1. “MOLECULAR MODELING USING RAPID PROTOTYPE TECHNOLOGY
An Interdisciplinary Undergraduate Research Experience”
Jacquelyn Pohl1, Sam Antoline2, Muthar Al-Ubaidi2 and Rajiv S. Soman1
1 Department of Chemical Technology, University of Cincinnati, 2220 Victory Parkway, Cincinnati, OH Department of Mechanical Engineering Technology, University of Cincinnati, 2220 Victory Parkway, Cincinnati, OH 45206
ABSTRACT: The difficulty of visualizing structural formulae in chemistry is due to a lack of dimensional variation. The molecule may have a tetrahedral structure, however, on paper, the two dimensional depiction contributes to a difficulty in visualizing it in three dimensions. With three dimensional molecular modeling of chemical structures, the comprehension of chemistry is more easily and better accomplished. As chemical structure is the basis of most bonding, reactions, and stability in chemistry, the understanding of structure is a vital part of understanding the chemistry. A Z-Corp 2510 Rapid Prototype instrument, based on 3D Printing technology has been used to form three dimensional models, not solely of simple compounds such as CCl4, but of more complex compounds such as aspirin and glucose. The rapid prototype machine was compatible with a printing program called Z Print. The structural chemistry program used was Accelry's Discovery Studio Visualizer 1.7, which allows for manipulation of chemical formulae and chemical structures. Incorporating this inter-disciplinary research gives the benefits of a higher understanding of chemistry with a different and improved perspective on how structure affects chemical properties and reactivity. This poster highlights some of the findings of this research.
INTRODUCTION:
- Rapid Prototyping is defined as three dimensional printing technology. It has many uses and has had many breakthroughs.
-It is currently used in many disciplines:
Mechanical Engineering
Gear Prototype
Parts for Size/Function
Architectural Engineering
House models
Prototypes for builds
Medical
Organ models
Prostheses
Prototypes for implants
PRINTING PROCESS:
Import file of molecule, protein, DNA, etc into Accelrys.
It is possible to create a molecule by using toolbars and knowledge of chemical formulas in Accelrys
Change the structure of the molecule to ball and stick, ribbon, space filling, etc.
Colors of the structure may be based on element, residue, chain, parent color, etc.
Using Accelrys, convert the file type from protein data bank (PDB) to virtual reality modeling program (VRML)
VRML files are compatible with Z Print and the rapid prototype machine
Once in Z-Print with file, set dimensions on the parts in the build file and prepare machine to print
Set X, Y, and Z planes along with where in the print area the part should be built
Re-verify all parts of the machine and build are ready and begin build
Allow 30 minutes to 10 hours for full process
Dig out parts, being careful not to break anything using the cleaning tools
Harden the parts using an infiltration binder
Allow parts to dry and clean/reset the machine
PRINTING PROCESS
Create or import file being, molecules, protein, etc.
Program formatting using Accelrys Discovery Studio Visualizer
Program Conversion to Z Print, a program compatible with the Rapid Prototype machine
Set dimensions on parts in the build file and prepare machine for printing
Re-verify all parts of the machine and dimensions of the parts
Begin build, allowing anywhere from 30 minutes to 10 hours for the full process
Dig out parts from powder, ensuring not to break any parts using the cleaning tools
Harden the parts using an infiltration binder
Allow parts to dry and clean the machine
CHEMICAL ENGINEERING DISCIPLINE:
Ball and Stick Models
Allows for basic understanding of chemical structure
Allows for comprehension of bonding, reactions, and chemical properties
Shows the difference in atom sizes and positioning of bonds
Ribbon Models
Allows for the viewing of protein structure
Demonstrates the difference between alpha helices and beta folds along with the turns
CAPABILITIES:
All Stick and ball models with chemical formula given
Ribbon Models that are able to have additional support added
FUTURE INTENTIONS:
All ribbon models, without additional support
DNA and other ribbon/ball and stick combinations
Complex chemical compounds in any form being stick, ball and stick, flat ribbon, solid ribbon, tube, schematic, and choice others
TECHNOLOGY AND SOFTWARE:
Z-Corp 2510 Rapid Prototype Instrument: A 3-D printing instrument using powder and .004 layer binder infusion
Z-Print: A program compatible with the rapid prototype machine which allows for the placement and planning of each individual part
SolidWorks: A program which allows for the manipulation of parts or the building of additional structures
Accelrys Discovery Studio Visualizer: A program which allows for the manipulation of chemical formulae and chemical structures
Myoglobin
Z-Corp 2510 Rapid Prototype Instrument
Phospholipid
Print Area
Valium
Planetary Gear Set
Heroin
Architectural Building
Aspirin
Caffeine