Copper(II) complexes with unsymmetrical pentadentate ed3a-type diamino-tricarboxylate ligands. Crystal structures, configurational analysis and DFT study of complexes

The O–O–N–N–O-type pentadentate ligands H3ed3a, H3pd3a and H3pd3p (H3ed3a stands ethylenediamine-N,N,N′-triacetic acid; H3pd3a stands 1,3-propanediamine-N,N,N′-triacetic acid and H3pd3p stands 1,3-propanediamine-N,N,N′-tri-3-propionic acid) and the corresponding novel octahedral or square-planar/trigonal-bipyramidal copper(II) complexes have been prepared and characterized. H3ed3a, H3pd3a and H3pd3p ligands coordinate to copper(II) ion via five donor atoms (three deprotonated carboxylate atoms and two amine nitrogens) affording octahedral in case of ed3a3− and intermediate square-pyramidal/trigonal-bipyramidal structure in case of pd3a3− and pd3p3−. A six coordinate, octahedral geometry has been established crystallographically for the [Mg(H2O)6][Cu(ed3a)(H2O)]2 · 2H2O complex and five coordinate square-pyramidal for the [Mg(H2O)5Cu(pd3a)][Cu(pd3a)] · 2H2O. Structural data correlating similar chelate Cu(II) complexes have been used for the better understanding the pathway: octahedral → square-pyramidal ↔ trigonal- bipyramid geometry. An extensive configuration analysis is discussed in relation to information obtained for similar complexes. The infra-red and electronic absorption spectra of the complexes are discussed in comparison with related complexes of known geometries. Molecular mechanics and density functional theory (DFT) programs have been used to model the most stable geometric isomer yielding, at the same time, significant structural data. The results from density functional studies have been compared with X-ray data.

Intonation contour realisation for Standard Yorùbá text-to-speech synthesis:a fuzzy computational approach

This paper presents a novel intonation modelling approach and demonstrates its applicability using the Standard Yorùbá language. Our approach is motivated by the theory that abstract and realised forms of intonation and other dimensions of prosody should be modelled within a modular and unified framework. In our model, this framework is implemented using the Relational Tree (R-Tree) technique. The R-Tree is a sophisticated data structure for representing a multi-dimensional waveform in the form of a tree. Our R-Tree for an utterance is generated in two steps. First, the abstract structure of the waveform, called the Skeletal Tree (S-Tree), is generated using tone phonological rules for the target language. Second, the numerical values of the perceptually significant peaks and valleys on the S-Tree are computed using a fuzzy logic based model. The resulting points are then joined by applying interpolation techniques. The actual intonation contour is synthesised by Pitch Synchronous Overlap Technique (PSOLA) using the Praat software. We performed both quantitative and qualitative evaluations of our model. The preliminary results suggest that, although the model does not predict the numerical speech data as accurately as contemporary data-driven approaches, it produces synthetic speech with comparable intelligibility and naturalness. Furthermore, our model is easy to implement, interpret and adapt to other tone languages.

A computational model of intonation for yorùbá text-to-speech synthesis:design and analysis

In this paper we present the design and analysis of an intonation model for text-to-speech (TTS) synthesis applications using a combination of Relational Tree (RT) and Fuzzy Logic (FL) technologies. The model is demonstrated using the Standard Yorùbá (SY) language. In the proposed intonation model, phonological information extracted from text is converted into an RT. RT is a sophisticated data structure that represents the peaks and valleys as well as the spatial structure of a waveform symbolically in the form of trees. An initial approximation to the RT, called Skeletal Tree (ST), is first generated algorithmically. The exact numerical values of the peaks and valleys on the ST is then computed using FL. Quantitative analysis of the result gives RMSE of 0.56 and 0.71 for peak and valley respectively. Mean Opinion Scores (MOS) of 9.5 and 6.8, on a scale of 1 - -10, was obtained for intelligibility and naturalness respectively.

Synthesis of a novel and stable g-C3N4–Ag3PO4 hybrid nanocomposite photocatalyst and study of the photocatalytic activity under visible light irradiation

A facile and reproducible template free in situ precipitation method has been developed for the synthesis of Ag3PO4 nanoparticles on the surface of a g-C3N4 photocatalyst at room temperature. The g-C3N4–Ag3PO4 organic–inorganic hybrid nanocomposite photocatalysts were characterized by various techniques. TEM results show the in situ growth of finely distributed Ag3PO4 nanoparticles on the surface of the g-C3N4 sheet. The optimum photocatalytic activity of g-C3N4–Ag3PO4 at 25 wt% of g-C3N4 under visible light is almost 5 and 3.5 times higher than pure g-C3N4 and Ag3PO4 respectively. More attractively, the stability of Ag3PO4 was improved due to the in situ deposition of Ag3PO4 nanoparticles on the surface of the g-C3N4 sheet. The improved performance of the g-C3N4–Ag3PO4 hybrid nanocomposite photocatalysts under visible light irradiation was induced by a synergistic effect, including high charge separation efficiency of the photoinduced electron–hole pair, the smaller particle size, relatively high surface area and the energy band structure. Interestingly, the heterostructured g-C3N4–Ag3PO4 nanocomposite significantly reduces the use of the noble metal silver, thereby effectively reducing the cost of the Ag3PO4 based photocatalyst.

I.~Synthesis, isolation, and characterization of 1-(2-anthryl)-2-cyclopropylethylene and 1-(2-naphthyl)-2-cyclopropylethylene. II.~Titanium dioxide photocatalysis of haloethers: A mechanistic study

I. The target molecules are classified as 1-aryl 2-cyclopropyl substituted ethylene. In the ground state, these molecules have a number of conformers, which are in equilibrium through rotation about single bonds. Once excited, the conformers have fixed conformation and are no longer in equilibrium and can be distinguished by their UV-vis as well as fluorescence spectra. The synthetic strategy involves standard steps. Both 2-methylanthracene and 2-methylnaphthalene were brominated using N-bromosuccinimide to give the bromomethyl adduct, which then was reacted with triphenylphosphine to form the phosphonium salt. This was followed by the formation of the phosphorus ylide, which upon treatment with cyclopropanecarboxaldehyde gave the product.^ II. The degradation of three aliphatic haloethers: bis-(2-chloroethyl) ether, bis-(2-chloroisopropyl) ether, and bis-(2-chloroethoxy)methane and two aromatic haloethers: 4-chlorodiphenyl ether and 4-bromodiphenyl ether was studied. Product studies have been conducted on the titanium dioxide photocatalysis of these compounds including mass balance, monitoring and identifying intermediates to establish the reaction pathways to deduce a mechanism for their degradation. The extent of mineralization was determined from the measurement of halogen anion (Cl$\sp-$/Br$\sp-$) as well as total organic carbon. The relative rates of disappearance of the individual haloethers appear to be related to the hydrophobic character of the given compound. Reaction mechanisms involving hydroxyl radical are proposed to explain the observed results. ^

Computational modeling of biodegradable starch based polymer composites

Purpose. The goal of this study is to improve the favorable molecular interactions between starch and PPC by addition of grafting monomers MA and ROM as compatibilizers, which would advance the mechanical properties of starch/PPC composites. ^ Methodology. DFT and semi-empirical methods based calculations were performed on three systems: (a) starch/PPC, (b) starch/PPC-MA, and (c) starch-ROM/PPC. Theoretical computations involved the determination of optimal geometries, binding-energies and vibrational frequencies of the blended polymers. ^ Findings. Calculations performed on five starch/PPC composites revealed hydrogen bond formation as the driving force behind stable composite formation, also confirmed by the negative relative energies of the composites indicating the existence of binding forces between the constituent co-polymers. The interaction between starch and PPC is also confirmed by the computed decrease in stretching CO and OH group frequencies participating in hydrogen bond formation, which agree qualitatively with the experimental values. ^ A three-step mechanism of grafting MA on PPC was proposed to improve the compatibility of PPC with starch. Nine types of 'blends' produced by covalent bond formation between starch and MA-grafted PPC were found to be energetically stable, with blends involving MA grafted at the 'B' and 'C' positions of PPC indicating a binding-energy increase of 6.8 and 6.2 kcal/mol, respectively, as compared to the non-grafted starch/PPC composites. A similar increase in binding-energies was also observed for three types of 'composites' formed by hydrogen bond formation between starch and MA-grafted PPC. ^ Next, grafting of ROM on starch and subsequent blend formation with PPC was studied. All four types of blends formed by the reaction of ROM-grafted starch with PPC were found to be more energetically stable as compared to the starch/PPC composite and starch/PPC-MA composites and blends. A blend of PPC and ROM grafted at the ' a&d12; ' position on amylose exhibited a maximal increase of 17.1 kcal/mol as compared with the starch/PPC-MA blend. ^ Conclusions. ROM was found to be a more effective compatibilizer in improving the favorable interactions between starch and PPC as compared to MA. The ' a&d12; ' position was found to be the most favorable attachment point of ROM to amylose for stable blend formation with PPC.^

Synthesis of M2AC (M = Ti, V, Cr, Nb, Zr, A = Al, Sn, S) (MAX) carbide phases and study of their physical behavior under extreme conditions

Materials known as Mn+1AXn phases, where n is 1, 2, or 3, and M represents an early transition metal, A an A-group element, and X is either Carbon and/or Nitrogen [1], are fast becoming technologically important materials due to the interesting combination of unique properties. However, a lot of important information about the high temperature and high pressure behavior of many of these compounds is still missing, which needs to be determined systematically. ^ In this dissertation the synthesis of M2AC (M = Ti, V, Cr, Nb, Zr) and A = (Al, Sn, S) compounds by arc melting, vacuum sintering and piston cylinder synthesis is presented along with the synthesis of Zr 2SC, which has been synthesized for first time in bulk form, by piston cylinder technique. The microstructural analysis by electron microscopy and phase analysis by x-ray diffraction is presented next. Finally, a critical analysis of the behavior of these compounds under the application of extreme pressure (as high as 50 GPa) and temperature (≈ 1000°C) is presented. ^ The high pressure studies, up to 50 GPa, showed that these compounds were structurally intact and their bulk moduli ranged from 140 to 190 GPa. The high temperature studies in the inert atmosphere showed that the M 2SnC compounds were unstable above 650°C and the expansion along the a-axis was higher than that along the c-axis, unlike the other phases. M2SC compounds on the other hand showed negligible difference in the thermal expansion along the two axes. The oxidation study revealed that Ti2AC (Al, S) compounds had highest resistance to oxidation while the M2SnC compounds had the least. Furthermore, from the oxidation study of these compounds, which were short time oxidation experiments, it was found that all of these compounds oxidized to their respective binary oxides. ^

Synthesis, characterization and study of physical properties of novel M(n+1)AX(n) compounds

Mn+1AXn compounds, the ternary layered nanolaminates have gathered momentum in the last decade since its advent because of their unusual but exciting properties. These technologically important compounds combine some of the best properties of metals and ceramics. Like ceramics they are refractory, oxidation resistant, elastically stiff and relatively light. They also exhibit metallic properties like excellent machinability, thermal and electrical conductivity. This dissertation concentrates on the synthesis of germanium-based 211 Mn+1AXn compounds. The main objective of the research was to synthesize predominantly single phase samples of Cr2GeC, V2GeC and Ti2GeC. Another goal was to study the effect of solid substitutions on the M-site of Mn+1AXn compounds with Ge as an A-element. This study is in itself the first to demonstrate the synthesis of (Cr0.5V0.5)2GeC a novel Mn+1AXn compound. Scanning electron microscopy coupled with energy dispersive spectroscopy, x-ray diffraction and electron probe microanalysis were employed to confirm the presence of predominantly single phase samples of M2GeC compounds where M = Ti, V, Cr and (Cr 0.5V0.5). A large part of the dissertation also focuses on the effect of the compressibility on the Ge-based 211 Mn+1AXn compounds with the aid of diamond anvil cell and high energy synchrotron radiation. This study also concentrates on the stability of these compounds at high temperature and thereby determines its suitability as high temperature structural materials. In order to better understand the effect of substitutions on A-site of 211 Mn+1 AXn compounds under high pressure and high temperature, a comparison is made with previously reported 211 Mn+1AXn compounds with Al, Ga and S as A-site elements.

A predictive computational fluid dynamics study of carotid artery

Abstract not available

A computational fluid dynamics study of the stencil printing process

Abstract not available

Synthesis of Iodinated Naphthoquinones Using Morpholine-Iodine Complex

artículo (arbitrado)--Universidad de Costa Rica. Escuela de Química, 2004. Este documento es privado debido a limitaciones de derechos de autor.

A study of computational methods to analyze gene expression data

The recent advent of new technologies has led to huge amounts of genomic data. With these data come new opportunities to understand biological cellular processes underlying hidden regulation mechanisms and to identify disease related biomarkers for informative diagnostics. However, extracting biological insights from the immense amounts of genomic data is a challenging task. Therefore, effective and efficient computational techniques are needed to analyze and interpret genomic data. In this thesis, novel computational methods are proposed to address such challenges: a Bayesian mixture model, an extended Bayesian mixture model, and an Eigen-brain approach. The Bayesian mixture framework involves integration of the Bayesian network and the Gaussian mixture model. Based on the proposed framework and its conjunction with K-means clustering and principal component analysis (PCA), biological insights are derived such as context specific/dependent relationships and nested structures within microarray where biological replicates are encapsulated. The Bayesian mixture framework is then extended to explore posterior distributions of network space by incorporating a Markov chain Monte Carlo (MCMC) model. The extended Bayesian mixture model summarizes the sampled network structures by extracting biologically meaningful features. Finally, an Eigen-brain approach is proposed to analyze in situ hybridization data for the identification of the cell-type specific genes, which can be useful for informative blood diagnostics. Computational results with region-based clustering reveals the critical evidence for the consistency with brain anatomical structure.

Computational and experimental study of the behavior of cyano-based ionic liquids in aqueous solution

The solvation of cyano- (CN-) based ionic liquids (ILs) and their capacity to establish hydrogen bonds (H-bonds) with water was studied by means of experimental and computational approaches. Experimentally, water activity data were measured for aqueous solutions of ILs based on 1-butyl-3-methylimidazolium ([BMIM](+)) cation combined with one of the following anions: thiocyanate ([SCN](-)), dicyanamide ([DCA](-)), or tricyanomethanide ([TCM](-)), and of 1-ethyl-3-methylimidazolium tetracyanoborate ([EMIM][TCB]). From the latter data, water activity coefficients were estimated showing that [BMIM][SCN] and [BMIM][DCA], unlike [BMIM][TCM] and [EMIM][TCB], are able to establish favorable interactions with water. Computationally, the conductor like screening model for real solvents (COSMO-RS) was used to estimate the water activity coefficients which compare well with the experimental ones. From the COSMO-RS results, it is suggested that the polarity of each ion composing the ILs has a strong effect on the solvation phenomena. Furthermore, classical molecular dynamics (MD) simulations were performed for obtaining an atomic level picture of the local molecular neighborhood of the different species. From the experimental and computational data it is showed that increasing the number of CN groups in the ILs' anions does not enhance their ability to establish H-bonds with water but decreases their polarities, being [BMIM][DCA] and [BMIM][SCN] the ones presenting higher propensity to interact.

Synthesis and antibacterial study of some s-substituted aliphatic analogues of 2-mercapto-5-(1-(4-toluenesulfonyl) piperidin-4-yl)-1,3,4-oxadiazole

Purpose: To synthesize a series of analogues of 1,3,4-oxadiazole and to evaluate their antibacterial activity. Methods: Ethyl piperidin-4-carboxylate (1) was mixed with 4-toluenesulfonyl chloride (2) in benignant conditions to yield ethyl 1-(4-toluenesulfonyl)piperidin-4-carboxylate (3) and then 1-(4- toluenesulfonyl)piperidin-4-carbohydrazide (4). Intermolecular cyclization of 4 into 2-mercapto-5-(1-(4- toluenesulfonyl) piperidin-4-yl)-1,3,4-oxadiazole (5) was obtained on reflux with CS2 in the presence of KOH. Molecule 5 was stirred with alkyl halides, 6a-i, in DMF in the presence of LiH to synthesize the final compounds, 7a-i. The structures of these molecules were elucidated by Fourier transform infra-red (FTIR) spectroscopy, proton nuclear magnetic resonance (1H-NMR) and electron impact mass spectrometry (EI-MS). Antibacterial activity was evaluated against five bacterial strains, namely, Salmonella typhi, Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus and Bacillus subtilis, with ciprofloxacin used as standard antibacterial agent. Results: Out of nine synthesized derivatives, compound 7a was the most active against three bacterial strains, S. typhi, E. coli and P. aeruginosa, with minimum inhibitory concentration (MIC) of 9.11 ± 0.40, 9.89 ± 0.45 and 9.14 ± 0.72 μM, respectively, compared with 7.45 ± 0.58, 7.16 ± 0.58 and 7.14 ± 0.18 μM, respectively, for the reference standard (ciprofloxacin). Similarly, compounds 7a - 7c showed relatively good antibacterial activity against B. subtilis strain while compound 7e - 7g revealed good results against S. typhi bacterial strain. Conclusion: The results indicate that S-substituted derivatives of the parent compound are more effective antibacterial agents than the parent compound, even with minor differences in substituents

A THEORETICAL STUDY OF INTERACTION OF NANOPARTICLES WITH BIOMOLECULE

Many types of materials at nanoscale are currently being used in everyday life. The production and use of such products based on engineered nanomaterials have raised concerns of the possible risks and hazards associated with these nanomaterials. In order to evaluate and gain a better understanding of their effects on living organisms, we have performed first-principles quantum mechanical calculations and molecular dynamics simulations. Specifically, we will investigate the interaction of nanomaterials including semiconducting quantum dots and metallic nanoparticles with various biological molecules, such as dopamine, DNA nucleobases and lipid membranes. Firstly, interactions of semiconducting CdSe/CdS quantum dots (QDs) with the dopamine and the DNA nucleobase molecules are investigated using similar quantum mechanical approach to the one used for the metallic nanoparticles. A variety of interaction sites are explored. Our results show that small-sized Cd4Se4 and Cd4S4 QDs interact strongly with the DNA nucleobase if a DNA nucleobase has the amide or hydroxyl chemical group. These results indicate that these QDs are suitable for detecting subcellular structures, as also reported by experiments. The next two chapters describe a preparation required for the simulation of nanoparticles interacting with membranes leading to accurate structure models for the membranes. We develop a method for the molecular crystalline structure prediction of 1,2-Dimyristoyl-sn-glycero-3-phosphorylcholine (DMPC), 1,2-Dimyristoyl-sn-glycero-3-phosphorylethanolamine (DMPE) and cyclic di-amino acid peptide using first-principles methods. Since an accurate determination of the structure of an organic crystal is usually an extremely difficult task due to availability of the large number of its conformers, we propose a new computational scheme by applying knowledge of symmetry, structural chemistry and chemical bonding to reduce the sampling size of the conformation space. The interaction of metal nanoparticles with cell membranes is finally carried out by molecular dynamics simulations, and the results are reported in the last chapter. A new force field is developed which accurately describes the interaction forces between the clusters representing small-sized metal nanoparticles and the lipid bilayer molecules. The permeation of nanoparticles into the cell membrane is analyzed together with the RMSD values of the membrane modeled by a lipid bilayer. The simulation results suggest that the AgNPs could cause the same amount of deformation as the AuNPs for the dysfunction of the membrane.