This work aimed at studying biophysical properties of two membrane proteins, one of potential nanotechnological use, bacteriorhodopsin, and one potential drug target, the NTS1 neurotensin receptor, at the single molecule scale. Bacteriorhodopsin (BR) is the only protein in the purple membrane (PM) of the halophilic organism Halobacterium salinarium. It is a light-driven proton pump converting light into a transmembrane proton gradient through isomerization of its retinal chromophore. Its stability, as well as its photoactivity remaining in dry protein layers, has made BR an attractive material for biomolecular devices. Numerous studies have been published on this topic; however, they have all used BR within the PM, on relatively large (µm-wide) surfaces. Here, conducting-probe atomic force microscopy (C-AFM) analysis was performed after removing most of the membrane lipids. For the first time, it was shown that the molecular conductance of BR can be reversibly photoswitched with predictable wavelength sensitivity. Intimate and robust coupling to gold electrodes was achieved by using a strategically engineered cysteine which, combined with partial delipidation, generated protein trimers homogenously orientated on the surface. Numerous controls using biophysical (SPR, ellipsometry, Kelvin-probe AFM) and chemical (photocurrent, cyclic voltammetry) techniques confirmed the wavelength specificity of the photoswitch, the anchoring role of the mutation and the homogenous orientation of the protein on the gold surface. Neurotensin is a brain and gastrointestinal 13 amino acid peptide acting as a neuromodulator in the central nervous system and as a hormone in the periphery. Its wide range of biological activities is primarily mediated through its binding to the neurotensin type 1 receptor (NTS1). NTS1 expressed in E.coli was purified and inserted into 100 nm brain polar lipid liposomes in a conformation which retained its ligand-binding capabilities. Initial AFM characterisation was performed as a prelude for ligand-receptor interaction studies, including high resolution imaging, force spectroscopy and solid state NMR approaches.

abstract: This dissertation describes the work on two projects which involves measuring molecular conductance and studying their properties on the nanoscale using various Scanning Tunneling Microscopy (STM) techniques. The first molecule studied was a porphyrin-fullerene moiety known as a molecular Dyad for photovoltaic applications. This project is further divided into two section, the first one involving the characterization of the Dyad monolayers and conductance measurement in the dark. The Dyads are designed to form charge separated states on illumination. The lifetime of the charged states have been measured efficiently but the single-molecule conductance through the molecules have yet to be characterized. The second part of the project describes the set-up of a novel sample stage which enables the study of molecular conductance under illumination. This part also describes the subsequent study of the molecule under illumination and the observation of a unique charge-separated state. It also contains the verification of the presence of this charge-separated using other characterization techniques like transient absorption spectroscopy. The second project described in the dissertation was studying and comparing the predicted rectifying nature of two molecules, identical in every way except for one stereocenter. This project describes the formation of monolayers of the molecule on gold and then studying and analyzing the current-voltage characteristics of the molecules and looking for rectification. Both the molecules proved to be rectifying, one more than the other as predicted by theoretical calculations. / Dissertation/Thesis / Ph.D. Chemistry 2011

abstract: Charge transport in molecular systems, including DNA (Deoxyribonucleic acid), is involved in many basic chemical and biological processes. Studying their charge transport properties can help developing DNA based electronic devices with many tunable functionalities. This thesis investigates the electric properties of double-stranded DNA, DNA G-quadruplex and dsDNA with modified base. First, double-stranded DNA with alternating GC sequence and stacked GC sequence were measured with respect to length. The resistance of DNA sequences increases linearly with length, indicating a hopping transport mechanism. However, for DNA sequences with stacked GC, a periodic oscillation is superimposed on the linear length dependence, indicating a partial coherent transport. The result is supported by the finding of delocalization of the highest occupied molecular orbitals of Guanines from theoretical simulation and by fitting based on the Büttiker’s theory. Then, a DNA G4-duplex structures with a G-quadruplex as the core and DNA duplexes as the arms were studied. Similar conductance values were observed by varying the linker positions, thus a charge splitter is developed. The conductance of the DNA G-tetrads structures was found to be sensitive to the π-stacking at the interface between the G-quadruplex and DNA duplexes by observing a higher conductance value when one duplex was removed and a polyethylene glycol (PEG) linker was added into the interface. This was further supported by molecular dynamic simulations. Finally, a double-stranded DNA with one of the bases replaced by an anthraquinone group was studied via electrochemical STM break junction technique. Anthraquinone can be reversibly switched into the oxidized state or reduced state, to give a low conductance or high conductance respectively. Furthermore, the thermodynamics and kinetics properties of the switching were systematically studied. Theoretical simulation shows that the difference between the two states is due to a difference in the energy alignment with neighboring Guanine bases. / Dissertation/Thesis / Doctoral Dissertation Chemistry 2016

Cette thèse en électronique moléculaire porte essentiellement sur le développement d’une méthode pour le calcul de la transmission de dispositifs électroniques moléculaires (DEMs), c’est-à-dire des molécules branchées à des contacts qui forment un dispositif électronique de taille moléculaire. D’une part, la méthode développée vise à apporter un point de vue différent de celui provenant des méthodes déjà existantes pour ce type de calculs. D’autre part, elle permet d’intégrer de manière rigoureuse des outils théoriques déjà développés dans le but d’augmenter la qualité des calculs. Les exemples simples présentés dans ce travail permettent de mettre en lumière certains phénomènes, tel que l’interférence destructive dans les dispositifs électroniques moléculaires. Les chapitres proviennent d’articles publiés dans la littérature. Au chapitre 2, nous étudions à l’aide d’un modèle fini avec la méthode de la théorie de la fonctionnelle de la densité de Kohn-Sham un point quantique moléculaire. De plus, nous calculons la conductance du point quantique moléculaire avec une implémentation de la formule de Landauer. Nous trouvons que la structure électronique et la conductance moléculaire dépendent fortement de la fonctionnelle d’échange et de corrélation employée. Au chapitre 3, nous discutons de l’effet de l’ajout d’une chaîne ramifiée à des molécules conductrices sur la probabilité de transmission de dispositifs électroniques moléculaires. Nous trouvons que des interférences destructives apparaissent aux valeurs propres de l’énergie des chaînes ramifiées isolées, si ces valeurs ne correspondent pas à des états localisés éloignés du conducteur moléculaire. Au chapitre 4, nous montrons que les dispositifs électroniques moléculaires contenant une molécule aromatique présentent généralement des courants circulaires qui sont associés aux phénomènes d’interférence destructive dans ces systèmes. Au chapitre 5, nous employons l’approche « source-sink potential » (SSP) pour étudier la transmission de dispositifs électroniques moléculaires. Au lieu de considérer les potentiels de sources et de drains exactement, nous utilisons la théorie des perturbations pour trouver une expression de la probabilité de transmission, T(E) = 1 − |r(E)|2, où r(E) est le coefficient de réflexion qui dépend de l’énergie. Cette expression dépend des propriétés de la molécule isolée, en effet nous montrons que c’est la densité orbitalaire sur les atomes de la molécule qui sont connectés aux contacts qui détermine principalement la transmission du dispositif à une énergie de l’électron incident donnée. Au chapitre 6, nous présentons une extension de l’approche SSP à un canal pour des dispositifs électroniques moléculaires à plusieurs canaux. La méthode à multiples canaux proposée repose sur une description des canaux propres des états conducteurs du dispositif électronique moléculaire (DEM) qui sont obtenus par un algorithme auto-cohérent. Finalement, nous utilisons le modèle développé afin d’étudier la transmission du 1-phényl-1,3-butadiène branché à deux rangées d’atomes couplées agissant comme contacts à gauche et à la droite. / This thesis is on molecular electronics concentrates mostly on the development of a method for the calculation of the transmission probability of molecules that are connected to contacts. On the one hand, this method aims at bringing a different point of view among the other methods for such calculations. On the other hand, it allows the integration of already developed theoretical tools in a rigorous manner, which increases the quality of the calculations. The work presented here often contains simple examples that shine some light on phenomena, such as the destructive interference, in molecular electronic devices. The chapters are from articles already published in the litterature. In chapter 2, we study a molecular quantum dot using a finite model with Kohn-Sham density functional theory. Moreover, using an implementation of the Landauer formula, we calculate the conductance of the quantum dot. We find that the electronic structure and molecular conductance depend strongly on the exchange and correlation functional employed. In chapter 3, we discuss the effect of adding a side chain to conducting molecules on the transmission probability of molecular electronic devices. We find that destructive interferences appear approximately at the energy eigenvalues of the isolated side chain, if these values do not correspond to localized states far away from the conductor. In chapter 4, we show that molecular electronic devices containing an aromatic molecule generaly possess circular currents which are associated with destructive interference phenomena in these systems. In chapter 5, we use the source-sink potential (SSP) approach to study the electronic transmission of some devices. Instead of considering the source and sink potentials exactly, we use perturbation theory to find an expression for the transmission probability T(E) = 1 − |r(E)|2 that depends on the properties of the bare molecule, where r(E) is the energy-dependent reflection coefficient. We show that in the first-order, it is the orbital density on the atoms connected to the contacts that largely determines the transmission probability for a given incoming electron energy. In chapter 6, we present an extension of the single channel source-sink potential approach for molecular electronic devices to multiple channels. The proposed multichannel method relies on an eigenchannel description of the conducting states of the molecular electronic device, which are obtained by a self-consistent algorithm. We use the model to study the transport of the 1-phenyl-1,3-butadiene molecule connected to two coupled rows of atoms that act as contacts on the left and right sides.

Submitted by TIAGO AZEVEDO BENITES null (tiagoazb@gmail.com) on 2017-10-09T17:59:58Z No. of bitstreams: 1 Tese Tiago.pdf: 5384805 bytes, checksum: 86cf0d44920d96e8154badd25a07c674 (MD5) / Approved for entry into archive by Monique Sasaki (sayumi_sasaki@hotmail.com) on 2017-10-09T19:38:54Z (GMT) No. of bitstreams: 1 benites_ta_dr_araiq.pdf: 5384805 bytes, checksum: 86cf0d44920d96e8154badd25a07c674 (MD5) / Made available in DSpace on 2017-10-09T19:38:54Z (GMT). No. of bitstreams: 1 benites_ta_dr_araiq.pdf: 5384805 bytes, checksum: 86cf0d44920d96e8154badd25a07c674 (MD5) Previous issue date: 2017-09-01 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / Dentro da eletroquímica, o estudo de reações de transferência de elétrons (TE) pode ser explorado por meio de eletrodos de ouro modificados com monocamadas auto-organizadas (SAMs), visto que elas são capazes de modificar as propriedades físico-químicas superficiais e controlar a cinética de TE. Este trabalho investigou as reações de TE em eletrodos de ouro modificados com SAMs eletroativas. Especificamente, foi estudado a cinética de TE em SAMs de 11-ferrocenil-undecanotiol sobre superfícies de ouro, por meio de análise de voltametria cíclica e espectroscopia de impedância/capacitância eletroquímica (EIE/ECE). Por meio dessas técnicas foi possível estimar variáveis como a densidade de estados redox (aproximadamente 3,4×〖10〗^14 estados cm-2 próximos aos valores reportados na literatura), de capacitância eletroquímica ou redox (137(±9) μF 〖cm〗^(-2)), a constante cinética de transferência de elétrons em 1,05×〖10〗^4 s^(-1) similares às reportadas por Creager, além da estimativa da energia de reorganização de Marcus (λ) em torno de 1,0 eV, valores similares a outros já previamente estimados para funcionalizações de SAMs eletroativas. Expandiram-se essas análises por meio da imobilização de complexos eletroativos de Bis(2,2′-bipiridina)-(5-Aminofenantrolina)rutênio bis(hexafluorofosfato) sobre superfícies de Au, por síntese orgânica com tióis ancoradores de diferentes cadeias (cisteína e 3-ácido carboxílico-6-mercaptopiridina), utilizando reação de ativação com DIC/HOBt em acetonitrila. Neste caso, obteve-se uma densidade de estados redox de cerca de 8,9×〖10〗^14 estados cm-2 e 9,3×〖10〗^14 estados cm-2, além de uma constante cinética de 2,6×〖10〗^3 s^(-1) e 1,07×〖10〗^3 s^(-1) para as abordagens I (3-ácido carboxílico-6-mercaptopiridina) e II (Cisteína) respectivamente. Resultados sugeriram uma maior capacidade das moléculas ancoradoras compostas de anel piridinico (abordagem I) na condução de carga quando comparados com a abordagem II, o que foi posteriormente confirmado por análise de condutância em que a abordagem I apresentou G=6×〖10〗^(-3) S contra G=2×〖10〗^(-3) S da abordagem II. Este trabalho apresentou uma abordagem teórico-experimental que relaciona as componentes físico-químicas quânticas através de uma nova perspectiva baseada nos estudos teóricos de Marcus-Buttiker e em análises experimentais centradas na capacitância eletroquímica. / In electrochemistry, the study of electron transfer reactions (TE) can be explored using Au electrodes modified with self-assembled monolayers (SAMs), since they are able to modify the physicochemical properties of electrodes surface and control the TE kinetics. This work investigated TE reactions on Au electrodes modified with SAMs. Specifically, TE kinetics were studied using 11-ferrocenyl-undecanethiol SAMs on Au surfaces by means of cyclic voltammetry and electrochemical impedance/capacitance spectroscopy (EIS/ECS) analysis. By means of these techniques, it was possible to estimate variables such as the density of redox states (approximately 3.4 × 1014 states per cm-2 , near the reported results in the literature), electrochemical or redox capacitance (137(±9) �� ��−2 ), the kinetic electron transfer constant at 1.05 × 104 � −1 similar to those reported by Creager, in addition to the estimation of the Marcus´ reorganization energy (�) of around 1.0 eV, value similar to others already previously estimated for functionalization of electroactive SAMs. These analyzes were expanded by immobilization of Bis(2,2'-bipyridine)-(5-Aminophenanthroline)ruthenium-bis (hexafluorophosphate) electroactive complexes on Au surfaces by organic synthesis with anionic thiols of different chains (cysteine and 3-carboxylic acid-6-mercaptopyridine), using activation reaction with DIC/HOBt in acetonitrile. In this case, a redox state density of about 8.9 × 1014 states cm-2 and 9.3 × 1014 states cm-2 , in addition to a kinetic constant of 2.6 × 103 � −1 and 1.07 × 103 � −1 to I (3-carboxylic acid-6- mercaptopyridine) and II (Cysteine) approaches, respectively, were used in the present study. Results suggesting a higher capacity of the pyridinium ring compound anchoring molecules (I approach) in charge conduction when compared to the II approach, which was later confirmed by conductance analysis: the I approach presented � = 6 × 10−3 � and � = 2 × 10−3 � for approach II. This work presented a theoretical-experimental approach relating the quantum physicochemical components through a new perspective based on the theoretical studies of Marcus-Buttiker and on experimental analyzes focused on the electrochemical capacitance.