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Title: DENSITY FUNCTIONAL THEORY STUDY OF MOLECULES AND CRYSTALS CONTAINING D AND F METALS.
Creator: Gangopadhyay, Shruba, Masunov, Artem, University of Central Florida
Abstract / Description: Density Functional Theory (DFT) method is applied to study the crystal structure of transition metal and lanthanide oxides, as well as molecular magnetic complexes. DFT is a widely popular computational approach because it recasts a many-body problem of interacting electrons into an equivalent problem of non-interacting electrons, greatly reducing computational cost. We show that for certain structural properties like phase stability, lattice parameter and oxygen migration energetics pure DFT...
Show moreDensity Functional Theory (DFT) method is applied to study the crystal structure of transition metal and lanthanide oxides, as well as molecular magnetic complexes. DFT is a widely popular computational approach because it recasts a many-body problem of interacting electrons into an equivalent problem of non-interacting electrons, greatly reducing computational cost. We show that for certain structural properties like phase stability, lattice parameter and oxygen migration energetics pure DFT can give good agreement with experiments. But moving to more sensitive properties like spin state energetic certain modifications of standard DFT are needed. First we investigated mixed ionic-electronic conducting perovskite type oxides with a general formula ABO3 (where A =Ba, Sr, Ca and B = Co, Fe, Mn). These oxides often have high mobility of the oxygen vacancies and exhibit strong ionic conductivity. They are key materials that nd use in several energy related applications, including solid oxide fuel cell (SOFC), sensors, oxygen separation membranes, and catalysts. Different cations and oxygen vacancies ordering are examined using plane wave pseudopotential density functional theory. We nd that cations are completely disordered, whereas oxygen vacancies exhibit a strong trend for aggregation in L-shaped trimer and square tetramer structure. On the basis of our results, we suggest a new explanation for BSCF phase stability. Instead of linear vacancy ordering, which must take place before the phase transition into brownmillerite structure, the oxygen vacancies in BSCF prefer to form the nite clusters and preserve the disordered cubic structure. This structural feature could be found only in the rst-principles simulations and cannot be explained by the effect of the ionic radii alone. In order to understand vacancy clustering and phase stability in oxygen-deficient barium strontium cobalt iron oxide (BSCF), we predict stability and activation energies for oxygen vacancy migration. Using symmetry constrained search and Nudged Elastic Band method, we characterize the transition states for an oxygen anion moving into a nearby oxygen vacancy site that is surrounded by different cations and find the activation energies to vary in the range 30-50 kJ/mol in good agreement with experimental data. Next we study spin alignments of single molecule magnets (SMM). SMMs are a class of polynuclear transition metal complexes, which characterized by a large spin ground state and considerable negative anisotropy. These properties lead to a barrier for the reversal of magnetization. For these reasons SMM are expected to be promising materials for molecular spintronics and quantum computing applications. To design SMM for quantum computation, we need to accurately predict their magnetic properties. The most important property is, Heisenberg exchange coupling constant (J). This constant appears in model Heisenberg Hamiltonian that can be written in general form as here Jij represents the coupling between the two magnetic centers i and j with the spin states Si and Sj. The positive J values indicate the ferromagnetic ground state and the negative ones indicate the antiferromagnetic ground state. We found pure DFT is not accurate enough to predict J values. We employ density functionals with a Hubbard U term that helps to counteract the unphysical delocalization of electrons due to errors in pure exchange-correlation functionals. Unlike most previous DFT+U studies, we calibrate U parameters for both metal and ligand atoms using five binuclear manganese complexes as the benchmarks. We note delocalization of the spin density onto acetate ligands due to À-back bonding, inverting spin-polarization of the acetate oxygen atoms relative to that predicted from superexchange mechanism. This inversion may affect performance of the models assuming strict localization of the spins on magnetic centers for the complexes with bridging acetate ligands. Next, we apply DFT+U methodology for Mn12(mda) and Mn12(ada) complexes to calculate all six nearest neighbor Jij value. Our result shows both qualitative and quantitative agreement with experiments unlike other DFT studies. Using the optimized geometry of the ground spin state instead of less accurate experimental geometry was found to be crucial for this good agreement. The protocol tested in this study can be applied for the rational design of single-molecule magnets for molecular spintronics and quantum computing applications. Finally we apply hybrid DFT methodology to calculate geometrical parameters for cerium oxides. We review the experimental and computational studies on the cerium oxide nanoparticles, as well as stoichiometric phases of bulk ceria. Electroneutral and nonpolar pentalayers are identified as building blocks of type A sesqioxide structure. The idealized structure of the nanoparticles is described as dioxide covered by a single pentalayer of sesquioxide, which explains the exceptional stability of subsurface vacancies in nanoceria. The density functional theory (DFT) predictions of the lattice parameters and bulk moduli for the Ce(IV) and Ce(III) oxides at the hybrid DFT level are also presented. The calculated values for both compounds agree with experiment and allow to predict changes in the lattice parameter with decreasing size of the nanoparticles. The results validate hybrid DFT as a promising method for future study the structure of oxygen vacancies and catalytic properties of ceria nanoparticles.
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Date Issued: 2011
Identifier: CFE0003741, ucf:48762
Format: Document (PDF)
PURL: http://purl.flvc.org/ucf/fd/CFE0003741

Title: DFT STUDY OF GEOMETRY AND ENERGETICS OF TRANSITION METAL SYSTEMS.
Creator: Goel, Satyender, MASUNOV, ARTEM, University of Central Florida
Abstract / Description: This dissertation focuses on computational study of the geometry and energetics small molecules and nanoclusters involving transition metals (TM). These clusters may be used for various industrial applications including catalysis and photonics. Specifically, in this work we have studied hydrides and carbides of 3d-transition metal systems (Sc through Cu), small nickel and gold clusters. Qualitatively correct description of the bond dissociation is ensured by allowing the spatial and spin...
Show moreThis dissertation focuses on computational study of the geometry and energetics small molecules and nanoclusters involving transition metals (TM). These clusters may be used for various industrial applications including catalysis and photonics. Specifically, in this work we have studied hydrides and carbides of 3d-transition metal systems (Sc through Cu), small nickel and gold clusters. Qualitatively correct description of the bond dissociation is ensured by allowing the spatial and spin symmetry to break. We have tested applicability of new exchange-correlation functional and alternative theoretical descriptions (spin-contamination correction in broken symmetry DFT and ensemble Kohn-Sham (EKS)) as well. We studies TM hydrides and carbides systems to understand the importance of underlying phenomenon of bond breaking in catalytic processes. We have tested several exchange-correlation functionals including explicit dependence on kinetic energy density for the description of hydrides (both neutral and cationic) and carbides formed by 3d-transition metals. We find M05-2x and BMK dissociation energies are in better agreement with experiment (where available) than those obtained with high level wavefunction theory methods, published previously. This agreement with experiment deteriorates quickly for other functionals when the fraction of the Hartree-Fock exchange in DFT functional is decreased. Higher fraction of HF exchange is also essential in EKS formalism, but it does not help when spin-adapted unrestricted approach is employed. We analyze the electron spin densities using Natural Bond Orbital population analysis and find that simple description of 3d electrons as non-bonding in character is rarely correct. Unrestricted formalism results in appreciable spin-contamination for some of the systems at equilibrium, which motivated us to investigate it further in details. In order to correct the spin contamination effect on the energies, we propose a new scheme to correct for spin contamination arising in broken-symmetry DFT approach. Unlike conventional schemes, our spin correction is introduced for each spin-polarized electron pair individually and therefore is expected to yield more accurate energy values. We derive an expression to extract the energy of the pure singlet state from the energy of the broken-symmetry DFT description of the low spin state and the energies of the high spin states (pentuplet and two spin-contaminated triplets in the case of two spin-polarized electron pairs). We validate our spin-contamination correction approach by a simple example of H2 and applied to more complex MnH system. Ensemble KS formalism is also applied to investigate the dissociation of C2 molecule. We find that high fraction of HF exchange is essential to reproduce the results of EKS treatment with exact exchange-correlation functional. We analyze the geometry and energetics of small nickel clusters (Ni2-Ni5) for several lowest energy isomers. We also study all possible spin states of small nickel cluster isomers and report observed trends in energetics. Finally we determine the geometry and energetics of ten lowest energy isomers of four small gold clusters (Au2, Au4, Au6, and Au8). We have also investigated the influence of cluster geometry, ligation, solvation and relativistic effects on electronic structure of these gold clusters. The effect of one-by-one ligand attachment in vacuum and solvent environment is also studied. Performance of five DFT functionals are tested as well; Local Spin Density Approximation (SVWN5), Generalized Gradient Approximation (PBE), kinetic energy density-dependent functional (TPSS), hybrid DFT (B3LYP), and CAM-B3LYP which accounts for long-range exchange effects believed to be important in the analysis of metal bonding in gold complexes and clusters. Our results exhibit the ligand induced stability enhancement of otherwise less stable isomers of Au4, Au6 and Au8. Ligands are found to play a crucial role in determining the 2D to 3D transition realized in small gold clusters. In order to select an appropriate theory level to use in this study, we investigate the effect of attachment of four different ligands (NH3, NMe3, PH3, PMe3) on cluster geometry and energetics of Au2 and Au4 in vacuum and in solution. Our results benchmark the applicability of DFT functional model and polarization functions in the basis set for calculations of ligated gold cluster systems. We employ five different basis sets with increasing amount of polarization and diffuse functions; LANL2DZ, LANL2DZ-P, def2-SVP, def2-TZVP, and def2-QZVP. We obtain NMe3 = NH3 < PH3 < PMe3 order of ligand binding energies and observe shallow potential energy surfaces in all molecules. Our results suggest appropriate quantum-chemical methodologies to model small noble metal clusters in realistic ligand environment to provide reliable theoretical analysis in order to complement experiments.
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Date Issued: 2010
Identifier: CFE0003293, ucf:48498
Format: Document (PDF)
PURL: http://purl.flvc.org/ucf/fd/CFE0003293

Title: SIMULATION OF PHOTOCHROMIC COMPOUNDS USING DENSITY FUNCTIONAL THEORY METHODS.
Creator: Patel, Pansy, Masunov, Artem, University of Central Florida
Abstract / Description: This Thesis describes the systematic theoretical study aimed at prediction of the essential properties for the functional organic molecules that belong to diarylethene (DA) family of compounds. Diarylethenes present the distinct ability to change color under the influence of light, known as photochromism. This change is due to ultrafast chemical transition from open to closed ring isomers (photocyclization). It can be used for optical data storage, photoswitching, and other photonic...
Show moreThis Thesis describes the systematic theoretical study aimed at prediction of the essential properties for the functional organic molecules that belong to diarylethene (DA) family of compounds. Diarylethenes present the distinct ability to change color under the influence of light, known as photochromism. This change is due to ultrafast chemical transition from open to closed ring isomers (photocyclization). It can be used for optical data storage, photoswitching, and other photonic applications. In this work we apply Density Functional Theory methods to predict 6 of the related properties: (i) molecular geometry; (ii) resonant wavelength; (iii) thermal stability; (iv) fatigue resistance; (v) quantum yield and (vi) nanoscale organization of the material. In order to study sensitivity at diode laser wavelengths, we optimized geometry and calculated vertical absorption spectra for a benchmark set of 28 diarylethenes. Bond length alternation (BLA) parameters and maximum absorption wavelengths (λmax) are compared to the data presently available from X-ray diffraction and spectroscopy experiments. We conclude that TD-M05/6-31G*/PCM//M05-2X/6-31G*/PCM level of theory gives the best agreement for both the parameters. For our predictions the root mean square deviation (RMSD) are below 0.014 ÃƒÂ… for the BLAs and 25 nm for λmax. The polarization functions in the basis set and solvent effects are both important for this agreement. Next we consider thermal stability. Our results suggest that UB3LYP and UM05-2X functionals predict the activation barrier for the cycloreversion reaction within 3-4 kcal/mol from experimental value for a set of 7 photochromic compounds. We also study thermal fatigue, defined as the rate of undesirable photochemical side reactions. In order to predict the kinetics of photochemical fatigue, we investigate the mechanism of by-product formation. It has been established experimentally that the by-product is formed from the closed isomer; however the mechanism was not known. We found that the thermal by-product pathway involves the bicyclohexane (BCH) ring formation as a stable intermediate, while the photochemical by-product formation pathway may involve the methylcyclopentene diradical (MCPD) intermediate. At UM05-2X/6-31G* level, the calculated barrier between the closed form and the BCH intermediate is 51.2 kcal/mol and the barrier between the BCH intermediate and the by-product 16.2 kcal/mol. Next we investigate two theoretical approaches to the prediction of quantum yield (QY) for a set of 14 diarylethene derivatives at the validated M05-2X/6-31G* theory level. These include population of ground-state conformers and location of the pericycylic minimum on the potential energy surface 2-A state. Finally, we investigate the possibility of nanoscale organization of the photochromic material based on DNA template, as an alternative to the amorphous polymer matrix. Here we demonstrate that Molecular Dynamic methods are capable to describe the intercalation of π-conjugated systems between DNA base pairs and accurately reproduced the available photophysical properties of these nanocomposites. In summary, our results are in good agreement with the experimental data for the benchmark set of molecules we conclude that Density Functional Theory methods could be successfully used as an important component of material design strategy in prediction of accurate molecular geometry, absorption spectra, thermal stability of isomers, fatigue resistance, quantum yield of photocyclization and photophysical properties of nanocomposites.
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Date Issued: 2010
Identifier: CFE0003136, ucf:48633
Format: Document (PDF)
PURL: http://purl.flvc.org/ucf/fd/CFE0003136

Title: Theoretical Study of Negative Molecular Ions Relevant to the Interstellar and Laboratory Plasma.
Creator: Khamesian, Marjan, Kokoouline, Viatcheslav, Argenti, Luca, Saha, Haripada, Masunov, Artem, University of Central Florida
Abstract / Description: Recently, several negative molecular ions, CnN? (n = 1, 3, 5) and CnH? (n = 4, 6, 8), were observed in the interstellar medium (ISM). It was suggested that the anions are formed in the ISM by the process of radiative electron attachment (REA). A simple statistical model was developed in 1980's to estimate rate coefficients of the REA reactions. Some of the rate coefficients obtained in the model are consistent with the observations, the others are not. More importantly, some of the...
Show moreRecently, several negative molecular ions, CnN? (n = 1, 3, 5) and CnH? (n = 4, 6, 8), were observed in the interstellar medium (ISM). It was suggested that the anions are formed in the ISM by the process of radiative electron attachment (REA). A simple statistical model was developed in 1980's to estimate rate coefficients of the REA reactions. Some of the rate coefficients obtained in the model are consistent with the observations, the others are not. More importantly, some of the approximations employed in the model are not physically justified.The aim of this thesis is a development of a quantum-mechanical approach to study the process of radiative electron attachment to linear molecules of astrophysical interest. The approach is based on accurate ab initio calculations of electronic bound and continuum states of the negative ion. Cross sections and rate coefficients for formation of the following molecular negative ions by REA were determined: CN?, C2H?, C3N?, C4H?, C5N?, C6H?, and C8H?. All the calculations presented in the thesis were carried out using the MOLPRO and UK R-matrix (Quantemol)suites of programs. Uncertainty quantification of the results, obtained for each studied system, was performed. A second process, closely related to the radiative electron attachment, photodetachment (PD), was also studied in the thesis. Photodetachment cross sections for the CnN? (n = 1, 3, 5), CnH? (n = 4, 6, 8) and C2? molecules were determined using an approach similar to the one employed for REA from the same transition dipole moment matrix elements. The obtained REA cross sections and rate coefficients were validated by comparing the present theoretical results with the experimental data from recent photodetachment experiments.The present results suggest that the observed abundance of these ions in the ISM can hardly be explained by the REA process. In other words, these anions are formed in the interstellar medium by a process different than radiative electron attachment.Dissociative electron attachment (DEA) is another process of anion formation, which could possibly explain formation of certain molecular anions in the ISM. The ClF attachment was studied using a first principle approach.A good agreement with experimental data was demonstrated.A theoretical approach to evaluate cross sections for rotational excitation of linear neutral molecules by an electron impact was developed and applied to acetylene, HCCH. The differential cross sections for e-HCCH scattering were calculated between energies 0.1 eV and 10 eV. The momentum transfer cross section and eigenphases for e-HCCH scattering were also calculated.
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Date Issued: 2017
Identifier: CFE0006612, ucf:51295
Format: Document (PDF)
PURL: http://purl.flvc.org/ucf/fd/CFE0006612

Title: Prediction of Optical Properties of Pi-Conjugated Organic Materials for Technological Innovations.
Creator: Nayyar, Iffat, Masunov, Artem, Saha, Haripada, Stolbov, Sergey, Gesquiere, Andre, University of Central Florida
Abstract / Description: Organic ?-conjugated solids are promising candidates for new optoelectronic materials. The large body of evidence points at their advantageous properties such as high charge-carrier mobility, large nonlinear polarizability, mechanical flexibility, simple and low cost fabrication and superior luminescence. They can be used as nonlinear optical (NLO) materials with large two-photon absorption (2PA) and as electronic components capable of generating nonlinear neutral (excitonic) and charged ...
Show moreOrganic ?-conjugated solids are promising candidates for new optoelectronic materials. The large body of evidence points at their advantageous properties such as high charge-carrier mobility, large nonlinear polarizability, mechanical flexibility, simple and low cost fabrication and superior luminescence. They can be used as nonlinear optical (NLO) materials with large two-photon absorption (2PA) and as electronic components capable of generating nonlinear neutral (excitonic) and charged (polaronic) excitations. In this work, we investigate the appropriate theoretical methods used for the (a) prediction of 2PA properties for rational design of organic materials with improved NLO properties, and (b) understanding of the essential electronic excitations controlling the energy-transfer and charge-transport properties in organic optoelectronics. Accurate prediction of these electro-optical properties is helpful for structure-activity relationships useful for technological innovations.In Chapter 1 we emphasize on the potential use of the organic materials for these two applications. The 2PA process is advantageous over one-photon absorption for deep-tissue fluorescence microscopy, photodynamic therapy, microfabrication and optical data storage owing to the three-dimensional spatial selectivity and improved penetration depth in the absorbing or scattering media. The design of the NLO materials with large 2PA cross-sections may reduce the optical damage due to the use of the high intensity laser beams for excitation. The organic molecules also possess self-localized excited states which can decay radiatively or nonradiatively to form excitonic states. This suggests the use of these materials in the electroluminescent devices such as light-emitting diodes and photovoltaic cells through the processes of exciton formation or dissociation, respectively. It is therefore necessary to understand ultrafast relaxation processes required in understanding the interplay between the efficient radiative transfer between the excited states and exciton dissociation into polarons for improving the efficiency of these devices. In Chapter 2, we provide the detailed description of the various theoretical methods applied for the prediction as well as the interpretation of the optical properties of a special class of substituted PPV [poly (p-phenylene vinylene)] oligomers. In Chapter 3, we report the accuracy of different second and third order time dependent density functional theory (TD-DFT) formalisms in prediction of the 2PA spectra compared to the experimental measurements for donor-acceptor PPV derivatives. We recommend a posteriori Tamm-Dancoff approximation method for both qualitative and quantitative analysis of 2PA properties. Whereas, Agren's quadratic response methods lack the double excitations and are not suitable for the qualitative analysis of the state-specific contributions distorting the overall quality of the 2PA predictions. We trace the reasons to the artifactual excited states above the ionization threshold. We also study the effect of the basis set, geometrical constraints and the orbital exchange fraction on the 2PA excitation energies and cross-sections. Higher exchange (BMK and M05-2X) and range-separated (CAM-B3LYP) hybrid functionals are found to yield inaccurate predictions both quantitatively and qualitatively. The failure of the exchange-correlation (XC) functionals with correct asymptotic is traced to the inaccurate transition dipoles between the valence states, where functionals with low HF exchange succeed. In Chapter 4, we test the performance of different semiempirical wavefunction theory methods for the prediction of 2PA properties compared to the DFT results for the same set of molecules. The spectroscopic parameterized (ZINDO/S) method is relatively better than the general purpose parameterized (PM6) method but the accuracy is trailing behind the DFT methods. The poor performances of PM6 and ZINDO/S methods are attributed to the incorrect description of excited-to-excited state transition and 2PA energies, respectively. The different semiempirical parameterizations can at best be used for quantitative analysis of the 2PA properties. The ZINDO/S method combined with different orders of multi-reference configuration interactions provide an improved description of 2PA properties. However, the results are observed to be highly dependent on the specific choice for the active space, order of excitation and reference configurations.In Chapter 5, we present a linear response TD-DFT study to benchmark the ability of existing functional models to describe the extent of self-trapped neutral and charged excitations in PPV and its derivative MEH-PPV considered in their trans-isomeric forms. The electronic excitations in question include the lowest singlet (S1) and triplet (T1†) excitons, positive (P+) and negative (P-) polarons and the lowest triplet (T1) states. Use of the long-range-corrected DFT functional, such as LC-wPBE, is found to be crucial in order to predict the physically correct spatial localization of all the electronic excitations in agreement with experiment. The inclusion of polarizable dielectric environment play an important role for the charged states. The particle-hole symmetry is preserved for both the polymers in trans geometries. These studies indicate two distinct origins leading to self-localization of electronic excitations. Firstly, distortion of molecular geometry may create a spatially localized potential energy well where the state wavefunction self-traps. Secondly, even in the absence of geometric and vibrational dynamics, the excitation may become spatially confined due to energy stabilization caused by polarization effects from surrounding dielectric medium.In Chapter 6, we aim to separate these two fundamental sources of spatial localization. We observe the electronic localization of P+ and P- is determined by the polarization effects of the surrounding media and the character of the DFT functional. In contrast, the self-trapping of the electronic wavefunctions of S1 and T1(T1†) mostly follows their lattice distortions. Geometry relaxation plays an important role in the localization of the S1 and T1† excitons owing to the non-variational construction of the excited state wavefunction. While, mean-field calculated P+, P- and T1 states are always spatially localized even in ground state S0 geometry. Polaron P+ and P- formation is signified by the presence of the localized states for the hole or the electron deep inside the HOMO-LUMO gap of the oligomer as a result of the orbital stabilization at the LC-wPBE level. The broadening of the HOMO-LUMO band gap for the T1 exciton compared to the charged states is associated with the inverted bond length alternation observed at this level. The molecular orbital energetics are investigated to identify the relationships between state localization and the corresponding orbital structure.In Chapter 7, we investigate the effect of various conformational defects of trans and cis nature on the energetics and localization of the charged P+ and P- excitations in PPV and MEH-PPV. We observe that the extent of self-trapping for P+ and P- polarons is highly sensitive on molecular and structural conformations, and distribution of atomic charges within the polymers. The particle-hole symmetry is broken with the introduction of trans defects and inclusion of the polarizable environment in consistent with experiment. The differences in the behavior of PPV and MEH-PPV is rationalized based on their orbital energetics and atomic charge distributions. We show these isomeric defects influence the behavior and drift mobilities of the charge carriers in substituted PPVs.
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Date Issued: 2013
Identifier: CFE0005110, ucf:50722
Format: Document (PDF)
PURL: http://purl.flvc.org/ucf/fd/CFE0005110

Title: A theoretical and experimental investigation of the physical and chemical properties of solid nanoscale interfaces.
Creator: Matos, Jeronimo, Kara, Abdelkader, Heinrich, Helge, Schelling, Patrick, Masunov, Artem, University of Central Florida
Abstract / Description: With the emerging interest in nanoscale materials, the fascinating field of surface science is rapidly growing and presenting challenges to the design of both experimental and theoretical studies. The primary aim of this dissertation is to shed some light on the physical and chemical properties of selected nanoscale materials at the interface. Furthermore, we will discuss the effective application of cutting edge theoretical and experimental techniques that are invaluable tools for...
Show moreWith the emerging interest in nanoscale materials, the fascinating field of surface science is rapidly growing and presenting challenges to the design of both experimental and theoretical studies. The primary aim of this dissertation is to shed some light on the physical and chemical properties of selected nanoscale materials at the interface. Furthermore, we will discuss the effective application of cutting edge theoretical and experimental techniques that are invaluable tools for understanding the systems at hand. To this effect, we use density functional theory (DFT) with the inclusion of van der Waals (vdW) interactions to study the effect of long-range interactions on the adsorption characteristics of various organic molecules (i.e. benzene, olympicene radical, and sexithiophene) on transition metal surfaces. Secondly, the detailed analysis of x-ray absorption spectroscopy (XAS), scanning transmission electron microscopy (STEM), x-ray photoelectron spectroscopy (XPS) and atomic force microscopy (AFM) measurements will be presented. These investigations will be dedicated to the study of (i) the effect of pre-treatment on the coarsening behavior of Pt nanoparticles (NPs) supported on ?-Al2O3 and (ii) deconvoluting the intrinsic (size effects) and extrinsic (ligand effects) physical and electronic properties of Au NPs encapsulated by polystyrene 2-vinylpiridine ligands.
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Date Issued: 2015
Identifier: CFE0005975, ucf:50783
Format: Document (PDF)
PURL: http://purl.flvc.org/ucf/fd/CFE0005975

Title: Theoretical and Computational Studies of the electronic, Structural, Vibrational, and Thermodynamic Properties of Transition Metal Nanoparticles.
Creator: Sadatshafaie, Ghazal, Rahman, Talat, Stolbov, Sergey, Ishigami, Masa, Masunov, Artem, University of Central Florida
Abstract / Description: The main objective of this dissertation is to provide better understanding of the atomic configurations, electronic structure, vibrational properties, and thermodynamics of transition metal nanoparticles and evaluate the intrinsic (i.e. size and shape) and extrinsic (i.e. ligands, adsorbates, and support) effects on the aforementioned properties through a simulational approach. The presented research provides insight into better understanding of the morphological changes of the nanoparticles...
Show moreThe main objective of this dissertation is to provide better understanding of the atomic configurations, electronic structure, vibrational properties, and thermodynamics of transition metal nanoparticles and evaluate the intrinsic (i.e. size and shape) and extrinsic (i.e. ligands, adsorbates, and support) effects on the aforementioned properties through a simulational approach. The presented research provides insight into better understanding of the morphological changes of the nanoparticles that are brought about by the intrinsic factors as well as the extrinsic ones. The preference of certain ligands to stabilize specific sizes of nanoparticles is investigated. The intrinsic and extrinsic effects on the electronic structure of the nanoparticles are presented. The physical and chemical properties of the nanoparticles are evaluated through better understanding of the above effects on the experimentally observed properties as well as the applied techniques. The unexpected experimental results are tested and interpreted by deconvolution of the affecting factors. The application of Debye model to nanoparticles is tested and its shortcomings at nanoscale are discussed. Predictions which can provide insight into intelligent choice of candidates to cater to certain properties are provided. The results of this thesis can be used in the future in design and engineering of functionalized materials. We use ab initio calculations based on Density Functional Theory (DFT) to obtain information about the energetics, atomic configuration, and electronic structure of the nanoparticles. Ab initio Molecular Dynamics (MD) is used to study the evolution of the structures of the nanoparticles. To calculate vibrational frequencies, the finite displacement method is employed.
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Date Issued: 2015
Identifier: CFE0006385, ucf:51536
Format: Document (PDF)
PURL: http://purl.flvc.org/ucf/fd/CFE0006385

Title: Computational Approach to Electrocatalysis.
Creator: Dhakal, Nagendra, Stolbov, Sergey, Rahman, Talat, Ishigami, Masa, Masunov, Artem, University of Central Florida
Abstract / Description: The main objective of this work is to understand the theoretical basis of the working principle of the Hydrogen fuel cell. We seek the physical basis of the Rational Design Technique, the smart way of preselecting materials from the material-pool, implemented in our study anticipating highly promising electrocatalysts for promoting the conversion of chemical energy stored in hydrogen molecules into the electrical energy. It needs the understanding of the relationship among the compositions of...
Show moreThe main objective of this work is to understand the theoretical basis of the working principle of the Hydrogen fuel cell. We seek the physical basis of the Rational Design Technique, the smart way of preselecting materials from the material-pool, implemented in our study anticipating highly promising electrocatalysts for promoting the conversion of chemical energy stored in hydrogen molecules into the electrical energy. It needs the understanding of the relationship among the compositions of the materials under consideration, their electronic structure and catalytic activities. We performed the first principle DFT calculations to achieve the goal.Our work is focused first on the issues in hydrogen oxidation reaction taking place in anode compartment of the cell. Next comes up with the issues with Oxygen Reduction Reaction taking place in cathode compartment. Finally, we focus on mechanisms underlying binding of small molecules on substrates.Platinum perfectly catalyzes hydrogen oxidation reaction on the hydrogen fuel cell anodes. However, it has at least two drawbacks: a) it is too expensive; b) it has a low tolerance to CO poisoning. Pt-Ru bi-functional catalysts are more tolerant to CO, but they are still very expensive. In this work, we performed first-principle studies of stability and reactivity of M/W (110) structures, where M = Pd, Ru, Au monolayers. All three systems are found to be stable: formation energy of MLs is significantly higher than cohesive energy of the M-elements. The calculated binding energies of H, H2, OH, CO, and H2O were used to obtain the reaction free energies. Analysis of the free energies suggests that Au-W bonding does not activate sufficiently Au monolayer, whereas Ru/W (110) is still too reactive for the CO removal. Meanwhile, Pd/W (110) is found to catalyze hydrogen oxidation and at the same time to be highly tolerant to the CO poisoning. The latter finding is explained by the fact that CO binds much weaker to Pd on W (110) than to Pt, while the OH binding is strong enough to ensure CO oxidation. The obtained results are traced to the electronic structure of the systems.Oxygen Reduction Reaction (ORR) is the heart core reaction in fuel cells, Proton Exchange Membrane Fuel cell and DEMFC. However, the reaction is not so obvious and need suitable electrocatalyst. Pt or Pt-based catalysts are found to be the best catalyst so far. But, its cost and shortage make it not feasible economically. Moreover, lower onset potential (maximal electrode potential at which the reaction can proceed) of such catalysts is offering another limitation to fuel cell performance. Research has been conducted in many directions for lowering the cost by replacing the Pt with some other elements of lower cost or reducing the Pt-load in the material; and even more finding the material performing better than Pt. In this paper, we've tried to understand the ORR mechanism and look for the material that could be potential option to Pt. Our calculations suggest that for monolayer of Pt on 5 layered slab of Nb or Mo the onset potential is the same as for Pt, while cost of these systems are much lower than that of Pt. Presence of water changes the reaction rate very minimum. Rational design method facilitates the research of selecting the appropriate catalyst and saves time and effort significantly. The result shows that the d-band center model is not accurate to describe the reactivity of the catalyst.For decades, adsorbates' binding energy (????) has been used as an indicator of the adsorbate-substrate bond strength (??????). Thus, although one can compute accurately any ?? models to gauge bond-strength are developed and applied to rationalize and anticipate ????'s because that is a key aspect in the rational search for efficient catalysts. Yet bond-strength alone fails to predict ???? trends. Therefore, quantifying and understanding the difference between ???? and ?????? is essential to catalysts design. Indeed, the adsorbate-substrate bond formation perturbs the substrate's electronic charge density, which reduces ???? by the energy attached to such perturbation: ??????????. Here, with the example of carbon monoxide adsorption on metal-doped graphene, we show that ?????????? may exceed 1 eV and render an unusual situation: although the EB of CO to the Au-doped graphene indicates that binding does not happen, we find evidence of a strong bond between CO and the substrate. Thus, in this case, the large ?????????? totally disrupt the equivalency between ?????? and ???? we also propose a method to compute ?????????? that bypasses dealing with an excited electronic state of the system.
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Date Issued: 2017
Identifier: CFE0006583, ucf:51336
Format: Document (PDF)
PURL: http://purl.flvc.org/ucf/fd/CFE0006583

Title: Electronic transport properties of carbon nanotubes: the impact of atomic charged impurities.
Creator: Tsuchikawa, Ryuichi, Ishigami, Masa, Mucciolo, Eduardo, Peale, Robert, Masunov, Artem, University of Central Florida
Abstract / Description: Even changing one atom in nanoscale materials is expected to alter their properties due to their small physical sizes. Such sensitivity can be utilized to modify materials' properties from bottom up and is essential for the utility of nanoscale materials. As such, the impact of extrinsic atomic adsorbates was measured on pristine graphene and a network of carbon nanotubes using atomic hydrogen, cesium atoms, and dye molecules. In order to further quantify such an atomic influence, the...
Show moreEven changing one atom in nanoscale materials is expected to alter their properties due to their small physical sizes. Such sensitivity can be utilized to modify materials' properties from bottom up and is essential for the utility of nanoscale materials. As such, the impact of extrinsic atomic adsorbates was measured on pristine graphene and a network of carbon nanotubes using atomic hydrogen, cesium atoms, and dye molecules. In order to further quantify such an atomic influence, the resistance induced by a single potassium atom on metallic and semiconducting carbon nanotubes was measured for the first time. Carbon nanotubes are sensitive to adsorbates due to their high surface-to-volume ratio. The resistance arising from the presence of extrinsic impurity atoms depends on the types of nanotubes. Metallic carbon nanotubes are resilient to a long-ranged, Coulomb-like potential, whereas semiconducting carbon nanotubes are susceptible to these impurities. The difference in the scattering strength originates from the chirality of carbon nanotubes, which defines their unique electronic properties. This difference had not directly measured experimentally because of the issue of contact resistance, the difficulty of chirality identification, and the uncertainty in the number of impurity atoms introduced on carbon nanotubes.We synthesized atomically clean, long ((>)100 ?m) carbon nanotubes, and their chirality was identified by Rayleigh scattering spectroscopy. We introduced potassium atoms on the nanotubes to impose a long-range, Coulomb potential and measured the change in resistivity, excluding the contact resistance, by plotting the resistance as a function of the carbon nanotube length. The flux of potassium atoms coming onto the nanotubes was monitored by quartz crystal microbalance, and the scattering strength of a single potassium atom was deduced from the change in resistivity and the density of potassium atoms on the nanotubes. We found that the scattering strength of potassium atoms on semiconducting nanotubes depends on the charge carrier type (holes or electrons). Metallic nanotubes were found to be less affected by the presence of potassium atoms than semiconducting nanotubes, but the scattering strength showed a large dependence on Fermi energy. These experimental results were compared to theoretical simulations, and we found a good agreement with the experiments. Our findings provide crucial information for the application of carbon nanotubes for electronic devices, such as transistors and sensors.
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Date Issued: 2015
Identifier: CFE0005729, ucf:50078
Format: Document (PDF)
PURL: http://purl.flvc.org/ucf/fd/CFE0005729

Title: Self-assembly of Amyloid Aggregates Simulated with Molecular Dynamics.
Creator: Berhanu, Workalemahu, Masunov, Artem, Kolpashchikov, Dmitry, Ye, Jingdong, Zou, Shengli, Schulte, Alfons, University of Central Florida
Abstract / Description: ABSTRACTAmyloids are highly ordered cross-? sheet aggregates that are associated with many diseases such as Alzheimer's, type II diabetes and prion diseases. Recently a progress has been made in structure elucidation, environmental effects and thermodynamic properties of amyloid aggregates. However, detailed understanding of how mutation, packing polymorphism and small organic molecules influence amyloid structure and dynamics is still lacking. Atomistic modeling of these phenomena with...
Show moreABSTRACTAmyloids are highly ordered cross-? sheet aggregates that are associated with many diseases such as Alzheimer's, type II diabetes and prion diseases. Recently a progress has been made in structure elucidation, environmental effects and thermodynamic properties of amyloid aggregates. However, detailed understanding of how mutation, packing polymorphism and small organic molecules influence amyloid structure and dynamics is still lacking. Atomistic modeling of these phenomena with molecular dynamics (MD) simulations holds a great promise to bridge this gap. This Thesis describes the results of MD simulations, which provide insight into the effects of mutation, packing polymorphism and molecular inhibitors on amyloid peptides aggregation. Chapter 1 discusses the structure of amyloid peptides, diseases associated with amyloid aggregation, mechanism of aggregation and strategies to treat amyloid diseases. Chapter 2 describes the basic principles of molecular dynamic simulation and methods of trajectory analysis used in the Thesis. Chapter 3 presents the results of the study of several all-atom molecular dynamics simulations with explicit solvent, starting from the crystalline fragments of two to ten monomers each. Three different hexapeptides and their analogs produced with single glycine replacement were investigated to study the structural stability, aggregation behavior and thermodynamics of the amyloid oligomers. Chapter 4 presents multiple molecular dynamics (MD) simulation of a pair polymorphic form of five short segments of amyloid peptide. Chapter 5 describes MD study of single-layer oligomers of the full-length insulin with a goal to identify the structural elements that are important for insulin amyloid stability, and to suggest single glycine mutants that may improve formulation. Chapter 6 presents the investigation of the mechanism of the interaction of polyphenols molecules with the protofibrils formed by an amyloidogenic hexapeptide fragment (VQIVYK) of Tau peptide by molecular dynamics simulations in explicit solvent. We analyzed the trajectories of the large (7(&)#215;4) aggregate with and without the polyphenols.Our MD simulations for both the short and full length amyloids revealed adding strands enhances the internal stability of wildtype aggregates. The degree of structural similarity between the oligomers in simulation and the fibril models constructed based on experimental data may explain why adding oligomers shortens the experimentally observed nucleation lag phase of amyloid aggregation. The MM-PBSA free energy calculation revealed nonpolar components of the free energy is more favorable while electrostatic solvation is unfavorable for the sheet to sheet interaction. This explains the acceleration of aggregation by adding nonpolar co-solvents (methanol, tri?uoroethanol, and hexa?uoroisopropanol). Free energy decomposition shows residues situated at the interface were found to make favorable contribution to the peptide -peptide association.The results from the simulations might provide both the valuable insight for amyloid aggregation as well as assist in inhibitor design efforts. First, the simulation of the single glycine mutants at the steric zipper of the short segments of various pathological peptides indicates the intersheet steric zipper is important for amyloid stability. Mutation of the side chains at the dry steric zipper disrupts the sheet to sheet packing, making the aggregation unstable. Thus, designing new peptidomimetic inhibitors able to prevent the fibril formation based on the steric zipper motif of the oligomers, similar to the ones examined in this study may become a viable therapeutic strategy. The various steric zipper microcrystal structures of short amyloid segments could be used as a template to design aggregation inhibitor that can block growth of the aggregates. Modification of the steric zipper structure (structure based design) with a single amino acid changes, shuffling the sequences, N- methylation of peptide amide bonds to suppress hydrogen bonding ability of NH groups or replacement with D amino acid sequence that interact with the parent steric zipper could be used in computational search for the new inhibitors. Second, the polyphenols were found to interact with performed oligomer through hydrogen bonding and induce conformational change creating an altered aggregate. The conformational change disrupts the intermolecular amyloid contact remodeling the amyloid aggregate. The recently reported microcrystal structure of short segments of amyloid peptides with small organic molecules could serve as a pharamcophore for virtual screening of aggregation inhibitor using combined docking and MD simulation with possible enhancement of lead enrichment. Finally, our MD simulation of short segments of amyloids with steric zipper polymorphism showed the stability depends on both sequence and packing arrangements. The hydrophilic polar GNNQQNY and NNQNTF with interface containing large polar and/or aromatic side chains (Q/N) are more stable than steric zipper interfaces made of small or hydrophobic residues (SSTNVG, VQIVYK, and MVGGVV). The larger sheet to sheet interface of the dry steric zipper through polar Q/N rich side chains was found to holds the sheets together better than non Q/N rich short amyloid segments. The packing polymorphism could influence the structure based design of aggregation inhibitor and a combination of different aggregation inhibitors might be required to bind to various morphologic forms of the amyloid peptides.
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Date Issued: 2011
Identifier: CFE0004088, ucf:49131
Format: Document (PDF)
PURL: http://purl.flvc.org/ucf/fd/CFE0004088

Title: Combustion kinetics of advanced biofuels.
Creator: Barari, Ghazal, Vasu Sumathi, Subith, Kapat, Jayanta, Kassab, Alain, Masunov, Artem, University of Central Florida
Abstract / Description: Use of biofuels, especially in automotive applications, is a growing trend due to their potential to lower greenhouse gas emissions from combustion. Ketones are a class of biofuel candidates which are produced from cellulose. However, ketones received rather scarce attention from the combustion community compared to other classes such as, alcohols, esters, and ethers. There is little knowledge on their combustion performance and pollutant generation. Hence their combustion chemistry needs to...
Show moreUse of biofuels, especially in automotive applications, is a growing trend due to their potential to lower greenhouse gas emissions from combustion. Ketones are a class of biofuel candidates which are produced from cellulose. However, ketones received rather scarce attention from the combustion community compared to other classes such as, alcohols, esters, and ethers. There is little knowledge on their combustion performance and pollutant generation. Hence their combustion chemistry needs to be investigated in detail. Diisopropyl ketone (DIPK) is a promising biofuel candidate, which is produced using endophytic fungal conversion. A detailed understanding of the combustion kinetics of the oxidation of DIPK in advanced engines such as, the homogeneous charge compression ignition (HCCI) engine is warranted. This dissertation concentrates on the combustion kinetics of DIPK over a wide range of temperature and pressure with a focus on HCCI engine application.An existing DIPK kinetic mechanism has been reviewed and a single zone HCCI engine model has been modeled and validated against recent experimental data from Sandia National Lab. Therefore different HCCI modeling assumptions were tested and the DIPK reaction mechanism was modified with missing reactions and the required thermochemical data. As a result, the HCCI pressure trace, heat release rate and reactivity have been improved. In order to improve the ignition delay time simulation results, the low temperature oxidation of DIPK was studied as the fuel chemistry effects on the autoignition behavior becomes important in low temperature. Therefore DIPK low temperature oxidation experimental data was obtained from the synchrotron photoionization experiments conducted at the Advanced Light Source (ALS) so that the primary products as well as the dominant oxidation pathways are identified. Furthermore, the aldehydes oxidation, as a result of partial or incomplete combustion and as the primary stable intermediate products in oxidation and pyrolysis of biofuel were studied at low temperature in ALS. A high temperature reaction mechanism was created using the reaction class approach. The reaction mechanism for DIPK was improved using the experimental data along with quantum chemical calculation of activation energies and barriers as well as vibrational modes for the important reactions identified in ALS experiment. The rate constants for important reactions were calculated based on modified Arrhenius equation. DIPK oxidation and pyrolysis were studied at high temperature and pressure using UCF shock tube. The ignition delay times as well as the product (methane) time histories were investigated and used as validation targets for the new model.
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Date Issued: 2015
Identifier: CFE0005921, ucf:50847
Format: Document (PDF)
PURL: http://purl.flvc.org/ucf/fd/CFE0005921

Title: Structure-Property Relationship of the Two-Photon Circular Dichroism of Compounds with Axial and Helical Chirality.
Creator: Diaz, Carlos, Hernandez, Florencio, Uribe Romo, Fernando, Kuebler, Stephen, Masunov, Artem, Del Barco, Enrique, University of Central Florida
Abstract / Description: Back in 1894 Lord Kelvin coined the term (")chiral(") in order to refer to molecules whose mirror images were not superimposable with themselves. Over the years, research has demonstrated the important role that chiral molecules play in life, chemistry, and biology as well as their importance in the development of new drugs and technologies.The efforts to understand chiral systems have been mainly driven by spectroscopic methods that leverage on the opposite responses that enantiomers have to...
Show moreBack in 1894 Lord Kelvin coined the term (")chiral(") in order to refer to molecules whose mirror images were not superimposable with themselves. Over the years, research has demonstrated the important role that chiral molecules play in life, chemistry, and biology as well as their importance in the development of new drugs and technologies.The efforts to understand chiral systems have been mainly driven by spectroscopic methods that leverage on the opposite responses that enantiomers have to linear or circularly polarized light of both handedness. More specifically, Electronic Circular Dichroism (ECD) which measures the differences in linear absorption of left and right circularly polarized light has been the method par excellence for the spectroscopic characterization of chiral compounds. Unfortunately, the fact that ECD is based on linear absorption severely limits the use of this method in the near to far UV region. This is mainly due to the interferences generated by the strong linear absorption of common organic solvents and buffers in this portion of the light spectrum. Nevertheless, the fact remains that many chiral biomolecules of interest related to deceases like Alzheimer and Parkinson, exhibit most of their linear absorption in the near to far UV region where ECD cannot be employed for their study. Therefore, it has become an urgent necessity to develop spectroscopic methods to study chiral molecules that can circumvent the limitations of ECD at shorter wavelengths. In order to overcome the existent limitations in linear chiral spectroscopy, the nonlinear equivalent of ECD arises as a promising alternative, i.e. Two-Photon Circular Dichroism (TPCD). Although, this phenomenon was theoretically predicted in 1975, it was not until 2008, with the introduction of the double-L scan, that a reliable and versatile method for the measurement of TPCD was introduced. The high sensitivity of this method is based on the use of (")twin(") pulses that allow accounting for fluctuations in the excitation source that prevented the experimental realization of the measurement. The first measurement of a full TPCD spectrum was performed on BINOL enantiomers and the results were supported and discussed with the help of theoretical calculations. After that seminal work, we embarked in expanding the understanding of the structure-property relationship of TPCD by performing, systematically, a series of theoretical-experimental studies in chiral biaryl derivatives and compounds with helical chirality.In Chapter 2 we present the theoretical-experimental study of the effect of the ?-electron delocalization curvature on the TPCD of molecules with axial chirality. The targeted molecules for this part of our investigation were S-BINOL, S-VANOL, and S-VAPOL. Our findings revealed that an increase in the TPCD signal, within this series of compounds, was related to the curvature of the ?(-)electron delocalization. The contributions of the different transition moments to the two-photon rotatory strength support our outcomes. Then, in Chapter 3 we introduce the development of the Fragment-Recombination Approach (FRA) for the calculation of the TPCD spectra of large molecules. This simple but powerful method is based on the additivity of the TPCD signal, and is subject to a strict conditional fragmentation approach. FRA-TPCD is demonstrated, theoretically, in two hypothetical molecular systems from the biaryl derivatives family. Afterward, in Chapter 4 we show the first experimental demonstration of FRA-TPCD through the conformational analysis of an axially-chiral Salen ligand in solution (AXF-155). The FRA-TPCD spectra calculated for the different isomers of AXF-155 allowed narrowing the number of possible isomers of this complex molecule in THF solution to only two. This represents a significant improvement from previously reported results using ECD. Subsequently, in Chapter 5 we present the study of the effect of intramolecular charge transfer (ICT) in S-BINAP, an axially dissymmetric diphosphine ligand with strong ICT. The evaluation of the performance of two different exchange-correlation functional (XCF) confirmed that in order to properly predict the theoretical TPCD spectrum of a molecule exhibiting strong ICT, it is required to use an XCF such as CAM-B3LYP. In addition, our findings revealed the importance of considering an adequate number of excited states in order to be able to fully reproduce the experimental TPCD spectrum, thus avoiding wrong assignments of theoretical transitions to experimental spectral features. Finally, and expanding on our previous study, in Chapter 6 we investigated the effect of the nature of ICT on two hexahelicene derivatives. Our investigation demonstrated that the TPCD signal of chiral molecules with strong ICT does not only depend on the strength of this effect but on its nature, i.e. extension of the ?(-)electronic delocalization increasing beyond (EXO-ICT) or within (ENDO-ICT) the helicene core. In summary, with the results presented in this thesis we closed a first loop in the understanding of the structure-property relationship of TPCD. In the future, we expect to deepen in our knowledge of the structure-property relationship of this phenomenon by studying further helicene derivatives with donor-acceptor motif, and through the application of FRA-TPCD to the conformational analysis of amino acids in peptides. We foresee numerous applications of TPCD for the study of optically active molecules with implications in biology, medicine, and the drug and food industry, and applications in nanotechnology, asymmetric catalysis and photonics.
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Date Issued: 2015
Identifier: CFE0005787, ucf:50067
Format: Document (PDF)
PURL: http://purl.flvc.org/ucf/fd/CFE0005787

Title: Computational Approach to the Problems of Electro- and Photo-Catalysis.
Creator: Zuluaga, Sebastian, Stolbov, Sergey, Schelling, Patrick, Roldan Cuenya, Beatriz, Masunov, Artem, University of Central Florida
Abstract / Description: The main objective of this work is to gain basis for rational design of catalysts used in fuel cells for conversion of chemical energy stored in hydrogen molecules into electric energy, as well as photo-catalysts used for hydrogen production from water under solar irradiation. This objective is achieved by applying the first principles computational approach to reveal relationship among compositions of materials under consideration, their electronic structure and catalytic activity. A major...
Show moreThe main objective of this work is to gain basis for rational design of catalysts used in fuel cells for conversion of chemical energy stored in hydrogen molecules into electric energy, as well as photo-catalysts used for hydrogen production from water under solar irradiation. This objective is achieved by applying the first principles computational approach to reveal relationship among compositions of materials under consideration, their electronic structure and catalytic activity. A major part of the work is focused on electro-catalysts for hydrogen fuel cells. Platinum (Pt) is widely used in the electrodes of fuel cells due to its good catalytic properties. However, Pt is an expensive and scarce element, its catalytic activity is not optimal and also it suffers from CO poisoning at anode. Therefore the search for new catalytic materials is needed for large scale implementation of fuel cells. The main direction of search of more efficient electro-catalysts is based in the design in which an active element monoatomic layer (AE) is deposited on a metal substrate (MS) made of a cost-effective material. Two goals are achieved by doing this: on the one hand, the cost of the catalytic system is reduced by reducing the amount of the AE in the system and on the other hand the catalytic properties of the AE can be tuned through its interactions with the MS. In the first part of this work the Pd-based alloys and layered structures have been studied as promising electro-catalysts for the ORR on the fuel cell cathodes, more precisely Pd-Co alloys and Pd/M/Pd (M=Co,Fe). There exists a robust model linking the activity of a surface toward ORR to computable thermodynamic properties of the system and further to the binding energies of the ORR intermediates on the catalyst surface. A more challenging task is to find how to tune these binding energies through modification of the surface electronic structure that can be achieved by varying the surface composition and/or morphology. To resolve this challenge, the electronic structure, binding energies of intermediates and the ORR free energies have been calculated within the density functional theory (DFT) approximation. The results presented in this work show that in contrast to the widely accepted notion, the strain exerted by a substrate on AE hardly affects the surface activity toward ORR, while the hybridization of the electronic states of the AE-and MS-electronic states is the key factor controlling the catalytic properties of these systems. Next it is shown that the catalytic activity of the promising anode electrocatalysts, such as Pt/M, M=Au, Ru and Pd, is also determined by the AE-MS hybridization with a minor effect of the strain. Furthermore, we have shown that, if AE is weakly bound to the substrate (as it is for Pt/Au), surface reconstruction occurs. This leads to the breaking of the relation between the electronic structure of the clean surface and the reactivity of the sytem. Other kind of promising ORR catalysts is designed in the form of Ru nanoparticles modified by chalcogens. In this work, I present the results obtained for small Ru clusters and flat Ru facets modified with chalcogens (S, Se and Te). The O and OH binding energies are chosen as descriptors of the ORR. The results on the two systems are compared, concluding that large clusters with relative large flat facets have higher catalytic activity due to the absence of low coordinated and thus high reactive Ru atoms. Regarding the problem of the hydrogen production via photo-catalytic splitting of water, one of the challenges is tuning the band gap of the photo-anodes to optimal levels. Graphitic carbon nitride (g-C3N4) is a promising material to be used as a photo-anode, however, a reduction of the band gap width by rational doping of the material would improve the efficiency significantly. This issue is addressed in the last chapter of this work. Two problems are considered: a) the stability of the doped system and b) the band gap width. To address the first problem the ab-initio thermodynamics approach has been used, finding that the substitution of C and N with the doping agent (B, C, N, O, Si and P) is thermodynamically preferred over the interstitial addition of dopant to the g-C3N4 structure. However, due to high kinetic energy barriers for the detachment of C and N atoms, involved in the substitution doping, the interstitial addition found to be kinetically more favorable. Since the density functional theory fails to reproduce the band gap of semiconductors correctly, the GW approximation was used to study the band gap of the system. The results indicate that the g-C3N4 system maintain its semiconductor character if doped with B, O and P under certain conditions, while reducing the band gap.
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Date Issued: 2013
Identifier: CFE0005288, ucf:50546
Format: Document (PDF)
PURL: http://purl.flvc.org/ucf/fd/CFE0005288

Title: Quantum Chemical Studies for the Engineering of Metal Organic Materials.
Creator: Rivera Jacquez, Hector, Masunov, Artem, Balaeff, Alexander, Harper, James, Heider, Emily, Zou, Shengli, Kaden, William, University of Central Florida
Abstract / Description: Metal Organic Materials (MOM) are composed of transition metal ions as connectors and organic ligands as linkers. MOMs have been found to have high porosity, catalytic, and optical properties. Here we study the gas adsorption, color change, and non-linear optical properties of MOMs. These properties can be predicted using theoretical methods, and the results may provide experimentalists with guidance for rational design and engineering of novel MOMs. The theory levels used include semi...
Show moreMetal Organic Materials (MOM) are composed of transition metal ions as connectors and organic ligands as linkers. MOMs have been found to have high porosity, catalytic, and optical properties. Here we study the gas adsorption, color change, and non-linear optical properties of MOMs. These properties can be predicted using theoretical methods, and the results may provide experimentalists with guidance for rational design and engineering of novel MOMs. The theory levels used include semi-empirical quantum mechanical calculations with the PM7 Hamiltonian and, Density Functional Theory (DFT) to predict the geometry and electronic structure of the ground state, and Time Dependent DFT (TD-DFT) to predict the excited states and the optical properties.The molecular absorption capacity of aldoxime coordinated Zn(II) based MOMs (previously measured experimentally) is predicted by using PM7 Theory level. The 3D structures were optimized with and without host molecules inside the pores. The absorption capacity of these crystals was predicted to be 8H2 or 3N2 per unit cell. When going beyond this limit, the structural integrity of the bulk material becomes fractured and microcrystals are observed both experimentally and theoretically.The linear absorption properties of Co(II) based complexes are known to change color when the coordination number is altered. In order to understand the mechanism of this color change TD-DFT methods are employed. The chromic behavior of the Co(II) based complexes studied was confirmed to be due to a chain in coordination number that resulted in lower metal to ligand distances. These distances destabilize the occupied metal d orbitals, and as a consequence of this, the metal to ligand transition energy is lowered enough to allow the crystals to absorb light at longer wavelengths.Covalent organic frameworks (COFs) present an extension of MOM principles to the main group elements. The synthesis of ordered COFs is possible by using predesigned structures andcarefully selecting the building blocks and their conditions for assembly. The crystals formed by these systems often possess non-linear optical (NLO) properties. Second Harmonic Generation (SHG) is one of the most used optical processes. Currently, there is a great demand for materials with NLO optical properties to be used for optoelectronic, imaging, sensing, among other applications. DFT calculations can predict the second order hyperpolarizability ?2 and tensor components necessary to estimate NLO. These calculations for the ?2 were done with the use of the Berry's finite field approach. An efficient material with high ?2 was designed and the resulting material was predicted to be nearly fivefold higher than the urea standard.Two-photon absorption (2PA) is another NLO effect. Unlike SHG, it is not limited to acentric material and can be used development of in vivo bio-imaging agents for the brain. Pt(II) complexes with porphyrin derivatives are theoretically studied for that purpose. The mechanism of 2PA enhancement was identified. For the most efficient porphyrin, the large 2PA cross-section was found to be caused by a HOMO-LUMO+2 transition. This transition is strongly coupled to 1PA allowed Q-band HOMO-LUMO states by large transition dipoles. Alkyl carboxyl substituents delocalize the LUMO+2 orbital due to their strong ?-acceptor effect, enhancing transition dipoles and lowering the 2PA transition to the desirable wavelengths range.The mechanism 2PA cross-section enhancement of aminoxime and aldoxime ligands upon metal addition of is studied with TD-DFT methods. This mechanism of enhancement is found to be caused by the polarization of the ligand orbitals by the metal cation. After polarization an increase in ligand to ligand transition dipole moment. This enhancement of dipole moment is related to the increase in 2PA cross-sections.
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Date Issued: 2015
Identifier: CFE0005990, ucf:50777
Format: Document (PDF)
PURL: http://purl.flvc.org/ucf/fd/CFE0005990

Title: Monitoring Crystal Structure Refinements Using Solid-State NMR Chemical Shift Tensors.
Creator: Kalakewich, Keyton, Harper, James, Campiglia, Andres, Elsheimer, Seth, Chumbimuni Torres, Karin, Masunov, Artem, Moore, Sean, University of Central Florida
Abstract / Description: Inclusion of lattice-fields in density functional theory (DFT) methods has enabled the accurate calculation of solid-state nuclear magnetic resonance (SSNMR) chemical shift tensors. Calculated 13C and 15N tensors (i.e. 3 principle values per nucleus) can be used to monitor crystal structure refinements and to select the correct structure from a large population of computationally generated candidates. In this dissertation, chapter 2 describes a methodology to improve established crystal...
Show moreInclusion of lattice-fields in density functional theory (DFT) methods has enabled the accurate calculation of solid-state nuclear magnetic resonance (SSNMR) chemical shift tensors. Calculated 13C and 15N tensors (i.e. 3 principle values per nucleus) can be used to monitor crystal structure refinements and to select the correct structure from a large population of computationally generated candidates. In this dissertation, chapter 2 describes a methodology to improve established crystal structures from three different diffraction techniques involving geometric refinement monitored using SSNMR tensor values. The calculated 13C tensors for three relatively simple organic compounds (i.e. acetaminophen, naphthalene, and adenosine) are shown to markedly improve upon DFT refinement. The so-called GGA-PBE functional provided the best agreement with experimental data. The use of the three principle values of the tensor is required for such results as the average (i.e. the isotropic) is less accurate. Chapter 3 applies this method to differentiate between hundreds of computationally predicted crystal structures. Typically, lattice energy of each candidate is used to select the correct structure, a process which is seldom successful. Herein, it is demonstrated that when 13C tensors from DFT refined structures are used for structural ranking by comparison to experimental data, only the correct structure agrees with experimental data in all cases. Chapter 4 illustrates the use of 15N tensors to monitor DFT refinement as an alternative to the 13C approach of Chapter 2. 15N tensors have been very difficult to obtain previously, thus a novel experimental method is developed here which improves signal-to-noise by as much as 300% and allows routine measurement. This improvement also improves the accuracy of the tensor values. Overall, the 15N tensors are found to be at least 5 times more sensitive to DFT refinements than 13C values.
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Date Issued: 2017
Identifier: CFE0006888, ucf:51726
Format: Document (PDF)
PURL: http://purl.flvc.org/ucf/fd/CFE0006888

Density Functional Theory (4)	+ -
Two-Photon Absorption (3)	+ -
DFT (2)	+ -
Oxygen Reduction Reaction (2)	+ -
AFM (1)	+ -

Amyloid fibril (1)	+ -
Beta sheet inhibitor (1)	+ -
Binding energy (1)	+ -
Bond Formation Energy (1)	+ -
C2H/C2H? (1)	+ -
C3N/C3N? (1)	+ -
C4H/C4H? (1)	+ -
C5N/C5N? (1)	+ -
C6H/C6H? (1)	+ -
C8H/C8H? (1)	+ -
CASTEP (1)	+ -
CN/CN? (1)	+ -
Carbon-13 Chemical Shift Tensors (1)	+ -
Chrage Transport (1)	+ -
ClF/ClF- (1)	+ -
Combustion (1)	+ -
Computational Chemistry (1)	+ -
Crystal Structure Refinement (1)	+ -
Diarylethenes (1)	+ -
EXAFS (1)	+ -
Electro-Catalysis (1)	+ -
Electrocatalyst (1)	+ -
Electrocyclic Reactions (1)	+ -
Electronic Circular Dichroism (1)	+ -
Electronic Structure (1)	+ -

University of Central Florida (15)	+ -
Masunov, Artem (14)	+ -
Stolbov, Sergey (4)	+ -
Ishigami, Masa (3)	+ -
Harper, James (2)	+ -

Rahman, Talat (2)	+ -
Saha, Haripada (2)	+ -
Schelling, Patrick (2)	+ -
Zou, Shengli (2)	+ -
Argenti, Luca (1)	+ -
Balaeff, Alexander (1)	+ -
Barari, Ghazal (1)	+ -
Berhanu, Workalemahu (1)	+ -
Campiglia, Andres (1)	+ -
Chumbimuni Torres, Karin (1)	+ -
Del Barco, Enrique (1)	+ -
Dhakal, Nagendra (1)	+ -
Diaz, Carlos (1)	+ -
Elsheimer, Seth (1)	+ -
Gangopadhyay, Shruba (1)	+ -
Gesquiere, Andre (1)	+ -
Goel, Satyender (1)	+ -
Heider, Emily (1)	+ -
Heinrich, Helge (1)	+ -
Hernandez, Florencio (1)	+ -
Kaden, William (1)	+ -
Kalakewich, Keyton (1)	+ -
Kapat, Jayanta (1)	+ -
Kara, Abdelkader (1)	+ -
Kassab, Alain (1)	+ -

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