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Computational Chemistry G UEST E DITORS’ I NTRODUCTION COMPUTATIONAL CHEMISTRY omputational chemistry has come of chemical, physical, and biological phenomena. age. With significant strides in com- The Nobel Prize award to John Pople and Wal- puter hardware and software over ter Kohn in 1998 highlighted the importance of the last few decades, computational these advances in computational chemistry. Cchemistry has achieved full partnership with the- With massively parallel computers capable of ory and experiment as a tool for understanding peak performance of several teraflops already on and predicting the behavior of a broad range of the scene and with the development of parallel software for efficient exploitation of these high- end computers, we can anticipate that computa- tional chemistry will continue to change the scientific landscape throughout the coming cen- tury. The impact of these advances will be broad and encompassing, because chemistry is so cen- tral to the myriad of advances we anticipate in areas such as materials design, biological sci- ences, and chemical manufacturing. Application areas Materials design is very broad in scope. It ad- dresses a diverse range of compositions of matter that can better serve structural and functional needs in all walks of life. Catalytic design is one such example that clearly illustrates the promise and challenges of computational chemistry. Al- most all chemical reactions of industrial or bio- chemical significance are catalytic. Yet, catalysis is still more of an art (at best) or an empirical fact than a design science. But this is sure to change. A recent American Chemical Society Sympo- sium volume on transition state modeling in catalysis illustrates its progress.1 This sympo- sium highlighted a significant development in the level of modeling that researchers are em- 1521-9615/00/$10.00 © 2000 IEEE ploying as they focus more and more on the DONALD G. TRUHLAR highly quantum mechanical activated complexes of catalytic reactions. The complexity of cat- University of Minnesota alytic processes had previously restricted full- VINCENT MCKOY scale computational efforts to the structure and California Institute of Technology binding of the reactive precursors. The impli- NOVEMBER/DECEMBER 2000 19 cations of this shift will be profound but not im- of such calculations for the design of cleaner, mediate. A relevant comparison is computer- more efficient combustion processes should be aided drug design—it became clear some 20 obvious. years ago that the computer-aided approach held tremendous promise. Although there has been impressive progress in the area,2,3 the majority Theme issue of successful drugs currently on the market were This theme issue cannot possibly cover all the developed without the aid of computers or on excitement of the computational chemistry field, the basis of rudimentary computational tech- but the articles presented here provide a varied niques that are no longer state of the art. How- picture of four exciting research areas. ever, this is changing ever more rapidly. “Simulating Complex Systems without Ad- A major challenge to materials design, as well justable Parameters” by Michele Parrinello looks as to many other areas of chemical modeling at the progress, computational challenges, and such as the environment, is the wide range of future potential of molecular dynamics. The po- length and time scales that we must address.4 tential applications of molecular dynamics are The operative objective is nanoscale modeling. almost unlimited. The fascination and usefulness For example, a cubic sample 5 nm × 5 nm × 5 of this approach stem from its ability to provide nm on edge contains thousands of atoms, and a a window of increasing spatial and temporal res- simulation over 5 ns encompasses 105 vibra- olution on the behavior of complex systems. tional periods of a strong bond to a hydrogen In “Atomic Scale Modeling of Polymerization atom. Following the motion of such a large Catalysts,” Tom Woo, Serguei Patchkovskii, and number of atoms for a long time is challenging, Tom Ziegler discuss an application of molecular but computational chemists are not waiting for modeling to examine a catalytic cycle’s elemen- computers to get faster. They are devising algo- tary reaction steps at the atomic level. They also rithms specifically designed to address these is- illustrate how such a fundamental understand- sues. An example is the hyperdynamics algo- ing of the way catalysts operate can provide a ba- rithm5 of Art Voter at Los Alamos National sis for rational design of catalysts and further Laboratory, which “floods the valleys” and lifts technological innovations in the plastic industry. every molecule like a ship (so to speak) so it can The third article, “The Computational Chal- more easily reach the high-energy dynamical lenges in Simulating Large DNA over Long bottlenecks. The algorithm then carefully cor- Times” by Tamar Schlick, Daniel Beard, Jing rects for the artificial bias so that we can predict Huang, Daniel Strahs, and Xiaoliang Qian, de- observables in real time. scribes the computational challenges and solu- Improving manufacturing processes to make tion strategies in simulations of the long-time them more environmentally benign and to ra- dynamics of DNA, with example applications. tionally design new materials will increasingly Such simulations call for a sophisticated array of rely on computational chemistry. The rapid and algorithms appropriate to DNA’s impressive efficient design of new materials, chemical in- spectrum of spatial and time scales. termediates, and products will be necessary to Lastly, “Methods in Computational Chem- achieve the goals of greater energy efficiency and istry” by Siddharth Dasgupta uses two specific increased productivity while minimizing envi- examples to illustrate computational chemistry’s ronmental impact. role in solving industrial problems. The first Combustion is another area where the com- looks at a major challenge oil refineries face: the putational approach really shines. A better un- crude from different oil wells has different hy- derstanding of the underlying processes in drocarbon composition, and even crude from combustion can have significant impact on our the same well can have different composition de- utilization of energy resources. A typical com- pending on its remaining useful life. However, bustion system involves hundreds of unstable each refinery must produce specific target prod- chemical intermediates, most of which re- ucts; quantum chemistry has provided valuable searchers have never isolated for individual ex- answers to these challenges. The next example perimental study. Theory can predict their addresses issues underlying the mechanism by heats of formation and their subsequent reac- which a polymeric film prevents oxygen from tion fates almost as easily as we can calculate diffusing through it and thus avoids oxidative the properties of the stable molecules for which damage to food. This example links molecular we have measured these attributes. The value dynamics and mesoscale simulation. 20 COMPUTING IN SCIENCE & ENGINEERING e hope this issue gives a flavor Donald G. Truhlar is Institute of Technology Distin- of both the kind of accom- guished Professor of Chemistry, Chemical Physics, and plishments that computational Scientific Computation at the University of Minnesota, chemists are proud of and the where he is also the director of the Minnesota Super- challengesW that excite and stimulate us. computer Institute. His research interests focus on computational chemical dynamics. He received his PhD from the California Institute of Technology. Con- tact him at the Dept. of Chemistry, Univ. of Minnesota, 139 Smith Hall, 207 Pleasant St. SE, Minneapolis, MN 55455-0431; [email protected]. References 1. D.G. Truhlar and K. Morokuma, Transition State Modeling for Vincent McKoy is a professor of theoretical chemistry Catalysis, American Chemical Soc., Washington, DC,1999. at the California Institute of Technology. His primary 2. A.L. Parrill and M.R. Reddy, Rational Drug Design, American interests include developing methodologies and ad- Chemical Soc., New York, 1999. vanced computational strategies for studying electron 3. D.G. Truhlar, W.J. Howe, A.J. Hopfinger, J. Blaney, and R.A. Dammkoehler, Rational Drug Design, Springer-Verlag, New York, collisions with polyatomic gases used in the plasma- 1999. processing steps in semiconductor fabrication and of 4. V.V. Bulatov, T.D. de la Rubia, R. Phillips, E. Kaxiras, and N. ultrafast pump-probe photoelectron spectroscopy of Ghoniem, Multiscale Modeling of Materials, Materials Research wavepackets in molecules. He received his PhD from Soc., Warrendale, Pa., 1999. Yale University. Contact him at the California Inst. of 5. A.F. Voter, “Hyperdynamics: Accelerated Molecular Dynamics of Infrequent Events,” Physical Rev. Letters, Vol. 78, No. 20, May Technology, Caltech Chemistry 127-72, Pasadena, CA 1997, pp. 3908–3911. 91125; [email protected]..
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