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Anthropogenic release of the greenhouse gas carbon dioxide is believed to be a leading cause in the global rise in temperature. The main source of the carbon dioxide released is from combustion of fossil fuels. Thus, its necessary to mitigate the release of CO2, look for alternatives for fossil fuels and capture and sequester or capture and convert CO2 to other useful fuels and chemicals hence creating carbon neutral or carbon negative energy cycles. This thesis work was primarily focused on design, adapt and understand the chemistry of two-dimensional (2D) layered materials, particularly transition metal dichalcogenide (TMD) molybdenum disulfide and transition metal carbides (MXenes) as catalytic materials for the conversion of renewable energy into fuels and chemicals as an alternative for fossil fuels. This investigation was accomplished by combining electrochemistry, state of the art characterization and density functional theory (DFT) calculations. We hypothesized that it would be possible to improve the electrocatalytic hydrogen evolution reaction (HER) on MoS2 by engineering catalytically active sites on the plane, their edges and their interlayer regions. We also hypothesized 2D MXene sheets would serve as good carbon dioxide reduction reaction (CO2RR) catalysts under aprotic conditions. Conceivably the broad impact of this thesis work utilizing experimental and theoretical studies is the realization of transition metal doped metallic MoS2 as a potential candidate towards HER in alkaline conditions. Initially the interlayer region of MoS2 were investigated for the HER by introducing Na+, Ca2+, Ni2+ and Co2+ cations in the interlayers of metallic phase MoS2. Experimental results show that intercalation of cations (Na+, Ca2+, Ni2+, and Co2+) into the interlayer region of 1T-MoS2 to lower the overpotential for the HER. In acidic media the overpotential to reach 10 mAcm-2 for 1T-MoS2 with intercalated ions is lowered by ~60 mV relative to pristine 1T-MoS2 (~230 mV). DFT calculations suggest that the introduction of states from the intercalated metals whether sp or d, to lower the Gibbs free energy for H-adsorption (ΔGH) relative to intercalant-free 1T-MoS2. The DFT calculations suggest that Na+ intercalation results in ΔGH closest to zero, which is consistent with our experiments where the lowest overpotential for the HER is observed with Na+ intercalation. In order to explore the activity of the edge sites of MoS2 and the effect of a conductive support we used a microwave-assisted growth technique to synthesize interlayer expanded MoS2 with a vertically orientation on conductive two-dimensional Ti3C2 MXene nanosheets (MoS2⊥Ti3C2). Judicious choice of reaction temperature allows a control over the density of the edges obtained. Compared to pure MoS2 this unique inorganic hybrid structure allows an increased exposure of catalytically active edge sites of MoS2. The produced materials were investigated as electrocatalysts for the hydrogen evolution reaction (HER) in acidic conditions. The MoS2⊥Ti3C2 catalyst synthesized at 240 0C exhibited a low onset potential (-95 mV vs RHE) for the HER and a low Tafel slope (~40 mV dec-1). The decrease in the overpotential is linked to decrease in the charge transfer resistance of the materials with the electrode and the increased edge site density. In a third study the basal plane of metallic MoS2 was engineered by doping with transition metals Co and Ni to be evaluated as a catalyst for the alkaline HER. Due to a lack of oxygen evolution catalysts that can oxidize water at the anode under acidic conditions, there is an urgency to realize HER catalysts that can efficiently reduce water to hydrogen gas under alkaline conditions. Though metallic MoS2 has an optimum H binding free energy for the HER, the sluggish water dissociation step under alkaline conditions has made the implementation of MoS2 as a catalyst at higher pHs harder. We hypothesized that doping transition metals in the basal plane of metallic MoS2 that can efficiently catalyze the water dissociation step in alkaline conditions would help to reduce the overpotential required for the HER under alkaline conditions. Ni and Co were doped in orthorhombic MoO3 which was then converted metallic MoS2 under hydrothermal conditions. The polarization plots obtained in 1.0 M KOH solution shows a low onset overpotential of -75 mV vs RHE for the 10% Ni doped metallic MoS2 with an overpotential of -145 mV to reach a current density of 10 mA/cm2. Pure metallic MoS2 reaches the same current density at an overpotential of -238 mV vs RHE while samples doped with 10% Co atoms reached 10 mA/cm2 at -165 mV. This improvement in the doped samples is attributed to the improved kinetics of the water dissociation step under the alkaline reaction conditions. DFT calculations suggests that an optimal binding of water for the water dissociation step, H binding free and low free energy of binding for OH intermediates. Rigorous cycling of the catalysts shows extremely high stability with the doped samples while the pure metallic MoS2 loses its activity with continuous cycling. DFT calculations show that the doped samples provide extra stability to the metastable metallic MoS2 thus improving their long-term stability. Photo/electrochemical conversion of CO2 is an important step in the path to renewable production of carbon-based fuels and chemicals. Activity and selectivity have been major concerns on the CO2RR catalysts. The activity of known materials are hindered by the scaling relationship in the binding energies of the many intermediates involved in the CO2RR. Thus, the simplest of CO2RR products CO and HCOOH are of great value. Nano structured precious metals like silver and gold have shown promise as cathode materials for the conversion of CO2 to CO. In this thesis work we evaluate the electrocatalytic properties of Mo2C and Ti3C2 MXenes towards the electrochemical CO2 reduction reaction (CO2RR) as cheaper alternatives for precious metals. Though there have been theoretical predictions of the ability of MXenes with certain composition to have the ability to reduce CO2 to hydrocarbons, there are no experimental findings to support these calculations. In this study we observe very high faradaic efficiencies, ~90% for the CO2 reduction to CO at low overpotentials ~250 mV in acetonitrile/ionic liquid electrolytes on Mo2C MXene while Ti3C2 shows ~65% FE at an overpotential of ~600 mV for the cathodic half reaction. Density functional theory calculations suggests that the enhanced activity of Mo2C relative to Ti3C2 is due to relative lowering of the energy barrier for the initial proton couple electron transfer step of CO2 and the spontaneous dissociation of the absorbed *COOH species to *CO and H2O on the Mo2C surface. The calculations also predict the most probable active sites for the CO2 conversion to be vacant oxygen sites. High selectivity and high FE of CO2 reduction to CO makes these earth abundant materials an attractive electrocatalyst for the CO2RR. / Chemistry

Two dimensional (2D) materials, including graphene, hexagonal boron nitride and layered transition metal dichalcogenides (TMDs), have been a revolution in condensed matter physics and they are at the forefront of recent scientific research. They are being explored for their unusual electronic, optical and magnetic properties with special interest in their potential uses for sensing, information processing and memory. Molybdenum disulfide (MoS2) has been the flagship semiconducting TMD over the past ten years due to its unique electronic, optical and mechanical properties. In this thesis, we grow mono- to few layer MoS2 films using ambient pressure chemical vapor depositions (AP-CVD) to obtain high quality samples. We employ low temperature scanning tunneling microscopy and spectroscopy (LT-STM/STS) to study the effect of layer number on the electronic density of states (DOS) of MoS¬2. We find a reduction of the magnitude of the quasiparticle band gap from one to two monolayers (MLs) thick. This reduction is found to be due mainly to a shift of the valence band maxima (VBM) where the conduction band minimum (CBM) does not change dramatically. Density functional theory (DFT) modeling of this system shows that the overlap of the interfacial S-pz orbitals is responsible for shifting the valence band edge at the Γ-point toward the Fermi level (EF), reducing the magnitude of the band gap. Additionally, we show that the crystallographic orientation of monolayer MoS2 with respect to the HOPG substrate can also affect the electronic DOS. This is demonstrated with five different monolayer regions having each with a unique relative crystallographic orientation to the underlying substrate. We find that the quasiparticle band gap is closely related to the moiré pattern periodicity, specifically the larger the moiré periodicity the larger the band gap. Using DFT, we find that artificially increasing the interaction between the film and the substrate means that the magnitude of the band gap reduces. This indicates that the moiré pattern period acts like a barometer for interlayer coupling. We investigate the effect of defects, both point and extended defects, on the electronic properties of mono- to few layer MoS¬2 films. Atomic point defects such including Mo interstitials, S vacancies and O substitutions are identified by STM topography. Two adjacent defects were investigated spectroscopically and found to greatly reduce the quasiparticle band gap and arguments were made to suggest that they are Mo-Sx complex vacancies. Similarly, grain boundaries were found to reduce the band gap to approximately ¼ of the gap found on the pristine film. We use Kelvin probe force microscopy (KPFM) to investigate the affect of annealing the films in UHV. The work function measurements show metastable states are created after the annealing that relax over time to equilibrium values of the work function. Scanning transmission electron microscopy (STEM) is used to show that S vacancies can recombine over time offering a feasible mechanism for the work function changes observed in KPFM. Lastly, we report how strain affects the quasiparticle band gap of monolayer MoS2 by bending the substrate using a custom built STM sample holder. We find that the local, atomic-scale strain can be determined by a careful calibration procedure and a modified, real-space Lawler Fujita algorithm. We find that the band gap of MoS2 reduces with strain at a rate of approximately 400 meV/% up to a maximum strain of 3.1%, after which the film can slip with respect to the substrate. We find evidence of this slipping as nanoscale ripples and wrinkling whose local strain fields alter the local electronic DOS. / Physics

Mechanisms for charge transport in organic electronics allows them to perform with disordered internal morphology, something which is not possible for traditional crystalline semiconductors. Improvements to performance can occur when the materials change their relative positions to each other, resulting as a different spatial dispersion with lower electrical loss over the device area. A numerical method has been developed using interaction models for molecules from colloidal self-assembly. Colloids are rigid particles with a volume which is embodied by their shape and their collective behaviour depends on its density. The self-assembly mechanism used is condensation, which increases the density by removing the spaces between molecules while they lose thermal energy due to the increasing steric interactions with neighbours. The molecular chemical structure determines the spatial probability of electron orbitals that (for a given energy) outlines their geometric shape. Because these shapes are localized onto the molecule, their intermolecular positions determine how close these orbitals can be to each other which is important for electron charge transport. During operation, the organic active layer may have thermal energy to cause molecular reorganization before cooling, which increases the probability to find disordered states within the device. A comprehensive suite of tools has been developed which can classify disorder in the physical characteristics of morphology; such as density, internal spacing, and angular orientation symmetry. These tools where used to optimize the experimental preparations for depositing nanoparticle dispersions on surfaces within organic electronic devices. These have also been used to quantify the statistical variations in structure between configurations produced from our Monte Carlo method and a similar molecular dynamics approach. Simulated self-assembly within highly confined areas showed repeatedly sampled microstates, suggesting that at thermodynamic equilibrium confined particles have quantized density states. We conclude with morphologies resulting from non-circular shapes and systems of donor-acceptor type molecules. / Thesis / Doctor of Philosophy (PhD)

Materials with three-dimensional (3D) hierarchical architectures exhibit attractive mechanical, energy conversion and thermal radiative cooling properties not found in their bulk counterparts. However, implementation of hierarchically structured 3D transition metal dichalcogenides (TMDs) is widely deemed not possible, by the lack of manufacturing solutions that overcome the hierarchy, quality, and scalability dilemma. Here we report dewetting-driven destabilization (DDD) process that enables simple, template-free, high throughput printing of 3D architected MoS2 Foam with hierarchy spanning seven orders of magnitude — from angstroms to centimeters. Although extremely simple, our manufacturing process combines electrohydrodynamic printing with dewetting-induced-patterning. This technique can be applied to a range of dissimilar twodimensional (2D) layered materials, including Ti3C2Tx MXene and reduced graphene oxide (rGO). The deposited MoS2 Foam achieves amplification of resilience and conductivity. It constructs hierarchically porous and spatially interconnected networks for both ions and electrons transfer. We further demonstrate the 3D MoS2 architected foam as high-performance anodes with an otherwise unachievable combination of a 99% battery yield, a dynamic recovery (up to 85%) to withstand excessive volume expansion, a strain-induced reduction in diffusion barrier (0.2 eV), and improved electron transport abilities across the entire structure. The result is the high Li-ion charge storage capacity with robust cycling stability at a bulk scale (~3.5 mg/cm2) and under a high current density (10,000 mA/g). The outstanding electrochemical performance arises from the architected structure-induced pseudocapacitive energy storage mechanism based on the redox reaction of Mo, rather than the traditional conversion reaction. Notably, the performance achieved is on par with or surpasses state-of-the-art anodes made of black phosphorus composites, Si-graphene and mesoporous graphene particle anodes, while the technique offers an evaporation-like simplicity for industrial scalability. This work is foundational, and the developed DDD process opens a new sight to manufacture structurally robust, multifunctional hierarchical structures from 2D materials. Given the high adjustability of synthesis conditions and a wide variety of 2D materials, we anticipate previously unattainable possibilities in the energy storage, flexible electronics, catalysis, separation and drug delivery.

To keep downsizing transistors, new materials must be explored since traditional 3D materials begin to experience tunneling and other problematic physical phenomena at small sizes. 2D materials are appealing due to their thinness and bandgap. The relatively weak van der Waals forces between layers in 2D materials allow easy exfoliation and device fabrication but they also result in poor heat transfer to the substrate, which is the main path for heat removal. The impaired thermal coupling is exacerbated in few-layer devices where heat dissipated in the layers further from the substrate encounters additional interlayer thermal resistance before reaching the substrate, which results in self-heating and degradation of mobility. This study explores the electro-thermal properties of five materials (MoS2, MoSe2, WS2, WSe2, and 2D black phosphorous) which have been identified as possible replacements for Si in future sub-5-nm channel-length devices. We have developed a coupled electro-thermal model to calculate device mobility. The carrier wavefunctions and distribution are obtained from solving the coupled Schrodinger and Poisson equations in the cross-plane direction. The screening length is then calculated from the screening wavenumber. We calculate TBC for each layer in the stack into the substrate from a model based on first-principles phonon dispersion. We determine the local temperature in each layer from a ratio of its dissipated energy and its TBC. We simulate various devices with self-heating (Delta T does not equal 0, where Delta T is the temperature rise of the few-layer device) under several parameters and examined the effects on mobility and change in device temperature. The effects are compared to the isothermal case (Delta T = 0). We observe that self-heating has a significant effect on temperature rise, layer-wise drain current, and effective mobility. Black phosphorous performs the best electrothermally and WS2 performs the worst overall. This thesis will inform future thermally aware designs of nanoelectronic devices based on 2D materials.

Grafenoxid (GO) har potential att användas i läkemedelsleveransapplikationer. Dess stora specifika yta gör det intressant som en effektiv bärare och skyddare av olika aktiva substanser för genterapi, såsom DNA och mRNA. Denna studie har fokuserat på att undersöka förhållandena för att ladda negativt laddat mRNA på GO. Kitosan (CS) och linjär polyetylenimin (PEI) har preadsorberats på GO för att underlätta mRNA-adsorption. Studien undersökte vid vilka förhållanden zeta-potentialen av GO/polyelektrolyt för det negativt laddade GO blir positivt. Dessa komplexerades sedan med mRNA vid olika N/P-förhållanden. Dessutom bedömde studien mRNA-frisättningskapaciteten genom att reducera pH.  GO/CS-komplexet vid förhållandet 1:2 visade positiv zeta-potential med N/P-förhållandena som sträcker sig från 1:1 till 10:1 visade att all mRNA och polyA har adsorberat till komplexet. N/P-förhållandet 10:1 var den enda som uppnådde en neutral zeta-potential, vilket tyder på tillräckligt mRNA för mättnad. Genom att öka koncentrationen av CS, kunde zeta-potentialen skifta till positivt vilket potentiellt förbättrar transfektionseffektiviteten. Visade en förbättring i signalen av det fria mRNA ökade när GO/CS/mRNA-komplexet utsattes för ett mer surt pH. Detta tyder på en potentiell frisättning när vektorn transfekteras in i cellen, eftersom den transporteras till lysosomerna som kännetecknas av sin sura miljö. GO/PEI-komplex visade endast negativ zeta-potential vid GO:PEI-förhållanden som når upp till 1:10, och därmed kommer det negativt laddade mRNA inte att adsorbera på dessa GO/PEI-komplex.  Resultaten tyder på en lovande utgångspunkt för pre-formuleringen av GO/CS-komplexet för vidare forskning. Detta arbete ger ett bidrag för framtida studier inom detta område. / Graphene oxide (GO) has a potential to be used in drug delivery applications. The large surface-to-mass ratio makes it interesting as efficient carrier and protector of various substances aimed for therapy, including DNA and mRNA. This study has focused on determining the ideal conditions for loading negatively charged mRNA onto GO using chitosan (CS) and linear polyethyleneimine (PEI) to facilitate mRNA adhesion. This was achieved by examining at what ratios of GO/polyelectrolyte the zeta potential of the negatively charged GO becomes positive, which were then subjected to mRNA complexation at different N/P (nitrogen/phosphate) ratios. Moreover, the study assessed the mRNA release capability by altering the pH.  The GO/CS complex at ratio 1:2 showed positive zeta potential with the N/P ratios ranging from 1:1 to 10:1 presented 100% loading efficiency of the added nucleic acids. With the N/P ratio 10:1 standing out as it achieved a neutral zeta potential, suggesting enough mRNA for saturation. By increasing the concentration of CS, the zeta potential could shift to positive potentially enhancing transfection efficiency. During the release assessment, the GO/CS/mRNA complex displayed increased amount of unbound mRNA when subjected to a more acidic pH. This suggests potential release when transfected into the cell, as the vector is transported to the lysosomes characterized by their acidic environment. GO/PEI complexes demonstrated only negative zeta potential at GO:PEI ratios reaching to 1:10, and thus the negatively mRNA will not adsorb on these GO/PEI complexes.  The findings suggest a promising starting point for the pre-formulation of the GO/CS complex for further research. This work provides a solid foundation for future studies in this area.

In recent years, two-dimensional (2D) van der Waals (vdW) materials have aroused much interest for their unique structural, thermal, optical, and electronic properties and have become a hot topic in condensed matter physics and material science. Many research methods, including scanning tunneling microscopy (STM), transmission electron microscopy (TEM), optical and transport measurements, have been used to investigate these unique properties. Among them, STM stands out as a powerful characterization tool with atomic resolution and is capable of simultaneously revealing both atomic structures and local electronic properties. This dissertation focuses on scanning tunneling microscopy and spectroscopy (STM/S) investigation of 2D metal chalcogenides and heterostructures. The first part of the dissertation focuses on the continuous interface in WS2/MoS2 heterostructures grown by the chemical vapor deposition (CVD) method. We observed a closed interface between the MoS2 monolayer and the heterobilayer with atomic resolution. Furthermore, our scanning tunneling spectroscopy (STS) results and density functional theory (DFT) calculations revealed band gaps of the heterobilayer and the MoS2 monolayer agree with previously reported values for MoS2 monolayer and MoS2/WS2 heterobilayer on SiO2 fabricated through the mechanical exfoliation method. The results could deepen our understanding of the growth mechanism, interlayer interactions and electronic structures of 2D transition metal dichalcogenides (TMD) heterostructures synthesized via CVD. The second part of the dissertation focuses on phase transformation in 2D In2Se3. We observed that 2D In2Se3 layers with thickness ranging from single to ~20 layers stabilized at the beta phase with a superstructure at room temperature. After cooling down to around 180 K, the beta phase converted to a more stable beta' phase that was distinct from previously reported phases in 2D In2Se3. The kinetics of the reversible thermally driven beta-to-beta' phase transformation was investigated by temperature dependent transmission electron microscopy and Raman spectroscopy, combined with the expected minimum-energy pathways obtained from our first-principles calculations. Furthermore, DFT calculations reveal in-plane ferroelectricity in the beta' phase. STS measurements show that the indirect bandgap of monolayer beta' In2Se3 is 2.50 eV, which is larger than that of the multilayer form with a measured value of 2.05 eV. Our results on the reversible thermally driven phase transformation in 2D In2Se3 will provide insights to tune the functionalities of 2D In2Se3 and other emerging 2D ferroelectric materials and shed light on their numerous potential applications like non-volatile memory devices. The third part of the dissertation focuses on domain boundaries in 2D ferroelectric In2Se3. The atomic structure of domain boundaries in two-dimensional (2D) ferroelectric beta' In2Se3 is visualized with scanning tunneling microscopy and spectroscopy (STM/S) combined with DFT calculations. A double-barrier energy potential across the 60° tail to tail domain boundaries in monolayer beta' In2Se3 is also revealed. The results will deepen our understanding of domain boundaries in 2D ferroelectric materials and stimulate innovative applications of these materials. / Doctor of Philosophy / Two-dimensional (2D) materials are materials consisting of a single layer or a few layers of atoms. They exhibit unique and interesting properties distinct from their bulk counterparts. Over the past decade, much effort has been devoted to a large family of 2D materials — 2D metal chalcogenides that exhibit fascinating structural and electronic properties. These 2D metal chalcogenides can also be stacked together to form various heterostructures. The scanning tunneling microscope (STM) is a powerful tool to study these materials with atomic resolution and is capable of simultaneously revealing both atomic structures and local electronic properties. It can also be used to manipulate nanometer-scale structures on the material surface. In this dissertation, we use scanning tunneling microscopy and spectroscopy (STM/S) to investigate 2D metal chalcogenides and heterostructures. The first part of the dissertation focuses on WS2/MoS2 heterostructures grown by the chemical vapor deposition (CVD) method. We observed a closed interface between the MoS2 monolayer and the heterobilayer with atomic resolution. Furthermore, our scanning tunneling spectroscopy (STS) results and density functional theory (DFT) calculations revealed band gaps of the heterobilayer and the MoS2 monolayer. The results could deepen our understanding of the growth mechanism, interlayer interactions and electronic structures of 2D transition metal dichalcogenides (TMD) heterostructures synthesized via CVD. The second part of the dissertation focuses on phase transformation in 2D In2Se3. We observed that 2D In2Se3 layers transform from beta phase to a more stable beta' phase when the sample is cooled down from room temperature to 77 K. This thermally driven beta-to-beta' phase transformation was found to be reversible by temperature dependent transmission electron microscopy and Raman spectroscopy, corroborated with the expected minimum-energy pathways obtained from our first-principles calculations. Furthermore, DFT calculations reveal in-plane ferroelectricity in the beta' phase. Our results on the reversible thermally driven phase transformation in 2D In2Se3 will provide insights to tune the functionalities of 2D In2Se3 and other emerging 2D ferroelectric materials. The third part of the dissertation focuses on domain boundaries in 2D ferroelectric In2Se3. The atomic structure of domain boundaries in 2D ferroelectric beta' In2Se3 is visualized by using STM/S combined with DFT calculations. A double-barrier energy potential across the 60° tail to tail domain boundaries in monolayer beta' In2Se3 is also revealed. The results will deepen our understanding of domain boundaries in 2D ferroelectric materials and stimulate innovative applications of these materials.

Graphene, one-atom-thick planar sheet of carbon atoms densely packed in a honeycomb crystal lattice, has grabbed appreciable attention due to its exceptional electronic, mechanical and optical properties. Chemical functionalization schemes are needed to integrate graphene with the different materials required for potential applications. Molecular self-assembly behavior on graphene is a key method to investigate the mechanism of interaction between molecules and graphene and the promising applications related to molecular devices. In this thesis, we report the molecular self-assembly behavior of phenyl-C61-butyric acid methyl ester (PCBM), C60, perylenetetracarboxylic dianhydride (PTCDA) and Gd3N@C80 on flat and rippled graphene 2D material by the experimental methods of scanning tunneling microscope (STM) and atomic force microscope (AFM) and by the theoretical method of density functional theory (DFT). We found that molecules form ordered structures on flat graphene, while they form disordered structure on rippled graphene. For example, PCBM forms bilayer and monolayer structures, C60 and Gd3N@C80 form hexagonal close packed (hcp) structure on flat graphene and PTCDA forms herringbone structure on flat graphene surface. Although C60 and Gd3N@C80 both form hcp structure, C60 forms a highly ordered hcp structure over large areas with little defects and Gd3N@C80 forms hcp structure only over small areas with many defects. These differences of structure that forms on flat graphene is mainly due to the molecule-molecule interactions and the shape of the molecules. We find that the spherical C60 molecules form a quasi-hexagonal close packed (hcp) structure, while the planar PTCDA molecules form a disordered herringbone structure. From DFT calculations, we found that molecules are more effected by the morphology of rippled graphene than the molecule-molecule interaction, while the molecule-molecule interaction plays a main role during the formation process on flat graphene. The results of this study clearly illustrate significant differences in C60 and PTCDA molecular packing on rippled graphene surfaces. / Doctor of Philosophy / As the first physical isolated two-dimensional (2D) material, graphene has attracted exceptional scientific attention. Due to its impressive properties including high carrier density, flexibility and transparency, graphene has numerous potential applications, such as solar cell, sensors and electronics. 2D molecular self-assembly is an area that focuses on organization and interaction between self-assembly behaviors of molecules on surface. Graphene is an excellent substrate for the study of molecular self-assembly behavior, and study of molecular study is very important for graphene due to potential applications of molecules on graphene. In this thesis, we present investigations of the molecular self-assembly of PCBM, C60, PTCDA and Gd3N@C80 on graphene substrate. First, we report the two types of bilayer PCBM configuration on HOPG with a step height of 1.68 nm and 1.23 nm, as well as two types of monolayer PCBM configuration with a step height of 0.7 nm and 0.88 nm, respectively. On graphene, PCBM forms one type of PCBM bilayer with a step height of 1.37 nm and one type of PCBM monolayer with a step height of 0.87 nm. By building and analyzing the models of PCBM bilayers and monolayers, we believe the main differences between two configurations of PCBM bilayer and monolayer is the tilt angle between PCBM and HOPG, which makes type I configuration the higher molecule density and binding energy. Secondly, we report the investigation of self-assembly behaviors of C60 and PTCDA on flat graphene and rippled graphene by experimental scanning tunneling microscope (STM) and theoretical density functional theory (DFT). On flat graphene, C60 forms hexagon close pack (hcp) structure, while PTCDA forms herringbone structure. On rippled graphene, C60 forms quasi-hcp structure while PTCDA forms disordered herringbone structure. By DFT calculation, we study the effect of graphene curvature on spherical C60 and planar PTCDA. Finally, we report a STM study of a monolayer of Gd3N@C80 on graphene substrate. Gd3N@C80 forms hcp structure in a small domain with a step height of 0.88 nm and lattice constant of 1.15 nm. According to our DFT calculation, for the optimal organization of Gd3N@C80 and graphene, the gap between Gd3N@C80 and graphene is 3.3 Å and the binding energy is 0.95 eV. Besides, the distance between Gd3N@C80 and Gd3N@C80 is 3.5 Å and the binding energy is 0.32 eV.