Theoretical Studies On Electronic Transport Properties And Their Controllability Of Hydrogen-Bonded Molecular Junctions

As an important weak interaction, hydrogen bond (H-bond) widely exists in chemistry and life sciences. Recent studies have indicated that some H-bond linked compounds, especially some biological molecules, may be used in molecular electronics with the functions as biological sensors, molecular wires and others. However, compared with the large numbers of studies on covalently linked conjugate complexes, the studied on the electronic transport properties of the complexes linked by H-bond and other weak interactions are relatively few. Moreover, the existing results about the conductivities of the weak interaction connected systems (such as proteins, DNA) are controversial. Many issues need to be clarified. The research about how to adjust and control the conductivity of H-bonded system, will not only benefit the design of nanoelectronic devices, but also help us to understand some basic issues in life activities, for example the charge migration in some biological processes. Inspired by the recent progresses about the conductances of some weakly interacted systems, this thesis presents a detailed investigation on the electronic transport of some H-bonded complexes by a first-principles method that combined the nonequilibrium Green's function method with density functional theory. In particularly, we pay more attention to the issues to enhance the electronic transport and electronic communication between the H-bond linked units by using the change or modification of the electronic properties of H-bond. We carried out a series of meaningful works and obtained some valuable results. The primary innovations can be summarized as follows:(1) Design of a novel redox-induced molecular switch base on the easy oxidation of hydrogen bond. The first contribution of this paper is the design of a conformation-dependent molecular switch using the different conductivities of H-bond and three-electron bond (3e-bond). Switch is one of the most widely used electronic devices in the circuit, which can be controlled by external triggers, such as electric field, light, electrochemistry and pH. Most of the central molecules of these devices are covalently interacted conjugated complexes. But it is reported that some weak non-covalent interactions, like H-bond and two-center, three-electron (2c-3e) bond, play crucial roles in many chemical and biological processes, especially in the long-range charge transfer in proteins. Therefore, the exploration of the conductivity of such weak interactions is of great importance both in understanding of charge transfer in proteins and in design of novel conducnce-adjustable molecular wires or junctions. Amide unit is one of important units in protein peptide backbone, and also widely exist in nucleic acid molecules. To modeling the properties of amide unit, we selected thioacetamide dimer (TAD) as a model. This is because TAD can represent the general properties of thioamide and even amide dimers, but possesses a lower ionization potential than amide, thus favoring the formation of a 2c-3e bond as a bridge for charge migration between the molecular units. The neutral TAD is composed of two thioamide monomers by forming the weak double N-H···S H-bonds. More interestingly, one-electron oxidation (the corresponding adiabatic ionization potential energy is 7.14 eV) may lead to a S-S linkage through a stronger S∴S 2c-3e bond between the two moieties, while the initial two H-bonds are considerable distorted. The molecule orbital and absorption spectra analyses also confirm this change. The initial double H-bonds are distorted following the remarkable decrease of the distance of the two S atoms. The calculated binding energies indicate that the formed S∴S 2c-3e bond is far stronger than that of the general S-containing H-bonds. This finding implicates that a S∴S 3e-bond would provide a better intermediate for the charge transfer between two moieties compared with the traditional H-bonds. We further examined the electron transport properties of the molecular junctions of the above two kinds of TADs inserted between electrodes. The calculated results show that theⅠ-Ⅴcharacteristic curves of the two configurations exhibit a switching behavior with an On-Off ratio in the range of 4.3-7.6 within the applied biases. This evident difference of the conductivities induced by oxidation/reduction of the molecular junctions implies a promising application for a molecular switch. That is, the two states of TAD unit with different conductivities could correspond to the 'Off' and 'On' states of a molecular switch. The analysis of transmission spectra confirms that the 3e-bond indeed provides a more favorable channel for the charge transfer compared with that of the H-bond. To our knowledge, there are no reports of molecular switches which ground on the different conductivities between the H-bonded and 3e-bonded molecular junctions in the previous literatures. Thus, the design of utilizing the different conductivities between the 3e-bond and the H-bond is original, and can provide an alternative way for the devices with an On-Off function, though the calculated On-Off ratio of the present switch is not very high in contrast with some ideal molecular switches.(2) Promotion effect of double proton transfer (DPT) on the conductivity of DNA based on the controllability of hydrogen bond. Charge migration in DNA attracts permanent attention due to both the potential application of DNA as a component in nanoelectronic devices and the fundamental role of conductivity in the oxidative damage and mutation of DNA. In addition, it is well established that proton transfer (PT) between two pairing bases plays a significant role in spontaneous, radiation-induced or oxidation-induced mutations in DNA. In particular, many researches suggested that charge transfer (CT) in DNA is generally accompanied by PT, leading to a diversity of cooperative proton-coupled electron transfer (PCET) migration mechanisms of protons and electrons. Although the mechanisms associated with DPT in various systems are nowadays well understood from the energetic, thermodynamic or kinetic viewpoints, their effects on the electronic transport along DNA are still less clear. Inspired by the recent progresses related to the contradicting results of the conductivity of DNA, we make a bottom-up exploration to clarify the essential role of DPT in promoting the charge migration in DNA from a new viewpoint:the base-to-base transverse electronic communication. The reason why we selected this special viewpoint is that many recent experimental and theoretical studies have revealed that the transverse conductivity of a base pair can be utilized to sequence DNA, exhibiting a potential role of the transverse electronic communication. We obtained the following results. Geometrically, DPT subtly changes the structures of a base pair, and thus makes the two base moieties in the base pair bonded more tightly. Electronically, besides lowering ionization potentials, DPT can improve the conjugation between two pairing bases which can delocalize the localizedπ-MOs at each base moiety toward the whole base pair through adjusting energy levels and spatial distributions of their MOs. Accompanyingly, DPT also leads to strengthening of the second-order interactions of the N-H···O and N-H···N in the Watson-Crick H-bond zones and the effectiveness of the charge transfer transitions between two pairing bases. As an overall result, DPT can enhance not only the transverse base-to-base electronic communication, but also the longitudinal electronic conductivity, as evidenced by the calculated currents along the H-bond direction in a base pair and along the DNA duplex axis direction. The transverse currents of DPT derivatives are enhanced by about 2 fold within the applied biases compared with the corresponding natural base pairs. And AT is more sensitive to DPT than GC. These observations about the increase of the transverse current, which is a measurable parameter, confirm our above conclusion that DPT can really enhance the transverse base-to-base electronic communication. We also calculated the longitudinal currents of three DNA fragments (two-layer stacked base pairs, GC:GC, GC:CG and DPT-GC:CG) under the bias of 0.5V. The longitudinal currents follow the order of GC:GC>DPT-GC:CG>GC:CG. Interestingly, the current of DPT-GC:CG is about 3.3 times that of GC:CG. In other words, DPT really improves the longitudinal electronic transport along DNA duplex for the specific GC:CG segment. The reason why the current increase, we think, is that DPT can adjust the energy levels and the spatial distributions of the MOs of a base pair, thus making a suitable condition for the DPT-GC unit to match with the MOs of its adjacent CG. The MO coupling interactions in the GC:CG unit can be enhanced by DPT. Clearly, this work would provide an understanding on the conduction of DNA, which can be promoted and regulated by DPT electronically.(3) Enhancement the conductivity of DNA based on the metal modification of hydrogen bond. DNA is one of potential candidate materials for molecular devices because of its unique effect of nano-size, superior properties of self-recognition and self-assembly. But nowadays, the conductivity of DNA remains controversial, thus shifting the development of functionalized DNA structures into the limelight. And the metal modification of DNA is one of the most promising avenues towards the goal of constructing complex functional nanoarchitetures. The exact structures and electronic properties of the formed metal-DNA complexes are, however, still less clear. Recently, our group also designed a class of multi-copper-mediated DNA. We obtained modified G3CuC and A2CuT base pairs by substituted all the Waston-Crick H-bond protons with Cu(I). The geometrical and electronical analyses indicate that the equi-number H-by-Cu replacement can enhance the transverse electronic communication and have positive effect on the conductivity of DNA. Herein, we present a detailed investigation on the electronic transport of the above mentioned multi-copper-mediated DNA by a first-principles method that combined the nonequilibrium Green's function method with density functional theory to reflect the effect of copper on the conductivity of DNA by some measurable parameters, such as current, conductance, et al. Firstly, we calculated the transverse currents along hydrogen bond direction of G3CuC andA2cuT and compared them with those of the canonical base pairs. The results show that the transverse currents both for GC and AT increase almost 20 times though the molecule size of copper modified base pairs expand by nearly 1 A. This fully confirms that Cu modification can significantly enhance the transverse base-to-base electronic communication of the pairing bases in DNA. Secondly we analyzed the longitudinal electronic transport along DNA helix and found that the effect of Cu-modification on longitudinal direction is more notably than on the transverse. For the two-layer-stacked repeating GC base pairs, the longitudinal current increases by 1 order of magnitude through the Cu(I) substitution. Following the increase of the length of the studied DNA segments, the effect of Cu modification is more distinct. For the three-layer-stacked repeating GC (3-GC), the increased ratio is up to 3 orders of magnitude. Furthermore, we found that the electronic transfer mechanism is super-exchange tunneling for the short repeating DNA segments. And the decay factor for poly(GC) is 1.22 A-1 while for poly(G3CuC) is 0.61 A-1. The decrease of the decay factor implies the charge could transfer more far in Cu-DNA than in native DNA. Clearly, this is more promising for the goal of constructing nano molecular wire. In addition, our results imply that the Cu modification may result in the change of the carrier in charge migration following the lengthening of DNA segments. In other words, Cu-mediated DNA may be more favor of the electron migration, not the hole transport.In summary, we presented a detailed investigation of the electronic transport properties of a series of hydrogen-bonded molecular junctions and made regulations on their electrical conductivities from three different aspects. The obtained interesting results may not only provide some good ideas for the design of bio-molecular device, but also help us to understand the charge migration in biological systems. In the meanwhile, it should be noted that the proposed hydrogen-bonded molecular junctions are only rational models, and probably can not de directly applied in a realistic experimental situation due to some other factors need considering in realization of a promising molecular device. In addition, the applied theoretical methods still have many imperfections, thus the obtained currents must be used more as a guide to rationally predict the trends in the conductivities of the designed systems rather than to quantify them. Certainly, the modulation effects could be enhanced by adding some modifying groups or extending conjugation of the conducting units, and the relevant explorations are in progress.