Dissertations / Theses on the topic 'Molecular materials'

Esta Tesis está centrada en el diseño, síntesis y caracterización de nuevos materiales moleculares multifuncionales basados en sistemas Dador-Aceptor (D-A) formados por la unidad dadora de electrones tetratiafulvaleno (TTF) enlazada a la unidad aceptora de electrones el radical policlorotrifenilmetilo (PTM) mediante diferentes puentes -conjugados. Estos compuestos pueden exhibir propiedades físicas muy interesantes como biestabilidad o propiedades ópticas no lineales en solución, conductividad en estado sólido o rectificación cuando son anclados en superficies. Por tanto, estos sistemas podrían encontrar aplicación en el campo de la electrónica molecular como interruptores, conductores o rectificadores. En la primera parte de esta Tesis, se estudiará el fenómeno de biestabilidad en solución de un sistema D-A basado en un radical PTM conectado a un TTF mediante un puente vinileno. Este sistema puede exhibir un cambio inducido por la temperatura entre dímeros diamagnéticos a temperatura ambiente y monómeros paramagnéticos a alta temperatura. Los dos distintos estados presentan diferentes propiedades ópticas y magnéticas utilizando la temperatura como estímulo externo. Por otra parte, también se presentará el diradical A-D-A compuesto por dos subunidades PTM radicalarias conectadas mediante un puente TTF-vinileno que puede modificar reversiblemente sus propiedades ópticas, magnéticas y electrónicas al oxidarse o reducirse en solución. La modificación de la deslocalización electrónica y del acoplamiento magnético se observa cuando generamos las especies cargadas y los cambios han sido racionalizados mediante cálculos teóricos. En la segunda parte de la Tesis, se presentará la síntesis y caracterización de distintos derivados TTF--PTM incrementando el número de vinilenos entre las unidades D y A. También se estudiará la transferencia de carga intramolecular y las propiedades ópticas no lineales (NLO) en solución y su dependencia con la estructura electrónica abierta así como con la longitud del puente de cada uno de los compuestos. En la tercera parte de la Tesis, se estudiará las arquitecturas auto-ensambladas en estado sólido de un nuevo sistema TTF-PTM. La estructura cristalina muestra un ordenamiento supramolecular con una segregación de las unidades dadoras y aceptoras. Además, se estudiará la aparición de conductividad en los cristales del mismo sistema al aumentar la presión. El comportamiento de semiconductor a altas presiones se relacionará con el aumento de interacciones intermoleculares así como con el incremento de la deslocalización de carga. Finalmente, en la última parte de la Tesis se presentará un nuevo compuesto TTF-PTM que ha sido funcionalizado con un grupo disulfuro para preparar monocapas auto-ensambladas (SAMs) en superficies de oro. Estas SAMs han sido caracterizadas mediante diversas técnicas espectroscópicas para estudiar la estructura electrónica del sistema. Además, se estudiará el transporte de carga a través de las SAMs para evaluar un posible comportamiento de rectificación.
This Thesis is focused on the design, synthesis and characterization of new multifunctional molecular materials based on donor-acceptor (D-A) dyads formed by the electron-donor tetrathiafulvalene (TTF) unit linked to the electron-acceptor polychlorotriphenylmethyl (PTM) radical moiety through different -conjugated bridges. These compounds can exhibit interesting physical properties such bistability and nonlinear optical properties in solution, conductivity in the solid state or electrical rectification when anchored on surfaces. Thus, these systems could find potential applications in the field of molecular electronics as switches, conductors or rectifiers. In the first part of the Thesis, we have studied the bistability phenomenon in solution of a D-A dyad based on a PTM radical linked to a TTF moiety through a vinyelene bridge. This system exhibited a temperature-induced switching between diamagnetic dimers at room temperature and paramagnetic monomers at high temperature. The two different states showed different optical and magnetic properties when using the temperature as external input. On the other hand, we have also reported the A-D-A diradical triad based on two PTM radical subunits connected through a TTF-vinylene bridge that can reversibly modify the optical, electronic and magnetic properties by one-electron reduction and oxidation in CH2Cl2 solution. The modification of electron delocalization and magnetic coupling was observed when the charged species were generated and the changes were rationalized by theoretical calculations. In the second part of the Thesis, we have reported the synthesis and characterization of different TTF--PTM dyad derivatives increasing the number of vinylene units between the D and A moieties. We have studied the intramolecular charge transfer and non-linear optical (NLO) properties in solution and their dependence on the open-shell structure as well as on the bridge length for this family of compounds. In the third part of the Thesis, we have studied self-assembled architectures in the solid state of a new D-A dyad based on a PTM radical linked to a TTF moiety through a -phenyl-pyrrole bridge. The crystal structure showed an interesting supramolecular arrangement with segregated donor and acceptor units. Moreover, we reported the appearance of conductivity in single crystals of the same system when increasing the pressure. The semiconducting behavior at high pressures has been attributed to the enhanced intermolecular interactions and charge delocalization due to incorporation of TTF units which force the formation of close packed stacks of molecules. Finally in the last part of the Thesis, we have reported a new TTF-PTM dyad that was functionalized with a disulfide group in order to prepare self-assembled monolayers (SAMs) on gold. These SAMs were fully characterized by different spectroscopic techniques in order to study the electronic structure of the system. Moreover, charge transport measurements through the SAMs were performed in order to evaluate the possible rectification behavior.

Els interruptors moleculars han estat un camp de recerca important en els últims anys degut a la seva capacitat per interconvertir-se entre múltiples estats al estar exposats a un estímul (escriptura) i al fet de modificar les seves propietats després del canvi (lectura). Els interruptors moleculars que interaccionen amb llum per canviar d’estat o bé que modifiquen les seves propietats òptiques són d’especial interès ja que la llum permet un alt control espai temporal de forma no invasiva i la seva detecció té una alta sensibilitat. Per aquest motiu, durant aquesta tesis s’han desenvolupat múltiples materials i processos fotofuncionals els quals poden resumir-se en dues parts: Per una banda, el caràcter multiestat d’una família de interruptors molecular (fluoro)cròmics basats en compostos espirocíclics zwitteriònics de Meisenheimer (SZMC), es va ampliar mitjançant la identificació d’un nou estat catiònic amb propietats òptiques distintives, el qual és pot generar tant electroquímicament com a través de l’adició d’un àcid. A més, es va investigar el comportament termo(fluoro)cròmic dels SZMC i es va demostrar que podien respondre tant a canvis en el dissolvent com a la presència d’anions. Aquest comportament multiestat i de resposta a múltiples estímuls va ser emprat en la preparació de una sèrie de materials fotofuncionals basats en SZMC com: un detector de pH d’ampli espectre, dispositius electro(fluoro)cròmics i sensors iònics, termals i de dissolvents. Per altra banda, es van controlar tres processos químics amb ditieniletens (DTE) mitjançant llum. Primer, la introducció d’un grup electroacceptor EWG va permetre la modulació del pKa de fenols funcionalitzats amb DTEs. Després, el control amb dues longituds d’ona d’una reacció d’amidació es va aconseguir amb un estratègia similar a l’anterior utilitzant un éster activat basat en DTE. Aquest va reaccionar fins a 24 vegades més ràpid en el estat tancat generat amb llum UV (ie. activació amb UV) que amb l’estat obert obtingut sota irradiació amb llum visible (ie. desactivació amb visible). Finalment, la estratègia de controlar reaccions amb dos colors també va ser aplicada en la fotoligació mitjançant una reacció de oxo-Diels Alder d’un dienòfil basat en DTE actiu en la forma tancada (ie. Activacióamb llum UV, desactivació amb llum visible) i un diè generat en llum UV basat en orto-metilbenzaldèhid.
Los interruptores moleculares han sido un campo de investigación importante en los últimos años debido a la capacidad de interconvertir-se entre múltiples estados al exponerse a un estímulo (escritura) y modificar sus propiedades (lectura). De especial interés han sido los interruptores moleculares que interaccionan con la luz ya sea para cambiar de estado o bien modificar sus propiedades ópticas en la transformación. Esto és debido a que la luz permite un alto control espaciotemporal al mismo tiempo que és no invasiva y altamente sensible a la detección. Por estos motivos, durante esta tesis se han desarrollados múltiples materiales y procesos fotofuncionales los cuales pueden resumirse en dos partes: Por un lado, el carácter multiestado de una familia de interruptores moleculares (fluoro)crómicos basados en compuestos espirocíclicos zwitteriònicos de Meisenheimer (SZMC) se amplió mediante la identificación de un nuevo estado catiónico, con propiedades ópticas distintivas, que se puede generar tanto electroquímicamente, como a través de la adición de ácido. Además, se investigó el comportamiento termo(fluoro)crómico de los SZMC y se demostró que podían responder tanto a cambios en el disolvente como a la presencia de iones. Este comportamiento multiestado i de respuesta a múltiples estímulos fue utilizado en la preparación de varios materiales fotofuncionales basados en SZMC como: un detector de pH de amplio espectro, dispositivos electro(fluoro)crómicos i sensores iónicos, termales i de disolventes. Por otro lado, se controlaron tres procesos químicos diferentes con interruptores moleculares fotoinducidos de tipo ditienileteno (DTE) mediante luz. Primero, la introducción de un grupo electroacceptor permitió la modulación del pKa de un fenol funcionalizado con un DTE. Segundo el control de una reacción de amidación con dos longitudes de onda fue conseguido con una estrategia similar a la anterior utilizando un ester activado basado en DTE. Este reacciona hasta 24 veces más rápido en el estado cerrado generado con luz ultravioleta (ie. activación con UV) que en el estado abierto que se obtiene al irradiar con luz visible (ie. desactivación con visible). Finalmente, el control de reacciones con dos colores de luz fue utilizado para controlar la reacción de oxo-Diels Alder entre un dienófilo basado en DTE activo en el estado cerrado (ie. activación con UV, desactivación con luz visible) i un dieno generado con luz UV basado en orto-metilbenzaldehido.
Molecular switches have been an important research field in the recent years due to its capacity to interconvert between multiple states through a stimulus (writing) and change their properties (reading). Of special interest are molecular switches that interact with light by either changing their optical properties or reacting as stimulus, due to its noninvasive high spatiotemporal control and sensitivity. As a result, several photofunctional materials and processes based on molecular switches were developed during this thesis which can be summarized in two topics. On the one hand, the multistate character of a family of (fluoro)chromic molecular switches based on spirocyclic zwitterionic Meisenheimer compounds (SZMC) was broadened by identifying a novel cationic state with distinctive optical properties, which could be achieved electrochemically or via acid addition. Moreover, the thermo(fluoro)chromic behavior of SZMCs was investigated and successfully demonstrated that they can respond to certain ions and solvents. This multistimuli-responsive and multistate character was then exploited for the preparation of a variety of photofunctional materials based on SZMCs: wide-range pH detectors, electro(fluoro)chromic displays, and thermal, ionic and solvent sensors. On the other hand, light controlled reactivity with dithienylethenes (DTE) was achieved for three chemical processes. First, the introduction of electrowithdrawing groups (EWG) allowed the modulation of the pKa in acetonitrile of a series of DTEs tethering phenol moieties. Second, a similar strategy allowed for the dual-color control of an amidation reaction employing DTE-based active esters which react up to 24 times faster in the UV-generated closed state (ie. activation with UV irradiation) than in the open state formed under visible illumination (ie depletion with visible light). Finally, two-wavelength control was also achieved for an oxo-Diels Alder reaction between a DTE-dienophile active in the closed state and a UV-generated diene based on orto-methylbenzaldehyde.
Universitat Autònoma de Barcelona. Programa de Doctorat en Química

Materiales orgánicos basados en moléculas pequeñas con propiedades optoelectrónicas son particularmente atractivos en los campos de celdas solares orgánicas y en el campo de la electrónica molecular. Porfirinas y curcuminoides (CCMoids) son moléculas que suscitan interés, siendo buenas candidatas en los campos mencionados, debido a que presentan estructuras químicas modificables y excelentes propiedades electrónicas. En esta tesis, se han estudiado la preparación y diseño de moléculas pertenecientes a las dos familias aquí indicadas, la capacidad de autoensamblaje de dichas moléculas conjuntamente con sus posibles aplicaciones. En el capítulo II, se han sintetizado dos metaloporfirinas (Zn(4R-PPP) y Zn(PPP)) ligandos largos que contienen centros quirales o aquirales conjutantemente con grupos carbonilos en las cuatro posiciones meso de sus respectivos núcleos de porfirina. Posteriorment, se ha sintetizado un estudio completo relacionado con las interacciones intermoleculares no covalentes de dichas multiporfirinas y experimentos iniciales con la creación de celdas solares orgánicas de hetero-unión (BHJ-OCs) donde este tipo de porfirinas han sido procesadas en solución para el estudio de su comportamiento como sistemas donadores en dichas celdas. Dicho estudio se extendió en el capítulo III a dos nuevas porfirinas (TEP y Zn (TEP)) con sustituyentes carbonilos pero más cortos donde se investigó el efecto de las dimensiones de los ligandos en las interacciones intermoleculares finales, y cómo esto afecta el rendimiento de OSCs. En el capítulo IV se explica como con los mismos centros quirales en las posiciones meso, se obtuvo una nueva porfirina, Zn(4R-CPP), que contiene grupos carboxílicos. También se muestran los estudios con dicho sistema y porfirinas adicionales con la formación de sistemas de autoensamblaje binarios basados en interacciones no covalentes o de autoensamblaje iónico para su posible aplicación como nanomateriales. En el Capítulo V, se sintetizaron CCMoides que contienen grupos quirales, de forma similar al capítulo II, así como el estudio del efecto de la quiralidad de dichos materiales. Además, la investigación hace énfasis en el logro de grupos ácidos terminales a partir de la hidrolización de los grupos ésteres (como se muestra en el capítulo IV) que permitió investigar la posible creación de sistemas con diferente dimensionalidades. Después, en el Capítulo VI, se exploró la síntesis de CPs /redes mediante el uso de CCMoides que contienen grupos piridínicos en sus terminaciones (3Py-CCM). El último capítulo está dedicado al diseño de nuevos derivados de porfirina que contienen grupos de anclaje basados en azufre para su aplicación en electrónica molecular conjuntamente con el estudio de sus propiedades electrónicas en solución y en estado sólido. Además, una familia de CCMoids también se ha analizado de manera similar a los derivados de porfirina, con el objetivo de recopilar información para mejorar su diseño molecular para aplicaciones electrónicas.
Organic small molecules materials with optoelectronic properties are particularly attractive in the fields of organic solar cells and molecular electronics. Porphyrins and curcuminoids (CCMoids) are prospective candidates in these fields due to their modifiable chemical structures and outstanding properties. In this thesis, the design and preparation of these two families of molecules, together with their self-assembly abilities and potential applications have been studied. In chapter II, two metalloporphyrins (Zn(4R-PPP) and Zn(PPP)) containing long chiral or achiral moieties with carbonyl substituents in the four meso-positions of their porphyrin cores have been synthesized. Then, a complete study related to non-covalent multiporphyrin assemblies has been performed, and initial solution-processed bulk heterojunction organic solar cell experiments were presented. To extend the above study, in chapter III, new porphyrins (TEP and Zn(TEP)) with shorter carbonyl substituents have been investigated and the effect of the length of the ligands in intermolecular interactions was studied, searching how this factor affects as well the OSCs performance. With the same chiral centres in the meso-positions, a porphyrin Zn(4R-CPP) involving carboxylic groups was obtained in chapter IV. And the binary self-assembling systems based on its derivations were achieved through non-covalent interaction or ionic self-assembly towards their potential application as active components in nanomaterials. In Chapter V, CCMoids containing chiral groups, in a similar manner as chapter II, were synthesized. In addition, research towards the achievement of terminal acid groups from the hydrolyzation of the ester groups (as chapter IV shows) allowed the investigation of the possible creation of systems with different dimensionalities. Then in Chapter VI, the synthesis of CPs/networks was explored by the use of a CCMoid containing pyridine moieties at its endings (3Py-CCM). The last chapter is devoted to the design of new porphyrin derivatives containing sulphur-based anchoring groups for their application in single molecular electronics together with the study of their electronic properties in solution and solid state. In addition, a family of CCMoids has also been analysed in a similar manner as the porphyrin derivatives, with the aim of gathering information to improve their molecular design for electronic applications.

Assessing hazards due to energetic or reactive chemicals is a challenging and complicated task and has received considerable attention from industry and regulatory bodies. Thermal analysis techniques, such as Differential Scanning Calorimeter (DSC), are commonly employed to evaluate reactivity hazards. A simple classification based on energy of reaction (-H), a thermodynamic parameter, and onset temperature (To), a kinetic parameter, is proposed with the aim of recognizing more hazardous compositions. The utility of other DSC parameters in predicting explosive properties is discussed. Calorimetric measurements to determine reactivity can be resource consuming, so computational methods to predict reactivity hazards present an attractive option. Molecular modeling techniques were employed to gain information at the molecular scale to predict calorimetric data. Molecular descriptors, calculated at density functional level of theory, were correlated with DSC data for mono nitro compounds applying Quantitative Structure Property Relationships (QSPR) and yielded reasonable predictions. Such correlations can be incorporated into a software program for apriori prediction of potential reactivity hazards. Estimations of potential hazards can greatly help to focus attention on more hazardous substances, such as hydroxylamine (HA), which was involved in two major industrial incidents in the past four years. A detailed discussion of HA investigation is presented.

The work within this thesis is concerned with several different magnetic systems all involving materials that are rich in sulphur and are thus predicted to have strong magnetic coupling through these sulphur atoms. Firstly, a range of molecular salt materials of [dithiazolyl]_x[M(dithiolene)₂] were synthesised and their magnetic behaviour analysed. Dithiolene complex salts of [BDTA]⁺ [2]-[6] were found to have a mainly mixed anion-cation stacked structural motif and show a number of interesting magnetic properties, such as an almost perfect one dimensional antiferromagnetic chain system ([BDTA]₂[Cu(mnt)₂ [2], as well as the conducting charge transfer salt [BDTA][Ni(dmit)₂]₂ [3] that is the first example of the [BDTA]⁺ cation behaving as an open shell cation. The [BDTA]₂[Fe(tdas)₂Cl] salt [5] has the first mixed stacking structural motif of this anion (as it usually dimerises) and this material was found to be paramagnetic. The paramagnetic radical dithiazolyl cation [BBDTA]⁺ was also co-precipitated with dithiolene complexes to create magnetic salts [11]-[15]. These all showed mixed magnetic effects with some unusual magnetic interactions occurring. [BDTA]⁺ was also co-crystallised with MC1₄^2- anions to form molecular materials containing two dimensional magnetic structure with a square lattice magnetic pathway. This magnetic mechanism provides ideal materials for the study of ground state quantum magnetic effects that are thought to be related to the fundamental mechanism of superconductivity. This work also contains the study of the non interacting magnetic molecular thiophosphine complexes of the form [M((SPR¹R²)₂N)₂] (M = Mn, Co, Ni, R¹ = R² = Ph, ⁱPr and R¹=Ph and R²=ⁱPr) which behave as simple paramagnets ([16]-[24]). All M = Mn and Co complexes were found to be simple paramagnetic materials with a strong ligand field splitting.

Work on modelling compounds possessing die tetraaza[14]annulene (TAA) fragment is described. Modelling studies have been conducted to investigate both structural and electronic properties, of both single molecules and extended arrays of these compounds. The structural aspects have been investigated using molecular mechanics and crystallographic database investigations. Molecules based on the tetraaza[14] annulene structure have been found to adopt one of four conformations. The geometries of these conformations are planar, saddle-shaped, slightly twisted, and dome-shaped. The complexed metal centre and the arrangement of substituents on the periphery of the ligand, have been found to determine which conformation a molecule adopts. In order to model the compounds, three new atom types have been created for the Universal Force Field. The electronic aspects have been investigated using Hartree Fock based calculations for single molecules and Extended Huckel based calculations for extended systems. The electronics of die single molecules have shown there to be a linear trend in the LUMO energies, although die HOMO energies vary very little. The reason for this trend in the LUMOs is unknown, but appears not to be related to any obvious structural feature.

Molecular materials have raised much interest in the last decades in the quest for new multifunctional devices. Among the multiple properties that those materials may present, one of the most typical is magnetism, which arises from the presence of unpaired electrons in the molecules that constitute the three-dimensional crystal. Magnetism has a macroscopic observable, the magnetic susceptibility (Ji), which is usually rationalized in terms of a set of JAB magnetic interactions between pairs of molecules. However, any experimental technique allows for such direct correspondence and, thus, the experimental interpretation of the magnetic properties usually requires further analysis from the point of view of computational chemistry. Consequently, the present PhD thesis is a contribution to the computational modeling of molecule-based magnetic materials. Specifically, we describe how the tools of computational chemistry may be used in order to study those materials from different perspectives. With this aim in mind, we have applied computational chemistry techniques to rationalize the magnetic properties of several systems of interest, ranging from metal-organic compounds, based on Cu(II), to pure organic radicals based on the DTA and Benzotriazinyl building blocks, and including compounds based on the metal-radical synthetic approach, and also spin crossover materials based on Fe(II). Along the thesis we have demonstrated that computational chemistry is a helpful discipline, capable to aid in the interpretation of experimental results and in the prediction of interesting properties, especially when working in close collaboration with experimentalists. In particular, the First Principles Bottom-Up (FPBU) procedure, extensively developed in our group, is a useful tool to rationalize the magnetic properties of any molecular magnetic material. To this purpose, the magnetic topology (i.e. the network of JAB within the crystal) is the key element. Regarding the magnetic topology, we have also demonstrated that it can be more intricate and complex than expected, and that it cannot be directly inferred from the coordination pattern of the molecule-based material. Therefore, the experimental assignation of the magnetic topology, by means of a fitting procedure, must be taken with caution. About the JAB values, we have proved that they depend on temperature, and that this dependence may be especially important when working with organic radicals. On this class of materials, we have analyzed how the JAB values evolve with time, and seen that this evolution may involve huge fluctuations of their magnitude as a consequence of the thermal motion at finite temperatures. Interestingly, we demonstrate herein that, when the JAB values depend non-linearly with the thermal vibrations of a material, the standard static perspective of magnetism is not valid to fully understand their magnetic properties, and that it is then required to adopt a dynamic perspective. Regarding the computational modeling of JAB values, we have seen that the combination of UB3LYP and the Broken-Symmetry approach yields JAB values, when transformed into the macroscopic observables, are in good agreement with experiment. In fact, we have demonstrated that, in order to predict the strength of a given JAB value, small distortions in the crystal structure can induce large variations, which may be much more important than the intrinsic error associated with the theoretical method employed. We have also observed that the counterions and diamagnetic ligands may have an important effect in defining the magnetic properties of a system. Overall, we have demonstrated that the magnetic topology and, thus, the macroscopic magnetic properties of a given material, cannot be understood without the proper knowledge of their crystal structure.
Els materials moleculars han despertat molt d'interès en les últimes dècades degut a la seva possible aplicació en nous dispositius multifuncionals. Entre les diferents propietats que aquests materials poden presentar, una de les més típiques és el magnetisme, el qual sorgeix de la presència d’electrons desaparellats en les molècules que constitueixen el cristall tridimensional. El magnetisme té un observable macroscòpic, la susceptibilitat magnètica (Ji), que sol ser racionalitzada en termes microscòpics mitjançant el conjunt d'interaccions magnètiques JAB entre determinats parells de molècules. No obstant això, cap tècnica experimental permet aquesta correspondència directa i, per tant, la interpretació experimental de les propietats magnètiques sol requerir d’un posterior anàlisi des del punt de vista de la química computacional. La present tesi doctoral pretén doncs contribuir en el camp del magnetisme molecular i, més concretament, en com es poden utilitzar les eines de la química computacional per a modelitzar materials magnètics moleculars des de diferents perspectives. Amb aquest objectiu en ment, s’han racionalitzat les propietats magnètiques de diversos sistemes d'interès, que van des de compostos metal•lorgànics basats en ions de Cu(II) o de Co(II), radicals orgànics purs, compostos basats en l’estratègia sintètica de “metall-radical”, i finalment també materials de spin crossover basats en Fe(II). Al llarg de la tesi s'ha demostrat que la química computacional és una disciplina útil, capaç d'ajudar a la interpretació dels resultats experimentals i en la predicció de propietats interessants, especialment quan es treballa en estreta col•laboració amb els experimentadors. En particular, el procediment de primers principis Bottom-Up (FPBU, per les seves sigles en anglès), desenvolupat àmpliament en el nostre grup, és una eina útil per racionalitzar les propietats magnètiques de qualsevol material magnètic molecular. Per a aquest propòsit, la topologia magnètica (és a dir, la xarxa de JAB dins del cristall) és l'element clau. A més, hem analitzat diversos factors que afecten aquesta topologia magnètica, com els contraions, els radicals diamagnètics o l’efecte de la temperatura, mitjançant el la seva manifestació en les vibracions del cristall i en la contracció (expansió) que pateix al refredar-se (escalfar-se).

Post-functionalization of 3,5-bis(2-pyridyl)-4-hydro-1,2,4,6-thiatriazine (Py2TTAH) and its synthetic precursors have been explored through alkylation, arylation, and coordination. While alkylation was initially pursued at the central nitrogen atom of Py2TTAH, functionalization instead occurred on the sulfur atom. Consequently, the proclivity of the sulfur towards alkylation and arylation was studied. Neutral 3,5-bis(2-pyridyl)-S-methyl-1,2,4,6-thiatriazine (S-Me-Py2TTA) and 3,5-bis(2-pyridyl)-S-ethyl-1,2,4,6-thiatriazine were achieved via either anionic or cationic intermediates, and all isolable species were fully characterized. In addition, an aromatic derivative, 3,5-bis(2-pyridyl)-S-phenyl-1,2,4,6-thiatriazine was obtained through reactions using hypervalent iodide as an electrophile. Functionalization of Py2TTAH and S-Me-Py2TTA was also explored through coordination with iron. The synthesis and crystal structures of two different iron complexes are described. The incorporation of boron with Py2TTAH and its precursor, N-2-pyridylimidoyl-2-pyridylamidine was also considered. Both compounds afforded the same boratriazine ring. Overall, this thesis describes the groundwork for future functionalization of the Py2TTA framework, and its potential for molecular materials applications.

This work seeks to lay the foundation for improved art conservation epoxies by addressing two of the problems which currently limit their use. The first problem with current conservation epoxies is the difficulty of removal post-cure. This can be solved by synthesizing epoxies with thermally re-workable Diels-Alder weak links. The second problem relates to difficulty in identifying epoxy joints in reconstructed artifacts and can be solved by incorporating fluorescent monomers within the epoxy network. The challenge in both of these projects is to ensure that the modified epoxies are still suitable for conservation use.

Nowadays, material, energy and information technologies are three pillar industries. The materials that have close relation with our life have also been the foundation for the development of energy and information technologies. As the new member of the material family, functional molecular materials have become increasingly important for many applications, for which the design and characterization by the theoretical modeling have played the vital role. In this thesis, three different categories of functional molecular materials, the endohedral fullerenes, the fullerene derivatives and the self-assembled monolayers (SAMs), have been studied by means of first principles methods. The non-metal endohedral fullerene N@C60 is a special endohedral fullerene that is believed to be relevant to the construction of future quantum computer. The energy landscape inside the N@C60 has been carefully explored by density functional theory (DFT) calculations. The most energy favorable potential energysurfaces (PESs) for the N atom to move within the cavity have been identified. The effect of the charging on the PESs has also been examined. It is found that the inclusion of dispersion force is essential in determining the equilibriumstructure of N@C60. Furthermore, the performance of several commonly useddensity functionals with or without dispersion correction has been verified for ten different endohedral fullerenes A@C60 with the atom A being either reactive nonmetal or nobel gases elements. It shows that the inclusion of the dispersion forcedoes provide better description for the binding energy (BE), however, none ofthem could correctly describe the energy landscape inside all the ten endohedral fullerenes exclusively. It thus calls for the further improvement of current density functionals for weak interacting systems. Soft X-ray spectroscopy is a powerful tool for studying the chemical and electronic structures of functional molecular materials. Theoretical calculations have been proven to be extremely useful for providing correct assignments for spectraof large systems. In this thesis, we have performed first principles simulations forthe near-edge X-ray absorption fine structure (NEXAFS) and X-ray photoelectron spectra (XPS) of fullerene derivatives and aminothiolates SAMs. Our calculatedspectra can accurately reproduce experimental results available for all the systemsunder investigations, and identify the species or structures that are responsible for those unexpected spectral features observed in experiments. We have suggested a modified building block (MBB) approach that allows to calculate NEXAFS spectraof a large number of fullerene derivatives with very small computational cost, and resolved the long standing puzzle around the experimental XPS and NEXAFS spectra of SAMs with aminothiolates.

QC 20120523

Carbon is one of the most versatile materials available to man, for hundreds of years the 3D forms of carbon (diamond and graphite) have been exploited for their electrical and physical properties, however only in recent decades have the OD (fullerenes), 1D (nanotubes) and 2D (graphene) forms of carbon been available to study and use for new technologies. The experimental realisation of single layer (SLG) and few layer (FLG) graphene has led to an explosion of interest in the properties and capabilities of this material. Although single layer graphene had been considered theoretically a number of years earlier, it had long been the consensus that a single atom thick material would not be stable in the free state.

Chapter 1 contains a brief background into subjects such as Robin-Day classes, binary code, logic gates and electrochemistry in order to aid understanding of the rest of the chapter. The unique paradigm of Molecular Quantum Cellular Automata (MQCA) is presented along with the advantages it offers to traditional silicon based electronics. A summary of the existing modelled and synthesised MQCA systems is included along with an explanation of the characteristics required for materials to be suitable for MQCA. The subject of chapter 2 is cyclopentadiene cobalt cyclobutadiene complexes for the application of MQCA. The introduction examines the mechanism for the formation of cyclopentadiene cobalt cyclobutadiene complexes and the bonding in these compounds. A range of acetylenes were prepared for the formation of cyclopentadiene cobalt cyclobutadiene complexes were examined and characterised. Metal fragments including {Ru(dppe)2Cl} and AuPPh3Cl were attached to a cyclopentadiene cobalt cyclobutadiene core and these materials were characterised. The subject of chapter 3 is benzene based materials for the application of MQCA. 1,2,4,5-tetrakis(ferrocenylethynyl)benzene was prepared, characterised and the electrochemistry was examined for electronic communication between the ferrocene sites. A range of two metal centre compounds were examined for solubility and electrochemical stability with the view of preparing four metal centre compounds with a benzene core. The subject of chapter 4 is porphyrin based materials. This was the first area of work for this thesis and was discontinued. A brief summary of the synthetic work carried out is described, along with some literature work that was published whilst this work was being carried. Chapter 5 contains the experimental information for chapters 2-4.

Molecular sieve films and colloidal particles may have great potential for further utilization in novel technological sophisticated applications such as structured catalysts, sensors and membranes. The work presented in this thesis concerns the synthesis molecular sieve films and the crystallization of zoned MFI materials for novel catalyst and sensor applications. The seeding method developed at the division has been modified for the preparation of MFI and FAU type films on a variety of steel substrates ranging from ordinary carbon steel to highly corrosion resistant stainless steel. The films were characterized by SEM, XRD and gas adsorption techniques. The results revealed that the type of steel did not affect the film morphology, the thickness or the preferred orientation of the crystals, whereas the thermal stability was dependent on the steel. Films on various stainless steel supports were stable during calcination, whereas films on carbon steel supports peeled off upon rinsing after calcination because a relatively thick magnetite/hematite film formed. Pre-calination of carbon steel improved the zeolite film stability upon calcination. Zoned MFI materials (colloidal zoned MFI crystals and zoned films) were synthesized in this work in order to improve the catalytic performance of MFI. A two-step crystallization method was developed to prepare zoned MFI materials, in which precursor ZSM-5 colloidal particles or film were grown in a silicalite-1 synthesis solution directly or after acid treatment. It was shown that zoned MFI materials did not form when the ZSM-5 surface had a high aluminum content. In this case, polycrystalline aggregates or a sandwich film formed due to secondary nucleation. After reducing the aluminum content to half by acid treatment of ZSM-5, secondary nucleation of new silicalite-1 crystals was inhibited and zoned MFI material was obtained.
Godkänd; 2003; 20070216 (ysko)

The investigation of the mechanisms lying behind the (photo-)chemical processes is fundamental to address and improve the design of new organic functional materials. In many cases, dynamics simulations represent the only tool to capture the system properties emerging from complex interactions between many molecules. Despite the outstanding progresses in calculation power, the only way to carry out such computational studies is to introduce several approximations with respect to a fully quantum mechanical (QM) description. This thesis presents an approach that combines QM calculations with a classical Molecular Dynamics (MD) approach by means of accurate QM-derived force fields. It is based on a careful selection of the most relevant molecular degrees of freedom, whose potential energy surface is calculated at QM level and reproduced by the analytic functions of the force field, as well as by an accurate tuning of the approximations introduced in the model of the process to be simulated. This is made possible by some tools developed purposely, that allow to obtain and test the FF parameters through comparison with the QM frequencies and normal modes. These tools were applied in the modelling of three processes: the npi* photoisomerisation of azobenzene, where the FF description was extended to the excited state too and the non-adiabatic events were treated stochastically with Tully fewest switching algorithm; the charge separation in donors-acceptors bulk heterojunction organic solar cells, where a tight-binding Hamiltonian was carefully parametrised and solved by means of a code, also written specifically; the effect of the protonation state on the photoisomerisation quantum yield of the aryl-azoimidazolium unit of the axle molecule of a rotaxane molecular shuttle. In each case, the QM-based MD models that were specifically developed gave noteworthy information about the investigated phenomena, proving to be a fundamental key for a deeper comprehension of several experimental evidences.

In the past, we have demonstrated that 1,8-anthraquinone-18-crown-5 (1) and its heterocyclic derivatives act as luminescent hosts for a variety of cations of environmental and clinical concern. We report here a series of heteroatom-substituted macrocycles containing an anthraquinone moiety as a fluorescent signaling unit and a cyclic polyheteroether chain as the receptor. Sulfur, selenium, and tellurium derivatives of 1,8-anthraquinone-18-crown-5 (1) were synthesized by reacting sodium sulfide (Na₂S), sodium selenide (Na₂Se) and sodium telluride (Na₂Te) with 1,8-bis(2-bromoethylethyleneoxy)anthracene - 9,10-dione in a 1:1 ratio (2,3, and 6). These sensors bind metal ions in a 1:1 ratio (7 and 8), and the optical properties of the new complexes were examined and the sulfur and selenium analogues show that selectivity for Pb(II) is markedly improved as compared to the oxygen analogue 1 which was competitive for Ca(II) ion.

Selective reduction of 1 yields secondary alcohols where either one or both of the anthraquinone carbonyl groups has been reduced ( 15 and 9). A new mechanism for the fluorescence detection of metal cations in solution is introduced involving a unique keto-enol tautomerization. Reduction of 1 yields the doubly reduced secondary alcohol, 9. 9 acts as a chemodosimeter for Al(III) ion producing a strong blue emission due to the formation of the anthracene fluorophore, 10, via dehydration of the internal secondary alcohol in DMSO/aqueous solution. The enol form is not the most thermodynamically stable form under these conditions however, and slowly converts to the keto form 11.

Currently we are focusing on cucurbituril derivatives, also described as molecular clips due to their folded geometry used as molecular recognition hosts. We first investigated the synthesis and characterization of aromatic methoxy/catechol terminated cucurbituril units that act as hosts for small solvent molecules, such as CH₂Cl₂, CH₃CN, DMF, and MeOH, through dual pi…H-C T-shaped interactions. We have calculated the single-point interaction energies of these non-covalent interactions and compared them to the dihedral angle formed from the molecular clip. We have also synthesized a molecular clip that contains terminal chelating phenanthroline ligands. This tetradentate ligand shows 2:3 metal:ligand binding with Fe(II) and 1:2 metal:ligand binding with Co(II) and Ni(II) cations.

Los surfactantes son moléculas anfifílicas, con una cabeza solvofílica y una cola solvofóbica. Cuando la concentración de surfactante en solución es suficientemente alta, las moléculas se agregan entre ellas para proteger las partes solvofóbicas del contacto con el medio. Tales agregados pueden tener forma y tamaño muy diferentes, dependiendo del surfactante y de las condiciones del sistema. La auto-organización de los surfactantes (self-assembly), debida a un compromiso energético y entrópico de su estructura molecular, es la clave que permite observar cristales líquidos muy ordenados. En presencia de un precursor inorgánico y dependiendo de las interacciones que este precursor establece con el surfactante, se puede observar la formación del material híbrido. Los materiales híbridos constituyen un paso intermedio fundamental para la síntesis de los materiales mesoporosos ordenados, los cuales se obtienen eliminando la matriz orgánica (surfactante) del substrato inorgánico.
El presente estudio tiene como principal objetivo estudiar bajo cuales condiciones los sistemas formados por un surfactante, un precursor inorgánico y un solvente, se auto-organizan para dar lugar a estructuras híbridas muy ordenadas. En particular nos proponemos individuar cuales son las características más importantes que los precursores inorgánicos deberían tener para poder observar la formación de materiales mesoporosos ordenados.
Simulaciones Monte Carlo en el colectivo canónico han sido utilizadas para analizar la agregación de los surfactantes en estructuras complejas, como micelas, cilindros organizados en forma hexagonal, o laminas, a partir de configuraciones totalmente desordenadas. Con particular interés hemos analizado el rango de condiciones que llevan a la formación de las estructuras cilíndricas, y estas mismas estructuras han sido comparadas en función de algunas importantes características morfológicas, como el tamaño de poro, el grosor de las paredes, la presencia y accesibilidad de los grupos funcionales en los poros. El modelo usado representa las moléculas de surfactante y de precursor inorgánico como cadenas de segmentos en una red tridimensional que discretiza el espacio en sitios de volumen unitario. Este modelo no entra en el detalle de las características físicas y químicas de las moléculas, pero permite reproducir su agregación en estructuras complejas en un tiempo de cálculo muy razonable. La separación de fase ha sido también evaluada recorriendo a una teoría de campo medio, la quasi-chemical theory, que, aunque no pueda predecir la formación de estructuras ordenadas, ha sido muy útil para confirmar los resultados de las simulaciones, sobretodo cuando no se observa formación de fases ordenadas.
El estudio de surfactantes distintos, uno modelado por una cadena lineal y otro con una cabeza ramificada, nos ha permitido evaluar algunas diferencias estructurales de los materiales obtenidos. La ramificación de la cabeza, que merecería un estudio más profundo del que hemos descrito en este trabajo, ha evidenciado unas interesantes consecuencias en el tamaño de los poros. Este mismo surfactante con cabeza ramificada ha sido elegido para la síntesis de agregados cilíndricos utilizados como templates en la formación, agregación, y condensación de una capa de sílica modelada a través de un modelo atomístico. En particular, hemos aislado uno de los cilindros presentes en los cristales líquidos de estructura hexagonal, y a su alrededor hemos simulado la formación de una capa de sílica utilizando un modelo atomístico. De esta forma, hemos obtenido un poro típico de una estructura mesoporosa más realista, sin necesidad de asumir una forma mas o menos cilíndrica del template, por ser este generado de la auto-agregación del surfactante.
Surfactants are amphiphilic molecules with a solvophilic head and a solvophobic tail. When the surfactant concentration in a given solution is high enough, the molecules aggregate between them to shield the solvophobic part from the contact with the solvent. Such aggregates can show very different sizes and shapes, according to the surfactant and the conditions of the system. The surfactants self-assembly, being due to an energetic and entropic compromise of their molecular structure, is fundamental to observe the formation of very ordered liquid crystals. In the presence of an inorganic precursor and depending on the interactions established between such a precursor and the surfactant, it is possible to synthesize a hybrid material. Hybrid materials are the key step for the formation of periodic ordered mesoporous materials, which can be obtained by eliminating the organic soft matter (the surfactants) from the inorganic framework. Periodic ordered mesoporous materials represent an important family of porous materials as they find a large number of applications in several industrial fields, such as separations, catalysis, sensors, etc. In the last decade, the range of potential applications has increased with the possibility of functionalizing the pore walls by incorporating organic groups during the synthesis, or with post-synthesis treatments.
In this work, we are interested in studying the formation of ordered materials when hybrid organic-inorganic precursors are used. Lattice Monte Carlo simulations in the NVT ensemble have been used to study the equilibrium phase behavior and the synthesis of self-assembling ordered mesoporous materials formed by an organic template with amphiphilic properties and an inorganic precursor in a model solvent. Three classes of inorganic precursors have been modeled: terminal (R-Si-(OEt)3) and bridging ((EtO)3-Si-R-Si-(OEt)3)) organosilica precursors (OSPs), along with pure silica precursors (Si-(OEt)4). Each class has been studied by analyzing its solubility in the solvent and the solvophobicity of the inorganic group.
At high surfactant concentrations, periodic ordered structures, such as hexagonally-ordered cylinders or lamellas, can be obtained depending on the OSPs used. In particular, ordered structures were obtained in a wider range of conditions when bridging hydrophilic OSPs have been used, because a higher surfactant concentration was reached in the phase where the material was formed. Terminal and bridging OSPs produced ordered structures only when the organic group is solvophilic. In this case, a partial solubility between the precursor and the solvent or a lower temperature favored the formation of ordered phases.
With particular interest, we have analyzed the range of conditions leaving to the formation of cylindrical structures, which have been evaluated according to the pore size distribution, the pore wall thickness, the distribution and the accessibility of the functional organic groups around the pores. The phase behavior has been also evaluated by applying the quasi-chemical theory, which cannot predict the formation of ordered structures, but was very useful to confirm the results of simulations, especially when no ordered structures were observed.
The study of the phase and aggregation behavior of two different surfactants, one modeled by a linear chain of head segments and the other modeled by a branched-head, permitted us to evaluate some structural differences of the materials obtained.

The present thesis honors contemporary molecular dynamics simulation methodologies which provide powerful means to predict data, interpret observations and widen our understanding of the dynamics, structures and interactions of carbohydrate systems. With this as starting point my thesis work embarked on several cutting edge problems summarized as follows. In my first work the thermal response in crystal cellulose Iβ was studied with special emphasis on the temperature dependence of the crystal unit cell parameters and the organization of the hydrogen bonding network. The favorable comparison with available experimental data, like the phase transition temperature, the X-ray diffraction crystal structures of cellulose Iβ at room and high temperatures, and temperature dependent IR spectra supported our conclusions on the good performance of the GLYCAM06 force field for the description of cellulose crystals, and that a cautious parameterization of the non-bonded interaction terms in a force field is critical for the correct prediction of the thermal response in cellulose crystals. The adsorption properties of xyloglucans on the cellulose Iβ surface were investigated in my second paper. In our simulations, the interaction energies between xyloglucan and cellulose in water were found to be considerably lower than those in vacuo. The van der Waals interactions played a prevailing role over the electrostatic interactions in the adsorption. Though the variation in one side chain did not have much influence on the interaction energy and the binding affinity, it did affect the structural properties of the adsorbed xyloglucans. The interaction of the tetradecasaccharide XXXGXXXG in complex with the hybrid aspen xyloglucan endo-transglycosylase PttXET16-34 was studied in the third paper. The effect of the charge state of the “nucleophile helper” residue Asp87 on the PttXET16-34 active site structure was emphasized. The results indicate that the catalysis is optimal when the catalytic nucleophile is deprotonated, while the “helper” residue and general acid/base residue are both protonated. In my forth paper, the working mechanism for a redox-responsive bistable [2]rotaxane based on an α-cyclodextrin ring was investigated. The umbrella sampling technique was employed to calculate the free energy profiles for the shuttling motion of the α-cyclodextrin ring between two recognition sites on the dumbbell of the rotaxane. The calculated free energy profiles verified the binding preferences observed experimentally. The driving force for the shuttling movement of the α-cyclodextrin ring was revealed by the analysis of the free energy components.
QC 20110513

Neutral molecular radicals have received increasing attention as building blocks for functional molecular materials owing to their intrinsic conductive and magnetic properties. However, for these systems to be technologically viable, the molecular framework must be capable of stabilizing the unpaired electron, but also enable a degree of control and modulation of the desired properties. To achieve these goals, the design of the radical template requires consideration of the intrinsic effects on the electronic structure and those from a supramolecular perspective. In that regard, thiazyl radicals are promising candidates, as their physical attributes can be tuned systematically for the application at hand. In the pursuit of tunable thiazyl frameworks, two thiatriazinyl radicals have been synthesized and functionalized with heteroaromatic substituents. The contrasting nature between the attached thienyl and pyridyl substituents was evident upon establishing the preparative routes towards the neutral radical, and further demonstrated when the radicals were characterized spectroscopically. Structural analysis has emphasized the ability for the heteroaromatic moieties to direct the assembly of molecules into different supramolecular arrangements, in addition to self-associating into tightly bound structures. While dimerization voids the spin properties of these radicals, the redox-versatile thiatriazinyls were designed to explore the physical properties originating from metal coordination. Using the more robust anionic precursor, a dinuclear dysprosium complex was isolated and structurally analyzed, where oxidation of the ligand occurred in the process. A mechanism towards the self-assembly of the complex has been proposed by NMR studies using the isostructural yttrium analogue, which has provided insights on the metal-ligand reactivity. Furthermore, single-molecule magnet behaviour was observed for the dysprosium complex following magnetic investigations. In contrast to thiatriazinyls, the resonance-stabilized pyridine-bridged bisthiadiazinyls can remain undimerized in the solid state. Three derivatives have been developed with thienyl attachments and vary by the atomic substitution at the basal carbon position (i.e., R = H, F, Cl). Solution measurements illustrated spin delocalization extending across the π-framework, while halogenation provided a handle to fine-tune the energies of frontier molecular orbitals. Moreover, the ability of the thienyl rings to engage in various interactions was manifested in the polymorphic behaviour for each derivative. The solid-state structures were analyzed from single-crystal X-ray diffraction and highlighted the range of supramolecular architectures afforded by these systems. Lastly, two crystallographic phases of a bisdithiazolyl derivative were isolated selectively, such that the low-temperature phase possess an unprecedented high-symmetry trigonal space group. The mix-matched sizes of the beltline substituents afforded a honeycomb arrangement of stacked radicals. Magnetic measurements depicted a transition to an antiferromagnetically ordered state below 8 K, from which a high-temperature series expansion function was developed to model the magnetic data. Analysis of the results suggest the presence of two equivalent spin-spiral sublattices spanning across the crystal lattice three-dimensionally.

The main purpose of this Ph. D. Thesis is to study the photo-induced transformations by a laser pulse in molecular materials. The results have been obtained thanks the use of pump-probe optical techniques. This required innovative experimental developments, including first attempts with a single shot technique. In the spincrosover family of molecular materials, in which light may induce the switching from a non magnetic to a magnetic state, for the first time we followed the transformation dynamics over ten decades in time scale, from 100 femtoseconds to a millisecond. It reveals that the process follows a complex pathway from molecular to material scale through a sequence of steps. A charge transfer organic compound, which exhibits an insulatior-to-metal phase transition, has also been investigated. A dynamics implying several coherent optical phonon modes has been clearly observed. The behaviour as a function of laser pulse intensity and temperature shows that the state photo-induced from the insulating phase differs from the metallic phase at thermal equilibrium. The newly developed single shot set-up proved able of recording changes upon an irreversible transformation, for instance inside a hysteresis regime. This set has been tested by observing photo-induced damages of a thin gold layer
L'objectif principal de ce travail de thèse de doctorat est l'étude de transformations photo-induites par un pulse laser dans des matériaux moléculaires. Les résultats ont été obtenus grâce à l'utilisation de techniques optiques pompe-sonde. Ceci a nécessité des développements expérimentaux innovants, incluant des premières tentatives de techniques « single shot ». Dans un matériau à transition de spin, où la lumière peut induire la commutation d'un état non magnétique à un état magnétique, nous avons pu suivre pour la première fois la dynamique de la transformation sur plusieurs ordres de grandeurs en temps, de 100 femtosesecondes à la milliseconde. Ceci a permis de montrer que le processus se produit en plusieurs étapes successives, de l'échelle de la molécule à celle du matériau. Un composé organique à transfert de charge, qui présente une transition métal-isolant, a aussi été étudié. Une dynamique mettant en jeu plusieurs modes de phonons optiques cohérents a clairement été observée. Le comportement en fonction de l'intensité du pulse laser et de la température permet de conclure que l'état photo-induit à partir de la phase isolant diffère de la phase métallique observée à l'équilibre thermique. La mise en place du nouveau montage optique « single shot » va permettre d'observer des changements d'état irréversible, comme dans un régime d'hystérèse. Ce montage a été testé en observant le comportement non thermique d'une couche mince d'or

The work described in this thesis is an attempt to provide improved understanding of the effects of several factors affecting diffusion in hydrated cement pastes and to aid the prediction of ionic diffusion processes in cement-based materials. Effect of pore structure on diffusion was examined by means of comparative diffusion studies of quaternary ammonium ions with different ionic radii. Diffusivities of these ions in hydrated pastes of ordinary portland cement with or without addition of fly ash were determined by a quasi-steady state technique. The restriction of the pore geometry on diffusion was evaluated from the change of diffusivity in response to the change of ionic radius. The pastes were prepared at three water-cement ratios, 0.35, 0.50 and 0.65. Attempts were made to study the effect of surface charge or the electrochemical double layer at the pore/solution interface on ionic diffusion. An approach was to evaluate the zeta potentials of hydrated cement pastes through streaming potential measurements. Another approach was the comparative studies of the diffusion kinetics of chloride and dissolved oxygen in hydrated pastes of ordinary portland cement with addition of 0 and 20% fly ash. An electrochemical technique for the determination of oxygen diffusivity was also developed. Non-steady state diffusion of sodium potassium, chloride and hydroxyl ions in hydrated ordinary portland cement paste of water-cement ratio 0.5 was studied with the aid of computer-modelling. The kinetics of both diffusion and ionic binding were considered for the characterization of the concentration profiles by Fick's first and second laws. The effect of the electrostatic interactions between ions on the overall diffusion rates was also considered. A general model concerning the prediction of ionic diffusion processes in cement-based materials has been proposed.

La construction de nouvelles architectures d'aimant moléculaire basé sur l'approche métal-radical repose sur la conception de nouvelles molécules radicalaires. Dans cette optique, notre stratégie s'est concentrée sur la synthèse de porphyrins incorporant des composés radicaux libres. En effet, les porphyrines sont des composés π conjugués qui devraient favoriser la délocalisation de spin et la transmission des interactions magnétiques sur l'entier macrocycle et de plus sur l'ensemble du composé obtenu. A cause de leur excellente stabilité dans une grande diversité d'environnements chimiques et leur capacité à coordonner avec des métaux de transitions, notre choix s'est porté sur les radicaux nitroxides. Dans cette thèse, une série de porphyrines contenant des tBUNO, nitronyl and imino nitroxide directement liés sur le squelette de la molécule ont été synthétisées. Les macrocycles obtenus ont été caractérisés par UV-Vis, Masse et RPE spectroscopie. De plus, durant ce travail, des intermédiaires réactionnaires intéressant ont été obtenus et caractérisés pour la première fois. Ce fut le cas pour la meso-tetrakis(4-formylphenyl)porphyrin et ses équivalents métallés pa le Cu(II) et le Mn(II). Ainsi que pour quelques précurseurs prometteurs de macrocycle tetrapyrroliques comme 2-(3,4-dicyanophenyl)-4,4,5,5-tetramethylimidazoline-3-oxide-1oxyl, 2-(3,4-dicyanophenyl)-4,4,5,5-tetramethylimidazoline-1-oxyl and 2-(4-benzaldehyde)-4,4,5,5-tetramethylimidazoline-1-oxyl. D'après ce que nous savons, ces composés représentent le premier exemple de porphyrines substituées par des nitronyl et imino nitroxide radical, ayant été caractérisées sans ambiguïté par des méthodes spectroscopiques
The preparation of Molecule-Based Magnets is based on the assembling carriers of magnetic moment. These may be the metal ions only with diamagnetic linkers or the metal ions connected through open-shell organic molecule. The building of novel Molecule-Based Magnets architectures following the metal-radical approach relies on the design of innovative open-shell organic molecular blocks. In this regard, we focus our strategy on the synthesis of porphyrins incorporating free radicals. Indeed, porphyrins compounds are π-conjugated systems which should favor spin delocalization and the transmission of the magnetic interactions on the overall macrocycle and further over the all architecture. Due to their excellent stability in a wide variety of chemical environments, and their abilities to coordinate with transition metal we focus our attention on nitroxide radicals. In this dissertation a series of porpyrin macrocycles were synthesized, bearing tBuNO, nitronyl and imino nitroxide covalently linked to the skeleton. Characterization was done by UV-Vis, Mass and EPR spectroscopy. Moreover during this work some interesting synthetic intermediates were obtained with good yield and characterize for the first time. This was the case for meso-tetrakis(4-formylphenyl)porphyrin and its corresponding metallated derivatives by Cu(II) and Mn(II). Some novel promising tetrapyrrolic macrocycle precursors bearing nitronyl and imino nitroxides free radicals as 2-(3,4- dicyanophenyl)-4,4,5,5-tetramethylimidazoline-3-oxide-1-oxyl, 2-(3,4- dicyanophenyl)-4,4,5,5-tetramethylimidazoline-1-oxyl and 2-(4-benzaldehyde)-4, 4, 5, 5-tetramethylimidazoline-1-oxyl. To the best of our knowledge, these compounds represent the first example of nitronyl and imino nitroxide substituted porphyrin derivatives that have been unambiguously characterized by spectroscopic techniques

A series of zwitterionic materials of general formula R-D*-CH=C(CN)- CÖH4-C(CN)2', where D* is a pyridirium or quinolinium acceptor and R is a hydrophobic alkyl chain or an aryl group, were deposited using the Langmuir- Blodgett (LB) technique and their photochromic and nonlinear optical properties characterised. The materials are highly solvatochromic, exhibiting a broad photochromic charge transfer band in the visible region which bleaches when irradiated. LB films of the zwitterions, Z-ß-(1-hexadecyl-4-pyridinium)-a-cyano-4- styryldicyanomethanide (CMH33-P3CNQ) and the quinolinium analogue, Z-ß-(1- hexadecyl-4-quinolinium)-a-cyano-4-styryldicyanomethanide (CIÖH33-Q3CNQ), are non-centrosymmetric (Z-type). They exhibit sharp charge transfer bands at 495 n ana ses n respecivey with haf widths ai half maximum of 27 and zz mi. Unusually, mixed LB films of CIGH33-P3CNQ and C161-133-Q3CNQ exhibit a single sharp charge transfer band whose position is dependent upon the mole fraction and is finely tunable in the range 495 to 565 nm. These films are photobleached when irradiated at wavelengths which overlap the absorption bands, and may find potential applications a components of a multifrequency optical memory. Also, the unique peak wavelength tuning of the heteromolecular films enabled the effect of the position of the absorption band on second harmonic generation to be investigated for the first time. The zwitterionic materials have exciting norlinear optical properties and the strongest second harmonic intensity from any LB film has been obtained. LB films of the quinolinium zwitterion (CMH33-Q3CNQ) are non-centrosymmetric and the second harmonic intensity increases quadratically with the number of layers deposited to thicknesses of ca. 1 m. It is one of only five known materials to show such behaviour and the second-order susceptibility (xa) = 180 pm V* at 1064 nm) is the highest value obtained for a multilayer structure.

Passive permeation through biological membranes is an important mechanism for transporting molecules and regulating the cellular content. Studying and understanding passive permeation is also extremely relevant to many industrial applications, including drug design and nanotechnology. In vivo membranes typically consist of mixtures of lamellar and nonlamellar lipids. Lamellar lipids are characterised by their tendency to form lamellar bilayer phases, which are predominant in biology. Nonlamellar lipids, when isolated, instead form non-bilayer structures such as inverse hexagonal phases. While mixed lamellar/nonlamellar lipid membranes tend to adopt the ubiquitous bilayer structure, the presence of nonlamellar lipids is known to have profound effects on key membrane properties, such as internal distributions of stress and elastic properties. This dissertation examines permeation through lamellar and nonlamellar lipid membranes by utilising atomistic molecular dynamics simulations in conjunction with two di erent methods, the z-constraint and the z-restraint, in order to obtain transfer free energy profiles, diffusion profiles and permeation coefficients. An assessment of these methods is performed in search for the optimal, with the goal to create an automated, accurate and robust permeation study framework. Part of the dissertation involves the creation of the corresponding software. Furthermore, this work examines the effect of changing the lamellar vs. nonlamellar lipid composition on the passive permeation mechanism of a series of 13 small molecules and drugs. These nonlamellar lipids are known to affect the lateral pressure distribution inside the membranes. This work investigates the hypothesis that the differences in lateral pressure should increase the resistance to permeation. The results indicate that, upon addition of nonlamellar lipids, permeation is hindered for small molecules but is facilitated for the largest. All results are in agreement with previous experimental and computational studies. This work represents an advancement towards the development of more realistic in silico permeability assays, which may have a substantial future impact in the area of rational drug design.

Biointerfaces bridge across inorganic and biological substances within a watercontaining environment. It is related to health care, environmental engineering and bioenergy generation. However, there is a lack of fundamental understanding of bonding and stability of biointerfaces, due to limited capabilities of experimental techniques. The research project employs molecular dynamics (MD) as the basic methodology to study selected biointerfaces, involving five carbon surfaces (amorphous carbon surface, basal graphite surface, basal graphite surface doped with hydrogen and hydroxyl groups, basal graphite surface with Stone-Wales defects, and edge graphite surface). The selected molecules are: a small alpha-helix and a beta-sheet peptide, each with 16 amino acids; and a mid-sized peptide (amyloid peptide). The systematic study of the molecular adsorption on carbon surfaces has shown that it is a very complex process, which depends on several factors such as the molecular structure, the hydropathy of the peptide molecule, the charge and defects of the substrate surface, and the orientation of the molecule upon adsorption. It is clear that the amino acids which face the surface initiate the adsorption process and influence subsequent stages of adsorption. The considered carbon surfaces have different levels of reactivity for the molecule adsorption. The amorphous and charged surfaces tend to stabilise the beta sheet secondary structure. The interaction between the amyloid peptide and the carbon surfaces seems to depend on its molecular orientation, as well as the nature of the carbon surface: it was clearly attracted to the hydrophobic basal surface of graphitic carbon but pushed away from the hydrophilic charge-doped surface in one of the orientations (the second), but the opposite is true for another orientation (the third). Details of the structural change were shown in the Ramachandran plot. The energy change of the system mainly comes from the configurational variation, and electrostatic interactions are more prominent than the others. Water molecules tend to accumulate above a hydrophobic surface, forming a dense water layer, with an estimated distance of 2.9 Å from the carbon surface, whereas they distribute relatively evenly on hydrophilic surfaces.

In this thesis, the phase behavior in water of a technical grade diglycerol-based surfactant (C41V) and a group of dyes (Quinaldine Red, Pyronin Y, N-Alkylthiacarbocyanines, Oxacarbocyanines, Pinacyanol and Alcian Blue) was studied. Several experimental techniques such as polarized optical microscopy, small and wide X-ray scattering, dynamic light scattering, UV-Vis and NMR spectroscopy, were used to characterize the different phases and get insight into the molecular self- assembly behavior. The phase diagram of the water/C41V system is characterized by a wide region at temperatures lower than 70 ºC in which an inverse hexagonal liquid crystal (H2) coexists with excess water. The H2 phase could be successfully dispersed in water in the form of nanoparticles (hexosomes). A hydrophobic drug (Ketoprofen) was encapsulated in the hexosomes and its release to a receptor solution showed a non-Fickian diffusion profile. Excess of glycerol and surfactants with higher degree of esterification were separated from C41V. It was found that glycerol causes phase segregation at high C41V concentrations. The spontaneous curvature of the surfactant system can be tuned by mixing the purified C41V with the surfactants with higher degree of esterification. Structural characterization of dyes in water reveals that the molecules stack in columnar aggregates, which increase in size with concentration. At relatively high concentrations (ca. > 30 wt%) Quinaldine Red and Pyronin Y form a Nematic chromonic liquid crystal composed by columns with unimolecular cross-section. Additionally, at higher concentrations, Quinaldine Red forms a chromonic rectangular phase, which indicates that the columns cross-section is anisotropic. UV-Vis spectroscopy suggests that N-Alkylthiacarbocyanines stack face to face. The dimer model was used to fit the UV-Vis spectra and to estimate the dimeric constant and the intermolecular dissociation. The intermolecular interactions increase with the alkyl chain length (from 19.2 kBT to 20.5 kBT) suggesting that not only aromatic p-p interactions but also the hydrophobic effect contribute to the aggregation process. From small angle X-ray scattering measurements it can be inferred that the molecular columns are hollow. By applying the exciton theory to the UV-Vis spectra of Oxacarbocyanines it was found that the stacking angle of these dyes is around 54.7 º. It was also found that the molecular interactions can also be tuned by varying the carbon atoms in the poly- methine spacer of cyanine dyes. Alcian Blue showed evidence of stacking in aqueous solution, however, due to the poor solubility of this dye in water no liquid crystal was formed; nevertheless, Alcian blue solubility increases at acidic pH and liquid crystals can be formed. Cyanine dye aggregates were used as templates for silica synthesis by a sol-gel reaction. Silica nanofibers with high surface area (i.e. 230 m2/g) and hierarchical arranged mesopores were obtained. Furthermore, silica nanofibers were used as hard templates to produce carbon materials. The resulting templated carbon nanofibers were used as functional materials in energy storage and sensing applications. Carbon nanofibers showed superior performance as double layer capacitors (capacitance values of ca. 3000 F/g) and presented potential as sensing materials for aromatic compounds, especially pyridine.
En las últimas décadas, el auto-ensamblaje molecular ha ganado importancia debido a su potencial tecnológico. El estudio de nuevas moléculas con capacidad de formar agregados funcionales es un área de investigación relevante en la ciencia de materiales. Los tensioactivos son los ejemplos más representativos de moléculas auto-ensambladas. Los tensioactivos están formados por una cadena hidrocarbonada (hidrófoba) y un grupo polar (hidrófilo). Los tensioactivos se auto- agregan en solución debido a segregación entre el solvente y las cadenas hidrofóbicas formando un amplio rango de nanoestructuras, desde micelas esféricas hasta cristales líquidos. No obstante, el auto-ensamblaje molecular no es una propiedad que está restringida a los tensioactivos. Algunas moléculas planas y aromáticas, como las llamadas cromónicas, pueden también auto-organizarse en solución. Las propiedades de las moléculas cromónicas son diferentes de aquellas mostradas por los tensioactivos. El estudio de las propiedades de auto-agregación de las moléculas cromónicas está restringida a unos pocos sistemas. Es por eso que se conoce muy poco sobre la relación entre su estructura molecular y su comportamiento de auto-agregación en solución. Los nanomateriales han sido una de las áreas de mayor enfoque científico y tecnológico de los últimos años debido a que estos presentan propiedades únicas. Estas propiedades dependen en gran medida de la composición química, tamaño y morfología, es por eso que controlar estos parámetros es fundamental. Principalmente hay dos metodologías de síntesis de nanomateriales: aquellas que parten de un material en el estado masivo (“bulk”) para obtener unidades más pequeñas (“top- down”) y aquellas que consisten en partir de átomos y moléculas para construir nanomateriales (“bottom-up”). La metodología “bottom-up” produce estructuras estables y robustas; adicionalmente es económico, versátil y fácil. Entre los métodos de bottom-up quizás los que están más ampliamente estudiados son aquellos que utilizan auto-agregados (especialmente tensioactivos) en solución como plantillas. En este caso la morfología y tamaño del material final están determinados por el tipo de agregado utilizado. Desde un punto de vista industrial, se prefiere el uso de tensioactivos de grado técnico (disponibles comercialmente) debido a que son más económicos; no obstante, las propiedades de auto-ensamblaje de tensioactivos pueden cambiar por la presencia de impurezas y es por ello que el estudio del efecto de dichas impurezas es relevante. Por otra parte, es de interés el uso de otro tipo de agregados con morfologías distintas a aquellas presentadas por sistemas tensioactivos. A este respecto, las moléculas cromónicas son atractivas ya que poseen propiedades ópticas que, combinadas con materiales inorgánicos, pueden usarse en un amplio rango de aplicaciones. En este contexto, el objetivo principal de este trabajo de tesis es el de estudiar y caracterizar el comportamiento de auto-ensamblaje molecular de tensioactivos de grado comercial y moléculas cromónicas en medio acuoso y utilizar estos agregados para sintetizar nanomateriales funcionales. Para ello el plan de trabajo se dividió en tres partes: * Estudio del comportamiento fásico de las moléculas seleccionadas en medio acuoso. * Preparación de materiales usando los agregados identificados en el estudio del comportamiento fásico como plantillas. * Estudio de las posibles aplicaciones de los materiales preparados en liberación controlada de fármacos, almacenaje de energía y tecnología de sensores. Se determinó el comportamiento fásico mediante determinación de diagramas de fase en función de la concentración y temperatura de los distintos compuestos elegidos. Los límites de las distintas fases se determinaron mediante microscopia de luz polarizada (POM) con control de temperatura. La estructura de los agregados se caracterizó por técnicas de dispersión de radiación, tales como dispersión de rayos X a ángulo pequeño (SAXS/WAXS) y dispersión dinámica de luz (DLS). Para los tensioactivos derivados de di-glicerol poli-isostearatos, se demostró que el di-glicerol mono-isostearato (C41V) en medio acuoso se autoagrega formando estructuras de cristal líquido hexagonal inverso (H2). Este cristal líquido H2 se dispersó en agua mediante distintos métodos formando los denominados ‘’hexosomas’’. El método de evaporación de solvente proporcionó los mejores resultados, obteniéndose tamaños de hexosomas más pequeños y con baja polidispersidad. Se encapsuló en los hexosomas obtenidos un fármaco hidrófobo (ketoprofeno)se estudió su liberación a un medio gastrointestinal simulado. Estos estudios pusieron de manifiesto que puede controlarse la difusión del fármaco a una solución receptora. Adicionalmente los hexosomas formados por C41V se degradan en condiciones gastro-intestinales, lo cual evita que estos se acumulen en los órganos corporales. El glicerol y los tensioactivos con grados de esterificación más altos presentes en C41V se separaron y se estudió la influencia de las impurezas en el comportamiento fásico del tensioactivo. Se encontró que el glicerol produce una segregación de fases a altas concentraciones de C41V. Adicionalmente se demostró que variando la cantidad de tensioactivo con mayor grado de esterificación en C41V se pueden obtener distintos cristales líquidos en coexistencia con un exceso de agua. En los sistemas acuosos de colorantes estudiados, se evidenció que todas las moléculas seleccionadas (Quinaldine red, Pyronin Y, Tiacarbocianinas, Oxacarbocianinas, Alcian Blue) se auto-agregan formando columnas moleculares apiladas cara-a-cara. Estas columnas crecen a medida que la concentración del colorante aumenta. A concentraciones suficientemente altas se forma una fase cristal líquido nemático (Fase N) y una fase de cristal líquido hexagonal (Fase M). En el sistema de agua/Quinaldine Red se identificó una estructura a concentraciones altas en la cual las columnas moleculares están ordenadas en una estructura rectangular. Los estudios con las Tiacarbocianinas y Oxacarbocianinas pusieron de manifiesto que las fuerzas inter-moleculares se pueden modular cambiando el tamaño de cadena de las cadenas alquílicas laterales o la cadena de metinos que separa los grupos aromáticos. Los estudios con Alcian Blue muestran que este colorante se auto-agrega en solución, pero se disocia poco en agua por lo cual no forma cristales líquidos. Alcian Blue en medio acido forma cristales líquidos debido que su disociación aumenta al disminuir el pH. Los agregados de los colorantes se han utilizado como plantillas para sintetizar nano-fibras de sílice con una nano-estructura determinada y una elevada superficie específica (230 m2/g). Los materiales derivados se han estudiado mediante diferentes técnicas tales como SEM, SAXS y adsorción/desorción de gases. Las nano-fibras de sílice se usaron como plantillas para obtener fibras de carbono Se exploraron aplicaciones de las fibras de carbono obtenidas en súper-capacitores mediante técnicas electroquímicas y se encontró que los materiales muestran un excelente rendimiento (capacitancias de hasta 300 F/g). Adicionalmente se estudió el uso de las fibras de carbono como sensores de vapores orgánicos, obteniéndose una alta sensibilidad respecto a compuestos aromáticos.

The subject of the present work is the characterization of potential materials for molecular hydrogen storage with a stress on the use of Small Angle Neutron Scattering (SANS). This research is dedicated mainly to a study of the porous structure of activated carbon. Employment of the contrast matching technique together with SANS led to an understanding of the process of pore filling resulting from an increase of partial pressure of contrast matching liquid (deuterated toluene). The Author has designed a special Al alloy sample cell for the variable vapour pressure SANS experiments. The accessible empty pores fraction at each p/po is calculated using the Porod Invariant. The data obtained matches the results from gravimetric measurements of D-toluene adsorption. The fractal nature of activated carbon is determined via application of the neutron scattering technique. The density of activated carbon - an important characteristic affecting the total hydrogen uptake - is found to be Q-dependent with an average saturation limit of 1.85 g/cc. The effect of the carbon activation process, i.e. the formation of micropores, is illuminated by SANS. Finally, a novel model, implying exponential decay of the pore size distribution with a lower cut-off, is proposed and the minimum pore radius is calculated for each experimental partial pressure of wetting liquid. These results are compared with those derived from the standard Guinier approximation. The proposed model yields the exact value of D-toluene surface tension when the derived pore radii are associated to the corresponding pressures via the Kelvin equation (within the range of its applicability), whereas the Guinier approximation gives an average value of the D-toluene surface tension approximately twice the tabulated value. Thus, it is concluded that the novel model presented in this thesis is an improved approximation to the porous structure of activated carbon. Additionally, a complimentary double-Gaussian pore size distribution model is suggested. It highlights the presence of ultramicro- and microporosity and shows a good agreement with the SANS data for dry activated carbon.

Computer simulations can be used in parallel with experimental techniques to gain valuable insights into physical systems, test theoretical models or predict new be- haviour of molecular materials. Long time and large length scales, in combination with problems of phase space sampling, present a grand challenge for simulations of self-organising molecular materials. In the work presented in this thesis, the aim has been to develop and apply new or recent simulation models and methods to address these issues, with the aim of producing improved simulations of molecular materials. A new anisotropic model for simulating mesogenic systems has been developed, based on a soft core spherocylinder potential. This model is tested for single site systems and a multipedal liquid crystalline molecule, using conventional molecular dynamics simulations. It is used also to map out an approximate phase diagram for a main chain liquid crystalline polymer as a function of the volume fraction of the mesogenic unit; and to study the effects of a chiral medium on flexible achiral dopant molecules. Results here, show a preferential selection of conformations of similar chirality to the solvent. Later in the thesis, this new soft core spherocylinder model, is combined with a recently developed simulation methdology, Statistical Temperature Molecular Dynamics, to study the isotropic-nematic phase transition of a single site mesogen and the isotropic-lamellar phase transition of a model rod- coil diblock copolymer, using a single simulation to span the temperature window corresponding to the phase transition. Additional simulations combine a mesoscopic simulation method, Stochastic Ro- tational Dynamics, with a coarse grained surfactant model. This allows a computa- tionally efficient solvent description while maintaining correct hydrodynamics. Re- sults presented here include the formation of a bilayer, via spontaneous self-assembly of surfactant molecules, and information on the pathways of micelle formation. In the final result chapter of this thesis, Hamiltonian replica exchange simulations are performed employing soft-core replicas for a Gay-Berne system. The simulation results show an order of magnitude increase in equilibration speed of the ordered phase when compared to conventional simulations of a Gay-Berne fluid.

Supported ionic liquid phase catalysis is a thriving area of research with many applications. Currently, investigations in this area have focussed on the applications of these systems and there are relatively few reports on the understanding of the interactions of the ionic liquid with the porous support. The aim of this research is observe and analyse these interactions for a number of model systems. The supported ionic liquid phases (SILPs) discussed herein are made up of an ionic liquid physisorbed onto a mesoporous silica host. The ionic liquids used were chosen because of their ease of handling and similarity in structure. Mesoporous silicas were chosen due to their tunable properties. The potential applications of the systems described here in range from catalysis to gas processing and storage. As the focus of this research is characterisation of the interactions between the ionic liquid and the porous silica support, storage of CO2 gas is the . only application explored herein. NMR spectroscopy has been extensively used in this research. Not only has it been a versatile tool for elucidation of structures, it has also allowed the measurement of changes in the dynamics of the ionic liquid upon encapsulation. Combination of high resolution and solid state NMR spectroscopy has also been used to identify the presence of gases in clathrate hydrates. A semi-clathrate hydrate was loaded with methane gas. Solid state NMR experiments were then used to indentify methane molecules present in the cages of the clathrate and quantify the percentage uptake with respect to the semi-clathrate hydrate host.

In this thesis, bio-nanocomposites made from two alternative biopolymers and montmorillonite (Mnt) clay have been investigated by molecular modelling. These biopolymers are xyloglucan (XG) and chitosan (CHS), both of which are abundant, renewable, and cost-effective. After being reinforced by Mnt clay nanoparticles, the polymer nanocomposites gains in multifunctionality and in the possibility to register unique combinations of properties, like mechanical, biodegradable, electrical, thermal and gas barrier properties. I apply molecular dynamics (MD) simulations to study the interfacial mechanisms of the adhesion of these biopolymers to the Mnt nanoplatelets at an atomic level. For the XG-Mnt system, a strong binding affinity of XG to a fully hydrated Mnt interface was demonstrated. It was concluded that the dominant driving force for the interfacing is the enthalpy, i.e. the potential energy of the XG-Mnt interacting system. The adsorbed XG favors a flat conformation with a galactose residue in its side chain that facilitates the adsorption of the polymer to the nanoclay.  The XG adsorption was found do depend strongly on the hydration ability of counterions. The binding affinity of XG to Mnt was found to be strongest in the K-Mnt/XG system, followed by, in decreasing order, Na-Mnt/XG, Li-Mnt/XG, and Ca-Mnt/XG. The competing mechanism between ions, water and the XG in the interlayer region was shown to play an important role. The dimensional stability upon moisture exposure, i.e. the ability of a material to resist swelling, is an important parameter for biopolymer-clay nanocomposites. While pure clay swells significantly even at low hydration levels, it is here shown that for the XG-Mnt system, at a hydration level below 50%, the inter-lamellar spacing is well preserved, suggesting a stable material performance. However, at higher hydration levels, the XG-Mnt composite was found to exhibit swelling at the same rate as the pure hydrated Mnt clay. For the CHS-Mnt system, the significant electrostatic interactions from the direct charge-charge attraction between the polymer and the Mnt clay play a key role in the composite formation. Varying the degree of acetylation (DA) and the degree of protonation (DPr) resulted in different effects on the polymer-clay interaction. For the heavily acetylated CHS (DA > 50%, also known as chitin), the strong adhesion of the neutral chitin to the Mnt clay was attributed to strong correlation between the acetyl functional groups and the counterions which act as an electrostatic “glue”. Similarly, the poor adhesion of the fully deprotonated (DPr = 0%) neutral CHS to the clay is attributed to a weak correlation between the amino functional group and the counterions. The stress-strain behavior of the CHS-Mnt composite shows that the mechanical properties are highly affected by the volume fraction of the Mnt clay and the degree of exfoliation of the composite. The material structure has a close relationship to the material properties. Biopolymer-clay nanocomposites hold a bright future to replace petroleum-derived polymer plastics and will become widely used in common life. The theme of the thesis is that further critical improvements of these materials can be accomplished by development of the experimental methods in conjunction with increased understanding of the interactions between polymer, clay, water, ions, solutions in the polymer-clay mixtures provided by molecular modelling.
I denna avhandling har molekylär modellering och molekyldynamisk (MD) simulering använts för att studera modellsystem för bio-nanokompositer bestående av montmorillonit-lera samt två olika sorters biopolymerer – xyloglukan (XG) och kitosan (CHS). Båda dessa polymerer är naturligt förekommande och mycket vanliga. De är dessutom förnyelsebara och kostnadseffektiva. Då polymererna förstärkts med nanopartiklar av montmorillonit får det resulterande kompositmaterialet en unik kombination av egenskaper såsom mekaniska, elektriska, termiska och barriär egenskaper etc. Genom att använda molekyldynamiska (MD) simuleringar, studeras här växelverkan mellan dessa biopolymerer och lernanopartiklar (Mnt) på grundläggande atomistisk detaljnivå. Mellan XG och Mnt i ett fullt hydrerat system kunde stark bindningsaffinitet påvisas. Den dominerande drivkraften för affiniteten var entalpi, d.v.s. potentiell växelverkansenergi. Den adsorberade XG-kedjan antar en platt konformation på ytan. Ett förslag utifrån simuleringsresultaten var att galaktosresidyn i xyloglukanets sidokedja underlättar adsorptionen till lerytan. Simuleringarna kunde också visa att adsorption av XG till Mnt beror starkt på motjonernas hydreringsförmåga. Bindningsaffiniteten mellan XG och Mnt var som starkast i K-Mnt/XG- systemet. Därefter följde, i minskande ordning, Na-Mnt/XG, Li-Mnt/XG och Ca-Mnt/XG. Det kunde visas att strukturen vid gränsytan styrs av konkurrerande mekanismer mellan joner, vatten och XG. Dimensionsstabilitet vid fuktexponering, d.v.s. förmågan hos ett material att motverka svällning, är en viktig egenskap för biopolymer-lernanokompositer. Ren lera sväller signifikant även vid låga fukthalter. Dock kunde MD simuleringar visa att ett modellsystem av XG-Mnt behåller sitt ursprungliga interlamellära avstånd vid hydreringsnivåer under 50%, vilket indikerar ett stabilare material. Vid högre hydrering uppmättes dock svällningen vara densamma som för ren lera. I CHS-Mnt-systemet visade det sig att direkt elektrostatisk växelverkan med signifikant styrka mellan laddningar på polymer och Mnt-yta spelar störst roll för kompositformeringen. Olika effekt på polymer-lerväxelverkan uppnåddes genom att variera acetyleringsgraden (DA) respektive protoneringsgraden (DPr). För den tungt acetylerade CHS-polymeren (DA > 50%, även kallad kitin) visade sig den starka vidhäftningen bero på korrelation mellan acetylgrupperna och motjonerna som i sin tur verkade som ett elektrostatiskt “lim”. På liknande sätt kunde den svaga vidhäftningen mellan fullt deprotonerad (DPr = 0%) neutral CHS och lera förklaras med en betydligt svagare korrelation mellan aminogrupperna och motjonerna. Spänning-töjningsbeteendet hos CHS-Mnt modellen visar att dess mekaniska egenskaper beror kraftigt på volymsandelen Mnt och graden av exfoliering i kompositen. Materialets struktur är nära relaterat till materialegenskaperna. Framtiden för nanokompositer av biopolymerer och lera är ljus då de kan komma att ersätta oljebaserade plaster och användas frekvent i våra dagliga liv. Materialen kommer successivt förbättras genom utveckling av experimentella metoder i kombination med molekylmodellering för ökad förståelse för växelverkan mellan polymer, lera, vatten, joner och lösningsmedel.
本论文利用分子动力学模拟技术研究了两种备选生物大分子与蒙脱土(Montmorillonite, Mnt)（一种粘土）组成的生物纳米复合材料，分别是木葡聚糖（Xyloglucan, XG）/蒙脱土和壳聚糖(Chitosan, CHS)/蒙脱土。木葡聚糖与壳聚糖都是自然界广泛存在的生物大分子，资源丰富且取材面宽，提取及加工成本低廉，加之可以生物降解并可再生，是优秀的生物复合材料备选原料。经过蒙脱土纳米颗粒加固后，这些基于生物大分子的复合材料将获得多功能且有多种独特特性相结合的优点，比如，更好的力学性能，生物可降解，良好的导电性能，传热性能和屏蔽气体与液体侵扰的能力等等。论文中，我们采用分子动力学模拟的方法着重对生物大分子与蒙脱土在界面上的粘附相互作用机理进行了深入探讨。  首先，对于木葡聚糖/蒙脱土纳米复合材料，我们发现糖分子与土分子间有着很强的天然亲和力。研究证明它们之间的这种相互作用，热焓是主要的推动力，也就是糖和土分子间的相互作用势能。含有半乳糖残基的木葡聚糖分子（本文中亦称天然木葡聚糖分子）吸附到粘土表面后，分子构型呈现扁平状，半乳糖残基似有辅助木葡聚糖大分子吸附到粘土颗粒上的作用。  进一步研究发现，木葡聚糖分子在粘土表面上的吸附与溶液中抗衡离子的水和作用密切相关。在钾离子平衡的糖/粘土系统中，糖分子与土分子的相互作用最强，钠离子平衡的糖/粘土系统次之，紧接着是锂离子平衡的糖/粘土系统，最弱的是钙离子平衡的糖/粘土系统。研究发现，离子，水分子，以及糖分子在粘土层间的竞争机制在糖分子的粘附过程中起着重要的作用。  材料暴露于潮湿环境中的尺寸稳定性，也就是材料抗肿胀的能力是生物大分子/蒙脱土所构成的复合材料的重要参数。蒙脱土自身即使在很低的潮湿环境下就会有明显地膨胀现象，然而，对木葡聚糖/蒙脱土复合材料来说，尺寸稳定性可以在水和值低于50%以下有效保存。其夹层尺寸的稳定保持暗示了材料在这个程度的潮湿环境下的稳定性。然而，当水和值高于50%时，木葡聚糖/蒙脱土复合材料将出现明显的肿胀现象，表现在夹层尺寸的明显增大，且其膨胀速率与粘土自身的膨胀速率逐渐趋于相当水平。  其次，对于壳聚糖/蒙脱土复合材料，我们发现由电荷-电荷间直接产生地强烈的静电吸引作用是壳聚糖分子与蒙脱土分子相互粘附并构成复合材料的关键因素。通过改变壳聚糖分子的乙酰化程度（Degree of acetylation, DA）和质子化程度(Degree of protonation, DPr)，糖分子与土分子的相互作用有着显著地不同。对于乙酰化程度（DA）高于50%的壳聚糖分子（亦成为甲壳素分子chitin, CHT），电中性的甲壳素分子与土分子间的强吸附作用源于乙酰基功能团与抗衡离子的强相关性。抗衡离子此时扮演着类似于“电子胶”的作用，可以有效地将电中性的甲壳素分子与土分子粘结在一起。类似地，当质子化程度最低时，亦即壳聚糖分子完全非质子化，即呈现电中性时，较差的糖/土吸附作用源于氨基功能团与抗衡离子的较弱的相关性。  进一步对壳聚糖/蒙脱土复合材料的分子系统进行应力应变计算发现，复合材料的力学性能直接受蒙脱土体积分数和其剥离程度的影响，通常，粘土的体积分数越大体系的力学性能越高，且剥离程度对材料的整体性能也有直接影响。因此，材料的结构与其性能的表征有着密切联系。  我们相信生物大分子与蒙脱土构成的生物复合材料有着光明的前景，可以取代石油提取物制成的塑料材料，并将能够广泛应用在日常生活中。通过实验技术的改善和应用分子模拟技术对复合材料体系中生物大分子，蒙脱土分子，水分子，离子，溶液环境等混合物质相互作用的理解增加，这种可再生的新材料将会得到重要改进，这也是整本论文的主旋律。

QC 20150520

Bio-nanocomposites

The work described in this thesis centres around our desire to use triphenylene as the scaffold for building new molecular materials. This has been approached in three different ways; firstly a twin linked by pyrrole units, secondly by twinning with triazoles, and finally via the formylation of triphenylene. A tetra-hexyloxysubstituted dipyrrolyltriphenylene twin had previously been synthesised in the group, however characterisation was difficult and therefore a twin with improved solubility was designed. The synthesis of tetra-decyloxysubstituted dipyrrolyltriphenylene was completed successfully, but the twinning of the compound could not be achieved. One possible explanation was interference of the long alkyl chains in the neighbouring positions to the pyrrole units. A new target precursor was designed with just two alkyl chains on the triphenylene. Previous work in the group had shown difficulties in the synthesis of the di-hexyloxysubstituted triphenylene, however with careful manipulations the synthesis was successful. New complications were found with the solubility of the di-hexyloxysubstituted dipyrrolyltriphenylene that could not be overcome. At this point crystals of the tetra-hexyloxysubstituted dipyrrolyltriphenylene twin had been obtained and full characterisation achieved. With the explosion of Click chemistry in the recent years, a twin linked by triazoles was targeted. The twin was designed from a tetra-hexyloxysubstituted diazidetriphenylene, coupled with di-hexyloxysubstituted diacetylenetriphenylene. The diacetylene triphenylene was synthesised successfully following on from the work achieved in the first project. Two routes were explored for the synthesis of the diazide. The first, a direct conversion of the dibromide to the diazide, gave no reaction. The second route was a series of manipulations starting from the dinitrotriphenylene. Some difficulties were found with the reduction of the dinitro compound to the diamine, however these were overcome using carefully controlled conditions. The corresponding diamide was synthesised to allow for full characterisation, as the diamine was found to decompose rapidly. Crystals were grown of the diamide and the x-ray structure was obtained, this showed an unexpected structure. The expected 3,6-substitution pattern had not been formed, in fact we had synthesised the 1,8-bisimide-2,7,10,11-tetrakis(hexyloxy) triphenylene. As the triazole linked triphenylene twin was not accessible, the diacetylenetriphenylene was twinned with itself. High dilution conditions were followed and the twin was successfully isolated. The twin showed no mesophase behaviour and remained stable beyond 300 oC. The third part of the thesis is based on the formylation of tetra-hexyloxysubstituted triphenylene. The formation of the triphenylene dialdehyde had previously eluded our group, however following a new protocol gave a successful synthesis. There were a number of potential compounds to investigate from this versatile precursor. We chose to target BODIPY-triphenylene hybrid compounds. Two compounds were designed, one from the dialdehyde where the BODIPY fragment would be attached via the central meso-carbon, and one from the dipyrrole where the BODIPY would be attached via the alpha positions of the pyrrole. Kryptopyrrole was used in the synthesis from the dipyrrole, to attempt to discourage potential polymer formation, however the reactions were not successful. The bis-BODIPYtriphenylene via the dialdehyde was successfully synthesised and the compound was observed for potential mesophase behaviour; it was seen to melt with decomposition at 150-160 oC. Finally, the triphenylene dialdehyde was used to synthesise a twin linked by diamines. The novel twinned structure has a central “void” region that we know to disfavour columnar organisation. The compound was observed for potential mesophase behaviour, and the twin was seen to exhibit only a stable nematic discotic mesophase up to 300 oC.

It is impossible to determine the amount of money that is spent every replacing products damaged from wear, but it is safe to assume that it is in the millions of dollars. With metallic materials, liquid lubricants are often used to prevent wear from materials rubbing against one another. However, with polymeric materials, liquid lubricants cause swelling, creating an increase in friction and therefore increasing the wear. Therefore, a different method or methods to mitigate wear in polymers should be developed. For better understanding of the phenomenon of wear, scratch resistance testing can be used. For this project, classic molecular dynamics is used to study the mechanics of nanometer scale scratching on amorphous polymeric materials. As a first approach, a model was created for polyethylene, considering intramolecular and intermolecular interactions as well as mass and volume of the CH2 monomers in a polymer chain. The obtained results include analysis of penetration depth and recovery percentage related to indenter force and size.

[EN] The present work examines the influence of the chemical structure of polymers on thermal, mechanical and dielectric behavior. The experimental techniques used for the purpose are differential scanning calorimetry, dynamo-mechanical analysis and dielectric spectroscopy. Additionally, in order to confirm the results obtained using the above methods, other techniques such as ray diffraction have also been employed. Chapters 1 and 2 contain the introduction and the objectives, respectively. Chapter 3 briefly describes the experimental techniques used. Chapter 4 contains the findings of the comparative analysis of the response to electrical noise fields for three poly(benzyl methacrylates) with different structures. The analysis was carried out under a wide range of frequencies and temperatures on three poly(benzyl methacrylates) containing two dimethoxy groups in positions 2,5-, 2,3- and 3,4-. The results show that the position of the dimethoxy groups on the aromatic ring has a significant effect on the molecular dynamics of poly(benzyl methacrylate). The spectra obtained were of high complexity and therefore, in order to perform a better analysis, numerical methods for time-frequency transformation including the use of parametric regularization techniques were used. We studied the effect of this structural change on the secondary relaxation processes and relaxation process , relating to the glass transition. We also analyzed the effect of the dimethoxy group position on the formation of nanodomains, in which the side chains are predominant, and on the conduction processes of the materials tested. In Chapter 5, the conductivity of rubbery liquids was studied by analyzing poly(2,3-dimethoxybenzyl methacrylate), which exhibits its own particular behavior. The chapter analyzes the principle of time-temperature superposition, employing different interrelated variables. Chapter 6 focuses on how the presence of crosslinking affects the molecular mobility of polymethacrylates containing aliphatic alcohol ether residues. In this case, the effect of crosslinking on the secondary and primary relaxation processes was analyzed. The creation of nanodomains in the side chains as a result of the presence of crosslinking was also studied.
[ES] En este trabajo se presenta un estudio de la influencia de la estructura química de los polímeros en su comportamiento térmico, mecánico y dieléctrico. Las técnicas experimentales empleadas para ello han sido la calorimetría diferencial de barrido, el análisis dinamo-mecánico y la espectroscopia dieléctrica. Adicionalmente, se han empleado otras técnicas como la difracción de rayos, con objeto de corroborar los resultados obtenidos por las primeras. En los Capítulos 1 y 2 se recoge la introducción y los objetivos, respectivamente. El Capítulo 3 presenta una breve descripción de las técnicas experimentales empleadas. En el Capítulo 4 se recogen los resultados obtenidos en el análisis comparativo de la respuesta a campos de perturbación eléctrica en un amplio rango de frecuencias y temperaturas para tres polimetacrilatos de bencilo con dos grupos dimetoxi en posiciones 2,5-, 2,3- y 3,4-. Los resultados obtenidos señalan el importante efecto de la posición de los grupos dimetoxi en el anillo aromático, sobre la dinámica molecular del polimetacrilato de bencilo. Los espectros obtenidos fueron muy complejos, por ello en orden a llevar a cabo un mejor análisis se emplearon métodos numéricos para la transformación tiempo-frecuencia que incluyeron el uso de técnicas de regularización paramétrica. Se ha estudiado el efecto que dicho cambio estructural ejerce tanto sobre los procesos de relajación secundaria como sobre el proceso de relajación α, relacionado con la transición vítrea. Así mismo, se ha analizado el efecto de la posición de los grupos dimetoxi en la formación de iii nanodominios en los que predominan las cadenas laterales, y su efecto en los procesos de conducción de los materiales analizados. En el Capítulo 5 se recoge el estudio de la conductividad de líquidos gomosos tomando como modelo el poli (metacrilato de 2,3-dimetoxibencilo), por su peculiar comportamiento. En este capítulo se ha realizado un análisis del principio de superposición tiempo-temperatura, empleando para ello diferentes variables relacionadas entre sí. En el Capítulo 6 se recoge el efecto de la presencia de entrecruzante en la movilidad molecular de polimetacrilatos que contienen residuos de éteres de alcoholes alifáticos. En este caso, se ha analizado el efecto de la presencia de entrecruzante tanto en los procesos de relajación secundarios, como en el proceso de relajación principal. También se llevó a cabo un análisis del efecto que la presencia de entrecruzante tiene sobre la creación de nanodominios gobernados por las cadenas laterales.
[CAT] En aquest treball es presenta un estudi de la influència de l'estructura química dels polímers en el seu comportament tèrmic, mecànic i dielèctric. Les tècniques experimentals utilitzades han sigut la calorimetria diferencial de rastreig, l'anàlisi dinamo-mecànic i l'espectroscòpia dielèctrica. Addicionalment, s'han empleat altres tècniques com la difracció de rajos X a fi de corroborar els resultats obtinguts per les primeres. En els Capítols 1 i 2 s'arreplega la introducció i els objectius, respectivament. Al Capítol 3 es presenta una breu descripció de les tècniques experimentals emprades. En el Capítol 4 es recull els resultats obtinguts en l'anàlisi comparativa de la resposta a camps de pertorbació elèctrica en un ampli rang de freqüències i temperatures de tres polimetacrilats de benzil amb dos grups metoxi en posicions 2,5-, 2,3- i 3,4-. Els resultats obtinguts assenyalen l'important efecte de la posició dels grups metoxi en l'anell aromàtic, sobre la dinàmica molecular del polimetacrilat de benzil. Els espectres obtinguts van ser molt complexos, per aquesta raó per a dur a terme un millor anàlisi es van emprar mètodes numèrics per a la transformació temps-freqüència que van incloure l'ús de tècniques de regularització paramètrica. S'ha estudiat l'efecte que el dit canvi estructural exerceix tant sobre els processos de relaxació secundària com sobre el procés de relaxació , relacionat amb la transició vítria. Així mateix, s'ha analitzat l'efecte de la posició dels grups metoxi en la formació de nanodominis en els que predominen les cadenes laterals, i el seu efecte en els processos de conducció dels materials analitzats. En el Capítol 5 s'arreplega l'estudi de la conductivitat de líquids gomosos prenent com a model el poli-(metacrilat de 2,3-dimetoxibencilo), pel seu peculiar comportament. En aquest capítol s'ha realitzat un anàlisi del principi de superposició temps-temperatura, emprant per a això diferents variables relacionades entre sí. En el Capítol 6 s'arreplega l'efecte de la presència d'entrecreuat en la mobilitat molecular de polimetacrilats que contenen residus d'èters d'alcohols alifàtics. En aquest cas, s'ha analitzat l'efecte de la presència d'entrecreuat tant en els processos de relaxació secundaris, com en el procés de relaxació principal. També es va dur a terme un anàlisi de l'efecte que la presència d'entrecreuat químic té sobre la creació de nanodominis governats per les cadenes laterals.
Carsí Rosique, M. (2015). Molecular mobility. Structure-property relationship of polymeric materials [Tesis doctoral no publicada]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/59460
TESIS
Premiado

Despite having significant applications in the nuclear industry, there have been virtually no molecular dynamics (MD) simulations of radiation damage in graphite. The difficulties in developing an accurate yet computationally inexpensive description of carbon have limited the number of detailed investigations. Although previous work has reported point defect energies and estimates of threshold displacement energies, very little is known about the cascade behaviour and the evolution of damage at the atomic level. Gaining an understanding of the processes caused by irradiation in graphite is central to extending the life span of the current advanced gas-cooled nuclear reactors in the UK. In addition, this will provide crucial information to aid next-generation nuclear technology such as the high-temperature graphitemoderated reactors, which were recently selected for development in the USA. The Environment Dependent Interaction Potential (EDIP) has been employed along with the Zeigler-Biersack-Littmark potential to model radiation damage in graphite. Statistical sampling of 20 initial directions and over a range of energies has revealed that nuclear graphite behaves in a manner distinct from metals and oxides, with damage primarily in the form of isolated point defects as apposed to connected regions of transient damage. Simulations have given evidence of channelling occurring along the <10¯12> channel which has previously not been observed in graphite simulations. Graphite cascades have exhibited a fractal-like branching structure and binary-collision-type behaviour. Results produced agree with historical defect prediction models. Important quantities such as the range of the primary knock-on atom and the average energy loss per collision have been calculated. Results indicate that graphite cascades are not dependent on the initial cell temperature. EDIP has been further employed to simulate the effects of radiation damage in carbon allotropes. Results reveal how a material’s structure affects the collision cascade and have highlighted the unique radiation response of graphite.