N1005 IBM Research: STM

Molecule Suggested in 1902 Gets its First Close-Up

Today, chemistry teachers and students can breath a sigh of relief. After teaching and learning about a particular family of molecules for decades, scientists have finally proven that they do in fact exist. <table cellpadding="0" cellspacing="0" class="tr-caption-container" style="float: right; margin-left: 1em; text-align: right;"><tbody><tr><td style="text-align: center;"><a href="https://farm4.staticflickr.com/3832/19307906738_488d5c573c_n.jpg" imageanchor="1" style="clear: right; margin-bottom: 1em; margin-left: auto; margin-right: auto;"><img border="0" src="https://farm4.staticflickr.com/3832/19307906738_488d5c573c_n.jpg" /></a></td></tr><tr><td class="tr-caption" style="text-align: center;">AFM image of an aryne molecule imaged with a CO tip</td></tr></tbody></table>In a new paper published online today in <a href="http://dx.doi.org/10.1038/nchem.2300" target="_blank">Nature Chemistry</a>, scientists from IBM Research and <a href="http://www.usc.es/ciqus/en" target="_blank">CIQUS at the University of Santiago de Compostela, Spain</a>, have confirmed the existence and characterized the structure of arynes (pronounced "ärēən"), a family of highly-reactive short-lived molecules which was first suggested 113 years ago. The technique has broad applications for on-surface chemistry and electronics, including the preparation of graphene nanoribbons and novel single-molecule devices. “Arynes are discussed in almost every undergraduate course on organic chemistry around the world. Therefore, it’s kind of a relief to find the final confirmation that these molecules truly exist,” said Prof. Diego Peña, a chemist at the University of Santiago de Compostela. “I look forward to seeing new chemical challenges solved by the combination of organic synthesis and atomic force microscopy." <a name="more"></a> There are trillions of molecules in the universe and some of them are stable enough to be isolated and characterized, but many others are so short-lived that they can only be proposed indirectly, via chemical reactions or spectroscopic methods. One such species are arynes, which were first suggested in <a href="http://dx.doi.org/10.1002/cber.19020350286" target="_blank">1902</a>, and since then have been used as intermediates or building blocks in the synthesis of a variety of compounds for applications including medicine, organic electronics and molecular materials. The challenge with these particular molecules is that they only exist for several milliseconds making them extremely challenging to image, until now. The imaging was accomplished by means of atomic force microscopy (AFM), a scanning technique that can accomplish nanometer-level resolution. After the preparation of the key aryne precursor by CIQUS, IBM scientists used the sharp tip of a scanning tunneling microscope (STM) to generate individual aryne molecules from precursor molecules by atomic manipulation. The experiments were performed on films of sodium chloride, at temperatures near absolute zero, to stabilize the aryne. Once the molecules were isolated, the team used AFM to measure the tiny forces between the STM tip, which is terminated with a single carbon monoxide molecule, and the sample to image the aryne’s molecular structure. The resulting image was so clear that the scientists could study their chemical nature based on the minute differences between individual bonds. “Our team has developed several state-of-the-art techniques since <a href="https://www-03.ibm.com/press/us/en/pressrelease/28267.wss" target="_blank">2009</a>, which made this achievement possible,” said <a href="http://researcher.ibm.com/researcher/view.php?person=zurich-PAV" target="_blank">Dr. Niko Pavliček</a>, a physicist at IBM Research - Zurich and lead author of the paper. “For this study, it was absolutely essential to pick an insulating film on which the molecules were adsorbed and to deliberately choose the atomic tip-terminations to probe them. We hope this technique will have profound effects on the future of chemistry and electronics." Prof. Peña, added that "These findings on arynes can be compared with the long-standing search for the giant squid. For centuries, fishermen had found clues of the existence of this legendary animal. But it was only very recently that scientists managed to film a giant squid alive. In both cases, state-of-the-art technologies were crucial to observe these elusive species alive: a low-noise submarine for the giant squid; a low-temperature AFM for the aryne." This research is part of <a href="https://www-03.ibm.com/press/us/en/pressrelease/44357.wss" target="_blank">IBM’s five-year, $3 billion investment</a> to push the limits of chip technology and semiconductor innovations needed to meet the emerging demands of cloud computing and Big Data systems. This work is a result of the large European project called <a href="http://pams-project.eu/">(Planar Atomic and Molecular Scale Devices)</a>. PAMS’ main objective is to develop and investigate novel electronic devices of nanometric-scale size. Part of this research is also funded by a <a href="http://erc.europa.eu/sites/default/files/press_release/files/press_release_adg2011_results.pdf">European Research Council Advanced Grant</a> awarded to IBM scientist <a href="http://researcher.ibm.com/researcher/view.php?person=zurich-GME" target="_blank">Gerhard Meyer</a>, who is also a co-author of the paper. <iframe allowfullscreen="" frameborder="0" height="360" src="https://www.youtube.com/embed/NOGaYWbrkaY" width="640"></iframe>

Today, chemistry teachers and students can breath a sigh of relief. After teaching and learning about a particular family of molecules for d...

IBM scientists use the STM to image molecules in liquid

12:24 AM N1000 0

<table cellpadding="0" cellspacing="0" class="tr-caption-container" style="float: right; margin-left: 1em; text-align: right;"><tbody><tr><td style="text-align: center;"><a href="https://farm6.staticflickr.com/5558/15030498715_07a6f97660_n.jpg" imageanchor="1" style="clear: right; margin-bottom: 1em; margin-left: auto; margin-right: auto;"><img border="0" height="200" src="https://farm6.staticflickr.com/5558/15030498715_07a6f97660_n.jpg" width="183" /></a></td></tr><tr><td class="tr-caption" style="text-align: center;">Nirmalraj in the Noise Free Lab</td></tr></tbody></table>Since the first microscope was invented, researchers and scientists around the world have searched for new ways to stretch their understanding of the microscopic world. In 1981, two IBM researchers, Gerd Binnig and Heinrich Rohrer, broke new ground in the science of the very, very small with their invention of the scanning tunneling microscope (STM). Like no instrument before it, Binnig and Rohrer’s invention enabled scientists to visualize the world all the way down to its molecules and atoms. The STM was recognized with the Nobel Prize in Physics in 1986 and is widely regarded as the instrument that opened the door to nanotechnology and a wide range of explorations in fields as diverse as electrochemistry, semiconductor science, and molecular biology. <a name="more"></a> In a new paper appearing today titled "<a href="http://www.nature.com/srep/2015/150511/srep10116/full/srep10116.html">Capturing the embryonic stages of self-assembly - design rules for molecular computation</a>" in <a href="http://www.nature.com/srep/2015/150511/srep10116/full/srep10116.html" target="_blank">Nature Scientific Reports</a>, IBM scientists in Zurich are adding a new chapter to the STM's legacy by reporting on a new methodology for the reliable extraction of incredibly high resolution images of the swarming behavior of molecules in situ or which translates to "on site". I spoke with the lead author of the paper <a href="http://researcher.ibm.com/researcher/view.php?person=zurich-PNI">Dr. Peter Nirmalraj</a> about his research and what's next. <div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhIoUvr2UVXCrjEOIMRs1nsUKp7lRLt7DzuTPx2EYM5fUOeHF-iryKpqWlsNLuqV6XcIL-xBOcyLbwc4YiDsxRA4A9wf5SqMTOQy_z8kPPmabF4TOucltptDf3GdNuePyXiKlZaZd2ZON0/s1600/Table+of+contents+graphic.jpg" imageanchor="1" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em;"><img border="0" height="320" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhIoUvr2UVXCrjEOIMRs1nsUKp7lRLt7DzuTPx2EYM5fUOeHF-iryKpqWlsNLuqV6XcIL-xBOcyLbwc4YiDsxRA4A9wf5SqMTOQy_z8kPPmabF4TOucltptDf3GdNuePyXiKlZaZd2ZON0/s320/Table+of+contents+graphic.jpg" width="208" /></a></div> Q. Why has it taken so long to use the STM for in situ imaging in liquid?  Peter Nirmalraj (PN): In situ STM imaging (imaging in liquids at room-temperature) has been around for the last 20 years, however extracting high resolution data comparable to UHV STM standards has remained a challenge, mainly due to the electrochemical congestion and external noise interference occurring when performing such measurements in liquids at room temperature. Q. How did you come up with the idea to make it work? PN: We have <a href="http://www.nature.com/nmat/journal/v13/n10/full/nmat4060.html">previously demonstrated</a> how to control molecular motion for stable electrical readouts.  In the current work we employ the same STM tool capable of measuring dynamics of individual molecules at the liquid-solid interface, with excellent spatio-temporal sensitivity. In particular we chose electrically inert and low vapor pressure liquids as the medium, that does not interfere with the tunneling mechanism. The entire setup is located within our state-of-the-art noise free laboratories located in the <a href="http://www.zurich.ibm.com/nanocenter/">Binnig and Rohrer Nanotechnology Center</a> which immensely aids such nanoscopic measurements in liquids. The question we asked ourselves, can we record in real-time the evolution of an organic molecular layer and in particular capture the very early-stages of self-assembly rather than only imaging a fully packed thermodynamically stable molecular matrix?  <div class="separator" style="clear: both; text-align: center;"></div><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjPF3EXRkC8Jmqpaxa2GTg_Gn0TeOJxfODtkx-8I5wPveOBvYmbsIT4DRl3e6l3a-Bnq78e5VhEPTR7mPT5JYo6gbjeabECIrc7nGLI4lLv14IAjW_vhzBb8lna6B2mFIUqCqwzlkwtkvk/s1600/STM.jpg" imageanchor="1" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em;"><img border="0" height="195" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjPF3EXRkC8Jmqpaxa2GTg_Gn0TeOJxfODtkx-8I5wPveOBvYmbsIT4DRl3e6l3a-Bnq78e5VhEPTR7mPT5JYo6gbjeabECIrc7nGLI4lLv14IAjW_vhzBb8lna6B2mFIUqCqwzlkwtkvk/s200/STM.jpg" width="200" /></a>Information obtained from such carefully designed experiments can and have provided deeper insights on the fundamentals of molecular self assembly, which is central in molecular computation and in refining step-by-step equilibration rules for agent-based algorithms (algorithmic self-assembly). Q. Why did you choose C60 molecules for the molecular solution? PN: Fullerenes are a well studied class of molecules. This makes it easier to calibrate our STM tool as the dimensions and intermolecular packing arrangements of this system is known from both theory and previous STM studies. More importantly fullerenes are compatible with our solvent of choice, n-tetradecane and form a stable molecular solution (molecules are well dispersed with minimal treatment and does not aggregate in solution). Currently we are exploring other molecules with different dimensions from porphyrins to ferrocene. Q. Could this technique be used for healthcare, to image bacteria and and viruses for example? PN: Yes, biomolecules which are generally not highly rigid and less conductive in nature can be imaged using STM when drop casted from a liquid-phase onto conductive metal surfaces. However, the solvents that generally support biomolecules are polar which necessitates an additional step for insulating the STM probe, minus the apex, to minimize parasitic currents during tunneling. Such measurements also need to be performed under closed-liquid cells with larger volume to contain rapid solvent evaporation. Q. What's next for your research? PN: The next step would be to investigate naturally occurring pattern formation and understand better the local structural dynamics of organic molecules such as porphyrins as they evolve from a disordered phase to an energetically stable stage and verify their internal response to external electrical pulses.  Large data sets generated from such studies will then be directed towards constructing predictive algorithms for assembly of new 2D and 3D molecular configurations and for testing basic logic gate operations in molecular layers. Follow the authors on Twitter at <a href="https://twitter.com/stm_pnn">@stm_pnn</a> and <a href="https://twitter.com/HeikeRiel">@HeikeRiel </a> This research is partly funded by the Marie Curie Actions-Intra-European Fellowship (IEF-PHY) under grant agreement N° 275074 “To Come” within the 7th European Community Framework Programme.

nano Nature STM IBM scientists use the STM to image molecules in liquid

Nirmalraj in the Noise Free Lab Since the first microscope was invented, researchers and scientists around the world have searched for new ...

Oil Applies Brakes to Molecules under STM at Room Temp

9:01 AM N1000 0

<div style="text-align: right;"></div><table cellpadding="0" cellspacing="0" class="tr-caption-container" style="float: right; margin-left: 1em; text-align: right;"><tbody><tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgcqdFz6oCMZJRGYOM5A50FsddPZm4MG5tddVxd_LOByIlSHb62cL7-Po8C1F7iKGv2jEmdVTSPkHl4Hsq3f-aCmFC9jxEdO8kJ9Rz4byZejNJP5wljvJGedosf13wIFOs-bNPkeTxGkJw/s1600/Peter_Nirmalraj_15.jpg" imageanchor="1" style="clear: right; margin-bottom: 1em; margin-left: auto; margin-right: auto;"><img border="0" height="171" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgcqdFz6oCMZJRGYOM5A50FsddPZm4MG5tddVxd_LOByIlSHb62cL7-Po8C1F7iKGv2jEmdVTSPkHl4Hsq3f-aCmFC9jxEdO8kJ9Rz4byZejNJP5wljvJGedosf13wIFOs-bNPkeTxGkJw/s1600/Peter_Nirmalraj_15.jpg" width="320" /></a></td></tr><tr><td class="tr-caption" style="text-align: center;">IBM scientists <a class="name" href="http://www.nature.com/nmat/journal/vaop/ncurrent/full/nmat4060.html#auth-4">Marilyne Sousa</a>, <a class="name" href="http://www.nature.com/nmat/journal/vaop/ncurrent/full/nmat4060.html#auth-1">Peter Nirmalraj</a>, <a class="name" href="http://www.nature.com/nmat/journal/vaop/ncurrent/full/nmat4060.html#auth-7">Heike Riel</a> and <a class="name" href="http://www.nature.com/nmat/journal/vaop/ncurrent/full/nmat4060.html#auth-6">Bernd Gotsmann</a> </td></tr></tbody></table>Since the first microscope was invented, researchers and scientists around the world have searched for new ways to stretch their understanding of the microscopic world. In 1981, two IBM researchers, who went on to become Nobel Laureates, <a href="https://www.youtube.com/watch?v=FczS5y4mmZc">Gerd Binnig and Heinrich Rohrer</a>, broke new ground in the science of the miniscule with their invention of the <a href="http://www-03.ibm.com/ibm/history/ibm100/us/en/icons/microscope/">scanning tunneling microscope</a> (STM), which enabled scientists to visualize the world all the way down to its molecules and atoms using a a quantum phenomenon called tunneling. Tunneling atoms escape the surface of a solid to form a kind of cloud that hovers above the surface; when another surface approaches, its atomic cloud overlaps and an atomic exchange occurs. By maneuvering a sharp metal conducting tip over the surface of a sample at an extremely small distance, Binnig and Rohrer found that the amount of electrical current flowing between the tip and the surface could be measured. Variations in this current could provide information about the inner structure and the height-relief of the surface. And from this information, one could build a three-dimensional atomic-scale map of the sample’s surface to reveal what atoms look like for the first time. IBM scientists in Zurich continue to push the boundaries of this instrument and in a paper appearing in Nature Materials today titled <a href="http://www.nature.com/nmat/journal/vaop/ncurrent/full/nmat4060.html">Nanoelectrical analysis of single molecules and atomic-scale materials at the solid/liquid interface</a> they have developed a new and frugal technique which enables the direct imaging and stable electrical read outs of single-molecules in a liquid environment using STM at room temperature. In the unique and ultra-controlled environment of the Noise Free Labs of the <a href="http://www.zurich.ibm.com/nanocenter/">Binnig and Rohrer Nanotechnology Center</a>, scientists are using a high-density liquid called silicone oil to serve as liquid-brakes to nearly freeze single molecular motion and ultra-thin organic spacers to electronically decouple the molecules from the contact metals. <table cellpadding="0" cellspacing="0" class="tr-caption-container" style="float: left; margin-right: 1em; text-align: left;"><tbody><tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgHY3lHZav9hRX1Vxe4M9djF1NMZVuZT4mMVj1TpU30ldQpKXC9tn4gWCnMgPiRuhXph41VuKJKNpu_2zkRgH7wmYOI_xeyISR9OLYmropAt5vBU-eah22Bceva9XVcjmSQu-4xterlTm4/s1600/Picture1.png" imageanchor="1" style="clear: left; margin-bottom: 1em; margin-left: auto; margin-right: auto;"><img border="0" height="246" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgHY3lHZav9hRX1Vxe4M9djF1NMZVuZT4mMVj1TpU30ldQpKXC9tn4gWCnMgPiRuhXph41VuKJKNpu_2zkRgH7wmYOI_xeyISR9OLYmropAt5vBU-eah22Bceva9XVcjmSQu-4xterlTm4/s1600/Picture1.png" width="320" /></a></td></tr><tr><td class="tr-caption" style="text-align: center;">In-situ STM image of individual fullerene molecules adsorbed on spacer-coated gold substrate. </td></tr></tbody></table><div class="separator" style="clear: both; text-align: center;"></div>The combinatorial effect allows the scientists to record high resolution real-space images and decode the intrinsic electronic structure of single-molecules. The technique has been successfully extended to further resolve the atomic-lattice, quantify topological defects and map the band structure of monoatomic graphene. In addition to applications in hybrid electronics, where electronically active molecules (organic switches) are embedded into 2-D crystal matrices, these findings provide new pathways and insights in mapping DNA electronic structure and dynamics as they interact with graphene nanopores, which has direct implications in engineering genome sequencing devices. This research was done in collaboration with chemists from IMDEA-Spain and Theoritical Physists from University of Limerick, Ireland.

IBM Research - Zurich nano STM Oil Applies Brakes to Molecules under STM at Room Temp

IBM scientists Marilyne Sousa , Peter Nirmalraj , Heike Riel and Bernd Gotsmann Since the first microscope was invented, rese...