Dissertations / Theses on the topic 'Metal-Molecule-Metal structure'

Il est bien connu que les propriétés optiques des nanoparticules de métaux nobles, en particulier d'or et d'argent, s'écartent fortement de celles de métaux macroscopiques. Pour les tailles comprises entre dix et quelques centaines de nanomètres, elles sont dominées par les plasmons de surface (SP) décrites par des modèles purement classiques. En revanche, les agrégats de quelques dizaines d’atomes se comportent comme des systèmes quantiques, ce qui induit des comportements optiques nouveaux. La structure des nanoparticules et l'environnement diélectrique peuvent affecter les propriétés optiques. Dans cette thèse, j'ai utilisé un microscope électronique à transmission à balayage (STEM) équipé d'un spectromètre à perte d'énergie des électrons (EELS) pour mesurer, en parallèle, les propriétés optiques et structurales de nanoparticules individuelles. Je présente comment des expériences complémentaires (STEM-EELS et absorption optique) sur de petites nanoparticules d'argent triées en taille et encapsulées dans une matrice de silice donnent au premier abord des résultats incohérents: tandis que, d’une part, l'absorption optique ne montre aucun effet de taille entre quelques atomes et environ 10 nm, un décalage en énergie est observé dans les mesures STEM-EELS. Notre interprétation quantitative, fondée sur un modèle mixte classique/quantique qui prend en compte tous les effets quantiques pertinents, a résolu les apparentes contradictions non seulement dans nos données expérimentales, mais également dans celles de la littérature. Notre modèle décrit comment l'environnement local est le paramètre crucial contrôlant la manifestation ou l'absence d'effets de taille quantique. En second lieu, je me suis intéressé à la région purement classique à travers des structureslithographiées de quelques centaines de nanomètres. Bien que les cavités plasmoniques triangulaires aient été largement étudiées dans la littérature, une classification en termes de modes de respiration et de bords plasmoniques manquait. Dans cette étude, les résultats expérimentaux de STEM-EELS, des modèles analytiques et des simulations classiques nous ont permis de décrire la nature des différents modes
It is well known that the optical properties of nanoparticles of noble metals, in particular gold and silver, deviate strongly from those of macroscopic metals. For sizes between ten and a few hundred nanometers, they are dominated by surface plasmons (SPs) described by purely classical models. On the other hand, clusters of a few tens of atoms behave like quantum systems inducing new optical behaviors. The structure of the nanoparticles and the dielectric environment can affect the optical properties. In this thesis I used a scanning transmission electron microscope (STEM) fitted with an electron energy loss spectrometer (EELS) to measure, in parallel, the optical and structural properties of individual nanoparticles. I present how complementary experiments (STEM-EELS and optical absorption) on sizeselected small silver nanoparticles embedded in silica yield at first inconsistent results: while optical absorption shows no size-effect in the range between only a few atoms and ~10 nm, a clear spectral shift is observed in STEM-EELS technique. Our quantitative interpretation, based on a mixed classical/quantum model which takes into account all the relevant quantum effects, resolves the apparent contradictions, not only within our experimental data, but also in the literature. Our comprehensive model describes how the local environment is the crucial parameter controlling the manifestation or absence of quantum size effects. Secondly, I was interested in the purely classical region through lithographed structures of a few hundred nanometers. Although triangular plasmonic cavities have been widely studied in the literature, a classification in terms of plasmonic modes of breathing and edge was missing. In this study, experimental STEM-EELS results, analytical models and classical simulations enabled us to describe the nature of the different modes

Molecular transport characterization is an active part of the research field in nanotechnology. In this interesting branch the self-assembly approach is highly exploited; it consists in spontaneous formation of highly ordered monolayers on various substrate surfaces. Self-assembled monolayers (SAMs) have found their applications in various areas, such as nanoelectronics, surface engineering, biosensing, etc. An important area in biosensing is the electrochemical detection, that enables sensing of dierent biomarkers with an important role, for many dierent applications in biomedical diagnostics or in monitoring of biological systems. Various test structures have been developed in order to carry out characterizations of self-assembled molecules, and numerous reports have been published in the past several years on the transport characteristics. This thesis' purpose is the single protein biomolecular sensing, that could become the starting point for monitoring drugs, developing clean energy systems, realizing bio-opto-electronic transistors... The possibility to cover so many fields is related to the kind of proteins, molecules, bioelements that will be inserted inside sensors. Biomolecular sensing has to be thought in order to reach a result with the better compromise between instrumentation versatility and measurements precision. The main underlying idea is to use single molecules as active elements in nano-devices. As a consequence, the proper realization of a molecule-electrode contact is a crucial issue. What is needed by author is something versatile, precize, cheap, at single molecule level and able to record measurements in few time in order to do statistical characterizations. The final goal of this work is a platform system adapt for both industry and research field. Electrical nanogap devices are the main character of this work. They have proven good performances as element for detecting small quantities of biomolecules, allowing direct transduction of biomolecular signals into useful electrical ones such as resistance/impedance, capacitance/dielectric, or field effect. Nanogaps are now one of the most busy area of research in the nanotechnology world. Moreover, these structures do not require feedback to maintain the mutual arrangement (comparing with conducting tip AFM) and are less stochastic with respect to electrochemical cells. Several techniques can be applied to nanogap fabrication: mechanically broken or positioned junctions, nano-scale lithography by Synchrotron radiation sources, electrochemical deposition and etching, and electromigration. None of these techniques is presently able to give precise control as to thefinal gap size. In this thesis the electromigration approach has been choosen, because of several useful characteristics. It is cost eective, because of the relatively low complexity of the required equipment. It can be embedded into a lab-on-chip system, thus exploiting the possibility to tailor the gap formation process by means of a digital loop control system. To this end, it just requires a conventional microchip fabrication process. It allows the parallelization with a smart packaging through which it is possible to produce more probes at the same time and perform many measurements in contemporary. The employment of nanogaps, as an instrumentation for the molecular charac- terization, has also some issues that have to be considered in order to obtain useful measurements. To characterize molecules the leakedge must be not higher than some pA to avoid the noise overcome the signal. Nanogap platform is perfect for molecular electronics. The experiments have been developed in dry way, as a consequence the solutions were evaporated before the measurement starting. This brought several problems cause biochemical analysis requires liquid solution in order to avoid an untimely death of the bio-elements tha has to be characterized. Considering a future developement, an improvement is necessary in terms of a system able to work with salty solutions without damaging the microchip's probes. Therefore it is a necessary a set-up allowing the anchorage of a microfluidic part. At the same time it is necessary to keep in mind that the presence of a new system has to not overcome the molecule signal, maintaining the leakedge under some tens of pA.

The discovery of new anticancer targets is the key factor for the development of more efficacious therapies. Sequence selective binding of double stranded DNA in the classical B form has been extensively employed to target small molecules to defined polynucleotide portions. More recently, ligand recognition of non canonical DNA foldings has been additionally considered a useful approach to selectively target distinct genomic regions. In this connection, G-quadruplexes represent an interesting system since they are believed to be physiologically significant arrangements. These non-canonical DNA structures are found at the ends of the human chromosomes (telomeres) as well as at promoter regions of several oncogenes where there is a cluster of guanine-rich sequences and they are likely to play important roles in the regulation of biological events. The induction and stabilization of the G-quadruplex arrangement by small molecules can lead to the inhibition of the telomerase activity by interfering with the interaction of the enzyme and its single stranded template. A similar molecular mechanism is likely involved in the transcriptional control that leads to the suppression of the oncogene transcription and, ultimately, in the regulation of the gene expression. As a result, the quadruplex topic is very attractive for the development of a specific anticancer strategy defined by a dramatic reduction of side effects, typical of chemotherapy. The purpose of this work is to investigate the interactions between novel classes of small molecules and different quadruplex DNA sequences and conformations. These new molecules were properly designed providing systematic atom-wise substitutions based on rational evaluations of previous studied compounds in order to increase their selectivity for G-quadruplex structures and to reduce toxic effects. Biophysical and biological properties of all new derivatives are herein evaluated at molecular and cellular level. The thesis work is divided into three main sections based on the structural features of the compounds object of study. The first part focuses on heterocyclic dications: upon changing their molecular binding shape, a correlation with G-quadruplex binding have been drawn. In particular it was possible to rationalize a shift in the binding modes, in particular between end stacking and groove recognition. Nevertheless a correlation between biophysical (G-quadruplex affinity) and biological (telomerase inhibition and cytotoxicity) results was not always clear. This feature may suggest the involvement of cellular targets different from the telomere and that are now under investigation. In Chapter 3, the DNA binding properties of some phenantroline derivatives in presence and in absence of Ni(II) and Cu(II) are investigated. We confirmed that different complex geometries involving one, two or three ligands per metal ion can affect the pattern of DNA recognition by driving nucleic acid conformational changes. Finally, in Chapter 4 some transplatin derivatives are evaluated. We focused our attention on defining the compounds capability to form adducts, with the nucleic acids, the nature of adducts and the kinetics of adduct formation not only on double strand DNA but also using single strand as well as G-quadruplex as targets. The results showed how different structural modifications can cooperate to greatly affect the potential interaction of the compounds. Interestingly it turned out their preference to react on single stranded DNA portions than to double stranded ones. This is probably due to an unfavourable orientation of the reactive groups when the molecule interacts with the DNA substrate. As a result, they appear to crosslink unpaired strands. By extending these results at cellular level they can reflect distinct distribution of platination site along the genome in comparison to cisplatin and even transplatin. The results obtained increment the available knowledge of DNA-small molecules interaction. In particular it emerged that a conserved interaction mode is consistent with biological effects. On the other hand, a shift in the binding mode can drive to different cytotoxic effects. This can provide a rationale for subsequent drug structure optimization leading to the development of new efficient and selective anticancer agents.
La scoperta di nuovi target anticancro è il fattore chiave per lo sviluppo di terapie sempre più efficaci. Lo studio del legame selettivo a sequenze di DNA a doppia elica nella classica forma B è stato largamente impiegato al fine di direzionare piccole molecole verso porzioni polinucleotidiche definite. Più recentemente, il riconoscimento (da parte di ligandi) di porzioni non canoniche di DNA si può tradurre in un metodo vantaggioso per indirizzare questi composti verso regioni distinte del genoma. A tale proposito, le strutture G-quadruplex rappresentano un sistema interessante poiché sono ritenute fisiologicamente significative. Queste strutture “non-canoniche” di DNA si trovano alle estremità del cromosoma (telomeri) così come in varie regioni promotrici di oncogeni in cui vi è un’abbondante presenza di residui guaninici e sembrano coinvolte nella regolazione di importanti eventi biologici. Pare infatti che l'induzione e la stabilizzazione di strutture G-quadruplex dalle parte di piccole molecole porti all'inibizione dell'attività della telomerasi interferendo con l'interazione tra l’enzima e il suo substrato a singola catena. Un simile meccanismo molecolare è probabilmente coinvolto anche nel controllo della regolazione dell'espressione genica e può portare alla soppressione della trascrizione di un oncogene. Di conseguenza, “l’approccio G-quadruplex” si rivela molto interessante per lo sviluppo di una strategia anticancro specifica caratterizzata anche da una riduzione drammatica degli effetti collaterali, tipici della chemioterapia. Lo scopo di questo lavoro è lo studio delle interazioni tra nuove famiglie di piccole molecole e diverse conformazioni di DNA G-quadruplex. Queste nuove molecole sono state opportunamente progettate apportando sostituzioni di atomi o gruppi funzionali basate sulla valutazione di composti precedentemente studiati al fine di aumentare la loro selettività per strutture G-quadruplex e di ridurre gli effetti tossici. Le proprietà biofisiche e biologiche di tutti i nuovi derivati sono state valutate al livello molecolare e cellulare. Il lavoro di tesi si divide in tre parti in base alle caratteristiche strutturali dei composti. La prima parte è dedicata alla studio di dicationi eterociclici: si è cercato correlare modifiche nella conformazione molecolare con l’affinita’ verso strutture G-quadruplex. In particolare è stato possibile razionalizzare cambiamenti della modalità di legame in base alla struttura dei composti esaminati. Tuttavia una correlazione fra i risultati biofisici (affinità G-quadruplex) e biologici (inibizione della telomerasi e citotossicità) non è risultata sempre definita. Ciò può suggerire il coinvolgimento di bersagli cellulari diversi dal telomero umano. Nel capitolo 3, sono state studiate le proprietà di legame al DNA di alcuni derivati fenantrolinici in presenza ed in assenza di Ni (II) e Cu (II). Abbiamo confermato che complessi caratterizzati da diverse geometrie che coinvolgono una, due o tre molecole per ione possono compromettere o meno il riconoscimento del DNA o determinare cambiamenti conformazionali dell'acido nucleico. Per concludere, il capitolo 4 è dedicato allo studio di derivati del transplatino. In particolare ci siamo focalizzati nel definire la capacità dei composti di formare addotti, la natura dei complessi e la cinetica di formazione del complesso non solo con DNA a doppio filamento ma utilizzando anche substrati a singola catena come il G-quadruplex. I risultati hanno dimostrato come diverse modifiche strutturali possano avere un ruolo importante nell’interazione dei composti con gli acidi nucleici. E’ risultata interessante la loro preferenzialità a reagire con porzioni di DNA a singolo filamento rispetto a sequenze a doppia elica. Ciò è probabilmente dovuto ad uno sfavorevole orientamento dei gruppi reattivi quando la molecola interagisce con il substrato di DNA. Di conseguenza, i composti sembrano formare un cross-link tra due filamenti non appaiati. A livello cellulare, questi risultati riflettono una distinta distribuzione del sito di platinazione all’interno del genoma rispetto al cisplatino e perfino rispetto al transplatino. I risultati ottenuti incrementano la conoscenza disponibile sull’interazione tra DNA e piccole molecole. In particolare è emerso che la conservazione della modalità di interazione si correla con effetti biologici definiti. Al contrario, una variazione della modalità di legame può portare a effetti citotossici differenti. Ciò può fornire una spiegazione razionale per una successiva ottimizzazione della struttura dei composti finalizzata allo sviluppo di nuovi agenti antitumorali efficaci e selettivi.

Calcul des courbes de potentiel adiabatiques pour les géométries colinéaires et perpendiculaires, à l'aide d'un pseudopotentiel dépendant du moment orbital électronique et d'une approche à deux centres; bon accord avec les calculs ab initio existants. Examen des différentes symétries de ces systèmes dans le formalisme de la théorie des groupes, afin d'étudier les valeurs propres et facteurs propres de l'hamiltonien électronique. Calcul quantique des sections efficaces relatives des transitions de structure fine de Rb induites par collision avec H(2) ou D(2). En tenant compte des niveaux rotationnels moléculaires, obtention d'un très bon accord avec les résultats expérimentaux et interprétation de l'effet isotopique

In this thesis, we focus on theoretical investigations on metal interfaces where many heterogeneous chemical reactions take place. Surface-enhanced Raman scattering (SERS) spectroscopy and the modern electrochemical methods are important in-situ techniques that have been widely employed for a variety of applications. Theoretical simulations have become an indispensable tool to infer the molecular details of interfacial structures that are not directly accessible from experimental measurements. In this context, we have proposed several new theoretical models for both SERS and interfacial electrochemistry, which allow us to provide molecular-level understanding of the interfacial structures under the realistic experimental conditions.   The first part of the thesis has addressed the basic theory of SERS that offers the vibrational structure of the interfacial molecules. It is well known that the huge enhancement of Raman intensity in this technique can be attributed to two independent factors, namely the physical and chemical enhancements. The former is resulted from the enhanced electromagnetic field induced by the plasmonic excitations, while the latter comes from the changing of interaction between the molecule and the surface. The interplay between these two enhancement factors, which has long been an issue of debate, is revealed in this thesis. They are coupled through molecular polarizability. A practical computational approach is proposed and used to demonstrate the importance of the coupling on different molecular systems. It is found that for certain systems the coupling factor can be as large as 106. This finding is of great importance towards a comprehensive understanding of the SERS mechanisms and a quantitative prediction of the enhancement factor.   The other part of the thesis is devoted to the theory of interfacial electrochemistry, in particular the effects of water solution. A novel protocol that combines classical molecular dynamics (MD) and the first principles density functional theory (DFT) calculations is proposed to address the statistical behavior of interfacial properties. Special attention has been paid to the work function of Pt(111) surface and CO adsorption energy on Pt(111) surface in aqueous solution. It has been found that in this case the work function of Pt surface illustrates a surprisingly broad distribution under the room temperature, sheds new light on the understanding of reaction activity of the surface. The proposed protocol is able to provide results in very good agreement with experiments and should be applied routinely in future studies.

QC 20120515

Cette thèse est une étude théorique sur la interface de porphyrine de cobalt avec des surfaces métalliques avec le code VASP DFT. Le cadre DFT nécessaire a été introduit dans le chapitre 1. La structure de la jBardeen, une programme ecrit en Java, pour la simulation de la STM est expliqué dans le chapitre 2 et le code source est jointe en annexe. Une étude de l'adsorption de CoTPP sur les surfaces métalliques a été entrepris dans le chapitre 3. Différents paramètres de calcul ont été évalués: Le site d'adsorption et de la géométrie à la fois la molécule et la surface ont été étudiés par rapport à la xc-fonctionnel et correction de la dispersion utilisée. Une adsorption site le plus stable est identifié. Par conséquent, ce site plus stable a été étudiée pour sa structure électronique. Calculés images STM avec le code jBardeen ont été comparés avec une experimentation de CoTPP Cu sur une surface (111) avec une couverture sous monocouche. Dans le chapitre 4, un adatome Fe a été présenté à la CoTPP sur Ag système (111). Trois sites de liaison symétrique différentes pour l'atome Fe ont été identifiés sur le macrocycle, marqué les , bi-, brd- et bru-positions. Un moment magnétique pouvait être attestée qui a été principalement situé sur l'atome Fe. Voies possibles entre les quatre, symétriquement équivalentes, sites bi- ont été étudiées avec des méthodes différentes. Simples calculs dans le vacuum et calculs de la “Nudged Elastic Band” (NEB) de l'ensemble du système a révélé une hauteur de barrière légèrement au-dessus de 0,2 eV allant de position bi à la posititon brd. Une analyse de vibration a montré que la commutation de l'atome Fe est susceptible, lorsqu'il est perturbé hors d'équilibre dans les positions brd et bru
This thesis is a theoretical study on the cobalt porphyrin - coinage metal surface interface with the DFT code VASP. The necessary DFT framework has been introduced in chapter 1. The structure of the Java program jBardeen for STM simulation is explained in chapter 2 and the source code is attached as Appendix. A study of the adsorption of CoTPP on coinage metal surfaces has been undertaken in chapter 3. Different parameters of the calculation have been evaluated: the adsorption site and the geometry of both the molecule and surface have been investigated with respect to the xc-functional and dispersion correction used. A most stable adsorption site -bridge down- is identified. Consequently, this most stable site was investigated for its electronic structure. Calculated STM images with the jBardeen code were compared with an experiment of CoTPP on a Cu(111) surface with sub monolayer coverage. In chapter 4 an Fe adatom was introduced to the CoTPP on Ag(111) system. Three symmetrically different binding sites for the Fe atom were identified on the macrocycle, labelled the bi-, brd- and bru-positions for bisector, bridge down and bridge up respectively. A magnetic moment could be evidenced which was mainly located on the Fe atom. Possible pathways between the four symmetrically equivalent bisector sites were investigated with different methods. Single point calculations in vacuum and Nudged Elastic Band (NEB) of the whole system revealed a barrier height of slightly above 0.2 eV going from bi- to the brd-position. A vibrational analysis showed that switching of the Fe atom is likely, when perturbed out of equilibrium in the brd- and bru- positions

Calculs ab initio sur le systeme hautement degenere cr h: mise en evidence d'un fort couplage entre etats ioniques et neutres et analyse des fonctions d'onde dans une description diabatique. Proposition d'une methode perturbative pour calcul des energies de dispersion entre un systeme versatil a (decrit dans une grande base) et un systeme quasi passif b (traite a l'approximation en coeur gele et caracterise par sa polarisabilite); calcul scf + ci de (a + b gele), du champ electrique exerce par a sur b, et de ses fluctuations, a l'aide d'un hamiltonien effectif; application a l'etude des courbes de potentiel des premiers etats excites des molecules diatomiques de ar avec na, k ou mg. Emploi de la theorie des pseudopotentiels et des potentiels modeles pour le calcul de potentiels impulsifs d'atomes inertes transferables a des systemes moleculaires; a partir de ces potentiels, calcul d'energies de dispersion applicable a la spectroscopie d'atomes alcalins en matiere de gaz rare

Die vorliegende Promotionsarbeit “Density functional study of the electronic and magnetic properties of selected transition metal complexes” beschäftigt sich mit dem Zusammenhang zwischen strukturellen Merkmalen sowie elektronischen und magnetischen Eigenschaften von Einzelmolekül-Magneten. Im Wesentlichen konnte dabei gezeigt werden, dass die magnetischen Eigenschaften sowohl von strukturellen Merkmalen als auch von den elektronischen Eigenschaften bestimmt werden. Des Weiteren ergab sich, dass verschiedene Kenngrößen der magnetischen Eigenschaften (im speziellen der magnetische Grundzustand S sowie die magnetische Anisotropie D) miteinander korreliert sind. Dies ist im Besonderen für eine mögliche Anwendung von Einzelmolekül-Magneten im Bereich der Datenspeicherung von Bedeutung.

The Grätzel photovoltaic cell is described in the introductory chapter and the main experimental method used in this study, X-ray crystallography, in the second chapter. The work described in chapter 3 and 4 was inspired by the Grätzel cell namely, the synthesis and characterisation of iodide and poly-iodides in chapter 3 and transition metal complexes synthesised using 2,2’-dipyridyl ketone in chapter 4.Chapter five looks in detail at a series of tri-angular lanthanide complexes, a chance discovery made while synthesising the 2,2’-dipyridyl ketone complexes described in chapter 4. These tri-angular clusters have interesting magnetic properties that are also described.

La Spectroscopie par Effet Tunnel Inélastique (IETS) avec un Microscope à Effet Tunnel (STM) est une nouvelle technique de spectroscopie vibrationnelle, qui permet de caractériser des propriétés très fines de molécules adsorbées sur des surfaces métalliques. Des règles de selection d’excitation vibrationnelle basées sur la symétrie ont été proposées, cependant, elles ne semblent pas exhaustives pour expliquer la totalité du mécanisme et des facteurs en jeu; elles ne sont pas directement transposables pour les propriétés d'un adsorbat et sont lourdes d'utilisation. Le but de cette thèse est donc d'améliorer ces règles de selection par une étude théorique. Un protocole de simulation de l'IETS a été développé, paramétré, et évalué, puis appliqué pour calculer des spectres IETS pour différentes petites molécules, qui sont systématiquement liées, sur une surface de cuivre. Des principes additifs de l'IETS ont été developpés, notamment concernant l’extension dans le vide de l’état de tunnel, l'activation/ quench sélectif de certains modes du aux propriétés électroniques de certains fragments moléculaires, et l'application de certaines règles d'addition de signaux IETS. De plus, des empreintes vibrationnelles par des signaux IETS ont été determinées pour permettre de différentier entre les orientations des adsorbats, la nature chimique des atomes et les isomères de structures. Une stratégie simple utilisant les propriétés de distribution de la densité électronique de la molécule isolée pour prédire les activités IETS sans des couts importants de calculs a aussi été développée. Cette expertise a été utilisée pour rationaliser et interpréter les mesures expérimentales des spectres IETS pour des métalloporphyrines et métallophtalocyanines adsorbées. Ces études sont les premières études IETS pour des molécules aussi larges et complexes. L'approche expérimentale a permis de déterminer les limitations actuelles des simulations IETS. Les défauts associés à l'identification ont été résolus en faisant des simulations d'images STM complémentaires
Inelastic Electron Tunneling Spectroscopy (IETS) with the Scanning Tunneling Microscope (STM) is a novel vibrational spectroscopy technique that permits to characterize very subtle properties of molecules adsorbed on metallic surfaces. Its proposed symmetry-based propensity selection rules, however, fail to fully capture its exact mechanism and influencing factors; are not directly retraceable to an adsorbate property and are cumbersome. In this thesis, a theoretical approach was taken to improve them. An IETS simulation protocol has been developed, parameterized and benchmarked, and consequently used to calculate IETS spectra for a set of systematically related small molecules on copper surfaces. Extending IETS principles were deduced that refer to the tunneling state’s vacuum extension, the selective activating/quenching of certain types of modes due to the moieties’ electronic properties, and the applicability of a sum rule of IETS signals. Also, fingerprinting IETS-signals that enable discrimination between adsorbate orientations, the chemical nature of atoms and structural isomers were determined and a strategy using straightforward electronic density distribution properties of the isolated molecule to predict IETS activity without (large) computational cost was developed. This expertise was used to rationalize and interpret experimentally measured IETS spectra for adsorbed metalloporphyrins and metallophthalocyanines, being the first IETS studies of this large size. This experimental approach permitted to determine the current limitations of IETS-simulations. The associated identification shortcomings were resolved by conducting complementary STM-image simulations

Metal complexes play fundamental roles in synthetic, biological, and catalytic processes, and when doing so they are often present at very low concentrations. Determining the coordination structure of complexes at trace levels or in complicated mixtures, however, is a very difficult task. This dissertation focuses on the investigation of a new methodology, based on ion-molecule (I-M) reactions and mass spectrometry (MS), to determine the coordination structure of metal complexes sensitively. This work describes the study of the gas-phase reactivity exhibited by a variety of model transition metal complexes with different reagent ligands in a quadrupole ion trap mass spectrometer. A series of tetradentate and pentadentate ligands containing N, O, and/or S donor atoms were synthesized and complexed with late first-row transition metals. Noticeable differences in reactivity were found as the ligand field around the central metal ion was changed. The electronic structure of the metal center was also found to exert a remarkable effect on the gas-phase reactions of metal complexes, and in fact, complexes with different geometric structures could be distinguished. Angular overlap model (AOM) and density functional theory (DFT) calculations were used to explain the experimental observations. The analytical utility of the I-M reactions was also investigated. Fluctuations in reagent and buffer gas pressures and vacuum system temperature were examined as possible error sources affecting the conclusions drawn from the I-M reaction procedure. Reagent gas pressure and temperature were found to be the most important factors affecting the reproducibility of the experimental data. Because the analytical information derived from these I-M reactions relies on complexation of a reagent ligand, steric factors that might affect these reactions were also evaluated. In summary, I-M reactions can distinguish complexes with different coordinating functional groups and geometries, and these reactions have some potential for providing coordination structure information for complexes present at trace levels.

This thesis reports the theoretical investigations aimed at understanding the structure, stability and properties of a few inorganic compounds. The first chapter presents an introductory overview of the theories used to solve the questions addressed in the thesis. A brief discussion of the work is also presented here. The second chapter deals with electron reservoirs which have been one of the basic motifs of single-electron device. Mononuclear vinylidene complexes of type Mn(C5H4R’)(R” 2 PCH2CH2PR "2)= C = C(R1)(H) were synthesized and reported [Venkatesan et al, Organometallics 25, 5190 (2006)] as potential electron reservoirs capable of storing and releasing electrons in a reversible fashion. These compounds have been of great interest because their red-ox chemistry (reversible oxidative coupling and reductive decoupling) is governed by the C - C bond. However slow oxidation of the mononuclear vinylidene complexes leads to undesired product. In our model compound Mn(C5H5)(PH3)2 = C = C(R1)(H), we substituted the cyclopentadienyl moiety by isolobal dianionic dicarbollyl ligand Dcab2- (C2B9H2-11 ). This simple substitution could reduce the production of undesired product. Calculations of vertical detachment energy, thermodynamic feasibility and molecular orbital analysis showed that this substitution was thermodynamically feasible and led to easy oxidation and dimerization of the parent compound accompanied with better reversibility of the reaction. The effect of substituents (R = H,Me,Ph) on Cβ atom of our model system was also analyzed. The substituent on β carbon had a great effect on the stability and reactivity of these complexes. Our comparative study between Mn(C5H5)(PH3)2 = C = C(R)(H) and Mn(Dcab)(PH3)2 = C = C(R)(H)−1 (where R = H,Me,Ph) predicted the latter to be a more potential electronic reservoir. Gas-phase observations on MAl 4- (M = Li, Na, Cu) and Li3Al-4 coupled with computations led to the conclusion that Al42− [Boldyrev and Wang et al, Science 291, 859 (2001)] is “aromatic” while Al44- is “antiaromatic” [Boldyrev and Wang et al, Science 300, 522 (2003)]. It has been reported by Pati et al [J. Am. Chem. Soc. 125, 3496 (2005)] that co-ordination with a transition metal can stabilize the “antiaromatic” Al4Li4. In the first section of chapter three, it has been reported that Al4Li4 can also be stabilized by capping it with main group element like C and its isoelectronic species BH. Calculations of binding energy, nuclear independent chemical shift (NICS), energy decomposition analysis and molecular orbital analysis supported the capping induced stability, reduction of bond length alternation and increase of aromaticity of these BH/C capped Al4Li4 systems. The interaction between px and py orbitals of BH/C and the HOMO and LUMO of Al4Li4 was responsible for such stabilization. Calculations suggested that capping might introduce fluxionality in the molecule at room temperature. Al has valence electronic configuration of s2p1 and Al42− has been shown to have multiple aromaticity [Boldyrev and Wang et al, Science 291, 859 (2001)]. Analogy between electronic configuration s2pof Al and d1sof Sc/Y prompted us to explore the aromaticity of M42− clusters (M = Sc, Y ) which have been described in the second section of chapter three. Different geometries of M42− clusters (M = Sc, Y ) were explored, and the planar butterfly-like D2h geometry (two fused triangles) was found to be the most stable isomer. This is unlike the case of Al42− where D4h isomer was the most stable one as reported in the literature. In D2h geometry of M42− clusters (M = Sc, Y ), significant electron delocalization in each wing of the butterfly indicated fused d aromaticity. Atomization energy and chemical hardness supported the preference of D2h geometry over the D4h geometry. Molecular orbital analysis showed that the d-electrons were delocalized in each triangle of D2h geometry. Our interest in the search of new kinds of binuclear sandwich compounds led us to consider sandwiched metal dimers CB5H6M - MCB5H6 (M = Si, Ge, Sn) which are at the minima in the potential energy hypersurface with a characteristic M - M single bond. This work has been described in the first section of chapter four. The NBO analysis and the M - M distances ( ˚A) (2.3, 2.44 and 2.81 for M= Si, Ge, Sn respectively) indicated substantial M - M bonding. Consecutive substitution of two boron atoms in B7H7−2 by M (Si, Ge, Sn) and carbon respectively led to neutral MCB5H7, where M - H bond bent towards the carbon side of the five membered ring. Dehydrogenation of two MCB5H7 might lead to our desired CB5H6M - MCB5H6 where similar bending of M -M bond has been observed. The bending of M - M bond in CB5H6M -MCB5H6 was more than the M - H bending in MCB5H7. Molecular orbital analysis has been done to understand the bending. Larger M - M bending observed in CB5H6M - MCB5H6 in comparison to M - H bending observed in MCB5H7 was suspected to be favored by stabilization of one of the M - M π bonding MO’s. Preference of M to occupy the apex of pentagonal skeleton of MCB5H7 over its icosahedral analogue MCB10H11 has been observed. Structures of sandwiched binuclear L- M – M - L where M = Ti, Zr and L = Cp, C3B3H6 were also investigated as described in second section of chapter four. We found that these compounds having bent geometry with short M - M distance (1.87˚A for M=Ti and 2.29˚A for M=Zr) lie at the minima in the potential energy hypersurface. Bending from the linear geometry led to the stabilization of M - L antibonding interaction in L - M – M - L. Molecular orbital analysis, NBO calculations, Wiberg bond index and charge analysis suggested M2+ unit to be embedded in between two L’s in L - M – M - L. Molecules that have the ability to perform interesting mechanical motions have always been of great interest. Umbrella inversion of ammonia is one of the most interesting and well studied phenomena. This study has led to the development of the MASER. The possibility of inversion of the molecule C9H9−Li+ by the movement of Li+ through the C9H9−ring was studied earlier [Das et al, Chem. Phys. Lett. 365, 320 (2002)]. In the fifth chapter theoretical investigation on a B12 cluster has been reported, which could exhibit a through ring umbrella inversion. Calculations showed that a part of the molecule, consisting of a three membered boron ring could invert through the rest, viz., a nine membered boron ring. Using a simple model, the double well potential for the motion was calculated. The barrier for inversion was found to be 4.31 kcal/mol. The vibrational levels and tunneling splitting were calculated using this potential. It was found that the vibrational excitation to the v = 17 level caused large amplitude “inversion oscillation” of the molecule. After considering the tunneling effect, inversion rate at 298K was calculated by using transition state theory and was found to be 1.17 x 1010/s. Finally, in the last chapter the main results of the thesis have been summarized.

Die vorliegende Promotionsarbeit “Density functional study of the electronic and magnetic properties of selected transition metal complexes” beschäftigt sich mit dem Zusammenhang zwischen strukturellen Merkmalen sowie elektronischen und magnetischen Eigenschaften von Einzelmolekül-Magneten. Im Wesentlichen konnte dabei gezeigt werden, dass die magnetischen Eigenschaften sowohl von strukturellen Merkmalen als auch von den elektronischen Eigenschaften bestimmt werden. Des Weiteren ergab sich, dass verschiedene Kenngrößen der magnetischen Eigenschaften (im speziellen der magnetische Grundzustand S sowie die magnetische Anisotropie D) miteinander korreliert sind. Dies ist im Besonderen für eine mögliche Anwendung von Einzelmolekül-Magneten im Bereich der Datenspeicherung von Bedeutung.