Foresight Update 25

Page 4

A publication of the Foresight Institute

A Review: 3D Molecular Modeling

Software For Windows and Mac

By Patrick Salsbury

Molecules-3D, and its extended version, Molecules-3D Pro, are inexpensive and surprisingly powerful molecular modeling programs for use on home PCs. The version reviewed runs on the Microsoft Windows platform; a version for Macintosh operating platform is also available.

Molecules-3D allows one to explore the three dimensional relationships between atoms, and provides for quick and easy construction (on-screen) of novel and complex structures. It uses the Dreiding force field for energy minimization, originally developed for high-end molecular modeling packages such as that produced by Biosym.

The Windows version requires a minimum of Windows 3.1, a 386 or better CPU, at least 4Mb of RAM, VGA graphics, and 3Mb of hard disk space. Of course, more computing power will make things run quicker, but it is not required for general operation. The program ran very well on a 486/50MHz, with 20Mb of RAM and SVGA graphics.

The basic package is affordably priced for a student budget, at approximately US$30. It comes with dozens of features, including several hundred 3D examples in a chemical structures library. The professional version, priced at US$70, comes with an advanced structural library of more than 1000 different molecules, some advanced memory handling for Windows (to allow construction of larger molecules) and energy calculations for things such as van der Waals forces, bond stretch, inversion, etc. The Pro version also allows one to manipulate more than one molecule on screen at once, for creating page layouts and reports. It permits creation of pages with 15 or so different molecular structures arranged on a single page.

The student version routinely handles construction of molecular structures in the 1 to 200 atom range without problem. It was only with models that were over 300 or so atoms that memory limitations of my machine became a problem. The Pro version handles Windows' memory limitations much better, allows modeling of structures in the 6 to 700 atom range quite easily. The company states that with a Pentium, structures up to 2000 atoms can be modeled.

One of the most impressive things about the program is its 3-D Builder module. This allows users to select atoms from a customizable palette of the various elements, to choose from single, double, triple, resonant, and lone-pair bonds, and to choose the appropriate valence geometries for the atoms you wish to build with. The module then begins by placing a single "ball and stick" atom on-screen, to which you may begin adding other atoms, or previously stored molecular fragments. A 4-valent carbon here, a bridging oxygen atom there, a terminal (double-bonded) oxygen over there, 3 more carbons, and perhaps a sulfur. Clicking one button will add hydrogens to all remaining open valences, and presto: you have a structure.

Molecular Octet-truss
©1996 Patrick G. Salisbury

The program keeps track of bond angles, torsion between atoms (for example, carbon prefers a twist of 60 degrees between groups linked by a single bond), atomic radius, bond length, etc. It also has a chemical syntax checker, to make sure that you haven't forgotten anything, or attached something in the wrong way (a carbon with only 3 bonds, for example.) And when you're happy with your structure, another button will perform energy minimization calculations, to "relax" the structure into its final form, making sure that no bonds are over-strained.

Molecules-3D will display these structures in simple line-form, in ball-and-stick form, or in rendered, space-filling style. These images may be cut to the clipboard and pasted into other programs in the Windows or Macintosh environments, such as word processors and graphics packages. Structures may also be exported to a variety of file formats. These include the native Molecular Arts .M3D file, as well as .MOL, .GMF, .CTA, and .CTB formats. The manual also provides a detailed breakdown of each file's formatting structure, so porting to other modeling formats should be relatively easy. I would hope to see support in the future for chemical MIME-types to facilitate easy transmission of 3D molecular data over the Web. (More information on chemical MIME-types can be found at http://www.ch.ic.ac.uk/chemime/ )

Extensible Nanotube Segment
©1996 Patrick G. Salisbury

All-in-all, I've found Molecules-3D, in both the student and the professional editions, to be of extreme value in helping with the design of complex molecular structures. With the rich feature set that is included, one can hardly go wrong for the price, and it would help to augment almost anyone's visualization of chemistry, regardless of their level of experience.

For more information, or to order, contact:
Molecular Arts Corporation
Hanover Corporate Centre
1532 East Katella Avenue, Suite 1000
Anaheim, CA 92805-6627 USA
Email: info@molecules.com or
71644.3626@compuserve.com

FAX: 714-634-1999 (Attn: Sales)
Phone: 800-431-5222 (USA/Canada)
714-634-8100 (USA or International)

Patrick Salsbury is a design scientist living in the San Francisco Bay Area. He works on creating solutions for social problems such as traffic congestion, homelessness, poverty, hunger, and poor education. A Foresight Institute Fellow, he is actively following nanotechnology development with an eye towards employing it to reduce some of these global issues. He can be reached at <salsbury@sculptors.com>.

Foresight Update 25 - Table of Contents

Nanotechnology in the Textile Industry

Focusing on a single industry -- textiles-- David R. Forrest has shed more light on the changes that nanotechnology will bring to industrial processes.

Dr. Forrest is a research specialist at Allegheny Ludlum Steel's Technical Center in Brackenridge, PA. His paper, presented to the Industrial Fabric and Equipment Exposition in October 1995 in Charlotte, NC., 20 pages plus 21 figures and 70 footnotes, begins with an excellent introduction to the concepts of molecular nanotechnology and ends with a thoughtful review of economic and social policy issues, including a comprehensive timeline of past developments in the field. In the body of the paper, he discusses potential applications of molecular nanotechnology in the manufacture of industrial fabrics.

"Clearly, there are enormous advantages to having materials that are 100 times stronger than we have now," Forrest writes. "At the molecular level, and given the capabilities of molecular nanotechnology, an obvious approach to improving the strength and toughness of a fabric would be to reinforce the fiber with carbyne molecules. Carbyne is a linear chain of carbon atoms with alternating single and triple bonds...with molecular manufacturing, arbitrarily long chains will be possible." He calculates that a packed array of carbyne molecules would have a tensile strength greater than 50 GPa, compared with 0.45 GPa for rayon and 0.083 for nylon -- an improvement of more than 110 times and 600 times, respectively. "Yet the carbyne molecule is quite flexible, allowing many options for twisting into fibers."

Further, "a carbyne molecule could be cross-linked to other carbyne molecules using the same sorts of structures that Drexler designed for gate knobs in the mechanical nanocomputer (in Nanosystems). The strength and stiffness of the resulting array could be adjusted by varying the number, length and geometry of the cross-links. Carbyne fibers made of non-cross linked molecular arrays would have an extraordinary degree of toughness since cracks would not propagate from one molecule to the next."

More can be gained than just strength in fabric manufacture, Forrest says. Smart materials could:

transport coolant or a heated medium to needed parts of clothing using micropumps and flexible microtubes.
create semipermeable membranes using "sorting rotors" (Nanosystems, page 374).
adjust their shape to the needs of the user; such material would be made of small cellular units connected with screws. Computers would direct the cells, powered with electrostatic motors, to adjust their relative spacing with the screws. "A rigid, solid object could be made to behave like a fabric by effecting rapid changes in its shape, or with temporary disconnections between some cells," Forrest writes.
self-clean, using robotic mites.
self-repair, using embedded sensors to detect flaws and robotic repair "crews."
allow creation of large sections of fabrics without visible seams, by joining panels of fabric with microscopic mechanical couplings along their edges. "Similarly, surfaces could contain mechanical couplings that, when pressed together, would bond with nearly the strength of the bulk material. This 'smart velcro' could latch and unlatch at the user's request."

Forrest concludes from calculations of theoretical properties and measurement of near-perfect whiskers of materials that "with the capabilities of molecular nanotechnology we can expect materials that are 10-50 times stronger and tougher, and 100 times more elastic, than today's commercial products." At the same time, we can achieve "very fine-grained integration of computers and sensors with materials (intelligent materials systems). Material will be viewed as active systems with programmable shapes and properties."

Copies of Forrest's complete paper are available from the author's Web site at
http://www.salsgiver.com/people/forrest/IFAI_paper.html. He also will provide paper copies upon request, sent either by email to forrest@salsgiver.com or by mail to David R. Forrest, Research Specialist, Allegheny Ludlum Steel, Technical Center, Alabama & Pacific Aves., Brackenridge, PA 15014-1597. [Note: Dr. Forrest's current mailing address]

Foresight Update 25 - Table of Contents

Dr. James Lewis Becomes New Foresight Webmaster

Dr. James Lewis, a long-time Senior Associate of both Foresight Institute and Institute for Molecular Manufacturing, has joined Foresight as Webmaster. Dr. Lewis is expected to take over super-vision of the IMM web site as well. Formerly a molecular biologist at Bristol-Meyers Squibb, Dr. Lewis is redirecting his career toward using the Web to further nanotechnology R&D. His interest in the connection between nanotechology and hypertext is not new: he built a large HyperCard stack on nanotechnology years ago, and has now uploaded this structure to the web at his personal site http://www.halcyon.com/nanojbl/

He is also co-editor on both Foresight conference proceedings books: Prospects in Nanotechnology: Toward Molecular Manufacturing (Wiley, 1995, with Markus Krummenacker) and Nanotechnology: Research and Perspectives (MIT Press, 1992, with BC Crandall). He is the author of over forty research publications in biochemistry, virology, and molecular biology.

Plans for the Foresight web site include posting of all Foresight publications (ten years' worth), a frequently updated news section, continual posting of new material from which the quarterly Update newsletter will be compiled, and a searchable database of a wide range of information in Foresight interest areas, especially nanotechnology. Technical papers, such as the 1981 Proceedings of the National Academy of Sciences paper on nanotechnology (http://www.imm.org/PNAS.html), are being posted at the Institute for Molecular Manufacturing site by Dr Lewis.

Foresight is in the process of setting up a group of volunteers to assist with html coding, scanning, proofreading of scanned material, and obtaining copyright permissions. Those interested can send relevant information on their skills and equipment to the Foresight office, foresight@foresight.org. We will be in touch when needed skills match those submitted by a prospective volunteer.

Foresight's previous Webmaster, Robert Armas, will be heading up the new Foresight Database Project, to be covered in future issues of Update. Both Lewis and Armas are expected to speak at the upcoming Senior Associates meeting this October in Palo Alto.

-Chris Peterson

From Foresight Update 25, originally published 15 July 1996.