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 LaboratoryAIT-CU Workshop on Nano, Continuum, Material and

Computational Mechanics

http://ep.llnl.gov/msds/AIT-presentation.htm Enhanced Version: http://ep.llnl.gov/msds/AIT-symposium.htm

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/

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!)

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 =1/10,000of the atom

Anders Jöns Ångström(1814-1874)

1 Å = 10 picometers = 0.1 nanometers = 10-4 microns = 10-8 centimeters

DNA: Picture 51http://info.bio.cmu.edu/courses/03231/ProtStruc/ProtStruc.htm

B-DNA: The advent of modeling

http://molvis.sdsc.edu/pdb/dna_b_form.pdb

46 Å

12 base sequence

(1953-2003)

DNA: Size, Shape & Self Assemblyhttp://www.umass.edu/microbio/chime/beta/pe_alpha/atlas/atlas.htm

Views & Algorithms

10.85 Å10.85 Å

QuickTime™ and aAnimation decompressorare needed to see this picture.

Several formats are commonly used but all rely on plotting atoms in 3 dimensional space; .pdb is one of the most popular.

http://www.rcsb.org/pdb/

PROTEIN DATA BANK

What are PDB files? http://chemistry.Gsu.EDU/glactone/PDB/pdb.htmlThe 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 GLACTONESEQRES 1 A 1 GSEQRES 1 B 1 CATOM 1 P G A 1 -6.620 6.196 2.089ATOM 2 OXT G A 1 -6.904 7.627 1.869ATOM 3 O2P G A 1 -7.438 5.244 1.299ATOM 4 O5' G A 1 -5.074 5.900 1.839ATOM 5 C5' G A 1 -4.102 6.424 2.779ATOM 6 C4' G A 1 -2.830 6.792 2.049ATOM 7 O4' G A 1 -2.044 5.576 1.839ATOM 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.

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

Globular proteins:A larger number of atoms rolled into relative small volumes

RNA polymerase II-transcription factor J. Biol. Chem., Vol. 274, Issue 11, 6813-6816, 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, The interaction of a globular protein, acetylcholinesterase, with a relatively small acetylcholinesterase, with a relatively small molecule, acetylcholine. molecule, acetylcholine.

Richard Short (Cornell University)

QuickTime™ and aYUV420 codec decompressorare needed to see this picture.

myosin-actin: muscle

Some Examples of Structural Proteins http://info.bio.cmu.edu/courses/03231/ProtStruc/ProtStruc.htm

collagen: connective tissue

Michael Ferenczi

Mechanical proteinsPathogens & Cell Invasion

http://ep.llnl.gov/msds/Staph-infection/infection.html

Streptococcus pyogenes96,000 x

Vincent A. Fischetti Ph.D., Rockefeller University

Human’s total ~ 100 x 10 6 immunoproteins

AntibodiesProlific Immunoproteins

Immunoglobin

Human Genome ~30,000 proteins

Combinatorial syntheses from libraries of 250, 10, and 6 possible contributors

Gecko & it’s toe, setae, spatulae6000x Magnification

http://micro.magnet.fsu.edu/primer/java/electronmicroscopy/magnify1/index.html

Geim, Nature Materials (2003) Glue-free Adhesive100 x 10 6 hairs/cm2

Full et. al., Nature (2000)5,000 setae / mm2

600x frictional force; 10-7 Newtons per seta

The “Lotus Effect” Biomimicry

http://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

The “Lotus Effect” Biomimicry

http://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

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 

Web MOhttp://c4.cabrillo.cc.ca.us/projects/webmo/index.html

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 MOhttp://c4.cabrillo.cc.ca.us/projects/webmo/index.html

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 & PropertiesOzone and Water

• The Lotus flower• Water & dirt repellancy

0.1278 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

pz

TIP

H

O+

Imaging: acetylene on Pd(111) at 28 K

Molecular Image Tip cruising altitude ~700 pmΔz = 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-

((( ) ( )))

M. Salmeron (LBL)

QuickTime™ and aYUV420 codec decompressorare needed to see this picture.

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 ClassroomBridging 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

• 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 ClassroomBridging 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/Chem120/learning.html

Crystals for the ClassroomBridging the realms of the macro and atomic/nano scale

http://crystals.llnl.gov

Instructor - StudentActivities, Exercises & Resources

http://crystals.llnl.gov• Seeing - Hearing - Doing

• Powerpoint Presentations

• Visualizations: Time lapsed Growth

QuickTime™ and aSorenson Video decompressorare needed to see this picture.

• Seeing - Hearing - Doing

• Powerpoint Presentations

• Visualizations: Time lapsed Growth

• Simulations: Fusion - Fission

Instructor - StudentActivities, 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

Instructor - StudentActivities, Exercises & Resources

http://crystals.llnl.gov

Acknowledgements

QuickTime™ and aGIF decompressorare needed to see this picture.