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New molecular CAD tools are needed for the design of diamondoid nanostructures. They are needed for research to produce detailed designs for analysis by computational chemistry packages, to allow search of the design space for promising paths to molecular manufacturing, to provide designs for general discussion and to generally reduce the time required to develop molecular manufacturing capabilities [1]. When molecular manufacturing capabilities emerge, molecular CAD software will be required to control molecular manufacturing systems.
Molecular CAD draws on the principles and techniques of both mechanical CAD and of molecular modeling. However, molecular CAD requires a body of principles and techniques appropriate for its domain. Diamondoid materials are of fundamental interest in nanotechnology. Diamondoid materials are crystalline. Molecular CAD software for diamondoid materials must therefore include some form of crystal editor which provides natural and intuitive operators for selecting and manipulating crystal lattices. Another consideration arises from an approach to the design of curved diamondiod structures. By introducing arrays of dislocations into the diamond lattice, thick walled, curved diamondoid structures with low bond strain are possible [2], [3], Molecular CAD needs to incorporate techniques like the introduction of dislocations as fundamental operations. A rudimentary molecular CAD program - called Crystal Clear - incorporating crystal lattice operators which facilitate the incorporation of periodic dislocations has been described [4]. In this paper we present a number of improvements to Crystal Clear and discuss some new principles and techniques appropriate for the field of molecular CAD. One example is the ability to select some part of the structure under design as a unit cell and then "grow" the structure using in any direction consistent with the definition of that unit cell. We discuss the design of several stuctures utilizing the new techniques.
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