News
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Sept. 2018. Congratulations Enrique! Enrique wins a postdoctoral fellowship in the International Mobility Mezinárodní mobilita MSCA-IF II program, which is co-funded by the EU and the Czech Ministry of Education, Youth and Sports. Enrique will work for the next 2 years on electronic structure and transport modeling beyond a DFT description. We look forward to a productive fellowship!
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July 2018. Single molecule circuits with N-Heterocyclic Carbene linkers. In this paper with the Roy and Venkataraman groups at Columbia University, we demonstrate for the first time NHCs as linkers for single molecule junctions. In JACS we show how NHC-bonded single molecule circuits can be made from a series of air-stable metal-NHC complexes that are reduced in situ. The conductance of the molecule is modulated by the identity of this single metal atom bonded to the NHC. Calculations substantiate the important role of the NHC group to the electronic properties and transport characteristics of the molecule, and demonstrate the strong electronic coupling of the NHC termination to the leads. Publications
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The group in June 2018. Héctor, Giuseppe, Enrique and Narendra (not in picture: Martin).
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June 2018. Goodbye, Giuseppe! Giuseppe’s Marie Skłodowska-Curie fellowship has come to an end. He joined the group at the start of 2015 under Czech (GAČR) funding. He then won the Marie Skłodowska-Curie fellowship, which lasted from July 2016 until the end of June 2018. In the 3.5 years he was in the group, he published 6 papers. In June we had a barbeque at the Institute together with our friends from the Nanosurf group to say goodbye! The grill was great, and we enjoyed some Bohemian champagne. Thanks Shayan Ed for the pictures!
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May 2018. Workshop on European grants at the Institute. As supervisor of a Marie Skłodowska-Curie fellowship, I collaborated in a seminar on European grants at the Institute organized by the new grant support unit. The goal was to give an overview of Marie Skłodowska-Curie and ERC grants and to provide insight on the evaluation process. I contributed to the training session by steering a group of participants in evaluating some sections of a Marie Skłodowska-Curie application. The participants in my group were very stern reviewers! The workshop included Marie Skłodowska-Curie and ERC grantees, supervisors and evaluators. Hopefully this will result in many successful European grants!!!
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May 2018. New predictions for current-induced vibrational instabilities in single molecule circuits. An electrical current can release energy to molecular vibrational modes and excite vibrations localized at the molecule. If this is not balanced by cooling mechanisms, no steady-state solution for the population of vibrational modes can be found, and the junction breaks. Previous works had shown that vibrational instabilities could be expected in donor -acceptor molecules where the donor state was lifted above the acceptor state by the applied bias, a regime known as population inversion. In J. Phys. Chem. Lett. we now show that vibrational instabilities are a much more general phenomenon than previously reported and that instabilities can occur in a broader class of molecules in a less restrictive physical regime. We calculate the rates of absorption and emission of vibrations and demonstrate vibrational instabilities for a small LUMO-conducting oligophenyl, without the requirements of donor-acceptor structure or population inversion. Bulky side groups were added, which result in a large twist angle between the benzene rings due to steric repulsion. This is important since it reduces conjugation and electronically separates states at both ends of the molecule, allowing for the tuning of their relative position under bias. In addition to DFT-NEGF calculations, we develop a two-site model which generalizes these findings, disentangles the effects of electronic properties and internal structure of vibrational modes, and maps junction (in)stability as a function of the different interface parameters. Publications
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April 2018. Stable bipodal platform for single molecule transport based on biphenylene. In this paper we proposed a new molecular platform for single molecule conductance based on biphenylene. It is a bipodal platform with stable mechanical properties and highly-conducting Au-C bonds. Biphenylene is an antiaromatic molecule consisting of two benzene rings connected via single bonds: the chemical structure has 6-4-6 member rings. The conjugated system has 12 pi electrons, making it antiaromatic (4n pi electrons in Hückel’s rule). Since antiaromatic structures are unstable, in our work we considered that the antiaromatic instability of biphenylene leads to the breaking of Carbon-Carbon bonds inside the molecule. These Carbon atoms then form covalent bonds with the Au substrate. The resulting geometry has benzene rings with a large twist angle that stand almost upright on the surface, a good platform for contacting this molecule with an STM tip. For the top contact we investigated a series of chemical linkers spanning low to high interaction with the tip. We showed how the proposed molecular architecture based on biphenylene is very stable mechanically and highly transparent electronically, demonstrating its potential in single molecule transport studies. Publications
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April 2018. Outreach and recruitment in the Physics Career Day. On April 24, I presented the group's research and PhD student activities in the Physics Career Day. This event was organized by Careermarket at the Charles University Faculty of Mathematics and Physics. Some of us from the Institute of Physics gave short presentations of PhD work in our groups intended for physics undergrads. I outlined for students what molecular transport theory consists on and mentioned the main research areas in the group. I also described the knowledge desirable for DFT-based simulations and what range of skills one might learn in a PhD.
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Jan. 2018. Conductance of helical molecules and demonstration of the converse piezoelectric effect. In the converse piezoelectric effect, an applied voltage results in mechanical strain. Together with our colleagues from the groups of Pavel Jelinek here at the Institute of Physics and Ivo Starý at the Institute of Organic Chemistry and Biochemistry, we investigated this effect and the electron transport properties in helicene derivatives on a Ag substrate. These molecules consist of 7 benzene rings coupled together forming a helix. In contrast to many other conjugated molecules, their geometry is not planar but three-dimensional: helicene molecules have a spring-like structure, with each ring spiralling ‘upwards’ and where the seventh ring is positioned above the first one. These terminal rings have acetylsufanyl (-SCOCH3) groups and one of them binds to the Ag(111) surface. Individual molecules were contacted using simultaneous AFM/STM at 5K. Topographic images showed both bright and dark helicene molecules, whose appearance is related to the geometry of the linker group. A conformer with the top CO group pointing up (towards vacuum) appears bright on the STM, while if it points down it appears dark. At contact, the tip binds to the S atom and dark molecules have a higher conductance due to their shorter tunnelling distance. The formation of the metal-molecule bond was studied by AFM/STM at various applied voltages. We saw that the distance at which tip-molecule contact was established varied linearly with applied voltage, and showed that this is due to the bias-induced vertical deformation of the spring-like scaffold. Publications
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Oct 2017. High-resolution submolecular imaging at 5K using the IETS amplitude. This paper combining measurements and simulations is a collaboration with our colleagues from Pavel Jelinek’s group here at the Institute and from the DIPC. In a seminal paper, W. Ho’s group showed that submolecular structure could be imaged from the spatial variation of the IETS frequencies. However, the high resolution needed to track the changes in mode energies at different tip positions was only possible at sub-Kelvin temperatures, limiting the wider application of this technique. Here we show how submolecular resolution is possible at 5K from the spatial variation of the IETS intensity. We approached a FePc molecule on Au with CO-functionalized tip: as the lateral position of the CO+tip was changed, the amplitude of the FR modes of CO remained almost constant, while that of the FT modes changed substantially. The contribution of our group was to explain the sensitivity of these modes to tip position. We used a technique we had developed previously to map the spatial origin of the IETS peaks and found clear differences between FT and FR modes. FR modes are generated mostly on the CO molecule and tip, and the contribution from other atoms is small. To correctly describe the intensity of FT modes, on the other hand, it is necessary to also include the interaction of the CO molecule with the molecular substrate. FT modes will therefore be more sensitive to the lateral position of the CO molecule relative to the molecule. Our colleagues also extended their probe-particle model to describe the common imaging mechanism for all three STM, AFM and IETS channels. Altogether, this paper demonstrates that it is possible to achieve submolecular resolution at 5K comparable to AFM from the spatial variation of the IETS amplitude. Publications
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Oct 2017. Paper on the role of molecular adsorbates in current-induced cooling. In the past we had studied how, when applying a voltage across a molecular junction, the electrical current could heat (but also cool!) the junction. In this new paper, we again consider a biscarbene molecule but this time with an electron-withdrawing NH2 species adsorbed on only one of the tip terminations. We compare the changes in current-induced energy exchange of this system with the ‘clean’ junction (which has no co-adsorbed species). Despite the absence of chemical bonds between the bridging molecule and the adsorbate, the NH2 group in the vicinity results in the cooling of biscarbene modes at all applied voltages. The population and energy stored in biscarbene modes are smaller with co-adsorbed NH2 than for the clean junction, and NH2 modes are heated while biscarbene modes cooled with applied voltage. We find that this is a rather indirect effect, caused by the shift in the biscarbene DOS induced by the presence of the NH2 species, while the effect of the adsorbate DOS itself is small. By changing the nature of the adsorbate (from electron-donating to withdrawing), it should be possible to tune the heating and cooling of molecular junctions. Publications
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July 2017. Conductance of an antiaromatic molecule measured for the first time! Together with our Japanese collaborators the Kiguchi group from Tokyo Institute of Technology and the Shinokubo group from Nagoya University, we study the conductance of a genuinely antiaromatic molecular circuit for the first time. Cyclic and planar molecules are said to be aromatic if they have 4n+2 pi electrons, and antiaromatic if they have 4n pi electrons. There are many aromatic species in molecular nanoscience (oligophenyls, thiophenes, porphyrins…) but antiaromatic molecules are very unstable and hard to synthesize. Antiaromatic molecules had been predicted by Breslow in the 70s to be highly conducting based on electrochemical measurements of oxidation/reduction potentials. In single molecule circuits it was recently shown that less aromatic molecules are more conducting but no genuinely antiaromatic molecule had been measured up to now. In our work we compare porphyrin (aromatic) and norcorrole (antiaromatic) units. The norcorrole core has two fewer Carbon atoms than the porphyrin (thus going from 4n+2 to 4n) but is structurally similar. The antiaromatic molecule is ~25× more conducting than its aromatic counterpart due to a more favorable alignment of frontier orbitals at the interface. Publications
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May 2017. Our paper on Au-C bonds in fullerenes is out! We form fullerene-based structures on Au(111) which are stable at room temperature against diffusion on the surface. We do this by low-energy Ar+ sputtering of fullerene films. Sputtering at these low energies (120 eV) was shown in Carbon materials to result in predominantly single vacancy defects. After sputtering we see bright spots on the surface that do not diffuse at room temperature. DFT calculations show that molecules with one missing atom are much more stable at the surface than fullerenes or than molecules with double vacancies. This increased binding comes from the saturation of the bonds around the defect by the Au surface. We interpret the observed features as adsorbed fullerene-based molecules with C vacancies. This is a collaboration with the Nanosurf group here at the Institute, who did the measurements. Publications
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Jan. 2017. Welcome Enrique! Enrique joins the group as a postdoctoral researcher. He will work on single molecule transport theory. Group
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Dec. 2016. Our paper on current-induced cooling is out! We calculate the current-induced excitation and damping of vibrational modes in a carbene-based molecular circuit. Previously, we had seen that for this system, the width and position of the LUMO resonance was determined by the atomistic details of the tip (adatom, pyramid,...). Here we calculate the energy exchange between electronic and vibrational degrees of freedom. Energy transferred to vibrational modes will heat the junction, while in the opposite case it is released in the electrodes far from the junction, which is effectively cooled. We find that for chain-like tip structures (which can result from the stretching of strong Au-C bonds), current can cool the junction at high applied voltage. Current-induced heating and cooling processes are important as they strongly influence the stability of the molecular junction under an applied voltage. Publications
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July 2016. Postdoc position available! A postdoc position is available in the group. Candidates should have experience with first-principles simulations. Preference will be given to candidates with expertise in (Tran)SIESTA codes and FORTRAN programming. Informal inquiries are welcome.
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July 2016. Our paper on the local contributions to IETS is out! Here we completely characterize the different contributions to the inelastic spectrum of a representative molecular junction. These contributions encode information on both the vibrational modes and the electronic structure and thus go beyond the usual figures of the modes. Since we use a local orbital basis, we can determine the spatial origin of all contributions to the vibrational modes, mapping the origin of the inelastic signal. We thereby provide, across all vibrational modes, a quantitative relation between the degree of symmetry of each mode, its inelastic signal, and the locality of selection rules. Publications
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July 2016. Giuseppe starts his Marie Skłodowska-Curie fellowship! In this project we will study current-induced vibrational heating and cooling of molecular junctions. The interaction of vibrational degrees of freedom with the tunneling electrons can result in the heating and, under certain circumstances, even cooling of the junction, and the endless number of chemical structures opens many possibilities to tune and control these processes. To study the electronic structure and the inelastic processes associated to the emission and absorption of molecular vibrations, we will carry out first-principles simulations based on DFT. We look forward to a fruitful fellowship!
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Feb. 2016. Our paper on tip-induced gating of carbene-based junctions is out! We calculate the transport properties of N-heterocyclic carbene-based (NHC) molecules on gold and see a very strong dependence of the LUMO position on the atomistic details of the tip. Depending on whether the tips have tetrameric, pyramidal, chain-like or adatom terminations, the position of the LUMO shifts by almost ~0.8 eV. We explain these changes through an analysis of the electron density difference. Since transport is LUMO-derived, the calculated transmission at the Fermi level changes by a factor 8× and the tip is effectively gating the carbene-based circuit. Publications
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Feb. 2016. Welcome Narendra! Narendra joins the group. He will work on using and developing DFT-based methods to calculate conductance single in molecular junctions. Group
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Nov. 2015. Welcome Martin! In addition to his experimental work on nanoprobes in the group of Antonín Fejfar, we are happy Martin is interested in carrying out ab-initio simulations. He will calculate the interface properties of carboranes at metal surfaces. Group