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The idea to use molecules as a basic building block in electronic circuits was developed about 50 years ago when a molecular rectifier was developed, but it has been a challenge for this field to make its way to real-world application. Now, due to the advancement in technologies, the properties of single molecules are better understandable and controllable. Some of the main motivations to build molecular electronics devices are that the conductive molecules can be as small as about 1 nm, that they are stable objects and can be tailor-made with desired electronic properties. This small size of molecule poses a challenge in their usage, one solution is to develop the hybrid devices whose properties are based on single and few molecules.

In this study, a portable hybrid device is used and further developed called a nanoMoED device, a nano-molecular electronic device. These devices consist of gold nanoparticles (AuNPs), gold nanoelectrodes and conjugated organic molecules. The electrical resistance of the device depends on the molecules functionalizing it and, in this work, they contain phenyl rings such as 4,4’-biphenyldithiol (BPDT), p-ter-phenyl-4,4''-dithiol and oligo phenylene-ethynylene.

The 20 nm wide nanogaps are fabricated by a focused ion beam (FIB) creating thus true nanodevices. The molecular nanojunctions are formed by dielectrophoretic trapping of molecule functionalized AuNPs into a nanogap. The distance between the NPs, measured from transmission electron microscopy images is similar to the size of the targeted functionalizing organic molecule that shall bridge the NP-NP gap. We have reported that the primary molecular ligand shell of the AuNPs can be tuned in the synthesis process by the secondary molecular functionalization process. The experimental results showed that this process depends on the interparticle spacing and the structure of the primary functionalizing molecules. The nanoMoED devices showed a successful cyclic molecular place exchange process where alternately BPDT and octanethiol (OT) were moved into the devices. This is confirmed by a change in the electrical resistance of devices showing higher conductance for BPDT than OT.

The nanoMoED devices when tested in NO2, ethanol, and NH3 gas atmosphere showed a significant change in device electrical resistance. Density functional theory calculations explain this observation. The analyte molecules bind with the aromatic conjugated molecule and induce additional charge transport channels near the Fermi level of the sensing molecule. In graphene-based, i.e., 2D, micron-sized devices, we could show that the non-covalent molecular functionalization of graphene improves its NH3 gas sensing response by 3 times as compared to pristine graphene. Further experiments are required to understand the device properties under different working conditions as well as to evidence different functionalities for example as a switch. 

The advent of technological furtherance in the biomedical sector and the renaissance of interdisciplinary science enable us to comprehend human lifestyle, and diseases at molecular and nanoscale levels. Lacking a shared theoretical foundation and terminological lexicon between various scientific domains might impede efforts to incorporate biological principles into nanoscience. In retrospect, it's possible to draw some instructive learnings from the fact that the development of contemporary nanoscience and biology was the consequence of the convergence of fields that had previously been kept separate. 

In this Ph.D. thesis, I have given the catchy moniker “GENOME2QUNOME” (an acronym for "Genetic organization of multicellular organisms and their enzymatic reaction 2 Quantum nanostructured materials for energy scavenging applications"), encompassing a combinatorial approach using computational methodologies in biophysics and nano/materials science. Structure-property correlations, a unifying paradigm based on understanding how nanomaterials behave and what qualities they exhibit at the molecular and nanoscale levels, are now widely acknowledged and are critical in the incorporation of bioinspired materials into nanoscience. Therefore, a unified framework have been elucidated in this thesis for the study of nanoscale materials ranging from 0D to 3D that may be useful in combining various strategies that characterize this interdisciplinary approach. 

This thesis is also a part of broader interdisciplinary research strategy aimed at depicting electronic transport in the nanoscale regime, elucidating interface mechanisms for contact electrification, and understanding the complex architectures of nanomaterials. The central hypothesis of this thesis is concentrated on the behavioral transition from the nanoscale regime to macromolecules, which is fascinating in real world scenario but theoretically challenging to bring it in reality or practice. To bridge this gap, I have made an attempt by integrating a wide range of computational methods, ranging from density functional theory (DFT) for systems with few atoms to classical dynamics dealing with billions of atoms.