UNT Research, Volume 16, 2006 Page: 26
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Wilson says the accomplishment means that, as computational
chemists, "we have reached the Holy Grail, and now we can actually
address larger chemical molecules at much higher levels of accuracy
than other groups have been able to do. That's very important."
Cundari, a professor of chemistry whose focus is on practical
applications, explains why: "This allows us to design and predict
the feasibility of chemical processes from the ground up. It's not
just better bean counting but a level of accuracy that you need to
design new chemical processes."
In about a decade, Cundari foresees the new approach
resulting in, for example, faster idea-to-market delivery of new
"One thing we are trying to understand is the thermodynamics
of drugs interacting with enzymes, which determines how effective
a drug is, and that effectiveness is reduced to thermodynamic dif-
ferences between useful and toxic," says Cundari. "There's a very
CGnda2I rn cmntatinns h
Not that this will happen immediately. Wilson and Cundari
worked with small molecules, such as water, which has two hydro-
gen atoms and one oxygen atom. Scaling up to larger, more com-
plex molecules means vastly more number crunching, but they're
working on it.
As of late spring, in fact, the professors and their team of
graduate students had achieved the critical one kilocalorie per mole
with hydrocarbon compounds containing up to 15 carbon atoms,
"and we think we can do better than that," Wilson says. "Our com-
puter and mathematical methods seem to be working quite well."
She acknowledges that there are other, more cumbersome,
methods for obtaining similar results, but she says her team's work
is the first practical technique.
"We thought others weren't going about the methodology the
right way," she says. "They worked, but there were a lot of 'fudge
factors' involved. We did it with pure mathematics, without fudge
ad hben C just a single computer
:quired 3.3 years to complete
,while their method would have taken just 20 days.
small energy difference between good for you and bad for you.
"Every molecular state has an energy associated with it," he
continues. "You want a good molecular state to have a favorable
energy - it sounds very Zen-like. In chemistry, the differences
between a good state and a bad state are very small, close to one
kilocalorie per mole. What we are doing has a difference of one
kilocalorie or less."
With their new method, dubbed the "correlation consistent
Composite Approach,"or ccCA, pharmaceutical companies eventu-
ally could bring out new drugs "faster, safer and cheaper," Cundari
That's because chemists now look at tens of thousands of
compounds searching for those that will produce the desired result
with the fewest side effects.
But with ccCA, "we can now predict the properties of those
compounds with high accuracy and confidence. This approach
allows us to become better handicappers, like in a horse race. We
can isolate the best material to be tested, with the least side effects,
the most effective, and so on," he says.
Wilson notes that on an octane molecule containing eight
carbon atoms, a Pacific Northwest National Laboratory group
used 1,400 computer processors computing simultaneously for a
day to reach one kilocalorie per mole. The UNT team took five
days - but significantly used only four processors, or basically
four desktop computers. That, of course, is much more realistic
computing power for the typical pharmaceutical lab wanting to
follow their lead.
To explain the significance, she draws an analogy of how
much time their method saves: If all their computations had been
done using just a single computer processor, previous state-of-the-
art methods would have required 3.3 years to complete them, while
their method would have taken just 20 days.
"A 20-day calculation is doable by most researchers," Wilson
points out. "A 3.3-year calculation is not. And most people don't
have access to 1,400 processors."
Kirk Peterson, a chemistry and materials science professor at
Washington State University in Pullman, Wash., says what Wilson
26 4 2006 UNT RESEARCH
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University of North Texas. UNT Research, Volume 16, 2006, periodical, 2006; Denton, Texas. (digital.library.unt.edu/ark:/67531/metadc29777/m1/26/: accessed December 12, 2017), University of North Texas Libraries, Digital Library, digital.library.unt.edu; crediting University Relations, Communications & Marketing department for UNT.