The influence of the charging effects on the transport characteristics of a molecular wire bridging two metallic electrodes in the limit of weak contacts is studied by generalized Breit-Wigner formula. Molecule is modeled as a quantum dot with discrete energy levels, while the coupling to the electrodes is treated within a broad band theory. Owing to this model we find self-consistent occupation of particular energy levels and orbital energies of the wire in the presence of transport. The nonlinear conductance and current-voltage characteristics are investigated as a function of bias voltage in the case of symmetric and asymmetric coupling to the electrodes. It is shown that the shape of that curves are determined by the combined effect of the electronic structure of the molecule and by electron-electron repulsion.
Based on large-scale molecular dynamics simulations, we propose a new charging method that should be capable of charging a Lithium-ion battery in a fraction of the time needed when using traditional methods. This charging method uses an additional applied oscillatory electric field. Our simulation results show that this charging method offers a great reduction in the average intercalation time for Li+ ions, which dominates the charging time. The oscillating field not only increases the diffusion rate of Li+ ions in the electrolyte but, more importantly, also enhances intercalation by lowering …
When electric current flows through a molecular junction, the molecule constantly charges and discharges by tunnelling electrons. These charging and discharging events occur at specific but random times and separated by stochastic time intervals. These time intervals can be associated with dwelling time for a charge (electron or hole) to reside on the molecule. In this paper, the statistical properties of these time intervals are studied and general formula for their distribution is derived. The theory is based on the Markovian master equation which takes into account transitions between vibra…
Supercapacitors are electric devices able to deliver a large power, enabling their use e.g. for the recovery of breaking energy in cars. This is achieved by using two carbon electrodes and an electrolyte solution or a pure ionic liquid (Room Temperature Ionic Liquid, RTIL). Energy is stored by the adsorption of ions at the surface of the electrodes, but the microscopic mechanism underlying the exceptional performance of Carbide Derived Carbon (CDC) electrodes remained unknown. Using molecular simulation with realistic electrode structures and under constant voltage conditions, we investigate t…
The potential profile across a biased molecular junction is calculated within the framework of a simple Thomas-Fermi type screening model. In particular, the relationship between this profile and the lateral molecular cross section is examined. We find that a transition from a linear potential profile to a potential that drops mainly near the molecule-metal contacts occurs with increasing cross section width, in agreement with numerical quantum calculations.
A very stable binding site for the interaction between an pentameric oligothiophene and an amyloid-$β$(1-42) fibril has been identified by means of non-biased molecular dynamics simulations. In this site, the probe is locked in an all-trans conformation with a Coulombic binding energy of 1,200 kJ/mol due to the interactions between the anionic carboxyl groups of the probe and the cationic $ε$-amino groups in the lysine side chain. Upon binding, the conformationally restricted probes show a pronounced increase in molecular planarity. This is in-line with the observed changes in luminescence pro…
Many recently introduced enhanced sampling techniques are based on biasing coarse descriptors (collective variables) of a molecular system on the fly. Sometimes the calculation of such collective variables is expensive and becomes a bottleneck in molecular dynamics simulations. An algorithm to treat smooth biasing forces within a multiple time step framework is here discussed. The implementation is simple and allows a speed up when expensive collective variables are employed. The gain can be substantial when using massively parallel or GPU-based molecular dynamics software. Moreover, a theoret…
We study the electrostatic potential of a molecular wire bridging two metallic electrodes in the limit of weak contacts. With the use of a tight-binding model including a fully three-dimensional treatment of the electrostatics of the molecular junction, the potential is shown to be poorly screened, dropping mostly along the entire molecule. In addition, we observe pronounced Friedel oscillations that can be related to the breaking of electron-hole symmetry. Our results are in semi-quantitative agreement with recent state-of-the-art ab initio calculations and point to the need of a three-dimens…
Molecular simulations can provide microscopic insight into the physical and chemical driving forces of complex molecular processes. Despite continued advancement of simulation methodology, model errors may lead to inconsistencies between simulated and reference (e.g., from experiments or higher-level simulations) observables. To bound the microscopic information generated by computer simulations within reference measurements, we propose a method that reweights the microscopic transitions of the system to improve consistency with a set of coarse kinetic observables. The method employs the well-…
One of the molecular properties most intuitive to the human perception is the geometrical shape. However, when exploring a large chemical space the determination of shape needs to be automated. We present a fast and simple approach to identify a molecule as linear, planar, cube, cuboid, disk, elliptical disk, spheroid and sphere which is more fine grained than existing approaches. The method is applied to more than one billion molecules ranging from small organic molecules to whole proteins. The results show that current chemistry research is biased towards planar geometries. Moreover, we demo…
We consider a biased molecular junction subjected to external time-dependent electromagnetic field. We discuss local field formation due to both surface plasmon-polariton excitations in the contacts and the molecular response. Employing realistic parameters we demonstrate that such self-consistent treatment is crucial for proper description of the junction transport characteristics.
Supercapacitors are energy storage devices able to deliver electricity with a high power. They consist of porous carbon electrodes in a concentrated electrolyte. Charged is stored by the adsorption of ions at the electrode surface. Nanoporous carbons allow to store more electricity thanks to a charging mechanism that differs from carbons with larger pores. This mechanism has recently been uncovered by combining in situ experiments (nuclear magnetic resonance, electrochemical quartz microbalance) and molecular simulations.
A variety of enhanced statistical and numerical methods are now routinely used to extract comprehensible and relevant thermodynamic information from the vast amount of complex, high-dimensional data obtained from intensive molecular simulations. The characterization of kinetic properties, such as diffusion coefficients, of molecular systems with significantly high energy barriers, on the other hand, has received less attention. Among others, Markov state models, in which the long-time statistical dynamics of a system is approximated by a Markov chain on a discrete partition of configuration sp…
Biased sampling of collective variables is widely used to accelerate rare events in molecular simulations and to explore free energy surfaces. However, computational efficiency of these methods decreases with increasing number of collective variables, which severely limits the predictive power of the enhanced sampling approaches. Here we propose a method called Temperature Accelerated Sliced Sampling (TASS) that combines temperature accelerated molecular dynamics with umbrella sampling and metadynamics to sample the collective variable space in an efficient manner. The presented method can sam…
Li+ transport within a solid electrolyte interphase (SEI) in lithium ion batteries has challenged molecular dynamics (MD) studies due to limited compositional control of that layer. In recent years, experiments and ab initio simulations have identified dilithium ethylene dicarbonate (Li2EDC) as the dominant component of SEI layers. Here, we adopt a parameterized, non-polarizable MD force field for Li2EDC to study transport characteristics of Li+ in this model SEI layer at moderate temperatures. The observed correlations are consistent with recent MD results using a polarizable force field, sug…
We present a consistent theory of energy balance and conversion in a single-molecule junction with strong interactions between electrons on the molecular linker (dot) and phonons in the nuclear environment where the Marcus-type electron hopping processes predominate in the electron transport. It is shown that the environmental reorganization and relaxation that accompany electron hopping energy exchange between the electrodes and the nuclear (molecular and solvent) environment may bring a moderate local cooling of the latter in biased systems. The effect of a periodically driven dot level on t…
Estimating the free energy in molecular simulation requires, implicitly or explicitly, counting how many times the system is observed in a finite region. If the simulation is biased by an external potential, the weight of the configurations within the region can vary significantly, and this can make the estimate numerically unstable. We introduce an approach to estimate the free energy as a simultaneous function of several collective variables starting from data generated in a statically-biased simulation. The approach exploits the property of a free energy estimator recently introduced by us …
