First-principles based matrix Green's function approach to molecular electronic devices: general formalism

Molecular conductance calculations of single-molecule junctions using projection-based density functional embedding

Single-Molecule Junctions (SMJs) are key platforms for the exploration of electron transport at the molecular scale. In this study, we present a method that employs different exchange-correlation density functionals for the molecule and the lead domains in an SMJ, enabling the selection of the optimal one for each part. This is accomplished using a formally exact projection-based density-functional theory (DFT-in-DFT) embedding technique combined with the non-equilibrium Green's function method to predict zero-bias conductance. The effectiveness of this approach is illustrated through transport calculations on SMJs with benzene-1,4-diamine and its tetramethylated and tetrafluorinated variants, using the CAM-B3LYP range-separated hybrid functional for the embedded molecule and the Perdew-Burke-Ernzerhof (PBE) functional for the electrodes. The findings indicate a substantial improvement in the accuracy of the predicted zero-bias conductance compared to traditional modeling using the PBE functional across the entire system. The causes for the noted improvement are demonstrated through the examination of alterations in the energy levels of the embedded molecule, along with variations in the electrode-molecule interactions.

σ Interference: Through-Space and Through-Bond Dichotomy

Dividing orbital interactions into through-space (TS) and through-bond (TB) modes is valuable for understanding various molecular properties. In this paper, we elucidate how the quantum interference phenomenon known as σ interference in electron transport through σ systems arises from TS and TB interactions. We performed electron transport calculations using a combination of density functional theory and nonequilibrium Green's function methods, focusing on ethylenediamine, a classical molecule that effectively highlights the contrast between TS and TB interactions. Our results confirm that destructive σ interference occurs in the syn and gauche conformers of this molecule. To further investigate both TS and TB interactions, we employed two analytical methods: the fragment molecular orbital (FMO) method, which captures the effects of both TS and TB interactions, and the chemical graph theory method, which specializes in TB interactions. The FMO analysis demonstrated that TB interactions lead to the characteristic distribution and energy level alignment of the frontier orbitals. Additionally, it was clarified that a change in TS interaction, due to a variation in the dihedral angle of the molecule, alters the energy gap between these orbitals, resulting in the manifestation of σ interference in the syn and gauche conformers, but not in the trans conformer. The chemical graph theory analysis based on the ladder C model, aimed at exploring the topological origin of σ interference from the network of TB interactions, revealed that σ interference is caused by the cancellation between the walk associated with geminal interactions (σ-conjugation) and the one related to vicinal interaction (σ-hyperconjugation). Notably, it was found that the vicinal interaction, which changes sign with the dihedral angle, has a decisive influence on whether this cancellation occurs. These findings clarify that σ interference arises from the interplay between TS and TB interactions. This insight will be valuable for designing molecular systems that utilize σ interference.

The electric regulation mechanism of drug molecules intercalating with DNA

The insertion of small drug molecules into DNA can change its electrical properties, thereby controlling the probability of its electrical transmission. This characteristic has enabled its widespread application in molecular electronics. However, the current understanding of the intercalation properties and electronic transmission mechanisms is still not deep enough, which severely restricts its practical application. In this paper, the density functional theory and the non-equilibrium Green's function formula are combined to bind three different small drug molecules to the same sequence of DNA through intercalation, in order to discuss the impact of intercalation and molecular structure on the electrical properties of DNA. After inserting two MAR70 molecules, the conductivity decreased from 2.38×10-5 G0 to 3.37×10-7 G0 . Upon the insertion of Nogalamycin, the conductivity dropped to 2.01×10-5 G0, only slightly lower than that of bare B-DNA. However, when cyanomorpholinodoxorubicin was inserted, the conductivity was 2.65×10-6 G0. In our study, we observed some common characteristics. After intercalating with drug molecules, new energy levels were induced, altering the positions of the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) energy levels, resulting in a narrowed bandgap and consequently reduced conductivity of the complex. Furthermore, the conductivity was also related to the number of inserted drug molecules, fewer inserted molecules led to a decrease in conductivity. The results of this study indicate that embedding drug molecules can reduce or regulate the conductivity of DNA, providing new insights for its application in the field of nanoelectronics.

Application of the shift-invert Lanczos algorithm to a nonequilibrium Green's function for transport problems

Nonequilibrium Green's function theory and related methods are widely used to describe transport phenomena in many-body systems, but they often require a costly inversion of a large matrix. We show here that the shift-invert Lanczos method can dramatically reduce the computational effort. We apply the method to two test problems, namely a simple model Hamiltonian and to a more realistic Hamiltonian for nuclear fission. For a Hamiltonian of dimension 66 103 we find that the computation time is reduced by a factor of 33 compared to the direct calculation of the Green's function.

Interpretation of molecular electron transport in ab initio many-electron framework incorporating zero-point nuclear motion effects

A computational methodology, founded on chemical concepts, is presented for interpreting the role of nuclear motion in the electron transport through single-molecule junctions (SMJ) using many-electron ab initio quantum chemical calculations. Within this approach the many-electron states of the system, computed at the SOS-ADC(2) level, are followed along the individual normal modes of the encapsulated molecules. The inspection of the changes in the partial charge distribution of the many-electron states allows the quantification of the electron transport and the estimation of transmission probabilities. This analysis improves the understanding of the relationship between internal motions and electron transport. Two SMJ model systems are studied for validation purposes, constructed from a conductor (BDA, benzene-1,4-diamine) and an insulator molecule (DABCO, 1,4-diazabicyclo[2.2.2]octane). The trends of the resulting transmission probabilities are in agreement with the experimental observations, demonstrating the capability of the approach to distinguish between conductor and insulator type systems, thereby offering a straightforward and cost-effective tool for such classifications via quantum chemical calculations.

Effective Coupling Model to Treat the Odd-Even Effect on the Current-Voltage Response of Saturated Linear Carbon Chains Single-Molecule Junctions

The calculation of the electrical charge transport properties of alkanes C n H 2n S 2 with (n = 4-11) was performed to understand the odd-even effect on its current-voltage response. The extended molecule and broadband limit models were used to describe the molecular junction and covalent coupling with the electrodes. It was shown that among the participating molecular orbitals, HOMO and HOMO-1 are the ones with the most charge transport contribution. Moreover, the odd-even effect is caused by the alternation of the eigenvalues of some frontier orbitals as a function of the number of carbons, especially the HOMO that dominates the electrical transport. It could also be noted that when the current is analyzed outside the resonance, the relationship with the number of carbons exponentially decays, confirming the reports in the literature. To the best of our knowledge, a first principle study of the odd-even effect in symmetric systems composed by linear saturated carbon chains covalently coupled to electrodes has not been reported yet.

Enabling Ab Initio Molecular Dynamics under Bias: The CP2K+SMEAGOL Interface for Integrating Density Functional Theory and Non-Equilibrium Green Functions

Density functional theory (DFT) combined with non-equilibrium Green's functions (NEGF) is a powerful approach to model quantum transport under external bias potentials at reasonable computational cost. In this work, we present a new interface between the popular mixed Gaussian/plane waves electronic structure package, CP2K, and the NEGF, code SMEAGOL, the most feature-rich implementation of DFT-NEGF available for CP2K to date. The CP2K+SMEAGOL interface includes the implementation of current induced forces. We verify this implementation for a variety of systems: an infinite 1D Au wire, a parallel-plate capacitor, and a Au-H2-Au junction. We find good agreement with SMEAGOL calculations performed with SIESTA for the same systems and with the example of a solvated Au wire demonstrating for the first time that DFT-NEGF can be used to perform molecular dynamics simulations under bias of large-scale condensed phase systems under realistic operating conditions.

Exploring Aromaticity Effects on Electronic Transport in Cyclo[n]carbon Single-Molecule Junctions

Cyclo[n]carbon (Cn) is one member of the all-carbon allotrope family with potential applications in next-generation electronic devices. By employing first-principles quantum transport calculations, we have investigated the electronic transport properties of single-molecule junctions of Cn, with n = 14, 16, 18, and 20, connected to two bulk gold electrodes, uncovering notable distinctions arising from the varying aromaticities. For the doubly aromatic C14 and C18 molecules, slightly deformed complexes at the singlet state arise after bonding with one Au atom at each side; in contrast, the reduced energy gaps between the highest occupied and the lowest unoccupied molecular orbitals due to the orbital reordering observed in the doubly anti-aromatic C16 and C20 molecules lead to heavily deformed asymmetric complexes at the triplet state. Consequently, spin-unpolarized transmission functions are obtained for the Au-C14/18-Au junctions, while spin-polarized transmission appears in the Au-C16/20-Au junctions. Furthermore, the asymmetric in-plane π-type hybrid molecular orbitals of the Au-C16/20-Au junctions contribute to two broad but low transmission peaks far away from the Fermi level (Ef), while the out-of-plane π-type hybrid molecular orbitals dominate two sharp transmission peaks that are adjacent to Ef, thus resulting in much lower transmission coefficients at Ef compared to those of the Au-C14/18-Au junctions. Our findings are helpful for the design and application of future cyclo[n]carbon-based molecular electronic devices.

Boron-doped graphene topological defects: unveiling high sensitivity to NO molecule for gas sensing applications

Global air quality has deteriorated significantly in recent years due to large emissions from the transformation industry and combustion vehicles. This issue requires the development of portable, highly sensitive, and selective gas sensors. Nanostructured materials, including defective graphene, have emerged as promising candidates for such applications. In this work, we investigated the B-doped topological line defect in graphene as a sensing material for various gas molecules (CO, CO2, NO, and NH3) based on a combination of density functional theory and the non-equilibrium Green's function method. The electronic transport calculations reveal that the electric current can be confined to the line defect region by gate voltage control, revealing highly reactive sites. The B-doped topological line defect is metallic, favoring the adsorption of NO and NH3 over CO and CO2 molecules. We notice changes in the conductance after gas molecule adsorption, producing a sensitivity of 50% (16%) for NO (NH3). In addition, the recovery time for nitride gases was calculated for different temperatures and radiation frequencies. At 300 K the ultraviolet (UV) has a fast recovery time compared to the visible (VIS) one by about two orders of magnitude. This study gives an understanding of how engineering transport properties at the microscopic level (by topological line defect and chemical B-doping) leads to promising nanosensors for detecting nitride gas.

Enhancing Spin-Transport Characteristics, Spin-Filtering Efficiency, and Negative Differential Resistance in Exchange-Coupled Dinuclear Co(II) Complexes for Molecular Spintronics Applications

Single-molecule spintronics, where electron transport occurs via a paramagnetic molecule, has gained wide attention due to its potential applications in the area of memory devices to switches. While numerous organic and some inorganic complexes have been employed over the years, there are only a few attempts to employ exchange coupled dinuclear complexes at the interface, and the advantage of fabricating such a molecular spintronics device in the observation of switchable Kondo resonance was demonstrated recently in the dinuclear [Co2(L)(hfac)4] (1) complex (Wagner et al., Nat. Nanotechnol. 2013, 8, 575-579). In this work, employing an array of theoretical tools such as density functional theory (DFT), the ab initio CASSCF/NEVPT2 method, and DFT combined with nonequilibrium Green Function (NEGF) formalism, we studied in detail the role of magnetic coupling, ligand field, and magnetic anisotropy in the transport characteristics of complex 1. Particularly, our calculations not only reproduce the current-voltage (I-V) characteristics observed in experiments but also unequivocally establish that these arise from an exchange-coupled singlet state that arises due to antiferromagnetic coupling between two high-spin Co(II) centers. Further, the estimated spin Hamiltonian parameters such as J, g values, and D and E/D values are only marginally altered for the molecule at the interface. Further, the exchange-coupled state was found to have very similar transport responses, despite possessing significantly different geometries. Our transport calculations unveil a new feature of the negative differential resistance (NDR) effect on 1 at the bias voltage of 0.9 V, which agrees with the experimental I-V characteristics reported. The spin-filtering efficiency (SFE) computed for the spin-coupled states was found to be only marginal (∼25%); however, if the ligand field is fine-tuned to obtain a low-spin Co(II) center, a substantial SFE of 44% was noted. This spin-coupled state also yields a very strong NDR with a peak-to-valley ratio (PVR) of ∼56 - a record number that has not been witnessed so far in this class of compounds. Additionally, we have established further magnetostructural-transport correlations, providing valuable insights into how microscopic spin Hamiltonian parameters can be associated with SFE. Several design clues to improve the spin-transport characteristics, SFE and NDR in this class of molecule, are offered.

Theoretical Study on the Open-Shell Electronic Structure and Electron Conductivity of [18]Annulene as a Molecular Parallel Circuit Model

Herein, the electron conductivities of [18]annulene and its derivatives are theoretically examined as a molecular parallel circuit model consisting of two linear polyenes. Their electron conductivities are estimated by elastic scattering Green's function (ESGF) theory and density functional theory (DFT) methods. The calculated conductivity of the [18]annulene does not follow the classical conductivity, i.e., Ohm's law, suggesting the importance of a quantum interference effect in single molecules. By introducing electron-withdrawing groups into the annulene framework, on the other hand, a spin-polarized electronic structure appears, and the quantum interference effect is significantly suppressed. In addition, the total current is affected by the spin polarization because of the asymmetry in the coupling constant between the molecule and electrodes. From these results, it is suggested that the electron conductivity as well as the quantum interference effect of π-conjugated molecular systems can be designed using their open-shell nature, which is chemically controlled by the substituents.

Stereoelectronic Switches of Single-Molecule Junctions through Conformation-Modulated Intramolecular Coupling Approaches

Stereoelectronic effects in single-molecule junctions have been widely utilized to achieve a molecular switch, but high-efficiency and reproducible switching remain challenging. Here, we demonstrate that there are three stable intramolecular conformations in the 9,10-diphenyl-9,10-methanoanthracen-11-one (DPMAO) systems due to steric effect. Interestingly, different electronic coupling approaches including weak coupling (through-space), decoupling, and strong coupling (through-bond) between two terminal benzene rings are accomplished in the three stable conformations, respectively. Theoretical calculations show that the molecular conductance of three stable conformations differs by more than 1 order of magnitude. Furthermore, the populations of the three stable conformations are highly dependent on the solvent effect and the external electric field. Therefore, an excellent molecular switch can be achieved using the DPMAO molecule junctions and external stimuli. Our findings reveal that modulating intramolecular electronic coupling approaches may be a useful manner to enable molecular switches with high switching ratios. This opens up a new route for building high-efficiency molecular switches in single-molecular junctions.

Tunnel junction sensing of TATP explosive at the single-molecule level

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.

Synthesis of Hidden Subgroup Quantum Algorithms and Quantum Chemical Dynamics

We describe a general formalism for quantum dynamics and show how this formalism subsumes several quantum algorithms, including the Deutsch, Deutsch-Jozsa, Bernstein-Vazirani, Simon, and Shor algorithms as well as the conventional approach to quantum dynamics based on tensor networks. The common framework exposes similarities among quantum algorithms and natural quantum phenomena: we illustrate this connection by showing how the correlated behavior of protons in water wire systems that are common in many biological and materials systems parallels the structure of Shor's algorithm.

Quantum Chemical Studies on Possible Molecular Devices Based on Electric Field-Induced Intramolecular Charge Transfer

We report quantum chemical studies on possible molecular devices working based on electric field-induced intramolecular charge transfer (EFIMCT). In the case of donor-acceptor (DA)-type molecular systems, intramolecular charge transfer (IMCT) can be induced by applying the external electric field to molecular systems along the charge transport direction, providing a possible switching mechanism which does not depend upon the electron-phonon coupling effect and is different from the negative differential resistance mechanism observed in the well-known NO2-substituted phenylene ethynylene oligomers. When the EFIMCT proceeds, the molecular systems have strong static electron correlation effects, where the standard nonequilibrium Green's function-density functional theory (DFT) approach cannot be applied to the molecular junction. As a first step toward practical switching devices, we do quantum chemical studies on the EFIMCT in such molecular systems as an isolated molecule, instead of using the electrode-junction-electrode open quantum system model. A prototype molecule P1 is designed as a tentative candidate molecule where the EFIMCT can proceed. The complete active space self-consistent field (CASSCF) molecular orbital calculations on P1 indicate that the EFIMCT can proceed at the external electric field intensity of 0.003 au, corresponding to about 2.25 V bias voltage. This calculated result strongly suggests that the development of this type of switching devices working at practically low bias voltage is feasible if the molecular system is properly designed. Broken symmetry unrestricted Hartree-Fock and spin-polarized Kohn-Sham DFT calculations also qualitatively reproduce the CASSCF results on P1, to some extent, indicating that these approaches can be employed for rough estimations on the EFIMCT such as the first screening of a large quantity of candidate molecules for this type of molecular devices. The possibility of molecular memory devices based on the EFIMCT is also discussed by analyzing the ground and excited potential energy surface model. Remaining challenges to develop practical molecular devices are discussed.

Potential differentiation of successive SARS-CoV-2 mutations by RNA: DNA hybrid analyses

The constant mutation of SARS-CoV-2 has triggered a new round of public health crises and has had a huge impact on existing vaccines and diagnostic tools. It is essential to develop a new flexible method to distinguish mutations to prevent the spread of the virus. In this work, we used the combination of density functional theory (DFT) and non-equilibrium Green's function formulation with decoherence, to theoretically study the effect of viral mutation on charge transport properties of viral nucleic acid molecules. We found that all mutation of SARS-CoV-2 on spike protein was accompanied by the change of gene sequence conductance, this is attributed to the change of nucleic acid molecular energy level caused by mutation. Among them, the mutations L18F, P26S, and T1027I caused the largest conductance change after mutation. This provides a theoretical possibility for detecting virus mutation based on the change of molecular conductance of virus nucleic acid.

Learning Conductance: Gaussian Process Regression for Molecular Electronics

Experimental studies of charge transport through single molecules often rely on break junction setups, where molecular junctions are repeatedly formed and broken while measuring the conductance, leading to a statistical distribution of conductance values. Modeling this experimental situation and the resulting conductance histograms is challenging for theoretical methods, as computations need to capture structural changes in experiments, including the statistics of junction formation and rupture. This type of extensive structural sampling implies that even when evaluating conductance from computationally efficient electronic structure methods, which typically are of reduced accuracy, the evaluation of conductance histograms is too expensive to be a routine task. Highly accurate quantum transport computations are only computationally feasible for a few selected conformations and thus necessarily ignore the rich conformational space probed in experiments. To overcome these limitations, we investigate the potential of machine learning for modeling conductance histograms, in particular by Gaussian process regression. We show that by selecting specific structural parameters as features, Gaussian process regression can be used to efficiently predict the zero-bias conductance from molecular structures, reducing the computational cost of simulating conductance histograms by an order of magnitude. This enables the efficient calculation of conductance histograms even on the basis of computationally expensive first-principles approaches by effectively reducing the number of necessary charge transport calculations, paving the way toward their routine evaluation.

Increased Surface Density of States at the Fermi Level for Electron Transport Across Single-Molecule Junctions

Fermi's golden rule, a remarkable concept for the transition probability involving continuous states, is applicable to the interfacial electron-transporting efficiency via correlation with the surface density of states (SDOS). Yet, this concept has not been reported to tailor single-molecule junctions where gold is an overwhelmingly popular electrode material due to its superior amenability in regenerating molecular junctions. At the Fermi level, however, the SDOS of gold is small due to its fully filled d-shell. To increase the electron-transport efficiency, herein, gold electrodes are modified by a monolayer of platinum or palladium that bears partially filled d-shells and exhibits significant SDOS at the Fermi energy. An increase by 2-30 fold is found for single-molecule conductance of α,ω-hexanes bridged via common headgroups. The improved junction conductance is attributed to the electrode self-energy which involves a stronger coupling with the molecule and a larger SDOS participated by d-electrons at the electrode-molecule interfaces.

Electrical modulation properties of DNA drug molecules

DNA drug molecules are not only widely used in gene therapy, but also play an important role in controlling the electrical properties of molecular electronics. Covalent binding, groove binding and intercalation are all important forms of drug-DNA interaction. But its applications are limited due to a lack of understanding of the electron transport mechanisms after different drug-DNA interaction modes. Here, we used a combination of density functional theory calculations and nonequilibrium Green's function formulation with decoherence to study the effect of drug molecules on the charge transport property of DNA under three different binding modes. Conductance of DNA is found to decrease from 2.35E-5 G0 to 1.95E-6 G0 upon doxorubicin intercalation due to modifications of the density of states in the near-highest occupied molecular orbital region, δG = 1105.13%. Additionally, the conductance of DNA after cis-[Pt(NH3)2(py)Cl]+ covalent binding increases from 1.02E-6 G0 to 5.25E-5 G0, δG = 5047.06%. However, in the case of pentamidine groove binding, because there is no direct change in DNA molecular structure during drug binding, the conductance changes before and after drug binding is much smaller than in the two above cases, δG = 90.43%. Our theoretical calculations suggest that the conductance of DNA can be regulated by different drug molecules or switching the interaction modes between small molecules and DNA. This regulation opens new possibilities for their potential applications in controllable modulation of the electron transport property of DNA.

A Green's Function Approach for Determining Surface Induced Broadening and Shifting of Molecular Energy Levels

Upon adsorption of a molecule onto a surface, the molecular energy levels (MELs) broaden and change their alignment. This phenomenon directly affects electron transfer across the interface and is, therefore, a fundamental observable that influences electrochemical device performance. Here, we propose a rigorous parameter-free framework, built upon the theoretical construct of Green's functions, for studying the interface between a molecule and a bulk surface and its effect on MELs. The method extends beyond the usual wide-band limit approximation, and its generality allows its use with any level of electronic structure theory. We demonstrate its ability to predict the broadening and shifting of MELs as a function of intramolecular coupling, molecule/surface coupling, and the surface density of states for a molecule with two MELs adsorbed on a one-dimensional model metal surface. The new approach could help provide guidelines for the design and experimental characterization of electrochemical devices with optimal electron transport.

A multiscale approach for electronic transport simulation of carbon nanostructures in aqueous solvent

Theoretical works addressing electronic nano-devices operating in an aqueous environment often neglect solvent effects. In order to assess the role played by the polarization effects on the electronic transport properties of solvated graphene, for example in possible bio-sensing applications, we have used here a combination of polarizable force-field molecular dynamics, hybrid quantum mechanics/molecular mechanics (QM/MM) approach, density functional theory, and non-equilibrium Green's function method. We considered different solvation conditions, the presence of defects in graphene, as well as various choices for the partitions between the quantum and classical regions in QM/MM, in which we explicitly account for polarization effects. Our results show that the polarization effects on graphene lead to changes in the structure of interfacial water molecules which are more pronounced in the vicinity of defects. The presence of water leads to increased scattering due to the long-range charge interactions with graphene. At the same time, changes in the conductance due to polarization or salt concentration are found to be small, paving the way for robust electronic nano-devices operating in aqueous environments.

Charge transport properties of SARS-CoV-2 Delta variant (B.1.617.2)

The B.1.617.2 (Delta) variant of concern is causing a new wave of infections in many countries. In order to better understand the changes of the SARS-CoV-2 mutation at the genetic level, we selected six mutations in the S region of the Delta variant compared with the native SARS-CoV-2 and get the conductance information of these six short RNA oligonucleotides groups by construct RNA: DNA hybrids. The electronic characteristics are investigated by the combination of density functional theory and non-equilibrium Green's function formulation with decoherence. We found that conductance is very sensitive to small changes in virus sequence. Among the 6 mutations in the Delta S region, D950N shows the largest change in relative conductance, reaching a surprising 4104.75%. These results provide new insights into the Delta variant from the perspective of its electrical properties. This may be a new method to distinguish virus variation and possess great research prospects.

Robust covalent pyrazine anchors forming highly conductive and polarity-tunable molecular junctions with carbon electrodes

In molecular electronics, electrode-molecule anchoring strategies play a crucial role in the design of stable and high-performance functional single-molecule devices. Herein, we employ aromatic pyrazine as anchors to connect a central anthracene molecule to carbon electrodes including graphene and armchair single-walled carbon nanotubes (SWCNTs), and theoretically investigate their atomic structures and electronic transport properties. These molecular junctions can be constructed via condensation reactions of the central molecules terminated with ortho-phenylenediamines with ortho-quinone-functionalized nanogaps of graphene and SWCNT electrodes. With two direct C-N covalent bonds connecting the central molecule site-selectively to carbon electrodes in a coplanar way, pyrazine anchors are advantageous for forming stable and structurally well-defined molecular junctions, being expected to reduce the uncertainty about the electrode-molecule linkage motifs. The junction transport is highly efficient due to the coplanar geometry and the ensuing strong π-type molecule-electrode electronic coupling. Furthermore, our calculations show that molecular junctions with pyrazine anchors and carbon electrodes are usually n-type electronic devices; upon hydrogenation of pyridinic nitrogen atoms, the device polarity can be tuned to p-type, indicating that the pyrazine anchors can also serve as a powerful platform for tailoring in situ the polarity of charge carriers in carbon-electrode molecular electronic devices.

Light-Driven Charge Transport and Optical Sensing in Molecular Junctions

Probing charge and energy transport in molecular junctions (MJs) has not only enabled a fundamental understanding of quantum transport at the atomic and molecular scale, but it also holds significant promise for the development of molecular-scale electronic devices. Recent years have witnessed a rapidly growing interest in understanding light-matter interactions in illuminated MJs. These studies have profoundly deepened our knowledge of the structure–property relations of various molecular materials and paved critical pathways towards utilizing single molecules in future optoelectronics applications. In this article, we survey recent progress in investigating light-driven charge transport in MJs, including junctions composed of a single molecule and self-assembled monolayers (SAMs) of molecules, and new opportunities in optical sensing at the single-molecule level. We focus our attention on describing the experimental design, key phenomena, and the underlying mechanisms. Specifically, topics presented include light-assisted charge transport, photoswitch, and photoemission in MJs. Emerging Raman sensing in MJs is also discussed. Finally, outstanding challenges are explored, and future perspectives in the field are provided.

Optoelectronic Current through Unbiased Monolayer Amorphous Carbon Nanojunctions

Monolayer amorphous carbon (MAC) is a recently synthesized disordered 2D carbon material. An ensemble of MAC nanofragments contains diverse manifestations of lattice disorder, and because of disorder the key unifying characteristic of this ensemble is poor electronic conductance. Curiously, our computational analysis of the electronic properties of MAC nanofragments revealed an additional commonality: a robust presence of charge-transfer character for electronic transitions from the occupied to virtual orbitals. This charge-transfer property suggests possible applications in optoelectronics. In this Letter, we demonstrate computationally that a laser pulse induces directional electronic currents in unbiased MAC nanojunctions and discuss the effects of pulse intensity on the magnitude of electron transfer.

Edge Effect in Electronic and Transport Properties of 1D Fluorinated Graphene Materials

A systematic examination of the electronic and transport properties of 1D fluorine-saturated zigzag graphene nanoribbons (ZGNRs) is presented in this article. One publication (Withers et al., Nano Lett., 2011, 11, 3912-3916.) reported a controlled synthesis of fluorinated graphene via an electron beam, where the correlation between the conductivity of the resulting materials and the width of the fluorinated area is revealed. In order to understand the detailed transport mechanism, edge-fluorinated ZGNRs with different widths and fluorination degrees are investigated. Periodic density functional theory (DFT) is employed to determine their thermodynamic stabilities and electronic structures. The associated transport models of the selected structures are subsequently constructed. The combination of a non-equilibrium Green's function (NEGF) and a standard Landauer equation is applied to investigate the global transport properties, such as the total current-bias voltage dependence. By projecting the corresponding lesser Green's function on the atomic orbital basis and their spatial derivatives, the local current density maps of the selected systems are calculated. Our results suggest that specific fluorination patterns and fluorination degrees have significant impacts on conductivity. The conjugated π system is the dominate electron flux migration pathway, and the edge effect of the ZGNRs can be well observed in the local transport properties. In addition, with an asymmetric fluorination pattern, one can trigger spin-dependent transport properties, which shows its great potential for spintronics applications.

Recent Progress and Future Prospects on All-Organic Polymer Dielectrics for Energy Storage Capacitors

With the development of advanced electronic devices and electric power systems, polymer-based dielectric film capacitors with high energy storage capability have become particularly important. Compared with polymer nanocomposites with widespread attention, all-organic polymers are fundamental and have been proven to be more effective choices in the process of scalable, continuous, and large-scale industrial production, leading to many dielectric and energy storage applications. In the past decade, efforts have intensified in this field with great progress in newly discovered dielectric polymers, fundamental production technologies, and extension toward emerging computational strategies. This review summarizes the recent progress in the field of energy storage based on conventional as well as heat-resistant all-organic polymer materials with the focus on strategies to enhance the dielectric properties and energy storage performances. The key parameters of all-organic polymers, such as dielectric constant, dielectric loss, breakdown strength, energy density, and charge-discharge efficiency, have been thoroughly studied. In addition, the applications of computer-aided calculation including density functional theory, machine learning, and materials genome in rational design and performance prediction of polymer dielectrics are reviewed in detail. Based on a comprehensive understanding of recent developments, guidelines and prospects for the future development of all-organic polymer materials with dielectric and energy storage applications are proposed.

Electrode effects on the observability of destructive quantum interference in single-molecule junctions

Destructive quantum interference (QI) has been a source of interest as a new paradigm for molecular electronics as the electronic conductance is widely dependent on the occurrence or absence of destructive QI effects. In order to interpret experimentally observed transmission features, it is necessary to understand the effects of all components of the junction on electron transport. We perform non-equilibrium Green's function calculations within the framework of density functional theory to assess the structure-function relationship of transport through pyrene molecular junctions with distinct QI properties. The chemical nature of the anchor groups and the electrodes controls the Fermi level alignment, which determines the observability of destructive QI. A thorough analysis allows to disentangle the transmission features arising from the molecule and the electrodes. Interestingly, graphene electrodes introduce features in the low-bias regime, which can either mask or be misinterpreted as QI effects, while instead originating from the topological properties of the edges. Thus, this first principles analysis provides clear indications to guide the interpretation of experimental studies, which cannot be obtained from simple Hückel model calculations.

A multiconfiguration pair-density functional theory-based approach to molecular junctions

Due to their small size and unique properties, single-molecule electronics have long seen research interest from experimentalists and theoreticians alike. From a theoretical standpoint, modeling these systems using electronic structure theory can be difficult due to the importance of electron correlation in the determination of molecular properties, and this electron correlation can be computationally expensive to consider, particularly multiconfigurational correlation energy. In this work, we develop a new approach for the study of single-molecule electronic systems, denoted NEGF-MCPDFT, which combines multiconfiguration pair-density functional theory (MCPDFT) with the non-equilibrium Green's function formalism (NEGF). The use of MCPDFT with NEGF allows for the efficient inclusion of both static and dynamic electron correlations in the description of the junction's electronic structure. Complete active space self-consistent field wave functions are used as references in the MCPDFT calculation, and as with any active space method, effort must be made to determine the proper orbital character to include in the active space. We perform conductance and transmission calculations on a series of alkanes (predominantly single-configurational character) and benzyne (multiconfigurational character), exploring the role that active space selection has on the computed results. For the alkane junctions explored (where dynamic electron correlation dominates), the MCPDFT-NEGF results agree well with the DFT-NEGF results. For the benzyne junction (which has a significant static correlation), we see clear differences in the MCPDFT-NEGF and DFT-NEGF results and evidence that NEGF-MCPDFT is capturing additional electron correlation effects beyond those provided by the Perdew-Burke-Ernzerhof functional.

In Situ Tuning of the Charge-Carrier Polarity in Imidazole-Linked Single-Molecule Junctions

Manipulating the nature of the charge carriers at the single-molecule level is one of the major challenges of molecular electronics. Using first-principles quantum transport calculations, we have investigated the electronic transport properties of imidazole-linked single-molecule junctions and identified the hydrogen atom bonded to the pyrrole-like nitrogen in imidazole as a switch to tune the polarity of the charge carriers. Our calculations show that the chemical nature of the imidazole anchors is dramatically altered by dehydrogenation, which changes the dominant charge carriers from electrons to holes. It is also revealed that upon dehydrogenation the interfacial Au-N bonds are modified from donor-acceptor-like to covalent, along with a significant promotion of the low-bias conductance and the junction stability. At variance with other traditional methods that always require drastic modifications of the junction structure, our findings provide a promising approach to tailor in situ the polarity of charge carriers in molecular electronic devices.

Electronic characteristics of BRCA1 mutations in DNA

The efficient and low-cost way for gene mutation detection and identification are conducive for the detection of disease. Here, we report the electronic characteristics of the gene of breast cancer 1 in four common mutation types: duplication, single nucleotide variant, deletion, and indel. The electronic characteristics are investigated by the combination of density functional theory and non-equilibrium Green's function formulation with decoherence. The magnitude of conductance of these DNA molecules and mutational changes are found to be detectable experimentally. In this study, we also find the significant mutation type dependent on the change of conductance. Hence these mutations are expected to be identifiable. We find deletion type mutation shows the largest change in relative conductance (~97%), whereas the indel mutation shows the smallest change in relative conductance (~27%). Therefore, this work presents a possibility of electronic detection and identification of mutations in DNA, which could be an efficient method as compared to the conventional methods.

Excitation Energy Transfer Efficiency in Fluctuating Environments: Role of Quantum Coherence in the Presence of Memory Effects

Several recent studies have interrogated the role of quantum coherence in affecting the transfer efficiency of an optical excitation to the designated "trap" state where the energy can be used for subsequent reactions, as in photosynthesis. However, these studies invoke a Markovian approximation for the time correlation function describing the environment-induced stochastic fluctuations. Here, we employ Kubo's quantum stochastic Liouville equation (QSLE) to include memory effects. We extend the existing QSLE scheme to introduce decay of a newly created excitation due to radiative and nonradiative channels and also by desired trapping toward the targeted chromophore. We show that the theoretical formalism based on the QSLE correctly reproduces the rate equation description in the Markovian limit, with the rate constants determined by an appropriate quantum limiting procedure. We find that under certain conditions, the efficiency of excitation transfer to the trap gains from the combined presence of quantum coherence and temporally correlated stochastic fluctuations. We work out different limiting situations in order to discover and quantify the optimum conditions for the energy transfer to the trapped state. We find that maximum energy transfer efficiency is achieved in the intermediate limit between coherent and incoherent transport.

Nonexponential Length Dependence of Molecular Conductance in Acene-Based Molecular Wires

In the nonresonant regime, molecular conductance decays exponentially with distance, limiting the fabrication of efficient molecular semiconductors at the nanoscale. In this work, we calculate the conductance of a series of acene derivatives connected to gold electrodes using density functional theory (DFT) combined with the nonequilibrium Green's function (NEGF) formalism. We show that these systems have near length-independent conductance and can exhibit a conductance increase with molecular length depending on the connection to the electrodes. The analysis of the molecular orbital energies and transmission functions attribute this behavior to the dramatic decrease of the highest occupied molecular orbital-lowest unoccupied molecular orbital (HOMO-LUMO) gap with length, which shifts the transmission peaks near the Fermi level. These results demonstrate that the anchoring configuration determines the conductance behavior of acene derivatives, which are optimal building blocks to fabricate single-molecule devices with tunable charge transport properties.

Quantum interference enhances rectification behavior of molecular devices

A theoretical and computational study of the effect of quantum interference on the rectification behavior of unimolecular devices.

Adenine based molecular junction as biosensor for detection of toxic phosgene gas

The possibility of adsorption of toxic phosgene gas (COCl₂) molecule on one of the nucleobase of DNA-adenine-has been analyzed using the first principle calculations based on density function theory. In accordance with the geometry of the nucleobase, two possible positions have been considered for effective adsorption of gas molecule. The calculations performed on adsorption energies suggest that the gas molecule is able to physisorb at both the considered positions with negligibly small values of charge transfer. The in-depth analysis of electron charge densities depicts that there is no orbital overlapping between the gas molecule and adenine. We observe a significant variation of transport properties of adenine-based molecular junction on adsorption of phosgene molecule while calculation the transport parameters at both the equilibrium as well as non-equilibrium. Also, the variation of HOMO-LUMO gap of adenine molecule on adsorption of phosgene leads to alteration of current and voltage, thus implying that adenine-based sensor can be effectively utilized to sense the presence of phosgene gas in a given environment. Small adsorption energies and recovery time suggest that the rate of desorption of phosgene is very high; thus, the proposed adenine sensor can be effectively used as a highly stable and selective reusable sensor.

A molecular device providing a remarkable spin filtering effect due to the central molecular stretch caused by lateral zigzag graphene nanoribbon electrodes

Through the density functional theory, we studied molecular devices composed of single tetrathiafulvalene (TTF) molecules connected with zigzag graphene nanoribbon electrodes by four different junctions. Interestingly, some devices have exhibited half-metallic behavior and can bring out a perfect spin filtering effect and remarkable negative differential resistance behavior. The current-voltage characteristics show that these four devices possess different spin current values. We found that all the TTF molecules were stretched due to interactions with the electrodes in the four devices. This leads to the Fermi levels of the three devices being down-shifted to the valence band; therefore, these devices exhibit half-metallic properties. The underlying mechanisms of the different spin current values are attributed to the different electron transmission pathways (via chemical bonds or through hopping between atoms). These results suggest that the device properties and conductance are controlled by different junctions. Our work predicts an effective way for designing high-performance spin-injected molecular devices.

Theoretical study of nitrogen, boron, and co-doped (B, N) armchair graphene nanoribbons

The electronic properties of the graphene nanoribbons (GNR) with armchair chirality were studied using the density functional theory (DFT) combined with non-equilibrium green's function method (NEGF) formalism. The role of donor and acceptor dopants of nitrogen and boron was studied separately and also in the situation of co-doping. The charge density, electronic density of states (DOS), and transmission coefficient at different bias voltages are presented for comparison between pure and doped states. It was found that this doping plays the main role in the distortion of the GNR lattices for cases of B and N as it affects straightly on the DOS and transmission coefficient of the systems under study. The band structure of edge was engineered by differently selecting the doping positions of B, N, and B-N hexagonal rings and it was found that there are significant changes in the electronic properties of these systems due to doping. This study can be used for developing GNR device based on doping B and N atoms.

Beyond Marcus theory and the Landauer-Büttiker approach in molecular junctions. II. A self-consistent Born approach

Marcus and Landauer-Büttiker approaches to charge transport through molecular junctions describe two contrasting mechanisms of electronic conduction. In previous work, we have shown how these charge transport theories can be unified in the single-level case by incorporating lifetime broadening into the second-order quantum master equation. Here, we extend our previous treatment by incorporating lifetime broadening in the spirit of the self-consistent Born approximation. By comparing both theories to numerically converged hierarchical-equations-of-motion results, we demonstrate that our novel self-consistent approach rectifies shortcomings of our earlier framework, which are present especially in the case of relatively strong electron-vibrational coupling. We also discuss circumstances under which the theory developed here simplifies to the generalized theory developed in our earlier work. Finally, by considering the high-temperature limit of our new self-consistent treatment, we show how lifetime broadening can also be self-consistently incorporated into Marcus theory. Overall, we demonstrate that the self-consistent approach constitutes a more accurate description of molecular conduction while retaining most of the conceptual simplicity of our earlier framework.

Non-equilibrium steady state conductivity in cyclo[18]carbon and its boron nitride analogue

A ring-shaped carbon allotrope was recently synthesized for the first time, reinvigorating theoretical interest in this class of molecules.