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 AIT-CU Workshop on Nano, Continuum, Material and Computational Mechanics Enhanced Version:

What is considered too large for the nano realm? Powers of 10 (10 x ) Earth = 12,760,000 meters wide (12.76 x 10 6 ), million meters Plant Cell = meters wide (12.76 x ) (12.76 millionths of a meter) (12,760 nanometers!) 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.)

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 ( ) 1 Å = 10 picometers = 0.1 nanometers = microns = centimeters

DNA: Picture 51 B-DNA: The advent of modeling 46 Å 12 base sequence ( )

DNA: Size, Shape & Self Assembly Views & Algorithms Å Several formats are commonly used but all rely on plotting atoms in 3 dimensional space;.pdb is one of the most popular.

PROTEIN DATA BANK What are PDB files? 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 ATOM 2 OXT G A ATOM 3 O2P G A ATOM 4 O5' G A ATOM 5 C5' G A ATOM 6 C4' G A ATOM 7 O4' G A ATOM 8 C3' G A 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.

Proteins: Size, Shape & Self Assembly

Globular proteins: A larger number of atoms rolled into relative small volumes RNA polymerase II-transcription factor J. Biol. Chem., Vol. 274, Issue 11, , 1999 The yellow dashed line is ~ 110-Å 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.

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

myosin-actin: muscle Some Examples of Structural Proteins collagen: connective tissue Michael Ferenczi

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

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

Gecko & it’s toe, setae, spatulae 6000x Magnification 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; Newtons per seta Yurdumakan, Chem Comm (2005) 200X Gecko’s Force

The “Lotus Effect” Biomimicry 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

The “Lotus Effect” Biomimicry 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 , H. Yldrm Erbil, A. Levent Demirel, Yonca Avc, Olcay Mert

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 login: dvc1 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 login: dvc1 password:chem Output: –Dipole moment –Bond Orders –Partial Charges –Vibrational Modes –Molecular Orbitals –Ultraviolet-Visible-Infrared Graphics –NMR Chemical Shifts

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 nm

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

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)

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

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 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

Chemistry lessons 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. Crystals for the Classroom Bridging the realms of the macro and atomic/nano scale

Web based, distributed freely Activities provide a diverse collection that support a wide variety of learning and teaching styles: Crystals for the Classroom Bridging the realms of the macro and atomic/nano scale

Instructor - Student Activities, Exercises & Resources Seeing - Hearing - Doing Powerpoint Presentations Visualizations: Time lapsed Growth

Seeing - Hearing - Doing Powerpoint Presentations Visualizations: Time lapsed Growth Simulations: Fusion - Fission Instructor - Student Activities, Exercises & Resources

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 Instructor - Student Activities, Exercises & Resources

Acknowledgements