Thesis (Ph. D.)--University of Chicago, Department of Chemistry, March 2001. / Includes bibliographical references. Also available on the Internet.

O grupo amida é encontrado em biomoléculas como as proteínas, ácidos nucleícos, bem como em polímeros sintéticos. A molécula mais simples que contém o grupamento amida é a formamida. Um grande número de estudos sobre essa molécula tem sido realizados no vácuo, no estado líquido e em solventes utilizando-se as mais diferentes técnicas experimentais e computacionais, mas ainda restam questões fundamentais sobre a sua estrutura eletrônica e solvatação. O conhecimento preciso da ressonância e das barreiras conformacionais desse composto é de fundamental importância para uma compreensão do comportamento conformacional de biomoléculas e polímeros sintéticos. Uma compreensão detalhada das interações dessa molécula com água é igualmente importante, pois o grupamento amida é um dos principais sítios de hidratação de proteínas. Este trabalho teve o objetivo de se estudar as interações existentes entre a formamida e água, nas formas de mínima energia e nos estados de transição do grupo amida, e as alterações na estrutura eletrônica da formamida. Constatou-se a existência de grandes diferenças entre a estrutura eletrônica da formamida na sua forma mais estável e a dos estados de transição da rotação do grupo amida. Através do método NBO (Natural Bond Orbitals), verificou-se uma diminuição nos efeitos de ressonância nos estados de transição provocada pela diminuição da interação entre o par de elétrons isolados do nitrogênio e o orbital 'pi' antiligante do grupo carbonila (nN→'pi'*CO). A hidratação provocou alterações na estrutura eletrônica da formamida planar e dos estados de transição. As interações intermoleculares entre formamida e água foram intensas, sobretudo nos casos em que o solvente interagiu simultaneamente com os grupos carbonila e amida. Nos estados de transição, a interação entre o par de elétrons isolado do nitrogênio da amida e a molécula de água se torna importante. As energias das ligações de hidrogênio entre a formamida e as moléculas de água são, de um modo geral, estabilizadoras das supermoléculas. Pode-se verificar que há cooperatividade apenas nas energias e não em outras propriedades. Com o auxílio das análises NBO (Natural Bond Orbitals) e NRT (Natural Resonance Theory), verificou-se um aumento da ressonância da formamida planar com a adição sucessiva de moléculas de água. Tal observação pode sugerir que as ligações de hidrogênio entre formamida e água possuem algum caráter covalente. O estudo da solvatação da formamida utilizando o modelo discreto/contínuo demonstrou que as moléculas de água explícitas exercem larga influência na energia livre de solvatação. Constatou-se a preferência pela solvatação no oxigênio do grupo carbonila e a validade do modelo discreto/contínuo. / The amide group is found in biomolecules such as proteins, nucleic acids, as well as synthetic polymers. The simplest molecule that contains the amide group is formamide. A large number of studies have been made on vacuum, liquid state and on various solvents, using the most different computational and experimental techniques, but there are many fundamental questions to be answered about its electronic structure and solvation. The precise knowledge about resonance and conformational barriers of this compound is of fundamental importance for the understanding of conformational behavior of biomolecules and synthetic polymers. A detailed understanding about the interactions of this molecule with water is equally important, for the amide group is one of the major sites of solvation in proteins. This work has the objective of studying the interactions of formamide and water, on the minimum energy conformation and the transition conformations of the amide group and the electronic structure of formamide. It has been found the existence of great differences between the electronic structure of formamide on its more stable conformation and the conformational transition states of the amide group rotation. Using the Natural Bond Orbital (NBO) analysis, a decrease of resonance effects on the transitions states was verified, due to the loss of interaction between the electrons of the nitrogen lone pair and the carbonyl 'pi' anti-bonding orbital (nN→'pi'*CO). The solvation of formamide has changed the electronic structure of planar formamide and the conformational transition states. The intermolecular interactions between planar formamide and water are very strong, specially when the solvent molecules interact simultaneously with the carbonyl and amide groups. Regarding the conformational transition states, the interaction between the nitrogen lone pairs of amide and the water molecule is observed. The hydrogen bond energies of formamide and water stabilizes the supermolecules. It can be verified that there is cooperativity only with energies and not in other properties. Using the NBO and the Natural Resonance Theory (NRT) methods, an increase of resonance for the planar form with the successive addition of water molecules has been verified. This observation suggests that the hydrogen bonds between formamide and water have some covalent character. The solvation study of formamide using the discrete/continuous model shows that the explicit waters influence the free energy of solvation. A preference for the solvation of carbonyl oxygen and the validity of the discret/continuous model has been verified.

The current environmental situation, with respect to global warming and the ever– approaching depletion of fossil fuel sources, places significance on the development of green fuel and platform chemical production methods. In this context, processes that utilise biomass sources as feedstock, are of great interest. Cellulose, which is the most abundant biopolymer in nature, is a renewable low–cost carbon resource derived from harvest residues and sources like wood and straw. Glucose generation from cellulose requires a saccharide conversion, whereby the β-(1,4)-glycosidic bond linkages in the cellobiose polymer repeating units are cleaved. Problems arise in the hydrolysis of cellulose as experimental and theoretical studies have shown cellulose to have very low solubility in water and most other general molecular solvents. This results in the use of harsh pretreatments at high temperatures and pressures to extract cellulose from lignocellulosic material and strong acids catalysts (pKa < −3.2). Room temperature ionic liquids (RTILs) provide potentially environmentally friendly alternative. It has been shown that ILs can dissolve cellulose under relatively benign conditions and can possibly be adapted into a one-pot-like process of hydrolysis using acid-functionalised IL catalysts. This dissertation investigated the effect of various ionic liquids on the thermodynamics of cellobiose acid hydrolysis, as both a catalyst and as a solvent, using computational means. An appropriate thermodynamic cycle protocol, a DLPNO-CCSD(T)/ccpVTZ//TPSS/def2-TZVP [M05-2X/6-31+G** (SMD)] proton exchange cycle, was established through benchmarking for the prediction of Brønsted acid-functionalised ionic liquid pKa values in ionic liquids. The sulfonyl-functionalised acidic IL was shown to be the most acidic IL resulting in a lower protonation free energy. Solvation in ionic liquids resulted in higher protonation and barrier height free energies relative to solvation in water. The current environmental situation, with respect to global warming and the ever– approaching depletion of fossil fuel sources, places significance on the development of green fuel and platform chemical production methods. In this context, processes that utilise biomass sources as feedstock, are of great interest. Cellulose, which is the most abundant biopolymer in nature, is a renewable low–cost carbon resource derived from harvest residues and sources like wood and straw. Glucose generation from cellulose requires a saccharide conversion, whereby the β-(1,4)-glycosidic bond linkages in the cellobiose polymer repeating units are cleaved. Problems arise in the hydrolysis of cellulose as experimental and theoretical studies have shown cellulose to have very low solubility in water and most other general molecular solvents. This results in the use of harsh pretreatments at high temperatures and pressures to extract cellulose from lignocellulosic material and strong acids catalysts (pKa < −3.2). Room temperature ionic liquids (RTILs) provide potentially environmentally friendly alternative. It has been shown that ILs can dissolve cellulose under relatively benign conditions and can possibly be adapted into a one-pot-like process of hydrolysis using acid-functionalised IL catalysts. This dissertation investigated the effect of various ionic liquids on the thermodynamics of cellobiose acid hydrolysis, as both a catalyst and as a solvent, using computational means. An appropriate thermodynamic cycle protocol, a DLPNO-CCSD(T)/ccpVTZ//TPSS/def2-TZVP [M05-2X/6-31+G** (SMD)] proton exchange cycle, was established through benchmarking for the prediction of Brønsted acid-functionalised ionic liquid pKa values in ionic liquids. The sulfonyl-functionalised acidic IL was shown to be the most acidic IL resulting in a lower protonation free energy. Solvation in ionic liquids resulted in higher protonation and barrier height free energies relative to solvation in water.

No description available.

Calculating the solvation energies of surfactants is a way to predict the cmc. The solvation energies were determined for a homologous series of betaines, (CH₃)₃N+(CH₂)nCOO- where n = 1 to 6. Their structure is composed of only the hydrophilic head group of a surfactant. The solvation energies were determined from both the gas phase energy and free energy of solution. Conformational analysis was performed on each molecule to locate the lowest energy structures and determine the Boltzmann population of each conformation for each molecule. The final solvation energies for each molecule are expectation values based on their energies and Boltzmann populations. The plotted solvation energies versus n form a parabolic curve that is similar to the literature cmc data where the betaine has a long hydrocarbon tail. However, the solvation energies peak at n = 3 and the cmc data peaks at n = 4. The dipole moments were also examined. The gas phase dipole moments were graphed and have a maximum at n = 3, similar to the solvation energy. The solution dipole moments have a linear graph, not comparable to the solvation energies. Therefore, the stability of the gas phase structures contributes more to the final solvation energy than the stability of the molecule in water. The correlation between the plots of log cmc vs n and solvation energy vs n indicates that it is possible to computationally predict the cmc with this method. The hydrophobic contribution can be accounted for based on a known correlation between chain length and the cmc, and the hydrophilic contribution can be examined with this method. Therefore, it is possible to design a new surfactant molecule that has a cmc within the range of the biological activity to be sent for synthesis. / Master of Science

In this experiment, more than one hundred volatile organic compounds were analyzed with the gas chromatograph. Six capillary columns ZB wax plus, ZB 35, TR1MS, TR5, TG5MS and TG1301MS with different polarities have been used for separation of compounds and illicit drugs. The Abraham solvation model has five solute descriptors. The solute descriptors are E, S, A, B, L (or V). Based on the six stationary phases, six equations were constructed as a training set for each of the six columns. The six equations served to calculate the solute descriptors for a set of illicit drugs. Drugs studied are nicotine (S= 0.870, A= 0.000, B= 1.073), oxycodone(S= 2.564. A= 0.286, B= 1.706), methamphetamine (S= 0.297, A= 1.570, B= 1.009), heroin (S=2.224, A= 0.000, B= 2.136) and ketamine (S= 1.005, A= 0.000, B= 1.126). The solute property of Abraham solvation model is represented as a logarithm of retention time, thus the logarithm of experimental and calculated retention times is compared.

One of the essential requirements of biomolecular modeling is an accurate description of water as a solvent. The challenge is to make this description computationally facile -- reasonably fast, simple, robust and easy to incorporate into existing software packages, yet accurate. The most rigorous procedure to model the effect of aqueous solvent is to explicitly model every water molecule in the system. For many practical applications, this approach is computationally too intense, as the number of required water atoms is on an average at least one order of magnitude larger than the number of atoms of the molecule of interest. Implicit solvent models, in which solvent molecules are replaced by a continuous dielectric, have become a popular alternative to explicit solvent methods. However, implicit solvation models often lack various microscopic details which are crucial for accuracy. One such missing effect that is currently missing from popular implicit models is the so called effect of charge hydration asymmetry (CHA). The missing effect of charge hydration asymmetry -- the asymmetric response of water upon the sign of solute charge -- manifests a characteristic, strong dependence of solvation free energies on the sign of solute charge. Here, we incorporate this missing effect into the continuum solvation framework via the conceptually simplest Born equation and also in the generalized Born model. We identify the key electric multipole moments of model water molecules critical for the various degrees of CHA effect observed in studies based on molecular dynamics simulations using different rigid water models. We then use this gained insight to incorporate CHA first into the Born model, and then into the generalized Born model. The proposed framework significantly improves accuracy of the hydration free energy estimates tested on a comprehensive set of varied molecular solutes -- monovalent and divalent ions, small drug-like molecules, charged and uncharged amino acid dipeptides, and small proteins. We finally develop a methodology to resolve the issue with unacceptably large uncertainty that stems from a variety of fundamental and technical difficulties in experimental quantification of CHA from charged solutes. Using the proposed corrections in the continuum framework, we untangle the charge-asymmetric response of water from its symmetric response, and further circumvent the difficulties by extracting accurate estimate propensity of water to cause CHA from accurate experimental hydration free energies of neutral polar molecules. We show that the asymmetry in water's response is strong, about 50% of the symmetric response. / Ph. D.

Concerns over industrial emissions and nuclear waste have led to the need to study ways to sequester industrial gasses, and recycle nuclear fuel. Two projects were done to study solvent systems for these two problems using computational methods. Current methods for SO₂ sequestration are wasteful in that the gasses cannot be extracted from the solvent, and the solvent cannot be reused. One possible solution, which this work focuses on, is the use of an ionic liquid as a sequestration agent for the adsorption of SO₂. Separation technology for heavy elements has not changed for over 60 years and issues with radiation contamination and low efficiency lead to high solvent waste. Biphasic alkane-water extraction systems are a possible solution as they have been used for the extraction of heavy elements. This work focuses on characterizing the factors that control partitioning in biphasic systems which increase extraction efficiency.

Modeling systems in liquid is imperative to chemistry, as many reactions take place in liquid, and nearly all of biochemistry is in the liquid state. Solvation Model 12 (SM12) is the newest Generalized Born Approximation iteration of a series of solvation models from Minnesota, it shows great promise for accurate, description of solutions. Shown is the full implementation of SM12 in to the pure Slater Type Orbital code, the Amsterdam Density Functional (ADF) package in particular. The model performs as well as its Gaussian Type Orbital counterpart. The model has been extended to account for periodic boundary conditions, as presented by the ADF-BAND code. The extension to infinite boundaries creates interesting edge effects that need to be taken into consideration, and are accounted for through cut off approximations and a screening function to ensure the potential is well-behaved. / October 2016

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.