The world’s oceans absorb a significant percentage of anthropogenic carbon emissions, and CO2 levels have profound effects on the marine environment. Of primary concern is the acidification of the oceans due to dissolved CO2. The goal of this research is to design new sensing technologies for deployment in the marine environment to detect CO2 pollutant. A series of carbon dioxide (CO2) receptors that are complexed to fluorene oligomers were studied computationally. In chapter 1, an overview of CO2 chemistry and various CO2 sensors is discussed. A short overview of the method (Kohn-Sham density functional theory and time-dependent density functional theory (TDDFT)) employed in this work is given. Chapter 2 presents a study on the interaction energy and electronic excitations of fluorene-receptors as CO2 sensors. The aim of this work is to gain an understanding of the nature of interactions between these receptors and CO2. The structural, electronic, and optical properties of these receptor complexes have been determined computationally. The monomer-receptor complexes show remarkable redshifts in their absorption spectra, which decrease on moving to dimer and trimer-receptor complexes (all blue-shifted).

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he interactions of the chemical warfare agent sulfur mustard with amorphous silica were investigated using electronic structure calculations. In this thesis, the binding energies of sulfur mustard and mimic species used in the laboratory were calculated using density functional theory and fully ab initio calculations. The wB97XD and B97D functionals, which include functions to account for long-range dispersion interactions, were compared to experimental trends. The hydroxylated amorphous silica surface was approximated using a gas-phase silanol molecule and clusters containing a single hydroxyl moiety. Recent temperature programmed desorption experiments performed in UHV concluded that sulfur mustard and its less toxic mimics undergo molecular adsorption to amorphous silica. Hydrogen bonding can occur between surface silanol groups and either the sulfur or chlorine atom of the adsorbates, and the calculations indicate that the binding energies for the two hydrogen bond acceptors are similar. The adsorption of sulfur mustard and its mimics on silica also exhibits the presence of significant van der Waals interactions between alkyl of the adsorbates and the surface. These interactions, in combination with the formation of a hydrogen bond between a surface silanol group and the Cl or S atoms of the adsorbates, provide remarkably large binding energies. / Master of Science

Yes / The predilection of sp-, sp2-, and sp3-hybridized chalcogen-bearing molecules to engage in type I chalcogen···chalcogen interactions was comparatively unveiled in like···like/unlike CY···YC, YCY···YCY, and F2Y···YF2 (where Y = O, S, and Se) complexes, respectively. Upon the optimized monomers, a potential energy surface (PES) scan was conducted to pinpoint the most favorable complexes. The energetic findings unveiled the ability of the investigated systems to engage in the interactions under study with binding energy values ranging from −0.36 to −2.33 kcal/mol. Notably, binding energies were disclosed to align in the posterior sequence; sp2- (i.e., YCY···YCY) > sp- (i.e., CY···YC) > sp3- (i.e., F2Y···YF2) hybridized complexes, except the like···like oxygen-bearing complexes. Instead, the highest negative binding energy values were detected for the OCO···OCO followed by those of the F2O···OF2 and CO···OC complexes. Furthermore, the like···like selenium-bearing complexes demonstrated the most considerable binding energies compared to the other investigated complexes. Remarkably, the quantum theory of atoms in molecules and noncovalent interaction index analyses revealed the highly directional and closed-shell nature of the investigated chalcogen···chalcogen interactions. Symmetry adapted-perturbation theory findings outlined the dispersion forces as the commanding forces for all the studied complexes. These observations will provide convincing justifications for the nature of chalcogens within type I chalcogen···chalcogen interactions, leading to increased progress in various domains regarding drug design and materials science. / Researchers Supporting Project number (RSPD2024R678), King Saud University, Riyadh, Saudi Arabia

The knowledge on the conformations of amino acids is essential to understand the biochemical behaviors and physical properties of proteins. Comprehensive computational study is focused to understand the conformational landscape of three aromatic amino acids (AAAs): tryptophan, tyrosine, and phenylalanine. Three different density functionals (B3LYP, M06-2X and wB97X-D) were used with two basis sets of 6-31G(d) and 6-31+G(d,p) for geometry optimizations of the conformers of AAAs followed by the vibrational frequencies. The goal was to identify the right choice of density functional theory (DFT) level for conformational analysis of amino acids by comparing the computational data against the available experimental results. Calculated infrared (IR) frequency values indicated that wB97X-D/6-31+G(d,p) level is less favorable than other DFT levels in case of O-H and N-H stretching frequencies for the conformers of AAAs. The C=O stretching frequencies at different computational levels were in good agreement with the experimental results. Interactions of AAAs (tryptophan, tyrosine, and phenylalanine) and two cyclic amino acids (histidine and proline) individually with two finite-sized graphene sheets (C62H20 and C186H36) were explored using M06-2X/6-31G(d) level. Computational investigations of the binding of amino acids with graphene provide knowledge for designing of new graphene-based biological/biocompatible materials. Selected conformers for each amino acid with different orientations on the surface of graphene were examined. The purpose of computational study on graphene-amino acids interactions was to identify the preferred conformer of amino acid to bind on graphene as well as to find the influence of amino acid binding on the band gap of graphene. Different conformers of AAAs generally prefer parallel orientation through π-π interactions to bind with graphene. However, bent orientation is more preferred over parallel to bind on the surface of graphene in case of conformer having relative energy approximately equal to 5 kcal/mol for all three AAAs. Histidine generally exhibits higher binding affinity than proline to form complex with graphene. The binding energies in the aqueous medium were slightly lower than those obtained in the gas phase with some exceptions. The adsorption of amino acids did not affect the band gap of graphene.

Thesis advisor: Kevin S. Bedell / We investigate the structure of the equation of state of finite nuclear matter by examining the nature of isospin dependence in the (a)symmetry energy term. In particular, we include in the description of the binding energy fourth-order dependence with respect to the asymmetry factor, (N-Z)/A, and the regime of the l=0 Landau parameter, F0´ , is required to be less than –1. This modified equation predicts a minimum binding energy where N≠Z, in addition to the standard symmetric minimum when N=Z. Results with the new asymmetry energy term are compared with experimental binding and symmetry energies from standard semi-empirical mass formulas. Importantly, this method reveals one possible mechanism for producing the phenomenon of neutron excess which is seen in physical nuclei. / Thesis (BS) — Boston College, 2004. / Submitted to: Boston College. College of Arts and Sciences. / Discipline: Physics. / Discipline: College Honors Program.

Um estudo teórico detalhado das estruturas e energias do ligante 1, 7, 11, 17-tetraoxa-2, 6, 12, 16-trazaocicloocsano ([20]aneN4O4) coordenado com íons metálicos de transição Fe2+, Co2+, Ni2+, Ru2+, Rh2+ e Pd2+ foi realizado em nível de teoria B3LYP/Lanl2DZ. As geometrias dos complexos foram totalmente otimizados em simetria Cs com os íons metálicos coordenados com quatro átomos de nitrogênio (complexos 1a e 1aq) ou quatro átomos de oxigênios (complexos 1b e 1bq) e duas moléculas de água. Os arranjos octaédricos (1a e 1b) e quadrado-planares (1aq e 1bq) foram consideremos neste trabalho. A estrutura teórica está em excelente acordo com a estrutura de difração de raio-x experimental determinada para o complexo octaédrico de Ni2+ de [20]AneN4O4. Os cátions M2+ ligam-se preferencialmente aos átomos de nitrogênios com energia de ligação que aumenta na ordem Fe2+ < Ru2+ < Co2+ < Ni2+ < Rh2+ < Pd2+. Para os metais de transição da primeira fila, os complexos de spin alto são mais estáveis que os complexos de spin baixo. Em contraste, para os metais de transição da segunda fila, os estados de spin baixo mostraram-se mais estáveis que os estados de spin alto. As ligações metal-ligante nos complexos foram analisadas em termo das interações covalentes e iônicas e ajudaram a entender porque os complexos (1a e 1aq) são mais estáveis que os complexos (1b e 1bq). Os complexos poliaminas [20]aneN4 e poliéteres [20]aneO4 foram obtidos substituindo os átomos de nitrogênio e oxigênio da posição alfa dos macrociclos [20]aneN4O4 e [20]aneO4N4, respectivamente. O macrociclo [20]aneO4 tem preferência em complexar íons metálicos da primeira fila, enquanto o macrociclo [20]aneN4 prefere complexar os íons metálicos da segunda fila. / A detailed theoretical study of structures and energies of the 1,7,1l,17-tetraoxa-2,6,12,16-tetraaza-cycloeicosane ligand ([20]AneN4O4) coordinated to Fe2+, Co2+, Ni2+, Ru2+, Rh2+ and Pd2+ transition metals ions was carried out with the B3LYP/Lanl2DZ method. The geometries of the complexes were fully optimized in Cs symmetry with the metal ions coordinated either to four atoms nitrogen (complexes 1a e 1b) or to the four atoms oxygen (complexes 1aq e 1bq). The octahedral and square planar arrangements were considered in this work. The theoretical structure is in excellent agreement with the experimental X-ray diffraction structure determination for the [20]AneN4O4 octahedral Ni2+ complex. The M2+ cations bind preferentially to the nitrogen atoms with binding energies that increase in the order Fe2+ < Ru2+ < Co2+ < Ni2+ < Rh2+ < Pd2+. For the first-row transition metals, the highspin complexes are more stable than the low-spin complexes. In contrast, for the second-row of transition metals, the low-spin states were found more stable than the high spin states. The metal-ligand bonds in the complexes were analyzed in terms of the covalent and ionic interactions and helped to understand why complexes (1a e 1aq) are more stable than complexes (1b e 1bq). The polyamines [20]aneN4 and polyethers [20]aneO4 complexes were obtained substituting the atoms N or O of the alfa position of the macrocycles [20]aneN4O4 and [20]aneO4N4, respectively. The macrocycle [20]aneO4 prefers to complex first-row transition metals; however, the macrocycle [20]aneN4 prefers to complex second-row transition metals.

Energias de ligação do estado fundamental de doadores rasos em super-redes são consideradas teoricamente com o auxílio de um procedimento variacional que leva em conta a mistura do contínuo de estados da minibanda à qual o mesmo está associado. Os cálculos são realizados para um grande número de parâmetros de super-rede e qualquer posição da impureza na mesma. É mostrado que a dependência da energia de ligação com os vários parâmetros envolvidos pode ser completamente explicada em termos de um modelo simples unidimensional (tight-binding) onde a largura da respectiva minibanda de condução e a energia de ligação no Limite de poço isolado são os únicos parâmetros relevantes. A extrema concordância quantitativa entre as energias de ligação derivadas deste modelo e as obtidas pelo método variacional mais rigoroso vem enfatizar o papel fundamental desempenhado pela largura de minibanda com o único parâmetro relevante ao se levar em conta os efeitos de tunelamento existentes nas super-redes. / A variational procedure which takes into account the mixing of a continuum of subband states has been used to investigate the binding energies of shallow donors in superlattices. The calculations where performed for a wide range of superlattices parameters and impurity positions. It is shown that the dependence of the binding energy upon the various superlattice parameters can be completely explained in terms of a simple onedimensional tight-binding model where the bandwidth of the respective conduction subband and the binding energy in the isolated quantum well are the only relevant parameters. The quantitative overall agreement between the binding energies derived from this model and those found variationally is excellent and emphasizes the fundamental role played by the bandwidth as the only relevant parameter accounting for the tunneling effects.

The energy density formalism (EDF) is used to investigate two problems. The EDF is a phenomenological method that incorporates as much knowledge of infinite nuclear matter as possible. In this formalism the energy of the nucleus is expressed as a functional of its density. The nucleus energy is obtained by minimizing the function, with respect to the density. In this report, the EDF is used to investigate the mercury isotope shift anomaly following the aforementioned suggestion. Specifically, nucleon densities with different degrees of central depression are generated. Energies corresponding to these densities are obtained. The density with the minimum energy is the preferred one. Based on the findings of the present work, it can be concluded that a central depression in the lighter mercury isotopes does not-appear- to be a possible explanation for the isotope shift anomaly. And the anomaly remains unresolved.

Ethylene adsorption was studied by use of DFT/B3LYP with basis set 6-31G(d,p) in Gaussian&lsquo / 03 software. It was found that ethylene adsorbs molecularly on the Ni13 nanocluster with &amp / #960 / adsorption mode. &amp / #960 / adsorption mode is studied for the Ni10 (1 1 1), Ni13 (1 0 0) and Ni10 (1 1 0) surface cluster as well. Relative energy values were calculated as &amp / #8722 / 50.86 kcal/mol, &amp / #8722 / 20.48 kcal/mol, &amp / #8722 / 32.44 kcal/mol and &amp / #8722 / 39.27 kcal/mol for Ni13 nanocluster, Ni10 (1 1 1), Ni13 (1 0 0) and Ni10 (1 1 0) surface cluster models, respectively. Ethylene adsorption energy was found inversely proportional to Ni coordination number when Ni10 (1 1 1), Ni13 (1 0 0) and Ni10 (1 1 0) cluster models and Ni13 nanocluster were compared with each other. DFT/B3LYP and basis set of 86-411(41d)G in Gaussian&lsquo / 03 was used to investigate Ni55 nanocluster. Ethylene adsorption on Ni55 nanocluster was studied by means of equilibrium geometry calculations with &amp / #960 / adsorption modes for two different coordination numbers as 6 and 8. The related adsorption energies were approximately found as -22.07 and -14.82 kcal/mol for these coordination numbers of surfaces, respectively. In addition, the binding energies stated in literature that are for Ni2 dimer and Ni13 nanoclusters were considered together with our binding energy results for Ni55 nanocluster. Accordingly, when a correlation line was drawn and the intercept of binding energies was obtained against the value of &amp / #8213 / n&amp / #8722 / 1/3&amp / #8214 / where n is the number of atoms in the cluster / the result of interception gives a good estimation for bulk nickel binding energy at infinite &amp / #8213 / n&amp / #8214 / . This interception result was found as 4.58 eV/atom where the experimental value is reported as 4.45 eV/atom for bulk in the literature. Ehtylene hydrogenation mechanisms were also investigated in terms of the resultant geometries and total energy required for the related mechanism steps.