Molecular dynamics study of the stability of a carbon nanotube atop a catalytic nanoparticle

The stability of a single-walled carbon nanotube placed on top of a catalytic nickel nanoparticle is investigated by means of molecular dynamics simulations. As a case study, we consider the $(12,0)$ nanotube consisting of 720 carbon atoms and the icosahedral Ni$_{309}$ cluster. An explicit set of constant-temperature simulations is performed in order to cover a broad temperature range from 400 to 1200 K, at which a successful growth of carbon nanotubes has been achieved experimentally by means of chemical vapor deposition. The stability of the system depending on parameters of the involved interatomic interactions is analyzed. It is demonstrated that different scenarios of the nanotube dynamics atop the nanoparticle are possible depending on the parameters of the Ni-C potential. When the interaction is weak the nanotube is stable and resembles its highly symmetric structure, while an increase of the interaction energy leads to the abrupt collapse of the nanotube in the initial stage of simulation. In order to validate the parameters of the Ni-C interaction utilized in the simulations, DFT calculations of the potential energy surface for carbon-nickel compounds are performed. The calculated dissociation energy of the Ni-C bond is in good agreement with the values, which correspond to the case of a stable and not deformed nanotube simulated within the MD approach.Comment: 11 pages, 5 figures; submitted to Eur. Phys. J.

Classical molecular dynamics simulations of fusion and fragmentation in fullerene-fullerene collisions

We present the results of classical molecular dynamics simulations of collision-induced fusion and fragmentation of C$_{60}$ fullerenes, performed by means of the MBN Explorer software package. The simulations provide information on structural differences of the fused compound depending on kinematics of the collision process. The analysis of fragmentation dynamics at different initial conditions shows that the size distributions of produced molecular fragments are peaked for dimers, which is in agreement with a well-established mechanism of C$_{60}$ fragmentation via preferential C$_2$ emission. Atomic trajectories of the colliding particles are analyzed and different fragmentation patterns are observed and discussed. On the basis of the performed simulations, characteristic time of C$_2$ emission is estimated as a function of collision energy. The results are compared with experimental time-of-flight distributions of molecular fragments and with earlier theoretical studies. Considering the widely explored case study of C$_{60}$--C$_{60}$ collisions, we demonstrate broad capabilities of the MBN Explorer software, which can be utilized for studying collisions of a broad variety of nanoscale and biomolecular systems by means of classical molecular dynamics

Atomistic simulation of the FEBID-driven growth of iron-based nanostructures

The growth of iron-containing nanostructures in the process of focused electron beam-induced deposition (FEBID) of Fe(CO)$_5$ is studied by means of atomistic irradiation-driven molecular dynamics (IDMD) simulations. The geometrical characteristics (lateral size, height and volume), morphology and metal content of the grown nanostructures are analyzed at different irradiation and precursor replenishment conditions corresponding to the electron-limited and precursor-limited regimes (ELR & PLR) of FEBID. A significant variation of the deposit's morphology and elemental composition is observed with increasing the electron current from 1 to 4 nA. At low beam current (1 nA) corresponding to the ELR and a low degree of Fe(CO)$_5$ fragmentation, the nanogranular structures are formed which consist of isolated iron clusters embedded into an organic matrix. In this regime, metal clusters do not coalesce with increasing electron fluence, resulting in relatively low metal content of the nanostructures. A higher beam current of 4 nA corresponding to the PLR facilitates the precursor fragmentation and the coalescence of metal clusters into a dendrite-like structure with the size corresponding to the primary electron beam. The IDMD simulations enable atomistic-level predictions on the nanoscopic characterization of the initial phase of nanostructure growth in the FEBID process. These predictions can be verified in high-resolution transmission electron microscopy experiments.Comment: 13 pages, 7 figure

Reactive molecular dynamics simulations of organometallic compound W(CO)6 fragmentation

Irradiation- and collision-induced fragmentation studies provide information about geometry, electronic properties and interactions between structural units of various molecular systems. Such knowledge brings insights into irradiation-driven chemistry of molecular systems which is exploited in different technological applications. An accurate atomistic-level simulation of irradiation-driven chemistry requires reliable models of molecular fragmentation which can be verified against mass spectrometry experiments. In this work fragmentation of a tungsten hexacarbonyl, W(CO)$_6$, molecule is studied by means of reactive molecular dynamics simulations. The quantitatively correct fragmentation picture including different fragmentation channels is reproduced. We show that distribution of the deposited energy over all degrees of freedom of the parent molecule leads to thermal evaporation of CO groups and the formation of W(CO)$_n^+$ ($n = 0-5$) fragments. Another type of fragments, WC(CO)$_n^+$ ($n = 0-4$), is produced due to cleavage of a C--O bond as a result of the localized energy deposition. Calculated fragment appearance energies are in good agreement with experimental data. These fragmentation mechanisms have a general physical nature and should take place in radiation-induced fragmentation of different molecular and biomolecular systems.Comment: 11 pages, 6 figures, submitted to European Physical Journal

Irradiation driven molecular dynamics simulation of the FEBID process for Pt(PF3_3)4_4

This paper presents a detailed computational protocol for atomistic simulation of the formation and growth of metal-containing nanostructures during the Focused Electron Beam Induced Deposition (FEBID) process. The protocol is based upon the Irradiation-Driven Molecular Dynamics (IDMD) - a novel and general methodology for computer simulations of irradiation-driven transformations of complex molecular systems by means of the advanced software packages MBN Explorer and MBN Studio. Atomistic simulations performed following the formulated protocol provide valuable insights into the fundamental mechanisms of electron-induced precursor fragmentation and the related mechanism of nanostructure formation and growth using FEBID, which are essential for the further advancement of FEBID-based nanofabrication. The developed computational methodology is general and applicable to different precursor molecules, substrate types, irradiation regimes, etc. The methodology can also be adjusted to simulate the nanostructure formation by other nanofabrication techniques using electron beams, such as direct electron beam lithography. In the present study, the methodology is applied to the IDMD simulation of the FEBID of Pt(PF$_3$)$_4$ - a widely studied precursor molecule - on a SiO$_2$ surface. The simulations reveal the processes driving the initial phase of nanostructure formation during FEBID, including nucleation of Pt atoms, formation of small metal clusters on the surface, followed by their aggregation and the formation of dendritic platinum nanostructures. The analysis of the simulation results provides space resolved relative metal content, height and the growth rate of the deposits which represent valuable reference data for the experimental characterization of the nanostructures grown by FEBID.Comment: 19 pages, 12 figure

Atomistic modeling of thermal effects in focused electron beam induced deposition of Me2_2Au(tfac)

The role of thermal effects in the focused electron beam induced deposition (FEBID) process of Me$_2$Au(tfac) is studied by means of irradiation-driven molecular dynamics simulations. The FEBID of Me$_2$Au(tfac), a commonly used precursor molecule for the fabrication of gold nanostructures, is simulated at different temperatures in the range of $300-450$ K. The deposit's structure, morphology, growth rate, and elemental composition at different temperatures are analyzed. The fragmentation cross section for Me$_2$Au(tfac) is evaluated on the basis of the cross sections for structurally similar molecules. Different fragmentation channels involving the dissociative ionization (DI) and dissociative electron attachment (DEA) mechanisms are considered. The conducted simulations of FEBID confirm experimental observations that deposits consist of small gold clusters embedded into a carbon-rich organic matrix. The simulation results indicate that accounting for both DEA- and DI-induced fragmentation of all the covalent bonds in Me$_2$Au(tfac) and increasing the amount of energy transferred to the system upon fragmentation increase the concentration of gold in the deposit. The simulations predict an increase in Au:C ratio in the deposit from 0.18 to 0.25 upon the temperature increase from 300 K to 450 K, being within the range of experimentally reported values.Comment: 14 pages, 8 figure

On the mechanisms of radiation-induced structural transformations in deposited gold clusters

Physical mechanisms of structural transformations in deposited metallic clusters exposed to an electron beam of a scanning transmission electron microscope are analyzed theoretically and computationally. Recent experiments with size-selected Au$_{923}$ clusters softly deposited on a carbon substrate showed that the clusters undergo structural transformations from icosahedron to decahedron and face-center cubic (fcc) structures upon exposure to a 200-keV electron beam. However, a detailed theoretical description of the underlying physical mechanisms of the observed phenomena is still lacking. We demonstrate that the relaxation of plasmon excitations formed in deposited metal clusters is a plausible mechanism for the experimentally observed structural transformations. Plasmon excitations in the clusters are formed mainly due to the interaction with low-energy secondary electrons emitted from a substrate. The characteristic occurrence times for plasmon-induced energy relaxation events are several orders of magnitude shorter than those for the momentum transfer events by energetic primary electrons to atoms of the cluster. The theoretical analysis is supported by the results of molecular dynamics simulations. The simulations show that an icosahedral Au$_{923}$ cluster softly deposited on graphite undergoes a structural transformation to an fcc structure due to the vibrational excitation of the cluster.Comment: 12 pages, 10 figure