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.
©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:
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 <firstname.lastname@example.org>.
Molecular Arts Corporation
Hanover Corporate Centre
1532 East Katella Avenue, Suite 1000
Anaheim, CA 92805-6627 USA
Email: email@example.com or
FAX: 714-634-1999 (Attn: Sales)
Phone: 800-431-5222 (USA/Canada)
714-634-8100 (USA or International)
Table of Contents - Foresight
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
"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
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:
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."
- transport coolant or a heated medium to needed parts of clothing using
micropumps and flexible microtubes.
- create semipermeable membranes using "sorting rotors" (Nanosystems,
- 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
- 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
Copies of Forrest's complete paper are available from the author's Web site
He also will provide paper copies upon request, sent either by email to
firstname.lastname@example.org or by mail
to David R. Forrest, Research Specialist, Allegheny Ludlum Steel, Technical
Center, Alabama & Pacific Aves., Brackenridge, PA 15014-1597.
Table of Contents - Foresight
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
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, email@example.com.
We will be in touch when needed skills match those submitted by a prospective
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.
Table of Contents - Foresight
From Foresight Update 25, originally published 15
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