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Despite the growing applications of silver nanoparticles, toxicity information on this nanomaterial is still deficient. Conclusions on the toxicity of silver nanoparticles vary and atomic level toxicity mechanisms are not yet achieved. Consequently, our group conducted combined computational and experimental toxicity studies of silver nanoparticles (AgNPs). Toxicity of 10 nm citrate stabilized AgNPs on HepG2 cells were investigated. Experimental results show that the 10 nm citrate stabilized AgNPs begin to be toxic to HepG2 cells at a dosage that exceeds 1 ppm and LD50 was observed at 3 ppm. Elevated reactive oxygen species levels were seen upon exposure to AgNPs with the maximum at the LD50 concentration of 3 ppm. Normal protein regulation of HepG2 cells were affected by exposure to AgNPs. TEM images of HepG2 cells exposed to AgNPs reveal that AgNPs can penetrate and agglomerate inside the cells. Our preliminary computational study was guided by one of the widely accepted toxicity mechanism of AgNPs in which the nanoparticles dissolute to Ag+. The computational model was composed of a 1:1 ratio of silver and phospholipid head. The silver employed are in atomic and anionic form while the phospholipid head are the phosphocholine (PC) and phosphoethanolamine (PE), which are abundant in HepG2 cells. Computational study shows that the presence of Ag+ results in partial oxidation of both the phospholipid heads. Our preliminary experimental and computational studies lead us to develop new computational methods that can accurately predict oxidation potentials (HOMO), reduction potentials (LUMO), and absorption spectra that can be used in studying toxicity mechanism of AgNPs through the oxidation pathway. Thus, computational methods for cyclic voltammetry and absorption spectroscopy that use DFT and TD-DFT, respectively, were improved to provide more accurate electronic and optical properties. Cyclopenta-fused polycyclic hydrocarbons (CP-PAHs) with available experimental data for HOMO, LUMO, ΔEgap and absorption spectra and have potential application as AgNP stabilizers were used in developing the improved computational methods for cyclic voltammetry and absorption spectroscopy. The improved computational method for cyclic voltammetry was developed by accounting for the anion species that occur experimentally and by using B3LYP the best density functional in predicting the HOMO, LUMO and ΔEgap of CP-PAHs with overall MAE of 014 eV. The best absorption spectra otef CP-PAHs were predicted using B3LYP for geometry optimizations followed by TD-CAMB3LYP with MAE of 29 nm. All calculations of CP-PAHs were implemented using the 6-311g (d,p) basis set and tetrahydrofuran (THF) as solvent. These two developed computational methods were tested on a group of methyl triphenyl amine (MTPA) derivatives with available experimental data for HOMO, LUMO, ΔEgap and absorption spectra and have potential application as AgNP stabilizers. The new computational methods for cyclic voltammetry and absorption spectroscopy also provided the most accurate predicted electronic and optical properties of MTPA derivatives. Among the ten density functionals employed, prediction of HOMO, LUMO and ΔEgap were most accurate using B3LYP and B3PW91 with overall MAE of 0.31 eV and 0.27 eV, respectively. Absorption spectra of MTPA derivatives were still best predicted using the B3LYP/TD-CAMB3LYP method with MAE of 13 nm. All calculations of MTPA were implemented using the 6-31+g (d,p) basis set and dichloromethane as solvent.

This licentiate thesis is devoted to the investigation of how bonding in simple organic molecules are affected by X-ray beam irradiation. The investigation targets molecules with three carbons as their main-chain structure. The stability of the bonds under ionization are simulated using the SIESTA package. SIESTA is a simulation package that provides molecular dynamics simulations based on density functional theory within the Born-Oppenheimer approximation. The aim of this study is to understand statistically the damaging process and selectivity among different types of bond. As the first targets, 4 hydrocarbons are investigated. They are propane, propene, propyne and propadiene, which have different combinations of single, double and triple bonds as their main-chain structures. Depending on the combinations, the structures can be either symmetric around the central atom or not. The structure of the symmetric molecules propane and propadiene are  stable until charge +3. In contrast, the asymmetric molecules propene and propyne, the  main-chain bonds show a tendency towards a more similar bond-distance as the level of ionization increases. In addition, hydrogens relocation occurs in propene, leading to a symmetric structure. Secondly, the bond fluctuations are investigated among 4 types of three-carbon molecules which have functional parts. Alcohol and carboxyl groups molecules show the stable bond integrities at charging 0 to +2. On the other hand, the carbon-carbon bonds in molecules with  acetyl and ketone groups are broken by ionization. Comparing the 8 kinds of bond breaking processes in these molecules, this statistical study gives an insight to organic molecules bonding systems.

Kohn-Sham density functional theory (KS-DFT) is one of the most widely used electronic structure methods. It is used to find the various properties of atoms, molecules, clusters, and solids. In principle, results for these properties can be found by solving self-consistent one-electron Schrödinger-like equations based on density functionals for the energy. In practice, the density functional for the exchange-correlation contribution to the energy must be approximated. The accuracy of practical DFT depends on the choice of density functional approximation (DFA) and also on the electron density produced by the DFA. The SCAN(strongly constrained and appropriately normed) functional developed by Sun, Ruzsinszky, and Perdew is the first meta-GGA (meta-generalized gradient approximation) functional that is constrained to obey all 17 known exact constraints that a meta-GGA can. SCAN has been found to outperform most other functionals when it is applied to aqueous systems. However, density-driven errors (energy errors occurring from an inexact density produced by a DFA) hinder SCAN from achieving chemical accuracy in some systems, including water. Density-corrected DFT (DC-DFT) can alleviate this shortcoming by adopting a more accurate electron density which, in most applications, is the electron density obtained at the Hartree-Fock level of theory, due to its relatively low computational cost. In the second chapter, calculations to determine the accuracy of the HF-SCAN functional for water clusters are performed. The interaction and binding energies of water clusters in the BEGDB and WATER27 data sets are computed, and then the spurious charge transfer in deprotonated, protonated, and neutral water dimer is interpreted. The density-corrected SCAN (DC-SCAN) functional elevates the accuracy of SCAN toward the CCSD(T) limit, not only for the neutral water clusters but also for all considered hydrated ion systems (to a lesser extent). In the third chapter, the barrier heights of the BH76 test set are analyzed. Three fully non-local proxy functionals (LC-ωPBE, SCAN50%, and SCAN-FLOSIC) and their selfconsistent proxy densities are used. These functionals share two important points of similarity to the exact functional. They produce reasonably accurate self-consistent barrier heights and their self-consistent total energies are nearly piecewise linear in fractional electron number. Somewhat-reliable cancellation of density - and functional-driven errors for the energy has been established. / Physics

<p>    Ceramics with novel optical properties have enabled substantial advances in technologies ranging from medical imaging to fish finding. Further development of optically transparent ceramics will allow the creation of novel devices with new capabilities, capable of functioning in previously inconceivable operating conditions. Hypersonic aerospace applications often utilize IR imaging for guiding and target identification. Sensors utilized in the detection and measurement of IR radiation cannot withstand the extreme environments intrinsic to hypersonic travel and thus must be protected from the surrounding environment while minimizing distortion of incident IR radiation. Towards this end, IR transparent ceramics have been developed that can withstand the extreme environments of hypersonic travel, while maintaining their optical and mechanical properties. </p> <p>The binary II-VI semiconductor Zinc Sulfide (ZnS) has been primarily utilized for this application due to its strong transmission of 8-10 μ𝑚 IR radiation in combination with the stability of its mechanical properties at elevated temperatures encountered at high airspeeds. While it has proven to be a capable material for the application, previous testing has found it to degrade and fail catastrophically when exposed to sand or water at subsonic speeds. This initiated a search for materials with similar IR transmittance properties to ZnS but with higher strength and resistance to degradation. </p> <p>The diamond allotrope of carbon has been found to have the most optimal mechanical properties for this application, but due to obvious limitations from cost and processing in bulk, it is not considered a realistic option for the application. The ternary sulfide Calcium Lanthanum Sulfide (CLS, CaLa2S4) was discovered in the early 1980s, with an extended IR transmission window of 8-12 μ𝑚 in contrast to the 8-10 μ𝑚 transmission window of ZnS. In combination with more favorable mechanical properties than ZnS, CaLa2S4 has become a promising candidate towards the manufacture of stronger IR windows for aerospace applications. To expand the existing body of knowledge on this ternary sulfide and towards the advancement of IR window materials, this work seeks to utilize density functional theory to characterize defects in CLS to guide future investigations of this material system.</p>

Although semilocal density functional approximations (DFA) are widely applied, none of them can capture the long-range van der Waals (vdW) attraction between the separated subsystems. However, they differ remarkably in the extent to which they capture intermediate-range vdW effects responsible for equilibrium bonds between neighboring small closed-shell subsystems. The local density approximation (LDA) often overestimates this effect, while the Perdew-Burke-Ernzerhof (PBE) generalized gradient approximation (GGA) underestimates it. The strongly-constrained and appropriately normed (SCAN) meta-GGA often estimates it well. All of these semi-local functionals require an additive correction like non-local correlation functionals (vdW-DFs, VV10, rVV10 etc.) or empirical methods ( DFT+D3, DFT+vdW, DFT+XDM etc.) to capture the long-range part. The molecular complexes bonded by vdW interactions, layered materials, and molecule-surface interactions are a few examples of the systems where the long-range effects play a crucial role.In the first part of this assessment, we investigate the adsorption of benzene and thiophene over the (111) surface of copper (Cu), gold (Au), and silver (Ag). Thiophene and benzene are the prototypes of their respective classes of aromatic compounds and are the most widely studied molecules to model such systems. We first combine a non-local correlation functional (rVV10) with the various generalized gradient approximations (GGAs), namely PBE and PBEsol, along with the meta-GGAs SCAN and revSCAN (collectively known as base functionals), through a set of parameters obtained by fitting against the argon-dimer interaction energy curve. These parameters bridge the base functionals and rVV10 and guide the delicate balance between the short- and long-range interaction. We also utilize the recently introduced vdW-dZK model based on the theory of Zaremba and Kohn. It is a proven method to yield RPA-quality results for the physisorption of graphene over different metallic surfaces. We assess the adsorption energies, vertical adsorption distances, and the molecular-orientation at various sites and compare the results to the experimental values whenever available. Based on our calculations, the semilocal functionals alone underestimate the adsorption energies, reflecting the need for additional corrections. The rVV10-based methods generally bring the molecules closer to the surface and increase the binding energies. However, there is a discrepancy in the description of rVV10 based methods when the base functional is changed. While rVV10 combined with PBE slightly underestimates the adsorption energies, revSCAN+rVV10 and PBEsol+rVV10 are significantly overestimating. The methods PBE+vdW-dZK and SCAN+vdW-dZK, in general, predict better adsorption energies. In particular, SCAN+vdW-dZK stands out in predicting adsorption distances, adsorption energies, sites, and orientation closest to the experimental values whenever available. Apart from the inability of the semilocal DFAs to capture the long-range vdW interaction, they suffer from the so-called self-interaction error (SIE), in which an electron density incorrectly interacts with itself. At the semilocal level, the self-exchange-correlation energy can not counter-balance the self-Hartree energy, giving rise to the SIE problem. About 40 years ago, Perdew and Zunger proposed a solution to it by introducing a method that could remove the spurious SIE on an orbital-by-orbital basis. However, for size-consistency of this orbital-dependent theory, localized orbitals instead of delocalized Kohn-Sham orbitals are required. Recently, Pederson \textit{et al.} introduced an elegant scheme, known as Fermi-L\"owdin orbital self-interaction correction (FLOSIC), which could generate size-extensive and localized orbitals. For an exact functional, free from SIE, the negative of the highest occupied orbital (HO) eigenvalue would equal the first ionization energy (IE). In the second part of this assessment, we evaluate the HO eigenvalue of a representative test set containing 14 small to moderate-sized organic molecules using FLOSIC. The SIE inherent in the semilocal DFAs seriously underestimates the magnitude of the HO energy. Although LDA-SIC and PBE-SIC correct them, IEs are still significantly overestimated. A similar previous work by Vydrov \textit{et al.} reported the over-correction of PZ-SIC in many-electron regions, and various schemes with moderate success have been introduced since then to scale SIC down on those regions. Recently Zope \textit{et al.} introduced a method (LSIC) based on locally scaling-down PZ-SIC using an iso-orbital indicator (z$_\sigma$) which ensures that the correction is made only in the regions where they are required. We introduce a few other approaches similar to LSIC and demonstrate that these methods significantly improve the agreement between the calculated HO eigenvalues and experimental IEs of molecules. / Physics

This dissertation investigates how the magnetic properties of strontium hexaferrite change upon the substitution of foreign atoms at the Fe sites. Strontium hexaferrite, SrFe12O19 is a commonly used hard magnetic material and is produced in large quantities (around 500,000 tons per year). For different applications of strontium hexaferrite, its magnetic properties can be tuned by a proper substitution of the foreign atoms. Experimental screening for a proper substitution is a cost-intensive and time-consuming process, whereas computationally it can be done more efficiently. We used the ‘density functional theory’ a first principles based method to study substituted strontium hexaferrite. The site occupancies of the substituted atoms were estimated by calculating the substitution energies of different configurations. The formation probabilities of configurations were used to calculate the magnetic properties of substituted strontium hexaferrite. In the first study, Al-substituted strontium hexaferrite, SrFe12-xAl x O19, with x = 0.5 and x = 1.0 were investigated. It was found that at the annealing temperature the nonmagnetic Al+3 ions preferentially replace Fe+3 ions from the 12k and 2a sites. We found that the magnetization decreases and the magnetic anisotropy field increases as the fraction, x of the Al atoms increases. In the second study, SrFe12-x Gax O19 and SrFe12-x Inx O19 with x = 0.5 and x = 1.0 were investigated. In the case of SrFe12-x Gax O19, the sites where Ga+3 ions prefer to enter are: 12k, 2a, and 4f1. For SrFe12-x Inx O19, In+3 ions most likely to occupy the 12k, 4f1, and 4f2 sites. In both cases the magnetization was found to decrease slightly as the fraction of substituted atom increases. The magnetic anisotropy field increased for SrFe12-x Gax O19, and decreased for SrFe12-x Inx O19 as the concentration of substituted atoms increased. In the third study, 23 elements (M) were screened for their possible substitution in strontium hexaferrite, SrFe12-x Mx O19 with x = 0.5. In each case the site preference of the substituted atom and the magnetic properties were calculated. We found that Bi, Ge, Sb, Sn, and Sc can effectively increase the magnetization, and Cr, P, Co, Al, Ga, and Ti can increase the anisotropy field when substituted into strontium hexaferrite.

Covariant density functional theory (CDFT) is a modern theoretical tool for the description of nuclear structure physics. Here different physical properties of the ground and excited states in atomic nuclei have been investigated within the CDFT framework employing three major classes of the state-of-the-art covariant energy density functionals. The global performance of CEDFs for even-even nuclei are investigated and the systematic theoretical uncertainties are estimated within the set of four CEDFs in known regions of the nuclear chart and their propagation towards the neutron drip line. Large-scale axial relativistic Hartree-Bogoliubov (RHB) calculations are performed for even-even nuclei to calculate different ground state observabvles. The predictions for the two-neutron drip line are also compared in a systematic way with the non-relativistic results. CDFT has been applied for systematic study of extremely deformed, rotating N ∼ Z nuclei of the A ∼ 40 mass region. At spin zero such structures are located at high energies which prevents their experimental observation. The rotation acts as a tool to bring these exotic shapes down to the yrast line so that their observation could become possible with a future generation detectors such as GRETA or AGATA. The major physical observables of such structures, the underlying single-particle structure and the spins at which they become yrast or near yrast are defined. The search for the fingerprints of clusterization and molecular structures is performed and the configurations with such features are discussed. CDFT has been applied to study fission barriers of superheavy nuclei and related systematic theoretical uncertainties in the predictions of inner fission barrier heights in superheavy elements. Systematic uncertainties are substantial in superheavy elements and their behavior as a function of proton and neutron numbers contains a large random component. The benchmarking of the functionals to the experimental data on fission barriers in the actinides allows reduction of the systematic theoretical uncertainties for the inner fission barriers of unknown superheavy elements. However, even then they on average increase when moving away from the region where benchmarking has been performed.

To capture the underlying chemistry and physics of a system on electronic structure platform, it is necessary to accurately describe the intermolecular interactions such as repulsion, polarization, hydrogen bonding, and van der Waals interactions. Among these interactions, van der Waals (dispersion) interactions are weak in nature as compare to covalent bonds and hydrogen bonding, but it is physically and chemically very important in accurately predicting condensed phase properties such as Vapor liquid equilibria. This presents a significant challenge in modeling VLE using a first principles approach. However, recent developments in dispersion corrected (DFT-D3) and nonlocal density functionals can model dispersion interactions with reasonable accuracy. Here, we will present some of results that quantify efficacy of recent density functionals in predicting phase equilibria of molecular systems via first principle Monte Carlo (FPMC) simulations. Our aim is to assess the performance of several density functional by determining VLE, critical properties, dimer potential energy curves, vibrational spectra, and structural properties. The functional used in our study includes PBE-D3, BLYP-D3, rVV10, PBE0- D3, and M062X-D3. In addition, we have used the second order Møller-Plesset perturbation theory (MP2) method for computing density of argon at single temperature. The organic compounds considered for this study involves argon, CO2, SO2, and various hydroflurocarbons (R14, R134a, CF3H, CF2H2, CFH3) molecules. Additionally, the development of new materials, ionic liquids, and modification of industrial processes are an ongoing effort by researchers to efficiently capture acidic gases. Our ability to model these sorption processes using a first principles approach can have significant impact in speeding up the discovery process. In our work, we have predicted CO2 solubility in triethyl(butyl)phosphonium ionic liquid via FPMC simulations. Our results reveal the infrared spectra, structural and transport properties for pure ionic liquid and its mixture with CO2 through ab initio molecular dynamics simulations.