Reply to the 'Comment on "Extent of conjugation in diazonium-derived layers in molecular junction devices determined by experiment and modelling"' by R. L. McCreery, S. K. Saxena, M. Supur and U. Tefashe, Phys. Chem. Chem. Phys., 2020, 22, DOI: 10.1039/d0cp02412k.

Our paper [Phys. Chem. Chem. Phys., 2019, 21, 16762] is the subject of a comment that clarifies a flaw in analysis of STM data. We accept the comment in regard to the aspect ratio considerations, but we also further clarify the main conclusions of our paper, and provide a molecular scale schematic using the data presented in the comment to help refine the original conclusions. Taken together, this shows that models presented in the literature may benefit from including more fine structure details, as better understanding may emerge from such considerations. This was the intent of our original article, and we thank the comment authors for the chance to clarify these points.

Solid-State Protein Junctions: Cross- Laboratory Study Shows Preservation of Mechanism at Varying Electronic Coupling.

Successful integration of proteins in solid-state electronics requires contacting them in a non-invasive fashion, with a solid conducting surface for immobilization as one such contact. The contacts can affect and even dominate the measured electronic transport. Often substrates, substrate treatments, protein immobilization, and device geometries differ between laboratories. Thus the question arises how far results from different laboratories and platforms are comparable and how to distinguish genuine protein electronic transport properties from platform-induced ones. We report a systematic comparison of electronic transport measurements between different laboratories, using all commonly used large-area schemes to contact a set of three proteins of largely different types. Altogether we study eight different combinations of molecular junction configurations, designed so that Ageoof junctions varies from 105 to 10-3 µm2. Although for the same protein, measured with similar device geometry, results compare reasonably well, there are significant differences in current densities (an intensive variable) between different device geometries. Likely, these originate in the critical contact-protein coupling (∼contact resistance), in addition to the actual number of proteins involved, because the effective junction contact area depends on the nanometric roughness of the electrodes and at times, even the proteins may increase this roughness. On the positive side, our results show that understanding what controls the coupling can make the coupling a design knob. In terms of extensive variables, such as temperature, our comparison unanimously shows the transport to be independent of temperature for all studied configurations and proteins. Our study places coupling and lack of temperature activation as key aspects to be considered in both modeling and practice of protein electronic transport experiments.

Extent of conjugation in diazonium-derived layers in molecular junction devices determined by experiment and modelling.

This paper shows that molecular layers grown using diazonium chemistry on carbon surfaces have properties indicative of the presence of a variety of structural motifs. Molecular layers grown with aromatic monomers with thickness between 1 and ∼15 nm display optical absorption spectra with significant broadening but no change in band gap or onsets of absorption as a function of layer thickness. This suggests that there is no extended conjugation in these layers, contrary to the conclusions of previous work. Density-functional theory modelling of the non-conjugated versions of the constituent aromatic monomers reveals that the experimental trends in optical spectra can be recovered, thereby establishing limits to the degree of conjugation and the nature of the order of as-grown molecular layers. We conclude that the absence of both shifts in band gap and changes in absorption onset is a consequence of resonant conjugation within the layers being less than 1.5 monomer units, and that film disorder is the main origin of the optical spectra. These findings have important implications for understanding charge transport mechanisms in molecular junction devices, as the layers cannot be expected to behave as ideal, resonantly conjugated films, but should be viewed as a collection of mixed nonresonantly- and resonantly-conjugated monomers.

Control of Rectification in Molecular Junctions: Contact Effects and Molecular Signature.

Thin layers of oligomers with thickness between 7 and 9 nm were deposited on flat gold electrode surfaces by electrochemical reduction of diazonium reagents, then a Ti(2 nm)/Au top contact was applied to complete a solid-state molecular junction. The molecular layers investigated included donor molecules with relatively high energy HOMO, molecules with high HOMO-LUMO gaps and acceptor molecules with low energy LUMO and terminal alkyl chain. Using an oligo(bisthienylbenzene) based layer, a molecule whose HOMO energy level in a vacuum is close to the Fermi level of the gold bottom electrode, the devices exhibit robust and highly reproducible rectification ratios above 1000 at low voltage (2.7 V). Higher current is observed when the bottom gold electrode is biased positively. When the molecular layer is based on a molecule with a high HOMO-LUMO gap, i.e., tetrafluorobenzene, no rectification is observed, while the direction of rectification is reversed if the molecular layer consists of naphtalene diimides having low LUMO energy level. Rectification persisted at low temperature (7 K), and was activationless between 7 and 100 K. The results show that rectification is induced by the asymmetric contact but is also directly affected by orbital energies of the molecular layer. A "molecular signature" on transport through layers with thicknesses above those used when direct tunneling dominates is thus clearly observed, and the rectification mechanism is discussed in terms of Fermi level pinning and electronic coupling between molecules and contacts.

Nanoalloying and phase transformations during thermal treatment of physical mixtures of Pd and Cu nanoparticles.

Nanoscale alloying and phase transformations in physical mixtures of Pd and Cu ultrafine nanoparticles are investigated in real time with in situ synchrotron-based x-ray diffraction complemented by ex situ high-resolution transmission electron microscopy. The combination of metal-support interaction and reactive/non-reactive environment was found to determine the thermal evolution and ultimate structure of this binary system. At 300 °C, the nanoparticles supported on silica and carbon black intermix to form a chemically ordered CsCl-type (B2) alloy phase. The B2 phase transforms into a disordered fcc alloy at higher temperature (> 450 °C). The alloy nanoparticles supported on silica and carbon black are homogeneous in volume, but evidence was found of Pd surface enrichment. In sharp contrast, when supported on alumina, the two metals segregated at 300 °C to produce almost pure fcc Cu and Pd phases. Upon further annealing of the mixture on alumina above 600 °C, the two metals interdiffused, forming two distinct disordered alloys of compositions 30% and 90% Pd. The annealing atmosphere also plays a major role in the structural evolution of these bimetallic nanoparticles. The nanoparticles annealed in forming gas are larger than the nanoparticles annealing in helium due to reduction of the surface oxides that promotes coalescence and sintering.