Stanislav M. Avdoshenko

Dynamic and electronic transport properties of DNA translocation through graphene nanopores.

Graphene layers have been targeted in the last years as excellent host materials for sensing a remarkable variety of gases and molecules. Such sensing abilities can also benefit other important scientific fields such as medicine and biology. This has automatically led scientists to probe graphene as a potential platform for sequencing DNA strands. In this work, we use robust numerical tools to model the dynamic and electronic properties of molecular sensor devices composed of a graphene nanopore through which DNA molecules are driven by external electric fields. We performed molecular dynamic simulations to determine the relation between the intensity of the electric field and the translocation time spent by the DNA to pass through the pore. Our results reveal that one can have extra control on the DNA passage when four additional graphene layers are deposited on the top of the main graphene platform containing the pore in a 2 × 2 grid arrangement. In addition to the dynamic analysis, we carried electronic transport calculations on realistic pore structures with diameters reaching nanometer scales. The transmission obtained along the graphene sensor at the Fermi level is affected by the presence of the DNA. However, it is rather hard to distinguish the respective nucleobases. This scenario can be significantly altered when the transport is conducted away from the Fermi level of the graphene platform. Under an energy shift, we observed that the graphene pore manifests selectiveness toward DNA nucleobases.

Understanding the catalyst-free transformation of amorphous carbon into graphene by current-induced annealing

We shed light on the catalyst-free growth of graphene from amorphous carbon (a–C) by current-induced annealing by witnessing the mechanism both with in-situ transmission electron microscopy and with molecular dynamics simulations. Both in experiment and in simulation, we observe that small a–C clusters on top of a graphene substrate rearrange and crystallize into graphene patches. The process is aided by the high temperatures involved and by the van der Waals interactions with the substrate. Furthermore, in the presence of a–C, graphene can grow from the borders of holes and form a seamless graphene sheet, a novel finding that has not been reported before and that is reproduced by the simulations as well. These findings open up new avenues for bottom-up engineering of graphene-based devices.

Organic Zener Diodes: Tunneling across the gap in organic semiconductor materials

Organic Zener diodes with a precisely adjustable reverse breakdown from -3 to -15 V without any influence on the forward current-voltage curve are realized. This is accomplished by controlling the width of the charge depletion zone in a pin-diode with an accuracy of one nanometer independently of the doping concentration and the thickness of the intrinsic layer. The breakdown effect with its exponential current voltage behavior and a weak temperature dependence is explained by a tunneling mechanism across the highest occupied molecular orbital-lowest unoccupied molecular orbital gap of neighboring molecules. The experimental data are confirmed by a minimal Hamiltonian model approach, including coherent tunneling and incoherent hopping processes as possible charge transport pathways through the effective device region.

Amorphous Carbon under 80 kV Electron Irradiation: A Means to Make or Break Graphene

Within graphene research, transmission electron microscopy (TEM) has proven to be an extremely useful and versatile characterization tool. [ 1 ] However, the electron beam can interact with the sample leading to its modifi cation during the process. This may be an undesirable effect and measures to avoid this do exist. In other cases, however, electron beam–sample interactions can be useful for nano-engineering or nano-manufacturing. [ 2 ] It is therefore crucially important to understand how a material responds to the electron beam and the environment inside a TEM. In general, carbon species are sensitive to a variety of irradiation effects including knock-on displacements, electronic excitations and radiolysis, and radiation-induced diffusion. [ 3 ] For example, the irradiation of amorphous carbon with a 100 or 200 keV electron beam has been shown to lead to the formation of sp 2 carbon onions. [ 4 ] The mechanism behind this catalyst-free electron beam induced graphitization is widely argued to arise from radiation-induced diffusion [ 5 ] which may qualitatively be thought of as similar to thermal diffusion. [ 3 ]

Direct in situ observations of single Fe atom catalytic processes and anomalous diffusion at graphene edges

Significance The single metal atom has been proposed to be a catalyst during the growth of carbon nanotubes; however, this hypothesis is still not confirmed. Our direct in situ transmission EM observation of the restructuring of the graphene edges interacting with an Fe atom directly revealed the intermediate states: pentagon and hexagon structures. In particular, our experiments and simulations show that the single Fe atom behaves differently on the graphene zigzag and armchair edges, giving insights to the growth mechanisms of various sp2 carbon structures. Single-atom catalysts are of great interest because of their high efficiency. In the case of chemically deposited sp2 carbon, the implementation of a single transition metal atom for growth can provide crucial insight into the formation mechanisms of graphene and carbon nanotubes. This knowledge is particularly important if we are to overcome fabrication difficulties in these materials and fully take advantage of their distinct band structures and physical properties. In this work, we present atomically resolved transmission EM in situ investigations of single Fe atoms at graphene edges. Our in situ observations show individual iron atoms diffusing along an edge either removing or adding carbon atoms (viz., catalytic action). The experimental observations of the catalytic behavior of a single Fe atom are in excellent agreement with supporting theoretical studies. In addition, the kinetics of Fe atoms at graphene edges are shown to exhibit anomalous diffusion, which again, is in agreement with our theoretical investigations.

Exploring the topography of the stress-modified energy landscapes of mechanosensitive molecules

We propose a method for computing the activation barrier for chemical reactions involving molecules subjected to mechanical stress. The method avoids reactant and transition-state saddle optimizations at every force by, instead, solving the differential equations governing the force dependence of the critical points (i.e., minima and saddles) on the systems potential energy surface (PES). As a result, only zero-force geometry optimization (or, more generally, optimization performed at a single force value) is required by the method. In many cases, minima and transition-state saddles only exist within a range of forces and disappear beyond a certain critical point. Our method identifies such force-induced instabilities as points at which one of the Hessian eigenvalues vanishes. We elucidate the nature of those instabilities as fold and cusp catastrophes, where two or three critical points on the force-modified PES coalesce, and provide a classification of various physically distinct instability scenarios, each illustrated with a concrete chemical example.

Substituent effects in a series of 1,7-C60(RF)2 compounds (RF = CF3, C2F5, n-C3F7, i-C3F7, n-C4F9, s-C4F9, n-C8F17): electron affinities, reduction potentials and E(LUMO) values are not always correlated

A series of seven structurally-similar compounds with different pairs of RF groups were prepared, characterized spectroscopically, and studied by electrochemical methods (cyclic and square-wave voltammetry), low-temperature anion photoelectron spectroscopy, and DFT calculations (five of the compounds are reported here for the first time). This is the first time that a set of seven RF groups have been compared with respect to their relative effects on E1/2(0/−), electron affinity (EA), and the DFT-calculated LUMO energy. The compounds, 1,7-C60(RF)2 (RF = CF3, C2F5, i-C3F7, n-C3F7, s-C4F9, n-C4F9 and n-C8F21), were found to have statistically different electron affinities (EA), at the ±10 meV level of uncertainty, but virtually identical first reduction potentials, at the ±10 mV level of uncertainty. The lack of a correlation between EA and E1/2(0/−), and between E(LUMO) and E1/2(0/−), for such similar compounds is unprecedented and suggests that explanations for differences in figures of merit for materials and/or devices that are based on equating easily measurable E1/2(0/−) values with EAs or E(LUMO) values should be viewed with caution. The solubilities of the seven compounds in toluene varied by nearly a factor of six, but in an unpredictable way, with the C2F5 and s-C4F9 compounds being the most soluble and the i-C3F7 compound being the least soluble. The effects of the different RF groups on EAs, E(LUMO) values, and solubilities should help fluorine chemists choose the right RF group to design new materials with improved morphological, electronic, optical, and/or magnetic properties.

Single molecule magnet with an unpaired electron trapped between two lanthanide ions inside a fullerene

Increasing the temperature at which molecules behave as single-molecule magnets is a serious challenge in molecular magnetism. One of the ways to address this problem is to create the molecules with strongly coupled lanthanide ions. In this work, endohedral metallofullerenes Y2@C80 and Dy2@C80 are obtained in the form of air-stable benzyl monoadducts. Both feature an unpaired electron trapped between metal ions, thus forming a single-electron metal-metal bond. Giant exchange interactions between lanthanide ions and the unpaired electron result in single-molecule magnetism of Dy2@C80(CH2Ph) with a record-high 100u2009s blocking temperature of 18u2009K. All magnetic moments in Dy2@C80(CH2Ph) are parallel and couple ferromagnetically to form a single spin unit of 21u2009μB with a dysprosium-electron exchange constant of 32u2009cm−1. The barrier of the magnetization reversal of 613u2009K is assigned to the state in which the spin of one Dy centre is flipped.

π-Extended and Curved Antiaromatic Polycyclic Hydrocarbons

Synthesis of antiaromatic polycyclic hydrocarbons (PHs) is challenging because the high energy of their highest occupied molecular orbital and low energy of their lowest unoccupied molecular orbital cause them to be reactive and unstable. In this work, two large antiaromatic acene analogues, namely, cyclopenta[pqr]indeno[2,1,7-ijk]tetraphene (CIT, 1a) and cyclopenta[pqr]indeno[7,1,2-cde]picene (CIP, 1b), as well as a curved antiaromatic molecule with 48 π-electrons, dibenzo[a,c]diindeno[7,1,2-fgh:7,1,2-mno]phenanthro[9,10-k]tetraphene (DPT, 1c), are synthesized on the basis of the corona of indeno[1,2-b]fluorene. These three antiaromatic PHs possess a narrow energy gap down to 1.55 eV and exhibit high kinetic stability under ambient conditions. Moreover, these compounds display reversible electron transfer processes in both the cathodic and anodic regimes. Their cation and anion radicals are characterized by in situ vis-NIR absorption and electron paramagnetic resonance spectroelectrochemistry. The X-ray crystallographic analysis confirms that while CIP and CIT manifest planar structures, DPT shows a curved π-conjugated carbon skeleton. The synthetic strategy starting from ortho-substituted benzene units to construct five-membered rings in this work provides a unique entry to novel pentagon-embedding or curved antiaromatic polycyclic hydrocarbons. In addition, besides the detailed chemical and physical investigations, microscale single-crystal fiber field-effect transistors were also fabricated.

Regioselective synthesis and crystal structure of C70(CF3)10[C(CO2Et)2]

The Bingel reaction of poly(trifluoromethyl)fullerene p7mp-C70(CF3)10 with diethyl malonate and CBr4 in the presence of bases yields the C70(CF3)10[C(CO2Et)2] cycloadduct as a major product, along with two C70(CF3)10[CH(CO2Et)] isomers. An XRD study of the main compound demonstrates that a [2 + 1] cycloaddition occurs at the unoccupied pole of the p7mp-C70(CF3)10 molecule. The observed regiochemical selectivity of the [2 + 1] cycloaddition is shown to be favored from both energetic and orbital reactivity viewpoints.