Towards Accurate and Efficient Description of Excited States

Thesis (Ph.D.)--University of Washington, 2016-06

Leading coordinate analysis of reaction pathways in proton chain transfer: Application to a two-proton transfer model for the green fluorescent protein

The ‘leading coordinate’ approach to computing an approximate reaction pathway, with subsequent determination of the true minimum energy profile, is applied to a two-proton chain transfer model based on the chromophore and its surrounding moieties within the green fluorescent protein (GFP). Using an ab initio quantum chemical method, a number of different relaxed energy profiles are found for several plausible guesses at leading coordinates. The results obtained for different trial leading coordinates are rationalized through the calculation of a two-dimensional relaxed potential energy surface (PES) for the system. Analysis of the 2-D relaxed PES reveals that two of the trial pathways are entirely spurious, while two others contain useful information and can be used to furnish starting points for successful saddle-point searches. Implications for selection of trial leading coordinates in this class of proton chain transfer reactions are discussed, and a simple diagnostic function is proposed for revealing whether or not a relaxed pathway based on a trial leading coordinate is likely to furnish useful information.

Nuclear magnetic resonance studies of molecular interactions and structures

This thesis is concerned with the investigation, by nuclear magnetic resonance spectroscopy, of the molecular interactions occurring in mixtures of benzene and cyclohexane to which either chloroform or deutero-chloroform has been added. The effect of the added polar molecule on the liquid structure has been studied using spin-lattice relaxation time, 1H chemical shift, and nuclear Overhauser effect measurements. The main purpose of the work has been to validate a model for molecular interaction involving local ordering of benzene around chloroform. A chemical method for removing dissolved oxygen from samples has been developed to encompass a number of types of sample, including quantitative mixtures, and its supremacy over conventional deoxygenation technique is shown. A set of spectrometer conditions, the use of which produces the minimal variation in peak height in the steady state, is presented. To separate the general diluting effects of deutero-chloroform from its effects due to the production of local order a series of mixtures involving carbon tetrachloride, instead of deutero-chloroform, have been used as non-interacting references. The effect of molecular interaction is shown to be explainable using a solvation model, whilst an approach involving 1:1 complex formation is shown not to account for the observations. It is calculated that each solvation shell, based on deutero-chloroform, contains about twelve molecules of benzene or cyclohexane. The equations produced to account for the T1 variations have been adapted to account for the 1H chemical shift variations in the same system. The shift measurements are shown to substantiate the solvent cage model with a cage capacity of twelve molecules around each chloroform molecule. Nuclear Overhauser effect data have been analysed quantitatively in a manner consistent with the solvation model. The results show that discrete shells only exist when the mole fraction of deutero-chloroform is below about 0.08.

Isolado protéico de farelo de arroz: obtenção, propriedades funcionais e aplicação

O arroz é o segundo cereal mais produzido no mundo e para que ele seja consumido é necessário o processo de beneficiamento, onde é retirada a casca, e com o polimento, o farelo. O farelo, após a retirada do óleo, é utilizado para alimentação animal, mas como corresponde a 8% do grão, são necessárias novas alternativas para o uso do mesmo, uma vez que contém em torno de 17% de proteína. As proteínas do farelo de arroz são consideradas de alta qualidade, hipoalergênicas e anticancerígenas. Devido ao excesso de fibras presentes no farelo, este não é utilizado diretamente na alimentação humana, podendo ser usado como fonte para a obtenção de extratos, concentrados ou isolados. A obtenção do isolado protéico pode ser por via química, que consiste na extração alcalina ou ácida, seguida de precipitação no ponto isoelétrico ou via enzimática, com o uso de enzimas amilolíticas, hemicelulases e carboidrases para a separação das proteínas. O objetivo deste estudo foi obter um isolado protéico a partir de farelo de arroz visando a inclusão deste em produto de panificação. Foi obtido isolado protéico pelo método químico que foi analisado pelo rendimento protéico, pelas propriedades funcionais, perfil aminoacídico, eletroforese e características térmicas. O isolado foi adicionado em bolos em diferentes concentrações sendo avaliado pelas características tecnológicas e sensoriais. O isolado protéico do farelo de arroz (IPFA) que apresentou maior rendimento protéico foi o obtido pelo método químico, com o farelo de granulometria de 42 mesh e desengordurado. Em relação às propriedades funcionais, foi verificado que o IPFA possui maior solubilidade e capacidade de retenção de água em pH 11, alta capacidade emulsificante e alta capacidade de formação de espuma. No aminograma, constatou-se que os aminoácidos encontrados no IPFA atendem as necessidades de bebês e crianças. No perfil eletroforético, o IPFA apresentou 3 grupos de proteínas. Na análise térmica com DSC, o IPFA apresentou alta temperatura de desnaturação e baixo valor de entalpia. Na elaboração dos bolos, à medida que foi adicionado o IPFA, aumentou o teor protéico, o pH e o volume específico e diminuiu o colapso, a luminosidade e a firmeza dos bolos. Na análise sensorial, os bolos com IPFA não apresentaram diferenças estatísticas do bolo controle (sem IPFA). Estes resultados indicam a potencialidade do IPFA em produtos de panificação.

Avaliação da ação bioinseticida de SBTI e vicilina de Erythrina velutina em enzimas digestivas e membrana peritrófica de larvas de Plodia interpunctella (Lepidoptera: Pyralidae)

Plodia interpunctella (Indian meal moth) is a cosmopolitan pest that attacks not only a wide range of stored grain as well other food products. Due to its economic importance several researches have focused in a method with ability to control this pest with few or no damage to the environment. The study of digestive enzymes inhibitors, lectins and chitin-binding proteins, has often been proposed as an alternative to reduce insect damage. In this study we report the major classes of digestive enzymes during larval growth in P. Interpunctella, being those proteinases actives at pH 9.5 and optimum temperature of 50 oC to both larvae of the 3rd instar and pre-pupal stage of development. In vitro and zymogram assays presented the effects of several inhibitors, such as SBTI, TLCK and PMSF to intestinal homogenate of 3rd instar larvae of 62%, 92% and 87% of inhibition and In pre-pupal stage of 87%, 62 % and 55% of inhibition, respectively. Zymograms showed inhibition of two low molecular masses protein bands by TLCK and that in presence of SBTI were retarded. These results are indicative of predominance of digestive serine proteinases in gut homogenate from Plodia interpunctella larvae. This serine proteinase was then used as a target to evaluate the effect of SBTI on larvae in in vivo assay. Effect of SBTI on mortality and larval mass was not observed at until 4% of concentration (w/w) in diets. Chitin, another target to insecticidal proteins, was observed by chemical method. Moreover, optic microscopy confirmed the presence of a peritrophic membrane. Established this target, in vivo effect of EvV, a chitin binding vicilin, evaluated during the larval development of P. interpunctella and was obtained a LD50 of 0,23% and WD50 of 0,27% to this protein. Mechanism of action was proposed through of the in vivo digestibility of EvV methodology. During the passage through the larval digestive tract was observed that EvV was susceptible to digestive enzymes and a reactive fragment, visualized by Western blotting, produced by digestion was recovered after dissociation of the peritrophic membrane. The bound of EvV to peritrophic membrane was confirmed by immunohystochemical assays that showed strong immunofluorescent signal of EvV-FITC binding and peritrophic membrane. These results are a indicative that vicilins could be utilized as potential insecticide to Plodia interpunctella and a control methods using EvV as bioinsecticide should be studied to reduce lost caused by storage insect pests

Evolution of genome sequencing techniques

The quality and the speed for genome sequencing has advanced at the same time that technology boundaries are stretched. This advancement has been divided so far in three generations. The first-generation methods enabled sequencing of clonal DNA populations. The second-generation massively increased throughput by parallelizing many reactions while the third-generation methods allow direct sequencing of single DNA molecules. The first techniques to sequence DNA were not developed until the mid-1970s, when two distinct sequencing methods were developed almost simultaneously, one by Alan Maxam and Walter Gilbert, and the other one by Frederick Sanger. The first one is a chemical method to cleave DNA at specific points and the second one uses ddNTPs, which synthesizes a copy from the DNA chain template. Nevertheless, both methods generate fragments of varying lengths that are further electrophoresed. Moreover, it is important to say that until the 1990s, the sequencing of DNA was relatively expensive and it was seen as a long process. Besides, using radiolabeled nucleotides also compounded the problem through safety concerns and prevented the automation. Some advancements within the first generation include the replacement of radioactive labels by fluorescent labeled ddNTPs and cycle sequencing with thermostable DNA polymerase, which allows automation and signal amplification, making the process cheaper, safer and faster. Another method is Pyrosequencing, which is based on the “sequencing by synthesis” principle. It differs from Sanger sequencing, in that it relies on the detection of pyrophosphate release on nucleotide incorporation. By the end of the last millennia, parallelization of this method started the Next Generation Sequencing (NGS) with 454 as the first of many methods that can process multiple samples, calling it the 2º generation sequencing. Here electrophoresis was completely eliminated. One of the methods that is sometimes used is SOLiD, based on sequencing by ligation of fluorescently dye-labeled di-base probes which competes to ligate to the sequencing primer. Specificity of the di-base probe is achieved by interrogating every 1st and 2nd base in each ligation reaction. The widely used Solexa/Illumina method uses modified dNTPs containing so called “reversible terminators” which blocks further polymerization. The terminator also contains a fluorescent label, which can be detected by a camera. Now, the previous step towards the third generation was in charge of Ion Torrent, who developed a technique that is based in a method of “sequencing-by-synthesis”. Its main feature is the detection of hydrogen ions that are released during base incorporation. Likewise, the third generation takes into account nanotechnology advancements for the processing of unique DNA molecules to a real time synthesis sequencing system like PacBio; and finally, the NANOPORE, projected since 1995, also uses Nano-sensors forming channels obtained from bacteria that conducts the sample to a sensor that allows the detection of each nucleotide residue in the DNA strand. The advancements in terms of technology that we have nowadays have been so quick, that it makes wonder: ¿How do we imagine the next generation?

Efecto de la extirpación de las espículas del glande del cuy como técnia de esterilización reproductiva y su influencia en agresividad y ganancia de peso en comparación con un método químico alcohol yodado al 2%

La presente investigación evaluó el efecto de la extirpación de las espículas del glande en cobayos como método de esterilización reproductiva y su influencia en agresividad y ganancia de peso en comparación con un método químico (alcohol yodado 2%) y un testigo. Se contemplaron dos etapas de estudio, la primera valoró agresividad y ganancia de peso en 90 cuyes machos de 45 días de edad con peso promedio de 658,3±8,54gr los cuales fueron distribuidos en grupos de 5 animales por jaula; para la segunda etapa se consideró fertilidad y prolificidad en 90 cuyes hembras sexualmente maduras de 3 meses de edad, las cuales fueron empadradas con 18 machos obtenidos al azar de una sub-muestra de la primera etapa, la relación de empadre fue cinco hembras un macho. Los animales en estudio fueron distribuidos en los siguientes tratamientos: T1 animales enteros (n=30), T2 animales extirpados las espículas (n=30) y T3 animales castrados con alcohol yodado 2% (n=30). Los datos obtenidos fueron procesados y analizados en el programa SPSS® versión 22.0 determinándose que la ganancia total de peso fue para T1 836,4±33,89gr, T2 860,5±24,54gr y T3 725,5±30,45 con significancia estadística (P<0,05) para T2 y T1 con relación a T3. En referencia a agresividad medida a través del daño de la canal a nivel de la zona dorso posterior se obtuvieron resultados porcentuales estadísticos no significativos (p>0,05) entre tratamientos. En cuanto a fertilidad se obtuvo: para T1 un valor de 66,7%, T2 86,7% y T3 12% existiendo significancia estadística (p<0,05) entre tratamientos. Para la variable prolificidad se obtuvo valores medios de: T1 2,47±0,34; T2 3,43±0,32 y T3 0,40±0.22, con diferencias significativas (p<0,05) únicamente para el T3 que fue el que menos crías obtuvo. En conclusión la extirpación de las espículas del glande del cuy no esteriliza reproductivamente por el contrario aumenta el porcentaje de fertilidad, no disminuye agresividad, obtiene pesos no distintos al testigo pero alcanza mejores pesos que el método químico.

Estudo da síntese e propriedade magnética de ferritas de manganês/cobalto dopadas com níquel

For the chemical method of synthesis of co-precipitation were produced ferrite powders manganese-cobalt equal stoichiometric formula Mn (1-x) Co (x) Fe2O4, for 0 < x < 1, first reagent element using as the hydroxide ammonium and second time using sodium hydroxide. The obtained powders were calcined at 400 ° C, 650 ° C, 900 ° C and 1150 ° C in a conventional oven type furnace with an air atmosphere for a period of 240 minutes. Other samples were calcined at a temperature of 900 ° C in a controlled atmosphere of argon, to evaluate the possible influence of the atmosphere on the final results the structure and morphology. The samples were also calcined in a microwave oven at 400 ° C and 650 ° C for a period of 45 minutes possible to evaluate the performance of this type of heat treatment furnace. It was successfully tested the ability of this group include isomorphic ferrite with the inclusion of nickel cations in order to evaluate the occurrence of disorder in the crystalline structures and their changes in magnetic characteristics.To identify the structural, morphological, chemical composition and proportions, as well as their magnetic characteristics were performed characterization tests of X-ray diffraction (XRD), scanning electron microscopy (SEM), transmission electron microscopy (TEM), energy dispersive spectroscopy (EDX), thermogravimetric (TG), vibrating sample magnetometry (MAV) and Mössbauer spectroscopy. These tests revealed the occurrence of distortion in the crystal lattice, changes in magnetic response, occurrence of nanosized particles and superparamagnetism

Uptake and toxicity of copper oxide nanoparticles in C6 glioma cells

Copper oxide nanoparticles (CuO-NPs) are frequently used for many technical applications, but are also known for their cell toxic potential. In order to investigate a potential use of CuO-NPs as a therapeutic drug for glioma treatment, we have investigated the consequences of an application of CuO-NPs on the cellular copper content and cell viability of C6 glioma cells. CuO-NPs were synthesized by a wet-chemical method and were coated with dimercaptosuccinic acid and bovine serum albumin to improve colloidal stability in physiological media. Application of these protein-coated nanoparticles (pCuO-NPs) to C6 cells caused a strong time-, concentration- and temperature-dependent copper accumulation and severe cell death. The observed loss in cellular MTT-reduction capacity, the loss in cellular LDH activity and the increase in the number of propidium iodide-positive cells correlated well with the specific cellular copper content. C6 glioma cells were less vulnerable to pCuO-NPs compared to primary astrocytes and toxicity of pCuO-NPs to C6 cells was only observed for incubation conditions that increased specific cellular copper contents above 20 nmol copper per mg protein. Both cellular copper accumulation as well as the pCuO-NP-induced toxicity in C6 cells were prevented by application of copper chelators, but not by endocytosis inhibitors, suggesting that liberation of copper ions from the pCuO-NPs is the first step leading to the observed toxicity of pCuO-NP-treated glioma cells.

Improved ultra-performance liquid chromatography with electrospray ionization quadrupole-time-of-flight high-definition mass spectrometry method for the rapid analysis of the chemical constituents of a typical medical formula: Liuwei Dihuang Wan

Liuwei Dihuang Wan (LWD), a classic Chinese medicinal formulae, has been used to improve or restore declined functions related to aging and geriatric diseases, such as impaired mobility, vision, hearing, cognition and memory. It has attracted increasingly much attention as one of the most popular and valuable herbal medicines. However, the systematic analysis of the chemical constituents of LDW is difficult and thus has not been well established. In this paper, a rapid, sensitive and reliable ultra-performance liquid chromatography with electrospray ionization quadrupole time-of-flight high-definition mass spectrometry (UPLC-ESI-Q-TOF-MS) method with automated MetaboLynx analysis in positive and negative ion mode was established to characterize the chemical constituents of LDW. The analysis was performed on a Waters UPLCTM HSS T3 using a gradient elution system. MS/MS fragmentation behavior was proposed for aiding the structural identification of the components. Under the optimized conditions, a total of 50 peaks were tentatively characterized by comparing the retention time and MS data. It is concluded that a rapid and robust platform based on UPLC-ESI-Q-TOF-MS has been successfully developed for globally identifying multiple-constituents of traditional Chinese medicine prescriptions. This is the first report on systematic analysis of the chemical constituents of LDW. This article is protected by copyright. All rights reserved.

A Near-Infrared Reflectance Spectroscopy Method for Direct Analysis of Several Chemical Components and Properties of Fruit, for Example, Chinese Hawthorn

Near-infrared spectroscopy (NIRS) calibrations were developed for the discrimination of Chinese hawthorn (Crataegus pinnatifida Bge. var. major) fruit from three geographical regions as well as for the estimation of the total sugar, total acid, total phenolic content, and total antioxidant activity. Principal component analysis (PCA) was used for the discrimination of the fruit on the basis of their geographical origin. Three pattern recognition methods, linear discriminant analysis, partial least-squares-discriminant analysis, and back-propagation artificial neural networks, were applied to classify and compare these samples. Furthermore, three multivariate calibration models based on the first derivative NIR spectroscopy, partial least-squares regression, back-propagation artificial neural networks, and least-squares-support vector machines, were constructed for quantitative analysis of the four analytes, total sugar, total acid, total phenolic content, and total antioxidant activity, and validated by prediction data sets.

Efficient simulation of stochastic chemical kinetics with the Stochastic Bulirsch-Stoer extrapolation method

Background Biochemical systems with relatively low numbers of components must be simulated stochastically in order to capture their inherent noise. Although there has recently been considerable work on discrete stochastic solvers, there is still a need for numerical methods that are both fast and accurate. The Bulirsch-Stoer method is an established method for solving ordinary differential equations that possesses both of these qualities. Results In this paper, we present the Stochastic Bulirsch-Stoer method, a new numerical method for simulating discrete chemical reaction systems, inspired by its deterministic counterpart. It is able to achieve an excellent efficiency due to the fact that it is based on an approach with high deterministic order, allowing for larger stepsizes and leading to fast simulations. We compare it to the Euler τ-leap, as well as two more recent τ-leap methods, on a number of example problems, and find that as well as being very accurate, our method is the most robust, in terms of efficiency, of all the methods considered in this paper. The problems it is most suited for are those with increased populations that would be too slow to simulate using Gillespie’s stochastic simulation algorithm. For such problems, it is likely to achieve higher weak order in the moments. Conclusions The Stochastic Bulirsch-Stoer method is a novel stochastic solver that can be used for fast and accurate simulations. Crucially, compared to other similar methods, it better retains its high accuracy when the timesteps are increased. Thus the Stochastic Bulirsch-Stoer method is both computationally efficient and robust. These are key properties for any stochastic numerical method, as they must typically run many thousands of simulations.

A novel near-infrared spectroscopy and chemometrics method for rapid analysis of several chemical components and antioxidant activity of mint (mentha haplocalyx briq.) samples

A novel near-infrared spectroscopy (NIRS) method has been researched and developed for the simultaneous analyses of the chemical components and associated properties of mint (Mentha haplocalyx Briq.) tea samples. The common analytes were: total polysaccharide content, total flavonoid content, total phenolic content, and total antioxidant activity. To resolve the NIRS data matrix for such analyses, least squares support vector machines was found to be the best chemometrics method for prediction, although it was closely followed by the radial basis function/partial least squares model. Interestingly, the commonly used partial least squares was unsatisfactory in this case. Additionally, principal component analysis and hierarchical cluster analysis were able to distinguish the mint samples according to their four geographical provinces of origin, and this was further facilitated with the use of the chemometrics classification methods-K-nearest neighbors, linear discriminant analysis, and partial least squares discriminant analysis. In general, given the potential savings with sampling and analysis time as well as with the costs of special analytical reagents required for the standard individual methods, NIRS offered a very attractive alternative for the simultaneous analysis of mint samples.