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A molecular dynamics study of selected polar liquids and their aqueous mixturesHaughney, Michael Francis January 1987 (has links)
No description available.
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Ab initio and empirical potentials for small moleculesKnowles, D. B. January 1986 (has links)
No description available.
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Accurate Non-Born--Oppenheimer Variational Calculations of Small Molelcular SystemsBubin, Sergiy January 2006 (has links)
The research overviewed in this dissertation concerns highly accurate variational calculations of small molecular systems without assuming the Born--Oppenheimer approximation. The centerpiece of the research is the use of different forms of explicitly correlated Gaussian basis functions. These basis functions allow analytical evaluation of all necessary matrix elements and provide a very powerful tool for solving quantum mechanical problems encountered in various areas of physics. Most of the derivations presented in the dissertation are done within the formalism of matrix differential calculus that has proven to be a very handy and effective way of dealing with explicitly correlated Gaussians. As this fomalism is not widely used in physics or chemistry, some mathematical background is provided. The expressions obtained theoretically were implemented in a computer code that was run quite extensively on several parallel computer systems during the period of the author's Ph.D. study. The results of many such calculations are presented and discussed. The dissertation is primarily based on the content of the papers that were published in coathorship with my scientific advisor and other collaborators in several scientific journals. It also includes some topics that were not considered in the publications but are essential for the completeness and good understanding of the presented work.
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A Density Approach to Chemical BindingPreston, Harry John Thomas 05 1900 (has links)
<p> The material presented in this thesis is an attempt to obtain an increased understanding of the electronic structure and chemical binding in molecular systems. The one-electron charge distribution in methane, which is derived by considering only one-electron dependent properties of the system, is used to analyze the chemical binding in this molecule. A theoretical method, which allows one to determine the effect of the Pauli exclusion principle on the one-electron density distribution, is used to test the concepts underlying the electron pair repulsion theory as applied to H2O and NH3. Kinetic energy distributions are defined in order to examine the relationship between the topographical features of the molecular one-electron charge distribution and the kinetic energy of the system.</p> / Thesis / Doctor of Philosophy (PhD)
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Espectroscopia vibracional, Raman ressonante e eletrônica de nitroderivados em sistemas conjugados / Vibrational, resonance Raman and electronic spectroscopies of nitroderivatives in conjugated systemsAndo, Rômulo Augusto 07 April 2005 (has links)
No presente trabalho foram investigados vários sistemas moleculares contemplando um ou mais grupos NO2 com características fortemente elétron atraentes, e por outro lado um grupo fortemente elétron doador (NH2, OH ou N3H) conectados através de um anel benzênico ou piridínico. A caracterização das propriedades de transferência de carga intramolecular (CT) nesses sistemas constitui um dos principais objetivos do trabalho, tendo sido para tanto utilizadas as técnicas de espectroscopia eletrônica, espectroscopia vibracional (Raman e infravermelho) e com grande destaque, a espectroscopia Raman ressonante. Essa investigação permitiu a caracterização dos grupos cromofóricos envolvidos na CT entre os vários substituintes e suas posições relativas. Em vários casos foi possível estender a investigação para as espécies aniônicas obtidas pela desprotonação dos grupos NH2, OH e N3H, quando então se nota mudança abrupta das características da transição de transferência de carga (energia e intensidade), o que por sua vez conduz a uma muito maior deslocalização eletrônica do cromóforo, como revelado pela análise dos espectros de absorção (UV-Vis) e Raman ressonante (RR). No caso de sistemas mais estendidos, como é o caso típico do ânion do 1,3-bis(4-nitrofenil)triazeno os dados de espectroscopia eletrônica e espectroscopia Raman ressonante mostram de maneira clara a presença de duas transições de transferência de carga na região do visível, o que caracteriza um sistema bicromofórico. / In the present work were investigated molecular systems bearing one or more NO2 groups, with strong electron withdrawing characteristics, in addition to a strong electron donating group (NH2, OH, N3H), connected to a benzene or pyridine ring. The characterization of the intramolecular charge transfer (CT) process in such systems is one of the main objects of this work and for such, electronic spectroscopy, vibrational spectroscopy (Raman and IR) and in special, resonance Raman spectroscopy were used. The study revealed the chromophoric moieties involved in the CT transitions in the several molecules investigated, included the ones where the relative positions of the substituents were changed. In several cases it was possible to extend the study to the anionic species that results from the deprotonation of the NH2, OH and N3H groups, where an abrupt change of the CT transition (energy and intensity) is observed, and what in its turn leads to a much more delocalized chromophore, as revealed by the UV-Vis and resonance Raman spectra. In the case of the more extended systems, as in the typical case of 1,3-bis(4-nitropheyl)triazene anion, the data show clearly the presence of two CT transitions in the visible region, what amounts to the formation of a bichromophoric system.
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Espectroscopia vibracional, Raman ressonante e eletrônica de nitroderivados em sistemas conjugados / Vibrational, resonance Raman and electronic spectroscopies of nitroderivatives in conjugated systemsRômulo Augusto Ando 07 April 2005 (has links)
No presente trabalho foram investigados vários sistemas moleculares contemplando um ou mais grupos NO2 com características fortemente elétron atraentes, e por outro lado um grupo fortemente elétron doador (NH2, OH ou N3H) conectados através de um anel benzênico ou piridínico. A caracterização das propriedades de transferência de carga intramolecular (CT) nesses sistemas constitui um dos principais objetivos do trabalho, tendo sido para tanto utilizadas as técnicas de espectroscopia eletrônica, espectroscopia vibracional (Raman e infravermelho) e com grande destaque, a espectroscopia Raman ressonante. Essa investigação permitiu a caracterização dos grupos cromofóricos envolvidos na CT entre os vários substituintes e suas posições relativas. Em vários casos foi possível estender a investigação para as espécies aniônicas obtidas pela desprotonação dos grupos NH2, OH e N3H, quando então se nota mudança abrupta das características da transição de transferência de carga (energia e intensidade), o que por sua vez conduz a uma muito maior deslocalização eletrônica do cromóforo, como revelado pela análise dos espectros de absorção (UV-Vis) e Raman ressonante (RR). No caso de sistemas mais estendidos, como é o caso típico do ânion do 1,3-bis(4-nitrofenil)triazeno os dados de espectroscopia eletrônica e espectroscopia Raman ressonante mostram de maneira clara a presença de duas transições de transferência de carga na região do visível, o que caracteriza um sistema bicromofórico. / In the present work were investigated molecular systems bearing one or more NO2 groups, with strong electron withdrawing characteristics, in addition to a strong electron donating group (NH2, OH, N3H), connected to a benzene or pyridine ring. The characterization of the intramolecular charge transfer (CT) process in such systems is one of the main objects of this work and for such, electronic spectroscopy, vibrational spectroscopy (Raman and IR) and in special, resonance Raman spectroscopy were used. The study revealed the chromophoric moieties involved in the CT transitions in the several molecules investigated, included the ones where the relative positions of the substituents were changed. In several cases it was possible to extend the study to the anionic species that results from the deprotonation of the NH2, OH and N3H groups, where an abrupt change of the CT transition (energy and intensity) is observed, and what in its turn leads to a much more delocalized chromophore, as revealed by the UV-Vis and resonance Raman spectra. In the case of the more extended systems, as in the typical case of 1,3-bis(4-nitropheyl)triazene anion, the data show clearly the presence of two CT transitions in the visible region, what amounts to the formation of a bichromophoric system.
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Computer-aided modeling and simulation of molecular systems and protein secondary structure predictionSoni, Ravi January 1993 (has links)
No description available.
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Computer-aided modeling and simulation of molecular systems and protein (WT-bGH) structure minimizationHuang, Zheng January 1995 (has links)
No description available.
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Application of Generalized Sturmian Basis Functions to Molecular Systems / Applications de bases Sturmiennes généralisées à des systèmes moléculairesGranados Castro, Carlos Mario 18 February 2016 (has links)
Dans cette thèse nous implémentons une approche Sturmienne, qui se sert de fonctions Sturmiennes généralisées (GSFs, en anglais), pour étudier l'ionisation de molécules par collisions de photons ou d'électrons. Comme l'Hamiltonian de la cible est non central, la description de l'ionisation des molécules n'est pas simple. En plus, puisque l'orientation spatiale de la molécule n'est généralement pas déterminée lors des expériences, une question importante à considérer est l'orientation aléatoire de la cible. Dans la littérature, des nombreuses méthodes théoriques ont été proposées pour traiter les molécules ; néanmoins, la plupart sont adaptées pour étudier, principalement, des états liés. Une description précise des états non-liés (continuum) des molécules reste un défi. Ici, nous proposons d'attaquer le problème avec les GSFs qui ont, par construction, un comportement asymptotique approprié au système étudié. Cette propriété permet de faire des calculs d'ionisation de façon plus efficace. Dans une première partie, nous validons l'implémentation de notre approche Sturmienne par l'étude de la photo-ionisation (PI) d'atomes. Différents potentiels effectifs sont utilisés pour décrire l'interaction de l'électron éjecté avec la cible ionisée. Les sections efficaces de PI sont calculées dans les jauges de longueur et de vitesse. Pour l'atome d'hydrogène la comparaison avec la formule analytique, indique qu'une convergence très rapide est obtenue avec un nombre modéré de GSFs. Pour He et Ne, nos résultats montrent, également, un très bon accord avec d'autres résultats théoriques et expérimentaux. Dans le cas des molécules, nous avons abordé l'orientation aléatoire avec deux stratégies : une utilise un potentiel moléculaire modèle (non-central), et l'autre un potentiel moyenné (central). Nous étudions la PI de CH4, NH3 et H2O à partir des orbitales de valence extérieure et intérieure, et aussi de SiH4 et H2S à partir des orbitales extérieures. Les sections efficaces de PI et les paramètres d'asymétrie (obtenus à partir des distributions angulaires) sont comparés avec ceux publiés dans la littérature. Nos résultats sont globalement satisfaisants et reproduisent les caractéristiques principales de ce processus d'ionisation. Dans une deuxième partie de la thèse, nous utilisons l'approche Sturmienne pour étudier l'ionisation de molécules par impact d'électrons. Pour le processus (e,2e), les sections efficaces triplement différentielles (TDCSs) sont examinées dans la première et deuxième approximation de Born, également en traitant de deux façons l'orientation aléatoire des molécules. Nous avons testé la méthode en comparent nos TDCSs pour l'atome d'hydrogène, montrant aussi son efficacité. Enfin, nous l'avons apliqué à l'ionisation de CH4, H2O et NH3, et nous avons comparé les résultats avec des données expérimentales et théoriques disponibles dans la littérature. Dans la plupart des cas, nos TDCSs sont en accord satisfaisant avec ces données, en particulier pour H2O et pour des électrons lents dans le cas de CH4 / In this PhD thesis we implement a Sturmian approach, based on generalized Sturmian functions (GSFs), to study the ionization of molecules by collision with photons or electrons. Since the target Hamiltonian is highly non-central, describing molecular ionization is far from easy. Besides, as the spatial orientation of the molecule in most experimental measurements is not resolved, an important issue to take into account is its random orientation. In the literature, many theoretical methods have been proposed to deal with molecules, but many of them are adapted to study mainly bound states. An accurate description of the unbound (continuum) states of molecules remains a challenge. Here we propose to tackle these problems using GSFs, which are characterized to have, by construction, the correct asymptotic behavior of the studied system. This property allows one to perform ionization calculations more efficiently. We start and validate our Sturmian approach implementation by studying photoionization (PI) of H, He and Ne atoms. Different model potentials were used in order to describe the interaction of the ejected electron with the parental ion. We calculated the corresponding PI cross sections in both length and velocity gauges. For H atom, the comparison with the analytical formula shows that a rapid convergence can be achieved using a moderate number of GSFs. For He and Ne we have also an excellent agreement with other theoretical calculations and with experimental data. For molecular targets, we considered two different strategies to deal with their random orientation: one makes use of a molecular model potential (non-central), while the other uses an angular averaged version of the same potential (central). We study PI for CH4, NH3, and H2O, from the outer and inner valence orbitals, and for SiH4 and H2S from the outer orbitals. The calculated PI cross sections and also the asymmetry parameters (obtained from the corresponding angular distributions) are compared with available theoretical and experimental data. For most cases, we observed an overall fairly good agreement with reference values, grasping the main features of the ionization process. In a second part of the thesis, we apply the Sturmian approach to study ionization of molecules by electron collisions. In the so-called (e,2e) processes, fully differential cross sections are investigated within both the first- or the second-Born approximations. Again, we show how to include in the description the random orientation of the molecule. We start with H atom, as a test system: the comparison of the calculated triple differential cross sections (TDCSs) with analytical results illustrates, similarly to the PI case, the efficiency of our GSF method. It is then applied to ionization of CH4, H2O and NH3, and comparisons are made with the few theoretical and experimental data available in the literature. For most cases, our TDCSs can reproduce such data, particularly for H2O and for slow ejected electrons in CH4
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Θεωρητική μελέτη νανοσωματιδίων και νανοσυστημάτων πυριτίουΚουκάρας, Εμμανουήλ Ν. 27 December 2010 (has links)
Στην εργασία αυτή μελετάμε μια σειρά από αντιπροσωπευτικά νανοφασικά συστήματα πυριτίου, στο πλαίσιο κοινών ιδιοτήτων και αρχών που θα βοηθήσουν σε μελλοντικές εφαρμογές σχεδιασμού μοριακών υλικών βασισμένων σε αυτά τα συστήματα. Οι κατηγορίες των συστημάτων με τα οποία ασχολούμαστε είναι (α) υδρογονωμένα και μη-υδρογονωμένα νανοσυσσωματώματα και νανοκρυσταλλικά συστήματα πυριτίου με ή χωρίς ενσωματωμένα μέταλλα μετάπτωσης, που αποτελούν χαρακτηριστικά μοντέλα ενδοεπιφάνειας μετάλλου−ημιαγωγού, (β) υπέρλεπτα υδρογονωμένα νανοσύρματα πυριτίου και (γ) οργανομεταλλικά πολλαπλών στρώσεων (multidecker-sandwiches) πυριτίου−άνθρακα. Εκτός από τη μελέτη των δομικών, ηλεκτρονικών, οπτικών, δονητικών και μαγνητικών ιδιοτήτων των συστημάτων, εστιάζουμε στην αναζήτηση μηχανισμών σταθεροποίησης και την εύρεση και καθορισμό κανόνων που μπορούν να λειτουργήσουν ως «εργαλεία μοριακού σχεδιασμού» με τη γενικότερη δυνατή ισχύ. Τα συσσωματώματα πυριτίου σταθεροποιούνται μέσου των μετάλλων μετάπτωσης σε δομές κλωβού και χαρακτηρίζονται συχνά από υψηλή συμμετρία και μεγάλα ενεργειακά χάσματα, ιδιότητες επιθυμητές για εφαρμογές στην οπτοηλεκτρονική και νανοηλεκτρονική. Στη μελέτη των νανοσυρμάτων πυριτίου συγκρίνουμε την σταθερότητα μεταξύ νανοσυρμάτων με διαφορετικές επιφανειακές δομές ενώ διατυπώνουμε κανόνα «μαγικότητας» νανοσυρμάτων με τον οποίο ερμηνεύουμε την σταθερότητά τους και την συνδέουμε με την ελαστικότητα και την κατανομή υδρογόνου στην επιφάνεια τους. Τέλος, βασιζόμενοι στην ισολοβική αρχή the boron connection, σχεδιάζουμε και μελετάμε μια νέα κατηγορία νανοδομών τύπου multidecker sandwiches οργανοπυριτίου. Στη διάρκεια εκπόνησης αυτής της διατριβής δημοσιεύτηκαν συνολικά 19 εργασίες σε διεθνή περιοδικά και σε πρακτικά συνεδρίων. / In this work we study a series of representative nanoscale systems based on silicon, in the context of common properties and principles which will assist in future applications in designing molecular materials based on these systems. The categories of the systems which we work on are (a) hydrogenated and non-hydrogenated silicon nanoclusters and nanocrystallic systems with or without embedded transition metals, which constitute models of metal−semiconductor interfaces, (b) ultrathin hydrogenated silicon nanowires and (c) organometallic silicon−carbon multidecker-sandwiches. In addition to the study of structural, electronic, optical, vibrational and magnetic properties of these systems, we focus on a search for stabilizing mechanisms and in finding and defining rules that can function as “molecular designing tools” with the broadest possible validity. The silicon nanoclusters are stabilized to cage-like structures by the insertion of transition metals and are characterized by high symmetry and large energy gaps, desirable properties for applications in optoelectronics and nanoelectronics. In the study of silicon nanowires we compare the stability between nanowires with different surface structures while we formulate “magicity” rules for nanowires with which we interpret their stability and associate it with their elasticity and the distribution of the surface hydrogen. Finally, based on the isolobal principle the boron connection, we design and study a new class of organometallic multidecker-sandwich type nanostructures. During the elaboration of this dissertation we published overall 19 papers in international scientific journals and conferences’ proceedings.
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