Low-lying LUMO Boosts Conductance in Antiaromatic Dibenzopentalene Versus Aromatic Analogues.

Antiaromaticity is a fundamental concept in chemistry, but the study of molecular wires incorporating antiaromatic units is limited. Despite initial predictions, very few studies show that antiaromaticity has a beneficial effect on electron transport. Dibenzo[a,e]pentalene (DBP) is a stable structure that displays appreciable antiaromaticity within the five-membered rings of the pentalene core. We have investigated derivatives of DBP furnished with pyridyl (Py) and F4-pyridyl (PyF4) anchor groups, and compared the conductance with purely aromatic phenyl and anthracene analogues. We find that the low-bias conductance of DBP-Py is approximately 60 % larger than that of the anthracene analogue Anth-Py and 250 % larger compared to the phenyl derivative Ph-Py. This is due to a better alignment of the LUMO with the gold Fermi level, which we confirm by conductance-voltage spectroscopy where the conductance of DBP-Py shows the greatest voltage-dependence. The F4-pyridyl compounds, which have lower LUMO energies compared to the pyridyl analogues, did not, however, form detectable molecular junctions. The strongly electron-withdrawing fluorine atoms reduce the donor capability of the nitrogen lone-pair to the point where stable N-Au bonds no longer form.

Efficient Electron Hopping Transport through Azurin-Based Junctions.

We conducted a theoretical study of electron transport through junctions of the blue-copper azurin from Pseudomonas aeruginosa. We found that single-site hopping can lead to either higher or lower current values compared to fully coherent transport. This depends on the structural details of the junctions as well as the alignment of the protein orbitals. Moreover, we show how the asymmetry of the IV curves can be affected by the position of the tip in the junction and that, under specific conditions, such a hopping mechanism is consistent with a fairly low temperature dependence of the current. Finally, we show that increasing the number of hopping sites leads to higher hopping currents. Our findings, from fully quantum calculations, provide deep insight to help guide the interpretation of experimental IV curves on highly complex systems.

A Group-Theoretic Approach to the Origin of Chirality-Induced Spin-Selectivity in Nonmagnetic Molecular Junctions.

Spin-orbit coupling gives rise to a range of spin-charge interconversion phenomena in nonmagnetic systems where certain spatial symmetries are reduced or absent. Chirality-induced spin-selectivity (CISS), a term that generically refers to a spin-dependent electron transfer in nonmagnetic chiral systems, is one such case, appearing in a variety of seemingly unrelated situations ranging from inorganic materials to molecular devices. In particular, the origin of CISS in molecular junctions is a matter of an intense current debate. Here, we derive a set of geometrical conditions for this effect to appear, hinting at the fundamental role of symmetries beyond otherwise relevant quantitative issues. Our approach, which draws on the use of point-group symmetries within the scattering formalism for transport, shows that electrode symmetries are as important as those of the molecule when it comes to the emergence of a spin-polarization and, by extension, to the possible appearance of CISS. It turns out that standalone metallic nanocontacts can exhibit spin-polarization when relative rotations which reduce the symmetry are introduced. As a corollary, molecular junctions with achiral molecules can also exhibit spin-polarization along the direction of transport, provided that the whole junction is chiral in a specific way. This formalism also allows the prediction of qualitative changes of the spin-polarization upon substitution of a chiral molecule in the junction with its enantiomeric partner. Quantum transport calculations based on density functional theory corroborate all of our predictions and provide further quantitative insight within the single-particle framework.

Chiral Single-Molecule Potentiometers Based on Stapled ortho- Oligo(phenylene)ethynylenes.

We report on the chemical design of chiral molecular junctions with stress-dependent conductance, whose helicity is maintained during the stretching of a single molecule junction due to the stapling of both ends of the inner helix. In the reported compounds, different conductive pathways are observed, with clearly different conductance values and plateau-length distributions, attributed to different conformations of the helical structures. The large chiro-optical responses and the potential use of these molecules as unimolecular spin filters have been theoretically proved using state-of-the-art Density Functional Theory (DFT) calculations, including a fully ab-initio estimation of the CISS-originating spin polarization which is done, for the first time, for a realistic molecular system.

Experimental Data Confirm Carrier-Cascade Model for Solid-State Conductance across Proteins.

The finding that electronic conductance across ultrathin protein films between metallic electrodes remains nearly constant from room temperature to just a few degrees Kelvin has posed a challenge. We show that a model based on a generalized Landauer formula explains the nearly constant conductance and predicts an Arrhenius-like dependence for low temperatures. A critical aspect of the model is that the relevant activation energy for conductance is either the difference between the HOMO and HOMO-1 or the LUMO+1 and LUMO energies instead of the HOMO-LUMO gap of the proteins. Analysis of experimental data confirms the Arrhenius-like law and allows us to extract the activation energies. We then calculate the energy differences with advanced DFT methods for proteins used in the experiments. Our main result is that the experimental and theoretical activation energies for these three different proteins and three differently prepared solid-state junctions match nearly perfectly, implying the mechanism's validity.

Adhesion of thin metallic layers on Au surfaces.

We carried out first-principles density-functional theory calculations to study the work of separation for five different metal-metal interfaces, each of them comprising thin layers of selected metals (Cr, W, Ta, Al or Ti) lying on top of Au surfaces. We found that the highest work of separation is obtained for one-atom-thick layers. Increasing the number of atomic layers leads the work of separation to oscillate with the thickness, and ultimately tend to a limiting value for a large number of layers. Interestingly, for most cases the lowest work of separation is obtained for two-atom layers. We find that this behaviour is mirrored by the quantity of charge transferred between the two metals on the one hand, and their spatial distance on the other.

Single-molecule conductance of dibenzopentalenes: antiaromaticity and quantum interference.

The effects of antiaromaticity and destructive quantum interference (DQI) are investigated on the charge transport through dibenzo-[a,e]pentalene (DBP). 5,10-Connectivity gives high single-molecule conductance whereas 2,7 gives low conductance due to DQI. Comparison of the 5,10-DBP with phenyl and anthracene analogues yields the trend GDBP ≈ GAnth > GPh, despite the aromatic anthracene having a larger HOMO-LUMO gap than 5,10-DBP. This is explained by unfavourable level alignment for 5,10-DBP.

Rational design of an unusual 2D-MOF based on Cu(i) and 4-hydroxypyrimidine-5-carbonitrile as linker with conductive capabilities: a theoretical approach based on high-pressure XRD.

Herein, we present, for the first time, a 2D-MOF based on copper and 4-hydroxypyrimidine-5-carbonitrile as the linker. Each MOF layer is perfectly flat and neutral, as is the case for graphene. High pressure X-ray diffraction measurements reveal that this layered structure can be modulated between 3.01 to 2.78 Å interlayer separation, with an evident piezochromism and varying conductive properties. An analysis of the band structure indicates that this material is conductive along different directions depending on the application of pressure or H doping. These results pave the way for the development of novel layered materials with tunable and efficient properties for pressure-based sensors.

Backbone charge transport in double-stranded DNA.

Understanding charge transport in DNA molecules is a long-standing problem of fundamental importance across disciplines1,2. It is also of great technological interest due to DNA's ability to form versatile and complex programmable structures. Charge transport in DNA-based junctions has been reported using a wide variety of set-ups2-4, but experiments so far have yielded seemingly contradictory results that range from insulating5-8 or semiconducting9,10 to metallic-like behaviour11. As a result, the intrinsic charge transport mechanism in molecular junction set-ups is not well understood, which is mainly due to the lack of techniques to form reproducible and stable contacts with individual long DNA molecules. Here we report charge-transport measurements through single 30-nm-long double-stranded DNA (dsDNA) molecules with an experimental set-up that enables us to address individual molecules repeatedly and to measure the current-voltage characteristics from 5 K up to room temperature. Strikingly, we observed very high currents of tens of nanoamperes, which flowed through both homogeneous and non-homogeneous base-pair sequences. The currents are fairly temperature independent in the range 5-60 K and show a power-law decrease with temperature above 60 K, which is reminiscent of charge transport in organic crystals. Moreover, we show that the presence of even a single discontinuity ('nick') in both strands that compose the dsDNA leads to complete suppression of the current, which suggests that the backbones mediate the long-distance conduction in dsDNA, contrary to the common wisdom in DNA electronics2-4.

Taming quantum interference in single molecule junctions: induction and resonance are key.

We have joined two fundamental concepts of organic chemistry to provide a deep, yet intuitive, understanding of how side groups influence destructive quantum interference (DQI) in the transport through conjugated molecules. Using density functional theory combined with Green's function techniques, and employing tight-binding models in which all the π-systems are considered, we elucidate the separate roles of bond-resonance and induction in tuning DQI. We show that the position of the anti-resonances produced by DQI is sensitive to the number of side groups, but not in a simple additive way. Instead, addition of multiple groups results in a weaker overall contribution per group, and this can be understood using a straight forward graphical analysis. Furthermore, we show that additional fine tuning of DQI is possible via attachment of a chain of atoms to a second site around the ring. DQI is controlled by modifying the length of the chain, thus providing exquisite control over the anti-resonance position. This insight provides chemists with a large number of options to tune DQI for unprecedented device optimization.

Can One Define the Conductance of Amino Acids?

We studied the electron-transport properties of ten different amino acids and one dimer (di-methionine) using the mechanically controlled break-junction (MCBJ) technique. For methionine and cysteine, additional measurements were performed with the scanning tunneling microscope break-junction (STM-BJ) technique. By means of a statistical clustering technique, we identified several conductance groups for each of the molecules considered. Ab initio calculations revealed that the observed broad conductance distribution stems from the possibility of various binding geometries which can be formed during stretching combined with a multitude of possible conformational changes. The results suggest that it would be helpful to explore different experimental techniques such as recognition tunneling and conditions to help identify the nature of amino-acid-based junctions even further, for example, with the goal to establish a firm platform for their unambiguous recognition by tunneling break-junction experiments.

Tuning Structure and Dynamics of Blue Copper Azurin Junctions via Single Amino-Acid Mutations.

In the growing field of biomolecular electronics, blue-copper Azurin stands out as one of the most widely studied protein in single-molecule contacts. Interestingly, despite the paramount importance of the structure/dynamics of molecular contacts in their transport properties, these factors remain largely unexplored from the theoretical point of view in the context of single Azurin junctions. Here we address this issue using all-atom Molecular Dynamics (MD) of Pseudomonas Aeruginosa Azurin adsorbed to a Au(111) substrate. In particular, we focus on the structure and dynamics of the free/adsorbed protein and how these properties are altered upon single-point mutations. The results revealed that wild-type Azurin adsorbs on Au(111) along two well defined configurations: one tethered via cysteine groups and the other via the hydrophobic pocket surrounding the Cu 2 + . Surprisingly, our simulations revealed that single amino-acid mutations gave rise to a quenching of protein vibrations ultimately resulting in its overall stiffening. Given the role of amino-acid vibrations and reorientation in the dehydration process at the protein-water-substrate interface, we suggest that this might have an effect on the adsorption process of the mutant, giving rise to new adsorption configurations.

Mechanical Deformation and Electronic Structure of a Blue Copper Azurin in a Solid-State Junction.

Protein-based electronics is an emerging field which has attracted considerable attention over the past decade. Here, we present a theoretical study of the formation and electronic structure of a metal-protein-metal junction based on the blue-copper azurin from pseudomonas aeruginosa. We focus on the case in which the protein is adsorbed on a gold surface and is contacted, at the opposite side, to an STM (Scanning Tunneling Microscopy) tip by spontaneous attachment. This has been simulated through a combination of molecular dynamics and density functional theory. We find that the attachment to the tip induces structural changes in the protein which, however, do not affect the overall electronic properties of the protein. Indeed, only changes in certain residues are observed, whereas the electronic structure of the Cu-centered complex remains unaltered, as does the total density of states of the whole protein.

A Solid-State Protein Junction Serves as a Bias-Induced Current Switch.

A sample-type protein monolayer, that can be a stepping stone to practical devices, can behave as an electrically driven switch. This feat is achieved using a redox protein, cytochrome C (CytC), with its heme shielded from direct contact with the solid-state electrodes. Ab initio DFT calculations, carried out on the CytC-Au structure, show that the coupling of the heme, the origin of the protein frontier orbitals, to the electrodes is sufficiently weak to prevent Fermi level pinning. Thus, external bias can bring these orbitals in and out of resonance with the electrode. Using a cytochrome C mutant for direct S-Au bonding, approximately 80 % of the Au-CytC-Au junctions show at greater than 0.5 V bias a clear conductance peak, consistent with resonant tunneling. The on-off change persists up to room temperature, demonstrating reversible, bias-controlled switching of a protein ensemble, which, with its built-in redundancy, provides a realistic path to protein-based bioelectronics.

Doping hepta-alanine with tryptophan: A theoretical study of its effect on the electrical conductance of peptide-based single-molecule junctions.

Motivated by a recent experiment [C. Guo et al., Proc. Natl. Acad. Sci. U. S. A. 113, 10785 (2016)], we carry out a theoretical study of electron transport through peptide-based single-molecule junctions. We analyze the pristine hepta-alanine and its functionalizations with a single tryptophan unit, which is placed in three different locations along the backbone. Contrary to expectations from the experiment on self-assembled monolayers, we find that insertion of tryptophan does not raise the electrical conductance and that the resulting peptides instead remain insulating in the framework of a coherent transport picture. The poor performance of these molecules as conductors can be ascribed to the strongly off-resonant transport and low electrode-molecule coupling of the frontier orbitals. Although the introduction of tryptophan increases the energy of the highest occupied molecular orbital (HOMO) of the peptides in the gas phase, the new HOMO states are localized on the tryptophan unit and therefore essentially do not contribute to coherent charge transport.

Ab initio electronic structure calculations of entire blue copper azurins.

We present a theoretical study of the blue-copper azurin extracted from Pseudomonas aeruginosa and several of its single amino acid mutants. For the first time, we consider the whole structure of this kind of protein rather than limiting our analysis to the copper complex only. This is accomplished by combining fully ab initio calculations based on density functional theory with atomic-scale molecular dynamics simulations. Beyond the main features arising from the copper complex, our study reveals the role played by the peripheral parts of the proteins. In particular, we find that oxygen atoms belonging to carboxyl groups which are distributed all over the protein contribute to electronic states near the HOMO. The contribution of the outer regions to the electronic structure of azurins had so far been overlooked. Our results highlight the need to investigate them thoroughly; this is especially important in prospect of understanding complex processes such as the electronic transport through metal-metalloprotein-metal junctions.

Electron Transport Through Homopeptides: Are They Really Good Conductors?

Motivated by recent experiments, we performed a theoretical study of electron transport through single-molecule junctions incorporating four kinds of homopeptides (based on alanine, glutamic acid, lysine, and tryptophan). Our results suggest that these molecules are rather insulating and operate in off-resonance tunneling as their main transport mechanism. We ascribe their poor performance as conductors to the high localization of their frontier orbitals. We found that binding scenarios in which side chains lie on the side of gold protuberances could give rise to an increase in conductance with respect to end-to-end binding configurations. These findings provide an insight into the conductance mechanism of the building blocks of proteins and identify key issues that need to be further investigated.

Bioengineering a Single-Protein Junction.

Bioelectronics moves toward designing nanoscale electronic platforms that allow in vivo determinations. Such devices require interfacing complex biomolecular moieties as the sensing units to an electronic platform for signal transduction. Inevitably, a systematic design goes through a bottom-up understanding of the structurally related electrical signatures of the biomolecular circuit, which will ultimately lead us to tailor its electrical properties. Toward this aim, we show here the first example of bioengineered charge transport in a single-protein electrical contact. The results reveal that a single point-site mutation at the docking hydrophobic patch of a Cu-azurin causes minor structural distortion of the protein blue Cu site and a dramatic change in the charge transport regime of the single-protein contact, which goes from the classical Cu-mediated two-step transport in this system to a direct coherent tunneling. Our extensive spectroscopic studies and molecular-dynamics simulations show that the proteins' folding structures are preserved in the single-protein junction. The DFT-computed frontier orbital of the relevant protein segments suggests that the Cu center participation in each protein variant accounts for the different observed charge transport behavior. This work is a direct evidence of charge transport control in a protein backbone through external mutagenesis and a unique nanoscale platform to study structurally related biological electron transfer.

Toward Multiple Conductance Pathways with Heterocycle-Based Oligo(phenyleneethynylene) Derivatives.

In this paper, we have systematically studied how the replacement of a benzene ring by a heterocyclic compound in oligo(phenyleneethynylene) (OPE) derivatives affects the conductance of a molecular wire using the scanning tunneling microscope-based break junction technique. We describe for the first time how OPE derivatives with a central pyrimidine ring can efficiently link to the gold electrode by two pathways presenting two different conductance G values. We have demonstrated that this effect is associated with the presence of two efficient conductive pathways of different length: the conventional end-to-end configuration, and another with one of the electrodes linked directly to the central ring. This represents one of the few examples in which two defined conductive states can be set up in a single molecule without the aid of an external stimulus. Moreover, we have observed that the conductance through the full length of the heterocycle-based OPEs is basically unaffected by the presence of the heterocycle. All these results and the simplicity of the proposed molecules push forward the development of compounds with multiple conductance pathways, which would be a breakthrough in the field of molecular electronics.

Single-molecule conductance of a chemically modified, π-extended tetrathiafulvalene and its charge-transfer complex with F4TCNQ.

We describe the synthesis and single-molecule electrical transport properties of a molecular wire containing a π-extended tetrathiafulvalene (exTTF) group and its charge-transfer complex with F4TCNQ. We form single-molecule junctions using the in situ break junction technique using a homebuilt scanning tunneling microscope with a range of conductance between 10 G0 down to 10(-7) G0. Within this range we do not observe a clear conductance signature of the neutral parent molecule, suggesting either that its conductance is too low or that it does not form a stable junction. Conversely, we do find a clear conductance signature in the experiments carried out on the charge-transfer complex. Due to the fact we expected this species to have a higher conductance than the neutral molecule, we believe this supports the idea that the conductance of the neutral molecule is very low, below our measurement sensitivity. This idea is further supported by theoretical calculations. To the best of our knowledge, these are the first reported single-molecule conductance measurements on a molecular charge-transfer species.