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Computational simulations using empirical force fields are frequently used to model guest-host interactions in porous periodic systems, where the interaction energy is broken into electrostatic and van der Waals contributions. While simulations such as these have been instrumental in progressing our understanding of neutral periodic systems, limitations in deriving partial atomic charges has largely contributed to the difficulty in modeling charged periodic frameworks. However, many nanoporous materials possess frameworks that have a net charge, which is balanced by counter-ions that intercalate through the pores. For example, virtually all zeolites used in practice contain a proportion of Al, which bestows the framework with a negative charge. In this respect, we investigate two methods for the generation of partial atomic charges in periodic systems having a net framework charge. First, we examine the validity of generating REPEAT electrostatic potential fitted charges derived from periodic electronic structure calculations, where a constant background charge is added to neutralize the net charge on the framework without adding neutralizing counter-ions. The second method we explore is the split charge equilibration (SQE) method for very rapid charge generation. In its original formulation, the SQE model cannot be applied to systems with a net charge. In this work, we reformulate the SQE method for non-neutral systems to be treated. The new SQE model, which we call SQEAB, was shown to give equivalent results to those of the original SQE model for neutral systems. For charged frameworks, the model was shown to provide partial atomic charges in good agreement with the DFT derived REPEAT method. Taking advantage of that work, we next focus on the development of a force field for modeling CO2, N2, and CH4 gas adsorption in both neutral and charged zeolites, which we call the AMP (Aluminosilicate MicroPorous) force field. Commonly, the electrostatic potential of zeolites is represented through the use of generic charges, where every atom of the same type in the framework is assigned the same atomic charge. Though this model is fast, it fails to account for structural differences between framework geometries. In this work, we have optimized a set of SQEAB parameters to reproduce the DFT derived electrostatic potentials (ESPs) of a structurally representative set of both neutral and charged zeolite frameworks. Comparing with other popular models, the SQEAB-AMP charges are shown to better reproduce the QM ESP by more than 30%, on average. Gas uptakes obtained using SQEAB AMP charges were found to be within 5% of those obtained using DFT derived charges. We have further optimized a set of Lennard-Jones parameters to be combined the SQEAB-AMP charges that reproduce experimental uptake data in zeolites.

Thesis (Ph.D.(Physics)) -- University of Limpopo, 2020 / The effects of O2, H2O and OH− and collectors are the major factors that determine the flotability behaviour of minerals. In particular, the influence of the chain length variation on xanthate collectors gives rise to increased recovery rates, and are still the most versatile collector for most minerals. This study explores the bonding behaviour, adsorption energies and electronic properties directly related to the reactivity of O2, H2O and OH−, ethyl xanthates (EX), normal propyl-xanthate (nPX), normal-butyl-xanthate (nBX–) and amyl-xanthate (AX) with the platinum antimony mineral surfaces: (100), (110) and (111) surfaces. We employed the ab-initio quantum mechanical density functional theory to investigate their adsorption and their electronic properties. In order to attain precise calculations, the cut-off energy of 500 eV was used for the bulk PtSb2, which was also transferred to the surfaces. To obtain accurate results the k point used for both the bulk and surfaces were 6x6x6 and 4x4x1, respectively. The bulk relaxation was found to give final lattice parameter of 6.531 Å. The DOS (Density Of States) indicated that both bulk and surfaces of PtSb2 had a metallic character, thereby indicating semiconducting behaviour. In cleaving the surfaces, all possible terminations were considered and the slab thickness was varied to obtain the desired stable surfaces. Their relaxed surface energies were 0.807 J.m-2, 1.077 J.m-2 and 1.074 J.m-2 for the (100), (111) and (110), respectively. These indicated that the (100) surface was the most stable and dominant plane for the platinum antimony. This fact is also observed in other minerals in general that low-index surfaces with lower surface energies indicates structural stability. The DOS showed stability with the EF (Fermi level/ Fermi energy) falling deep into the pseudo gap for all surface. The valence electrons on the surface were 5d96s1 for Pt and 5s25p3 for Sb as depicted from the Mulliken population charges and these electrons were actively involved in the hybridisation. The oxidation showed that the oxygen molecules preferred interacting with the Sb atoms than the Pt atoms for all surfaces. For the (100) surface we found that the Pt-O2peroxide adsorption site gave the strongest adsorption, while for the (110) surface we noted that the Sb2-O-O-Sb3 bridging gave the most exothermic adsorption. The case of the (111) surface showed the Sb2-O-O-Sb2 bridging to give the strongest exothermic adsorption, which dissociated and resulted in atomic bonding. Their atomic charges indicated that the oxygen molecules gain charges from the Pt and Sb atoms. In all cases, PtSb2 Bulk PtSb2 (100), (110) and (111) surfaces O2, H2O, OH-and Xanthates adsorptions the O2 interacting with Sb gained more charges, thus showing preferential adsorption to the Sb atoms. In addition, the Sb/Pt-bonded oxygens were more negative than the terminal or end-bonded oxygen atom for superoxide modes. These suggested that the 2p-orbital spin-down unoccupied orbital (LUMO) of O2 is fully occupied. The case of H2O molecules adsorptions on the three PtSb2 mineral surfaces indicated that the H2O adsorbed through van der Waals forces, in particular for multi adsorptions by physisorption process for the (100) and the (110) surfaces. However, on the (111) surface we observed chemisorption adsorption. For the (100) surface we found that the H2O-Pt was exothermic, while the H2O-Sb was endothermic and only showed exothermic from 5/8-8/8 H2O/Sb. The case of the (110) surface showed stronger adsorption of H2O on Pt than on Sb atoms, with a weaker adsorption on Sb2 atoms, while the adsorption on the (111) surface was stronger on Sb3 and weaker on Sb2 atoms. The full-coverage for the (110) surface gave –35.00 kJ/mol per H2O molecule, which is similar to the full coverage on the (100) surface (–38.19 kJ/mol per H2O molecule). Furthermore, the full monolayer adsorption on Sb2 and Sb3 for the (111) surface gave much stronger adsorption (–55.54 kJ/mol per H2O). In addition, the full-coverage on the (111) surface (i.e. on Pt1 and all Sb atoms) gave adsorption energy of –54.95 kJ/mol per H2O molecule. The adsorption of hydroxide on the surfaces showed stronger affinity than the water molecules. This suggested that they will bind preferentially over the water molecules. We also found that the OH–preferred the Sb atoms on the (100) surface, with a greater adsorption energy of –576.65 kJ/mol per OH– molecule for full-surface coverage. The (110) surface adsorption energy on full-surface coverage was –541.98 kJ/mol per OH molecule. The (111) surface full-coverage yielded adsorption energy of –579.53 kJ/mol per OH– molecule. The atomic charges related to both hydration and hydroxide adsorption showed charge depletion on both Pt/Sb and O atoms of the H2O and OH–. This suggested that there is a charge transfer into other regions within the orbitals. The adsorption of collectors on the PtSb2 surfaces to investigate their affinity with surfaces were performed considering different adsorption sites in order to find the most stable exothermic preferred site. In respect of the (100) surface, we noted that the bridging on Pt and Sb atoms by the collector involved the S atoms for all xanthates. Their adsorption energies showed that EX had strong affinity with the surface and the order was as: EX ≈ AX > nBX > nPX. In the case of the (110) surface the bridging on Pt atoms were PtSb2 Bulk PtSb2 (100), (110) and (111) surfaces O2, H2O, OH- and Xanthates adsorptions the most preferred sites for EX, nPX, nBX and AX. The order of adsorption energies was: nBX > nPX ≈ AX > EX. The (111) surface was observed to have the bridging on Sb2 and Sb3 atoms most exothermic for EX, nBX and AX, while the nPX showed the bridging on Pt1 and Sb3 atoms. The adsorption energies were found to have the nPX more stronger on the surface, with EX weaker and the order decreased as: nPX > nBX > AX > EX. This gave insights in the recovery of the minerals during flotation, that the use of EX or AX may float the platinum antimonide better based on the adsorption trends on the (100) surface, which is the most stable surface plane cleavage for platinum antimonide. The analysis of the electronic structures of the collector on the surface from density of states showed stability bonding of the collector on the surface, due to the EF falling deep into the pseudo gap for collector S atoms and surface Pt and Sb PDOS. The atomic charges computed indicated that the collectors behave as electron donors and acceptors to the Pt and Sb on the surface, respectively for the (100) surface. Interestingly for the (110) surface we observed that both surface Pt and Sb atoms lost charges, with a loss of charges on the collector S atoms. These observations suggested that the collectors S atoms offer their HOMO electrons to Pt and Sb atoms to form bond and simultaneously the Pt and Sb atoms donate their d-orbital and p-orbitals electrons to the LUMO of the collectors to form a back donation covalent bond, respectively. The (111) surface clearly showed that the surface Pt and Sb atoms lose charges to the collector S atoms, suggested a back donation covalent bonds. / National Research Foundation (NRF) and CSIR (Council for Scientific and Industrial Research) through Centre for High Performance Computing (CHPC)

Orientador: Roy Edward Bruns / Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Quimica / Made available in DSpace on 2018-08-08T20:57:48Z (GMT). No. of bitstreams: 1 Cesar_PauloHenrique_M.pdf: 1005998 bytes, checksum: a962e8dd40f25da4750c20492dd58820 (MD5) Previous issue date: 2007 / Resumo: A Teoria Quântica de Átomos em Moléculas (QTAIM) é utilizada para decompor as derivadas do momento dipolar e as intensidades de infravermelho das moléculas AB3 (A=N, P; B=H, F) em contribuições de carga¿fluxo de carga-fluxo de dipolo (CCFDF). Os cálculos realizados no nível MP2/6-311++G(3d,3p) obteve valores das intensidades de infravermelho com as cargas e dipolos atômicos QTAIM que diferem em 13,8 km mol dos valores experimentais não considerando as vibrações de estiramento das moléculas de NH3 e PH3, em que ocorrem sobreposição das bandas experimentais. Os dipolos atômicos dos átomos de nitrogênio e fósforo são muito importantes na determinação do momento dipolar das moléculas de NF3, PH3 e PF3, enquanto que as cargas atômicas são quase totalmente responsáveis pelo momento dipolar da molécula de NH3. O fluxo de dipolo do átomo central é mais importante na determinação das intensidades das bandas de estiramento de todas as moléculas, enquanto contribui muito pouco para as intensidades das bandas de deformação. As contribuições dos fluxos de dipolos dos átomos terminais devem ser consideradas para descrever com maior precisão as intensidades de todas as moléculas. A expectativa que se tem com o modelo momento de ligação simples, é do domínio da contribuição de carga para as derivadas do momento de dipolo e intensidades das moléculas NH3, NF3 e PF3. Entretanto, as contribuições de fluxo de carga e fluxo de dipolo são muito grandes para todas as vibrações do PH3, cancelando-se no modo de estiramento e reforçando-se nos modos de deformação. / Abstract: The quantum theory of atoms in molecules (QTAIM) has been used to decompose dipole moment derivatives and fundamental infrared intensities of the AB3 (A=N, P; B=H, F) molecules into charge-charge flux-dipole flux (CCFDF) contributions. Calculations were carried out at the MP2/6-311++G(3d,3p) level. Infrared intensities calculated from the QTAIM atomic charges and atomic dipoles are within 13.8 km mol of the experimental values not considering the NH3 and PH3 stretching vibrations for which the experimental bands are severely overlapped. Group V atomic dipoles are very important in determining the molecular dipole moments of NF3, PH3 and PF3 although the atomic charges account for almost all the NH3 molecular moment. Dipole fluxes on the Group V atom are important in determining the stretching band intensities of all molecules whereas they make small contributions to the bending mode intensities. Consideration of dipole flux contributions from the terminal atoms must also be made for accurately describing the intensities of all these molecules. As expected from a simple bond moment model, charge contributions dominate for most of the NH3, NF3 and PF3 dipole moment derivatives and intensities. Charge flux and dipole flux contributions are very substantial for all the PH3 vibrations, canceling each other for the stretching modes and reinforcing one another for the bending modes. / Mestrado / Físico-Química / Mestre em Química

No description available.

Diversas metodologias foram desenvolvidas nas últimas décadas para cálculo de propriedades que representassem quantitativamente a distribuição de carga eletrônica de forma mais simplista. A mais básica destas propriedades é chamada de carga atômica. Contudo, não havendo unanimidade quanto à utilização de um formalismo de cálculo de carga para situações abrangentes de estudo, há a necessidade de trabalhos voltados para uma análise comparativa entre as respostas destes formalismos em termos de carga atômica e parâmetros derivados. Assim, fez-se nesta dissertação uma investigação sobre valores de carga atômica e propriedades dinâmicas relacionadas, com importância em estudos sobre movimentos vibracionais em moléculas, como fluxo de carga e fluxo de dipolo, obtidos com os formalismos de cálculo de carga de Mulliken, NPA, CHELPG e QTAIM. Neste trabalho também se avaliou o efeito da escolha do método de cálculo, como Hartree-Fock e métodos que incluem correlação eletrônica (MP2, MP4(SDQ) e CCSD), e do conjunto de funções de base, através de funções como cc-pVDZ, cc-pVTZ e cc-pVQZ, sobre estas propriedades dinâmicas. Os sistemas analisados incluíram moléculas diatômicas e triatômicas lineares (HF, HCl, LiH, NaH, NaCl, LiF, NaF, LiCl, BF, AlF, BeO, MgO, CO, ClF, CO2, CS2, OCS, HCN e HNC) formadas por ligações de caráter variado, desde altamente iônicas até covalentes e incluindo ligações múltiplas. Também foram estudadas moléculas de clorofluorometanos (CH4, CH3Cl, CH3F, CH2Cl2, CH2F2, CH2ClF, CHCl3, CHF3, CHCl2F, CHClF2, CCl2F2, CClF3, CFCl3, CCl4, e CF4) para observação do efeito da troca de substituintes nas propriedades citadas. Pelos resultados obtidos, pode-se afirmar que apenas os formalismos NPA e QTAIM apresentam bom comportamento quanto à convergência em relação ao método de cálculo e/ou tamanho do conjunto de funções de base utilizados no estudo do fluxo de carga. Entretanto, apenas os valores QTAIM são consistentes com certas considerações químicas fundamentais, como fluxos de carga tendendo a zero durante o estiramento de ligações de predominante caráter iônico, em moléculas com estruturas próximas à geometria de equilíbrio. As cargas e seus fluxos obtidos com Mulliken apresentaram alta dependência e problemas de convergência com a escolha da função de base, além de valores incoerentes em alguns sistemas. Por sua vez, CHELPG não se mostrou adequado à aplicação da aproximação finita de dois pontos na obtenção dos valores numéricos de fluxos de carga. A análise da resposta destas propriedades à troca de substituintes em moléculas de clorofluorometanos seguiu destacando positivamente QTAIM em relação aos outros formalismos. Enquanto CHELPG demonstrou oscilações inconsistentes em gráficos destes valores em função do número de átomos de cloro e/ou flúor, NPA e Mulliken se mostraram sensíveis à troca de substituintes, entretanto, os valores de fluxo de carga observados em alguns casos estão em desacordo com a tendência esperada na troca de átomos de hidrogênio por átomos de cloro ou flúor. / Several methodologies were developed in the last few decades in order to obtain a property which could represent quantitatively electronic charge distributions in a simple way. The fundamental quantity in this treatment is called atomic charge. However, as long as there is not an agreement about the most indicated method to determine atomic charges for general systems or responses under study, it is necessary to analyze, comparatively, how these methods behave in given situations and how the values derived from them respond in each case. Hence, an investigation including charges and related quantities as charge flux and atomic dipole flux, which are of interest to vibrational analysis, was done by means of values resulting from four formalisms, that are, Mulliken, NPA, CHELPG and QTAIM. In this study were also evaluated the changes in such dynamic properties when the calculations are done by means of different methods, as Hartree-Fock and methods that include electron correlation (MP2, MP4(SDQ) and CCSD) and, with different basis sets as cc-pVDZ, cc-pVTZ and cc-pVQZ. The systems analyzed were diatomic and linear triatomic molecules (HF, HCl, LiH, NaH, NaCl, LiF, NaF, LiCl, BF, AlF, BeO, MgO, CO, FCl, CO2, CS2, OCS, HCN and HNC) including diverse bonding character, such as highly ionic or covalent bonds along with multiple bonds. Also, charge and charge flux parameters in chlorofluoromethane molecules (CH4, CH3Cl, CH3F, CH2Cl2, CH2F2, CH2ClF, CHCl3, CHF3, CHCl2F, CHClF2, CCl2F2, CClF3, CFCl3, CCl4 and CF4) were studied to analyze the effects in these properties during the exchange of substituent atoms. Considering the data obtained, one can infer that only NPA and QTAIM formalisms result in satisfactory convergence patterns with chosen methods and/or basis set sizes during the determination of charge and charge flux values. However, only QTAIM charge fluxes seem to follow certain chemical considerations, as low values for charge flux in a bond enlargement in systems with a predominant ionic character close to their equilibrium geometry. The Mulliken formalism shows high dependence and convergence issues in basis set size increments, as well as some inconsistent values. On other hand, CHELPG formalism is not suited to the finite approach for numerical derivatives in its two-point version. The study of substituent effects in chlorofluoromethanes reinforces the performance of QTAIM when compared to other formalisms. While CHELPG returned inconsistent oscillations in plots against the number of chlorine/fluorine atoms, NPA and Mulliken exhibited some sensibility with the change of substituent, though the flux values observed in a few cases are in disagreement with the tendencies expected when the hydrogen atoms are switched by chlorine or fluorine atoms.

Diversas metodologias foram desenvolvidas nas últimas décadas para cálculo de propriedades que representassem quantitativamente a distribuição de carga eletrônica de forma mais simplista. A mais básica destas propriedades é chamada de carga atômica. Contudo, não havendo unanimidade quanto à utilização de um formalismo de cálculo de carga para situações abrangentes de estudo, há a necessidade de trabalhos voltados para uma análise comparativa entre as respostas destes formalismos em termos de carga atômica e parâmetros derivados. Assim, fez-se nesta dissertação uma investigação sobre valores de carga atômica e propriedades dinâmicas relacionadas, com importância em estudos sobre movimentos vibracionais em moléculas, como fluxo de carga e fluxo de dipolo, obtidos com os formalismos de cálculo de carga de Mulliken, NPA, CHELPG e QTAIM. Neste trabalho também se avaliou o efeito da escolha do método de cálculo, como Hartree-Fock e métodos que incluem correlação eletrônica (MP2, MP4(SDQ) e CCSD), e do conjunto de funções de base, através de funções como cc-pVDZ, cc-pVTZ e cc-pVQZ, sobre estas propriedades dinâmicas. Os sistemas analisados incluíram moléculas diatômicas e triatômicas lineares (HF, HCl, LiH, NaH, NaCl, LiF, NaF, LiCl, BF, AlF, BeO, MgO, CO, ClF, CO2, CS2, OCS, HCN e HNC) formadas por ligações de caráter variado, desde altamente iônicas até covalentes e incluindo ligações múltiplas. Também foram estudadas moléculas de clorofluorometanos (CH4, CH3Cl, CH3F, CH2Cl2, CH2F2, CH2ClF, CHCl3, CHF3, CHCl2F, CHClF2, CCl2F2, CClF3, CFCl3, CCl4, e CF4) para observação do efeito da troca de substituintes nas propriedades citadas. Pelos resultados obtidos, pode-se afirmar que apenas os formalismos NPA e QTAIM apresentam bom comportamento quanto à convergência em relação ao método de cálculo e/ou tamanho do conjunto de funções de base utilizados no estudo do fluxo de carga. Entretanto, apenas os valores QTAIM são consistentes com certas considerações químicas fundamentais, como fluxos de carga tendendo a zero durante o estiramento de ligações de predominante caráter iônico, em moléculas com estruturas próximas à geometria de equilíbrio. As cargas e seus fluxos obtidos com Mulliken apresentaram alta dependência e problemas de convergência com a escolha da função de base, além de valores incoerentes em alguns sistemas. Por sua vez, CHELPG não se mostrou adequado à aplicação da aproximação finita de dois pontos na obtenção dos valores numéricos de fluxos de carga. A análise da resposta destas propriedades à troca de substituintes em moléculas de clorofluorometanos seguiu destacando positivamente QTAIM em relação aos outros formalismos. Enquanto CHELPG demonstrou oscilações inconsistentes em gráficos destes valores em função do número de átomos de cloro e/ou flúor, NPA e Mulliken se mostraram sensíveis à troca de substituintes, entretanto, os valores de fluxo de carga observados em alguns casos estão em desacordo com a tendência esperada na troca de átomos de hidrogênio por átomos de cloro ou flúor. / Several methodologies were developed in the last few decades in order to obtain a property which could represent quantitatively electronic charge distributions in a simple way. The fundamental quantity in this treatment is called atomic charge. However, as long as there is not an agreement about the most indicated method to determine atomic charges for general systems or responses under study, it is necessary to analyze, comparatively, how these methods behave in given situations and how the values derived from them respond in each case. Hence, an investigation including charges and related quantities as charge flux and atomic dipole flux, which are of interest to vibrational analysis, was done by means of values resulting from four formalisms, that are, Mulliken, NPA, CHELPG and QTAIM. In this study were also evaluated the changes in such dynamic properties when the calculations are done by means of different methods, as Hartree-Fock and methods that include electron correlation (MP2, MP4(SDQ) and CCSD) and, with different basis sets as cc-pVDZ, cc-pVTZ and cc-pVQZ. The systems analyzed were diatomic and linear triatomic molecules (HF, HCl, LiH, NaH, NaCl, LiF, NaF, LiCl, BF, AlF, BeO, MgO, CO, FCl, CO2, CS2, OCS, HCN and HNC) including diverse bonding character, such as highly ionic or covalent bonds along with multiple bonds. Also, charge and charge flux parameters in chlorofluoromethane molecules (CH4, CH3Cl, CH3F, CH2Cl2, CH2F2, CH2ClF, CHCl3, CHF3, CHCl2F, CHClF2, CCl2F2, CClF3, CFCl3, CCl4 and CF4) were studied to analyze the effects in these properties during the exchange of substituent atoms. Considering the data obtained, one can infer that only NPA and QTAIM formalisms result in satisfactory convergence patterns with chosen methods and/or basis set sizes during the determination of charge and charge flux values. However, only QTAIM charge fluxes seem to follow certain chemical considerations, as low values for charge flux in a bond enlargement in systems with a predominant ionic character close to their equilibrium geometry. The Mulliken formalism shows high dependence and convergence issues in basis set size increments, as well as some inconsistent values. On other hand, CHELPG formalism is not suited to the finite approach for numerical derivatives in its two-point version. The study of substituent effects in chlorofluoromethanes reinforces the performance of QTAIM when compared to other formalisms. While CHELPG returned inconsistent oscillations in plots against the number of chlorine/fluorine atoms, NPA and Mulliken exhibited some sensibility with the change of substituent, though the flux values observed in a few cases are in disagreement with the tendencies expected when the hydrogen atoms are switched by chlorine or fluorine atoms.