Supramolecular Chemistry of Addressable Biostructures:
 Engineering with Biological, Molecular Machines

Molecular model of the assembly formed between a duplex DNA 60mer containing dU moieties at target sites spaced 35nt apart and two molecules of the methyltransferase M·HhaI. The model shown is taken from the paper “Uracil as an Alternative to 5-Fluorocytosine in Addressable Protein Targeting”, by John A. Wendel and Steven S. Smith (used with the permission of Steven S. Smith). Larger version of this figure [712×800 pixels; 83K]

Alternative representation of above using space filling view of atoms.

 Molecular Manipulator Design

A Fine-Motion Controller for Molecular Assembly. An atomically detailed design for a fine-motion controller for molecular assembly, containing 2,596 atoms. As described by the designer, K. Eric Drexler:

“This illustration shows a structure resembling a Stewart platform that results from a long sequence of designs and redesigns aimed at specifying the atomic structure of a molecular-scale fine-motion controller. Its core consists of a shaft linking two hexagonal endplates, sandwiching a stack of eight rings. In a complete system, each ring would be rotated by a lever driven by a cam mechanism. Each ring supports a strut linked to a central platform (here shown raised, displaced, and twisted). Rotating a ring moves a strut; moving a strut moves the platform; positioning all eight rings (over-)determines a platform position in x, y, z, roll, pitch, and yaw. (If the struts were rigid, six would do the job; here, two struts have been added to increase stiffness, decrease elegance, and annoy Ralph Merkle.) The chief design problem is to enable an adequate range of motion without mechanical interference or unacceptable bond strains, and within the size constraints set by available modeling tools and patience. The illustrated structure can execute precise motions over several atomic diameters with associated 90-degree rotations, and contains fewer than 3,000 atoms.”

For further details, including a file of atomic coordinates, see http://www.imm.org/Parts/Parts2.html

 Nanotube Junctions for Nanoelectronic Devices

Simulation of a T-junction between a semi-conducting and a metallic nanotube. The nanotubes are formed by rolling up sheets of graphitic carbon, with the atoms arranged in hexagons. The T-junction is formed by inserting pentagons and heptagons of carbon atoms. The illustration shows the computationally fully relaxed (9,0)-(10,0)-(9,0) tube. The turquoise coloured balls denote the atoms forming the heptagons. Pentagons are denoted by white balls. The structure contains eight heptagons and two pentagons. (9,0) tubes are metallic while (10,0) tubes are semiconducting.

“These quasi-2D junctions could be the building blocks of nanoscale tunnel junctions in a 2D network of nanoelectronic devices” the authors write in “Carbon Nanotube ‘T-junctions’: Nanoscale Metal-Semiconductor-Metal Contact Devices”, M. Menon and D. Srivastava, Phys. Rev. Lett. 79, 4453 (1997).

Picture from Drs. Deepak Srivastava, NAS Nanotechnology Group and Madhu Menon, University of Kentucky, Lexington.

 A Synthetic Self-Assembling Spherical Complex

Synthetic Self-Assembling Spherical Complex. The above picture appeared on the cover of Science, 1 December, 1995. Cover caption “Tetramethyladamantane (green) is encapsulated by two molecules of a self-complementary synthetic receptor. An array of weak intermolecular forces are balanced to produce the assembly in solution. (Red spheres, oxygen atoms, blue spheres, nitrogen atoms.)” The complex is described in the paper “Autoencapsulation through intermolecular forces: a synthetic self-assembling spherical complex” R. S. Meissner, J. Rebek Jr., and J. de Mendoza. Science 270: 1485-1488.

Synthetic Self-Assembling Spherical Complex–Alternate View. The above complex viewed from another perspective.

Pictures provided by Michael Pique, The Scripps Research Institute, and Dr. Julius Rebek, Jr. Director of the Skaggs Institute for Chemical Biology, The Scripps Research Institute.

 Computational, Fullerene Nanotechnology

Carbon nanotube based gears. For further information, see the papers “Molecular Dynamics Simulations of Carbon Nanotube Based Gears” by Jie Han and Al Globus, MRJ, Inc., Richard Jaffe, NASA, and Glenn Deardorff, Sterling Software, NASA Ames Research Center, located at http://science.nas.nasa.gov/Groups/Nanotechnology/publications/MGMS_EC1/simulation/paper.html, and “Machine Phase Fullerene Nanotechnology” by Al Globus, Charles Bauschlicher, Jie Han, Richard Jaffe, Creon Levit, and Deepak Srivastava, located at http://science.nas.nasa.gov/Groups/Nanotechnology/publications/1997/fullereneNanotechnology/. A larger version of this figure [800×674 pixels; 116K] is located at http://science.nas.nasa.gov/Groups/Nanotechnology/gallery/gears/long.jpg