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a) Electrostatic potential energy Ep(X) of empty gap (Figure 1a) obtained by TranSIESTA along the midline parallel to the z‐axis in the electrode plane for different terminations X (N – black, F – blue, Cl – violet, S – olive, and H – red). In‐gap distance is measured from termination atoms on the left to the termination atoms on the right graphene sheet in the z‐direction. b) The difference E⊥HOMO(X) between the HOMO and the electrode Fermi energy for perpendicularly oriented benzene in X‐terminated nanogaps (see Figure 1b). c) Center‐of‐the‐gap Ep(X)–Ep(F) values and E⊥HOMO(X)–E⊥HOMO(F), represented with blue crosses and magenta diamonds, respectively.
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Functionalization of electrodes is a wide‐used strategy in various applications ranging from single‐molecule sensing and protein sequencing, to ion trapping, to desalination. We demonstrate, employing non‐equilibrium Green′s function formalism combined with density functional theory, that single‐species (N, H, S, Cl, F) termination of graphene nano...
Citations
... Article nanoslit device are also expected to reduce orientational fluctuations during experimental measurements. 48,58 The I−V pattern demonstrates that some of the amino acids (Ala, His, Lys, Pro, and Tyr) may be distinctly identified within the (0.05−0.10 V) bias window, as shown in Figure 55,59,60 The transmission function T(E, V) depends not only on the electronic structure of the targeted molecule but also on a number of other factors, such as the strength of coupling between targeted molecule and leads, which itself is a function of the geometry of the targeted molecule-lead system. Specifically, T(E, V) is very much sensitive to the energy matching of the asymptotic Bloch channels in the leads with the energy level of the targeted molecule, deformed by the coupling with electrodes and adapted to the drop in chemical potential of the molecule. ...
... Similarly, for both dCMP and dTMP, the LUMO orbital primarily occupies the nucleobase part (Figure 1b,d). At zerobias, the E P along the midline in the z-direction in an empty gap between H-terminated CNTs is given in Figure 2a, whose shape (magenta line) originates from the dipoles at CNT terminations [39,40]. Figure 2b shows the empty-gap electrostatic potential energy E P (bias) − E P (0) along the same line at different bias values and average z coordinates of HOMO and LUMO (<z HOMO > and <z LUMO >, orange and purple vertical lines, respectively, and also Figure 1) of nucleotides. ...
... Similarly, for both dCMP and dTMP, the LUMO orbital primarily occupies the nucleobase part (Figure 1b,d). At zerobias, the EP along the midline in the z-direction in an empty gap between H-terminated CNTs is given in Figure 2a, whose shape (magenta line) originates from the dipoles at CNT terminations [39,40]. Figure 2b shows the empty-gap electrostatic potential energy EP(bias) − EP(0) along the same line at different bias values and average z coordinates of HOMO and LUMO (<zHOMO> and <zLUMO>, orange and purple vertical lines, respectively, and also Figure 1) of nucleotides. ...
... At those voltages, 0.2 V for dTMP and 1 V for dCMP, both HOMO and LUMO energies of both nucleotides deviate from the WP lines. Simultaneously, the charge Q (Figure 3), obtained from the Hirshfeld population analysis, begins to accumulate on the molecule, causing the strong pinning of the orbitals to the electrochemical potential µ L of the left electrode (light blue line in Figure 3) [39,40]. ...
The electrical current properties of single-molecule sensing devices based on electronic (tunneling) transport strongly depend on molecule frontier orbital energy, spatial distribution, and position with respect to the electrodes. Here, we present an analysis of the bias dependence of molecule frontier orbital properties at an exemplar case of DNA nucleotides in the gap between H-terminated (3, 3) carbon nanotube (CNT) electrodes and its relation to transversal current rectification. The electronic transport properties of this simple single-molecule device, whose characteristic is the absence of covalent bonding between electrodes and a molecule between them, were obtained using density functional theory and non-equilibrium Green’s functions. As in our previous studies, we could observe two distinct bias dependences of frontier orbital energies: the so-called strong and the weak pinning regimes. We established a procedure, from zero-bias and empty-gap characteristics, to estimate finite-bias electronic tunneling transport properties, i.e., whether the molecular junction would operate in the weak or strong pinning regime. We also discuss the use of the zero-bias approximation to calculate electric current properties at finite bias. The results from this work could have an impact on the design of new single-molecule applications that use tunneling current or rectification applicable in high-sensitivity sensors, protein, or DNA sequencing.
Nanoporous membranes promise energy‐efficient water desalination. Hexagonal boron nitride (h‐BN), like graphene, exhibits outstanding physical and chemical properties, making it a promising candidate for water treatment. We employed Car‐Parrinello molecular dynamics simulations to establish an accurate modeling of Na⁺ and Cl⁻ permeation through hydrogen passivated nanopores in graphene and h‐BN membranes. We demonstrate that ion separation works well for the h‐BN system by imposing a barrier of 0.13 eV and 0.24 eV for Na⁺ and Cl⁻ permeation, respectively. In contrast, for permeation of the graphene nanopore, the Cl⁻ ion faces a minimum of energy of 0.68 eV in the nanopore plane and is prone toward blockade of the nanopore, while the Na⁺ ion experiences a slight minimum of 0.03 eV. Overall, the desalination performance of h‐BN nanopores surpasses that of their graphene counterparts.
Triacetone triperoxide (TATP) is a highly potent homemade explosive commonly used in terrorist attacks. Its detection poses a significant challenge due to its volatility, and the lack of portability of current sensing techniques. To address this issue, we propose a novel approach based on single-molecule TATP detection in the air using a device where tunneling current in N-terminated carbon-nanotubes nanogaps is measured. By employing the density functional theory combined with the non-equilibrium Green's function method, we show that current of tens of nanoamperes passes through TATP trapped in the nanogap, with a discrimination ratio of several orders of magnitude even against prevalent indoor volatile organic compounds (VOCs). This high tunneling current through TATP's highest occupied molecular orbital (HOMO) is facilitated by the strong electric field generated by N-C polar bonds at the electrode ends and by the hybridization between TATP and the electrodes, driven by oxygen atoms within the probed molecule. The application of the same principle is discussed for graphene nanogaps and break-junctions.
The requirement for controllable frontier orbital energy shift in single-molecule devices based on electronic (tunneling) transport yielded several rules for device design that lean on molecular level pinning to the electrochemical potential of nano-electrodes. We previously found that the pinning (designated as the strong pinning) was the consequence of the bias-induced molecular charge accumulation related to the hybridization of the highest occupied molecular orbital (HOMO) with one of the electrodes. However, in the wide bias range, only “partial” pinning (designated as the weak pinning) happens. In this work, we address the bias-induced shift of molecular orbitals in a weak pinning regime, where no hybridization or covalent bonds with electrodes exist. We found using density functional theory coupled with non-equilibrium Green’s functions that the energy shift of frontier molecular orbitals of benzene and nicotine, placed between H-terminated (3, 3) CNTs, in weak pinning regime, is driven only by the electrostatic potential energy of an empty gap. For nicotine, whose HOMO and LUMO (lowest unoccupied molecular orbital) are located on different sides of the gap center, we show that the HOMO-LUMO energy gap changes with bias. We developed a theoretical model of a dielectric in a gap to depict this behavior. Application-wise, we expect that the weak pinning effect would be observable in novel single-molecule sensors based on electronic transport and molecular rectifying as long as the system exhibits a non-resonant behavior, and could serve for molecular gap tuning in single-molecule readout such as DNA, RNA and protein sequencing, or harmful single-molecule detection in gas phase.
Fast, reliable and inexpensive DNA sequencing is an important pursuit in healthcare, especially in personalized medicine with possible deep societal impacts. Despite significant progress of various nanopore-based sequencing configurations, challenges that remain in resolution and chromosome-size long readout call for new approaches. Here we found strong rectification in transverse current during ssDNA translocation through a nanopore with side-embedded N-terminated carbon nanotube electrodes. Employing DFT and Non-Equilibrium Green’s Function formalism, we show that the rectifying ratio (response to square pulses of alternating bias) bears high nucleobase specificity. The rectification arises due to bias-dependent resistance asymmetry on the deoxyribonucleotide-electrode interfaces. The asymmetry induces molecular charging and HOMO pinning to the electrochemical potential of one of the electrodes, assisted by an in-gap electric field effect caused by dipoles at the terminated electrode ends. We propose rectifying ratio, due to its order-of-magnitude-difference nucleobase selectivity and robustness to electrode-molecule orientation as a promising read-out quantifier for single-base resolution in solid state nanopore sequencing devices.
