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Foresight Nanotech Update 58

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A publication of the Foresight Nanotech Institute

Software control of matter

Ideas factory produces three projects to be funded

Nanoscience and nanotechnology, broadly defined, are rapidly growing fields that receive major funding. There is widespread hope that current discoveries will soon provide solutions to great unmet needs (for example, the Foresight Nanotechnology Challenges). There is less investment in developing advanced nanotechnology of the type that J. S. Hall described in Nanofuture (see "Anticipating advanced nanotechnology" in this issue). One effort in this direction is the Technology Roadmap for Productive Nanosystems announced by the Foresight Nanotech Institute in partnership with The Waitt Family Foundation and Battelle. Another very interesting recent development comes from the UK.

A January Nanodot post ("U.K. nanotechnology project causing U.S. nanoenvy") is a measure of the admiration felt within the Foresight community for an "ideas factory" program announced by the UK's physical sciences research council, the EPSRC, with the theme "Software control of matter at the atomic and molecular scale". The director of the ideas factory program was Richard Jones, author of Soft Machines: Nanotechnology and Life (see review in Update 55), and the topic was proposed by Nottingham University nanophysicist Philip Moriarty, a member of the Nanofactory Collaboration organized by Robert A. Freitas Jr. and Ralph C. Merkle.

The Software control of matter ideas factory was announced by EPSRC in September of 2006 for 20 participants to spend a week in January developing research proposals, for which EPSRC had set aside £1.5 million (almost $3 million). The announced challenge:

"Can we design and construct a device or scheme that can arrange atoms or molecules according to an arbitrary, user-defined blueprint? This is at the heart of the idea of the software control of matter — the creation, perhaps, of a "matter compiler" which will interpret software instructions to output a macroscopic product in which every atom is precisely placed. Even partial progress towards this goal would significantly open up the range of available functional materials, permitting meta-materials with interesting electronic, optoelectronic, optical and magnetic properties.

"One route to this goal might be to take inspiration from 3-d rapid prototyping devices, and conceive of some kind of pick-and-place mechanism operating at the atomic or molecular level, perhaps based on scanning probe techniques. On the other hand, the field of DNA nanotechnology gives us examples of complex structures built by self-assembly, in which the program to guide the construction is implicit within the structure of the building blocks themselves. This problem, then, goes beyond surface chemistry and the physics of self-assembly to some fundamental questions in computer science.

"This ideas factory should attract surface physicists and chemists, including specialists in scanning probe and nanorobotic techniques, and those with an interest in self-assembling systems. Theoretical chemists, developmental biologists, and computer scientists, for example those interested in agent-based and evolutionary computing methods and emergent behaviour, will also be able to contribute."

The "sandpit"

The essence of the project was a 5-day "sandpit", a residential interactive workshop in which a highly multidisciplinary mix of 20 participants pursued intensive discussions to generate innovative, radical approaches to the research challenge. The sandpit began January 8, was led by Richard Jones, and included a team of professional facilitators to guide the participants through the process.

The development of the project, from December 2006 through January 2007, is archived on the public blog of the EPSRC Ideas Factory "Software Control of Matter". In addition to daily reports on the sandpit, dozens of insightful and informative comments were posted. However, the details of the sandpit discussions were not revealed.

Writing near the completion of the sandpit, Richard Jones said of the result: "But what's important is that we've got tremendously exciting projects to look forward to, which we really don't think would have been arrived at any other way. We were looking for a grand vision — real ambition, of a kind that scientists are sometimes reluctant to commit to. But we needed to be sure that, on the very first day of the project, it was clear exactly what the newly starting scientists on the project would do. And, while it's obvious that for a sufficiently big vision, one can't expect the route from here to there to be fully mapped out at the outset, we need to be sure that there are no obviously unbridgeable chasms in the way. We know, and the funders know too, that there is a significant risk of failure, but that's as it has to be."

Out of this process came three projects to be funded by the £1.5 million. As of the time they were announced on the blog, there remained a few administrative hurdles to be completed prior to EPSRC officially approving funding. There were two experimental projects (Software-controlled assembly of oligomers, Directed reconfigurable nanomachines), each to receive slightly less than half of the total funding, and one project (The matter compiler) based on theory and computer science. For each project, only a very general single paragraph overview is provided (along with the names of each project leader, the main collaborators, and other contributors). The numerous posted comments illuminate some of the issues involved. It is however, clear that many researchers were (quite reasonably) unwilling to release specific information about very novel multidisciplinary proposals before they had even begun the research.

The descriptions of the three projects provided on the blog:

Software-controlled assembly of oligomers

We propose to create a molecular machine that will build new materials under software control. The output of the machine will be chains of building blocks linked by covalent bonds. The machine is modular and is designed to accept many different building blocks, from small molecules to nanoparticles, with a wide range of physical and chemical properties. In order to drive its development we will concentrate on using it to create two target products: a molecular wire, capable of transporting energy and electrical charge, and a catalyst. Software control starts with specification by the end-user of a sequence of building blocks. The target sequence is encoded in an instruction tape which can be read by the machine: the tape is itself a molecule, a synthetic DNA oligomer. The target sequence of building blocks is automatically converted into a control sequence of DNA bases, and the tape is produced by commercial solid-phase synthesis. The job of the machine is to read the instruction tape and to form the bonds between building blocks in the specified sequence. Every component of this molecular factory is itself a molecule: our ambition is to develop the system to the point where it could be distributed to end users as chemicals in plastic vials.

Directed reconfigurable nanomachines

We propose a scheme to revolutionise the synthesis of nanodevices, nanomachines, and, ultimately, functional materials via the positional assembly of molecules and nanoscale building blocks. Computer-directed actuators will be used to drive (with sub-nanometre to sub-Angstrom precision) the elements of a nanosystem along pre-defined and entirely deterministic trajectories, thereby achieving structures not accessible by mimicing natural assembly strategies alone. Linkages and bonding between the building blocks will also be initiated, modulated, and — in some cases — terminated by direct computer control. Our proposal rests on the parallel development of novel surface-bound, reconfigurable nanoscale building blocks (molecules, functionalised clusters, nanoparticles) and a prototype computer-controlled matter manipulator best described as a nanoscale conveyor belt. We focus on the generation of two major and immensely challenging functionalities for positionally-assembled nanomachines: switchable energy transduction and conformationally-driven motion. Our archetypal system comprises the following units: an energy harvester, a switchable/gateable link, and an optical or mechanical output. By arranging, configuring, and triggering these fundamental units our long-term goal is no less than the fabrication of an autonomous, abiotic nanomachine.

The matter compiler

An ambition to assemble molecules and materials under atomically precise control demands a big leap forward in control engineering and computer science. Is it possible to anticipate the properties and needs of a 'nano-assembler'? If so, there is a need for a high level instruction language and a computer compiler that translates commands in this language into instructions for the 'nano-assembler'. This development will require a breakthrough in understanding of chemical synthesis that must embrace the radically new 'pick and place' assembly method which is now possible in scanning probe microscopy (SPM). The Matter Compiler project is thus both an exercise in foresight, to anticipate developments in this area, and a prototype implementation for the engineering control and computer science aspects of directed molecular assembly. It has as inputs data from SPM experiments of collaborators, energy landscapes for 'pick and place' reactions and the vast knowledge base of classical synthetic chemistry, including methodologies such as retrosynthesis. This will be supplemented by reaction schemes for 'pick and place' reactions deduced from first principles quantum chemistry calculations and the technology of object oriented databases and inference engines.

We hope these projects achieve their objectives. At the very least, these innovative efforts should lead to a clearer picture of the problems and opportunities along the path toward molecular manufacturing.

Rolling and carrying molecules across surfaces

Getting molecules on surfaces to do machine-like things

By James Lewis, PhD

Atomically precise placement of molecules on surfaces is only the first step towards the long term goal of assembling molecular machinery on surfaces. A next step is to make molecules move on surfaces in useful ways. The two projects described here—the nanocar and the nano-walker—have in common that thermally driven diffusion was controlled to accomplish the specified purpose.

Nanocars move and do work on the molecular scale

Rice University chemists led by James M. Tour reviewed their recent progress in making a variety of single-molecule nanovehicles [Yasuhiro Shirai, Jean-François Morin, Takashi Sasaki, Jason M. Guerrero and James M. Tour "Recent progress on nanovehicles" (free access), Chem. Soc. Rev., 2006, 35, 1043-1055]. They describe nanovehicles as "a new class of molecular machines consisting of a molecular scale chassis, axles, and wheels, that can roll across solid surfaces with structurally defined directions" The nanovehicles they have made are about 3x4 nm in size, and each batch is produced in a 100-ml laboratory flask in 30-mg quantities containing about 3.2x1018 (3.2 quintillion) nanovehicles.

Most previous work in which scanning probe microscopes (SPM) were used to move molecules across surfaces resulted in motion better described as stick and slip or sliding rather than rolling. The exceptions that did show rolling were fullerene structures. Thus the principal breakthrough so far has been to demonstrate "a new type of fullerene-based wheel-like rolling motion, not stick-slip or sliding translation". They presented a "nanocar" rolling across a gold surface on four C60 wheels, imaged using a scanning tunneling microscope (STM). The chassis and two axles were constructed from phenylene (aromatic six-carbon ring) and ethynylene (two carbons joined by a triple bond) moieties linked together to form a Z-shaped backbone for the nanocar, with four spherical C60 moieties attached as wheels. Alkyl groups were added to increase the solubility of the molecules. The ethynylene connections provide for free rotation of the wheels and chassis parts. The major technical challenge the team encountered was apparently how to attach the ethynylene groups to the C60 units.

The fullerene wheels appear as bright features in the STM image, but the chassis and axles could not be directly visualized. From molecular models, as confirmed by the spacing of the fullerene wheels in the STM images, the nanocars are 3.3 nm wide and 2.1 nm long. Because the nanocars are rectangular, not square, the chassis and axle orientation of the four-lobed nanocar molecules could be determined by measuring the separation of the fullerene wheels.

The nanocars are stationary on the gold surface at room temperature, as expected because of the strong adhesion between fullerenes and the gold surface previously observed, and remained stationary while heated to 170 degrees C. At higher temperatures, however, the molecules move across the surface, as followed by a series of STM images. The motion of the nanocars at 200 degrees C combines pivots with translation perpendicular to the axles. Translation parallel to the axles was not observed. The pivoting, instead of simple motion in one dimension, is thought to occur because the fullerene wheels can rotate independently of each other. Variant three-wheel molecules with axles designed so that they could not roll showed only pivoting, with little or no translation. The fact that the three-wheel variants showed no thermally induced translation further suggests that the translation seen with the nanocars is due to rolling of the fullerene wheels.

Attempting to push a nanocar with the STM tip did not result in rolling of the nanocar; however, a nanocar could be pulled in a direction perpendicular to the axles by lowering the tip of the STM in front of the molecule in the direction of motion. Presumably the nanocar is pulled by the electric field of the tip. "The use of spherical wheels based on fullerene-C60 and freely rotating axles based on alkynes permits directed nanoscale rolling of a molecular structure."

The next goal of Tour and his team is to integrate a light-powered molecular motor in a nanocar—a unidirectional motor, developed by BL Feringa and colleagues at the University of Groningen, based on a chiral helical alkene in which the central double bond undergoes photo-induced cis-trans isomerization when irradiated with 365 nm light was chosen. The plan they describe is to place the motor in the central portion of the chassis where it could propel the nanocar by turning against the metal surface like a paddlewheel. However, the presence of fullerene wheels rendered the motor inactive, probably by quenching the photoexcited state of the motor moiety. Therefore they substituted a different type of wheel. Because it is nearly spherical and does not absorb at a wavelength that interferes with the operation of the motor, p-carborane (an icosahedron in which the 12 vertices are each formed by either one of 10 boron atoms each linked to a hydrogen atom or by one of two 2 carbon atoms each linked to a hydrogen atom) was substituted for C60. The proposed design was synthesized and then irradiated in solution with 365 nm light. Nuclear magnetic resonance spectroscopy revealed that rotation of the motor was not inhibited by the bulky carborane wheels. Also, for technical reasons, nanovehicles with carborane wheels are considerably easier to synthesize than those with fullerene wheels. However, whether the carborane wheels will enable directional rolling on a surface, as has been shown with the fullerene wheels, is not yet known. Whether the motor will be able to propel this nanocar across a surface also remains to be determined.

A molecule carrier

A University of California Riverside team led by Ludwig Bartels has demonstrated that molecules derived from anthracene can "walk" in a straight line across a crystalline copper surface. Anthracene is a linear array of three fused benzene rings. Their first advance [abstract] used 9,10-dithioanthracene, in which two sulfur atoms are attached to the two carbon atoms of the middle hexagon, forming a molecule that has been described as resembling an ant missing all but its middle pair of legs. Combining scanning tunneling microscope (STM) images with detailed computer simulations they established that the molecule aligns with the copper atoms on the Cu(111) surface such that the sulfur atoms straddle two neighboring rows of copper atoms. When cooled to 50-70 K (somewhat below liquid nitrogen temperature) the molecule diffuses in a straight line across the copper surface such that "due to the molecular geometry, [the two sulfur atoms] move in alternation so that the stationary one guides the motion of the mobile one in the direction of the next step and prevents the molecule from rotating or veering off course." The authors note that the motion of the sulfur atoms "bears striking resemblance to bipedal locomotion (e.g., human walking), with one foot always on the ground to guide the motion of the other".

In their recent advance ["A molecule carrier"] the team showed that a related molecule (anthraquinone—a related molecule in which two oxygen atoms, instead of two sulfur atoms, are attached to the central pair of carbon atoms) not only "walked" in a straight line across the copper surface, but could reversibly carry one or two carbon dioxide molecules with it. Unattached, the carbon dioxide molecules would diffuse at random across the copper surface, but attached to the anthraquinone, the molecular "cargo" was carried along in a straight line. A carbon dioxide molecule attaches to an anthracene molecule either via random diffusion or via manipulation with the STM tip. Detachment occurs in the same way. The authors conclude "our observations are proof of principle for the application of molecules at surfaces as molecular-scale analogs of macroscopic machinery ('molecular machines')—that is, as entities that change the position or properties of separate, molecular-scale objects in a predetermined fashion."

The molecule carrier was the topic of a Nanodot post "Nanotechnology movie: Walking molecule now carries packages".

Foresight Nanotech Update 58 Spring 2007

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