by electron excitation: ((( ) ( Tip R = 94 M R = 150 M z ~ -0. 2 Å z R = 0. 55 G z ~ +0. 8 Å z ~ - 1 Å Translation by direct contact (orbital overlap): R = 10. 5 M M. Salmeron (LBL) Trajectories of molecule pushed by the tip )))

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)

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.

Crystals for the Classroom Bridging the realms of the macro and atomic/nano scale http: //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

Crystals for the Classroom Bridging the realms of the macro and atomic/nano scale http: //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.

Crystals for the Classroom Bridging the realms of the macro and atomic/nano scale http: //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/Chem 120/learning. html

Instructor - Student Activities, Exercises & Resources http: //crystals. llnl. gov • • • Seeing - Hearing - Doing Powerpoint Presentations Visualizations: Time lapsed Growth

Instructor - Student Activities, Exercises & Resources http: //crystals. llnl. gov • • Seeing - Hearing - Doing Powerpoint Presentations Visualizations: Time lapsed Growth Simulations: Fusion - Fission

Instructor - Student Activities, Exercises & Resources http: //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

Acknowledgements