Crystal Clear: a molecular CAD tool

Abstract

Molecular nanotechnology requires computer-based design and analysis tools. Currently they are needed-as part of a computational approach to nanotechnology-to allow detailed, analysed designs to be presented and discussed and to dovetail with efforts to develop fabrication capabilities. In the longer term, as fabrication capabilities emerge, they will be needed for similar reasons as are needed in today's manufacturing systems: to allow investigation of design alternatives and to control manufacturing systems. Given the huge number of 'parts' which may be required in molecular machines the need for computer-based tools will, however, be even more primary for molecular nanotechnology than for today's manufacturing technology, surpassing the CAD requirements of VLSI. Whilst molecular CAD clearly shares some traits with existing CAD, a fundamental difference is that the position and bonding of every atom is of key interest in molecular manufacturing. This necessitates new approaches and techniques. Molecular manufacturing will eventually use diamondoid materials; materials which are crystalline. Molecular CAD tools for the design of diamondoid structures must incorporate techniques for manipulating crystalline materials. In this paper, we describe a molecular CAD tool-Crystal Clear-which allows the design of simple diamondoid structures in full atomic detail using some novel techniques based on the crystalline nature of diamondoid materials.