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First-Principles-Based Multiscale, Multiparadigm Molecular Mechanics and Dynamics Methods for Describing Complex Chemical Processes

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Multiscale Molecular Methods in Applied Chemistry

Part of the book series: Topics in Current Chemistry ((TOPCURRCHEM,volume 307))

Abstract

We expect that systematic and seamless computational upscaling and downscaling for modeling, predicting, or optimizing material and system properties and behavior with atomistic resolution will eventually be sufficiently accurate and practical that it will transform the mode of development in the materials, chemical, catalysis, and Pharma industries. However, despite truly dramatic progress in methods, software, and hardware, this goal remains elusive, particularly for systems that exhibit inherently complex chemistry under normal or extreme conditions of temperature, pressure, radiation, and others. We describe here some of the significant progress towards solving these problems via a general multiscale, multiparadigm strategy based on first-principles quantum mechanics (QM), and the development of breakthrough methods for treating reaction processes, excited electronic states, and weak bonding effects on the conformational dynamics of large-scale molecular systems. These methods have resulted directly from filling in the physical and chemical gaps in existing theoretical and computational models, within the multiscale, multiparadigm strategy. To illustrate the procedure we demonstrate the application and transferability of such methods on an ample set of challenging problems that span multiple fields, system length- and timescales, and that lay beyond the realm of existing computational or, in some case, experimental approaches, including understanding the solvation effects on the reactivity of organic and organometallic structures, predicting transmembrane protein structures, understanding carbon nanotube nucleation and growth, understanding the effects of electronic excitations in materials subjected to extreme conditions of temperature and pressure, following the dynamics and energetics of long-term conformational evolution of DNA macromolecules, and predicting the long-term mechanisms involved in enhancing the mechanical response of polymer-based hydrogels.

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Acknowledgements

The material on single shock Hugoniot is based upon work supported by the Department of Energy’s National Nuclear Security Administration under Award Number DE-FC52-08NA28613. The material on hydrogel mechanics for tissue engineering scaffolding is based upon work supported by the National Science Foundation (CMMI 0727870). Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author/s and do not necessarily reflect the views of the National Science Foundation. The early developments of these multiscale multiparadigm methods were initiated with support by DOE under the ECUT program (Prog. Mgr. Minoo Dastoor) and continued DAPRA under the PROM and ONR programs (Prog. Mgr. Carey Swartz, Judah Goldwasser, and Steve Wax). Substantial support was provided by ARO-MURI, ONR-MURI, DURIP, and ASCI projects along with Chevron, Dow-Corning, Aventis, Asahi Kasei, Intel, PharmSelex, and many other industrial labs.

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Authors and Affiliations

  1. Chemistry and Chemical Engineering, California Institute of Technology, Mail code 139-74, 1200 E California Blvd, Pasadena, CA, 91125, USA

    Andres Jaramillo-Botero, Robert Nielsen, Ravi Abrol, Julius Su, Tod Pascal, Jonathan Mueller & William A. Goddard III

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  1. Andres Jaramillo-Botero
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  6. Jonathan Mueller
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  7. William A. Goddard III
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Corresponding authors

Correspondence to Andres Jaramillo-Botero or William A. Goddard III .

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Editors and Affiliations

  1. Wilhelm-Oswald Institut für, Physikalische und Theoretische Chemie, Universität Leipzig, Linnéstr. 2, Leipzig, 04103, Germany

    Barbara Kirchner

  2. , Lehrstuhl für Thermodynamik und Energiet, Universität Paderborn, Warburger Str. 100, Paderborn, 33098, Germany

    Jadran Vrabec

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© 2011 Springer-Verlag Berlin Heidelberg

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Jaramillo-Botero, A. et al. (2011). First-Principles-Based Multiscale, Multiparadigm Molecular Mechanics and Dynamics Methods for Describing Complex Chemical Processes. In: Kirchner, B., Vrabec, J. (eds) Multiscale Molecular Methods in Applied Chemistry. Topics in Current Chemistry, vol 307. Springer, Berlin, Heidelberg. https://doi.org/10.1007/128_2010_114

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