abstract: The goal of this theoretical study of infrared spectra was to ascertain to what degree molecules may be identified from their IR spectra and which spectral regions are best suited for this purpose. The frequencies considered range from the lowest frequency molecular vibrations in the far-IR, terahertz region (below ~3 THz or 100 cm-1) up to the highest frequency vibrations (~120 THz or 4000 cm-1). An emphasis was placed on the IR spectra of chemical and biological threat molecules in the interest of detection and prevention. To calculate IR spectra, the technique of normal mode analysis was applied to organic molecules ranging in size from 8 to 11,352 atoms. The IR intensities of the vibrational modes were calculated in terms of the derivative of the molecular dipole moment with respect to each normal coordinate. Three sets of molecules were studied: the organophosphorus G- and V-type nerve agents and chemically related simulants (15 molecules ranging in size from 11 to 40 atoms); 21 other small molecules ranging in size from 8 to 24 atoms; and 13 proteins ranging in size from 304 to 11,352 atoms. Spectra for the first two sets of molecules were calculated using quantum chemistry software, the last two sets using force fields. The "middle" set used both methods, allowing for comparison between them and with experimental spectra from the NIST/EPA Gas-Phase Infrared Library. The calculated spectra of proteins, for which only force field calculations are practical, reproduced the experimentally observed amide I and II bands, but they were shifted by approximately +40 cm-1 relative to experiment. Considering the entire spectrum of protein vibrations, the most promising frequency range for differentiating between proteins was approximately 600-1300 cm-1 where water has low absorption and the proteins show some differences. / Dissertation/Thesis / Ph.D. Physics 2012

A captura, estocagem e separaÃÃo de gases em processos de combustÃo à considerado um passo importante no desenvolvimento e consolidaÃÃo de novas tecnologias, devido as necessidades ambientais e ao grande interesse econÃmico envolvido. A separaÃÃo de gases Ãcidos (CO2 e H2S) à uma etapa de fundamental importÃncia para reduzir impactos ambientais e atender as especificaÃÃes de seguranÃa e mercado. A adsorÃÃo em faujasitas se apresenta como uma alternativa economicamente atraente em processos industriais, mas o elevado nÃmero de processos e condiÃÃes de temperatura e pressÃo onde pode ser utilizada, torna um estudo experimental impraticÃvel. Outro fator relevante sÃo as condiÃÃes de seguranÃa impostas durante o manuseio do Ãcido sulfÃdrico, necessitando de maior investimento em equipamentos, manutenÃÃo e sistemas de seguranÃa. Diante disse a simulaÃÃo molecular pode ser utilizada para obter propriedades imprescindÃveis para o dimensionamento e implantaÃÃo de PSAs. A base da utilizaÃÃo da simulaÃÃo molecular à a determinaÃÃo do campo de forÃa. Nesse trabalho um conjunto de parÃmetros de campo forÃa, baseados em campos de forÃa clÃssicos (UFF), foi proposto para CO2 em faujasitas sÃdicas. Em seguida a mesma metodologia de parametrizaÃÃo foi utilizada para H2S, N2, O2 e CH4. Os resultados obtidos a baixa pressÃo foram comparados com estudos experimentais e outros modelos propostos pela literatura, obtendo excelente concordÃncia em diferentes temperaturas e razÃes Si/Al, permitindo determinar o posicionamento dos sÃtios e do calor de adsorÃÃo. Outros cÃtions de compensaÃÃo foram testados para predizer a adsorÃÃo de nitrogÃnio em faujasitas. As isotermas para os cÃtions monovalentes obtiveram elevada precisÃo, para bivalentes os resultados representaram o padrÃo de adsorÃÃo experimental, embora com isotermas de menor precisÃo. Por fim, a adsorÃÃo da mistura N2/CO2 foi estudada apresentado boa concordÃncia com dados experimentais, demonstrando a eficiÃncia do mÃtodo como uma alternativa para determinaÃÃo de propriedades de misturas industriais. / The environmental needs and the great economic interest involved. The capture, storage and separation of gases in combustion processes is considered an important step in the development and consolidation of new technology, The separation of acidic gases (CO2 and H2S) is an important step to reduce environmental impacts and meet safety specifications and market. The adsorption on faujasitas presents itself as an economically attractive alternative in industrial processes, but the high number of processes and temperature and pressure conditions where it can be used, makes an experimental study impractical. Another relevant factor are security conditions imposed during the handling of hydrogen sulphide, necessitating greater investment in equipment, maintenance and safety systems. On said the molecular simulation can be used to obtain indispensable properties for the design and deployment of PSAs. The molecular simulation basis is the force field determination. In this work a set of force field parameters, based on classical force fields (UFF), has been proposed for CO2 in sodium faujasitas. The same methodology was used for H2S, N2, O2 and CH4 parameterization. The results obtained at low pressure were compared with experimental studies and other models proposed by literature, obtaining excellent concordance in different temperatures and Si/Al ratios, allowing determining the placement of adsorption sites and the heat. Other balancing cations were tested to predict nitrogen adsorption. The isotherms for the monovalent cations obtained high precision, to the bivalent results represented the standard experimental adsorption isotherms, albeit with less precision. Finally, the adsorption of mixture N2/CO2 was studied presented good agreement with experimental data, demonstrating the efficiency of the method as an alternative for determination of industrial properties of mixtures.

Submitted by Irene Nascimento (irene.kessia@ufpe.br) on 2017-03-27T17:41:33Z No. of bitstreams: 2 license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) TeseKeilaCunha-Química2016.pdf: 14937894 bytes, checksum: cac41daeb22968873c67113d6f511e66 (MD5) / Made available in DSpace on 2017-03-27T17:41:33Z (GMT). No. of bitstreams: 2 license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) TeseKeilaCunha-Química2016.pdf: 14937894 bytes, checksum: cac41daeb22968873c67113d6f511e66 (MD5) Previous issue date: 2016-10-21 / CNPQ / Materiais bionspirados em peptídeos e proteínas possuem ampla diversidade de aplicações científicas e tecnológicas. Este trabalho se concentrou na descrição de propriedades dinâmicas e conformacionais de dois biomiméticos: peptóides e catecóis. Peptóides são oligômeros de glicinas N-substituídas de interesse biológico devido à resistência a proteases, maior estabilidade térmica, ambiental e facilidade de síntese, em comparação a peptídeos. Todavia, os desafios à aplicação de peptóides são devidos a flexibilidade ocasionada pela perda das ligações de hidrogênio intra-cadeia principal e interconversão cis/trans à temperatura ambiente. A simulação molecular clássica de peptóides tem sido limitada pelos campos de força existentes que não permitem a rotação interna da ligação amida sem o uso de técnicas para melhorar a amostragem. Neste trabalho foi desenvolvido um conjunto de parâmetros para a simulação de peptóides que permitiu descrever corretamente as populações conformacionais cis/trans de unidades monomêricas, em comparação a dados de RMN. As simulações de oligômeros mostraram estruturas bastantes flexíveis, não condizentes com conclusões propostas a partir de espectros de dicroísmo circular, que tem atribuído estruturas helicoidais a estes oligômeros. Os resultados sugerem que as transições eletrônicas favorecidas pelas conformações cis são as principais responsáveis pelos espectros obtidos. Adicionalmente, simulações por dinâmica molecular foram utilizadas para caracterizar a adsorção de moléculas catecóis em superfícies minerais. Proteínas de pés de mexilhões inspiraram nossos colaboradores na síntese de dois tipos de moléculas: iniciadores acrilatos para aplicação em resinas odontológicas e surfactantes zwiteriônicos para transistores orgânicos de efeito de campo (OFETs). Dentre as moléculas sintetizadas, os catecóis apresentaram melhores resultados nas aplicações propostas e forte adesão a superfícies minerais. A modelagem molecular permitiu elucidar como mudanças na estrutura molecular de catecóis acrilatos e da superfície mineral afetaram a adsorção. Os nossos resultados mostraram ainda que a automontagem de monocamadas de catecóis zwiteriônicos é governada pelo balanço entre ligações de hidrogênio, interações entre anéis aromáticos e dessolvatação da superfície mineral. / Peptides and proteins bioinspired materials have wide range of scientific and technological applications. This work has focused on the description of dynamic and conformational properties of two biomimetics: peptoids and catechols. Peptoids are N-substituted glycine oligomers of biological interest due proteases resistance, higher thermal and environmental stability and easier synthesis, when compared to peptides. However, the flexibility caused by the lack of intra-backbone hydrogen bonds and cis/trans interconversion at room temperature represents the main challenge for applications based on structure-function relationship. Classical molecular simulation of peptoids has been limited by the existing force fields, which do not allow amide bond internal rotation without the use of enhanced sampling techniques. In this work, the development of a set of parameters for peptoids simulation allowed the correctly description of cis/trans conformational populations in monomeric units, when compared to NMR data. The oligomers simulations showed flexible structures and that are not consistent with the withdrawn conclusions from circular dichroism spectra that has attributed helical structures to these oligomers. The results suggested that electronic transitions favored by cis conformations are mainly responsible by the obtained spectra. In addition, molecular dynamics simulations were used to characterize the adsorption of catechol molecules on mineral surfaces. Mussel foot proteins inspired our coworkers to synthesize two types of molecules: acrylic primers for dental resins and zwitterionic surfactants for organic field effect transistors (OFETs). Among the synthesized molecules, catechols showed best results for the proposed applications and strongest adhesion on mineral surfaces. Molecular modeling allowed elucidating how changes in molecular structure of acrylic catechols and on mineral surface affected adsorption. Our results also showed that the self-assembling of zwiterionic catechol monolayers is governed by the balance between hydrogen bonds, interactions between aromatic rings and desolvation of the mineral surface.

Orientador: Yoshiyuki Hase / Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Quimica / Made available in DSpace on 2018-08-13T00:04:59Z (GMT). No. of bitstreams: 1 Sousa_Marcelode_M.pdf: 719258 bytes, checksum: c3faa35c86e3b8438789d2e27f5c2c51 (MD5) Previous issue date: 2008 / Resumo: Um novo método de correção de anarmonicidade está sendo proposto no atual trabalho em termos do campo de força. O objetivo deste método é simplificar a reprodução dos campos de força harmônicos, das freqüências harmônicas e da distribuição de energia potencial pela aplicação dos coeficientes de correção de anarmonicidade ao campo de força da análise de coordenadas normais. A simplificação proposta consiste em se agrupar os coeficientes segundo suas similaridades numéricas, reproduzindo resultados tão semelhantes quanto aos dos coeficientes não agrupados. Os coeficientes de correção de anarmonicidade agrupados e não agrupados foram calculados para o trans-ácido fórmico e aplicados aos campos de força do cis- e dímero da mesma molécula. Os resultados obtidos para as freqüências harmônicas para as espécies de trans-, cis- e dímero do ácido fórmico pelo método proposto foram muito similares àqueles obtidos método de Dennison / Abstract: A new anharmonicity correction method is proposed in this work. The aim of this method is to simplify the reprodution of the harmonic force fields, the harmonic frequencies and potential energy distribution by application of the anharmonicity correction coefficients to the normal coordinate analysis force field. The simplification proposed consists in grouping the coefficients according of their numerical similarities, producing results similar to those obtained without grouping. The grouping and non grouping anharmonicity correction coefficients were calculated for trans-formic acid and applied to the force fields of the cis- and dimer of this molecule. The results obtained for the harmonic frequencies for the trans-, cis- and dimer species by the proposed method are very close to those obtained Dennison method / Mestrado / Físico-Química / Mestre em Química

Abstract This thesis deals with infrared spectroscopy investigations on the linear DCCI molecule. The high resolution spectra between 200–5200 cm-1 were measured with the Fourier transform spectrometer at the University of Oulu. The spectra were analyzed taking into account various types of resonances between rovibrational energy levels. As a result, a set of molecular constants and resonance parameters describing the rotational and vibrational energy states of the molecule were obtained. From the resulting molecular constants, together with previous results from literature for HCCI, the structure of monoiodoacetylene was calculated. In addition, eight harmonic force constants with estimated uncertainties for monoiodoacetylene were determined.

Force fields of 3d objects are used for different purposes in computer graphics as skeletonization and collision detection. In this paper we present a novel method to approximate the force field of a discrete 3d object in linear time. Similar to the distance transformation we define a rule that describe how the forces associated with boundary points are propagated into the interior of the object. The result of this propagation depends on the order in which the points of the object are processed. Therefore we analyze how to obtain an order-invariant approximation formula. For a chosen iteration order (i, j, k) the set of boundary points that influence the force of a particular point p of the object can be described by a spatial region Rijk. The geometries of these regions are characterized both for the Cartesian and the body-centered cubic grid (bcc grid). We show that in the case of the bcc grid these regions can be combined in such a way that E3 is uniformly covered which basically means that each boundary point is contained in the same number of regions. Based on the covering an approximation formula for the force field is proposed that has linear complexity and gives good results for standard objects. We also show that such a uniform covering can not be built from the regions of influence of the Cartesian grid. With our method it becomes possible to use features of the force field for a fast and topology preserving skeletonization. We use a thinning strategy on the bcc grid to compute the skeleton and ensure that critical points of the force field are not removed. This leads to improved skeletons with respect to the properties of centeredness and rotational invariance.

Force field methods are used to investigate the properties of a wide variety of chemical systems on a routine basis. The expression for the electrostatic energy typically does not take into account the anisotropic nature of the atomic electron distribution or the dependence of that distribution on the system geometry. This has been suggested as a cause of the failure of force field methods to reliably predict the behaviour of chemical systems. A method for incorporation of anisotropy and polarisation is described in this work. Anisotropy is modelled by the inclusion of multipole moments centred at atoms whose values are determined by application of the methods of Quantum Chemical Topology. Polarisation, the dependence of the electron distribution on system geometry, is modelled by training machine learning models to predict atomic multipole moments from knowledge of the nuclear positions of a system. The resulting electrostatic method can be implemented for any chemical system. An application to progressively more complex systems is reported, including small organic molecules and larger molecules of biological importance. The accuracy of the method is rigorously assessed by comparison of its predictions to exact interaction energy values. A procedure for generating transferable atomic multipole moment models is defined and tested. The electrostatic method can be combined with the empirical expressions used in force field calculations to describe total system energies by fitting parameters against ab initio conformational energies. Derivatives of the energy are given and the resulting multipolar polarisable force field can be used to perform geometry optimisation calculations. Future applications to conformational searching and problems requiring dynamic descriptions of a system are feasible.

Chloroperoxidase (CPO) is a potential biocatalyst for use in asymmetric synthesis. The mechanisms of CPO catalysis are therefore of interest. The halogenation reaction, one of several chemical reactions that CPO catalyzes, is not fully understood and is the subject of this dissertation. The mechanism by which CPO catalyzes halogenation is disputed. It has been postulated that halogenation of substrates occurs at the active site. Alternatively, it has been proposed that hypochlorous acid, produced at the active site via oxidation of chloride, is released prior to reaction, so that halogenation occurs in solution. The free-solution mechanism is supported by the observation that halogenation of most substrates often occurs non-stereospecifically. On the other hand, the enzyme-bound mechanism is supported by the observation that some large substrates undergo halogenation stereospecifically. The major purpose of this research is to compare chlorination of the substrate beta-cyclopentanedione in the two environments. One study was of the reaction with limited hydration because such a level of hydration is typical of the active site. For this work, a purely quantum mechanical approach was used. To model the aqueous environment, the limited hydration environment approach is not appropriate. Instead, reaction precursor conformations were obtained from a solvated molecular dynamics simulation, and reaction of potentially reactive molecular encounters was modeled with a hybrid quantum mechanical/molecular mechanical approach. Extensive work developing parameters for small molecules was pre-requisite for the molecular dynamics simulation. It is observed that a limited and optimized (active-site-like) hydration environment leads to a lower energetic barrier than the fully solvated model representative of the aqueous environment at room temperature, suggesting that the stable water network near the active site is likely to facilitate the chlorination mechanism. The influence of the solvent environment on the reaction barrier is critical. It is observed that stabilization of the catalytic water by other solvent molecules lowers the barrier for keto-enol tautomerization. Placement of water molecules is more important than the number of water molecules in such studies. The fully-solvated model demonstrates that reaction proceeds when the instantaneous dynamical water environment is close to optimal for stabilizing the transition state.

Chalconas e flavonoides são compostos comumente presentes em plantas, e constituem uma grande família de produtos naturais com um amplo espectro de atividades farmacológicas. Mudanças na estrutura destas moléculas tem se provado úteis no desenvolvimento de novos agentes terapêuticos, sendo assim, esses compostos tem sido intensamente estudados. Métodos computacionais como a dinâmica molecular (DM) são ferramentas poderosas para o acesso a informações de difícil obtenção por outros meios experimentais. Campos de força acurados são essenciais para a descrição de sistemas biológicos em simulações de DM, assim, um conjunto de parâmetros associado a um composto necessita ser cuidadosamente calibrado para garantir a obtenção de resultados confiáveis. Considerando a relevância dessa família de moléculas e a falta de parâmetros validados para a estrutura básica de chalconas e flavonoides no campo de força GROMOS, o presente trabalho tem como objetivo prover um novo conjunto de parâmetros para a simulação destes compostos. Um protocolo que combina cálculos ab initio e simulações de DM foi aplicado para obter novas cargas atômicas e parâmetros torsionais Propriedades experimentais como densidade e entalpia de vaporização foram usadas como comparação aos valores obtidos em simulações, como forma de validação dos parâmetros. A comparação dos perfis torsionais obtidos por cálculos quânticos e por mecânica molecular auxiliou na geração de novos potenciais que permitem uma descrição conformacional mais acurada dos diedros de interesse. Diversos ajustes em grupos de cargas foram feitos, e os valores para propriedades termodinâmicas obtidos nas simulações estão em concordância com os dados experimentais. Simulações de metadinâmica foram realizadas para avaliar o comportamento conformacional de chalconas e flavonoides completos, e contatos de NOE foram medidos durante simulações de DM, obtendo uma reprodução quase completa das distâncias entre alguns grupos de prótons. O protocolo empregado gerou parâmetros de campo de força que reproduzem bem dados experimentais, e espera-se que estes resultados contribuam para a realização de estudos computacionais acurados envolvendo chalconas e flavonoides. / Chalcones and flavonoids are polyphenolic compounds extensively distributed in plants, constituting a large family of natural products with a broad spectrum of pharmacological activities. Changes in their structure have been proven useful for the development of new therapeutic agents, thus these biomolecules are being intensively studied and modified. Computational methods such as molecular dynamics (MD) simulations are powerful tools to assess information that is difficult to obtain experimentally. Accurate force fields are essential for describing biological systems in a MD simulation, thus a parameter set associated to a certain compound need to be carefully calibrated to ensure reliable results. Considering the relevance of this family of molecules and the lack of validated parameters for the basic structure of chalcones and flavonoids in the GROMOS force field, this work intends to provide a new parameter set for the simulation of these compounds. We employed a protocol combining ab initio calculations and MD simulations for the obtention of new atomic charges and torsional parameters Experimental properties such as density and enthalpy of vaporization were compared to the calculated values in order to validate the parameters. A fitting of molecular-mechanical to quantum-mechanical torsional profiles was performed for each of the dihedrals of interest in the structures, generating new torsional potentials that provide accurate description of conformational behavior. Additionally, adjustments in charge groups were made in topologies used for the MD simulations and the obtained values of the thermodynamic properties are in good agreement with experimental data. Metadynamics simulations were performed to evaluate the conformation of complete chalcones and flavonoids, and NOE contacts during MD simulations were measured, obtaining an almost complete reproduction of inter-proton interactions. The employed protocol generated force field parameters that reproduce well the target data and we expect they will contribute to more accurate computational studies on the biological role of chalcones and flavonoids.

In the search for a sustainable and environmentally friendly energy source, artificial photosynthesis has been proposed  as a promising solution. Using water as a substrate, solar energy can be utilised to store energy in the chemical form of hydrogen fuel. In part of this global scientific effort, this thesis work focuses on enabling molecular dynamics simulations of a particular set of ruthenium centred  water oxidation catalysts. The new catalysts show great success because of a binuclear  reaction  pathway in aqueous solution which makes it very interesting to model and investigate. Utilising quantum  mechanical tools, a set of molecular mechanics force field parameters for Ru-involved bonds, angles, torsions, and partial charges was successfully obtained and examined. The work allows future large scale simulation of water  oxidation and oxygen evolution in order to gain understanding and improve artificial photosynthesis.