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
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
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.
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/
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: firstname.lastname@example.org or
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 <email@example.com>.
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
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
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."
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, firstname.lastname@example.org.
We will be in touch when needed skills match those submitted by a
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