Neste trabalho, uma combinação de cálculos de mecânica quântica, simualções computacionais e teoria de perturbação termodinâmica, foi usada para estudar a solvatação do carbono de etileno (EC) e do carbonato de propileno (PC) em água. As estruturas do líquido foram geradas usando simulações com o método Monte Carlo e amostragem de Metropólis. A função de autocorrelação em energia foi usada para analisar a correlação estatística entre estas configurações. Após uma analise detalhada das ligações de hidrogênio, configurações supermoleculares descorrelacionadas ( carbonato + ligações de hidrogênio cercadas por 350 moléculas de água tratadas como cargas pontuais) foram amostradas das simulações e cálculos do momento de dipolo, no nível de cálculo MP2/ aug-cc-pvDZ, foram realizados. Em média foram formadas 1,4 ligações de hidrogênio entre a água e os solutos (EC ou PC). Foi obtido um momento de dipolo médio 9,9 ± 0,2 D para o EC-água e de 10,6 ± 0,2 D para o PC-água. Finalmente, simulações com o método de Monte Carlo no ensemble NPT e a técnica de perturbação de energia livre foram usados para determinar as energias livres de solvação, e os resultados foram Gsolv = -15,1 ± 0,8 Kcal/ mol para o EC em água e Gsolv = -15,3 ± 1,2 Kcal/mol para o PC em água. A análise destes resultados leva a conclusão de que o EC e o PC são igualmente estáveis em solução aquosa, ou seja, a metilação não tem efeito significativo na solvatação do PC e nem influência a formação das ligações de hidrogênio. / In this work, a combination of quantum mechanics, Monte Carlo simulations and thermodynamic perturbation theory was used to study the solvation of ethylene carbonate (EC) and propylene carbonate (PC) in water. The liquid structures was generated by NVT Monte Carlo simulation using standard procedures for the Metropolis sampling technique. The auto-correlation function of the energy was used to analyse the statistical correlation between the configurations (carbonates + hydrogen bonds sorrounded by 350 water molcules treated as point charges) were smpled from the simulations and dipole moment calculations, at the MP2/ aug-cc-pvDZ, were performed. On average, 1,4 hydrogen bonds were formed between water and the solutes (EC or PC). An average dipole momento of 9,9 ± 0,2 D was obtained for EC-water and 10,6 ± 0,2 D for PC-water. Finally, Monte Carlo simulations in the NPT ensemble combined with free energy pertubation technique were used to determine solvation free energies, and the results were Gsolv = -15,1 ± 0,8 kcal/mol for EC in water and Gsolv = -15,3 ± 1,2 kcal/mol for PC in water. The analysis of these results leads to the conclusion that EC and PC are equally stable in aqueous solution, i.e, the methylation hás no effect on the solvation of PC and no influence on the hydrogen bond formation.

Neste trabalho, foram caracterizados os estados eletrônicos fundamental e excitados de mais baixa energia dos sistemas 1;3[H,C,As]. Para isso, foram empregados vários métodos ab initio de estrutura eletrônica (MP2, CCSD(T), CCSD(T)-F12b e MRCISD) aliados a extensos conjuntos de funções de base consistentes na correlação (aug-cc-pVnZ, em que n = D, T, Q e 5). Buscando uma acurácia ainda maior, os resultados obtidos foram extrapolados para o limite do conjunto de base completa (CBS). O estado X1Σ+ da molécula HCAs e o estado eletrônico fundamental do sistema 1[H,C,As], com as seguintes distâncias internucleares: rHC=1,0748 Å e rCAs=1,6602 Å; para as frequências harmônicas, obtivemos ω1(&#963)=1068 cm-1, ω2(π)/ω3(&#960)= 626 cm-1 e ω4(σ)=3310 cm-1 no nível de teoria CCSD(T)-F12-CBS. A espécie 1Σ+ HAsC e um ponto de sela de segunda ordem sobre a superfície de energia potencial (localizado a 75,24 kcal.mol-1 do X1Σ+ HCAs), ou seja, chegamos a conclusão que esta espécie, neste estado eletrônico, em fase gasosa, não existe. Já para os estados tripletos, ha isomerização, sendo que o 13A\' HCAs e o 13A\' HAsC foram caracterizados como mínimos com uma energia relativa ao mínimo global de 59,27 kcal.mol-1 e 88,22 kcal.mol-1, respectivamente. Além disso, exploramos os canais de dissociação destas espécies no nível de teoria CCSD(T). Foram ainda calculadas as frequências fundamentais para os estados do HCAs e do HAsC, como também investigada a inclusão da correlação dos elétrons do caroço nos parâmetros estruturais, vibracionais e energéticos. Estimamos o calor de formação (ΔH0f) a 0 e 298,15 K para as espécies CH, AsH, CAs e HCAs, sendo que a maioria desses valores ainda não e conhecida na literatura. Para o X1Σ+ HCAs, obtivemos um valor de ΔH0f igual a 71,22 kcal.mol-1 a 0 K e 70,38 kcal.mol-1 a 298,15 K. Calculamos o potencial de ionização da molécula HCAs utilizando varias metodologias teóricas, obtendo valores muito próximos aos experimentais, por exemplo, o CCSD(T)-aVTZ forneceu 9,90 eV frente ao valor experimental de 9,8 eV. Os estados eletrônicos excitados singleto e tripleto das espécies HCAs e HAsC foram também caracterizados com a obtenção de dados estruturais, vibracionais e energéticos. A maioria dos dados das espécies HCAs e HAsC nesta dissertação são inéditos na literatura química. / In this work, the ground state and low-lying excited electronic states of system 1;3[H,C,As] were investigated theoretically. Several ab initio molecular electronic structure theory were employed (MP2, CCSD(T), CCSD(T)-F12b e MRCISD) along with extensive correlation-consistent basis sets (aug-cc-pVnZ, n= T, Q e 5). Seeking increasing accuracy, further extrapolation of the results to the complete-basis-set (CBS) limit were carried out. The ground electronic state of 1[H,C,As] is the 1Σ+ HCAs specie, with internuclear distances of rHC=1.0748 Å and rCAs=1.6602 Å, and with harmonic vibrational frequencies ω1(&#963)=1068 cm-1, ω2(π)/ω3(&#960)= 626 cm-1 ω4(σ)=3310 cm-1, at the CCSD(T)-F12-CBS level theory. The electronic state 1Σ+ HAsC is a second-order saddle point on the potential energy surface (located at 75.24 kcal.mol-1 above HCAs), thus providing evidence that this species does not exist in gas phase. However, there is isomerization for triplet electronic states 13A\' HCAs to 13A\' HAsC, with energy relative to global minimum of 59,27 kcal.mol-1 e 88,22 kcal.mol-1, respectively. Fundamental frequencies and the effects of correlation of core electrons in structural, vibrational, and energetic parameters were also evaluated for HCAs and HAsC. Furthermore, the dissociation channels of these species were also evaluated at the CCSD(T)-CBS level theory. The heats of formations (ΔH0f), at 0 and 298,15 K, for the species CH, AsH, CAs and HCAs, were estimated; for most of them these results are inexistent in the literature. For X1Σ+ HCAs, we obtained 71.22 kcal.mol-1 at 0 K and 70.38 kcal.mol-1 at 298.15 K for ΔH0f. The ionization potential was also calculated by several theoretical methodologies, and the results are close to the experimental data; using CCSD(T)-aVTZ, we predicted a value of 9,9 eV, in close agreement with experimental value of 9,8 eV. The singlet and triplet electronic excited states of HCAs and HAsC were investigated and their structural, vibrational and energetic properties evaluated. Most of the results of this work are new in the chemistry literature.

Neste trabalho, são utilizados diversos métodos de química teórica para estudar as propriedades eletrônicas e o espectro de absorção de seis corantes catiônicos: laranja de acridina (LA), proflavina (PF), safranina (SF), vermelho neutro (VN), azul de metileno (AM) e tionina (TN). Inicialmente é realizado um estudo para verificar a influência do solvente na geometria e no espectro desses corantes utilizando diversos métodos de química quântica, o método de solvatação contínuo IEFPCM e a simulação de Monte Carlo (MC). A seguir são estudados a diprotonação, a dimerização e alguns modelos para a argila do tipo montmorilonita e para a interação desta com os corantes, fenômenos esses que explicam a metacromasia observada experimentalmente. / This work presents a theoretical study on the electronic properties and the absorption spectra of six cationic dyes: acridine orange, proflavine, safranine, neutral red, methylene blue and thionine. First of all, we have carried out calculations to verify the solvent effects on geometries and spectra employing methods of Quantum Chemistry and including solvent effects with the polarizable continnum model and Monte Carlo (MC) simulation. Also, we have studied diprotonation, dimerization and some models of the montmorillonite clay and its interaction with the cationic dyes under study here, phenomena that explain the experimental methacromatic behavior of these dyes.

Orientador: Gustavo Troiano Feliciano / Coorientador: Paulo Roberto Bueno / Banca: Eduardo Maffud Cilli / Banca: Paula Homem de Mello / Resumo: O estudo de monocamadas eletroativas vem ganhando espaço na literatura pois tem se mostrado como uma ferramenta muito promissora para a obtenção de diagnósticos cada vez mais rápidos e precisos para uma grande variedade de condições. Embora o número de publicações sobre o assunto venha aumentando significativamente com o passar dos anos, ainda não existem estudos aprofundados sobre a relação entre a estrutura da monocamada e suas propriedades eletrônicas e redox e como estas influenciam na detecção mais ou menos sensível de moléculas-alvo. Esta dissertação apresenta o estudo teórico das propriedades estruturais, eletrônicas e redox de uma monocamada peptídica com ferroceno terminal preso a uma superfície de ouro. Os cálculos foram feitos numa interface GROMACS-ORCA através da qual se produziram dinâmicas clássicas, quânticas e híbridas (QM/MM). Os resultados obtidos incluem uma comparação de cálculos single point para a estrutura do ferroceno com três bases (6-31G*, DEF2-SVP e DEF2-TZVP) e cinco funcionais (B3LYP, BLYP, BP86, PBE0 e PBE) no qual o conjunto DEF2-TZVP/ BP86 obteve os melhores resultados. A mesma estrutura foi usada para calcular, por meio do QM/MM, a distribuição da energia potencial do ferroceno reduzido e oxidado com a finalidade de produzir curvas de Marcus e analisar se este complexo obedece aos princípios delineados por essa teoria. As curvas mostraram que o ferroceno segue a teoria de Marcus se o meio no qual ele se encontra for homogêneo. Por último, fiz... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: The study of electroactive monolayers has been gaining ground in the literature because it has proved to be a very promising tool for obtaining faster and more accurate diagnostics for a wide variety of conditions. Although the number of publications on the subject has increased significantly over the years, there are still no in-depth studies on the relationship between monolayer structure and its redox and electronic properties and how these influence in the sensitivity for detecting target molecules. This dissertation presents the theoretical study of the structural, electronic and redox properties of a peptidic monolayer with ferrocene attached to a gold surface. The calculations were made in a GROMACS-ORCA interface through which classical, quantum and hybrid dynamics (QM/MM) were produced. The results obtained include a comparison of single point calculations for the ferrocene structure with three bases (6-31G*, DEF2-SVP and DEF2-TZVP) and five functional ones (B3LYP, BLYP, BP86, PBE0 and PBE) in which the set DEF2-TZVP/ BP86 got the best results. The same structure was used to calculate the distribution of the potential energy of reduced and oxidized ferrocene by means of the QM / MM in order to produce Marcus curves and to analyze if this complex obeys the principles outlined by this theory. The curves showed that ferrocene follows Marcus's theory if the medium in which it is found is homogeneous. Finally, classical simulations were performed to obtain structural info... (Complete abstract click electronic access below) / Mestre

Emissions of soot and polycyclic aromatic hydrocarbons (PAHs) from incomplete burning of hydrocarbon fuels pose a great threat to the environment and human health. To reduce such emissions, a comprehensive understanding of their evolution process is essential. In this work, a series of research studies were conducted to evaluate sooting tendencies and to experimentally and theoretically develop PAH mechanisms. The sooting tendencies of oxygenated fuels were quantitively investigated in counterflow diffusion flames. Sooting limits are described by critical fuel and oxygen mole fractions, measured with a laser scattering technique. The addition of dimethyl ether displays non-monotonic behavior on sooting tendencies at elevated pressures, which is attributed to the chemical effect from kinetic simulations. The tendency of incipient soot formation of other oxygenated fuels (e.g., alcohol, acid, ether, ketone, and carbonate ester) was also assessed, using a similar approach. As the precursor of soot, PAH measurement using laser induced fluoresecnce was implemented to track the evolution processes from PAHs to incipient soot. Developing a PAH mechanism is essential to the understanding of soot formation; however, PAH formation and its growth process are not well understood. Based on previous research, PAHs with 5-membered rings are abundant in flames. Therefore, the growth of PAHs with 5-membered rings was investigated, using acenaphthylene (A2R5) as the example. The density functional theory (DFT) and the transition state theory (TST) were adopted to calculate potential energy surfaces and reaction rate coefficients. The existence of 5-membered rings appreciably impacts PAH production by facilitating the formation of planar PAHs with C2H substitution, thereby improving existing PAH mechanisms. In PAH mechanisms, the thermochemistry properties are not all calculated, but are hypothesized to be equal to those of a similar structure. The simulation accuracy of the hypothesis is explored here by discussing the sensitivity of the thermochemistry parameters in flame simulations. The group additivity method utilizing THERM codes is used to calculate thermochemistry properties. PAH loading affects the sensitivity of thermochemistry properties to both flame temperature and product yields. These results show that either accurate thermochemistry properties, or reverse reaction rates should be provided in the mechanism to improve simulation accuracy.

<p><br></p><p>The pharmaceutical industry depends on deeply understanding pharmaceutical excipients and active ingredients. The physicochemical properties must be sufficiently understood to create a safe and efficacious drug product. High-throughput methods have reduced the time and material required to measure many properties appropriately. However, some are more difficult to evaluate. One such property is solubility or the equilibrium dissolvable content of the material. Solubility is an essential factor in determining the bioavailability of an active ingredient and, therefore, directly impacts the effectiveness and marketability of the drug product.</p><p>Solubility can be a challenging, time-consuming, material-intensive property to measure correctly. Due to the challenge associated with determining experimental values, researchers have devoted a significant amount of time toward the accurate prediction of solubility values of drug-like compounds. This remains a difficult task as there are two hurdles to overcome: data quality and specificity of molecular descriptors. Large databases of reliable solubility values have become more readily available in recent years, lowering the first barrier to more accurate solubility predictions. The second hurdle has proven more challenging to overcome. Advances in artificial intelligence (AI) have provided opportunities for improvement in estimations. Expressly, the subsets of machine learning and neural networks have provided the ability to evaluate vast quantities of data with relative ease. The remaining barrier arises from appropriately selecting AI techniques with descriptors that accurately describe relevant features. Although many attempts have been made, no single set of descriptors with either data-driven approaches or <i>ab initio</i> methods has accurately predicted solubility.</p><p>The research within this dissertation focuses on an attempt to lower the second barrier to solubility prediction by starting with molecular features that are most important to solubility. By deriving molecular descriptors from the electronic properties on the surface of molecules, we obtain precise descriptions of the strength and locality of intermolecular interactions, critical factors in the extent of solubility. The novel molecular descriptors are readily integrated into a Deep-sets based Graph and Self-Attention Neural Network, which evaluates predictive performance. The findings of this research indicate significant improvement in predicting intrinsic solubility over other literature-reported methods.</p>

Computing the Fermi-Dirac operator is done through recursive polynomial expansions, using the SP2 and SP2 Acc algorithms. The Gateaux derivative is computed for both schemes by mapping the zeroth and first order matrices onto a block upper triangular matrix, which is implemented in Python using Numpy arrays to store full matrices and in C++ by first constructing a basic matrix library to use as blocks in a later created block upper triangular matrix library which only directly references two blocks in a 2 x 2 block matrix. Computations of the Fermi-Dirac operator were carried out on artificially created Hamiltonians to verify correct implementations, as well on real life examples of Fock matrices resulting from ergo calculations on water clusters(http://ergoscf.org/). It was found that the relative error in the first order response in the density matrix was not different when using SP2 Acc compared to when using SP2.

The variational quantum eigensolver (VQE) approach is currently one of the most promising strategies for simulating chemical systems on quantum hardware. In this work, I will describe a new quantum algorithm and a new set of classical algorithms based on VQE. The quantum algorithm, ADAPT-VQE, shows promise in mitigating many of the known limitations of VQEs: Ansatz ambiguity, local minima, and barren plateaus are all addressed to varying degrees by ADAPT-VQE. The classical algorithm family, O2DX-UCCSD, draws inspiration from VQEs, but is classically solvable in polynomial time. This group of algorithms yields equations similar to those of the linearized coupled cluster theory (LCCSD) but is more systematically improvable and, for X = 3 or X = ∞, can break single bonds, which LCCSD cannot do. The overall aim of this work is to showcase the richness of the VQE algorithm and the breadth of its derivative applications. / Doctor of Philosophy / A core goal of quantum chemistry is to compute accurate ground-state energies for molecules. Quantum computers promise to simulate quantum systems in ways that classical computers cannot. It is believed that quantum computers may be able to characterize molecules that are too large for classical computers to treat accurately. One approach to this is the variational quantum eigensolver, or VQE. The idea of a VQE is to use a quantum computer to measure the molecular energy associated with a quantum state which is parametrized by some classical set of parameters. A classical computer will use a classical optimization scheme to update those parameters before the quantum computer measures the energy again. This loop is expected to minimize the quantum resources needed for a quantum computer to be useful, since much of the work is outsourced to classical computers. In this work, I describe two novel algorithms based on the VQE which solve some of its problems.

Although semi-empirical quantum codes have existed for several years now, the computational chemistry has, by and large, remained the subject of major interest for organic chemists and quantum chemists. In this thesis numerous exercises are designed in order to explore various areas of chemical engineering where these quantum chemical software might be successfully utilized. In this sense, the following attempt is a feasibility study to bring these semi-empirical quantum codes to the attention of the chemical engineering community. / M.S.

Most research on solving the N-electron Schrödinger equation has focused on ground states; excited states are comparatively less studied, and represent a greater challenge for many ab initio methods. The challenge is exacerbated for systems with substantial multiconfigurational character (i.e., strongly-correlated systems) for which standard many-electron wavefunction methods relying on a single electronic configuration give qualitatively incorrect descriptions of electron correlation. This thesis explores approaches to molecular excited state properties that are computationally efficient, yet applicable to multiconfigurational systems. Specifically, we explore strategies that combine the Equation-of-Motion (EOM) approach with the types of correlated wavefunction ansätze that are suitable for strongly-correlated systems. While it is known that the EOM method provides a general strategy for computing electronic transition energies, the significant flexibility in how one formulates the EOM approach and how it can be applied as a post-processing tool for different wavefunctions is not always appreciated. We begin by reviewing the EOM approach, focussing on methods that can be formulated using the 1- and 2-electron reduced density matrices. We assess the accuracy of different EOM approaches for neutral and ionic excited states. We focus on EOM-based alternatives to the traditional extended Koopams’ Theorem for ionization energies and electron affinities as well as an EOM formulation for double ionization transitions that constitutes an extension of the hole-hole/particle-particle random phase approximation (RPA) to multideterminant wavefunction methods. Then we introduce FanEOM, an EOM extension of the Flexible Ansatz for N-electron Configuration Interaction (FANCI) [Comput. Theor. Chem. 1202, 113187 (2021)], and explore its application to spectroscopic properties. Using the EOM methods for electronic excitation and double ionization/double electron affinity transitions described in the initial part of this thesis (i.e., the extended random phase approximations, ERPA), we study adiabatic connection formulations (AC) for computing the residual dynamic correlation energy in correlated wavefunction methods. The key idea in these approaches is that the perturbation strength dependent 2-RDM that appears in the AC formula can be approximated through the solutions from the different variants of ERPA [Phys. Rev. Lett. 120, 013001 (2018)]. Finally, we present PyEOM, an open-source software package designed to help prototype and test EOM-based methods. / Thesis / Doctor of Philosophy (PhD)