ChemNews.Com VOL 6 NO 4
ChemOffice Sheds Light on Customers Problems
Charles R. Szmanda, Ph.D.
 |
Dr. Szmanda is a Senior Fellow at Shipley Company
in Marlboro, Massachusetts, where the primary goal of his research
is the development of new photoresist materials for nanolithography.
He holds his Ph.D. in physical chemistry from the University
of Wisconsin, and in the past has worked for Bell Laboratories,
Monsanto, and Aspect Systems. |
I've never been patient enough to read instruction manuals.
So, when my copy of ChemOffice Ultra arrived and I saw that pile
of manuals and the PDF formatted documentation on the CD-ROM, I
resigned myself to a marathon at the computer-with manuals in one
hand and a big pot of coffee in the other. It didn't work out that
way.
|
| The customer
had her answer and it was all done without cracking a single
manual |
|
A customer called with a problem. It appeared that the solvent
in one of our products, a polymer based photoresist solution, might
be causing the tubing that carried it to the point of use to undergo
a stress-related degradation. At first, this didn't make any sense.
The tubing was, after all, made of a fluoropolymer called PFA and
seemed highly unlikely that the solvent, ethyl lactate, could attack
it. One of our engineers came up with the key. Some grades of PFA
were not recommended for use with solvents such as esters and ketones
because the polymer chains were terminated with carboxylic acids.
The more suitable grades were terminated with trifluoromethyl groups.
The customer wanted to know why this would make a difference.
I had used ChemDraw before and was familiar with molecular mechanics
but had absolutely no idea how to use Chem3D-so I made a few guesses.
I drew the solvent molecule and a model polymer molecule with ChemDraw
and decided to try to paste the two-dimensional drawings into Chem3D.
It worked! Then, following the menus, I copied the PFA model polymer,
pasted it into the window several times and used MM2 to optimize
the bundle after each paste. Within minutes, I was able to begin
searching for the specific molecular interaction that caused the
polymer to degrade. There it was! The ethyl lactate found the carboxylic
acid-terminated chain ends. Once again, using the menus, I used
the molecular dynamics feature to warm the system slowly and the
degradation mechanism appeared. The solvent molecule, using the
acid chain-ends as the point of entry, invaded the PFA polymer matrix
and became a "wedge" that pushed the individual chains apart. A
quick comparison showed that without the solvent, the polymers held
together very well. This was amazing! The customer had her answer.
And it was all done without cracking a single manual.
Through a little more trial and error, I found that it was possible
to actually "dock" one molecule to another. This made the process
of determining molecular interactions even easier-it's actually
a lot of fun. This procedure was used to probe some of the molecular
interactions that might lead to crystallization. In this case, it
was quite simple to start with an associated dimer and build up
a series of hypothetical crystal structures with each layer docked
independently. While the results require experimental confirmation,
one can use the simulated structures to determine strategies for
avoiding crystal nucleation.
MOPAC
MOPAC can be used to do structure optimization and probe the electronic
structures of reactants, transition states and products. With this
tool, we have been able to assess quickly the influence of subtle
changes in structure and save considerable synthetic effort by targeting
the candidate materials that are most likely to give the desired results.
The MOPAC documentation does contain a few nuggets that are not
immediately obvious. This is to be expected with a program as sophisticated
as ChemOffice Ultra and here, a trip to the Chem3D manual, however
brief, pays off. The manuals are written so that the information
is available quickly and easily with most of the key points in easy
-to-find tables. If you're the type of person who likes to get into
the "nitty-gritty," the included CD-ROM version of the MOPAC manual
is packed with every possible detail about the program's operation
and use.
ChemFinder-A Terrific Partner
ChemFinder was another surprise. My first encounter was with ChemACX
and there, I was able to find commercially available chemicals quickly
and easily. Then there's the MSDS database, ChemMSDX, which gives
me quick and easy access to safety information on the most common
chemicals. What really adds value, however is the organic chemical
reaction database, ChemRXN, which is included with the package. With
this tool, even a non-organic chemist like myself can come up to speed
on synthetic procedures for making all sorts of new compounds. It's
certainly going to be my starting point from now on.
The included databases make ChemInfo quite valuable all by themselves.
But when I discovered that I can use a molecular fragment database
to construct complex molecules and polymers simply by typing simple
mnemonics (even ones I define myself) into the replacement text
box in Chem3D, I was delighted-again. ChemFinder was called up automatically
and the molecular fragments appeared and were bonded together with
no problem at all.
This makes it possible to define and run a model in seconds without
drawing a single structure.
A Word About ChemDraw- an Old Standby Gets Better
ChemDraw has been around for a long time. It created the standard
for electronic publication of chemical structures. Today, it is integrated
into the ChemOffice Ultra package in such a way as to provide a critical
interface to each of its partners. In addition, ChemDraw includes
a facility for calculating 1H and 13C NMR chemical shifts. One simply
draws the molecule and uses the pull-down menu to calculate them.
In most cases, the accuracy is excellent. 
All in all, ChemOffice Ultra is a very powerful, easy-to-use toolset
for any chemist who is interested in structure-function relationships-or
who just wants to be a better chemist. I give it a five. |
