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USA-Austrian and Swiss Nanocars finish first in first Nanocar race

If the current is high enough, the molecule starts to move and can be steered over the racetrack (University of Basel)

Our previous post announced a race around a 100 nm course of six NanoCars, each a unique concept created from only several dozen atoms and powered by electrical pulses. The race was run a few weeks later and two winners declared, due to two different tracks being used. From Swiss news “Swiss team wins shortest car race in the world“:

“Swiss Nano Dragster”, driven by scientists from Basel, has won the first international car race involving molecular machines. The race involved four nano cars zipping round a pure gold racetrack measuring 100 nanometres – or one ten-thousandth of a millimetre.

The two Swiss pilots, Rémy Pawlak and Tobias Meier from the Swiss Nanoscience Institute and the Department of Physics at the University of Basel, had to reach the chequered flag – negotiating two curves en route – within 38 hours.

The winning drivers, who actually shared first place with a US-Austrian team, were not sitting behind a steering wheel but in front of a computer. They used this to propel their single-molecule vehicle with a small electric shock from a scanning tunnelling microscope.

During such a race, a tunnelling current flows between the tip of the microscope and the molecule, with the size of the current depending on the distance between molecule and tip. If the current is high enough, the molecule starts to move and can be steered over the racetrack, a bit like a hovercraft.

[Includes 24-frame video from Basel University]

The race track was maintained at a very low temperature (-268 degrees Celsius) so that the molecules didn’t move without the current.

What’s more, any nudging of the molecule by the microscope tip would have led to disqualification.

Miniature motors

The race, held in Toulouse, France, and organised by the National Centre for Scientific Research (CNRS), was originally going to be held in October 2016, but problems with some cars resulted in a slight delay. In the end, organisers selected four of nine applicants since there were only four racetracks.

The cars measured between one and three nanometres – about 30,000 times smaller than a human hair. The Swiss Nano Dragster is, in technical language, a 4′-(4-Tolyl)-2,2′:6′,2”-terpyridine molecule.

The Swiss and US-Austrian teams outraced rivals from the US and Germany.

The race is not just a bit of fun for scientists. The researchers hope to gain insights into how molecules move.

Christian Joachim, head of research at CNRS, said that if they managed to control molecule movement, “we could create extremely miniature motors that could have all sorts of uses”.

Twenty years ago Dr. Joachim shared the 1997 Foresight Feynman Prize in Nanotechnology for Experimental Work with two researchers then at IBM Research Zurich for work using scanning probe microscopes to manipulate molecules. Eight years later he won the 2005 Foresight Feynman Prize in Nanotechnology for Theory for developing theoretical tools and establishing the principles for design of a wide variety of single molecule functional nanomachines.

Image from 22-second video. Rice and partner University of Graz run fastest single-molecule car in international event (Rice University)

Additional details and perspectives are provided by a Rice University news release written by Mike Williams. “Rice vehicle tops all in Nanocar Race“:

Rice University chemist James Tour [winner of the 2008 Foresight Institute Feynman Prize for Experimental work] and his international team have won the first Nanocar Race. With an asterisk.

The Rice and University of Graz team finished first in the inaugural Nanocar Race in Toulouse, France, April 28, completing a 150-nanometer course — a thousandth of the width of a human hair — in about 1½ hours. (The race was declared over after 30 hours.)

The team led by Tour and Graz physicist Leonhard Grill [winner of the 2011 Foresight Institute Feynman Prize for Experimental work] deployed a two-wheeled, single-molecule vehicle with adamantane tires on its home track in Graz, Austria, achieving an average speed of 95 nanometers per hour. Tour said the speed ranged from more than 300 to less than 1 nanometer per hour, depending upon the location along the course.

The Swiss Nano Dragster team finished next, five hours later. But organizers at the French National Center for Scientific Research declared them a co-winner of first place as they were tops among teams that raced on a gold track.

Because the scanning tunneling microscope track in Toulouse could only accommodate four cars, two of the six competing international teams — Ohio University and Rice-Graz — ran their vehicles on their home tracks (Ohio on gold) and operated them remotely from the Toulouse headquarters.

Five cars were driven across gold surfaces in a vacuum near absolute zero by electrons from the tips of microscopes in Toulouse and Ohio, but the Rice-Graz team got permission to use a silver track at Graz. “Gold was the surface of choice, so we tested it there, but it turns out it’s too fast,” Grill said. “It’s so fast, we can’t even image it.”

The team got permission from organizers in advance of the race to use the slower silver surface, but with an additional handicap. “We had to go 150 nanometers around two pylons instead of 100 nanometers since our car was so much faster,” Tour said.

Tour said the race directors used the Paris-Rouen auto race in 1894, considered by some to be the world’s first auto race, as precedent for their decision April 29. “I am told there will be two first prizes regardless of the time difference and handicap,” he said.

The Rice-Graz car, called the Dipolar Racer, was designed by Tour and former Rice graduate student Victor Garcia-Lopez and raced by the Graz team, which included postdoctoral researcher and pilot Grant Simpson and undergraduate and co-pilot Philipp Petermeier.

The purpose of the competition, according to organizers, was to push the science of how single molecules can be manipulated as they interact with surfaces.

“We chose our fastest wheels and our strongest dipole so that it could be pulled by the electric field more efficiently,” said Tour, whose lab has been designing nanocars since 1998. ‘We gave it two (side-by-side) wheels to minimize interaction with the surface and to lower the molecular weight.

“We built in every possible design parameter that we could to optimize speed,” he said.

While details of the Dipolar Racer remained a closely held secret until race time, Tour and Grill said they will be revealed in a forthcoming paper.

“This is the beginning of our ability to demonstrate nanoscale manipulation with control around obstacles and speed and will pave the way for much faster paces and eventually for carrying cargo and doing bottom-up assembly.

“It’s a great day for nanotechnology,” Tour said. “And a great day for Rice University and the University of Graz.”

Additional coverage:

In Science, by Robert F. Service “Watch the world’s smallest cars race along tracks thinner than a human hair“:

… To propel the molecular machines forward on their silver and gold tracks, researchers use electric jolts provided by the tip of a scanning tunneling microscope. After nearly 8 hours, the Austrian-U.S. entry, Dipolar Racer, has already crossed the finish line. The car, which resembles a molecular Segway without a handle, has completed two runs down its 150-nanometer silver track at an average speed of 35 nanometers per hour. At that pace, it would take hundreds of years to drive the car across a €1 coin. The Nano Dragster, entered by the Swiss team, was the first to complete a shorter, 100-nanometer-long gold race track. But the other four teams have struggled to even cross the starting line …

From National Public Radio, written by Merrit Kennedy “Microscopic Cars Square Off In Big Race” [includes 6:22 video]:

… The Austrian-U.S. team, driving the Dipolar Racer, finished hours before any of its competitors.

However, the two-wheeled car raced on its home track in Austria, on a silver track rather than a gold one. The team controlled it remotely. Rice University, where some of the scientists hail from, say silver was a handicap because it’s a slower surface. Race scientific director Christian Joachim tells The Two-Way that “they were unable to compete on gold because on gold the molecule was not stable enough.”

The next finisher, the Swiss Nano Dragster, was declared a co-winner – because it was the first team to finish on gold. …

From Chemistry World, written by Fernando Gomollón-Bel “World’s first nanocar race a success for science and engagement“:

…Steve Goldup, who works on interlocked molecules and molecular machines at the University of Southampton, UK, but didn’t take part in the race, says that the dipolar racer is a ‘really nice design’. He notes that the team ’optimised it to maximise the dipole (maximises the force created by the electric field of the STM tip) and minimise the molecular weight. It will be interesting to find out – and the experiments to work this out will be interesting in themselves – if the car skids along or if the wheels roll. Either way would achieve the goal as the wheels prevent the aromatic body from sticking to the surface.’ …

It is interesting that a small collection of molecular cars, all driven by electric pulses from an STM tip, differing substantially in design details, show such a wide range of performances. Perhaps this is not only an iconic event in the developing story of molecular machines, but a beginning of a systematic effort to understand function and engineer improved performance?
—James Lewis, PhD

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First International NanoCar Race showcases molecular vehicles

Entrants, not to scale. Top row (left to right): NanoMobile club (France); Nanocar Team: Rice(USA) & Graz (Austria) Universities; Nano-windmill Compagny, Dresden Technical University (Germany). Bottom row (left to right): MANA-NIMS, Nano-Vehicle (Japan); Ohio Bobcat nanowagon team, Ohio University (USA); Swiss-nano Dragster, University of Basel (CH) Credit: Nanocar Race http://www.cemes.fr/Molecule-car-Race?lang=fr./

Twenty years ago Dr. Christian Joachim of CEMES=CNRS (France) shared the 1997 Foresight Feynman Prize in Nanotechnology for Experimental Work with two researchers then at IBM Research Zurich for work using scanning probe microscopes to manipulate molecules. Eight years later he won 2005 Foresight Feynman Prize in Nanotechnology for Theory for developing theoretical tools and establishing the principles for design of a wide variety of single molecule functional nanomachines. For the past few years he has been organizing the first ever international nanocar race which will provide an arena to test half a dozen very different designs for vehicles comprising only several dozen atoms each to race along a 100-nm course powered by electrical pulses from an STM tip. The races will be held April 28-29 in Toulouse, France. From a CNRS March 13 news release “The world’s first international race for molecule-cars, the Nanocar Race is on“:

Nanocars will compete for the first time ever during an international molecule-car race on April 28-29, 2017 in Toulouse (south-western France). The vehicles, which consist of a few hundred atoms, will be powered by minute electrical pulses during the 36 hours of the race, in which they must navigate a racecourse made of gold atoms, and measuring a maximum of a 100 nanometers in length. They will square off beneath the four tips of a unique microscope located at the CNRS’s Centre d’élaboration de matériaux et d’études structurales (CEMES) in Toulouse. The race, which was organized by the CNRS, is first and foremost a scientific and technological challenge, and will be broadcast live on the YouTube Nanocar Race channel. Beyond the competition, the overarching objective is to advance research in the observation and control of molecule-machines.

More than just a competition, the Nanocar Race is an international scientific experiment that will be conducted in real time, with the aim of testing the performance of molecule-machines and the scientific instruments used to control them. The years ahead will probably see the use of such molecular machinery—activated individually or in synchronized fashion—in the manufacture of common machines: atom-by-atom construction of electronic circuits, atom-by-atom deconstruction of industrial waste, capture of energy…The Nanocar Race is therefore a unique opportunity for researchers to implement cutting-edge techniques for the simultaneous observation and independent maneuvering of such nano-machines.

The experiment began in 2013 as part of an overview of nano-machine research for a scientific journal, when the idea for a car race took shape in the minds of CNRS senior researcher Christian Joachim (now the director of the race) and Gwénaël Rapenne, a Professor of chemistry at Université Toulouse III – Paul Sabatier. Three years later, the nanocars are operational and ready to face off on the circuit’s gold surface. There were numerous challenges in organizing this race, from selecting the racecourse, which must accommodate all types of molecule-cars, to adapting the scanning tunneling microscope. The participating teams also had to overcome a series of difficult tasks (depositing and visualizing the molecules beneath the microscope), as well as meet numerous criteria (the molecules’ structure and form of propulsion) in order to participate in this race. Of the nine teams that applied before the end of May 2016, six were selected, and four will take their place at the 4-tip microscope’s starting line on April 28, 2017 for the 36-hour race in Toulouse.

The challenges facing researchers in the race will be so many steps forward in novel fields in chemistry and physics. In the process, each team will build up new skills, data, and know-how that will one day contribute to the development of surface chemistry (which enables chemical synthesis directly on a particular surface), or in the new science of surfaces known as membrane science, which makes it possible to deposit a molecule-machine on the surface of a cell, or to control the movement of a single molecule in a liquid.

The CEMES-CNRS microscope is the only one in the world allowing four different experimenters to work on the same surface. The development of such multi-tip microscopes will enable synchronizing a great number of molecule-machines in order to increase capacity, for instance for storing energy or capturing it from a hot metallic surface. A genuine “atom technology” is dawning.

The rules of the race:

  • The racecourse: 20 nm + one 45° turn + 30 nm + one 45° turn + 20 nm, for a total of 100 nm
  • 36 h maximum duration
  • Authorization to change one’s nanocar in case of an accident
  • Pushing one’s nanocar is forbidden
  • One sector of the gold surface per team
  • Maximum 6 hours to clean one’s portion of the course before starting
  • No tip changes allowed during the 36 hours

3D print4ed models of all six entrants to scale. Credit: Nanocar Race http://www.cemes.fr/Molecule-car-Race?lang=fr./

For more information, including where to watch the race on April 28, 2017 in Livestream or on YouTube or Facebook: http://nanocar-race.cnrs.fr/indexEnglish.php

Additional details about the gold nano-track, the placement of gold adatoms about which the nanocars must manuever, allowed methods of propulsion, and the six teams that have entered the competition can be found here.

The six teams and their vehices:

Casual inspection of the images of the six vehicles entered in this competition reveals that they differ substantially in size, shape, and design. It will be interesting to see
how these various designs perform under uniform conditions, and if general principles emerge to guide the design of various molecular machines.
—James Lewis, PhD

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Entrants, not to scale. Top row (left to right): NanoMobile club (France); Nanocar Team: Rice(USA) & Graz (Austria) Universities; Nano-windmill Compagny, Dresden Technical University (Germany). Bottom row (left to right): MANA-NIMS, Nano-Vehicle (Japan); Ohio Bobcat nanowagon team, Ohio University (USA); Swiss-nano Dragster, University of Basel (CH) Credit: Nanocar Race http://www.cemes.fr/Molecule-car-Race?lang=fr./

Twenty years ago Dr. Christian Joachim of CEMES=CNRS (France) shared the 1997 Foresight Feynman Prize in Nanotechnology for Experimental Work with two researchers then at IBM Research Zurich for work using scanning probe microscopes to manipulate molecules. Eight years later he won 2005 Foresight Feynman Prize in Nanotechnology for Theory for developing theoretical tools and establishing the principles for design of a wide variety of single molecule functional nanomachines. For the past few years he has been organizing the first ever international nanocar race which will provide an arena to test half a dozen very different designs for vehicles comprising only several dozen atoms each to race along a 100-nm course powered by electrical pulses from an STM tip. The races will be held April 28-29 in Toulouse, France. From a CNRS March 13 news release “The world’s first international race for molecule-cars, the Nanocar Race is on“:

Nanocars will compete for the first time ever during an international molecule-car race on April 28-29, 2017 in Toulouse (south-western France). The vehicles, which consist of a few hundred atoms, will be powered by minute electrical pulses during the 36 hours of the race, in which they must navigate a racecourse made of gold atoms, and measuring a maximum of a 100 nanometers in length. They will square off beneath the four tips of a unique microscope located at the CNRS’s Centre d’élaboration de matériaux et d’études structurales (CEMES) in Toulouse. The race, which was organized by the CNRS, is first and foremost a scientific and technological challenge, and will be broadcast live on the YouTube Nanocar Race channel. Beyond the competition, the overarching objective is to advance research in the observation and control of molecule-machines.

More than just a competition, the Nanocar Race is an international scientific experiment that will be conducted in real time, with the aim of testing the performance of molecule-machines and the scientific instruments used to control them. The years ahead will probably see the use of such molecular machinery—activated individually or in synchronized fashion—in the manufacture of common machines: atom-by-atom construction of electronic circuits, atom-by-atom deconstruction of industrial waste, capture of energy…The Nanocar Race is therefore a unique opportunity for researchers to implement cutting-edge techniques for the simultaneous observation and independent maneuvering of such nano-machines.

The experiment began in 2013 as part of an overview of nano-machine research for a scientific journal, when the idea for a car race took shape in the minds of CNRS senior researcher Christian Joachim (now the director of the race) and Gwénaël Rapenne, a Professor of chemistry at Université Toulouse III – Paul Sabatier. Three years later, the nanocars are operational and ready to face off on the circuit’s gold surface. There were numerous challenges in organizing this race, from selecting the racecourse, which must accommodate all types of molecule-cars, to adapting the scanning tunneling microscope. The participating teams also had to overcome a series of difficult tasks (depositing and visualizing the molecules beneath the microscope), as well as meet numerous criteria (the molecules’ structure and form of propulsion) in order to participate in this race. Of the nine teams that applied before the end of May 2016, six were selected, and four will take their place at the 4-tip microscope’s starting line on April 28, 2017 for the 36-hour race in Toulouse.

The challenges facing researchers in the race will be so many steps forward in novel fields in chemistry and physics. In the process, each team will build up new skills, data, and know-how that will one day contribute to the development of surface chemistry (which enables chemical synthesis directly on a particular surface), or in the new science of surfaces known as membrane science, which makes it possible to deposit a molecule-machine on the surface of a cell, or to control the movement of a single molecule in a liquid.

The CEMES-CNRS microscope is the only one in the world allowing four different experimenters to work on the same surface. The development of such multi-tip microscopes will enable synchronizing a great number of molecule-machines in order to increase capacity, for instance for storing energy or capturing it from a hot metallic surface. A genuine “atom technology” is dawning.

The rules of the race:

  • The racecourse: 20 nm + one 45° turn + 30 nm + one 45° turn + 20 nm, for a total of 100 nm
  • 36 h maximum duration
  • Authorization to change one’s nanocar in case of an accident
  • Pushing one’s nanocar is forbidden
  • One sector of the gold surface per team
  • Maximum 6 hours to clean one’s portion of the course before starting
  • No tip changes allowed during the 36 hours

3D print4ed models of all six entrants to scale. Credit: Nanocar Race http://www.cemes.fr/Molecule-car-Race?lang=fr./

For more information, including where to watch the race on April 28, 2017 in Livestream or on YouTube or Facebook: http://nanocar-race.cnrs.fr/indexEnglish.php

Additional details about the gold nano-track, the placement of gold adatoms about which the nanocars must manuever, allowed methods of propulsion, and the six teams that have entered the competition can be found here.

The six teams and their vehices:

Casual inspection of the images of the six vehicles entered in this competition reveals that they differ substantially in size, shape, and design. It will be interesting to see
how these various designs perform under uniform conditions, and if general principles emerge to guide the design of various molecular machines.
—James Lewis, PhD

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Precisely removing individual atoms with microscope creates novel molecule

Left: Schematic of triangulene, with six fused benzene rings comprising 22 carbon atoms and 12 hydrogen atoms. Two hydrogen atoms have been removed from dihydrotriangulene (22 carbon atoms and 14 hydrogen atoms) leaving two unpaired electrons, designated by black dots. Scale bar: 5 Â = 0.5 nm. Right: AFM image of triangulene on Cu(111) surface. Credit: Pavliček et al. Nature Nanotechnology.

The application of scanning probe microscopy to building individual molecules on a surface took another step forward with the fabrication of a fragment of graphene that was too reactive to be synthesized using conventional chemistry. Over at Quartz Akshat Rathi describes how “IBM researchers have created an ‘impossible’ molecule that could power quantum computers“. Additional details from an IBM Research press release “IBM & Warwick Image Highly Reactive Triangular Molecule for the First Time“:

Published today in Nature Nanotechnology, IBM scientists are truly making the invisible visible.

A few weeks ago IBM released its annual five predictions for the next five years based on this theme. IBM scientists in Zurich are making a good argument to add a sixth prediction with their latest scientific achievement – imaging some of the tiniest objects known to science.

While not household names, molecules including pentacene, olympicene, hexabenzocoronene and cephalandole A are all microscopic molecules which are traditionally represented using 2D structural stick models – think back to your high school chemistry class.

But thanks to a microscopy technique published by the IBM scientists in 2009, physicists, biologists and chemists around the world can now image these molecules with remarkable clarity and precision, in some cases for the first time, decades after they were first theorized allowing them to study and manipulate with incredible precision.

David Fox, University of Warwick, explains “For chemists it is amazing to be able to see individual molecules in such high resolution, especially unusual or highly reactive ones. It is the best way to confirm their structure.”

In addition to imaging, the IBM team, which includes two European Research Council (ERC) grant winners, Leo Gross and Gerhard Meyer [who are also two of the three-member IBM Research-Zurich team who won the 2012 Foresight Institute Feynman Prize for Nanotechnology for Experiment], is also able to manipulate molecules to cause chemical reactions so molecules can be synthesized from adsorbed precursor molecules.

For example, nearly one year ago in collaboration with CiQUS at the University of Santiago de Compostela, the scientists triggered and observed a fascinating molecular rearrangement reaction known as a Bergman cyclisation and the year before that they studied and visualized arynes, a family of highly-reactive short-lived molecules which was first suggested 115 years ago — proving that they do in fact exist. And now, they are doing it again.

Appearing today in Nature Nanotechnology [abstract], IBM scientists in collaboration with chemists at the University of Warwick have synthesized and characterized a tricky molecule called triangulene, also known as Clar’s hydrocarbon, which was first hypothesized in 1953.

Anish Mistry, University of Warwick continues, “Chemists have always thought that triangulene would be too unstable to isolate. Building on our previous olympicene collaboration, we have added an extra ring to the molecule, and an extra level of complexity to the science, but have managed to make a previously impossible molecule with potentially really interesting properties.”

First author on the paper, IBM researcher, Niko Pavliček comments, “In this work, we used our atomic manipulation technique from the aryne and Bergman papers to generate triangulene, which had never been synthesized before. It’s a challenging molecule because it’s highly reactive, but it’s also particularly interesting because of its magnetic properties.”

As they have demonstrated in previous papers, IBM scientists use a unique combined scanning tunneling microscope (STM) and atomic force microscope (AFM), both invented by former IBM scientists in the 1980s and recognized with the Nobel and Kavli Prizes, respectively.

In their latest research the sharp tip of the combined STM/AFM was used to remove two hydrogen atoms from the precursor molecule. The STM takes its measurement by quantum mechanical tunneling of electrons between a tip brought very close to a sample surface and applying a voltage between them. At appropriately high voltage, the ‘tunneling electrons’ can induce the removal of the specific bonds within the precursor molecule. The product molecule can then be characterized by its molecular orbitals when imaging at milder voltages.

These measurements, combined with density functional theory calculations, confirmed that triangulene keeps it free molecules’ properties on the surface.

The team also used the AFM, with a tip terminated with a single carbon monoxide molecule, to resolve or image the planar molecule with its six fused benzene rings, which appear in a symmetric triangle, for the first time. The results produced some pleasant surprises.

Gross explains, “Radicals feature unpaired electrons, and we previously were investigating sigma-radicals. In these, the unpaired electrons are assigned to certain atoms and we found that these always formed bonds with copper. But we were surprised that no bond formed for triangulene on copper. We think that is because triangulene is a pi-radical, which means it’s unpaired electrons are delocalized.”

It is exactly these unpaired electrons, which make the molecule interesting. In classical physics, a charged particle moving in space possesses angular momentum and produces a magnetic field around it. In quantum mechanics, every particle – moving in space or not – possesses an additional intrinsic angular momentum, which is called their ‘spin’. In most conventional hydrocarbons, electrons are always paired and the effect of their spins cancels. But in molecules like triangulene, the spin of the unpaired electrons leads to magnetism on the molecular scale.

The authors believe that beyond just the science there are also several interesting applications for this work.

Pavliček explains, “Triangulene-like segments incorporated into graphene nanoribbons have been suggested as an elegant way to design organic spintronic devices.”

Graphene nanoribbons are being researched for applications in nanocomposites materials, which are very strong and light. The field of spintronics is being studied by groups around the world, including at IBM, for information storage and processing.

Pavliček continues, “We could also demonstrate that its magnetism survives on xenon or sodium chloride surfaces. However, we cannot get a detailed picture of its magnetic state and possible excitations with our microscope (which lacks a magnetic field), so there is plenty to explore and discover for other groups.” …

This work is another impressive step forward by Leo Gross, Gerhard Meyer, and their IBM team members over the past dozen years imaging and manipulating individual chemical bonds using scanning probe microscopy, specifically an ultrastable combination STM/AFM with an ultrasharp tip terminating in a single carbon monoxide molecule. Previous milestones include:

Despite containing 22 carbon atoms and 12 hydrogen atoms arranged as six fused benzene rings, it is not possible to draw the familiar benzene resonant structures for the whole molecule without generating two unpaired valence electrons. The flat, triangular triangulene molecule is thus a diradical and very unstable and cannot be synthesized by conventional chemical methods. Several different isomers of dihydrotriangulene (22 carbon atoms and 14 hydrogen atoms) can be chemically synthesized, but these contain two or more tetrahedrally bonded methylene bridge carbon atoms instead of all flat aromatic carbon atoms. Dihydrotriangulene can be synthesized in a number of isomers—different molecules with the same number of each kind of atom, but joined together differently to form different structures.

The chemically synthesized dihydrotriangulene, consisting of mixtures of several structural isomers of dihydrotriangulene, was deposited in ultrahigh vacuum at 5 K on surface of either Cu(111), NaCl(100), or Xe(111). Imaging by STM and AFM revealed the presence of four isomers of dihydrotriangulene on the surface. The observed relative abundance of different isomers was consistent with energies calculated using density functional theory. By precise positioning of the tip over promising isomers, combined with careful control of current and voltage, followed by imaging, they were able to demonstrate the removal of single hydrogen atoms from methylene bridge CH2 groups. The voltage pulse was applied twice to individual dihydrotriangulene isomers to generate triangulene. Because the D3h symmetry of triangulene does not match the square lattice of (100)-oriented NaCl surfaces, the mismatch leads to frequent rotation between four equivalent adsorption geometries, the authors explain, so they chose further characterization of triangulene on Cu(111) and Xe(111) surfaces.

AFM results demonstrate stable adsorption of triangulene on Cu, with no indication of chemical bonding to the supporting Cu surface. This result contrasts with their previous observations of strong bonding to the Cu(111) surface of diradicals formed from arynes or Bergman cyclization products (above). They rationalize this discrepancy as due to the arynes and Bergman cyclization diradicals being σ radicals while the triangulene diradicals are π radicals. A comparison of STM and scanning tunneling spectroscopy results with density functional theory calculations indicate the properties expected of a triangulene diradical with two unpaired electrons having aligned spins.

A commentary in Nature by Philip Ball cites Philip Moriarty of the University of Nottingham, UK, describing the creation of triangulene as a new type of chemical synthesis in which atoms on individual molecules were physically manipulated using a microscope. In addition to the possible applications mentioned in spintronics and quantum computing, it will be interesting to see how far these recent discoveries can be extended building increasingly complex molecules, molecular machines, and molecular machine systems by assembling radicals on a surface. Perhaps a step on the path to general purpose, high throughput atomically precise manufacturing?
—James Lewis, PhD

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From de novo protein design to molecular machine systems

All the proteins in this image were designed with atomic accuracy, validated by X-ray crystal structures or NMR. Credit: Baker Lab, University of Washington

Regular readers will have noticed that the de novo design of proteins not found in nature has become an increasingly active area of nanotechnology research the past several years, including eight advances this past year that we have cited (here, here, here, here, here, here, here, here). To put this rapid acceleration of progress in perspective, David Baker’s group, source of 7 of the above 8 advances, recently published (Sept, 2016) a review “The coming of age of de novo protein design“:

Most protein design efforts to date have focused on reengineering existing proteins found in nature. By contrast, de novo protein design generates new structures from scratch, with sequences unrelated to naturally occurring proteins. Before 2011, the only successful de novo designed proteins were Top7 (2003), and an array of coiled coil peptides (helical bundles). In the past five years, the field of de novo protein design has exploded. The wealth of new structures, and advancements in methodology, should now now allow proteins to be precisely crafted and custom-made to solve specific modern-day problems.

The review is published in Nature (journal abstract) and the full text PDF is available courtesy of the Baker lab. The journal abstract:

There are 20200 possible amino-acid sequences for a 200-residue protein, of which the natural evolutionary process has sampled only an infinitesimal subset. De novo protein design explores the full sequence space, guided by the physical principles that underlie protein folding. Computational methodology has advanced to the point that a wide range of structures can be designed from scratch with atomic-level accuracy. Almost all protein engineering so far has involved the modification of naturally occurring proteins; it should now be possible to design new functional proteins from the ground up to tackle current challenges in biomedicine and nanotechnology.

The authors cite the diverse functions that natural proteins have evolved to execute through several hundred million years of random variation and selective pressure working on primordial proteins: using solar energy to manufacture complex molecules, ultrasensitive detection of small molecules and light, the conversion of pH gradients into chemical bonds, and transforming chemical energy into work. They estimate the total number of distinct proteins produced by extant organisms as 1012, an extremely tiny fraction of the 20200 (equals approximately 1.6 x 10260) distinct sequences possible for a 200-residue protein, indicating that evolution has explored only a tiny region of the sequence space available to proteins. Because evolution proceeds by incremental variation and selection, natural proteins are not spread uniformly across sequence space. Thus the vast spaces not sampled by evolution comprise the arena for de novo protein design based on the principles of protein biophysics, specifically that proteins fold into the lowest energy states accessible to their amino acid sequences.

The review describes the physical basis of the energy function used for design calculations, and the approaches used to overcome the problem of sampling an immense sequence space. This review is based on the authors’ experience with the Rosetta structure prediction and design methodology that they have developed; other de novo protein design software described elsewhere is cited. The authors attribute recent progress not only to advances in understanding and computer methods, but also to a steady increase in computing power, and a dramatic improvement in DNA synthesis methods, greatly lowering the cost of the synthetic genes needed to express designed proteins in bacteria. With respect to lower prices for synthetic DNA, it is interesting to note that a technical advance that accelerates one path to advanced nanotechnology (DNA nanotechnology) can also independently advance a different path (de novo protein design).

The physical principles that underlie protein design are described.

  • The force driving protein folding is the burial of hydrophobic residues in the protein’s core, away from solvent, with side chains packed as closely as possible without unfavorable atomic overlaps.
  • Polar groups that become buried upon folding must form intra-protein hydrogen bonds.
  • Steric and torsional effects favor certain backbone geometries and disfavor others.

The authors first consider the ab initio structure prediction problem: finding the lowest energy structure for a fixed amino acid sequence in the absence of information about the structures of evolutionarily related proteins. Because the size of the backbone conformational space is huge, predicting structure without information on related proteins is only possible for the smallest proteins. In general, successful structure prediction requires a number of distance constraints from a set of proteins that have co-evolved.

Because only a finite number of backbones can be sampled computationally, sequence-independent constraints on backbone geometry must be used. For example, polar atoms of the backbone with make hydrogen bonds within the chain in α-helices or β-sheets, or contact the solvent in exposed loops. Much de novo protein design work emphasizes designing ideal proptein structures with unkinked α-helices and β-strands. By contrast, most natural proteins contain irregular features, which reduce the free energy of folding, that arise either from selection for function or from neutral drift. The authors note that a free energy of folding of 8 kcal per mole would suffice to insure a folded population of more than 99.999%, so that evolution would have been under little pressure to optimize folding beyond that.

The procedure is described that was used to design a wide range of ideal αβ protein structures, including Top7, the first (2003) globular protein to be designed with a fold not observed in nature. Modifications and additions to the procedure are described, including designing proteins with internal symmetry in which a single idealized unit is repeated numerous times. such as toroids and barrels. The sequences that have been designed, expressed, and characterized are often exceptionally stable and differ greatly from those found in nature, suggesting that naturally occurring proteins sample only a tiny fraction of stable protein structures that can be realized. Some of the examples given in this review are among the eight advances cited at the top of this post.

The authors cite some of the many accomplishments that have resulted from computational protein-design efforts that have engineered new functions on scaffolds derived from natural proteins, and propose that the capabilities of next generation designed functional proteins could greatly exceed those of first-generation designed proteins based on native scaffolds. They further point to opportunities presented by incorporating new chemistries and unnatural amino acids {in the near future we will cover their work that they cite here on hyperstable constrained peptides}.

Addressing the limitations of protein design as currently practiced, they acknowledge that only a faction of protein designs adopt stable folded structures when produced in the bacterium E. coli. Failure is often due to lack of solubility and formation of unintended oligomers, both probably arising from unanticipated intermolecular hydrophobic interactions. The authors expect that it should become increasingly possible to identify the factors that differ between soluble and insoluble designs. They further note that their highest success rates have been with peptides that were synthesized chemically, so that part of the reason for failures might lie with toxicity of certain designs expressed in E. coli, or with complexities of the bacterium’s biology. Also, high successes with α-helical repeat designs indicates sequence repetition is probably favored over alternative structures.

The review finishes with a consideration of challenges and opportunities of ongoing work in de novo protein design. First, they note a fundamental problem encountered when redesigning natural proteins for new functions, such as new catalytic activities, altering many residues to introduce a new function can inadvertently alter the structure, such as by introducing unanticipated loops. Since native proteins are often only marginally stable, changes can lead to unfolding or aggregation. In contrast, the very high stability of de novo designed proteins should render them more suitable as starting points for creating new functions.

Although de novo designed proteins begin with ideal structures, the introduction of functional sites and binding interfaces will “inevitably compromise this ideality” and thus render the structure less stable. Binding surfaces usually contain hydrophobic residues, and are thus more prone to aggregation, and the active sites of enzymes have some mobility to allow substrates to enter and products to leave. To address these challenges, the authors first suggest designing recessed cavities into proteins to enable ligand and substrate binding. They have already addressed this challenge in a paper they have just published, which we will feature in an upcoming post. Finally, the authors note that sophisticated functions like allostery and signalling found in natural proteins …

… emerge in protein systems with multiple low-energy states and moving parts that can be toggled by external stimuli. To achieve such capabilities, which could have widespread applications in the design of molecular machines to tackle problems ranging from tumour recognition to computing, will require proteins to be designed with multiple, distinct energy minima.

The review cites a study published two years ago that demonstrates the capability to design a functional protein with two alternative states.

Overcoming these challenges in the years ahead is an exciting prospect. Success would signal a technological advance that is analogous to the transition from the Stone Age to the Iron Age. Instead of building new proteins from those that already exist in nature, protein designers can now strive to precisely craft new molecules to solve specific problems — just as modern technology does outside of the realm of biology.

By providing an overview of progress along a major path to atomically precise nanotechnology, and a clear view of near-term challenges and how they might be met, this review contributes significantly to a roadmap from current molecular science to a future technology of productive nanosystems and general purpose, high throughput atomically precise manufacturing.
—James Lewis, PhD

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Two-component, 120-subunit icosahedral cage extends protein nanotechnology

Ten designs spanning three distinct icosahedral architectures. Credit: Baker laboratory, Institute for Protein Design, University of Washington

Baker Lab researchers have extended their work that we cited last summer
assembling a large, stable, icosahedral protein molecular cage to a multi-component icosahedral protein complex. From a University of Washington Institute for Protein Design news release “Designed Protein Containers Push Bioengineering Boundaries“:

…Baker lab scientists and collaborators have taken this work to an exciting new level by engineering 120-subunit icosahedral nanocages that self-assemble from not one, but two distinct protein components. The new designed proteins are described in the latest issue of Science in a paper entitled “Accurate design of megadalton-scale multi-component icosahedral protein complexes” [abstract, full text PDF courtesy of Baker Lab].

In this paper, former Baker lab graduate student Jacob Bale, Ph.D. and collaborators describe the computational design and experimental characterization of ten two-component protein complexes that self-assemble into nanocages with atomic-level accuracy. These nanocages are the largest designed proteins to date with molecular weights of 1.8-2.8 megadaltons and diameters comparable to small viral capsids. The structures have been confirmed by X-ray crystallography (see figure). The advantage of a multi-component protein complex is the ability to control assembly by mixing individually prepared subunits. The authors show that in vitro mixing of the designed subunits occurs rapidly and enables controlled packaging of negatively charged GFP by introducing positive charges on the interior surfaces of the two components.

The ability to design, with atomic-level precision, these large protein nanostructures that can encapsulate biologically relevant cargo and that can be genetically modified with various functionalities opens up exciting new opportunities for targeted drug delivery and vaccine design. …

The above news release also links to a feature article, written by Robert F. Service, and video in ScienceThis protein designer aims to revolutionize medicines and materials” that provides an excellent overview and perspective on the work of David Baker, co-winner of the 2004 Feynman Prize, Theory category.

Citing their previous successes designing 24-subunit two-component tetrahedra, and noting the need for larger assemblies to package substantial amounts of cargo. Icosahedral symmetries generally enclose the maximum volumes, and the twofold, threefold, and fivefold rotational axes present within icosahedral symmetry provide three possible ways to construct complexes from pairwise combinations of oligomeric building blocks, designated I53, I52, and I32 architectural types. These three architectures are respectively formed from 12 pentameric and 20 trimeric building blocks, from 12 pentamers and 30 dimers, and from 20 trimers and 30 dimers.

From among several hundred thousand possible pairings of pentamers, trimers, and dimers, filtering based on a variety of metrics selected for experimental characterization 71 designs of type I53, 44 of I52, and 68 of type I32. These were derived from 23 pentameric, 57 trimeric, and 91 dimeric protein scaffolds. Experimental results are reported for two-component, 120-subunit icosahedral protein nanostructures of 1.8 to 2.8 megadalton molecular weight and 24 to 40 nm diameter. Ten designs spanning all three architectures form materials closely matching the design models.

The resolution obtained with x-ray crystal structures (0.35 to 0.56 nm) was not sufficient to determine side chain structures at the interfaces, the experimental structures matched the design structures with high accuracy at the level of polypeptide backbone structure. With more than 130,000 heavy atoms (all atoms except hydrogen) each, these are, to the best of the authors’ knowledge, the largest designed biomolecular nanostructures to date (July 2016) to be verified by x-ray crystallography.

The authors note that he designs presented here obey strict icosahedral symmetry, with the asymmetric unit in each case containing a heterodimer comprising one subunit from each of the two components. The authors are not aware of any natural protein complexes characterized to date that exhibit I52 or I32 architectures. “Our designs thus appear to occupy new regions of the protein assembly universe, which either have not yet been explored by natural evolution or are undiscovered at present in natural systems.”

The results presented here justify the authors’ conclusion in their abstract: “The ability to design megadalton-scale materials with atomic-level accuracy and controllable assembly opens the door to a new generation of genetically programmable protein-based molecular machines.” They suggest applications in areas like targeted drug delivery, vaccine design, and bioenergy. From the standpoint of productive nanosystems and atomically precise manufacturing, it will be interesting to see if such molecular machines can be adapted to the design of more complex and capable molecular machines, thus starting a virtuous cycle of tools producing better tools.
—James Lewis, PhD

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Cleanly placing atomically precise graphene nanoribbons

Researchers have made the first important step toward integrating atomically precise graphene nanoribbons (APGNRs) onto nonmetallic substrates. Credit: Radocea et al.

We have been following progress toward using graphene nanoribbons in nanotechnology for nearly a decade, most recently citing “Atomically precise boron doping of graphene nanoribbons“. Just published results from Joseph W. Lyding, winner of the 2014 Foresight Institute Feynman Prize, Experimental category, and his collaborators have demonstrated a major step toward integrating atomically precise graphene nanoribbons onto a semiconductor surface. A hat tip to first author Adrian Radocea for sending word of their accomplishment described in this Beckman Institute news release written by Maeve Reilly “Creating Atomic Scale Nanoribbons“:

Silicon crystals are the semiconductors most commonly used to make transistors, which are critical electronic components used to carry out logic operations in computing. However, as faster and more powerful processors are created, silicon has reached a performance limit: the faster it conducts electricity, the hotter it gets, leading to overheating.

Graphene, made of a single-atom-thick sheet of carbon, stays much cooler and can conduct much faster, but it must be [fabricated] into smaller pieces, called nanoribbons, in order to act as a semiconductor. Despite much progress in the fabrication and characterization of nanoribbons, cleanly transferring them onto surfaces used for chip manufacturing has been a significant challenge.

A recent study conducted by researchers at the Beckman Institute for Advanced Science and Technology [at the University of Illinois at Urbana-Champaign] and the Department of Chemistry at the University of Nebraska-Lincoln has demonstrated the first important step toward integrating atomically precise graphene nanoribbons (APGNRs) onto nonmetallic substrates. The paper, “Solution-Synthesized Chevron Graphene Nanoribbons Exfoliated onto H:Si(100),” was published in Nano Letters [abstract].

Graphene nanoribbons measure only several nanometers across, beyond the limits of conventional chip top-down patterning used in chip manufacturing. As a result, when carved from larger pieces of graphene by various nanofabrication approaches, graphene nanoribbons are neither uniform nor narrow enough to exhibit the desired semiconductor properties.

“When you’re going from the top-down, it’s very hard to get control over the width. It turns out that if the width modulates by just an atom or two, the properties change significantly,” said Adrian Radocea, a doctoral student in the Nanoelectronics and Nanomaterials Group.

As a result, the nanoribbons must be made from “the bottom up,” from smaller molecules to create atomically precise nanoribbons with highly uniform electronic properties.

“It’s like molecular building blocks: kind of like snapping Legos together to building something,” said Radocea. “They lock in place, and you end up with the exact control over the ribbon width.”

The “bottom-up” approach was first shown for graphene nanoribbons by Cai et al. in a 2010 Nature paper demonstrating the growth of atomically precise graphene nanoribbons on metallic substrates. In 2014, the research group of Alexander Sinitskii at the University of Nebraska-Lincoln developed an alternative approach for making atomically precise graphene nanoribbons in solution.

“The previously demonstrated synthesis on metallic substrates yields graphene nanoribbons of very high quality, but their number is rather small, as the growth it limited to the precious metal’s surface,” said Sinitskii, associate professor of chemistry at University of Nebraska-Lincoln and an author of the study. “It is difficult to scale this synthesis up. In contrast, when nanoribbons are synthesized in the unrestricted three-dimensional solution environment, they can be produced in large quantities.”

The difficulty in cleanly transferring nanoribbons stems from the high sensitivity to environmental contaminants. Both solution-synthesized and surface-grown nanoribbons are exposed to chemicals during the transfer process that can affect the performance of graphene nanoribbon devices. To overcome this challenge, the interdisciplinary team used a dry transfer in an ultra-high vacuum environment.

A fiberglass applicator coated in graphene nanoribbon powder was heated to remove contaminants and solvent residue and then pressed onto a freshly prepared hydrogen-passivated silicon surface. The nanoribbons were studied in great detail with ultra-high vacuum scanning tunneling microscope developed by Joseph Lyding, professor of electrical and computer engineering and an author of the study. The researchers obtained atomic-scale images and electronic measurements of the graphene nanoribbons that were critical for confirming their electronic properties and understanding the influence of the substrate.

Computational expertise available at Beckman, Radocea explained, was instrumental in understanding the experimental results. “I was still collecting more data trying to figure out what was going on. Once the modeling results came in and we started looking at the data differently, it all made sense.”

Members of Beckman’s Computational Multiscale Nanosystems Group, Tao Sun, a doctoral student, and Narayana Aluru, professor of mechanical science and engineering, provided expertise in computational modeling via density functional theory to investigate the properties of the nanoribbons.

“Density functional theory calculations provided a deeper understanding of the electronic properties of the integrated system and the interactions between graphene nanoribbons and the silicon substrate,” said Sun. “It was exciting that the computational results could help explain and confirm the experimental results and provided a coherent story.”

“Atomically precise graphene nanoribbons (APGNRs) are serious candidates for the post-silicon era when conventional silicon transistor scaling fails,” said Lyding. “This demonstrates the first important step toward integrating APGNRs with technologically relevant silicon substrates.”

“I find the project very exciting because you are building things with atomic level control, so you try to put every atom exactly where you want it to go,” said Radocea. “There aren’t many materials out there where you can say you have that ability. Nanoribbons are exciting because there is a real need and a real application.”

Dry contact transfer is used to press a fiberglass applicator coated with a powder of atomically precise graphene nanoribbons (that had been synthesized in solution and then degassed at high temperature to remove contaminants) against a hydrogen-passivated Si(100) surface under ultrahigh vacuum. The graphene nanoribbons (GNRs) cleanly exfoliate onto the surface. 80 of 115 GNRs imaged using scanning tunneling microscope spectroscopy were nontransparent (the lattice of the underlying Si substrate was not visible) with an average apparent height of 0.30 nm. The GNRs do not appear to align to the Si lattice, indicating a weak coupling interaction. The 35 semitransparent nanoribbons exhibited an average, apparent height of 0.20 nm. Semitransparency is an imaging artifact influenced by tip-sample separation, the work function of the STM probe, nanoribbon-surface interaction, and surface density of states within the GNR energy bandgap.

High resolution scanning tunneling spectroscopy and current imaging tunneling spectroscopy were used to determine the details of the electronic structure of the chevron GNRs and their interactions with the Si surface. Results are compared with previous studies of chevron GNRs on gold and of graphene nanoflakes on H:Si(100). The fact that the graphene lattice is only observed for nontransparent GNRs indicates the carbon plane is at a height near 0.30 nm, and a van der Waals bonding interaction between GNRs and the Si substrate is possible. The interaction between GNR and surface is weak enough to allow movement of the GNR using the STM tip. The average bandgap over 21 GNRs was determined to be 2.85 eV with a standard deviation of 0.13 eV.

Dry contact transfer also places overlapping nanoribbons on the surface, allowing study of multilayer GNRs. Although these multilayer cross-junctions formed accidentally, they could be formed deliberately by manipulation with an STM tip. The effect of GNR junctions on height and band gap were determined. The Si surface under part of a GNR was depassivated by holding sample bias at 8 V while moving the STM tip over the GNR. The height and width of a GNR are decreased after depassivation, indicating an increased coupling to the Si(100) surface and a change in the electronic structure of the GNR. Metallic behavior after hydrogen depassivation is attributed to changes in GNR electronic structure caused by Si-C bonding.

First principles DFT simulations were performed before and after hydrogen depassivation. After hydrogen depassivation, the projected density of states of the GNR shows finite states at the Fermi level, and there is no longer a band gap. The formation of covalent bonds between the Si surface and the GNR leads to metallic behavior. The Si surface atoms move outward, and the GNR changes from flat to distorted, with some C atoms moving in toward the Si surface.

Using their dry contact transfer process, the authors have cleanly placed atomically precise graphene nanoribbons on a technologically relevant semiconductor surface, manipulated position with an STM tip, and demonstrated controlled interactions between nanoribbon and surface using atomically precise hydrogen depassivation. Their conclusion seems well-founded:

The ability to cleanly place atomically precise GNRs onto H:Si(100) is unprecedented and is expected to have an enormous impact on GNR device prototyping.

This work should herald progress toward atomically precise transistors, qubits, and increasingly complex atomically precise nanolithography.
—James Lewis, PhD

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Adding modular hydrogen-bond networks to protein design

Molecular recognition in DNA is built upon a small set of hydrogen-bonding interactions in the core of the DNA double helix. Specificity in protein folding depends largely on buried packing of hydrophobic amino acid side chains complemented by irregular interactions of specific polar groups. A general method is described to design a wide range of protein oligomers that specifically interact via a network of hydrogen bonds. Credit: Baker Lab, University of Washington.

Advances last year in the bottom-up design and fabrication of increasingly complex atomically precise nanostrutures were so rapid we were not able to cover as many as we wanted. Before we dive into this year’s advances, we are catching up on some of the important advances we missed last year. Perhaps the most active area of molecular engineering research last year was the de novo protein design area, originally proposed by Foresight co-founder K. Eric Drexler as “a path to the fabrication of devices to complex atomic specifications”. Our most recent post in this area cites five earlier posts last year about protein design.

Continuing our coverage of important advances in protein design, the two co-winners of the 2004 Feynman Prize, Theory category (for developing the Rosetta software suite for biomolecular modeling and design) both reported important protein design advances in adjacent papers in Science last May. A perspective commentary “Inspired by nature” in the same issue by Ravit Netzer and Sarel J. Fleishman of the Weizmann Institute of Science points out that the great success over the past decade of de novo designing proteins that folded exactly as designed and were very stable has not produced all of the “important structural features seen in protein interfaces and enzyme active sites”. They note that computer algorithms like Rosetta used to design proteins optimize stability. “By contrast, evolution selects proteins for their ability to perform a vital molecular function, often at the expense of stability.” They discuss the complementary approaches to this issue taken by David Baker and his collaborators (today’s post) and by Brian Kuhlman and his collaborators (tomorrow’s post).

Writing in Geekwire, Alan Boyle reports “Scientists add twists to protein designs“:

Biochemists from the University of Washington have engineered complex protein molecules with additional chemical bonds that make it possible to mix and match them like the base pairs of DNA.

The designer proteins, described today in a paper published by the journal Science [abstract, full text PDF courtesy of Baker Lab], could open the way for a kind of synthetic coding system modeled after the groundbreaking double-helix DNA code system discovered by James Watson and Francis Crick back in 1953.

“Think of it this way: The principle of heredity is Watson-Crick base pairing between the two complementary strands of DNA. We invent in the paper an analogous pairing arrangement for proteins,” David Baker, director of the UW’s Institute for Protein Design, told GeekWire in an email.

Protein molecules can be folded into a wide variety of shapes, which help determine how they function in cells. A software platform called Rosetta was invented at the UW more than a decade ago to analyze protein-folding patterns. Rosetta, along with a more recently developed program called HBNet, played a key role in designing new breeds of protein molecules that include additional hydrogen bonds. …

As explained on the Baker Lab web site “De novo design of protein homo-oligomers with modular hydrogen-bond network-mediated specificity“:

General design principles for protein interaction specificity are challenging to extract. In DNA, specificity arises from a limited set of hydrogen-bonding interactions in the core of the double helix to design and build a wide range of shapes. In proteins, specificity arises largely from buried hydrophobic packing complemented by irregular peripheral polar interactions. Protein-based materials have the potential for even greater geometric and chemical diversity, including additional functionality. Here we describe a general approach for designing a wide range of protein oligomers that have interaction specificity determined by modular arrays of extensive hydrogen bond networks. We use the approach to design dimers, trimers, and tetramers consisting of two concentric rings of helices, including previously not seen triangular, square, and supercoiled topologies. X-ray crystallography confirms that the structures overall, and the hydrogen-bond networks in particular, are nearly identical to the design models, and the networks confer interaction specificity in vivo. The ability to design extensive hydrogen-bond networks with atomic accuracy enables the programming of protein interaction specificity for a broad range of synthetic biology applications; more generally, our results demonstrate that, even with the tremendous diversity observed in nature, there are fundamentally new modes of interaction to be discovered in proteins.

Because hydrogen bond networks play much more complex and subtle roles in protein structures than they do in the simple molecular recognition networks that make DNA nanotechnology possible, Boyken et al. begin by developing a general computational method, HBNet, to rapidly list all side-chain hydrogen-bond networks possible with a given protein backbone structure. There are a large number of possibilities because there are more polar amino acids than there are DNA bases, and each amino acid side chain can adopt multiple conformations (rotameric states) depending on the protein backbone. HBNet computes hydrogen-bonding and steric repulsion interactions between all conformations of all pairs of polar side chains. It then identifies networks of three or more residues connected by hydrogen bonds with little steric repulsion. Networks are rejected if they contain buried polar groups that do not make hydrogen bonds.

To take advantage of networks of repeating structures to build scaffolds, they turned to coiled coils, specifically oligomeric structures with two concentric rings of helices. Systematic variation of helix parameters was used to generate a wide range of backbone structures. HBNet then searched tens of thousands of backbones to identify the small fraction that can support networks that can span the intermolecular interface.

A total of 114 dimeric, trimeric, and tetrameric designs spanning a broad range of superhelical parameters and hydrogen-bond networks were selected for experimental characterization. Genes encoding these protein structures were synthesized and expressed in bacteria. 101 of these expressed soluble proteins, which were purified for further characterization. 66 of these had the design oligomerization state, with tetramers having the lowest success rate (3 of 13 soluble designs assembled properly).

Proteins with two-ring designs were compared with corresponding structures having only the inner ring of helices. X-ray crystallography was used to identify those proteins with structures nearly identical to the design goals. In the most successful designs, nearly all buried polar groups made hydrogen bonds.

To test the role of the hydrogen-bond networks in conferring specificity for assembly into oligomers, control designs were made using the same backbones, but without HBNet. These control designs yielded only hydrophobic interfaces. These control designs were calculated to be energetically more favorable, but when expressed, the proteins were less soluble than their hydrogen-bond network counterparts, and those that were soluble enough to purify yielded multiple higher-molecular-weight aggregates instead of the design oligomers. The authors conclude from this and other experiments that designs in which hydrogen bond networks partition hydrophobic interface area into relatively small areas are more specific than designs with large contiguous hydrophobic patches. The best designs had hydrogen bond networksspanning the entire oligomeric interface, with each helix contributing at lest one side chain.

An additional set of trimers was designed with identical backbones and identical hydrophobic packing motifs so that the only difference was the placement and composition of hydrogen-bond networks. The designs were based on two trimers originating from the same superhelical parameters, but with unique hydrogen bond networks designated as “A” and “B”. Interface with only nonpolar residues are designated “X”. The three-letter code A, B, X was used combinatorially to generate new designs by placing A, B, or X at each of the four repeating cross sections of the supercoil. Five of the six combinatorial designs synthesized were found to be folded, thermostable, and assembled to form trimers. These five along with the two parent designs AAXX and XXBB and the all-hydrophobic control XXXX were crossed in an all-by-all array in a yeast two-hybrid binding experiment, which uses the expression of a reporter gene to measure how specifically two protein domains bind to each other. The results showed the hydrophobic domains to be promiscuous while the hydrogen bond networks mediate specificity.

Having demonstrated that their program HBNet provides a general computational method to accurately design hydrogen-bond networks, the authors claim that the ability to preorganize polar contacts without buried unsatisfied polar atoms should be broadly useful for enzyme design, small molecule binding, and matching polar protein interfaces.

The authors further propose that their two-ring structures provide a new class of protein oligomers with potential for programmable interactions analogous to Watson-Crick base pairing. Although Watson-Crick base pairing is largely limited to the antiparallel double helix, they propose that their designed protein hydrogen-bond networks allow specification of two-ring structures with a range of oligomerization states and supercoil geometries.

It should now become possible to develop new protein-based materials with the advantages of both polymers: DNA-like programmability and tunable specificity coupled with the geometric variability, interaction diversity, and catalytic function intrinsic to proteins.

Considering the striking progress the past decade has seen with both DNA nanotechnology and protein design, it should be especially interesting to watch how this proposal plays out.
—James Lewis, PhD

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Designing novel protein backbones through digital evolution

Overview of the SEWING method. Each panel, from left to right: parental structures with extracted substructures; Graph schematic – colored nodes indicate substructures contained in final design model, superimposed structures show structural similarity indicated by adjacent edges; Design model before sequence optimization and loop design; Final design models. Credit: Jacobs et al.

Continuing yesterday’s discussion of two complementary approaches to balance designing protein structures with novel functions with designing protein structures with maximum stability, we focus on a method to create novel proteins by stitching together pieces of existing proteins, developed by Brian Kuhlman, one of two co-winners of the 2004 Feynman Prize, Theory category, and his collaborators. From the University of North Carolina Medical School newsroom “Scientists digitally mimic evolution to create new proteins“:

… researchers at the University of North Carolina School of Medicine have developed a method that creates novel proteins by stitching together pieces of already existing proteins.

The technique, called SEWING, is inspired by natural evolutionary mechanisms that also recombine portions of known proteins to produce new structures and functions. This approach can generate a diverse set of protein structures with many of the distinctive features that proteins require to carry out specific biological functions.

The findings, published today in the journal Science [“Design of structurally distinct proteins using strategies inspired by evolution” journal abstract, HHS Public Access author manuscript], could enable researchers to design proteins to play a variety of different roles in human biology and disease, such roles as catalysts, biosensors, and therapeutics.

“We can now begin to think about engineering proteins to do things that nothing else is capable of doing,” said senior study author Brian Kuhlman, PhD, professor of biochemistry and biophysics, and member of the UNC Lineberger Comprehensive Cancer Center. “The structure of a protein determines its function, so if we are going to learn how to design new functions, we have to learn how to design new structures. Our study is a critical step in that direction and provides tools for creating proteins that haven’t been seen before in nature.”

At the chemical level, proteins are composed of long chains of hundreds to thousands of subunits called amino acids – the building blocks of life. The sequence of these amino acids ultimately determines each protein’s unique geometry. Some sections of a protein might be folded back and forth onto itself like a paper fan; others might be coiled tightly like a spring. In all, scientists estimate that the human body contains about 100,000 different proteins, each the result of millions of years of evolutionary shuffling, culminating in a precise lineup of pleats, coils, and furrows required to carry out a specific job in the cell.

Traditionally, researchers have used computational protein design to recreate in the laboratory what already exists in the natural world. But in recent years, their focus has shifted toward inventing novel proteins with new functionality. These design projects all start with a specific structural “blueprint” in mind, and as a result are limited. Kuhlman and his colleagues believe that by removing the limitations of a pre-determined blueprint and taking cues from evolution they can more easily create functional proteins.

To mimic the mechanisms of natural protein evolution, they developed a computer design strategy called SEWING (Structure Extension With Native-substructure Graphs). First, the researchers took a slew of naturally occurring proteins and digitally chopped them up into well-defined pieces, as if turning a bunch of rag dolls into a pile of arms, legs, and heads. Then they performed a series of computational tests to figure out which pieces would fit well together. In nature, this step would involve looking for stretches of amino acid sequences that are similar between proteins. On the computer, it involved searching for regions of structural similarity so that – in the analogy of the rag doll – a hand would end up being stitched to an arm and then a shoulder, and not a head or a hip.

First author Tim M. Jacobs, PhD, a former graduate student in the Kuhlman lab, used this method to map out 50,000 of these stitched together proteins on the computer. He then tapped a number of different metrics to whittle down the list to the top 21 proteins, which he produced in the lab. Jacobs and colleagues took pictures of these proteins using x-ray crystallography and NMR, and found that the proteins contained all the unique structural varieties they had designed on the computer.

“We were excited that some had clefts or grooves on the surface, regions that naturally occurring proteins use for binding other proteins,” said Jacobs. “That’s important because if we wanted to create a protein that can act as a biosensor to detect a certain metabolite in the body, either for diagnostic or research purposes, it would need to have these grooves. Likewise, if we wanted to develop novel therapeutics, they would also need to attach to specific proteins.” …

Jacobs et al. propose that traditional efforts in protein design to produce idealized protein structures “may not always be the most effective starting points for engineering novel protein functions. Functional sites in proteins are often created from non-ideal structural elements, such as kinks, pockets and bulges.” Further, protein design methods begin with an idealized target structure in mind, while natural evolution depends on fitness provided by the evolved protein function, rather than predetermined structure. Their design strategy, called SEWING (Structure Extension With Native-substructure Graphs), builds new protein structures from small pieces of naturally occurring protein domains. They chose to extract two different types of substructures: the first, continuous stretches encompassing two secondary structure elements separated by a loop, to capture relative orientation and local packing interactions; the second, groups of 3-5 secondary structural elements that all make van der Waals contacts with each other but are not necessarily continuous in primary sequence, to maintain longer range tertiary interactions that are often conserved during protein evolution. A total of 33,928 continuous substructures and 4,584 discontinuous substructures were extracted from the protein data bank.

The above elements are combined and modified to develop new tertiary structures. Potential combinations are computationally tested to ensure structural fit, but without any target structure being required. This process produced about 7×1016 backbone structures for subsequent consideration. From this large number of possibilities 11 designs based on continuous SEWING and 10 designs based on discontinuous SEWING were selected for experimental characterization. Eight of the 11 continuous designs were soluble and readily purified. Two of these were hyperthermophiles, and one (CA01) exhibited an estimated melting temperature of 126 °C, with a crystal structure that exhibited excellent agreement with the design model, to an alpha-carbon root mean square deviation of only 80 pm.

Two of the 10 discontinuous SEWING were expressed well enough for purification. One of these, DA03, exhibited high thermostability. The other discontinuous design, DA05, did not readily crystallize, but NMR spectroscopy confirmed the presence of 4 of 5 of the designed helices, while the 5th was disordered. Redesigning that region using the continuous SEWING method yielded a new protein that adopts the designed conformation. The additional step of loop-building necessary for discontinuous SEWING may have accounted for the lower success using that method.

The diversity of models generated by SEWING is demonstrated, the authors claim, by the inclusion of kinked and curved helices, cavities and clefts, and a large range of helix-crossing angles. They note that the topologies of SEWING models is greater than seen with previously designed alpha-helical proteins, “which are restricted to coiled-coils, repeat proteins and up-down four helix bundles” The authors expect the diversity of SEWING designs to further increase when alternative substructures are included, such as β-α motifs and β-hairpins.

We anticipate that this structural diversity will be advantageous for functional design, as every backbone generated with SEWING has new surface and pocket features that provide potential binding sites for ligands or macromolecules. Additionally, SEWING offers an approach for stitching together functional motifs from naturally occurring proteins, an evolutionary mechanism to generate multi-functional proteins and allosteric systems.

The study described in our most recent post and this study together demonstrate substantial control over biomolecular shape and interactions, complementing previous accomplishments in designing protein stability and extending protein design space. We can hope that increasing control over the balance between stabilizing and functional features will lead to designing new protein functions, and eventually more complex and capable molecular machine systems.
—James Lewis, PhD

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A brief history of nanotechnology

Richard Feynman teaches a special lecture on March 13, 1964. Energy.gov/Flickr. United States government work.

Our two most recent posts (here and here) have been about efforts by the Advanced Manufacturing Office of the U.S. Department of Energy to promote atomically precise manufacturing—a specific vision for the future of nanotechnology—a vision upon which the Foresight Institute has been focused since our founding 30 years ago. The vision was far removed from then current laboratory technologies, but those current technologies were entering a period of very rapid progress. Progress in several areas led to very useful functional nanomaterials and nanodevices. Enthusiasm for near-term commercial applications became conflated with a long-term technology vision and combined to bring forth ambitious new funding in the US and elsewhere. The differing visions of what nanotechnology is and can become, and the resulting conflicts over funding and over the public image of nanotechnology, are part of the story of Foresight’s first 30 years “Thirty Years of Nanotechnology and Foresight“. An engaging perspective on the history of nanotechnology written by W. Patrick McCray, a professor in the history department at the University of California–Santa Barbara, was published by Slate earlier this year as part of its Futurography series: “Gods of Small Things“.

The field may seem new—but it dates back more than 50 years

… Since the 21st century began, few emerging technologies have been so heavily promoted, funded, and debated as nanotechnology. Defined (currently) by the U.S. government as “the understanding and control of matter at the nanoscale”—a nanometer is one-billionth a meter—nanotechnology as a field and research community has received billions of funding dollars, making it one of the nation’s largest technology investments since the space race.

Yet the idea that manipulation of the material world at the near-atomic scale was possible, even within grasp, possesses a historical arc stretching far back to the height of the Cold War. From the 1950s onward, investments in physics, chemistry, and the relatively new field of materials science provided a research foundation for the eventual emergence of nanotechnology. In fact, architects of a post–Cold War national nano-research program often traced its origins back to a discrete point in time and space. …

The story Prof. McCray recounts begins with Richard Feynman’s 1959 after-dinner talk, which predicted microscopic machines that would be able to build complex materials by precisely placing individual atoms in designed arrangements to achieve desired functions. Feynman’s ideas attracted little attention despite important progress in chemistry, surface physics, and other areas until the exploratory engineering work of Foresight’s co-founder Eric Drexler, then a student at MIT, popularized Feynman’s proposal under the banner of “nanotechnology”. However, this vision of the future of nanotechnology soon came into conflict with mainstream science’s funding priorities and focus on near-term applications.

… Ultimately, their clashing viewpoints were about making definitions and marking several boundaries: present-day science versus exploratory engineering; whether the point of view of chemistry or computer science was more representative of the nanoscale world; and ultimately, who had the authority to speak on behalf of “nanotechnology.” …

Prof. McCray estimates that by the time President Obama leaves office, the U.S. government will have spent close to $25 billion on nanotechnology-related research. Certainly the overwhelming majority of this funding has gone to mainstream science’s vision of nanotechnology, which will no doubt continue to make major contributions to materials science, medical science, and vastly improved membranes, catalysts, and computers. Increasingly, these advances will depend upon achieving atomic precision in manufacturing. Early on, atomically precise manufacturing will be achieved by various self-assembly processes developed to manufacture specific materials. We can expect, however, that as increasingly complex systems of molecular machines are developed using these simpler methods, eventually nanofactories will use molecular machine systems to place reactive molecular fragments on a workpiece with atomic precision to fabricate complex, functional nanometer scale building blocks, which will then be assembled hierarchically by robotic machinery to manufacture macroscopic products.
—James Lewis, PhD

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