This thesis describes stereospecific fluorination reactions, and addresses the synthesis of fluorosugars. In Chapter 1, the influence of fluorine on the physical properties of organic molecules, as well as its stereoelectronic effects, are introduced. Furthermore, an overview of nucleophilic and electrophilic fluorination reactions is given. Chapter 2 describes the dehydroxyfluorination of allylic alcohol diastereoisomers 155a and 155b, which can proceed either by direct or allylic fluorination. The regio- and stereo- selectivities were also assessed. Chapter 3 outlines the synthesis of the novel trifluoro D-glucose analogue 193 and trifluoro D-altrose analogue 216. The transport of these hexose analogues across the red blood cell membranes was then explored, to investigate the influence of polarity versus hydrogen bonding ability in carbohydrate-protein interactions. Chapter 4 describes the development and optimisation of Bio’s methodology, to promote stereospecific dehydroxyfluorination of benzylic alcohols (R)-213 and (R)-227 by addition of TMS-amine additives 226 and 229. And finally Chapter 5 reports the experimental procedures as well as the characterisation and the crystallographic data of the molecules prepared in this thesis.

Crystallographically solids with well defined crystal structures are normally assumed to be highly ordered. However, it is not uncommon to find considerable degree of disorder amongst many of these crystalline substances. Disorder among crystalline substances often arise from the rotational motion which leads to the well known class of plastic crystalline substances. Typically, globular molecules such as methane, carbon tetrachloride or adamantane exhibit plastic crystalline phase with significant amount of orientational disorder. In many other substances, disorder arises from torsional motion as in the case of biphenyl, p- or o-terphenyls, stilbene or azobenzenes. In case of molecules with flexible segment, such as alkanes or surfactants, motion of the terminal methyl group or terminal ethyl group is responsible for the observed disorder. Chapter 1 discusses various aspects of disorder in crystals. A new pressure induced solid phase of biphenyl is reported at room temperature. Isothermal-isobaric ensemble variable shape simulation cell Monte Carlo calculations are reported on biphenyl at 300K as a function of pressure between 0-4 GPa. The potential proposed by Williams for inter-molecular and Benkert-Heine-Simmons(BHS) for intramolecular interactions have been employed. Different properties indicating changes in the crystal structure, molecular structure, distributions of inter- and intra-molecular energy are reported as a function of pressure. With increase in pressure beyond 0.8 GPa, the dihedral angle distribution undergoes a change from a bimodal to an unimodal distribution. The changes in IR and Raman spectra across the transition computed from ab initio calculations are in agreement with the experimental measurements. It is shown that at pressures larger than 0.8 GPa, competition between inter-molecular interactions with intra-molecular terms v/z., conjugation energy and the ortho-ortho repulsion favors a planar biphenyl due to better packing and consequently a predominant inter-molecular term. The exact value of the transition pressure will depend on the accuracy of the inter- and intra-molecular potentials employed here. p-terphenyl has been modeled at 300K and atmospheric pressure with different potential models. Modified Fihppini parameters for mtermolecular interactions and BHS potential for inter-ring torsion predict the structure of p-terphenyl reasonably well. Pressure variation calculations are carried out with this combination of inter- and intra-molecular potential. The structure as a function of pressure upto 5 GPa has been compared with experimental structure provided by Puschnig et al. The transformation of functional form of the potential energy curve (associated with the inter-ring flipping) from W-shaped to [/-shaped form as a function of pressure has been observed. This is in excellent agreement with previous studies of polyphenyls including biphenyl and p-hexaphenyl. The complete planarization of molecules occurs when the pressure range is 1.0 GPa-1.5 GPa. Molecular simulation of solid stilbene in the isothermal-isobaric ensemble with variable shape simulation are reported. Structure has been characterized by means of lattice parameters and radial distribution functions. Simulations show existence of pedal-like motion at higher temperatures in agreement with the recent X-ray diffraction measurements by Ogawa and co-workers and several others previously. Difference in energy between the major and minor conformers, barrier to conformational change at both the crystallographic sites have been calculated. Temperature dependence of the equilibrium constant between the two conformers as well as the rate of conversion between the con-formers at the two sites have been calculated. These are in agreement with the recent analysis by Harada and Ogawa of non-equilibrium states obtained by rapid cooling of stilbene. Volume and total intermolecular energy suggest existence of two transitions in agreement with previous Raman phonon spectroscopic and calorimetric studies. They seem to be associated with change from order to disorder at the two sites. Ab initio calculations coupled with simulations suggest that the disorder accounts for only a small part of the observed shortening in ethylene bond ength. A Monte Carlo simulation with variable shape simulation cell has been carried out on stilbene. The study attempts to investigate the disorder at various pressures upto 4 GPa. It is seen that the population of minor conformers at sites 1 and 2 decrease with increase in pressure. Population of minor conformers at site 2 decreases to zero by 1.5 GPa. In contrast, the population of minor conformers at site 1 remains finite for the runs reported here. It is seen that the population of minor conformers at site 1 is higher than at site 2 at room temperature which is to be expected on the basis of the activation energies. Associated changes in the unit cell as well as molecular conformation are discussed. Isothermal-isobaric ensemble Monte Carlo simulation of adamantane has been earned out with variable shape simulation cell. Low temperature crystalline phase and the room temperature plastic crystalline phases have been studied employing the Williams potential. We show that at room temperature, the plastic crystalline phase transforms to the crystalline phase on increase in pressure. Further, we show that this is the same phase as the low temperature ordered tetragonal phase of adamantane. The high pressure ordered phase appears to be characterized by a slightly larger shift of the first peak towards lower value of r in C-C, C-H and H-H rdfs as compared to the low temperature tetragonal phase. Co-existence curve between the crystalline and plastic crystalline phase has been obtained approximately upto a pressure of 4 GPa. We investigate the equation of state, variation of lattice parameters and the distortion of molecular geometry of low temperature phase of adamantane upto 26 GPa pressure. A rigid and a flexible model of adamantane have been studied using variable shape simulation within the isothermal-isobaric ensemble. Including six low frequency modes obtained from density functional theory carried out on a single-molecule has incorporated the flexibility. These calculations used Becke 3-parameter method and Lee-Yang-Parr electron correlation functional with 6-31G(d) basis set. The simulated equation of state and variation of c/a ratio as a function of pressure are compared with the experimental results. The results are in good agreement with high pressure experiments. Nature of distortion in molecular geometry obtained from the calculation are also in good agreement with the experiment.

The thesis entitled “Controlling Stereochemistry at the Quaternary Center Using Bifunctional (Thio)urea Catalysis” is divided into five chapters. Chapter 1: Catalytic Enantioselective Construction of Quaternary Stereocenters through Direct Vinylogous Michael Addition of Deconjugated Butenolides to Nitroolefins The direct use of deconjugated butenolides in asymmetric C–C bond forming reaction is a powerful but challenging task because of the additional problem of regioselectivity along with the issues of diastereo- and enantioselectivity. In this chapter, a direct asymmetric vinylogous Michael addition of deconjugated butenolides to nitroolefins has been demonstrated for the construction of quaternary stereocenter at the γ-position of butenolides. A novel thiourea-based bifunctional organocatalyst, containing two elements of chirality, was synthesized starting from commercially available quinine and (S)-tert-leucine. Remarkably, the sense of stereoinduction in this process is dominated by the tert-leucine segment of the catalyst. Synthetically versatile & highly functionalized γ-butenolides with contiguous quaternary and tertiary stereocenters were synthesized stereoselectively. The reaction was found to be general and a wide range of nitroolefins, with both electron-rich and electron-deficient substituents, underwent smooth reaction under these mild conditions. Similarly, deconjugated butenolides, having various substituents at the γ-position were well tolerated under these reaction conditions and the products were obtained in excellent yields and with uniformly high diastereo- and enantioselectivities. Reference: Manna, M. S.; Kumar, V.; Mukherjee, S. Chem. Commun. 2012, 48, 5193–5195. Chapter 2: Catalytic Asymmetric Direct Vinylogous Michael Addition of Deconjugated Butenolides to Maleimides for the Construction of Quaternary Stereogenic Center In this chapter, a mild and operationally simple protocol for the direct vinylogous Michael addition of deconjugated butenolides to maleimides has been illustrated. Using bifunctional tertiary amino thiourea organocatalyst, derived from a ‘matched’ combination of trans-(1R,2R)-diaminocyclohexane (DACH) and (S)-tert-leucine, the Michael adducts were obtained in excellent yields and with good to high diastereoselectivities and outstanding enantioselectivities. Application of the corresponding diastereomeric catalyst indicated the dominance of the ‘DACH’ unit over the chiral side chain in determining the sense of stereoinduction. The practicality of this protocol is illustrated by substantial low catalyst loading (down to 5 mol%) and one-pot catalyst recycling. Based on the X-ray structure of the catalyst and observed stereochemistry of the Michael adduct, a stereochemical model is proposed which was further supported by additional experiment. Reference: Manna, M. S.; Mukherjee, S. Chem.–Eur. J. 2012, 18, 15277–15282. Chapter 3: Enantioselective Desymmetrization of Cyclopentenedione through Direct Catalytic Vinylogous Michael Addition of Deconjugated Butenolides Five-membered carbocycles containing one or more stereogenic centers on the ring are privileged structural motifs found in many biologically active natural and non-natural compounds. Among various methods for accessing these enantioenriched carbocyclic frameworks, desymmetrization of prochiral or meso-compounds through catalytic enantioselective transformations represents a powerful strategy. The biggest advantage of such asymmetric desymmetrization reactions lies in their ability in controlling stereochemistry remote from the reaction site. This chapter deals with a highly efficient desymmetrization protocol for 2,2-disubstituted cyclopentene-1,3-diones via direct vinylogous nucleophilic addition of deconjugated butenolides with the help of a tertiary amino thiourea bifunctional catalyst. In contrast to the existing desymmetrization protocols, this method represents a unique example where quaternary stereocenter is generated not only within the ring but also outside the cyclopentane ring. Densely functionalized products are obtained in excellent yields and with outstanding diastereo- and enantioselectivities. The robustness screening indicated that the reaction is highly tolerant to a variety of competing electrophiles and nucleophiles. The remarkable influence of the secondary catalyst site on the enantioselectivity points towards an intriguing mechanistic scenario. To the best of our knowledge, this is the first time such an effect is observed in the context of asymmetric catalysis. Reference: (1) Manna, M. S.; Mukherjee, S. Chem. Sci. 2014, 5, 1627–1633. (2) Manna, M. S.; Mukherjee, S. Org. Biomol. Chem. 2015, 13, 18–24. (Perspective) Chapter 4: Enantioselective Desymmetrization of Cyclopentenediones through Organocatalytic C(sp2)–H Alkylation Organic compounds are characterized by the presence of various C–H bonds. Functionalization of a specific C–H bond in a molecule with a selected atom or group are among the most straightforward and desirable synthetic transformations in organic chemistry. In this chapter, a simple protocol for the direct alkylation of olefinic C(sp2)–H bond has been developed, not only enantioselectively using an organocatalyst but more importantly without using any directing group. This alkylative desymmetrization of prochiral 2,2-disubstituted cyclopentene-1,3-diones is catalyzed by a dihydroquinine-based bifunctional urea derivative. Using easily accessible, inexpensive and air-stable nitroalkanes as the alkylating agent, this C(sp2)−H alkylation represents a near-ideal desymmetrization and delivers products containing an all-carbon quaternary stereogenic center in good to excellent yields and with high enantioselectivities. The mild reaction conditions allow for the introduction of various functionalized alkyl groups. The possibility of a second alkylation and its applications has also been demonstrated. This protocol is the first example of the use of nitroalkane as the alkyl source in an enantioselective transformation. It is expected that, these findings would have broader consequences and applications to other alkylative and related transformations. Reference: Manna, M. S.; Mukherjee, S. J. Am. Chem. Soc. 2015, 137, 130–133. (Highlighted in Synform 2015, 67–70) Chapter 5: Enantioselective Desymmetrization of Cyclopentenediones through Organocatalytic Formal C(sp2)–H Vinylation The development of catalytic enantioselective C(sp2)–H vinylation reactions remained relatively underexplored for a long time because of various challenges associated with it. As C(sp2)–H functionalization reactions do not generate any stereocenter at the reaction site, development of enantioselective C(sp2)−H functionalization must rely on desymmetrization of prochiral or meso-substrates. More important issue is the identification of a suitable directing group which can efficiently control the regioselectivity during the activation of C(sp2)−H bond. In this chapter, an efficient formal C(sp2)−H vinylation of prochiral 2,2-disubstituted cyclopentene-1,3-dione is developed without using any directing group. This formal C(sp2)−H vinylation of 2,2-disubstituted cyclopentene-1,3-dione is realized using a two-step operation: catalytic enantioselective Michael addition of deconjugated butenolides followed by a base mediated decarboxylation. The vinylated products, containing a remote all-carbon quaternary stereogenic center, are obtained in good yields and with good to high enantioselectivities. Synthetic utility of this protocol is demonstrated by converting the resulting chiral electron-deficient diene into various important building blocks. Significant erosion in enantioselectivity during the decarboxylation process was explained by a plausible mechanism, which was further supported by control experiments. Reference: Manna, M. S.; Sarkar, R.; Mukherjee, S. manuscript under preparation.

Section I of the thesis deals with the enantiospecific total synthesis of phomopsolide B. Phomopsolide B was isolated from a strain of Phomopsis Oblonga. Enantiospecific total synthesis of phomopsolide B was accomplished in 13 overall yield in 12 linear steps using (S)-lactic acid and L-tartaric acid as chiral pool precursors. Present approach involves the efficient use of -keto phosphonate derived from commercially available (S)-ethyl lactate. Horner-Wadsworth-Emmons reaction and Still-Gennari olefination were employed as key reactions in the synthesis (scheme 1). Scheme 1: Total synthesis of phomopsolide B. [This work has been published: Prasad, K. R.; Gutala, P. Tetrahedron 2012, 68, 7489-7493.] Section II of the thesis describes the total synthesis of macrosphelides A and E which are isolated from a culture broth of Microsphaeropsis sp. FO-5050 and from the strain Periconia byssoides. Total synthesis of macrosphelides A and E was accomplished in 19 overall yield from commercially available (S)-ethyl lactate. Horner-Wadsworth-Emmons reaction and Yamaguchi lactonization were employed as key reactions for the total synthesis of macrosphelides A and E (scheme 2). Scheme 2: Total synthesis of macrosphelides A and E. [This work has been published: Prasad, K. R.; Gutala, P. Tetrahedron 2011, 67, 4514-4520.] Section III of the thesis deals with total synthesis and determination of absolute configuration of synargentolide B 1. Synargentolide B 1 is a 5,6-dihydro--pyrone containing natural product and was isolated from Syncolostemon Argenteus by Rivett et al. in 1998 (fig 1). The relative stereochemistry at C-6, C-6′ positions in synargentolide B 1 was assigned to be R, S respectively based on the positive cotton effect in the CD spectrum. Threo stereochemistry was proposed for the C1′-C2′ diol unit in synargentolide B 1 based on the NMR studies. The stereochemistry at C-5 could not be assigned, hence the structure of synargentolide B 1 was tentatively proposed as 6R-[5,6S-(diacetyloxy)-1,2-(dihydroxy)-3Eheptenyl]-5,6-dihydro-2H-pyran-2-one (fig. 1). Figure 1: Putative structure of synargentolide B 1. Based on the tentative stereochemistry at the C-6, C-6′ positions proposed by Rivett et al. and taking into consideration the threo relationship for the C-1′-C-2′ diol unit, it is anticipated that the structure of synargentolide B 1 could be one of the four possible diastereomers 1a-1d (fig 2). Figure 2: Possible diastereomers of synargentolide B (1a-d). Incidentally, one of the diastereomers 6R-[5R,6S-(diacetyloxy)-1S,2R-(dihydroxy)- 3E-heptenyl]-5,6-dihydro-2H-pyran-2-one 1d was a reported natural product isolated in 1990 from Hyptis oblangifolia by Pereda-Miranda, R. et al. along with its corresponding diacetylated product 2 (fig 3). Fig. 3: Natural products isolated from Hyptis oblangifolia by Pereda-Miranda, R. et al. Total synthesis and determination of absolute configuration of synargentolide B 1 were accomplished by synthesizing four possible diastereomers of the natural product (1a-1d) and by comparison of the spectral data of all synthesized diastereomers with that of reported for the natural product. Wittig-Horner reaction of -keto phosphonate derived from (S)-lactic acid and ring closing metathesis reaction were employed as key reactions in the total synthesis of synargentolide B 1 (scheme 3 and 4). Scheme 3: Total synthesis of possible diastereomers of synargentolide B (1a, 1b). Scheme 4: Total synthesis of possible diastereomers of synargentolide B (1c, 1d). [This work has been published: Prasad, K. R.; Gutala, P. J. Org. Chem. (in press)]. It was found that spectral data of 1a, 1b, 1c were not in agreement with that reported for synargentolide B 1. However spectral data of 1d was in complete agreement with the data reported for synargentolide B 1. Spectral data of 1d was also in complete agreement with the data reported for the natural product isolated by Pereda-Miranda, R. et al. Since the absolute stereochemistry of tetraacetate 2 is identical to the absolute stereochemistry of 1d, we wanted to confirm the integrity of the diol 1d by synthesizing the corresponding acetate 2 which was also a natural product isolated by Pereda-Miranda et al. 1H NMR data of the synthesized tetraacetate 2 was in agreement with that reported for the isolated tetraacetate, while discrepancies were observed in the 13C NMR spectral data. To clear the uncertainty, X-ray crystal structure analysis of the tetraacetate 2 was performed. It was comprehensively proved that the structure of synthesized tetraacetate 2 was indeed same as the putative structure proposed for the isolated tetraacetate by Pereda-Miranda et al. The crystal structure analysis also confirmed the absolute stereochemistry of the tetraacetate 2 and 1d (synargentolide B 1). (For structural formula pl refer the abstract pdf file)

Les travaux de cette thèse ont porté sur le développement de deux méthodes de modélisation des enzymes contenant des groupes prosthétiques de la famille des flavines.La première méthode, PredFace, permet de prédire la stéréochimie des produits d'une réaction catalysée par des enzymes contenant des groupes prosthétiques, en identifiant la face libre d'interaction avec les substrats. Le protocole mis en place pour cette méthode implique l'utilisation de huit complexes "sondes", obtenus par des opérations de symétrie à partir de l'état de transition de la réaction de transfert d'un atome d'hydrogène entre le nicotinamide et la lumiflavine. Ces complexes sont positionnés dans le site actif avec le groupe prosthétique comme référence et dans chaque cas l'énergie d'interaction protéine-ligand est évaluée par la fonction de score implémentée dans le logiciel de docking utilisé (AutoDock). L'énergie d'interaction la plus favorable permet d'identifier la face du groupe prosthétique accessible pour la réaction enzymatique dans le site actif. La méthode PredFace a été validée par l'analyse de l'ensemble des structures de la Protein Data Bank contenant des groupes prosthétiques de la famille des flavines (2170). Le protocole mis au point est très rapide (moins d'une minute), ce qui nous a permis de développer un site web afin de mettre cette méthode à la disposition de la communauté.La seconde méthode, ProsthDock, est une nouvelle méthode de docking basée sur le mécanisme d'une réaction enzymatique catalysée par un groupe prosthétique et guidée par la présence de ce groupe prosthétique dans le site actif de l'enzyme. Le développement de cette méthode a été motivé par le fait que les méthodes actuelles de docking, en présence de groupes prosthétiques, se révèlent incapables de produire des poses correctes pour des substrats, en accord avec les réactions enzymatiques. Afin de remédier à ce problème nous avons ajouté à la fonction de score classique un terme supplémentaire, qui rendra compte de l'interaction du ligand avec le groupe prosthétique. Dans un premier temps, nous avons construit un modèle simplifié du complexe NADH/FMN et calculé l'état de transition de la réaction de transfert d'hydrogène entre les deux partenaires. Des surfaces d'énergie potentielle pour cette réaction ont été calculées en variant la distance, l'angle et l'angle dièdre entre les deux réactifs. Un docking sous contrainte est ensuite réalisé et en fonction du positionnement de chaque pose de docking dans le site actif le terme supplémentaire de la fonction de score est calculé à partir des surfaces d'énergie potentielle, ce qui nous permet de modifier le classement des résultats de docking en favorisant les poses qui sont en accord avec la réaction enzymatique. / During this PhD thesis we developped two new molecular modeling methods applied to enzymes containing flavin-type prosthetic groups.The first method, PredFace, predicts the stereochemistry of products from a reaction catalyzed by enzymes containing prosthetic groups, by automatically identifying the solvent-exposed face of the prosthetic group. The protocol involves the use of eigth complexes as "probes", obtained by symmetry operations starting from the transition state of a hydrogen atom transfer reaction between nicotinamide and lumiflavin. These complexes are positioned in the binding site with the prosthetic group as reference and the energy of the protein-ligand interaction is evaluated by the scoring function implemented in the docking software (AutoDock). The most favorable interaction energy allows the identification of the prosthetic group face that is available for the enzymatic reaction in the binding site. The PredFace method has been validated by analyzing all the structures in the Protein Data Bank containing flavin-derived prosthetic groups (2170). This method is very fast (less than a minute), which allowed us to develop a web site open to the scientific community.The second method, ProsthDock, is a new mechanism-based molecular docking method guided by prosthetic groups present in the active sites of enzymes. The development of this method was motivated by the incapacity of the currently available docking methods to provide, in the presence of prosthetic groups, ligand conformations that are compatible with the enzymatic reactions. In this regard, we have added a new term to the classical scoring function, to take into account the interaction between ligand and prosthetic group. We have built a simplified model of the NADH/FMN complex and calculated the transition state of the hydrogen transfer reaction between the two partners. Potential energy surfaces have been calculated for this reaction by variating the angle, diedral angle and distance between the two reaction partners. A subsequent docking with constraints provides binding site conformations of the ligand for which the new term of the scoring function is calculated using the potential energy surfaces. This results in a new ranking of the docking poses, favoring those in agreement with the enzymatic reaction.

<div>Enantioselective syntheses of hexacyclic aspidoalbidine alkaloids (+)-fendleridine and (+)-acetylaspidoalbidine are described. These syntheses feature an asymmetric decarboxylative allylation and photocyclization of a highly substituted enaminone. Also, the synthesis highlights the formation of a C19-hemiaminal ether via a reduction/condensation/intramolecular cyclization cascade with the C21-alcohol. The present synthesis provides convenient access to the aspidoalbidine hexacyclic alkaloid family in an efficient manner.</div><div>A copper-catalyzed cross-coupling is described. Use of Cu(I) salts in the presence of allyl bromides and organostannyl furans were found to undergo catalytic turnover under ambient conditions and afford the coupled products in good to great yields. Model substrate screening led to conditions used in the concise formal synthesis of FR901464 analogues. Optimization of the described coupling step led to suppression of undesired isomers and byproducts affording the desired diene coupled product in high yield, stereo-, and regioselectivity on a multigram scale. Novel protection of the resulting diene moiety as an unconventional protecting group, and a facile four-step single column chromatographic stereoselective sequence are also reported.</div>

No description available.

<p dir="ltr">Directed hydrogenation, in which product geometric selectivity is dictated by the binding of an ancillary directing group on the substrate to the catalyst, is typically achieved by homogeneous Rh and Ir complexes. No heterogeneous catalyst has been able to achieve equivalently high directivity due to a lack of control over substrate binding orientation at the catalyst surface. In this work, we demonstrate through structure-activity studies that careful control of surface ensemble geometry in bimetallic nanoparticle catalysts can confer hydroxyl-directed selectivity in heterogeneous double bond hydrogenation. We postulate that the oxophilic alloy component binds hydroxyl groups to pre-orient the molecule on the surface, while proximal noble metal atoms impart facially selective addition of hydride to the olefin. We found that controlling the degree of surface alloying between oxophilic and noble metal component as well as alloy component identity is critical to maximizing reaction selectivity and starting material conversion. Our optimized catalysts exhibit good functional group tolerance on a variety of cyclohexenol and cyclopentenol scaffolds, with Pd-Cu and Pt-Ni systems being developed for the diastereoselective hydrogenation of tri- and more challenging tetra-substituted olefins, respectively. The applicability of this method is then demonstrated in a four-step synthesis of a fine fragrance compound, (1<i>R</i>,2<i>S</i>)-(+)-<i>cis</i>-methyldihydrojasmonate (Paradisone®), with high yield and enantiopurity.</p>

La miniaturisation toujours plus poussée des composants électroniques a atteint une limite en arrivant à l’échelle atomique. Afin de fabriquer des circuits à cette échelle, il est nécessaire de intéresser aux plus petits composants pouvant être intégrés : les molécules individuelles et les groupes d’atomes. Dans cette optique, les molécules de 1,4-bis(pyridin-4-ylethynyl) benzène (BPEB), Dibenzo[a,h]thianthrene (DBTH), de Bis{82,92,152,162,222,232- hexa-(2,4,6-trifluorophenoxy)[g,l,q]-5,10,15,20-tetraazaporphyrino)}[b,e]-benzene (H4Pc2) ont été conçues, synthétisées et caractérisées afin d’en étudier le transport de charges et les changements induits proche de la surface. Des techniques de SPM, tels que le STM, le nc-AFM et l’usage conjoint de l’AFM avec le STM ont été mises en pratique pour analyser les molécules reposant intégralement ou partiellement sur un substrat. L’interprétation des résultats expérimentaux a été faite au moyen de calculs de DFT. De plus, l’autoassemblage en solution de nouvelles mono-phthalocyanines métalliques fluorées, MPc (M= Mg2+, 2H+, Co2+) a été étudié.Tout d’abord, les mesures de conductance mirent en évidence, lors d’expériences de manipulation de fils moléculaires (BEPB), les changements de conformation associés aux transport des électrons à travers les molécules. De plus, le mouvement dit de “retournement papillon” (anglais: butterfly flapping) ayant lieu dans la classe des thianthrènes fut bloqué à basse température grâce à l’interaction avec le substrat. Ce blocage a permit de conduire la première étude stéréochimique de dérivés de thianthrènes chiraux (DBTH). Les analyses STM du DBTH ont montrées que le passage entre deux configurations de DBTH est reproductible et non-destructif. Par ailleurs, le nc-AFM utilisé à résolution sub-moléculaire a constitué un outils important pour réaliser une caractérisation complète et distinguer entre les différents isomères de configuration et de constitution déposés sur une surface. D’autre part, la structure moléculaire de la phthalocyanine binucléaire (H4Pc2) a été confirmée en utilisant un STM en mode “courant constant” et un AFM en mode “fréquence constante”. Ces résultats jettent les bases d’une prochaine étude de transport (travail en cours). En outre, l’étude de l’agrégation dans les molécules de MPc mit en évidence le rôle important de la capacité de coordination de l’atome central de la cavité Pc sur la formation d’agrégat. Finalement, des mesures électrochimiques ont démontrées que l’agrégation moléculaire peut bloquer le nature active de l’atome Co2+. Dans ce travail, il a été clairement montré que le SPM est une technique adéquate pour étudier les changements de conformations et de configurations associés aux courant tunnel d’électrons à travers des molécules, qu’elles soient planaire ou pas. Les études d’agrégation des interrupteurs magnétiques ont permis de mieux comprendre l’organisation supramoléculaire. Cette organisation est un point crucial pour le développement de futurs circuits basés sur une fabrication “bottom-up”. / The demand of downscaling of technology will reach its limit at the atomic length scale. This claim creates the necessity of investigating the smallest components suitable to become devices, single molecules or group of atoms. Therefore, 1,4-bis(pyridin-4-ylethynyl) benzene (BPEB), Dibenzo[a,h]thianthrene (DBTH) and Bis{82,92,152,162,222,232-hexa-(2,4,6-trifluorophenoxy)[g,l,q]-5,10,15,20-tetraazaporphyrino)}[b,e]-benzene (H4Pc2) have been designed, synthesized and characterized to investigate transport of charge through molecules and surface confined molecular switching. Scanning Probe Microscopy (SPM), such as STM, nc-AFM and combined STM/AFM were used to study the molecules on near-surface conditions. Density Functional Theory (DFT) calculations were used to interpret the experimental results. Moreover, the self-assembly of new fluorinated metalo mono-phthalocyanines, MPc (M= Mg2+, 2H+, Co2+) was investigated in solution.Firstly, conductance experiments performed while a molecular wire (BPEB) was being lifted up from a surface revealed the conformational changes associated to the transport of electrons through molecules. Secondly, the “butterfly” flapping motion in the class of the thianthrenes was blocked due to the interaction with a surface at low temperature. This block leads to the first stereochemical study of a quiral thianthere derivative (DBTH). The STM experiments on DBTH revealed a reproducible and non-destructive switching between two surface confined configurations of DBTH. In addition, nc-AFM with submolecular resolution has been proved to be a powerful tool for the full characterization and distinction of configurational and constitutional isomers on surfaces. Thirdly, the molecular structure of a binuclear phthalocyanine (H4Pc2) was confirmed through constant current STM and constant high _f AFM experiments. These results set the state of future spintronic transport experiments (ongoing work). On the other hand, the aggregation studies on MPc revealed that the coordination character of the central atom of the Pc cavity has an important effect on the formation of aggregates. Additionally, electrochemical experiments demonstrated that molecular aggregations can lead to the quenching of the electrochemical-active nature of a Co2+ atom.Herein it has been demonstrated that SPM are suitable techniques to study the conformational and configurational changes associated with the tunneling of electrons through planar and non-planar molecules in real space. Aggregation studies of magnetic switches were carried out to better understand the supramolecular organization under near surface conditions, a key point for the design of future devices based on the bottom up approach.

Inspiriert von den natürlich vorkommenden Antibiotika der Gramicidin Familie und ihrer d-(alt)-l Aminosäuresequenz, die es diesen Oligopeptiden ermöglicht, eine beta–helikale Sekundärstruktur einzunehmen, war das Hauptziel dieser Arbeit die Synthese und Charakterisierung von Peptiden und diversen Pseudopeptiden mit regulärer all-l und d-(alt)-l Sequenz und die Untersuchung des Einflusses dieser stereochemischen Variation auf die Strukturen und Eigenschaften dieser Verbindungen. Zusätzlich ergab der Austausch von Amid-Bindungen im Peptid-Rückgrat durch verschiedene Isostere diverse, teils einzigartige Pseudopeptid-Strukturen, wohingegen Verzweigung des linearen Peptid-Rückgrates zu sphärischen Molekülen führte. Alle Projekte zielten auf die Entwicklung und Synthese diskreter Oligomere für Strukturuntersuchungen, sowie auf die Einbindung der jeweiligen Strukturelemente in Polymere. Die Polymerization geeigneter Monomere zu Polymeren soll zu makro- und supramolekularen Nano-Objekten führen. Die divergent/konvergente Synthese einer Serie von Oligo-d-(alt)-l-lysinen zielte auf die Generierung hydrophiler, pH-sensitiver nanotubularer Strukturen. Schrittweiser Austausch von Amid-Bindungen des Peptid-Rückgrates durch Ester-(alt)-Urea-Einheiten führte zu all-l und d-(alt)-l Oligopseudoleucinen mit 50% und 0% Amid-Bindungs-Anteil. Design, Synthese und Polymerisation von AB-“Click”-Monomeren, basierend auf all-l and l-(alt)-d lysin Dipeptiden, ergaben hochmolekulare, Triazol-enthaltende Polypseudopeptide, deren Seitenketten mit Pyrenbuttersäure quantitativ postfunktionalisiert werden konnten. Die Einführung von Verzweigung in Glutamat-Peptide ergab chirale Dendrimere mit adressierbaren fokalen und periphären Funktionalitäten, sowie variabler Ladungsdichte. Design, Synthese und Polymerisation eines Glutamat basierenden AB2-“Click”-Monomers lieferte verwandte chirale hyperverzweigte Polypseudopeptide. / Inspired by the naturally occurring antibiotics of the Gramicidin family and their d-(alt)-l amino acid sequence, enabling these oligopeptides to adopt a beta–helical secondary structure, the work presented in this thesis targeted the syn-thesis and characterization of peptides and diverse pseudopeptides with regular all-l and d-(alt)-l sequences and the influence of this stereochemical variation on the compounds’ structures and properties. Further diversification of the struc-tures as obtained by replacing amide bonds in the peptide backbone with differ-ent isosteres, affording unique pseudopeptide structures. In addition spherical molecules were generated by introducing branching into the linear peptide scaf-fold. Throughout all projects, the aim was the design and synthesis of discrete oligomers for structural investigations and the incorporation of the respective structural elements into polymers via the polymerization of suitable monomers, in order to generate nanoscale macromolecular and supramolecular objects. The divergent/convergent synthesis of a series of oligo-d-(alt)-l-lysines targeted the generation of hydrophilic, pH-sensitive nanotubular structures. The stepwise replacement of peptide backbone amide bonds with ester-(alt)-urea moieties afforded all-l and d-(alt)-l oligopseudoleucines with 50% and 0% amide content. The design, synthesis, and polymerization of an AB-“Click”-monomer, based on all-l and l-(alt)-d lysine dipeptides afforded high molecular weight, triazole con-taining polypseudopeptides. Quantitative coupling to pyrene butyric acid afforded the respective side chain labeled polymers. The introduction of branching into glutamate peptides afforded fully chiral den-drimers with addressable focal and peripheral functionalities and variable charge density. The design, synthesis, and polymerization of a glutamate based AB2-“Click”-monomer led to related chiral hyperbranched polypseudopeptides.