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<p> The need for higher bandwidth and people's desire to be "always connected" have spurred a new era of silicon photonics. The traditional integrated electrical transmission lines have been an obstacle preventing ultra high speed communication. Using monolithic chips of integrated optoelectronic circuits from silicon provides an economic way to realize Tetra Byte/Second bandwidth in a variety of areas such as "fiber to the home" and the buses linking chips inside computer.</p> <p> The heart of such optoelectronics-silicon laser-is still in pursuit. One of the most promising approaches is the erbium doped silicon nanocrystals embedded in silica system. External photon or hot electrons injection excites the silicon nanocrystals, which then transfer their energies to nearby erbium ions to emit light at 1.55 μm wavelength range.</p> <p> In this thesis, we investigate the effects of cavity and electric field on energy transfer from Si nanocrystals (Si-nc's) to Er ions, and simulate material gain in such systems. Our results show that microcavity can enhance the Forster energy transfer and material gain, reducing the requirements for Si-nc pumping. The electric field will hinder the radiation decay of Si-nc, but we have to further explore the tunneling mechanism before concluding the overall effect of electric field. Some future work needs to be done, which will shine some light on the design of the silicon laser.</p> / Thesis / Master of Applied Science (MASc)

The interior of the cell is a densely crowded and complex arena, full of a vast and diverse array of molecules and macromolecules. A fundamental understanding of cellular physiology will depend not only upon a reductionist analysis of the chemistry, structure, and function of individual components and subsystems, but also on a sagacious exegesis of the dynamic and emergent properties that characterize the higher-level system of living cells. Here, we present work on two aspects of the supramolecular organization of the cell: the controlled assembly of the mitotic spindle during cell division and the regulation of cellular metabolism through the formation of multienzyme complexes. During division, the cell undergoes a profound morphological and molecular reorganization that includes the creation of the mitotic spindle, a process that must be highly controlled in order to ensure that accurate segregation of hereditary material. Chapter 2 describes results that implicate the kinase, Zeste-white3/Shaggy (Zw3/Sgg), as having a role in regulating spindle morphology. The congregation of metabolic enzymes into macromolecular complexes is a key feature of cellular physiology. Given the apparent pervasiveness of these assemblies, it seems likely that some of the mechanisms involved in their organization and regulation might be conserved across a range of biosynthetic pathways in diverse organisms. The Winkel laboratory makes use of the flavonoid biosynthetic pathway in Arabidopsis as an experimental model for studying the architecture, dynamics, and functional roles of metabolic complexes. Over the past several years, we have accumulated substantive and compelling evidence indicating that a number of these enzymes directly interact, perhaps as part of a dynamic globular complex involving multiple points of contact between proteins. Chapter 3 describes the functional analysis of a predicted flavonol synthase gene family in Arabidopsis. The first evidence for the interaction of flavonoid enzymes in living cells, using fluorescent lifetime imaging microscopy fluorescent resonance energy transfer analysis (FLIM-FRET), is presented in Chapter 4. / Ph. D.

Materials with length scales in the nanometer regime demonstrate properties that are remarkably different from analogous bulk matter. As a result, researchers are striving to catalog the changes in properties that occur with decreasing size, and more importantly, understand the reason behind novel nanomaterial properties. By learning the true nature of nanomaterials, scientists and engineers can design better materials for a variety of applications. Inert gas-phase condensation synthesis of metal oxide nanoparticles was used to develop materials to explore the optical and chemical properties of metal oxide nanoparticles. One potential application for nanomaterials is use in optical applications. The possibility of interparticle energy transfer was investigated for lanthanide-doped yttrium oxide nanoparticles using laser spectroscopy. Experimental evidence collected with this study indicates that interparticle, lanthanide-mediated energy transfer may have been observed. In addition, lanthanide-doped gadolinium oxide nanoparticles were synthesized and investigated with optical spectroscopy to identify the best potential candidates for bioanalytical applications of this material. The influence of particle annealing and dopant concentration were also studied. Nanoparticle film structure was investigated with scanning electron microscopy. Two different film structures composed of oxide nanoparticles were found to grow under different synthesis conditions. The film structure was found to be determined by the degree of particle aggregation in the gas phase during synthesis. Aggregation of the particles was found to be controlled by a combination of gas pressure and properties. Chemical properties of metal oxide nanoparticles also are very important. Reflection-absorption Infrared Spectroscopy and vacuum surface analytical techniques were used to explore the chemistry of the chemical warfare agent dimethyl methylphosphonate (DMMP) on yttrium oxide as well as other metal oxide nanoparticles. DMMP was found to dissociate at room temperature on several types of metal oxide nanoparticles. Hydroxyl groups were found to be critical for the adsorption of DMMP onto the particles. Finally, the reactivity of the nanoparticles was found to increase with decreasing particle size. This was attributed to a relative increase in the number of high-energy surface defects for the smaller particles. / Ph. D.

A key component of natural photosynthesis are the antenna chromophores (chlorophylls and carotenoids) that capture solar energy and direct it towards the reaction centers of photosystems I and II. Highlighted by highly-ordered crystal structures and synthetic tunability via crystal engineering, metal–organic frameworks (MOFs) have the potential to mimic the natural photosynthetic systems in terms of the efficiency and directionality of energy transfer. Owing to their larger surface areas, MOFs have large absorption cross sections, which amplifies the rate of photon collection. Furthermore, MOFs can be constructed using analogues of chlorophyll and carotenoids that can participate in long-range energy transfer. Herein, we aimed to design photoactive MOFs that can execute one of the critical steps involved in photosynthesis - photon collection and subsequent energy transfer. The influence of spatial arrangement of chromophores on the efficiency and directionality of excitation energy transfer (EET) was investigated in a series of mixed-ligand pyrene- and porphyrin-based MOFs. Due to the significant overlap between the emission spectrum of 1,3,6,8-tetrakis(p-benzoic acid)pyrene (TBAPy) and the absorption spectrum of meso-tetrakis(4-carboxyphenyl)porphyrin (TCPP), the co-assembly of these two ligands in a MOF should enable facile energy transfer. Bearing this in mind, three TBAPy-based MOFs with markedly different network topologies (ROD-7, NU-901, and NU-1000) were chosen and a small number of TCPP units were incorporated in their backbone. To gain insight into the photophysical properties of mixed-ligand MOFs, we conducted time-resolved and steady-state fluorescence measurements on them. Stern-Volmer analysis was performed on the fluorescence lifetime data of mixed-ligand MOFs to determine the quenching constants. The quenching constant values for ROD-7, NU-901, NU-1000, and TBAPy solution were found to be 15.03 ± 0.82 M-1, 10.25 ± 0.99 M-1, 8.16 ± 0.41 M-1, and 3.35 ± 0.30 respectively. In addition, the ratio of the fluorescence intensities of TCPP and TBAPy was used to calculate the EET efficiencies in each of the three MOFs. EET efficiencies were in the following order: ROD-7 > NU-901 > NU-1000 > TBAPy-solution. Based on the trends observed for quenching constants and EET efficiencies, two conclusions were drawn: (1) the ligand-to-ligand energy transfer mechanism in MOFs outperforms the diffusion-controlled mechanism in solution phase, (2) energy transfer in MOFs is influenced by their structural parameters and spectral overlap integrals. The enhanced EET efficiency in ROD-7 is attributed to shorter interchromophoric distance, larger orientation factor, and larger spectral overlap integral. Directionality of energy transfer in these MOFs was assessed by calculating excitonic couplings between neighboring TBAPy linkers using the atomic transition charges approach. Rate constants of EET (kEET) along different directions were determined from the excitonic couplings. Based on the kEET values, ROD-7 is expected to demonstrate highly anisotropic EET along the stacking direction. In order to explore the mechanistic aspects of EET in porphyrin-based MOFs, we studied the energy transfer characteristics of PCN-223, a zirconium-based MOF containing TCPP ligands. After performing structural characterization, the photophysical properties of PCN-223 and free TCPP were investigated using steady state and time-resolved spectroscopy. pH-dependent fluorescence quenching experiments were performed on both the MOF and ligand. Stern-Volmer analysis of quenching data revealed that the quenching rate constants for PCN-223 and TCPP were 8.06 ± 1011 M-1s-1 and 2.71 ± 1010 M-1s-1 respectively. The quenching rate constant for PCN-223 is, therefore, an order of magnitude larger than that for TCPP. Additionally, PCN-223 demonstrated a substantially higher extent of quenching (q = 93%) as compared to free TCPP solution (q = 51%), at similar concentrations of quencher. The higher extent of quenching in MOF is attributed to energy transfer from neutral TCPP linkers to N-protonated TCPP linkers. Using the Förster energy transfer model, the rate constant of EET in PCN-223 was calculated. The magnitude of rate constant was in good agreement with the kEET values reported for other porphyrin-based MOFs. Nanosecond transient absorption measurements on PCN-223 revealed the presence of a long-lived triplet state (extending beyond 200 μs) that exhibits the characteristic features of a TCPP-based triplet state. The lifetime of MOF is shorter than that of free ligand, which may be attributed to triplet-triplet energy transfer in the MOF. Lastly, femtosecond transient absorption spectroscopy was employed to study the ultrafast photophysical processes taking place in TCPP and PCN-223. Kinetic analysis of the femtosecond transient absorption data of TCPP and PCN-223 showed the presence of three distinct time components that correspond to: (a) solvent-induced vibrational reorganization of excitation energy, (b) vibrational cooling, and (c) fluorescence. Materials that allow control over the directionality of energy transfer are highly desirable. Core-shell nanocomposites have recently emerged as promising candidates for achieving long-distance, directional energy transfer. For our project, we aim to employ UiO-67-on-PCN‐222 composites as model systems to explore the possibility of achieving directional energy transfer in MOF-based core-shell structures. The core–shell composites were synthesized by following a previously published procedure. Appropriate amounts of Ruthenium(II) tris(5,5′-dicarboxy-2,2′-bipyridine), RuDCBPY, were doped in the shell layer to produce a series of Ru-UiO-67-on-PCN‐222 composites with varying RuDCBPY loadings (CS-1, CS-2, and CS-3). The RuDCBPY-doped core–shell composites were characterized by powder X-ray diffraction (PXRD), scanning electron microscopy (SEM) imaging, Nitrogen adsorption-desorption isotherms, and diffuse reflectance spectroscopy. Efforts are currently underway to quantify RuDCBPY loadings in CS-1, CS-2, and CS-3. After completing structural characterization, the photophysical properties of CS-1, CS-2, and CS-3 will be investigated with the help of time-resolved and steady-state fluorescence spectroscopy. / Doctor of Philosophy / The pigment−protein complexes in natural photosynthetic units (also known as light harvesting antennas) efficiently capture solar energy and transfer this energy to reaction centers that carry out water splitting reactions. The collective chromophoric behavior of antennas can be replicated by metal-organic frameworks (MOFs). MOFs are crystalline, self-assembled materials composed of metal clusters connected by organic molecules. In this dissertation, we study the factors that govern the energy transfer and light harvesting capabilities of MOFs. In chapter 2, we examined the role of 3D structure of MOFs in energy transfer. In chapter 3, we investigated the influence of pH and temperature on the photophysical properties of MOFs. In chapter 4, we explored the possibility of energy transfer in novel MOF-on-MOF composites. This work is intended to pave the way for the construction of highly efficient MOF-based materials that can serve as the light harvesting and energy-transfer components in solar energy conversion devices.

Understanding interfacial interactions at the molecular level is important for interpreting and predicting the dynamics and mechanisms of all chemistry processes. A thorough understanding of the interaction dynamics and energy transfer between gas molecules and surfaces is essential for the study of various chemical reactions. The collisions of diatomic molecules on organic surfaces are crucial to the study of atmospheric chemistry. Molecular beam scattering experiments performed in ultra-high vacuum chambers provide insight into the dynamics of gas-surface interactions. Many questions remain to be answered in the study of gas-surface interfacial chemistry. For example, what affects the energy transfer between gas molecules and surfaces? How do intermolecular forces affect the interfacial interaction dynamics? We have approached these questions by scattering diatomic gas molecules from functionalized self-assembled monolayers (SAMs). Our results indicate that the intermolecular forces between gas molecules and surfaces play an important role in the energy transfer processes. Moreover, the stronger the intermolecular forces, the more often the incident molecules come into thermal equilibrium with the surface. Furthermore, most of the previous approaches toward understanding gas-surface interaction dynamics considered the interactions as independent incidents. By scattering O2, N2, CO and NO on both CH3- and OH- terminated SAM, we found a correlation between the gas-surface interactions and a bulk property, solubility. Both being strongly affected by intermolecular forces, the gas-surface energy transfer and solubility of gases in surface-similar solvents (water for OH-SAM, n-hexane for CH3-SAM) have a positive correlation. This correlation facilitates the understanding of interfacial dynamics at the molecular level, and helps predict the outcome of the similar-size gas collisions on surfaces. / Master of Science

A molecular-level understanding of gas-surface energy exchange and reaction mechanisms will aid in the prediction of the environmental fate of pollutants and enable advances toward catalysts for the decomposition of toxic compounds. To this end, molecular beam scattering experiments performed in an ultra-high vacuum environment have provided key insights into the initial collision and outcome of critical interfacial processes on model systems. Results from these surface science experiments show that, upon gas-surface collisions, energy transfer depends, in subtle ways, on both the properties of the gas molecules and surfaces. Specifically, model organic surfaces, comprised of long-chain methyl- and hydroxyl-terminated self-assembled monolayers (SAMs) have been employed to test how an interfacial hydrogen bonding network may affect the ability of a gas-phase compound to thermally accommodate (typically, the first step in a reaction) with the surfaces. Results indeed show that small organic compounds transfer less energy to the interconnected hydroxyl-terminated SAM (OH-SAM) than to the organic surface with methyl groups at the interface. However, the dynamics also appear to depend on the polarizability of the impinging gas-phase molecule. The π electrons in the double bond of ethene (C2H4) and the triple bond in ethyne (C2H2) appear to act as hydrogen bond acceptors when the molecules collide with the OH-SAM. The molecular beam scattering studies have demonstrated that these weak attractive forces facilitate energy transfer. A positive correlation between energy transfer and solubilities for analogous solute-solvent combinations was observed for the CH3-SAM (TD fractions: C2H6 > C2H4 > C2H2), but not for the OH-SAM (TD fractions: C2H6 > C2H2 > C2H4). The extent of energy transfer between ethane, ethene, and ethyne and the CH3-SAM appears to be determined by the degrees of freedom or rigidity of the impinging compound, while gas-surface attractive forces play a more decisive role in controlling the scattering dynamics at the OH-SAM. Beyond fundamental studies of energy transfer, this thesis provides detailed surface-science-based studies of the mechanisms involved in the uptake and decomposition of chemical warfare agent (CWA) simulants on or within metal-organic frameworks (MOFs). The work presented here represents the first such study reported in with traditional surface-science based methods have been applied to the study of MOF chemistry. The mechanism and kinetics of interactions between dimethyl methylphosphonate (DMMP) or dimethyl chlorophosphate (DMCP), key CWA simulants, and Zr6-based metal-organic frameworks (MOFs) have been investigated with in situ infrared spectroscopy (IR), X-ray photoelectron spectroscopy (XPS), powder X-ray diffraction (PXRD), and DFT calculations. DMMP and DMCP were found to adsorb molecularly (physisorption) to the MOFs through the formation of hydrogen bonds between the phosphoryl oxygen and the free hydroxyl groups associated with Zr6 nodes or dangling -COH groups on the surface of crystallites. Unlike UiO-66, the infrared spectra for UiO-67 and MOF-808, recorded during DMMP exposure, suggest that uptake occurs through both physisorption and chemisorption. The XPS spectra of MOF-808 zirconium 3d electrons reveal a charge redistribution following exposure to DMMP. Besides, the analysis of the phosphorus 2p electrons following exposure and thermal annealing to 600 K indicates that two types of stable phosphorus-containing species exist within the MOF. DFT calculations (performed by Professor Troya at Virginia Tech), were used to guide the IR band assignments and to help interpret the XPS features, suggest that uptake is driven by nucleophilic addition of a surface OH group to DMMP with subsequent elimination of a methoxy substituent to form strongly bound methyl methylphosphonic acid (MMPA). With similar IR features of MOF-808 upon DMCP exposure, the reaction pathway of DMCP in Zr6-MOFs may be similar to that for DMMP, but with the final product being methyl chlorophosphonic acid (elimination of the chlorine) or MMPA (elimination of a methoxy group). The rates of product formation upon DMMP exposure of the MOFs suggest that there are two distinct uptake processes. The rate constants for these processes were found to differ by approximately an order of magnitude. However, the rates of molecular uptake were found to be nearly identical to the rates of reaction, which strongly suggests that the reaction rates are diffusion limited. Overall, and perhaps most importantly, this research has demonstrated that the final products inhibit further reactions within the MOFs. The strongly bound products could not be thermally driven from the MOFs prior to the decomposition of the MOFs themselves. Therefore, new materials are needed before the ultimate goal of creating a catalyst for the air-based destruction of traditional chemical nerve agents is realized. / Doctor of Philosophy / A molecular-level understanding of gas-surface energy exchange and reaction mechanisms will aid in the prediction of the environmental fate of pollutants and enable advances toward catalysts for the decomposition of toxic compounds. Our gas-surface scattering experiments performed in an ultra-high vacuum environment have provided key insights into the outcome of critical interfacial processes on model systems. Results show that energy transfer upon gas-surface collisions depends on both the properties of the gas molecules and surfaces. Due to the formation of interfacial hydrogen bonding network in hydroxyl-terminated surface, the small organic compounds transfer less energy to it than to the organic surface with methyl groups at the interface. The dynamics also appear to depend on the properties of the impinging gas-phase molecule. The π electrons in the double bond of ethene and the triple bond in ethyne act as hydrogen bond acceptors when the molecules collide with the hydroxyl-terminated surface. The attractive forces facilitate energy transfer. A positive correlation between energy transfer and solubilities for analogous solute-solvent combinations was observed for the methyl-terminated surface, but not for the hydroxyl-terminated surface. The extent of energy transfer between ethane, ethene, and ethyne and the methyl-terminated surface appears to be determined by the degrees of freedom or rigidity of the gas, while gas-surface attractive forces play a more decisive role in controlling the scattering dynamics at the hydroxyl-terminated surface. Furthermore, this thesis provides detailed surface-science-based studies of the mechanisms involved in the uptake and decomposition of chemical warfare agent (CWA) simulants on or within metal-organic frameworks (MOFs). Dimethyl methylphosphonate (DMMP) and dimethyl chlorophosphate (DMCP), key CWA simulants, physisorbed to the MOFs through the formation of hydrogen bonds between the phosphoryl oxygen and the free hydroxyl groups associated with inorganic nodes or dangling -COH groups on the surface of crystallites. The infrared spectra for UiO-67 and MOF-808 suggest that uptake occurs through both physisorption and chemisorption. The XPS spectra of MOF-808 zirconium 3d electrons reveal a charge redistribution following exposure to DMMP. Besides, the analysis of the phosphorus 2p electrons following exposure and thermal annealing to 600 K indicates that two types of stable phosphorus-containing species exist within the MOF. DFT calculations suggest that uptake is driven by nucleophilic addition of a surface OH group to DMMP with subsequent elimination of a methoxy substituent to form strongly bound methyl methylphosphonic acid (MMPA). With similar IR features of MOF-808 upon DMCP exposure, the reaction pathway of DMCP in MOFs may be similar to that for DMMP, but with the final product being methyl chlorophosphonic acid (elimination of the chlorine) or MMPA (elimination of a methoxy group). The rates of product formation suggest that there are two distinct uptake processes. The rate constants for these processes were found to be nearly identical to the rates of physisorption, which suggests that the reaction rates are diffusion limited. Overall, this research has demonstrated that the final products inhibit further reactions within the MOFs. The strongly bound products could not be thermally driven from the MOFs prior to the decomposition of the MOFs themselves. Therefore, new materials are needed before the ultimate goal of creating a catalyst for the air-based destruction of traditional chemical nerve agents is realized.

Polypyridyl transition metal complexes containing ruthenium, rhodium and iridium centers are mainly studied due to their light absorbing and emitting properties. Lanthanide oxides such as europium oxide absorb light as well and exhibit strong luminescence and long lifetimes. The optical properties of these materials were significant especially in solar energy utilization schemes and optical applications. Energy transfer across a surface is important in several applications including phosphors and biomedical applications. Excited states of metal complexes with a carboxylate-containing ligand such as deeb = diethyl-2,2'-bipyridine-4,4'-dicarboxylate were studied on nanoparticle surfaces. In this work, [Rh(deeb)2Cl2](PF6), [Ir(deeb)2Cl2](PF6) and [Ir(deeb)2(dpp)](PF6)3 were synthesized using the building block approach. The metal complexes were characterized using 1H NMR spectroscopy, mass spectrometry, electronic absorption spectroscopy and electrochemistry. The 1H NMR spectra of the complexes were consistent with those of their ruthenium analogs. Mass spectra contain fragmentation patterns of the (M-PF6)+ molecular ion for [Rh(deeb)2Cl2](PF6) and [Ir(deeb)2Cl2](PF6), and (M-3PF6)3+ molecular ions for [Ir(deeb)2(dpp)](PF6)3. The electronic absorption spectrum of [Rh(deeb)2Cl2](PF6) shows a maximum at 328 nm, which is assigned as 1π→π*transition. The electronic absorption spectrum of [Ir(deeb)2Cl2](PF6) shows maxima at 308 nm and 402 nm, which are assigned as 1π→π* and metal-to-ligand charge transfer transitions, respectively. The [Ir(deeb)2(dpp)](PF6)3 complex exhibits peaks due to 1π→π* transitions at 322 nm and 334 nm. [Rh(deeb)2Cl2](PF6) has emission maxima from the 3LF state at 680 nm and 704 nm for the solid and glassy solutions at 77 K, respectively. [Ir(deeb)2Cl2](PF6) has emission maxima from the 3MLCT state at 538 nm in acetonitrile and 567 nm in the solid state at room temperature, with lifetimes of 1.71 μs and 0.35 μs, respectively. [Ir(deeb)2Cl2](PF6) has an unusually higher quantum yield than analogous compounds. [Ir(deeb)2(dpp)](PF6)3 has emission maxima from the 3IL state at 540 nm in acetonitrile and 599 nm in the solid state at room temperature, with lifetimes of 1.23 μs and 0.14 μs, respectively. Cyclic voltammetry of [Ir(deeb)2Cl2](PF6) and [Ir(deeb)2(dpp)](PF6)3 yield reversible and quasi-reversible couples corresponding to deeb ligand and Ir3+/+reductions, respectively. Attachment of the complexes were conducted by equilibration of complex solutions in acetonitrile with europium oxide nanoparticles. Europium oxide nanoparticles, which were synthesized by gas-phase condensation, have 11-nm diameters and exhibit sharp f-based luminescence in the visible and near IR regions. EDX, TEM, IR and reflectance spectroscopy measurements indicate substantial coating through various modes of attachment of the nanoparticle surface by the metal complexes while retaining the excited state properties of the metal complexes. Surface adsorption studies indicate monolayer coverage of the nanoparticle surface by the metal complexes, consistent with limiting surface coverages of previously reported analogous systems. Eu2O3 nanoparticles modified with [Rh(deeb)2Cl2]+ exhibit minimal to no energy transfer from emission spectra, and a reduction in the lifetime at 77K could be due to the rhodium complex preventing the excitation of Eu3+. Upon attachment of the Ir complexes [Ir(deeb)2Cl2]+ and [Ir(deeb)2(dpp)]3+ on as-prepared nanoparticles, Eu3+ luminescence was observed for nanoparticles modified with iridium complexes at room temperature, which could be due to energy transfer among other possibilities. Efficiencies of 68% and 50%, and energy transfer rate constants of 1.1 x 10-5 and 1.0 x 10-5 were calculated from lifetime data for [Ir(deeb)2Cl2]+ and [Ir(deeb)2(dpp)]3+ on Eu2O3 nanoparticles, respectively. Since iridium complexes are used as components of light-emitting diodes, europium oxide nanoparticles modified with iridium complexes have potential in optical applications which make studies of these compounds interesting. / Master of Science

Numerous pigment protein complexes exist in natural systems to harvest light energy such as photosystem II and Nanosalina xenorhodopsin. However, the mechanisms of these lipid embedded photo-active complexes have yet to be fully understood. Photosystem II is of interest due to being a compact complex which can perform the three initial key steps of photosynthesis: absorb light, transfer the excitation from the antennae to reaction center, and perform efficient charge separation. Despite considerable theoretical and experimental effort the exact mechanism of this process remains uncertain. Nanosalina xenorhodopsin is a more recently discovered inwards proton pump with minimal studies into the inwards proton pumping mechanism. Nanosalina xenorhodopsin is of interest as it contrasts with other known and well studied rhodopsins which serve as outwards proton pumps, moving H+ ions out of a cell. In this work, we use the Hamiltonian ensemble method to construct the first fully ab initio computational models of these systems which will be used to determine the mechanisms of these systems. To construct these models we first investigated the effect of the modeled surrounding membrane and simulated temperature. The effect of the extended modeled environment on calculated results is often overlooked but important for the construction of an accurate ab initio model. Our models showed that both membrane composition and temperature result in significant changes in the behavior of the extended membrane system, relative excitation energies of chromophores, and energy dynamics of a pigment protein complex. The absolute excitation energies of chromophores, absorption spectra, and linear dichroism spectra were comparatively insensitive to changes in the modeled environment. With the effect of the environment established, we present a preliminary method to extend our photosystem II model to include charge transfer states, and a preliminary model of Nanosalina xenorhodopsin which can determine the photocycle states through validation of calculated spectra against experimental results.