Fabrication of a Complex Two-Dimensional Adenine Perylene-3,4,9,10-tetracarboxylic Dianhydride Chiral Nanoarchitecture through Molecular Self-Assembly

International audienceThe two-dimensional self-assembly of a nonsymmetric adenine DNA base mixed with symmetric perylene-3,4,9,10-tetracarboxylic dianhydride (PTCDA) molecules is investigated using scanning tunneling microscopy (STM). We experimentally observe that these two building blocks form a complex close-packed chiral supramolecular network on Au(111). The unit cell of the adenine PTCDA nanoarchitecture is composed of 14 molecules. The high stability of this structure relies on PTCDA PTCDA and PTCDA adenine hydrogen bonding. Detailed theoretical analysis based on the density functional theory (DFT) calculations reveals that adenine molecules work as a "glue", providing additional strengthening to the PTCDA-based skeleton of this sophisticated multicomponent nanoarchitecture. At the same time, we find that orientation and chirality of adenine molecules across the monolayer is likely to vary, leading to a disorder in the atomistic structure of the entire assembly

Simulated structure and imaging of NTCDI on Si(1 1 1)-7 × 7 : a combined STM, NC-AFM and DFT study

The adsorption of naphthalene tetracarboxylic diimide (NTCDI) on Si(1 1 1)-7 × 7 is investigated through a combination of scanning tunnelling microscopy (STM), noncontact atomic force microscopy (NC-AFM) and density functional theory (DFT) calculations. We show that NTCDI adopts multiple planar adsorption geometries on the Si(1 1 1)-7 × 7 surface which can be imaged with intramolecular bond resolution using NC-AFM. DFT calculations reveal adsorption is dominated by covalent bond formation between the molecular oxygen atoms and the surface silicon adatoms. The chemisorption of the molecule is found to induce subtle distortions to the molecular structure, which are observed in NC-AFM images

Temperature control in molecular dynamic simulations of non-equilibrium processes

Thermostats are often used in various condensed matter problems, e.g. when a biological molecule undergoes a transformation in a solution, a crystal surface is irradiated with energetic particles, a crack propagates in a solid upon applied stress, two surfaces slide with respect to each other, an excited local phonon dissipates its energy into a crystal bulk, and so on. In all of these problems, as well as in many others, there is an energy transfer between different local parts of the entire system kept at a constant temperature. Very often, when modelling such processes using molecular dynamics simulations, thermostatting is done using strictly equilibrium approaches serving to describe the NV T ensemble. In this paper we critically discuss the applicability of such approaches to non-equilibrium problems, including those mentioned above, and stress that the correct temperature control can only be achieved if the method is based on the generalized Langevin equation (GLE). Specifically, we emphasize that a meaningful compromise between computational efficiency and a physically appropriate implementation of the NV T thermostat can be achieved, at least for solid state and surface problems, if the so-called stochastic boundary conditions (SBC), recently derived from the GLE (Kantorovich and Rompotis 2008 Phys. Rev. B 78 094305), are used. For SBC, the Langevin thermostat is only applied to the outer part of the simulated fragment of the entire system which borders the surrounding environment (not considered explicitly) serving as a heat bath. This point is illustrated by comparing the performance of the SBC and some of the equilibrium thermostats in two problems: (i) irradiation of the Si(001) surface with an energetic CaF2 molecule using an ab initio density functional theory based method, and (ii) the tribology of two amorphous SiO2 surfaces coated with self-assembled monolayers of methyl-terminated hydrocarbon alkoxylsilane molecules using a classical atomistic force field. We discuss the differences in behaviour of these systems due to applied thermostatting, and show that in some cases a qualitatively different physical behaviour of the simulated system can be obtained if an equilibrium thermostat is used

Quantum interference and the time-dependent radiation of nanojunctions

Using the recently developed time-dependent Landauer-Buttiker formalism and Jefimenko's retarded solutions to the Maxwell equations, we show how to compute the time-dependent electromagnetic field produced by the charge and current densities in nanojunctions out of equilibrium. We then apply this formalism to a benzene ring junction and show that geometry-dependent quantum interference effects can be used to control the magnetic field in the vicinity of the molecule. Then, treating the molecular junction as a quantum emitter, we demonstrate clear signatures of the local molecular geometry in the nonlocal radiated power.Peer reviewe

Atomistic insight into the formation dynamics of charged point defects:A classical molecular dynamics study of Formula Presented-centers in NaCl

This paper provides an atomistic exploration of the lattice dissipation mechanisms accompanying the formation of charged point defects through a femtosecond resolved study of Formula Presented-center creation in NaCl. Our findings, following from a classical molecular dynamics based investigation of this model system, point to general range of properties that should be present in similar systems. Immediately after the creation of such a charged defect center, its excess energy is imparted amongst the highest energy optical modes with no clear preference based on their degree of localization. This energy is then dissipated through equilibration amongst a bath of lower energy phonon modes. The temporal behavior primarily follows exponential decay trends at all the temperatures and energies explored, with a small degree of competition between phonon population and depopulation amongst lower energy bath modes. Moreover, the dissipation timescale is found to be approximately the same amongst all phonon energies. A temperature-dependent analysis shows the expected decrease in phonon lifetimes with increasing temperature. This is accompanied by similarly more rapid dissipation of thermal energy around the defect center at lower temperatures when the phonon mean free path is increased. An intuitive phenomenological model based on Langevin dynamics is also provided to interpret the atomistically derived phonon decay characteristics in the temporal domain. More broadly, these results are expected to aid the design and experimental investigation of strongly correlated materials where charged defect centers can play an important role in technological applications.</p

On-Surface Boronation of Porphyrin into a Molecular Dipole

Functionalized porphyrins by introducing exotic atoms into their central cavities have significant applications across various fields. As unique nanographenes, porphyrins functionalized with monoboron are intriguing, yet their synthesis remains highly challenging. Herein, we present the first on-surface boronation of porphyrin, bonding a single boron atom into the porphyrin’s cavity. The boronation is selective, being observed exclusively in molecules featuring a specific aromatic ring-fused structure (ARFS*), not the pristine porphyrin molecule or its other ARFS forms. The boron’s bonding geometry is noncentered, transforming the boronated porphyrin into a molecular dipole and imparting a markedly varied electronic structure. Well-ordered two-dimensional dipole arrays are achieved. Upon elevated thermoactivation, intermolecular O–B–O bonds provide robustness and flexibility to the molecular chains. This work demonstrates the high selectivity of on-surface porphyrin boronation and provides an effective strategy for tailoring molecules’ electronic structure, producing molecular dipoles, and promoting the robustness and flexibility of molecular chains

Partition-free theory of time-dependent current correlations in nanojunctions in response to an arbitrary time-dependent bias

Working within the nonequilibrium Green’s function formalism, a formula for the two-time current correlation function is derived for the case of transport through a nanojunction in response to an arbitrary time-dependent bias. The one-particle Hamiltonian and the wide-band limit approximation are assumed, enabling us to extract all necessary Green’s functions and self-energies for the system, extending the analytic work presented previously [Ridley et al. , Phys. Rev. B 91 , 125433 ( 2015 )]. We show that our expression for the two-time correlation function generalizes the Büttiker theory of shot and thermal noise on the current through a nanojunction to the time-dependent bias case including the transient regime following the switch-on. Transient terms in the correlation function arise from an initial state that does not assume (as is usually done) that the system is initially uncoupled, i.e., our approach is partition free. We show that when the bias loses its time dependence, the long-time limit of the current correlation function depends on the time difference only, as in this case an ideal steady state is reached. This enables derivation of known results for the single-frequency power spectrum and for the zero-frequency limit of this power spectrum. In addition, we present a technique which facilitates fast calculations of the transient quantum noise, valid for arbitrary temperature, time, and voltage scales. We apply this formalism to a molecular wire system for both dc and ac biases, and find a signature of the traversal time for electrons crossing the wire in the time-dependent cross-lead current correlations

Intramolecular bonds resolved on a semiconductor surface

Noncontact atomic force microscopy (NC-AFM) is now routinely capable of obtaining submolecular resolution, readily resolving the carbon backbone structure of planar organic molecules adsorbed on metal substrates. Here we show that the same resolution may also be obtained for molecules adsorbed on a reactive semiconducting substrate. Surprisingly, this resolution is routinely obtained without the need for deliberate tip functionalization. Intriguingly, we observe two chemically distinct apex types capable of submolecular imaging. We characterize our tip apices by "inverse imaging" of the silicon adatoms of the Si (111) -7 x 7 surface and support our findings with detailed density functional theory (DFT) calculations. We also show that intramolecular resolution on individual molecules may be readily obtained at 78 K, rather than solely at 5 K as previously demonstrated. Our results suggest a wide range of tips may be capable of producing intramolecular contrast for molecules adsorbed on semiconductor surfaces, leading to a much broader applicability for submolecular imaging protocols