Structure properties of water clusters are investigated in this study by means of molecular dynamics simulations. The oxygen density profile, dipole moment and hydrogen bond properties of water clusters are all examined. The temperature dependence and size dependence of the structure properties are also explored in the present study. Upon the molecular dynamics simulations, the flexible three-centered (F3C) water potential is used to model the inter- and intra-actions of the water molecule. It is found that as the temperature rises, the density of the oxygen and the average number of hydrogen bonds per water molecule will decrease. The effect of cluster size, however, is less significant on the structure properties. The differences between the structural properties for the surface region and those for the interior region of the cluster are also investigated. It is found that as the temperature rises, the average number of hydrogen bonds per water molecule decreases, but the ratio of surface water molecules increases. After comparing the water densities in interior regions and the average number of hydrogen bonds in those regions, we find there is no apparent size effect on water molecules in the interior region, whereas the size of the water cluster has a significant influence on the behavior of water molecules at the surface region.

No description available.

Recently, by performing molecular dynamics simulations in the methane-water system, we have measured the static lifetimes of cagelike water clusters (CLWC) immersed in bulk liquid water, during which the member-water molecules of CLWCs are not allowed to exchange with their surrounding water molecules [J. Phys. Chem. C, 2007, 111, 2595]. In this study, we measure the dynamic lifetimes of CLWCs with permitting such water exchanges. It is found that the dynamic lifetimes of CLWCs are not less than the static lifetimes previously obtained, and their ratio increases with the lifetime values. The results strengthen that CLWCs are metastable structures in liquid water and the occurrence probability of long-lived CLWCs will increase if one uses the dynamic lifetimes instead of the static lifetimes. The implications of this study for hydrate nucleation are discussed.

A variety of highly hydrated ions were generated and studied using electrospray ionization mass spectrometry (ESI-MS) including proton, a series of triply charged lanthanide ions, the doubly charged lead ion and various methylated guanidinium ions. In each case large hydrated water clusters were mass selected and fragmented through collision induced dissociation (CID) to investigate their properties. The fragmentation of protonated water clusters highlighted the stability of the “magic” water cluster [H(H2O)21]+. Typically unstable triply charge lanthanide water clusters and the previously unobserved doubly charged lead water clusters were generated. Fragmentation studies indicated that both the charge density and the geometry of the clusters affect their stability. The charge reduction of triply charged lanthanide clusters led to the direct observation of ion evaporation. Finally, the dehydration of various methylated guanidinium ions indicated a structural basis for differences in their ability to hydrogen bond.

No description available.

No description available.

Orientador: Herculano da SIlva Martinho. / Tese (doutorado) - Universidade Federal do ABC. Programa de Pós Graduação em Nanociências e Materiais Avançados, 2014. / A biópsia óptica utilizando espectroscopia vibracional emerge como uma técnica com boa sensibilidade e especificidade no diagnóstico de doenças. Entretanto, para melhor entender como as alterações bioquímicas se traduzem em alterações estruturais que conduzem a estes estados patológicos, são necessários estudos mais aprofundados e a simulação computacionalé a ferramenta adequada. Existem diversos estudos que envolvem macromoléculas e tecidos, porém ainda não é conhecido um modelo teórico para sua descrição e comparação aos resultados experimentais de espectroscopia Raman. Neste contexto, buscou-se encontrar um modelo teórico para o tecido, partindo de um peptídeo de colágeno, com diferentes graus de hidratação e a presença de água confinada em sua estrutura, a fim de contribuir para os estudos de biópsia óptica por espectroscopia vibracional. Os modelos foram construídos a partir de um peptídeo de colágeno, proveniente do Protein Data Bank e adicionados clustersde água confinada em cada modelo. Os modelos foram comparados quanto à energia, mínimo global, momento de dipolo e frequências Raman experimentais. Foi possível perceber que o modelo D1 é preferível para empacotar moléculas de água e é também aquele que menos favorece os processos de transferência eletrônica e, consequentemente, o mais próximo de um tecido de mucosa normal. Analisando também os espectros vibracionais observou-se que os modelos C1s e D1 são aqueles que melhor representam o espectro Raman experimental na região estudada. Também foram tabelados os modos vibracionais de cada modelo, o que contribui para entendimento dos picos espectrais. Pôde-se concluir que é possível a aplicação destes modelos a problemas biológicos reais, como estudos de cosmetologia e farmacologia de tecidos. / The optical biopsy using vibrational spectroscopy is emerging as a technique with good sensitivity and specificity in the diagnosis of diseases. However, for better understanding how the biochemical changes translate into structural changes that lead to these pathological conditions, further studies are needed and the computer simulation is the appropriate tool. Several studies involving macromolecules and tissues, but it is not yet known a theoretical model for the description and comparison to experimental results of Raman spectroscopy. In this context, we sought to find a theoretical model for the tissue, leaving a collagen peptide with different degrees of hydration and the presence of confined water in its structure, in order to contribute to the study of optical biopsy by vibrational spectroscopy. The models had beenbuilt from a collagen peptide found on the Protein Data Bank and added to confined water clusters in each model. The models were compared with regard to energy, dipole moment, global minimum and experimental Raman frequencies. It was possible to notice that the D1 model is preferable to package water molecules and and is also the one that least favours the electronic transfer processes and, consequently, the closest thing to a normal mucosa tissue. Analyzing the Vibrational Spectra also showed that C1s and D1 models are those which best represent the experimental Raman spectrum in the region studied. We also tabulated vibrational modes of each model, which contributes to understanding of the spectral peaks. It might be concluded that it is possible to apply these models to real biological problems, such as cosmetology and pharmacology studies of tissues.

La compréhension de l'irradiation à l'échelle du nanomètre dans les systèmes biomoléculaires nécessite l'observation de caractéristiques nouvelles auxquelles les développements techniques actuels nous permettent d'accéder. Ce travail se situe au coeur de la construction du nouveau dispositif DIAM Dispositif d’Irradiation d’Agrégats de Molécules biologiques développé à l’Institut de Physique Nucléaire de Lyon. Le développement d’une source d’agrégats associée à un spectromètre de masse à double focalisation a permis l’obtention des premiers faisceaux d’agrégats moléculaires protonés sélectionnés en masse. De plus, un système de détection innovant a été développé et validé dans des expériences de dissociations d’agrégats d’eau protonés par collision sur un gaz. Les résultats obtenus contribuent à la connaissance de la stabilité et de la structure des petits agrégats d’eau protonés et des agrégats mixtes d’eau et de pyridine protonés / Nanoscale characterization of irradiation in biomolecular systems requires observation of novel features which are now achievable with the recent technical progress. This work is a central part in the development of DIAM which is a new experimental set-up devoted to irradiation of biomolecular clusters at the Institut de Physique Nucléaire de Lyon. The development of the cluster source and of a double focusing mass spectrometer leads to the production of intense beams of mass selected protonated molecular clusters. Combined with this mass selected cluster beams an innovative detection technique is demonstrated in collision induced dissociation experiments. The results contribute to the knowledge of the stability and the structure of the small protonated water clusters and mixed clusters of water and pyridine

Density functional theory is the most commonly used computational tool to study properties of solids and molecules. Self-interaction error, that arises due to improper cancellation of the self-Hartree and the self exchange correlation energy, has long been identified as a major limitation of practical density functional approximations. We develop and test the performance of different self-interaction corrected functionals in accurately predicting a wide range of properties. This work focuses on use of the Fermi-L\"{o}wdin orbital self-interaction correction (FLOSIC) method to study neutral water complexes and interaction of ions with water clusters. The strongly constrained and appropriately normed (SCAN) density functional approximation (DFA) has been found to give the correct energy ordering of low-lying isomers of water hexamers, resolves the density anomaly between water and ice, and improves the relative lattice energy of ice polymorphs and the infrared spectra of liquid water. However, SCAN is not without its drawbacks. The binding energies of water clusters and lattice energies of ice phases are overestimated by SCAN. We find that by explicitly removing the self-interaction error, the hydrogen-bond binding energy of water clusters can be significantly improved. In particular, self-interaction correction to the SCAN functional (FLOSIC-SCAN) improves binding energies without altering the correct energetic ordering of the low-lying water hexamers. So, orbital-by-orbital removal of self-interaction error applied on top of a proper DFA can lead to an improved description of water complexes. To gain further insight into the performance of different functionals on the relative stability of water clusters, we decompose the total interaction energy into many-body components. We see that the major portion of error in SCAN comes from the two-body interaction, and the FLOSIC-SCAN improves two-body interactions over SCAN and predicts higher-order many-body interactions with about the same accuracy as SCAN. The SCAN functional gives good account of monomer deformation energy (one-body energy), PBE estimated it too low and self-interaction corrected methods FLOSIC-PBE and FLOSIC-SCAN estimated too high monomer deformation energies. Improvement in the total interaction energy by FLOSIC-PBE and FLOSIC-SCAN is happening because of error cancellation by one-body interaction energy. Aqueous solutions of ions are of particular interest due to their profound applications in environmental chemistry, solvation mechanics, the desalination process, etc. This motivated us to study ion-water systems, which include hydronium ion-water clusters, hydroxyl ion-water clusters, halide ion-water clusters, and alkali ion-water clusters. The erroneous delocalization of the extra-electron in anions obtained with DFAs is basis-set dependent. DFAs like LSDA, PBE, or SCAN can bind only a fraction of the excess electron in the complete basis set limit, implying that a moderate-sized localized basis would be a good choice for them. But, accurate description of hydrogen bonds often requires a large basis with some extra diffuse functions. So, in negatively charged hydrogen-bonded systems like deprotonated water clusters, the suitable choice of basis-set is both difficult and ambiguous. We explore this issue systematically in this work. Further, we have found that the better performance by application of FLOSIC is seen in all systems that are connected at least with one hydrogen bond and the error in the binding energy decreases with increase in the size of an ion or equivalently decreases with the length of the hydrogen bond. Moreover, within the same ion-water system, error in the binding energy decreases with increase in the size of the cluster. Non-hydrogen-bonded water-alkali clusters are not affected by the self-interaction errors. / Physics

Le Dispositif d'Irradiation d'Agrégats Moléculaires (DIAM) est conçu pour l'étude de mécanismes de dissociation résultant de l'interaction de nanosystèmes moléculaires avec des protons de 20-150 keV. Une technique originale de spectrométrie de masse appelée COINTOF (Correlated Ion and Neutral Time Of Flight) permet la mesure corrélée du temps de vol des fragments neutres et chargés issus de la dissociation d'un système moléculaire sélectionné en masse. Une stratégie de traitement des signaux a été développée afin de pouvoir distinguer des fragments proches en temps (< 1ns). Les données collectées sont structurées dans le logiciel ROOT® pour l'analyse statistique des corrélations. Le fonctionnement de la technique COINTOF est illustré par des expériences de dissociation induite par collision d'agrégats d'eau protonés sur une cible gazeuse. La méthodologie d'analyse des données est exposée à travers l'étude du canal de dissociation du trimère d'eau protoné produisant l'ion chargé H3O+ et deux molécules d'eau. La distribution de la différence de temps de vol entre les deux fragments neutres est mesurée, mettant en évidence une énergie libérée de quelques eV. En parallèle, un second spectromètre de masse à temps de vol adapté à l'évolution du dispositif a été développé. Il associe un temps de vol linéaire et un temps de vol orthogonal et intègre un détecteur à position (ligne à retard). Des simulations ont démontré les potentialités du nouvel analyseur. Enfin, des travaux ont été menés au laboratoire R.-J. A. Lévesque (Université de Montréal) portant sur les capacités d'imagerie de détecteurs à position multi-pixel de la collaboration MPX-ATLAS. / DIAM (Dispositif d'Irradiation d'Agrégats Moléculaires) is a n ewly designed experimental setup to investigate processes resulting from the irradaition of molecular nano-systems by 20-150 keV protrons. One of its specificities relies on the original techique of mass spectrometry named COINTOF (Correlated Ion and Neutral Time of Flight) consisting in correlated measurments of the time of fkight of charged and neutral fragments produced by the dissociation of a single molecular ion parent. A strategy of treatment and analysis of the detection signals was developed to distinguish two fragments close in time (<1ns). The collected data are structured in the software ROOT for the statistical analysis of the correlations. The COINTOF technique is illustrated in the case of collision induced dissociation of protonated water clusters on atomic targets. The methodology of the analysis is explained through the study of dissociation channel of the protonated water trimer producing the charged fragment H3O+ and two water molecules. The distribution of the time of flight difference between the two neutral fragments is measured providing a,n estimate of the kinetic energy release of a few eV. In parallel, a second time-of-flight mass spectrometer was designed. It associated a linear time-of-flight and an orthogonal time-of-flight and integrates position detectors (delay line anode). Simulations demonstrate the potentials of the new analyzer. Finally, research works were led at the laboratory R.-J. A. Lévesque (Université de Montréal) on the imaging capabilities of the multi-pixel detectors of the MPX-ATLAS collaboration.