In-Situ Formation of H-Bonding Imidazole Chains in Break-Junction Experiments

of H-Bonding Imidazole Chains in Break-Junction Experiments. As a small molecule possessing both strong H-bond donor and acceptor functions, 1H-imidazole can participate in extensive homo- or heteromolecular H-bonding networks. These properties are important in Nature, as imidazole moieties are incorporated in many biologically-relevant compounds. Imidazole also finds applications ranging from corrosion inhibition to fire retardants and photography. We have found a peculiar behaviour of imidazole during scanning tunnelling microscopy-break junction (STM-BJ) experiments, in which oligomeric chains connect the two electrodes and allow efficient charge transport. We attributed this behaviour to the formation of hydrogen-bonding networks, as no evidence of such behaviour was found in 1-methylimidazole (incapable of participating in intramolecular hydrogen bonding). The results are supported by DFT calculations, which confirmed our hypothesis. These findings pave the road to the use of hydrogen-bonding networks for the fabrication of dynamic junctions based on supramolecular interactions. Abstract As a small molecule possessing both strong H-bond donor and acceptor functions, 1 H imidazole can participate in extensive homo- or heteromolecular H-bonding networks. These properties are important in Nature, as imidazole moieties are incorporated in many biologically-relevant compounds. Imidazole also finds applications ranging from corrosion inhibition to fire retardants and photography. We have found a peculiar behaviour of imidazole during scanning tunnelling microscopy-break junction (STM-BJ) experiments, in which oligomeric chains connect the two electrodes and allow efficient charge transport. We attributed this behaviour to the formation of hydrogen-bonding networks, as no evidence of such behaviour was found in 1-methylimidazole (incapable of participating in intramolecular hydrogen bonding). The results are supported by DFT calculations, which confirmed our hypothesis. These findings pave the road to the use of hydrogen-bonding networks for the fabrication of dynamic junctions based on supramolecular interactions.


Introduction
Single-entity experiments 1 and the advancement of computational methods 2 have increased our understanding of the behaviour of matter at the molecular level. A novel approach to the characterisation of individual molecules has been the fabrication of molecular junctions, 3,4 where a single entity is sandwiched between two biased metallic electrodes, and the current flowing through the nanoscale device is used as a characterisation signal. The conductance of a junction is exquisitely correlated with the chemical nature of the molecular wire, and with the support of computational methods, can be used to extract structural, electronic and conformational information. As methods for single molecule electrical characterisation have advanced so have the complexity of molecular systems which can be studied. In recent years this has included the study of molecular assemblies, which has included dimeric molecular pairs and supramolecular assemblies. An example here is the study of pairs of fullerenes in an STM junctions sandwiched between gold electrical contacts, with one fullerene attached the surface and the other directly on-top and attached to the STM tip. 5 Fullerene functionalised STM tips have also been used to form single porphyrin-fullerene dyads through non-covalent interactions, 6 and -stacking has also been exploited to assemble molecular pairs in STM break junctions. 7,8 On the other hand, hydrogen bonding is widely exploited in both chemical and biochemical systems for the exquisite assembly of often complex supra-molecular structures, but it has only been used in a relatively few single molecule junction studies.
Nishino have assembled pairs of ω-carboxyl alkanethiols monolayers onto gold STM tip and substrates. 9 The carboxylic acid groups of these adsorbates then binding through hydrogen bonding across the junction in an STM electrical junction. Hydrogen bonding across molecular junctions has also been achieved with DNA base pairs and has been used to study hydrogenbonding dynamics. 10,11 In this contribution we explore new possibilities to exploit hydrogen bonding in nanoscale electrical junctions and show that hydrogen bonding can also be used to form extended chains of molecules spanning the nanogap. We deployed 1H-imidazole (1,3diazole, Figure 1a) as the molecular target and exploited the versatility of STM single-molecule electrical characterisation to study its behaviour of at a noble metal interface.
Many of its relevant properties arise from its high electric dipole moment (3.67 D) and its ability to form strong H-bonding networks both in the solid state 12 and in solution. 13 This results, for instance, in 1H-imidazole itself being a crystalline solid at standard temperature and pressure, with a relatively high melting point of 89 -91 °C despite its low molecular weight. In the solid state, 1H-imidazole forms one-dimensional molecular networks, linked by NH᠁N intermolecular hydrogen bonds 14,15 which are in essence very long coordination polymers ( Figure 1c) with a persistent tape motif. 16  Through the H-bonding axis (c crystallographic plane), charge transport of solid state 1Himidazole crystals is >10 3 times more efficient than along the other two axes. 17 This strong electrical anisotropy is mirrored in the shape of the crystal themselves, which are long and fragile fibrous needles. Imidazolic compounds also form a range of complexes with alkali and transition metal cations, via interactions of the lone pair electrons on the imine nitrogen. Hbonded coordination networks are formed in the complexes, either between the imidazolic nitrogens 18 or through interactions with water 19 or carboxylic acid functionalities, 20 highlighting the particular strength and resilience of such networks. The complexing properties of imidazolic compounds are further evidenced by their ability to adsorb at transition metal surfaces and passivate them. This phenomenon is exploited in their wide use as corrosion inhibitors. The structure of imidazolic films at metal surfaces is complex, with the passivating film thickness and arrangement depending on the deposition conditions and N-substituents.
As an illustrative example for its behaviour with coinage metals, 1H-imidazole etches the surface of copper to give coordinating species. Tri-and tetrameric fragments are formed, which are bound together with the substrate. 21 Raman spectroscopy suggests the adsorption proceeds mainly through interactions of the sp 2 N atom with the metal surface, coordinated through its lone electron pair, with the ring perpendicular (or at a small tilt angle) to the surface. 22 However, a parallel deprotonation mechanism, with formation of imidazolate-metal bonds, is evident in in-situ infrared spectroscopy. 23 Recently, it has also been successfully used as molecular contact in scanning tunnelling microscopy break junction (STM-BJ) studies, as an aurophilic terminus. 24 We came across an anomalous behaviour of imidazolic compounds during our singlemolecule conductance studies. In its protonated form, we would not expect junctions to form since the pair of electrons on the pyrrolic nitrogen are part of the aromatic sextet and thus not obviously available for bonding to a metal contact. The pair of electrons on the iminic (pyridinelike) nitrogen is not part of the aromatic sextet and thus "available", but this gives only one anchoring group, not the usual two needed for the formation of robust metal-molecule-metal junctions. On the other hand, a deprotonation of the pyrrolic nitrogen with formation of imidazolate-metal bonds as mentioned above opens the possibility to form bridging junctions across metallic nanogaps. These then might be expected to give a well-defined high conductance value for the imidazolate, similar to what has been observed for pyrazine 27,28 (1,4-diazabenzene), with clear signatures of charge transport through the molecule anchored between the two electrodes by the N atoms in the 1,3-positions, spaced 2.2 Å apart. In what follows, we will show that 1H-imidazole and benzimidazole (bicyclic fused benzene and imidazole, Figure 1b) are indeed capable of forming single-molecule junctions, but as the junctions are pulled apart, conductive H-bonding chains of length greatly surpassing the single-molecule N᠁N distance assemble between the two electrodes, and the structure and charge transport characteristics of these is dependent on the experimental medium.  The formation of conductive junctions that extend beyond the length of a single 1H-imidazole molecule in anhydrous environment can be rationalised by the formation of oligomeric chains, with junctions incorporating up to three molecules (Figure 2e), held together by strong hydrogen bonds. In water, a similar H-bonding mechanism could lead to the formation of chains of alternating imidazole and water molecules (Figure 2f). In order to test this, we performed measurements in deuterated water, which resulted again in a multiple peaks but at slightly different values of conductance (although the differences were smaller than the experimental uncertainty). We took this as a confirmation that water (or deuterium oxide) are incorporated in the conductive path and contribute directly to charge transport, but our data is not conclusive on a possible isotope effect. A similar behaviour was also found in benzimidazole (more details in the ESI). As a control experiment, we also performed measurements on 1-methylimidazole in anhydrous mesitylene:tetrahydrofuran (8:2, v:v), in which intermolecular hydrogen bonds cannot form owing to the lack of a suitable H-bond donor 26 . STM-BJ experiments resulted in no discernible conductance peak, but only a broad, raised noise level at low conductance values. 1-methylimidazole readily adsorbs on noble metal surfaces 27,28 through interactions with the lone pair on the sp 2 nitrogen, which would account for the increased tunnelling noise signal, but does not form well-defined junctions between two Au electrodes as the latter would require a demethylation mechanism (more details in the ESI). Evidence of 1-methylimidazole adsorption on the metallic electrode is further provided by the increased G0 signal, as adsorbates are known to stabilise point contacts. 29 We found no evidence of formation of π-stacked junctions as previously described in the literature, 24 and we ascribe this phenomenon to the different environment used in our study, where tetrahydrofuran can form a solvation shell around the imidazole and prevent the formation of π-stacked supramolecular structures.

Theoretical Modelling
To provide a framework for the interpretation of the data obtained from STM-BJ experiments, we performed density functional theory (DFT) and transport calculations (more details in the Methods section). We started by obtaining the relaxed geometries for 1H-imidazole oligomers, in the gas phase and in a nanoelectrode junction. The predicted hydrogen bond length in the gas phase (1.76 Å) is in good agreement with the value found in the solid state (2.04 Å) and the literature. 30 When imidazolic chains are confined within two nanoelectrodes, our calculations predict deprotonation of the imidazole, with formation of a strong Au-N coordination bond, that grants a high electronic coupling. We then calculated the ( ) curves (transmission coefficient as a function of energy, Figure 4c) for the supramolecular junctions.
The conductance of a molecular wire can be directly calculated from these curves via the   (Figure 4d). An interesting outcome of our calculations is that, to correctly account for the observed break-off distance of the highest conductance peak obtained in water (Figure 2d), the shortest junction needs to incorporate a single water molecule, adsorbed at the Au electrode and interacting by H-bonding with 1H-imidazole adsorbed on the other electrode. Theory also predicts that, with the sensitivity of our preamplifier (noise level at ~10 -6 G0), we can only measure the monomer and the dimer, with the trimer falling below our noise level. As can be observed in the histograms in Figure 2b, there is significant conductance peak splitting, that we ascribe to different H-bonding conformers in the junction (more details in the ESI). We repeated the calculations for benzimidazole, and a similar behaviour was found, albeit with slightly different conductance values (see ESI).

Conclusions
In conclusion, we demonstrated here the formation of oligomeric, hydrogen bonding chains of imidazolic compounds formed in situ during a break-junction experiments. This resulted in an unexpectedly complex conductance "spectrum" for such a simple, 5-member heterocyclic compound. In addition to the formation of imidazole dimers and trimers, we also observed, in aqueous environment, the formation of junctions incorporating H-bonded water. For the junctions to be stable at room temperature, the energetics of structural dissociation must be well above at room temperature. However, many compounds which have been measured as single-entity junctions in the literature might be capable of forming H-bonded chains, but evidence of in-situ formation of oligomeric entities during a break-junction experiment is scarce. Examples of such processes available in the literature are limited to those involving coordination or chemical bonds, such as metallopolymers formed by abstraction of metal atoms from the two electrodes, 32 spontaneous dimerization of organotin compounds, 33 and, recently, field-induced catalytic oligomerisation of terminal anilines. 34 We believe the peculiar behaviour of imidazole can be attributed to its particularly high moment of dipole, measured conductance vs electrode separation trace, which is aligned to the rupture of the metallic nanocontact at 0.5 0 and thousands of these traces are compiled into histograms and density plots without further data selection or processing. Additional details on the instrument used in this study and the data acquisition/analysis process can be found in our previous publications. 38,39 Computational Methods: The relaxed geometry of the isolated molecule is obtained using the DFT code SIESTA, 40,41 so that the force on all atoms is less than 0.01 eV/Å. We used double-basis set with polarization and norm-conserving pseudopotentials. Real space grid cut off is 150 Ry. We employed the GGA exchange-correlation functional with PBE parametrisation. 42 To calculate the geometry-optimized molecule is placed between two Au electrodes consisting of seven principle layers, with 12 Au atoms and an atomically sharp tip.
We then further relaxed the geometry and we obtained the mean-field Hamiltonian and overlap matrix of the system. The transport code GOLLUM 43 was then used to calculate ( ). The conductance is then obtained by where is the Boltzmann's constant and is the temperature.

Conflicts of Interest
The authors declare no competing financial interests.

STM-BJ experiments of 1H-imidazole in heavy water (D2O)
As discussed in the manuscript, we performed experiments with 1H-imidazole in heavy water.
Results are shown in Figure S1. As can be observed in Figure S1, changing the environment from H2O to D2O results in a shift of the conductance peaks towards a slightly lower conductance, and different ratio of the various contributions. D2O also forms slightly longer junctions, as can be seen by the density maps shown in Figure S2 the effect can be ascribed to the stronger D2O hydrogen bonds. It is however worth stressing that these might be just simple experimental fluctuations and are not indicative of a clear isotope effect.

STM-BJ experiments on Benzimidazole
We also performed the same set of experiments described in the manuscript on benzimidazole, to verify the robustness of the hydrogen bonding chains formed in situ, and to demonstrate that it is indeed mostly NH-N hydrogen bonding responsible for the observed behaviour. In a way similar to 1H-imidazole, benzimidazole forms long H-bonded tapes in the solid state, as can be seen in Figure S3.
Measurements of benzimidazole in thoroughly dry conditions, H2O or D2O gave sets of conductance peaks similar to what has been observed in 1H-imidazole, as can be observed in Figure S4-S6. Figure S4: Conductance histogram (left) and 2D density maps for benzimidazole in anhydrous conditions.  With a similar behaviour to 1H-imidazole, benzimidazole showed similar conductance values in D2O in respect to the measurements in H2O.
In addition, we also performed experiments in "wet" solvents, with no effort towards the exclusion of water in commercially available mesitylene and tetrahydrofuran ( Figure S7). The main results here is the presence of the peak we attribute to imidazole-H2O H-bonding complex in wet environment, appearing as two sharp peaks in the 10 -1 -10 -2 G0 region, and the suppression of the conductance peak we attribute to the imidazole H-bonding dimer at 10 -3 G0. The overall results therefore strengthen our claim of a strong influence of the environment (in this case, H-bonding environment) on the conductance behaviour of imidazolic compounds.   Figure S9 shows the transmission coefficient of the protonated imidazole and benzimidazole series.
Similar to the result shown for non-protonated junctions in Figure 4 of the main paper and Figure   S8, increasing the number of H-bonded units bridging the two electrodes reduces the conductance of the system. The overall conductance values are slightly lower than non-protonated series, as a result of a reduced electrode-molecule coupling.

Additional calculations in the presence of water
In addition to the structures presented in the main paper in Figure 4b, we performed calculations on other possible conformers of the junctions in the presence of water, either with water adsorbed at an electrode or with different motif of H-bonding.
The overall results help in understanding the peak splitting observed, for instance, in Figure 2b     download file view on ChemRxiv SI_Imidazole H-bonding Network.pdf (3.82 MiB)