One- and two-center energy components in the atoms in molecules theory

The energy decomposition scheme proposed in a recent paper has been realized by performing numerical integrations. The sample calculations carried out for some simple molecules show excellent agreement with the chemical picture of molecules, indicating that such an energy decomposition analysis can be useful from the point of view of connecting quantum mechanics with the genuine chemical concepts

CNDOL: A fast and reliable method for the calculation of electronic properties of very large systems. Applications to retinal binding pocket in rhodopsin and gas phase porphine.

Very large molecular systems can be calculated with the so called CNDOL approximate Hamiltonians that have been developed by avoiding oversimplifications and only using a priori parameters and formulas from the simpler NDO methods. A new diagonal monoelectronic term named CNDOL/21 shows great consistency and easier SCF convergence when used together with an appropriate function for charge repulsion energies that is derived from traditional formulas. It is possible to obtain a priori molecular orbitals and electron excitation properties after the configuration interaction of single excited determinants with reliability, maintaining interpretative possibilities even being a simplified Hamiltonian. Tests with some unequivocal gas phase maxima of simple molecules (benzene, furfural, acetaldehyde, hexyl alcohol, methyl amine, 2,5 dimethyl 2,4 hexadiene, and ethyl sulfide) ratify the general quality of this approach in comparison with other methods. The calculation of large systems as porphine in gas phase and a model of the complete retinal binding pocket in rhodopsin with 622 basis functions on 280 atoms at the quantum mechanical level show reliability leading to a resulting first allowed transition in 483 nm, very similar to the known experimental value of 500 nm of "dark state." In this very important case, our model gives a central role in this excitation to a charge transfer from the neighboring Glu(-) counterion to the retinaldehyde polyene chain. Tests with gas phase maxima of some important molecules corroborate the reliability of CNDOL/2 Hamiltonians.

A reação de metátese de olefinas: reorganização e ciclização de compostos orgânicos

The olefin metathesis reaction allows the exchange of complex alkyl units between two olefins, with the formation of a new olefinic link and a sub-product olefin usually ethylene. This reaction has found extensive application in the last ten years with the development of the Grubbs and Schrock catalysts, in total synthesis of complex organic molecules, as opposed to the very important use in the petrochemical industry with relatively simple molecules. This review intends to trace a historical and mechanistic pathway from industry to academy, before illustrating the more recent advances.

Studies on molecular structure and properties using microwave and infrared spectral data

The major objective of the thesis is essentially to evolve and apply certain computational procedures to evaluate the structure and properties of some simple polyatomic molecules making use of spectroscopic data available from the literature. It must be said that though there is dwindling interest in recent times in such analyses, there exists tremendous scope and utility for attempting such calculations as the precision and reliability of'experimental techniques in spectroscopy have increased vastly due to enormous sophistication of the instruments used for these measurements. In the present thesis an attempt is made to extract maximum amount of information regarding the geometrical structure and interatmic forces of simple molecules from the experimental data on microwave and infrared spectra of these molecules

Low energy elastic and electronically inelastic electron scattering from biomolecules.

Reactions initiated by collisions with low-energy secondary electrons has been found to be the prominent mechanism toward the radiation damage on living tissues through DNA strand breaks. Now it is widely accepted that during the interaction with these secondary species the selective breaking of chemical bonds is triggered by dissociative electron attachment (DEA), that is, the capture of the incident electron and the formation of temporary negative ion states [1,2,3]. One of the approaches largely used toward a deeper understanding of the radiation damage to DNA is through modeling of DEA with its basic constituents (nucleotide bases, sugar and other subunits). We have tried to simplify this approach and attempt to make it comprehensible at a more fundamental level by looking at even simple molecules. Studies involving organic systems such as carboxylic acids, alcohols and simple ¯ve-membered heterocyclic compounds are taken as starting points for these understanding. In the present study we investigate the role played by elastic scattering and electronic excitation of molecules on electron-driven chemical processes. Special attention is focused on the analysis of the in°uence of polarization and multichannel coupling e®ects on the magnitude of elastic and electronically inelastic cross-sections. Our aim is also to investigate the existence of resonances in the elastic and electronically inelastic channels as well as to characterize them with respect to its type (shape, core-excited or Feshbach), symmetry and position. The relevance of these issues is evaluated within the context of possible applications for the modeling of discharge environments and implications in the understanding of mutagenic rupture of DNA chains. The scattering calculations were carried out with the Schwinger multichannel method (SMC) [4] and its implementation with pseudopotentials (SMCPP) [5] at di®erent levels of approximation for impact energies ranging from 0.5 eV to 30 eV. References [1] B. Boudai®a, P. Cloutier, D. Hunting, M. A. Huels and L. Sanche, Science 287, 1658 (2000). [2] X. Pan, P. Cloutier, D. Hunting and L. Sanche, Phys. Rev. Lett. 90, 208102 (2003). [3] F. Martin, P. D. Burrow, Z. Cai, P. Cloutier, D. Hunting and L. Sanche, Phys. Rev. Lett. 93, 068101 (2004). [4] K. Takatsuka and V. McKoy, Phys. Rev. A 24, 2437 (1981); ibid. Phys. Rev. A 30, 1734 (1984). [5] M. H. F. Bettega, L. G. Ferreira and M. A. P. Lima, Phys. Rev. A 47, 1111 (1993).

Propriedades antioxidantes de constituintes fenólicos de macroalgas marinhas

Desde tempos remotos que as macroalgas marinhas são utilizadas por comunidades humanas, nomeadamente as orientais, como parte importante da sua dieta alimentar. A composição química das diferentes macroalgas marinhas (algas castanhas – Phaeophyta, algas vermelhas – Rhodophyta e algas verdes – Chlorophyta) confirma que além de terem um valor nutricional satisfatório podem ser uma fonte muito interessante de compostos bioativos como, por exemplo, os compostos fenólicos. Quimicamente os compostos fenólicos caracterizam-se por apresentarem um ou mais grupos hidroxilo ligados a um anel aromático. Estes compostos englobam desde moléculas simples até moléculas poliméricas de grandes dimensões. A maioria dos compostos fenólicos apresenta atividade antioxidante. O interesse pelo estudo de metabolitos secundários das macroalgas com propriedades antioxidantes surgiu, numa primeira fase, como uma tentativa de encontrar substitutos para os antioxidantes sintéticos usados como aditivos alimentares (nomeadamente o BHA e o BHT) que demonstravam possuir efeitos carcinogénicos. No entanto, rapidamente a comunidade científica reconheceu que a aplicação de novos compostos fenólicos naturais é muito mais vasta. Sabe-se hoje que é crucial para a promoção da saúde de um indivíduo que se verifique a manutenção do equilíbrio entre a produção de radicais livres e as respetivas defesas antioxidantes. Quando esse equilíbrio se altera e ocorre uma acumulação de radicais livres no organismo, este entra em stress oxidativo, situação que pode conduzir a danos dos lípidos celulares, proteínas e ácidos nucleicos, o que favorece o aparecimento de diversas doenças e acelera o envelhecimento celular. Assim, atualmente existe um crescente interesse por parte da indústria farmacêutica e da indústria da cosmética no estudo dos compostos fenólicos isolados de macroalgas. De entre estes, destacam-se os florotaninos, que para além das propriedades antioxidantes têm demonstrado possuir outras atividades farmacológicas importantes, tais como atividade antibacteriana, anti-viral, antineoplásica, anti-hipertensora e anti-diabética. Este trabalho consiste numa revisão bibliográfica sobre os diversos compostos fenólicos com atividade antioxidante isolados de macroalgas marinhas e que demonstraram vantagens na sua incorporação, quer em formulações cosméticas, quer em medicamentos, debatendo as suas ações farmacológicas, mecanismos de ação e possíveis aplicações futuras.

Investigating automated chemical evolution of oil-in-water droplets

One of the main unresolved questions in science is how non-living matter became alive in a process known as abiognesis, which aims to explain how from a primordial soup scenario containing simple molecules, by following a ``bottom up'' approach, complex biomolecules emerged forming the first living system, known as a protocell. A protocell is defined by the interplay of three sub-systems which are considered requirements for life: information molecules, metabolism, and compartmentalization. This thesis investigates the role of compartmentalization during the emergence of life, and how simple membrane aggregates could evolve into entities that were able to develop ``life-like'' behaviours, and in particular how such evolution could happen without the presence of information molecules. Our ultimate objective is to create an autonomous evolvable system, and in order tp do so we will try to engineer life following a ``top-down'' approach, where an initial platform capable of evolving chemistry will be constructed, but the chemistry being dependent on the robotic adjunct, and how then this platform can be de-constructed in iterative operations until it is fully disconnected from the evolvable system, the system then being inherently autonomous. The first project of this thesis describes how the initial platform was designed and built. The platform was based on the model of a standard liquid handling robot, with the main difference with respect to other similar robots being that we used a 3D-printer in order to prototype the robot and build its main equipment, like a liquid dispensing system, tool movement mechanism, and washing procedures. The robot was able to mix different components and create populations of droplets in a Petri dish filled with aqueous phase. The Petri dish was then observed by a camera, which analysed the behaviours described by the droplets and fed this information back to the robot. Using this loop, the robot was then able to implement an evolutionary algorithm, where populations of droplets were evolved towards defined life-like behaviours. The second project of this thesis aimed to remove as many mechanical parts as possible from the robot while keeping the evolvable chemistry intact. In order to do so, we encapsulated the functionalities of the previous liquid handling robot into a single monolithic 3D-printed device. This device was able to mix different components, generate populations of droplets in an aqueous phase, and was also equipped with a camera in order to analyse the experiments. Moreover, because the full fabrication process of the devices happened in a 3D-printer, we were also able to alter its experimental arena by adding different obstacles where to evolve the droplets, enabling us to study how environmental changes can shape evolution. By doing so, we were able to embody evolutionary characteristics into our device, removing constraints from the physical platform, and taking one step forward to a possible autonomous evolvable system.

Moléculas simples com aplicação na medicina

O trabalho apresentado, foi realizado no âmbito do mestrado em Química para o ensino, da Universidade de Évora e tem como tema " Moléculas Simples de Aplicação na Medicina". A abordagem deste tema deve-se à necessidade cada vez maior de um ensino que motive os alunos e lhes proporcione um gosto maior pelo estudo das ciências, uma vez que cada vez mais os jovens estudantes revelam pouca motivação e gosto pelo estudo das áreas científicas quer ao nível do ensino secundário quer ao nível do ensino superior. Pretende-se também tentar compreender e explicar o porquê das suas desmotivações e tentar adaptar novas abordagens a temas que suscitem nos jovens um maior interesse, uma melhor compreensão da importância das ciências, da tecnologia na vida quotidiana de todos nós no que respeita ao nosso bem-estar e à nossa saúde. Numa primeira parte é feita uma revisão sobre os principais conteúdos propostos a desenvolver em sala de aula, conteúdos esses que sustentam o estudo do xénon como anestésico e dos perfluorocarbonetos como substitutos do sangue. A segunda parte integra um programa orientador, seguindo as metodologias e estrutura do programa homologado pelo ME para o 12º ano de escolaridade, e protocolos de algumas actividades de carácter experimental laboratorial propostas. Estas actividades têm como finalidade estimular a curiosidade e facilitar a consolidação das matérias. ABSTRACT: The present study was carried out under the Master's Degree in Chemistry for Teaching, taught at the University of Évora under the theme "lmplementation of Simple Molecules in Medicine". The approach to this issue is due to an increasing need for teaching that motivates students and sharpen their senses for the study of science because, increasingly, young students show little motivation and passion for the study of science, both at secondary school and higher education terms. The aim is also trying to understand and explain the reason of their discouragement and try new approaches to issues that raise young in a better understanding of the importance of science and technology in everyday life for all of us in what concerns to our welfare and our health. ln the first part there is an overview of the major content areas to develop in the classroom. These contents support the study of xenon as an anesthetic and perfluorocarbons as blood substitutes. The second part includes the syllabus, following the methodologies and structure of the curriculum approved by the ME to the 12th grade and protocols of some activities for an experimental laboratory. These activities intend to stimulate curiosity and facilitate the consolidation of materials.

Sintesi e caratterizzazione di CaCu3Ti4O12 (CCTO) per applicazioni in fotoelettrocatalisi

A promising strategy to mitigate both the energy crisis and global warming is the development of solar fuels and chemicals using as feedstock CO2 in combination with simple molecules such as water. This process stores the solar energy into chemical bonds, leading to a carbon-neutral approach of fuels and chemicals production. Aim of this thesis was the synthesis and characterization of CaCu3Ti4O12 (CCTO)- based compounds to be used as visible light photocatalyst for CO2 to chemical conversion. Different compositions were produced doping CCTO with increasing concentration of iron into the perovskite’s A site in order to identify the materials with the highest photo- and photoelectrocatalytic properties. The most promising compositions were used to produce photoelectrodes by screen printing that were characterized by linear and cyclic voltammetry, impedance spectroscopy and Mott-Schottky analysis to evaluate the electrical conductivity and calculate the flat band potential and the number of charge carriers in the samples. The photoelectrodes were then tested in a photoelectrochemical (PEC) cell for the conversion of CO2 into fuel and chemicals. The results obtained confirm that CCTO-based materials can be considered promising materials for carbon dioxide photo-electrochemical reduction.

A brief introduction to molecular orbital theory of simple polyatomic molecules for undergraduate chemistry students

A simple, four-step method for better introducing undergraduate students to the fundamentals of molecular orbital (MO) theory of the polyatomic molecules H2O, NH3, BH3 and SiH4 using group theory is reported. These molecules serve to illustrate the concept of ligand group orbitals (LGOs) and subsequent construction of MO energy diagrams on the basis of molecular symmetry requirements.

Is the poly (methylene blue)-modified glassy carbon electrode an adequate electrode for the simple detection of thiols and amino acid-based molecules?

This paper describes the preparation, characterization, and use of poly (methylene blue) (PMB)-modified glassy carbon electrodes (GCE) (GCE-PMB) in the detection of the thiols L-cysteine (L-CySH) and N-acetyl cysteine (Acy), and the herbicide glyphosate (GLYP) in pH 5.3 aqueous solution. The polymer film prepared by electropolymerization showed different characteristics such as robustness, stability, and redox properties satisfactorily. The surface coverage concentration (Gamma) of PMB was found to be 7.90 x 10(-9) - mol cm(-2). Moreover, we observed strong adhesion of the polymer film to the electrode surface. The results using GCE-PMB as a sensor indicated that this modified electrode exhibited electrocatalytic activity toward the detection of thiols and glyphosate in 0.1 mol L-1 KO (pH 5.3). Meanwhile, strong adsorption of the analytes on the GCE-PMB electrodes was also observed. Otherwise, using a low concentration (1 x 10(-4) mol L-1) of L-cysteine and N-acetyl cysteine and 8.9 x 10(-6) mol L-1 of glyphosate, separately, it was possible to observe a well-defined electrochemical response, thus providing an opportunity to further understand the applicability of PMB as a sensor for amino acid-based molecules. (C) 2012 Elsevier B.V. All rights reserved.

Simple mechanochemistry describes the dynamics of kinesin molecules

Recently, Block and coworkers [Visscher, K., Schnitzer, M. J., & Block, S. M. (1999) Nature (London) 400, 184–189 and Schnitzer, M. J., Visscher, K. & Block, S. M. (2000) Nat. Cell Biol. 2, 718–723] have reported extensive observations of individual kinesin molecules moving along microtubules in vitro under controlled loads, F = 1 to 8 pN, with [ATP] = 1 μM to 2 mM. Their measurements of velocity, V, randomness, r, stalling force, and mean run length, L, reveal a need for improved theoretical understanding. We show, presenting explicit formulae that provide a quantitative basis for comparing distinct molecular motors, that their data are satisfactorily described by simple, discrete-state, sequential stochastic models. The simplest (N = 2)-state model with fixed load-distribution factors and kinetic rate constants concordant with stopped-flow experiments, accounts for the global (V, F, L, [ATP]) interdependence and, further, matches relative acceleration observed under assisting loads. The randomness, r(F,[ATP]), is accounted for by a waiting-time distribution, ψ\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} \begin{equation*}{\mathrm{_{1}^{+}}}\end{equation*}\end{document}(t), [for the transition(s) following ATP binding] with a width parameter ν ≡ 〈t〉2/〈(Δt)2〉≃2.5, indicative of a dispersive stroke of mechanicity ≃0.6 or of a few (≳ν − 1) further, kinetically coupled states: indeed, N = 4 (but not N = 3) models do well. The analysis reveals: (i) a substep of d0 = 1.8–2.1 nm on ATP binding (consistent with structurally based suggestions); (ii) comparable load dependence for ATP binding and unbinding; (iii) a strong load dependence for reverse hydrolysis and subsequent reverse rates; and (iv) a large (≳50-fold) increase in detachment rate, with a marked load dependence, following ATP binding.

Atomic Charge Transfer-counter Polarization Effects Determine Infrared Ch Intensities Of Hydrocarbons: A Quantum Theory Of Atoms In Molecules Model.

Atomic charge transfer-counter polarization effects determine most of the infrared fundamental CH intensities of simple hydrocarbons, methane, ethylene, ethane, propyne, cyclopropane and allene. The quantum theory of atoms in molecules/charge-charge flux-dipole flux model predicted the values of 30 CH intensities ranging from 0 to 123 km mol(-1) with a root mean square (rms) error of only 4.2 km mol(-1) without including a specific equilibrium atomic charge term. Sums of the contributions from terms involving charge flux and/or dipole flux averaged 20.3 km mol(-1), about ten times larger than the average charge contribution of 2.0 km mol(-1). The only notable exceptions are the CH stretching and bending intensities of acetylene and two of the propyne vibrations for hydrogens bound to sp hybridized carbon atoms. Calculations were carried out at four quantum levels, MP2/6-311++G(3d,3p), MP2/cc-pVTZ, QCISD/6-311++G(3d,3p) and QCISD/cc-pVTZ. The results calculated at the QCISD level are the most accurate among the four with root mean square errors of 4.7 and 5.0 km mol(-1) for the 6-311++G(3d,3p) and cc-pVTZ basis sets. These values are close to the estimated aggregate experimental error of the hydrocarbon intensities, 4.0 km mol(-1). The atomic charge transfer-counter polarization effect is much larger than the charge effect for the results of all four quantum levels. Charge transfer-counter polarization effects are expected to also be important in vibrations of more polar molecules for which equilibrium charge contributions can be large.

Molecules Clarify a Cnidarian Life Cycle - The ""Hydrozoan'' Microhydrula limopsicola Is an Early Life Stage of the Staurozoan Haliclystus antarcticus

Background: Life cycles of medusozoan cnidarians vary widely, and have been difficult to document, especially in the most recently proposed class Staurozoa. However, molecular data can be a useful tool to elucidate medusozoan life cycles by tying together different life history stages. Methodology/Principal Findings: Genetic data from fast-evolving molecular markers (mitochondrial 16S, nuclear ITS1, and nuclear ITS2) show that animals that were presumed to be a hydrozoan, Microhydrula limopsicola (Limnomedusae, Microhydrulidae), are actually an early stage of the life cycle of the staurozoan Haliclystus antarcticus (Stauromedusae, Lucernariidae). Conclusions/Significance: Similarity between the haplotypes of three markers of Microhydrula limopsicola and Haliclystus antarcticus settles the identity of these taxa, expanding our understanding of the staurozoan life cycle, which was thought to be more straightforward and simple. A synthetic discussion of prior observations makes sense of the morphological, histological and behavioral similarities/congruence between Microhydrula and Haliclystus. The consequences are likely to be replicated in other medusozoan groups. For instance we hypothesize that other species of Microhydrulidae are likely to represent life stages of other species of Staurozoa.45