Chemistry Reference
In-Depth Information
First-Principles-Based Multiscale,
Multiparadigm Molecular Mechanics and
Dynamics Methods for Describing Complex
Chemical Processes
Andres Jaramillo-Botero, Robert Nielsen, Ravi Abrol, Julius Su, Tod Pascal,
Jonathan Mueller and William A. Goddard III
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 signifi-
cant 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 multi-
scale, multiparadigm strategy. To illustrate the procedure we demonstrate the appli-
cation 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, includ-
ing understanding the solvation effects on the reactivity of organic and organome-
tallic 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, follo-
wing the dynamics and energetics of long-term conformational evolution of DNA
