Monte Carlo and molecular dynamics simulations of methane in potassium montmorillonite clay hydrates at elevated pressures and temperatures

The structure and dynamics of methane in hydrated potassium montmorillonite clay have been studied under conditions encountered in sedimentary basin and compared to those of hydrated sodium montmorillonite clay using computer simulation techniques. The simulated systems contain two molecular layers of water and followed gradients of 150 barkm-1 and 30 Kkm-1 up to a maximum burial depth of 6 km. Methane particle is coordinated to about 19 oxygen atoms, with 6 of these coming from the clay surface oxygen. Potassium ions tend to move away from the center towards the clay surface, in contrast to the behavior observed with the hydrated sodium form. The clay surface affinity for methane was found to be higher in the hydrated K-form. Methane diffusion in the two-layer hydrated K-montmorillonite increases from 0.39×10-9 m2s-1 at 280 K to 3.27×10-9 m2s-1 at 460 K compared to 0.36×10-9 m2s-1 at 280 K to 4.26×10-9 m2s-1 at 460 K in Na-montmorillonite hydrate. The distributions of the potassium ions were found to vary in the hydrates when compared to those of sodium form. Water molecules were also found to be very mobile in the potassium clay hydrates compared to sodium clay hydrates. © 2004 Elsevier Inc. All All rights reserved.

Dynamic complexity of chaotic transitions in high-dimensional classical dynamics:Leu-Enkephalin folding

Leu-Enkephalin in explicit water is simulated using classical molecular dynamics. A ß-turn transition is investigated by calculating the topological complexity (in the "computational mechanics" framework [J. P. Crutchfield and K. Young, Phys. Rev. Lett., 63, 105 (1989)]) of the dynamics of both the peptide and the neighbouring water molecules. The complexity of the atomic trajectories of the (relatively short) simulations used in this study reflect the degree of phase space mixing in the system. It is demonstrated that the dynamic complexity of the hydrogen atoms of the peptide and almost all of the hydrogens of the neighbouring waters exhibit a minimum precisely at the moment of the ß-turn transition. This indicates the appearance of simplified periodic patterns in the atomic motion, which could correspond to high-dimensional tori in the phase space. It is hypothesized that this behaviour is the manifestation of the effect described in the approach to molecular transitions by Komatsuzaki and Berry [T. Komatsuzaki and R.S. Berry, Adv. Chem. Phys., 123, 79 (2002)], where a "quasi-regular" dynamics at the transition is suggested. Therefore, for the first time, the less chaotic character of the folding transition in a realistic molecular system is demonstrated. © Springer-Verlag Berlin Heidelberg 2006.

Controlled growth of carbon nanotubes for high performance nanoelectronics

Unique electrical and mechanical properties of single-walled carbon nanotubes (SWNTs) have made them one of the most promising candidates for next-generation nanoelectronics. Efficient utilization of the exceptional properties of SWNTs requires controlling their growth direction (e.g., vertical, horizontal) and morphologies (e.g., straight, junction, coiled). ^ In this dissertation, the catalytic effect on the branching of SWNTs, Y-shaped SWNTs (Y-SWNTs), was investigated. The formation of Y-shaped branches was found to be dependent on the composition of the catalysts. Easier carbide formers have a strong tendency to attach to the sidewall of SWNTs and thus enhance the degree of branching. Y-SWNTs based field-effect transistors (FETs) were fabricated and modulated by the metallic branch of the Y-SWNTs, exhibiting ambipolar characteristics at room temperature. A subthreshold swing of 700 mV/decade and an on/off ratio of 105 with a low off-state current of 10-13 A were obtained. The transport phenomena associated with Y- and cross-junction configurations reveals that the conduction mechanism in the SWNT junctions is governed by thermionic emission at T > 100 K and by tunneling at T < 100 K. ^ Furthermore, horizontally aligned SWNTs were synthesized by the controlled modification of external fields and forces. High performance carbon nanotube FETs and logic circuit were demonstrated utilizing the aligned SWNTs. It is found that the hysteresis in CNTFETs can be eliminated by removing absorbed water molecules on the CNT/SiO2 interface by vacuum annealing, hydrophobic surface treatment, and surface passivation. SWNT “serpentines” were synthesized by utilization of the interaction between drag force from gas flow and Van der Waals force with substrates. The curvature of bent SWNTs could be tailored by adjusting the gas flow rate, and changing the gas flow direction with respect to the step-edges on a single-crystal quartz substrate. Resistivity of bent SWNTs was observed to increase with curvature, which can be attributed to local deformations and possible chirality shift at curved part. ^ Our results show the successful synthesis of SWNTs having controllable morphologies and directionality. The capability of tailoring the electrical properties of SWNTs makes it possible to build an all-nanotube device by integrating SWNTs, having different functionalities, into complex circuits. ^

X-Ray Diffraction of Highway Materials, HR-128, 1969

X-ray diffraction data during adsorption of water vapor on Na- and Ca-montmorillonites show that interlayer expansion is continuous but nonuniform. X-ray and adsorption isotherm data indicate an ice-like configuration of water molecules is completed with the fourth layer of interlayer water for the Ca-clay; a fifth layer intrudes to give a less ordered structure. Data for the Na-clay indicate a laminar stacking arrangement for up to three layers of interlayer water. The Na-clay adsorbs more than twice as much water and undergoes four times as large a volume change than the Ca-clay. The free energy change during adsorption of water vapor on the Ca-clay is nearly twice that for the Na-clay. Free energy changes with increasing relative pressure reflect interlayer expansion increments.

Tractographie de la matière blanche orientée par a priori anatomiques et microstructurels = White matter tractography guided by anatomical and microstructural priors

Résumé : L'imagerie par résonance magnétique pondérée en diffusion est une modalité unique sensible aux mouvements microscopiques des molécules d'eau dans les tissus biologiques. Il est possible d'utiliser les caractéristiques de ce mouvement pour inférer la structure macroscopique des faisceaux de la matière blanche du cerveau. La technique, appelée tractographie, est devenue l'outil de choix pour étudier cette structure de façon non invasive. Par exemple, la tractographie est utilisée en planification neurochirurgicale et pour le suivi du développement de maladies neurodégénératives. Dans cette thèse, nous exposons certains des biais introduits lors de reconstructions par tractographie, et des méthodes sont proposées pour les réduire. D'abord, nous utilisons des connaissances anatomiques a priori pour orienter la reconstruction. Ainsi, nous montrons que l'information anatomique sur la nature des tissus permet d'estimer des faisceaux anatomiquement plausibles et de réduire les biais dans l'estimation de structures complexes de la matière blanche. Ensuite, nous utilisons des connaissances microstructurelles a priori dans la reconstruction, afin de permettre à la tractographie de suivre le mouvement des molécules d'eau non seulement le long des faisceaux, mais aussi dans des milieux microstructurels spécifiques. La tractographie peut ainsi distinguer différents faisceaux, réduire les erreurs de reconstruction et permettre l'étude de la microstructure le long de la matière blanche. Somme toute, nous montrons que l'utilisation de connaissances anatomiques et microstructurelles a priori, en tractographie, augmente l'exactitude des reconstructions de la matière blanche du cerveau.

Investigations into the mechanism of orotidine 5'-monophosphate decarboxylase: Sources of substrate destabilization and transition state stabilization

Orotidine 5′-monophosphate decarboxylase (OMPDC) achieves a rarely paralleled rate acceleration, yet the catalytic basis prompting this enhancement have yet to be fully elucidated. To accomplish decarboxylation, OMPDC must overcome the high energy barrier due to the localized anionic charge of the intermediate. Mechanistic studies employing enzyme mutagenesis and product or intermediate analogues were used to investigate possible transition state stabilization by a carbene resonance structure. Viability of the carbene structure depends upon a key hydrogen bond between O4 of the substrate and the amide backbone of a conserved serine or threonine. Substitution of the conserved residue with Pro resulted in a kcat/KM of 1 M-1s-1; deletion of the FUMP O4 resulted in a product analogue that does not undergo H6 exchange or inhibit decarboxylation. Hence, indirect evidence reveals the O4-backbone interaction plays an important role for binding and catalysis. OMPDC likely has honed multiple mechanisms to attain its remarkable catalysis. The successful crystallizations of OMPDC a decade ago sparked hypotheses that structure and sequence conserved residues induced productive strain on the substrate-enzyme complex. Here, we demonstrate a new source of stress: a hydrophobic pocket adjacent to the OMP carboxylate that exhibits kinetic parameters characteristic of substrate destabilization. Substitution of these residues with hydrophilic side-chains, by providing hydrogen-bonding partners, decreased kcat by 10 to 10^4–fold. The same substitutions display very little change in the rate of product H6 exchange, supporting that this hydrophobic pocket affects the substrate-enzyme complex before the transition state. We also provide evidence that hydrophilic residues can insert water molecules into the pocket with detrimental effects to catalysis.

Synthesis and structural stability of metal-organic frameworks

Metal-organic frameworks (MOFs) have attracted significant attention during the past decade due to their high porosity, tunable structures, and controllable surface functionalities. Therefore many applications have been proposed for MOFs. All of them however are still in their infancy stage and have not yet been brought into the market place. In this thesis, the background of the MOF area is first briefly introduced. The main components and the motifs of designing MOFs are summarized, followed by their synthesis and postsynthetic modification methods. Several promising application areas of MOFs including gas storage and separation, catalysis and sensing are reviewed. The current status of commercialization of MOFs as new chemical products is also summarized. Examples of the design and synthesis of two new MOF structures Eu(4,4′,4′′,4′′′-(porphine-5,10,15,20-tetrayl)tetrakis(benzoic acid))·2H2O∙xDMF and Zn4O(azobenzene-4,4’-dicarboxylic acid)3∙xNMP are described. The first one contains free-base porphyrin centers and the second one has azobenzene components. Although the structures were synthesized as designed, unfortunately they did not possess the expected properties. The research idea to use MOFs as template materials to synthesize porous polymers is introduced. Several methods are discussed to grow PMMA into IRMOF-1 (Zn4O(benzene-1,4-dicarboxylate)3, IR stands for isoreticular) structure. High concentration of the monomers resulted in PMMA shell after MOF digestion while with low concentration of monomers no PMMA was left after digestion due to the small iii molecular weight. During the study of this chapter, Kitagawa and co-workers published several papers on the same topic, so this part of the research was terminated thereafter. Many MOFs are reported to be unstable in air due to the water molecules in air which greatly limited their applications. By incorporating a number of water repelling functional groups such as trifluoromethoxy group and methyl groups in the frameworks, the water stability of MOFs are shown to be significantly enhanced. Several MOFs inculding Banasorb-22 (Zn4O(2-trifluoromethoxybenzene-1,4-dicarboxylate)3), Banasorb-24 (Zn4O(2, 5-dimethylbenzene-1,4-dicarboxylate)3) and Banasorb-30 (Zn4O(2-methylbenzene-1,4-dicarboxylate)3) were synthesized and proved to have isostructures with IRMOF-1. Banasorb-22 was stable in boiling water steam for one week and Banasorb-30’s shelf life was over 10 months under ambient condition. For comparison, IRMOF-1’s structure collapses in air after a few hours to several days. Although MOF is a very popular research area nowadays, only a few studies have been reported on the mechanical properties of MOFs. Many of MOF’s applications involve high pressure conditions, so it is important to understand the behavior of MOFs under elivated pressures. The mechanical properties of IRMOF-1 and a new MOF structure Eu2(C12N2O4H6)3(DEF)0.87(H2O)2.13 were studied using diamond anvil cells at Advanced Photon Source. IRMOF-1 experienced an irriversible phase transtion to a nonporous phase followed by amorphization under high pressure. Eu2(C12N2O4H6)3(DEF)0.87(H2O)2.13 showed reversible compression under pressure up to 9.08GPa.

Desenvolvimento de magnetizador para tratamento magnético da água

Dissertação (mestrado)—Universidade de Brasília, Faculdade Gama, Programa de Pós-Graduação em Engenharia Biomédica, 2015.

INVESTIGATION OF MAGNESIUM ION CHARGE STORAGE MECHANISM IN MANGANESE DIOXIDE

Magnesium (Mg) battery is considered as a promising candidate for the next generation battery technology that could potentially replace the current lithium (Li)-ion batteries due to the following factors. Magnesium possesses a higher volumetric capacity than commercialized Li-ion battery anode materials. Additionally, the low cost and high abundance of Mg compared to Li makes Mg batteries even more attractive. Moreover, unlike metallic Li anodes which have a tendency to develop a dendritic structure on the surface upon the cycling of the battery, Mg metal is known to be free from such a hazardous phenomenon. Due to these merits of Mg as an anode, the topic of rechargea¬ble Mg batteries has attracted considerable attention among researchers in the last few decades. However, the aforementioned advantages of Mg batteries have not been fully utilized due to the serious kinetic limitation of Mg2+ diffusion process in many hosting compounds which is believed to be due to a strong electrostatic interaction between divalent Mg2+ ions and hosting matrix. This serious kinetic hindrance is directly related to the lack of cathode materials for Mg battery that provide comparable electrochemical performances to that of Li-based system. Manganese oxide (MnO2) is one of the most well studied electrode materials due to its excellent electrochemical properties, including high Li+ ion capacity and relatively high operating voltage (i.e., ~ 4 V vs. Li/Li+ for LiMn2O4 and ~ 3.2 V vs. Mg/Mg2+). However, unlike the good electrochemical properties of MnO2 realized in Li-based systems, rather poor electrochemical performances have been reported in Mg based systems, particularly with low capacity and poor cycling performances. While the origin of the observed poor performances is believed to be due to the aforementioned strong ionic interaction between the Mg2+ ions and MnO2 lattice resulting in a limited diffusion of Mg2+ ions in MnO2, very little has been explored regarding the charge storage mechanism of MnO2 with divalent Mg2+ ions. This dissertation investigates the charge storage mechanism of MnO2, focusing on the insertion behaviors of divalent Mg2+ ions and exploring the origins of the limited Mg2+ insertion behavior in MnO2. It is found that the limited Mg2+ capacity in MnO2 can be significantly improved by introducing water molecules in the Mg electrolyte system, where the water molecules effectively mitigated the kinetic hindrance of Mg2+ insertion process. The combination of nanostructured MnO2 electrode and water effect provides a synergic effect demonstrating further enhanced Mg2+ insertion capability. Furthermore, it is demonstrated in this study that pre-cycling MnO2 electrodes in water-containing electrolyte activates MnO2 electrode, after which improved Mg2+ capacity is maintained in dry Mg electrolyte. Based on a series of XPS analysis, a conversion mechanism is proposed where magnesiated MnO2 undergoes a conversion reaction to Mg(OH)2 and MnOx and Mn(OH)y species in the presence of water molecules. This conversion process is believed to be the driving force that generates the improved Mg2+ capacity in MnO2 along with the water molecule’s charge screening effect. Finally, it is discussed that upon a consecutive cycling of MnO2 in the water-containing Mg electrolyte, structural water is generated within the MnO2 lattice, which is thought to be the origin of the observed activation phenomenon. The results provided in this dissertation highlight that the divalency of Mg2+ ions result in very different electrochemical behaviors than those of the well-studied monovalent Li+ ions towards MnO2.

Proton conductivity and luminiscence properties of lanthanide aminotriphosphonates

Metal phosphonates are multifunctional solids with tunable properties, such as internal H-bond networks, and high chemical and thermal stability [1]. In the present work, we describe the synthesis, structural characterization, luminescent properties and proton conduction performance of a new family of isostructural cationic compounds with general formula [Ln(H4NMP)(H2O)2]Cl·2H2O [Ln = La3+, Pr3+, Sm3+, Gd3+, Tb3+, Dy3+, Ho3+, H6NMP = nitrilotris(methylphosphonic acid)]. These solids are formed by positively charge layers, which consist of isolated LnO8 polyhedra and bridge chelating NMP2- ligands, held apart by chloride ions and water molecules. This arrangement result in extended interlayer hydrogen networks with possible proton transfer pathways. The proton conductivity of Gd3+ sample, selected as prototype of the series, was measured. In the range between range 25º and 80 ºC, the conductivity increase with the temperature up to a maximum value of 3.10-4 S·cm-1, at relative humidity of 95 %. The activation energy obtained from the Arrhenius plot (Figure 1) is in the range corresponding to a Grotthuss transfer mechanism.

Synthesis of waterborne polyurethane-urea dispersions with chain extension step in homogeneous and heterogeneous media

Hypothesis: The possibility of tailoring the final properties of environmentally friendly waterborne polyurethane and polyurethane-urea dispersions and the films they produce makes them attractive for a wide range of applications. Both the reagents content and the synthesis route contribute to the observed final properties. Experiments: A series of polyurethane-urea and polyurethane aqueous dispersions were synthesized using 1,2-ethanediamine and/or 1,4-butanediol as chain extenders. The diamine content was varied from 0 to 4.5 wt%. Its addition was carried out either by the classical heterogeneous reaction medium (after phase inversion step), or else by the alternative homogeneous medium (prior to dispersion formation). Dispersions as well as films prepared from dispersions have been later extensively characterized. Findings: 1,2-Ethanediamine addition in heterogeneous medium leads to dispersions with high particle sizes and broad distributions whereas in homogeneous medium, lower particle sizes and narrow distributions were observed, thus leading to higher uniformity and cohesiveness among particles during film formation. Thereby, stress transfer is favored adding the diamine in a homogeneous medium; and thus the obtained films presented quite higher stress and modulus values. Furthermore, the higher uniformity of films tends to hinder water molecules transport through the film, resulting, in general, in a lower water absorption capacity.

Porous self-protonating spiropyran-based NIPAAm gels with improved reswelling kinetics

The final publication is available at Springer via http://dx.doi.org/[10.1007/s10853-015-9458-2]

Poli-líquidos iônicos e complexos solúveis de Eu3+ e Tb3+ : bioimageamento celular seletivo

Dissertação (mestrado)—Universidade de Brasília, Instituto de Química, Programa de Pós-Graduação em Química, 2015.

Radioprotective effect and other biological benefits associated with flavonoids

Ionizing radiation has the potential to cause extensive damage to living organisms. It can directly act on DNA, proteins and lipids, resulting in ionizing excitation and chemical bond cleavage, which can lead to molecular and cellular damage. Ionizing radiation can hydrolyze water molecules in the body, resulting in increased numbers of free radicals with strong oxidation ability. This process indirectly leads to tissue degeneration and necrosis, which can possibly result in cancer. In this paper, the intervention mechanism of flavonoids on ionizing radiation was analyzed. It has been revealed that the intervention mechanism associated with flavonoids may offer protective properties for DNA, prevent scavenging free radicals, and protect against auto-immune damage. In addition, this invention mechanism can protect the hematopoietic system and reduce inflammation.

Ammonia effects on proton conductivity properties of coordination polymers

Crystalline metal phosphonates are referred to as a type of structurally versatile coordination polymers [1]. Many of them contain guest molecules (H2O, heterocyclics, etc.), acidic sites and, furthermore, their structure can be also amenable for post‐synthesis modifications in order to enhance desired properties [2]. In the present work, we examine the relationships between crystal structure and proton conductivity for several metal phosphonates derive from multifunctional ligands, such as 5-(dihydroxyphosphoryl)isophthalic acid (PiPhtA) [3] and 2-hydroxyphosphonoacetic acid (H3HPAA). Crystalline divalent metal derivatives show a great structural diversity, from 1D to 3D open-frameworks, possessing hydrogen-bonded water molecules and acid groups. These solids present a proton conductivity range between 7.2·10-6 and 1.3·10−3 S·cm-1. Upon exposure to ammonia vapor, from an aqueous solution, solid state transformations are observed accompanied of enhance proton conductivities. The stability of these solids under different environment conditions (temperature and relative humidities) as well as the influence of the ammonia adsorption on the proton conduction properties of the resulting solids will be discussed.