Stephen Sligar
Beckman Institute
405 N. Mathews Avenue
Urbana, IL 61801

Faculty Participating in the Beckman Institute Molecular and Electronic Nanostructures Main Research Theme (MRT)

Ilesanmi Adesida, Stephen Bishop, Paul Bohn, David Brady, David Ceperley, Hyung Soo Choi, Martin Gruebele, Karl Hess, Steven Kang, Thomas Kerkhoven, Walter Klemperer, Jean-Pierre Leburton, Jennifer Lewis, Joseph Lyding, Nancy Makri, Richard Martin, Eric Michielssen, Jeffrey Moore, Yoshi Oono, George Papen, David Payne, Umberto Ravaioli, Klaus Schulten, Tsung Cheng Shen, Robert Skeel, Stephen Sligar, Samuel Stupp, John Tucker, Peter Wolynes, Charles Zukoski.


With goals of creating chains of interdisciplinary research from physics to function and from molecules to mind and of developing leading edge tools for characterization and manipulation of molecular scale structures, the Beckman Institute has fostered research in molecular and electronic nanostructures since its founding. Nanoscale structures and processes explored in the Institute include organic and inorganic self-organizing materials, quantum confined devices and quantum transport in semiconductors, molecular and atomic interactions in gases and on surfaces, synthesis and function in biological molecules, and complexity and coherence in quantum dynamics. These efforts impact physics through improved perspectives on quantum mechanics and complexity, chemistry through improved synthesis and characterization techniques, life sciences through improved understanding and control of biological materials, and technology through improved electronic and photonic materials and devices. We have created world-class laboratories in photonics, genetic engineering, surface chemistry, and advanced electronic, atomic, and optical imaging and lithography. We have developed numerical and theoretical tools to model nanoscale systems using modern developments in quantum transport and density functional theory.

Nanoscale research in the Beckman Institute was combined under the umbrella of the new Molecular and Electronic Nanostructures Main Research Theme (MRT) in 1994. The purpose of the MRT is to coordinate and encourage cross-disciplinary and cross-departmental research. This paper describes the "strategic plan" for the nanostructures MRT. After a brief overview of the nanostructures theme in this section, subsequent sections overview the background, or motivation, of the nanostructures theme, the laboratory and computational resources available to the MRT, and major opportunities in nanostructure research.

The nanostructures MRT has developed in a unique academic environment of cross-departmental communication and collaboration. Common themes, such as process complexity and quantum coherence, and telling contrasts, as between lithographic and self-organizing fabrication, have emerged from this experience. Close interaction between disciplines is essential in pursuit of the difficult and still elusive goals of understanding and controlling the functionality of nanometer scale molecules, processes and devices in biotechnology, chemical dynamics, materials science, and information systems. We are pursuing these goals by integrating our development of computational analysis tools and advanced scanning microscopes with ultrafast photonics and electronics, chemical synthesis, and bioscience. The Molecular and Electronic Nanostructures theme focuses on consultation and collaboration in developing

In contrast with departmentalized "tool oriented" traditional academic programs, the Molecular and Electronic Nanostructures theme merges work in mechanics, optics, electronics, chemistry, and biochemistry to create a problem-oriented research program. The program focuses on two specific problems: semiconductor nanostructures and self organizing synthesis. We are developing STM (scanning tunneling microscope) lithography, advanced scanning microscopy, chemical self-assembly, and optical and electronic characterization techniques to support these areas. Running through the problem areas are two analysis and development tools: ultrafast dynamical systems and quantum transport-based analysis of complex molecular and electronic systems.

The Molecular and Electronic Nanostructures theme is a model of how cross-disciplinary research programs can have broad and profound impact while remaining focused on excellence in a finite set of laboratory and analytical tasks. By establishing links between artificial and natural nanoscale fabrication, advanced imaging and probe tools, and computational visualization and analysis, we will develop a clear picture of mesoscopic systems and opportunities for their application. Nanostructures are a unique research opportunity from several perspectives. They are both the smallest structures in which artificial structure can be encoded and the largest structures for which nearly complete quantum mechanical models can be developed. They are simultaneously worthy objects of basic scientific research and crucial elements in the continuing development of the information technologies that make advanced research possible. In concert with Beckman Institute research themes in biological intelligence and human-computer interactions, the Molecular and Electronic Nanostructures theme uses unity of purpose and diversity of perspective to achieve understanding of information transfer mechanisms spanning the range from molecular self-assembly to supercomputing.


In 1960, Feynman described "bottomless" opportunities for research and development of smaller and smaller structures based on the microscopic and lithographic resolution of that time. The scanning tunneling microscope and related discoveries and inventions have opened possibilities beyond even Feynman's vision in the science and engineering of structures on the nanometer scale. Milestone progress has been made in various disciplines. Physics and materials science have achieved an understanding of mesoscopic systems and quantum transport phenomena in solids and solid heterolayers that were unknown before the last decade, the meaning of mechanical engineering has been expanded by the fabrication of springs, turning wheels, and moving pistons on the nanometer scale, and the ever denser integration of electron devices has made 106 transistors on a chip a household concept. Chemistry has dealt with nanometer-sized objects (i.e., molecules) all along, but increasingly turns its attention to organizational principles which operate on the supra-molecular length scale.

A broad view of nanostructure research reveals a picture in which mechanics, reaction dynamics, optics, and electronics merge and lose their conventional meaning, and an overlapping interest arises in the corresponding disciplines: physics, chemistry, biochemistry, and mechanical and electrical engineering. Arising from this melting pot of disciplines are three common foci:

  1. fabrication and self-assembly tools
  2. advanced imaging, visualization, and dynamical probe techniques
  3. numerical modeling and analysis tools

The Beckman Institute has fostered major interdisciplinary research in each of these areas. Fabrication of semiconductor nanostructures is the aim of the STM-based Nanolithography Program, and molecular self-assembly in organic and inorganic systems is being developed in several groups from chemical, biological, and mechanistic perspectives. Extensive experimental imaging facilities for scanning tunneling and atomic force microscopy (AFM) have been built and are being extended. The Beckman Institute has developed outstanding facilities for optical and electronic characterization and is developing unique ultrafast and scanning optical probe spectroscopy and microscopy systems.

Powerful computation facilities for scientific visualization and numerical modeling are present in the Institute, including the National Center for Supercomputing Applications and the National Center for Computational Electronics. Computers and computation play a unique role in nanostructure research. Artificial fabrication and imaging of nanoscale systems rely on computer-controlled scanning microscopes and computer-intensive data analysis. Analysis of self-assembling systems and nanostructure dynamics requires detailed computational modeling. Large computational resources and supercomputer applications are necessary to understand the quantum dynamics of nanostructures, and visualization tools are necessary to link these pictures to theoretical ideas and mental images. Of course, modern computers are made of integrated circuits with features approaching nanoscale dimensions. Using such computers, the Molecular and Electronic Nanostructures theme links the bottomless opportunities for spatial and temporal complexity in small structures and the opportunity for explosive growth in computational tools.

The next section of this paper overviews existing Institute resources in nanostructure research. Following this overview, we consider future opportunities and describe six areas of special strength and promise in Beckman Institute nanostructure research:

  1. Fabrication and Characterization of Semiconductor Nanostructures
  2. Self-Organizing Synthesis in Chemistry and Structural Biology
  3. Dynamics of Nanostructures
  4. Quantum Transport in Complex Systems
  5. Circuit Testbeds
  6. Theoretical Biophysics

The final section of this paper presents extremely brief synopses the specific research interests of the faculty participating in the MRT.


Scanning Tunneling Microscopy

The Beckman Institute houses one of the most advanced STM laboratories in the world. This laboratory is the central facility of the ONR-funded "STM-Based Nanolithography" URI and consists of several UHV-STM chambers that are interconnected to permit sample and tip transport between multiple experimental stations under UHV (ultra-high vacuum) conditions. In addition to the three UHV STMs, there is a full suite of sample preparation and conventional surface analysis tools in this system. Among these are LEED/Auger, residual gas analysis, gas dosing, sample heating and cleaving, ion sputtering, and annealing. The STMs employed in this system were developed at the University of Illinois and have a unique combination of features. They employ an inertial translation scheme for tip/sample approach that eliminates the bulky mechanical components other designs use, resulting in much greater rigidity and insensitivity to mechanical disturbances. The design is also highly thermally compensated, resulting in thermal drift below 1 Å/hour. This design is currently being marketed by two U.S. companies under patent license from the University of Illinois.

A more recent development is the incorporation of an integral coarse translation system in which the STM tip can be inertially translated by several millimeters in any direction. This feature enables alignment of the scan area with prepatterned device structures or molecular beam epitaxy (MBE)-grown heterolayers. Another key feature of this STM is the ability to relocate the same scan area even after the sample has been removed from the STM. This facilitates many important experiments in which the effects of sample treatments outside of the STM can be studied at a previously scanned or patterned region of the surface. A special etching chamber has been incorporated in this system for etching experiments using chlorine or other hazardous gases.

Currently under development is a variable temperature UHV-STM that connects directly to the existing facility for UHV transfers. This instrument will enable studies to be performed over the 1.5-400 K range. At low temperatures, the greatly enhanced spectroscopic resolution of the STM will enable electron wavefunction mapping for the studies of quantum size effects. In addition, by controlling the temperature, it will be possible to control the dynamics of absorbed surface species. This is expected to open new directions in the study of molecules on surfaces.

Also under development is a field ion microscope (FIM) combined with a STM to diagnose and control tip shapes. STM tips are generally prepared with empirical recipes using electrochemical etch solutions. The FIM will allow direct atomic imaging of the tip and will also be used to field evaporate atomic layers until the desired structure is achieved. This is especially important for STM nanolithography experiments in which the tip is operated in field emission. Tips prepared in the FIM will be transferred under UHV to all of the other experimental stations.

Additional commercial STM instruments are also available, including a Nanoscope III for imaging and manipulation of mesoscale biological systems and a suite of Topometrix instruments for surface chemistry characterization.

Atomic Force Microscopy

The Beckman Institute houses a fully operational AFM facility consisting of three instruments capable of standard AFM, lateral force, and non-contact imaging. An upgrade to add capabilities for magnetic force electrical imaging is in progress. The instruments are capable of producing both long range (100 nm) and atomic images in either a liquid or dry environment.

The AFM facility is an integral part of the Beckman Visualization Facility, which also houses instruments for electron, confocal, and light microscopy as well as extensive computational tools. The network linking all of the instruments and computers facilitates the transparent transfer of data from the atomic force microscopes to the computer workstations for further processing, analysis, and finally preparation for presentation.


The Beckman Institute maintains laser and computational laboratories to support studies of the photo-dynamics of molecules, solid-state materials, and quantum confined systems and to develop applications of ultrafast optics in communications, data storage, and polychromatic sensing. Facilities include five femtosecond mode-locked laser systems; a molecular beam spectroscopy system; cryogenic spectroscopy systems; a variety of ion, solid state, and semiconductor laser systems; high speed data acquisition and analysis systems; and computational modeling tools. The photonic systems program has unique capabilities for generating and detecting complex ultrafast optical fields. Using diffractive pulse shapers and interferometric cross-correlators, the capacity has been demonstrated to encode cross-spectrally coherent time domain optical fields to micron spatial resolution and 100 femtosecond temporal resolution over millimeter scale spatial windows and 100 picosecond scale temporal windows. These fields offer an unprecedented opportunity for direct time domain control of quantum dynamical processes. Complex space-time fields can be coded with sufficient degrees of freedom to coherently specify and manipulate the space-time dynamics of molecular and electronic nanostructures.

Under a major grant from the NSF's Optical Science and Engineering Initiative, construction of an integrated STM/ultrafast optical surface studies laboratory began September 1996. Completed in 1997, this laboratory allows programmable terahertz modulation of STM tip-surface interactions and surface nanostructures.

Proteins - Recombinant DNA Technology

State-of-the art facilities for the application of recombinant DNA technology to the understanding of protein, nucleic acid, and lipid functionalities are critical to the synthesis and manipulation of nanoscale biological systems. The Beckman Institute has available the complete suite of capabilities, from computational macromolecular modeling for de novo design, DNA-RNA synthesis, site-directed mutagenesis, combinatorial library generation and screening, heterologous expression through fermentation, macromolecule purification, characterization, and assay. Central problems under investigation include construction and characterization of protein-based Coulomb blockade devices, studies of quantum transport in condensed macromolecular arrays, subnanosecond initiation and documentation of protein folding events, de novo design of sensors of environmental pollutants and xenobiotic compounds, construction of artificial nanoscale materials for use as blood substitutes, and documentation of macromolecular dynamic modes linked to function.

Computational Electronics

The Beckman Institute hosts the NSF National Center for Computational Electronics (NCCE) which encompasses nationwide more than sixty groups mainly from universities but also from industry and government laboratories. Much of the work of the center is concerned with advanced numerical simulation of electronic transport in semiconductors with a very large fraction of researchers interested in semiconductor nanostructures. Emphasis is placed on the interdisciplinary aspect of computational electronics, and the center includes applied mathematicians, computer scientists, physicists, chemists, and electrical engineers. The topics attacked in the center range from conventional device simulation to standardizing Monte Carlo simulations and to solving difficult eigenvalue problems and problems related to quantum transport.

Beckman faculty associated with the center interact with many other NCCE groups, including groups at Stanford (K. Hess and R. Dutton co-direct NCCE), Notre Dame, NCSU, and Oregon State University, as well as with groups at IBM Watson, AT&T - Murray Hill, groups at NIST and ONR, and many foreign partnerships.

Near Field Scanning Optical Microscopy (NSOM)

Under development at the Beckman Institute is a NSOM facility that will feature a commercial turnkey instrument for general use as well as support the development of a state-of-the-art instrument with the capability of performing spectroscopy on single molecules. NSOM is a relatively new technology that takes the flexibility of optical microscopy down to the nanoscale regime. Although electron and other particle-based microscopies have superior spatial resolution to NSOM, the large number of contrast mechanisms, including (a) opacity, (b) refractive index variations, (c) polarization, (d) light emission (photoluminescence), (e) reflectivity, and (f) spectroscopy, that have been worked out for normal diffraction-limited optical microscopy can be carried over to NSOM but are not available to particle microscopies. Thus, NSOM is well suited for the optical characterization of fabricated mesoscale and nanoscale device structures, as well as comparably-sized biological structures, which opens rich opportunities for interactions with other thematic groups within the Beckman Institute. By establishing such a facility at the "ground floor" of this new field, Beckman researchers will have access to the latest developments and will be able to influence the evolution of commercial NSOM instruments. In addition, the NSOM facility is a near-perfect complement to existing UHV-STM and atomic force microscopic capabilities.

NCSA and Nanostructures

The National Center for Supercomputing Applications (L. Smarr, director) is one of four NSF-supported high performance computing and communications facilities. NCSA has a total staff of two hundred. The Beckman Institute houses the NCSA Applications group and its high performance visualization facilities. NCSA has long had a partnership with Illinois faculty in developing both theoretical simulations and experimental facilities. As a national center it has co-hosted workshops on both topics. The computational facilities at NCSA include state-of-the-art parallel supercomputers such as a Silicon Graphics Power CHALLENGE array, an HP/CONVEX Exemplar, an HP/CONVEX C3, and a Thinking Machines CM-5, as well as networks of high-end workstations. These are all interconnected at high speed and available over the network to both remote users and scientific instruments.

Over the last several years, NCSA and the scanning tunneling microscopy component of the Molecular and Electronic Nanostructures group have developed a distributed computing support structure for STMs that allows for real-time remote control and visualization of STM imaging and nanolithography. This system couples in high-end graphics systems as well as collaborative software and has been demonstrated over continental distances. It allows for restructuring silicon surfaces under remote visual control.

Similarly, NCSA has been a long-time partner with the National Center for Computational Electronics (NCCE), directed by Karl Hess. NCSA has provided both computational facilities as well as training in advanced topics through NCCE. What has emerged in the last five years is a move from the traditional semiclassical approximations of electron transport in semiconductors, appropriate to scales above 500 nanometers, to the emergence of pioneering attempts to model the full set of quantum effects appropriate to nanoelectronic scales. This will begin to allow for the design and simulation of novel new electronic effects not possible in the semiclassical regime.

These two approaches could come together in an interdisciplinary approach at the Beckman Institute to molecular and electronic nanostructures. One can easily imagine the next generation of scaleable supercomputers being powerful enough to perform real-time simulations of the atomic interaction of the STM tip with the underlying substrate. If these simulations were fed back into the loop of the nanolithography, one would have an experimental tool of unprecedented power. Similarly, one can foresee quantum electronic devices created first virtually by full quantum simulations, then created with nanolithographic techniques and measured, comparing the physical device with the predicted features of the virtual device. Because of the difficulty of precisely studying the properties of such tiny devices experimentally, the simulations will probably become an essential part of nanoelectronic design. Computational resources are also vital to the design of chemical and biological nanostructure and the prediction of macromolecular and polymer folding and assembly.

Opportunities in Nanostructure Research

Motivation for a "Molecular and Electronic Nanostructures" main research theme (MRT) arises from scientific and pragmatic considerations. From the scientific point of view, the nanostructure research theme is a sound and exciting approach to the broad Beckman Institute goal of research, which covers "physics to function" and "molecules to mind." The research goals of the nanostructure theme are to develop basic understanding of physical and chemical processes in molecular nanostructures, mesoscopic semiconductor structures, and macromolecular assemblies and to explore emergent function, dynamics, and structure in these systems. The molecular and electronic nanostructure project includes biochemists, chemists, physicists, electrical engineers, computer scientists, and material scientists working on topics with obscure disciplinary boundaries. For example, nanostructure dynamics occur on such fast time scales that they belong in the realm of optics but they encompass atomic, molecular, and electronic phenomena of interest to physicists, chemists, and electrical engineers. This blending of disciplines attracts us to nanoscale science and forces us to broaden our perspective. From the engineering side, device functionality is the overriding goal. Engineering nanostructure research begins with the idea of using semiconductor or molecular devices in information science. For example, one might use self-organizing synthesis to create dense or 3-D logic or memory arrays. However, experience shows that function is the least predictable result of research. A unique benefit of broad cross-disciplinary research is the diversity of perspective that will allow disparate groups to identify and develop new functions quickly. An example of novel function arising from cross-disciplinary fertilization might be the use of engineering control and information theoretical concepts in the design of self-organizing structures for biological or organic environmental control or sensing systems.

From a pragmatic point of view, the "Beckman experience" of common facilities for cross-disciplinary research has shown that groups pursuing disparate interests often require similar equipment. Chemistry groups use the same scanning microscopy systems to characterize macromolecular arrays as physics and engineering groups use to build and characterize solid state materials and devices. Electrical engineers working on high speed communications and control use the same laser and data acquisition equipment as chemists studying ultrafast reaction dynamics. Even without direct collaboration, shared resources are economically attractive. Imaging and visualization are common interests among groups in the nanostructures area and in the Biological Intelligence and Human-Computer Interface MRTs. Leading edge facilities that resolve the atomic structure of complex molecules (organic, inorganic, or biological) and of materials with complex composition (natural or artificial superlattices) are necessary to guarantee experimental and theoretical progress in many areas of Beckman Institute research. The expectation that coordinated development and application of leading-edge fabrication, characterization, and analysis facilities will simultaneously enable research in a number of areas is a driving force behind the foundation of the Molecular and Electronic Nanostructures theme. Participating researchers master the most advanced tools of their own discipline of engineering or chemical and physical science and contribute tools and perspective to the institute-wide effort to manipulate and characterize the smallest building blocks of complex matter. Imaging, visualization, and characterization tools developed through this collaboration will also be of service to other groups in the institute and around the world.

Interconnections and collaborations between individual research groups in the nanostructure area are dynamic and ongoing. Group membership also varies with topics as they evolve, research matures, and new horizons and frontiers open. We are currently focused on several opportunities based on the expertise of present researchers and on the current assessment of where progress is most likely and necessary. Participating groups maintain their individual identities but collaborate in the use and development of research tools such as imaging, computational and visualization facilities, and dynamical data acquisition and control systems. All groups overlap in developing scientific perspective and technological function. Opportunities in these areas are detailed in the following subsections.

(i) Fabrication and Characterization of Semiconductor Nanostructures

Advanced patterning of materials is central to research on electronic nanostructures. The Beckman Institute contains several unique resources in this area as the focus of the national DOD University Research Initiative for "STM-Based Nanolithography." This program involves nine faculty members from the Departments of Electrical and Computer Engineering, Physics, and Chemistry in a coordinated effort to develop a quasi-atomic scale lithography based on utilizing the low-energy electron beam from an STM to control surface chemistry on Si, GaAs, and related semiconductors.

The UHV-STM Laboratory headed by Joseph Lyding and John Tucker contains a five-chamber interconnected system designed specifically for atomic-level imaging, pattering, and processing of semiconductor nanostructures. A sixth chamber, currently under construction, will provide liquid-He-temperature spectroscopy and luminescence capabilities for characterizing devices in situ. Further analysis is available in the AFM laboratory maintained as a central facility. The adjacent Microelectronics Research Laboratory houses the primary facilities for several collaborating faculty. High-resolution conventional e-beam lithography and gaseous etching facilities are headed by I. Adesida, MBE of III-V layered materials by K.-Y. Cheng, and photo- and electro-luminescence analysis by Steven Bishop. These faculty and their students routinely participate in parallel experiments within their own laboratories and in the Beckman Institute in order to develop the techniques that will eventually be required to grow, fabricate, and test STM-patterned nanostructures entirely within a single UHV environment. Additional capabilities in Si advanced processing of device structures and air-STM exposure of resists are obtained through collaboration with groups outside Illinois (e.g., University of Minnesota). An effort to utilize molecular self-assembly in the development of new e-beam resists is headed by Paul Bohn, tying the STM-based lithography project to extensive research in molecular recognition and synthesis within the Beckman Institute.

To date, the most significant result achieved in the STM-based nanolithography program is the selective removal of hydrogen atoms from atomically clean H-passivated Si(100)2x1 surfaces in ultra-high vacuum. The highly-localized STM electron beam has been found to reproducibly eliminate H-atoms from the Si dangling bonds, yielding linewidths of ~15A corresponding to only two atomic dimer rows. This opens the door to a wide variety of nanoscale patterning possibilities on Si, including selective oxidation, nitridation, epitaxy, and doping, which are now beginning to be explored. For future industrial applications, an attractive feature of this technique is that it should be possible to deliver the low-energy electrons by a method other than STM, using e-beam microcolumns or mask exposure systems, for example.

Work on GaAs and other compound semiconductors within this program is based on combining STM lithography with in situ gaseous etching, to be performed in side chambers attached to the main UHV system. Recent work done elsewhere has demonstrated that gentle gaseous etching of heated samples can virtually eliminate the surface damage that ordinarily depletes carriers from nanostructures when etching is assisted by plasma ionization. Research in this area is now getting underway by employing more conventional gaseous etching facilities in the microelectronics group in parallel with those on the STM side-chambers in Beckman in order to develop the techniques. A major goal in this direction will be to pattern the 2-dimensional electron gas (2DEG), which forms naturally on the surface of thin InAs epitaxial layers due to Fermi level pinning above the conduction band edge. Since the 2DEG lies on the surface of this material, spectroscopic capabilities of (low-temperature) STM can be used to probe the wavefunctions and energy levels of laterally confined electrons, including aspects of carrier transport on a scale never before realized.

The unique coarse translation capability of the Beckman UHV-STM system is currently used to locate and examine cleaved III-V heterolayers and quantum wells, including state-of-the-art resonant tunneling diodes grown at MIT Lincoln Laboratories and Texas Instruments in addition to structures grown in the microelectronics group. Recent experiments with (-doped heterolayer interfaces appear to have yielded the first direct images of a 2DEG. This ability to readily locate nanoscale device structures within a macroscopic area of several millimeters while preserving atomic resolution is a major resource for the nanolithography effort, since it provides the capability to modify individual devices that have been pre-patterned by conventional e-beam techniques. In the future, we anticipate that there will be great opportunities to combine this unique atomic-scale STM imaging capability with femtosecond laser spectroscopy in order to help elucidate new areas of electron dynamics and surface chemistry in nanostructures.

(ii) Self Organizing Synthesis -- Chemistry and Structural Biology

This effort is parallel to and (see final section) in close collaboration with the solid state nanostructure research and emphasizes the molecular aspects. It seeks to understand the fundamental scientific principles relating to the mechanisms for assembly and function of mesoscale biological structures. Although there have been great advances in the visualization of biological structures at the angstrom scale with X-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy and the direct manipulation at these length scales using recombinant DNA technology, the synthesis, characterization, and structure determination at the mesoscale (10 - 500 mm) is in its infancy. Yet it is at these scales that Nature utilizes macromolecular assemblies for the key processes of life, including nucleic acid synthesis and processing, biopolymer synthesis, energy transduction, and control of cell growth and division. This region is the arena where physics and electrical engineering meet biochemistry. Advances in our ability to visualize and manipulate mesoscale structures will not only provide direct structural input, but also allow utilization of biological macromolecules as the building blocks for composite molecular structures and devices.

Our efforts to date have exploited our combined expertise in rational synthesis of complex molecular architectures, de novo gene synthesis routes to protein engineering, and sophisticated surface chemistry and characterization capabilities to pursue the development of structures and devices that have no counterparts in classical device technology. Characterization of natural and designed mesoscale structures makes use of our combined expertise in surface chemistry, electrochemistry, ultrafast photoinitiated electron transfer measurements, and STM, AFM and NSOM probe methodologies. We believe that the case for the study and manipulation of biological macromolecules at interfaces and rational engineering of quantum and chemical transformation is attainable.

1. Construction of chemical and biological mesoscale devices. Research in our joint laboratories over the past few years has resulted in significant advances in the ability to control the assembly of proteins on surfaces and at interfaces. The critical concept in our approach is that the utilization of oriented metalloprotein arrays will allow device functions to be realized that are simply inaccessible to classical device modalities. This key point is germane, as an organizational principle, to implementations of biological macromolecules in smart sensors, distributed signal processing schemes, nanoscale autonomous power systems, and to interfacing with electrooptic semiconductor materials, i.e., to the whole of the problem of nanoscale hybrid devices.

Nature has provided interesting systems with potential application in molecular devices. Indeed, some systems such as bacteriorhodopsin and the photosynthetic reaction center are being actively investigated in many laboratories. However, the systems that nature has provided gratis are most often not ideally suited for a particular application. They are often not assembled into useful superstructures, they have nonexistent or inefficient abilities to recognize neighbors, they have the wrong optical or electrical (i.e., electron transfer) properties, etc. Hence, genetic engineering is a key technology in our efforts. The coupling of recombinant DNA technology with sophisticated surface chemistries, spectroscopic measurements, and controlling technologies for external manipulation of structure offers an excellent opportunity to construct hybrid biomolecular devices in which real control over the function is designed into the device from the first planning steps. The first step in directing the complete three-dimensional control of assembly is one in which structures are assembled with defined orientation in a planar array. This "tethering" must be specific and selective in the control of protein orientation. Our efforts in this arena have resulted in the merging of genetic engineering, chemical synthetic, and bioanalytical methods to provide a unique attachment site at a predefined location on the macromolecular surface with resultant control of orientation. As an initial step, oriented arrays of metalloproteins have been achieved and characterized using both self-assembly and Langmuir-Blodgett fabrication strategies. This approach is useful for selective immobilization and assembly of other protein-based mesoscale assemblies, such as antibody and catalytic enzyme complexes, which will have a major impact on design of sensing and processing methods in diagnostics and industrial procedures.

To support these research goals it is necessary to develop fundamental understanding of the key molecular aspects of assembly, patterning, and control. Ability to simultaneously engineer the binding specificity and the surface attachment site in metalloproteins and other mesoscale systems and to introduce such engineered proteins into planar arrays that can subsequently be interrogated optically is crucial to this effort. We have already demonstrated that genetic engineering techniques can be used to place a unique amino acid residue (typically a cysteine) at an appropriate point to orient the binding site in the desired direction, and the geometric and electronic properties around the prosthetic group have been engineered to introduce a desired de novo specificity of molecular recognition and electronic property of the prosthetic group. We are developing specific changes in the metalloprotein properties, which can be coupled efficiently to an external electronic or optical interrogation scheme. As an example, we have generated a "molecular wire" of self-assembled protein monomers for the study of the fundamental properties of charge transport and its regulation through quantum interference pathways.

2. Mesoscale imaging, manipulation, and characterization. The Molecular and Electronic Nanostructures theme offers exciting possibilities for completely novel directions in self-organizing synthesis. Self-organizing synthesis refers to an assembly of units in which the units themselves are single molecules, genetically derived biomolecules, or complex molecular clusters in a predesigned pattern with control over molecular placement, orientation, spacing, and interaction, and in which this control is manifested over supermolecular length scales. Thus, these experiments really seek to marry the exciting advances of the last decade in the areas of scanning probe microscopies for both imaging and pattern delineation (nanolithography), genetic engineering for structural/functional control of biological macromolecules, complex synthetic routes to molecules approaching mesoscopic dimensions, and chemical characterization capabilities that have now evolved to examining samples at the level of a single molecule.

Characterization of these mesoscale assemblies employs techniques at the cutting edge of physics, chemistry, and biochemistry. For example, an understanding of the quantum charge transport in biological energy transducing oligomeric systems is being advanced in our group by the development of pulse and modulation methods for measurement of redox transfer events on the time scale of femtoseconds to milliseconds, over temperature scales from a few degrees Kelvin to ambient, and over pressure ranges from atmospheric to 100,000 psi. Only by having the assay capabilities over these extended decades of scale can a molecular understanding evolve. Likewise, only having a direct interface and contact across multidisciplinary boundaries connects the notion of biological electron transfer with the theories and experiments of semiconductor physics, condensed matter physics, and molecular motion and vibronic coupling.

As exciting as each of these advances is in and of itself, the possibilities which are opened by bringing them together with the right mix of highly creative and motivated investigators, state-of-the-art research facilities, and in an environment that actively promotes investigators sharing ideas across traditional disciplinary lines, are unprecedented. The types of fundamental questions that must be answered to address the experimental vehicles described herein are pertinent to the whole of nanoscale manipulation for fabrication of molecular devices:

The research groups of the principal investigators who are brought together, within the context of the Beckman Institute and with strong records of individual accomplishment, are particularly well-suited to tackle these challenges. These include the use of sophisticated modern techniques for the synthesis of mesoscopic molecular entities with exquisite control over structure and function; expertise in the use of scanned probe techniques for the study of interfaces in situ, in particular complex electrochemical interfaces where the properties are determined by the interplay of surface reconstruction; molecular adsorption and solution structuring; and developing and applying novel measurement schemes for the characterization of complex molecular assemblies, in particular composite assemblies in which self-assembled and Langmuir-Blodgett mulitlayers layers are exploited for the external control of molecular transport. This exciting interdisciplinary research initiative in mesoscale synthesis, visualization, manipulation, and characterization is ripe for discovery by a synergistic multi-investigator effort in the Molecular and Electronic Nanostructures Group.

3. Nanolithographic patterns (templates for the controlled assembly of molecular nanostructures). While nanolithographic techniques are well-suited for generating patterns on the submicron size scale, they are unlikely to become the method of choice for the manipulation of matter on the atomic size scale. Chemical synthetic techniques, although capable of generating extremely complex structures on the atomic-molecular level, are ill-suited for manipulating matter on a larger size scale, relying on spontaneous self-assembly as opposed to controlled assembly. A hybrid of the two approaches, however, should be capable of yielding materials whose structures can be controlled on both the atomic-molecular and the submicron size scales.

Nanolithographic patterns are being used as templates for assembling molecular nanostructures in a controlled fashion, thus generating supramolecular arrays whose structures are completely defined on both the atomic-molecular and the submicron size scales. Starting with passivated (protected) surfaces, nanolithography will be employed to generate arrays of points, lines, or polygons having nanoscale dimensions. These patterns, comprised of deprotected substrate surface atoms, will be exposed to large, molecular clusters capable of forming covalent bonds with the deprotected atoms. The dimensions of these clusters will be comparable to the dimensions of the surface patterns such that the patterns will serve as templates for generating ordered assemblies of molecular species. In the simplest case, for example, a square grid pattern could be generated nanolithographically from points whose dimensions allow binding of one and only one molecular cluster at each point. In this fashion, the nanolithographic pattern would serve as a template for the controlled assembly of a square grid of individual molecular clusters. The same approach could, of course, be applied to more complex patterns to generate more complex molecular arrays.

Research is conceptually advancing in three phases. First, passivated surfaces must be developed that can be patterned on the (1-2 nm size scale to generate reactive surface atoms surrounded by passivated substrate. In chemical terms, the lithographic pattern must be comprised of reactive functional groups in a sterically confined environment of protecting groups. Systems of potential interest include exposed Si atoms on a hydrogen-passivated silicon surface, exposed copper atoms on an oxide-passivated copper surface, exposed Au-OH groups on a gold surface protected with organic molecules, or exposed edges of MoS2. Exposure would be accomplished by using an STM or AFM, scanning with high tunneling currents or forces, respectively, over the surface. Exposure (deprotection) or etching using STM or AFM has been shown on each of the systems above. This etching occurs either through electron-stimulated desorption (in the case of the STM) or through local heating of the surface by the augmented tip-surface interaction (in the case of the AFM). The etching can be controlled to at least 1 nm in extent and in many cases down to true atomic dimensions. Patterning might also require more than one step. For example, reactive Au-OH patterns might be created on organic-passivated Au(111) surfaces by first forming patterns of exposed Au atoms and then electrochemically performing a one-electron oxidation of the exposed surface. There continue to be reports of preferential etching via SPM-surface interactions of a variety of passivated materials. Al and GaAs have been the subject of recent papers. In concept, almost any passivated material can be etched and deprotected with high spatial resolution using probe microscopy. The etching and exposure steps in this project both require the ability to operate in liquid environments (see below). The capability of operating in an aqueous environment has been developed at Illinois, and extension to nonaqueous environments using inert atmosphere techniques is anticipated.

The second phase of the program involves selection and synthesis of suitably sized and suitably reactive molecular species designed to react with the appropriate functional groups on previously prepared patterned surfaces. Reactive surface hydroxyl groups, for example, are known to be reactive toward metal alkoxides, and polynuclear alkoxides would therefore be appropriate molecular species in this case. Specifically, titanium oxoalkoxide clusters such as [Ti12O16](OPri)16 and [Ti16O16](OEt)32 display regioselective alkoxide exchange with alcohols and should react in a similar fashion with surface hydroxyls. For exposed metal surface atoms, polynuclear metal-sulfur clusters or large organic phosphines might possess suitable reactivity. For exposed metal sulfide surface atoms, transition metal carbonyl clusters with labile substituents are good candidates.

The final and critical research phase involves devising experimental procedures for assembling the molecular clusters on the patterned surface and examining their structures using SPM-based techniques. In order to avoid problems associated with sample transfer, researchers will perform nanolithography, cluster array assembly, and product analysis in a solution environment. The following sequence of events is envisioned: (a) preparation of a protected surface, for example, by oxidation or self-assembly of organics, (b) immersion into a suitably inert liquid that also serves as a solvent for the molecular clusters to be employed in a subsequent step, (c) deprotection or etching, at which point the exposed area is immediately decorated with the molecular cluster already present in solution, and (d) SPM-analysis using more modest interaction parameters. This protocol could be extended to include a second immersion-deprotection/decoration-analysis sequence involving assembly of a second molecular cluster on the surface, yielding a final product in which two types of molecular clusters are assembled in close proximity to each other. Post-processing, i.e., either thermal, chemical, or photochemical processing of the decorated areas, could follow emersion.

4. Rodcoils and supermolecular assemblies. This research (directed by S. Stupp) focuses on two areas, the self-assembly of organic molecules into nanostructures and the use of supermolecular assemblies as templates to generate nanostructured semiconductors. The self-assembling molecules of interest were synthesized for the first time in a Beckman laboratory and were termed "rodcoils" in the first publications. These molecules are either of oligomeric or polymeric dimensions and contain one molecularly rigid segment covalently bonded to a flexible one in a common molecular backbone. Between 1995 and 1997 this group discovered the self-organization of these structures into superlattices in which aggregates of the rigid parts with dimensions on the order of a few nanometers become dispersed in a specific geometry in a continuum of flexible segments. A hexagonal superlattice has been constructed in which 5 nanometer diameter discs have formed through segregation of the rod-like segments. The nature of the aggregates and of the superlattices is different from those previously known in block copolymers. We believe that this self-organization opens the door to the rational design of nanostructured organic patterns.

In the area of nanostructured semiconductors we are interested in the design and synthesis of amphiphilic block molecules that form ordered assemblies and can bind in selective nanocompartments the precursor ions for inorganic semiconductors. The basic concept is to explore the controlled nucleation and growth of semiconducting solids with nanoscale features produced by the imprint of nonbinding blocks of the amphiphiles. We have discovered one system in which a hexagonal assembly of organic molecules mediates the growth of II-VI semiconducting lattices containing cylindrical holes three nanometers in diameter and arranged periodically in a hexagonal lattice eight nanometers apart.

The synthetic laboratory, the visualization laboratory, the numerical laboratory, and the advanced chemical systems facilities available at the Institute have been critical for the development of this from 1995-7. Addition of electron microscopy to the Institute in the near future will be another important resource.

Future experiments will expand work on self-assembled nanostructures by developing rodcoil molecules in which the aggregates of rigid units will have interesting electronic, and possibly electro-optical, properties. Such structures could generate new sensor technologies or serve as templates to generate nanoscale patterns for electronic devices. There is also the possibility of using our nanostructures as templates to create two-dimensional arrays of special proteins produced in the Sligar group. The development of nanostructures with reasonable electronic conductivities will also allow exploration together with Lyding's group of the potential for further patterning using STM techniques. As the chemical structures are modified we will also develop a parallel computational effort that will use genetic algorithms to make predictions on the stability of molecular aggregates required for the formation of nanostructures

In the area of nanostructured semiconductors formed with supermolecular templates, we will pursue two specific directions. One will be to consider chemical vapor deposition of metals in periodic nanocavities formed in semiconductors and occupied in precursor phases by molecular assemblies. This will allow us to create semiconducting lattices with nanoscale periodic features of various metals. Working in collaboration with Hess and Tucker it may be possible to simulate the band structure of such systems and also to design model devices. The second direction we plan to follow is to explore synthetic methodologies to internalize in semiconducting lattices organic structures with specific functions. For example, we are interested in incorporating within the lattice organic molecules that act easily as electron donors or acceptors and thereby can impact directly on the electronic properties of the semiconductor. The presence of such organic inclusions could mediate the recombination rates of holes and electrons and produce novel semiconducting materials and devices.

5. Structural and dynamic aspects of molecular assemblies. This research (directed by P. Bohn) addresses fundamental aspects of molecular self-organization. In the last decade of this century and beyond, a fundamental thrust in the molecular sciences will be to understand the relationship of structure and function for molecularly engineered architectures. One subset of such structures are nanolayer arrays, in which structural regularity exists over coherence lengths of many hundreds to thousands of molecular diameters in-the-plane, but in which adjacent molecular planes may be completely different. Understanding structure-property relationships in these arrays is a central focus of this research, and Bohn's efforts are centered on exploiting powerful laser spectroscopic techniques coupled with optical phenomena for spatial localization. For example, we are building a near-field scanning optical microscope that will be capable of routinely measuring the spectroscopic properties of isolated single molecules at surfaces (see Existing Resources section).

In a new collaborative venture, Paul Bohn and Jeff Moore are using the unique structural properties of topologically diverse phenylacetylene macrocycles to build assemblies in which long-range ordering opens exciting possibilities for molecular recognition. In these assemblies subtle changes in molecular architecture, e.g., changing the steric bulk of meta-substituents, can produce dramatic changes in packing and, thus, in small-molecule binding properties of the supermolecular array. The full power of different structure elucidation tools in the Beckman Institute (STM, LB isotherm measurements) can be brought to bear on nanolayer arrays and provide the input for rational molecular engineering of structural properties on the supermolecular length scale.

Similar ideas are being pursued jointly with Steve Sligar (see Section ii.1 above) to fabricate, manipulate, and characterize two-dimensional assemblies of genetically engineered heme proteins (e.g., cytochromes b5 and c and myoglobin). The chief objective of this work is to develop techniques for making two-dimensional crystals of these materials and to use the unique selectivity of biological macromolecules to make electro-optically addressable devices for sensing, recognition, and separation.

Another project being carried out in collaboration with Lyding and Bishop seeks to understand how self-assembled monolayers (SAMs) of organic nucleophiles can be used for passivation and for resist function at III-V interfaces and how near-field scanning optical microscopy can be used as a parallel exposure tool for nanolithography of these SAM layers. These efforts are focused on developing the chemical principles pertinent to a massively parallel processing scheme, which has spatial capabilities in the nanometer size regime. Such capabilities are crucial for the eventual realization of nanometer-scale quantum electronic devices.


1 References removed by editor.

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Published: January 1998; WTEC Hyper-Librarian
14 S.G. Sligar