Molecular electronics aims to extend Moore's law to the molecular level, incorporating individual or groups of molecules into electronic circuits [1]. McCreery [2] introduced carbon-based molecular junctions that utilize quantum mechanical tunnelling for electronic music, marking the first commercial application of molecular electronics. These all-carbon junctions utilize covalent bonding and overcome the electromigration issue seen in metal contacts. The molecular junction consists of a layer (1–20+ nm) of covalently bonded oligomers between two conducting carbon electrodes. Short-range transport (<5 nm) occurs mainly through coherent tunnelling. However, when the molecular layer exceeds 5 nm, molecular orbitals become the pathways for transport. Various non-covalent interactions play a role in (supra)molecular junctions, including host-guest interactions, hydrogen bonding, π-π interactions, and interactions found in mechanically interlocked molecules [3]. Molecular electronics has the potential to enhance conventional microelectronics by adding chemical functionalities like redox charge storage, orbital transport, energy-selective photodetection, or single molecule junctions for monitoring molecular processes [4]. Advanced micro- and nano-manufacturing equipment allows for precise processing accuracy close to a single atom, ensuring increased manufacturing stability [5]. Moreover, molecular electronics can serve as a research tool that complements the development of various electronic functions, many of which are not present in conventional semiconductors. Molecular junctions consist of two electrodes – typically in a solid state – and the scattering region containing one or more molecules attached to the surfaces via different types of interactions. In the supramolecular variety, this linkage is non-covalent including π-π, σ-σ, host-guest, van der Waals or electrostatic interactions (including hydrogen bonds) [4]. This range of possibilities enables a plethora of different charge transfer mechanisms with anticipated strong applicational utility in sensing, construction of diodes, transistors, rectifiers and more [3,6,7]. Supramolecular solutions can be also particularly useful to solve the everlasting miniaturisation problem in modern electronics [6].

Polydopamine (PDA) and other melanins have complicated chemical structure and physical arrangements of the monomeric units [[8], [9], [10], [11], [12]] driven by hydrogen bonds, π-π and π-cation interactions, electrostatic and van der Waals forces. Such a diversity creates broad possibilities for synthesis and tailoring the physical and chemical properties [[8], [9], [10], [11], [12]]. Melanins, and PDA in particular, exhibit a complex set of electrical and electronic properties and many of them are still being investigated [13]. In general, PDA is a hybrid electronic-ionic conductor with temperature dependence similar to amorphous semiconductors [14]. Although the conductivity of the dry melanin is poor [15,16], after addition of water, there is an exponential increase due to the conduction of protons and hydroxyl ion radicals [17]. This aspect of the PDA can be applied in humidity sensing [18].

In addition to electronic properties, melanins have the strong ability of UV-VIs-IR absorption and energy dissipation over the 90 % of the light energy via the non-radiative (vibrational) means [19,20], which is a basis for photoprotection applications [21]. Mixed conduction has also a great advantage in bioelectronics as an ionic to electronic current transducers [22]. For example, as a coating for different types of semiconductors, it causes the photosensitisation effect on top of the enhancement of visible light absorption [13,23,24]. Furthermore, melanins themselves exhibit complex chemical and physical interactions [10,13,25] with other materials that strongly affect the realm of electronic properties.

The supramolecular junction involving PDA and gold nanoparticles (AuNPs) is among the most often experimentally studied, due to its wide application in biochemical, medical and environmental studies. PDA offers the ability to direct the growth of core-shell nanocrystals for highly active and phenomenally versatile nanocatalysts, with tailored sizes, morphologies, and chemical configurations, which 2D assemblies can be stably anchored on a diverse range of solid substrates [26]. AuNP loading on PDA is used in environmental remediation, such as nitroaromatics reduction for water purification [27], where the activity may be hundred times higher compared to freely dispersed AuNPs [28]. This superb catalytic activity is generally attributed to electronic transfer from PDA coating to catalytically-active sites [29]. Furthermore, PDA-AuNP heterojunction may be grafted on nanocomposite membranes [30], while not reducing the permeate flux significantly [31]. AuNP deposition on PDA-encapsulated Fe3O4 offers a new route towards green nanocatalysts, recyclable by using an external magnetic field [32]. Other studies on Fe3O4-PDA-AuNP composites reveal their specific interaction with bovine haemoglobin and potential in its removal in the proteomic analysis [33]. Since PDA can transfer electrons further entrapment of glucose oxidase (GOx) into these composites offers their use as glucose sensors [34].

The insolubility in water in the broad pH range from 0 to 11 accompanied by biocompatibility and low cytotoxicity [14,35] makes PDA a suitable material for biosensing applications [[36], [37], [38]]. Antibody functionalization via a Schiff base reaction offers superior efficiency, high sensitivity, and low immunosensor detection limits [39]. PDA-AuNP conjugates were reported as colorimetric immunoassays, with colour change resulting from the amplified catalytic reduction [40] but also as molecularly imprinted polymers, constituting an effective antifouling strategy in real environments [41]. AuNP-PDA with ultrathin PDA shell (1.3 nm) exhibits significantly higher surface-enhanced Raman spectroscopy effects compared to thicker PDA Forming AuNP-PDA heterojunction or more complex structures is vesting them with photothermal properties, desired in linked cancer therapies [42,43]. Overall, those properties make the PDA a unique type of (semi)conductor with a broad range of electronic applications depending on its chemical/physical structure. However – according to the best knowledge of authors – neither experimental, nor theoretical studies of the supramolecular junctions involving single PDA molecule have been performed so far. Moreover, there is little knowledge of the relation between the electronic structure and charge transfer properties of the PDA in different oxidation states when it is in contact with other materials [44].

This work employs comprehensive computational modelling to investigate supramolecular junctions of PDA tetramers oriented in various configurations. We thoroughly examine how different oxidation states, chemical structures, and physical arrangements on metallic surfaces modulate the electronic properties of PDA. The interactions between PDA model tetramers and Au (100) slabs are established across multiple orientations. We construct two-electrode devices with the tetramers weakly coupled to gold leads to elucidate the geometry and electronic structure. Calculations reveal the immense tunability of the electronic characteristics of PDA, which remain largely unexplored. Its properties strongly depend on oxidation state, precise chemical structure, and surface atomic arrangements. The configurations examined are designed to mirror the behaviour of PDA interacting with gold nanocrystal structures in electrochemical cells and catalytic systems. This provides fundamental insights into tailoring PDA electronics through systematic modifications to molecular structure and also interactions with metal electrodes. Overall, this work constitutes a robust computational investigation into elucidating structure-property relationships to guide optimization of PDA-based junctions and devices. The results showcase the rich tunability of PDA systems via chemical, structural, and environmental changes.