Molecular Modeling

The goal behind molecular modeling techniques is to provide realist 3D structures for a

molecule to allow the study of its properties. There are a number of resources available to

you.

Visualization of structures: http://undergrad-ed.chemistry.ohio-state.edu/jmol-viewer/.

This site has sections for VSEPR geometries, inorganic crystal structures, “Molecules”

contains approximate 500 organic, inorganic, biological and ESP (Electrostatic surface

potentials) and a limited number of reaction mechanisms, and finally the “Klotho”

database of organic and biological molecules (approximately 480 structures). All

structure can be manipulated in 3D, displayed in a variety of formats including 3D (using

anaglyphic glasses). There is a “Popup window” available to display the molecule in full

screen mode. New structures can be added on request.

This site (http://undergrad-ed.chemistry.ohio-state.edu/) contains are number of

additional resources under the “General Chemistry” link that maybe useful to you and

your students. The “Organic” link contains information on Organic chemistry, but at an

introductory university level. The “Spectroscopy” link contains information on IR, UV-

Vis and NMR spectroscopy including the.

The Protein Data Bank (http://www.rcsb.org/pdb/home/home.do).

Modeling Software

Wavefunction (http://www.wavefun.com/) sells a number of software packages for

molecular modeling.

ODYSSEY® is a unique teaching program for introductory and general chemistry

classes in high schools, colleges, and universities. Utilizing scientifically-based

molecular simulations, ODYSSEY provides an interactive environment for

learning and exploration. The instructor’s version is $200, the student version is

$60 or $100.

Spartan is a general modeling package and comes in a number of versions,

SpartanModel ($30) (the Jmol-viewer can do this for free), Student’s Edition

($60), Spartan Essential ($600), and Spartan 08 ($1,200).

Wavefunction will give discounts for bulk purchases.

WebMO (https://webmo.osc.edu/cgi-bin/login.cgi) is a new user interface for doing

molecular modeling using OSC’s (The Ohio Supercomputing Center) cluster. There is

limited help available in the software and at http://undergrad-ed.chemistry.ohio-

state.edu/webmo/. This is free to academics including high-school users. If you are

interested I can set up an account for you. Please email me a request at

rspinney@chemistry.ohio-state.edu.

Using the Power of Supercomputers and High-Resolution Graphics to Understand and Design Molecules Computers are powerful tools in the chemical and biological sciences. In this activity you will visualize how the atomic structure of molecules allows them to perform their functions. Jmol is available for free from http://jmol.sourceforge.net/. The files used in this exercise can be obtained from http://undergrad-ed.chemistry.ohio-state.edu/jmol-viewer/. 1. Powerful Catalysts for Chemical Synthesis Catalysts are molecules that accelerate chemical reactions without being consumed themselves. Nature uses catalysts in many different ways, and life on earth would be impossible without them. Using chemical knowledge and computers, chemists at OSU design powerful catalysts that are able to effect important reactions under mild, energy efficient and environmentally benign conditions. Small amounts of this nickel (Ni)-based catalyst help to stitch together inexpensive molecules of ethylene (a cheap gas from which polyethylene grocery bags are made) and vinylnaphthalene, to synthesize expensive pharmaceuticals, such as naproxen (the active ingredient in Aleve®). 2. Catalyzing Chemical Reactions with Urea Ureas have recently been discovered to catalyze reactions useful for preparation of new molecules, such as drugs or materials. Particularly attractive features of urea catalysts include their non-toxic nature and ease of use. The proposed mode of action by which ureas catalyze reactions is through hydrogen bonding, such as weak interactions between the N-H groups of the urea (blue) and the oxygens of the nitro group (-NO2). 3. ATP – adenosine triphosphate ATP is a small molecule that plays a central role in various aspects of biology. Breaking the bond that connects the terminal γ-phosphate group to the rest of the molecule releases energy that is used to drive a vast array of chemical, and mechanical transformations in the cell. It is also one of the fundamental building blocks of RNA, and without the 2'-hydroxyl group, DNA. 4. Nucleosome Core Particle, PDB entry 1KX5 DNA in each human cell consists of about three billion nucleotide building blocks. Extended, this DNA would measure over one meter in length. In cells, the DNA (yellow) is packaged into chromosomes by histone proteins (blue), which together with positively charged ions (pink), allows the otherwise rigid DNA molecule to wrap tightly around the proteins. Researchers at OSU

use chemical and biophysical methods to study how DNA is packaged into chromosomes, and how its genetic information is accessed by other cellular factors. 5. TRAP-Trp-RNA Ternary Complex, 1C9S In cells, gene expression is regulated in a variety of ways. One is by controlling access to the information in the cell's genetic code by alternately remodeling the way nucleic acid molecules (DNA, RNA) are packaged. The protein TRAP forms donut-shaped structures in which 11 copies of the protein assemble in to a ring (each a different color of ribbon), and upon binding to a small molecule (spheres), becomes activated to bind its target RNA (green), thereby rearranging its structure as it wraps around the outside of the ring. Researchers at OSU study how this happens, and how it allows genetic expression to be regulated. 6. The SMK Riboswitch Bound to SAM, 3E5C One of the most transformative discoveries of modern biology concerns the remarkable versatility of RNA molecules. Some RNA molecules are able to sense molecular signals directly, without the need of a protein sensor. The SMK riboswitch is an RNA molecule (rainbow ribbon) that remodels its own shape upon binding specifically to its feed-back activator, S-adenosyl methionine (SAM, spheres), a vital cellular metabolite. An important implication of the discovery is that researchers can now think about developing to drugs that interact directly with RNA molecules, in addition to more traditional targets, proteins and enzymes. OSU is the proud home of one of the discoverers of this activity of RNA molecules, who was recently named to the National Academy of Sciences. 7. Transmembrane Ion-transporting Rh proteins, 3B9Z Rh proteins are best known for their role as a human blood factor and antigen (Rh-positive/Rh-negative). Functionally, these proteins appear form channels that control the transport of small molecules across cellular membranes. Structural studies of membrane proteins are supremely challenging and are thus very poorly understood despite their widespread roles, and the fact that a large fraction of useful medicines interact directly with membrane proteins. Researchers at OSU use chemistry, biophysics and computers to determine the structures of the proteins and to understand how they function. 8. Zeolites – Marvelous Microstructures Zeolites are microporous, crystalline structures with simple chemical compositions. Because of their porous structures, zeolites are useful for a

variety of purposes, including the manufacture of gasoline, removal of organic impurities from water, and making hard water soft. Thus, it is likely that your detergent has zeolites. Researchers at OSU are developing specialized zeolites for these and a variety of other useful applications.

(2012-05-04)