yes / The density functional theory (DFT) based a unique model has been developed to predict the toxicity of ionic liquids using structural-feature based quantum chemical reactivity descriptors. Electrophilic indices (ω), the energy of highest occupied (EHOMO) and lowest unoccupied molecular orbital, (ELUMO) and energy gap (∆ E) were selected as the best toxicity descriptors of ILs via Pearson correlation and multiple linear regression analyses. The principle components analysis (PCA) demonstrated the distribution and inter-relation of descriptors of the model. A multiple linear regression (MLR) analysis on selected descriptors derived the model equation for toxicity prediction of ionic liquids. The model predicted toxicity values and mechanism are very consistent with observed toxicity. Cationic and side chains length effect are pronounced to the toxicity of ILs. The model will provide an economic screening method to predict the toxicity of a wide range of ionic liquids and their toxicity mechanism.

Doping in bulk semiconductors (e.g., n- or p- type doping in silicon) allows for precise control of their properties and forms the basis for the development of electronic and photovoltaic devices. Recently, there have been reports on the successful synthesis of doped semiconductor nanocrystals (or quantum dots) for potential applications in solar cells and spintronics. For example, nanocrystals of ZnSe (with zinc-blende lattice structure) and CdSe and ZnO (with wurtzite lattice structure) have been doped successfully with transition-metal (TM) elements (Mn, Co, or Ni). Despite the recent progress, however, the underlying mechanisms of doping in colloidal nanocrystals are not well understood. This thesis reports a comprehensive theoretical analysis toward a fundamental kinetic and thermodynamic understanding of doping in ZnO, CdSe, and ZnSe quantum dots based on first-principles density-functional theory (DFT) calculations. The theoretical predictions of this thesis are consistent with experimental measurements and provide fundamental interpretations for the experimental observations. The mechanisms of doping of colloidal ZnO nanocrystals with the TM elements Mn, Co, and Ni is investigated. The dopant atoms are found to have high binding energies for adsorption onto the Zn-vacancy site of the (0001) basal surface and the O-vacancy site of the (0001) basal surface of ZnO nanocrystals; therefore, these surface vacancies provide viable sites for substitutional doping, which is consistent with experimental measurements. However, the doping efficiencies are affected by the strong tendencies of the TM dopants to segregate at the nanocrystal surface facets, as indicated by the corresponding computed dopant surface segregation energy profiles. Furthermore, using the Mn doping of CdSe as a case study, the effect of nanocrystal size on doping efficiency is explored. It is shown that Mn adsorption onto small clusters of CdSe is characterized by high binding energies, which, in conjunction with the Mn surface segregation characteristics on CdSe nanocrystals, explains experimental reports of high doping efficiency for small-size CdSe clusters. In addition, this thesis presents a systematic analysis of TM doping in ZnSe nanocrystals. The analysis focuses on the adsorption and surface segregation of Mn dopants on ZnSe nanocrystal surface facets, as well as dopant-induced nanocrystal morphological transitions, and leads to a fundamental understanding of the underlying mechanisms of dopant incorporation into growing nanocrystals. Both surface kinetics (dopant adsorption onto the nanocrystal surface facets) and thermodynamics (dopant surface segregation) are found to have a significant effect on the doping efficiencies in ZnSe nanocrystals. The analysis also elucidates the important role in determining the doping efficiency of ZnSe nanocrystals played by the chemical potentials of the growth precursor species, which determine the surface structure and morphology of the nanocrystals.

Kohn-Sham density functional theory is a rigorous formulation of many-electron quantum mechanics which, for practical purposes, requires approximation of one term in its total energy expression: the exchange-correlation energy. This work elucidates systematic methods for constructing approximations to the exchange-correlation energy solely from first-principles physics. We review the constraints that can be built into approximate density functionals, and use thermochemical data to argue that satisfaction of these constraints permits a more general description of electronic matter. Contact with semiclassical physics is made by studying the turning surfaces of Kohn-Sham potentials in solids. Perfect metals and covalently-bound, narrow-gap insulators do not have turning surfaces at equilibrium, but do under expansive strain. Wide-gap insulators, ionic crystals, and layered solids tend to have turning surfaces at equilibrium. Chemical bonds in solids are classified using the turning surface radii of its constituent atoms. Depletion of the charge density, such as near a monovacancy in platinum, is shown to produce a turning surface. Further, this work demonstrates why generalized gradient approximations (GGAs) are often able to describe some properties of sp-bonded narrow-gap insulators well. A Laplacian-level pure-density functional is developed with the goal of describing metallic condensed matter. This functional is derived from the r2SCAN orbital-dependent meta-GGA, and reduces its tendency to over-magnetize ferromagnets; improves its description of the equation of state properties of alkali metals; and improves its description of intermetallic thermodynamics. It is constructed to enforce the fourth-order exchange gradient expansion constraint (not satisfied by r2SCAN), and a few free parameters are fitted to paradigmatic metallic systems: jellium surfaces and closed-shell jellium clusters. Last, we modify an exchange-correlation kernel that describes the density-density response of jellium to better satisfy known frequency sum rules. We also constrain the kernel to reproduce the correlation energies of jellium, and compare it to a wide variety of common kernels in use for linear response, time-dependent density functional theory calculations. / Physics

The development of the semi-empirical atomistic potential called the embedded atom method (EAM) has allowed for the efficient modeling of solid-state environments, at a lower computational cost than afforded by density functional theory (DFT). This offers the capability of EAM to model the energetics of solid-state phases of varying coordination, including defects, such as vacancies and self-interstitials. This dissertation highlights the development and application of two EAMs: a Ti potential constructed with the multi-state modified embedded atom method (MS-MEAM), and a Ni potential constructed with the fragment Hamiltonian (FH) method. Both potentials exhibit flexibility in the description of different solid-states phases and applications. This dissertation also outlines two applications of DFT. First, a study of structure and stability for solid-state forms of NixCy (in which x and y are integers) is investigated using plane-wave DFT. A ground state phase for Ni2C is elucidated and compared to known and hypothesized forms of NixCy. Also, a set of correlation consistent basis sets, previously constructed using the B3LYP and BLYP density functionals, are studied. They are compared to the well-known to the correlation consistent basis sets that were constructed with higher-level ab initio methodologies through computations of enthalpies of formation and combustion enthalpies. The computational accuracy with regard to experiment is reported.

Supercapacitors have emerged as a promising energy storage technology with unique characteristics that set them apart from conventional batteries and capacitors. Supercapacitors bridge the gap between these two technologies by combining the high power density of capacitors with the high energy storage capacity of batteries, offering a compelling solution for various applications. In the pursuit of enhancing supercapacitor performance, magnetite (Fe3O4) has been researched as a potential anode material. Fe3O4 offers several desirable properties, including high theoretical capacitance, low cost, and environmental friendliness. Compositing Fe3O4 with conductive additives has served to address the issue of limited conductivity in Fe3O4 anodes for practical uses, however, a focus must be shifted to enhancing the capacitive performance of such anodes to unlock their full potential. Achieving the full potential of Fe3O4 for supercapacitor applications requires addressing challenges in the colloidal fabrication of high-active mass electrodes. This is done by exploring the exceptional adsorption properties of two dispersing and capping agents: 3,4-dihydroxybenzoic acid and murexide. Exceptional adsorption properties of catecholate-type 3,4-dihydroxybenzoic acid molecules were explored for surface modification of Fe3O4 nanoparticles to enhance their colloidal dispersion as verified by sedimentation test results and Fourier-transform infrared spectroscopy measurements. Electrodes prepared in the presence of 3,4-dihydroxybenzoic acid exhibited nearly double the capacitance at slow charging rates as compared to the control samples without the dispersant or with benzoic acid as a non-catecholate dispersant. Density functional theory analysis of adsorption behavior of 3,4-dihydroxybenzoic acid and benzoic acid at the (001) surface of Fe3O4 corroborated these experimental results by providing an understanding of the basic mechanism of 3,4-dihydroxybenzoic acid adsorption on the surface of nanoparticles. Furthermore, murexide for surface modification of Fe3O4 nanoparticles effectively enhanced the performance of multi-walled carbon nanotube-Fe3O4 supercapacitor anodes. Our experimental results demonstrate significant improvements in electrode performance when murexide is used as a capping or dispersing agent compared to the case with no additives. From impedance measurements, we revealed a substantial decrease in the real part of impedance for samples prepared with murexide, indicating easier charge transfer at more negative electrode potentials, and reinforcing the role of murexide as a capping agent and charge transfer mediator. The theoretical investigation allowed us to identify the nature of chemical bonds between murexide and the surface, with significant charge transfer taking place between the Fe3O4 surface and murexide adsorbate. / Thesis / Master of Applied Science (MASc)

<p>Despite the unprecedented success achieved by Kohn-Sham density functional theory (KS-DFT) in the past few decades, the standard approximations used for the KS exchange-correlation functional typically lead to unacceptably large errors when applied to strongly-correlated electronic systems. Partition-DFT (P-DFT) is a formally exact reformulation of KS-DFT in which the ground-state density and energy of a system are obtained through self-consistent calculations on isolated fragments, with a partition energy introduced to account for the inter-fragment interactions. The unique advantage of this partitioning scheme lies in the fact that it adopts the electron density of fragments as the main variable, in place of the density of the entire system in KS-DFT, so that novel approximations can be constructed in terms of fragment properties. With a simple overlap approximation (OA) of the partition energy proposed for binary-partitioned systems, P-DFT is able to rectify the static correlation error caused by standard density functional approximations for strongly-correlated diatomic molecules. In this work, we first implement P-DFT on a one-dimensional (1D) real-space grid and calculate the ground-state energy and density of a series of 1D hydrogen chains using the local density approximation (LDA) as the density functional approximation for fragments. We then propose the generalized overlap approximation (GOA) and the corrected generalized overlap approximation (cGOA), which extends the applicability of OA to systems partitioned into more than two fragments. Combining LDA with cGOA leads to quantitatively correct dissociation curves of hydrogen chains. The static correlation error of LDA is suppressed by cGOA in the strongly-correlation regime when the calculations are performed in a spin-restricted manner, i.e., without the spin symmetry breaking. Additionally, GOA induces an improvement of the ground-state density upon LDA results, and hence helps P-DFT provide a better description of the density dimerization in hydrogen chains.</p>

Electronic band structure in the solid and its relation to the energy gap of the monomer is all about studying how intermolecular interactions change electronic structure. In experimental studies this results in broader absorption bands and by extension a lowering of the LUMO and raising of HOMO energy to the conduction and valence band edges respectively. This electronic change involves splitting of the molecular energy levels into bands of non-degenerate energies and can be calculated either quantum mechanically (QM) or by classical force field models through the change in ionization potential (IP) and electron affinity (EA), called the apparent polarization energy, and its relation to HOMO and LUMO through Koopman’s and Janak’s theorem. The study of the formation of a ‘band’ like structure is important in regimes and systems where conventional quantum mechanical (QM) methods become infeasible. Specifically, when systems are non-periodic and plane wave approximations fail, such as in amorphous structures, or in regimes between where the plane wave bulk approximation and the gas phase single molecule QM methods where the scaling of conventional gas phase atomic orbital methods becomes exorbitantly costly and the plane wave approximation fails for open systems. Therefore, the objective of this work is to highlight the changing optoelectronic properties of molecular solids within this regime using both density functional theory and molecular mechanics. The scalability of DFT limits it to multimer systems, leaving the larger nanoscale materials to be studied using molecular mechanics. Here we have utilized a variety of dispersion sensitive functionals in order to characterize the intermolecular interactions and splitting energies in small multimers of some of the smallest oligoacene species, benzene and anthracene. Benzene and anthracene nanoclusters from 0.8 to 5.0 nm in radius have had their changes in electronic band energy calculated due to polarization using the AMOEBA force field and bulk values have also been extrapolated. AMOEBA’s explicit polarization terms allow for direct handling of the polarization energy, control of nanocluster size and shape in a regime that QM methods cannot probe efficiently, and the ability to specify the position of charge carriers in order to examine specific electronic surface behavior. Using differing DFT methods the change in the HOMO and LUMO energy from the single molecule state to multimers of the size of 10 and 12 units for anthracene and benzene respectively. The HOMO band of benzene was raised by ~0.3 eV and LUMO lowered by 0.35 eV. In anthracene the HOMO was lowered by ~0.1 eV and the LUMO by ~0.15 eV. These values remain within 0.1 eV across all dispersion functionals. Using Ren’s parameterization procedure and MP2 for the AMOEBA force field he apparent polarization was calculated. The extrapolated values for the change in the HOMO and LUMO of benzene from single molecule to bulk were 1.42 eV and 0.49 eV respectively. For anthracene the crystalline bulk changes the HOMO and LUMO by 1.34 eV and 1.16 eV respectively. The regression for bulk extrapolation also predicts that benzene clusters of 12 units will be 0.77 eV for HOMO and -0.41 eV for LUMO. Similarly for an anthracene cluster made up of 10 molecular units the apparent polarization is predicted through linear regression to be 0.58 eV for HOMO and 0.53 eV for LUMO.

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 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 Å 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.

This dissertation describes the development and testing of modified embedded atom method (MEAM) interatomic potentials for Al, Si, Mg, Cu, Fe, and their alloys, with primary concentration on Mg-Al system. We performed the density functional theory (DFT) based ab initio calculations to determine the structural and elastic properties of element pairs that are impractical to obtain from experimental measurements. Specifically, we estimated the cohesive energy, equilibrium atomic volume, bulk modulus, and elastic moduli of every element pair in the NaCl reference structure. Based on the results of DFT calculations, MEAM parameters for each element pair were constructed. We extensively tested the new MEAM potential for Mg-Al alloy system. The new Mg-Al MEAM potential was compared with DFT calculations, previously published semi-empirical interatomic potentials, and experiments. Applicability of the new MEAM potential to atomistic modeling was demonstrated by calculating stress-strain responses from molecular dynamics (MD) simulations of Mg and Al systems in a variety of configurations. The effects of alloying, porosity, and strain rate conditions on the stress-strain response were quantified. The underlying mechanisms for tension-compression asymmetry observed in the macroscale experiments of Mg alloys were investigated at the nanoscale. This work presents a contribution to the task of bridging quantum-mechanical and classical atomistic scale simulations. Information from ab initio electronic structure calculations was used to construct parameters of semi-empirical MEAM potentials for large-scale atomistic simulations of alloys. The results of the new MEAM models compare extremely well to those from other published interatomic potentials. The applicability of the new MEAM potential to investigate nanoscale mechanisms of the deformation and fracture for Al, Mg and Mg-Al alloys was demonstrated. It has been shown that the MEAM provides a single universal formalism for classical atomistic simulations of a wide range of elements and their alloys.

No description available.