Strongly localised molecular orbitals for α\alpha-quartz

A previously proposed computational procedure for constructing a set of nonorthogonal strongly localised one-electron molecular orbitals (O. Danyliv, L. Kantorovich - physics/0401107) is applied to a perfect $\alpha$-quartz crystal characterised by an intermediate type of chemical bonding. The orbitals are constructed by applying various localisation methods to canonical Hartree-Fock orbitals calculated for a succession of finite molecular clusters of increased size with appropriate boundary conditions. The calculated orbitals span the same occupied Fock space as the canonical HF solutions, but have an advantage of reflecting the true chemical nature of the bonding in the system. The applicability of several localisation techniques as well as of a number of possible choices of localisation regions (structure elements) are discussed for this system in detail

Comparison of localization procedures for applications in crystal embedding

With the aim of future applications in quantum mechanical embedding in extended systems such as crystals, we suggest a simple and computationally efficient method which enables construction of a set of nonorthogonal highly localized one-electron orbitals for periodic nonmetallic crystals which reflect their chemical nature. The orbitals are also used to build up the Hartree-Fock (HF) electron density of the entire crystals. The simplicity of the method stems from the fact that it does not require usage and/or modification of periodic electronic structure codes, and is instead based on the HF calculation of a sequence of finite clusters with subsequent application of a localization procedure to transform the HF canonical molecular orbitals. Two extreme cases of chemical bonding, ionic (MgO crystal) and covalent (Si crystal), are considered for which a number of known localization schemes are applied and compared. With some modifications our method can also be applied to nonperiodic nonmetallic systems as well

Calculation of the current response in a nanojunction for an arbitrary time-dependent bias: application to the molecular wire

Recently [Phys. Rev. B 91, 125433 (2015)] we derived a general formula for the time-dependent quantum electron current through a molecular junction subject to an arbitrary time-dependent bias within the Wide Band Limit Approximation (WBLA) and assuming a single particle Hamiltonian. Here we present an efficient numerical scheme for calculating the current and particle number. Using the Pad\'e expansion of the Fermi function, it is shown that all frequency integrals occurring in the general formula for the current can be removed analytically. Furthermore, when the bias in the reservoirs is assumed to be sinusoidal it is possible to manipulate the general formula into a form containing only summations over special functions. To illustrate the method, we consider electron transport through a one-dimensional molecular wire coupled to two leads subject to out-of-phase biases. We also investigate finite size effects in the current response and particle number that results from the switch-on of such a bias

Non-equilibrium statistical mechanics of classical nuclei interacting with the quantum electron gas

Kinetic equations governing time evolution of positions and momenta of atoms in extended systems are derived using quantum-classical ensembles within the Non-Equilibrium Statistical Operator Method (NESOM). Ions are treated classically, while their electrons quantum mechanically; however, the statistical operator is not factorised in any way and no simplifying assumptions are made concerning the electronic subsystem. Using this method, we derive kinetic equations of motion for the classical degrees of freedom (atoms) which account fully for the interaction and energy exchange with the quantum variables (electrons). Our equations, alongside the usual Newtonian-like terms normally associated with the Ehrenfest dynamics, contain additional terms, proportional to the atoms velocities, which can be associated with the electronic friction. Possible ways of calculating the friction forces which are shown to be given via complicated non-equilibrium correlation functions, are discussed. In particular, we demonstrate that the correlation functions are directly related to the thermodynamic Matsubara Green's functions, and this relationship allows for the diagrammatic methods to be used in treating electron-electron interaction perturbatively when calculating the correlation functions. This work also generalises previous attempts, mostly based on model systems, of introducing the electronic friction into Molecular Dynamics equations of atoms.Comment: 18 page

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

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

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

Calculation of electron density of periodic systems using non-orthogonal localised orbitals

Methods for calculating an electron density of a periodic crystal constructed using non-orthogonal localised orbitals are discussed. We demonstrate that an existing method based on the matrix expansion of the inverse of the overlap matrix into a power series can only be used when the orbitals are highly localised (e.g. ionic systems). In other cases including covalent crystals or those with an intermediate type of chemical bonding this method may be either numerically inefficient or fail altogether. Instead, we suggest an exact and numerically efficient method which can be used for orbitals of practically arbitrary localisation. Theory is illustrated by numerical calculations on a model system.Comment: 12 pages, 4 figure