Chemical experiments and predictions by computer
Solid-like structure (with short-range order in three dimensions) of n-dodecane narrowly confined between solid surfaces is induced by interfacial forces. This effect may explain the orders-of-magnitude higher viscosity observed in confined-fluid experiments compared with bulk fluid values.
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The term “chemistry” conjures up images of people in white lab coats, pouring liquids
from test tubes into a beaker. But an increasing number of chemists do most of their
chemistry on computers, partly to save money and increase safety. Simulating chemistry
experiments on the computer instead of doing them in the lab can produce chemical
reactions and properties with a faster turnaround and better accuracy. Computational
chemistry also can aid understanding of actual lab results.
David Bernholdt, who helped develop the NWChem computational chemistry software
package while a postdoctoral scientist at DOE’s Pacific Northwest National Laboratory,
leads the chemistry initiative at DOE’s Center for Computational Sciences at ORNL.
Bernholdt knows the value of computational chemistry, so he is working to develop
scaling techniques that will allow chemists to work with even larger molecules on
ORNL’s new supercomputers.
“Computational chemistry allows you to predict which chemical
compounds are more likely to give the desired property or result,”
he says. “For instance, computational chemistry was used by
Kodak’s color film developers to predict which chemicals would
produce the right colors yet still hold up during chemical
processing to develop the film. It saves you from having to
synthesize lots of different chemicals and then screen them for the
needed properties, such as what might be effective in a therapeutic
At ORNL several researchers have been using supercomputers to
work on computational chemistry projects. Don Noid and Bobby
Sumpter, both in ORNL’s Computer Science and Mathematics
Division, were the first to computationally model the dynamics of
fluid flow inside carbon nanotubes—tiny cylinders resembling
rolled-up chicken wire. Their molecular dynamics simulations
showed that argon slowed down more quickly than helium and that
both fluids slowed down faster in a flexible nanotube than in a rigid
More recently, they found in their simulation studies with Clemson
University researchers that hydrocarbons break up more slowly
when heated in carbon nanotubes than in a furnace under vacuum.
They believe the rate of breakup of these polymers (similar to crude oil cracking under
pyrolysis) is altered by the chemistry of confined spaces.
Working with Mike Barnes of ORNL’s Chemical Sciences Division (CSD), Noid and
Sumpter showed both computationally and experimentally that a nanosized polymer
droplet can be formed from materials that don’t normally mix and that the droplet can be
forced through a micron-sized orifice. The resulting particles exhibit unique properties
that could make them useful for optical displays and industrial coatings. The researchers
also helped develop a software tool to calculate how far and which way thousands of
atoms move relative to their neighbors (vibrational modes), providing insight into the
structure and behavior of various materials.
Hank Cochran, Peter Cummings, and Shengting Cui, all with both CSD and the University
of Tennessee at Knoxville, are doing molecular simulations of microdispersions
stabilized by surfactants in supercritical carbon dioxide (CO2). Surfactants act like
detergent by reducing surface tension; they are being used in several new dry cleaning
establishments where CO2 replaces traditionally used carcinogenic solvents. DuPont is
building a big plant in North Carolina to produce Teflon and other fluoryl polymers using
other new surfactants with supercritical CO2 instead of ozone-destroying chlorinated
The CSD group is also simulating the effects of velocity
gradients (shear flow) on the arrangement and behavior of
long-chain molecules in such situations as during the
extrusion of filaments and the melting of polymers. In
addition, they are looking at the behavior of lubricants in
the narrowest nanoscale separations between motor
vehicle components, which can be substantially different
from their behavior in bulk.
Cochran and Cui are simulating the behavior of water that
contains salts and DNA or proteins in channels thousands
of times smaller than a hair in a “nanofluidic lab on a
chip.” When developed, under the leadership of
lab-on-a-chip inventor Mike Ramsey of CSD, such a
device might be used in a doctor’s office for ultrafast DNA
sequencing of blood drops from individual patients for
rapid disease diagnosis. Liquids containing DNA or
protein could be moved by the influence of electric fields
through ultrasmall channels, which might enable the
increase of sequencing and diagnostic speeds by a million
to a billion times. In their simulations, the researchers take into account the electric-field
and surface forces that extend through the liquid inside the nanoscale channel. These
simulations help to guide and interpret Ramsey’s experiments.
As devices get smaller, computational chemistry is likely to play a bigger role in figuring
out how to make them work.