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4-(12-mercaptododecyloxy)phenol (1), 3-(12-mercaptododecyloxy)phenol (2), 4-(12-mercaptododecyl)phenol (3), 4-(12-mercapto-dodecyl)phenol (4), 12-phenyldodecyl-mercaptan (5), 12-phenylundecyoxymercaptan (6), 4-(6-mercapto-hexyl)phenol (7), and 4-(12-mercaptododecyloxy)phenol (8) were synthesized. The thiol products were characterized by NMR, HRMS, and elemental analysis. Self-assembled monolayers (SAMs) on gold substrates were prepared from thiols 1-8, and the resulting monolayer surfaces were analyzed using Reflectance Absorbance Infrared Spectroscopy (RAIRS), contact angle goniometry, ellipsometry, reductive desorption cyclic voltametry, and impedance spectroscopy. Several aromatic C-C vibrational frequencies in the RAIRS spectra, for SAMs of 1-8, reveal a dependence of peak intensity on substitution regiochemistry of the aromatic ring. This result suggests that the orientation of the aromatic ring changes with substitution. Peak intensity, and peak widths of alkyl C-H vibrational features in the RAIRS spectra also reveal a dependence of the environment of the alkyl chain on structure of thiols 1-8. Meta-substitution seems to significantly alter the projection of the terminal -OH group relative to para-substitution. Contact angles were obtained for each SAM surface using water, glycerol, and ethylene glycol. From the contact angle data, Zisman and Fowkes analyses were performed in order to determine surface free energy values and also to determine the dispersive contribution to the surface energy. The energy values obtained from the Zisman plots as well as the dispersive contributions obtained from the Fowkes plots suggest a dependence of surface energy on substitution regiochemistry of the aromatic ring. The results are consistent with the interpretation of the RAIRS spectra as they relate to the effect substitution regiochemistry has on SAM structure and interfacial properties. The results of the reductive desorption measurements performed on each monolayer surface, indicate that changes in substitution regiochemistry do not seem to affect the surface coverage of SAMs 1-8. Desorption potentials however, are affected by the structure of the thiols composing the SAM, which suggests that the lateral stability resulting from interactions of the terminal groups and alkyl chains, is different for each monolayer surface. Specifically SAMs of 12-phenyldodecylmercaptan (5) and SAMs of 4-(12-mercaptododecyloxy)phenol (1) seem to be more stable due to interactions of the terminal aromatic ring in SAMs of (5) and due to an increase in van der Waals interactions in SAMs of (1). Film thicknesses, as determined by ellipsometry, also suggest that meta-substitution of the aromatic ring results in lower thicknesses for SAMs of (4), which is consistent with the interpretation of the structural changes resulting from meta-substitution, suggested by the interpretation of the RAIRS spectrum of SAMs of (4). Thickness measurements also indicate that most of the functionalized SAMs (1-4, 7, 8) react with OTS, which suggests the terminal -OH group is not shielded at the interface and is available for reaction. Following reaction with OTS the RAIRS spectra of the reacted surfaces reveal structural changes to the underlying SAM. Impedance spectroscopic measurements performed on SAMs of 1-8 reveal what seems to be a correlation between the orientation of the aromatic ring and the resistance properties of the SAM. It appears meta-substitution of the ring lowers the monolayers ability to resist electron transfer. These data suggest that meta-substitution of the aromatic ring has a significant impact upon the structure of the resulting monolayer relative to monolayers composed of para-substituted molecules. The data also suggests that there is a correlation between molecular structure and interfacial properties particularly as it relates to surface energy and reactivity. Small atomic changes in the molecules composing the SAM result in measurable differences in macroscopic properties of the interface. It is important to recognize the need for understanding structure-property relationships in self-assembled monolayers particularly if logical design of surfaces is to be achieved and applied towards solving problems associated with corrosion and adhesion of metal surfaces. / Ph. D.

Monocamadas auto-organizadas formadas pela quimissorção de alcanotióis sobre ouro apresentam estruturas bem definidas, organizadas e reprodutíveis. As propriedades de SAMs, aliadas à facilidade de síntese, têm atraído o interesse da comunidade cientifica o que ocasionou um grande avanço na área de nanotecnologia, especialmente em engenharia de superfícies. Neste trabalho, avaliou-se a modificação de um substrato de ouro com uma mistura dos ácidos 3-mercaptopropiônico e 11-mercaptoundecanóico. Com isso procurou-se controlar a configuração da superfície da SAM a fim de se obter um arranjo com ilhas de 3amp circundadas por 11amu, similar a um conjunto de ultramicroeletrodos. A SAM mista foi produzida por incubação de um substrato de ouro em solução etanólica contendo ambos os tiois. O estudo do processo redox do par [Fe(CN)6]4-/[Fe(CN)6]3- demonstrou que monocamadas de 3amp se comportam como a superfície de ouro não modificado, apresentando os mesmos valores de corrente de pico (Ip), potencial de pico (Ep) e resistência de transferência de carga (Rtc), pois permitem que ocorra a transferência eletrônica por efeito de tunelamento quântico dos elétrons através da monocamada. Entretanto monocamadas de 11amu demonstram comportamento isolante, apresentando uma Rtc 250 vezes maior e Ip significativamente menores que a observada para a SAM-3amp. As cargas de dessorção redutiva e variação de massa obtidas com a MECQ para a SAM mista evidenciaram alto recobrimento da superfície e um mecanismo de adsorção que varia com o tempo de incubação do substrato em solução contendo os tiois. Assim, a configuração da superfície com domínios de 3amp bem estabelecidos é alcançada com 20 horas de incubação do substrato. O perfil observado com a voltametria cíclica, aliado aos dados obtidos com a EIE comprova a existência de segregação de fases na SAM mista contendo regiões recobertas pelo 3amp (raio médio de 4,3 µm) circundadas por 11amu (com separação média de 75,42 µm). O estudo do comportamento eletroquímico do fisetin confirma o surgimento de propriedades diferenciadas com a SAM mista, onde observou-se apenas um processo redox sem que o analito permanecesse adsorvido na superfície da SAM. Todavia para a SAM-3amp e ouro não modificado foi observado dois processos redoxes seguido de adsorção irreversível do produto da reação na superfície eletródica. Utilizando a SAM mista como sensor eletroquímico para determinação de fisetin em água alcançou-se um limite de detecção de 1,67 x10-8 mol L-1. / Self-assembled monolayers obtained by chemiosorption of alkanethiols on gold present well-defined, organized and reproducible structures. The unique properties exhibited by such surfaces, allied to the great facility to obtain, have attracted the interest of the scientific community and caused a significant advance in the nanotechnology research, especially in the surface engineering one. In this work, the modification of gold substrate with a mixture of 3-mercaptopropionic acid and 11-mercaptoundecanoic acid was evaluated. The aim was control the surface of the SAMs in order to obtain an island arrangement of 3mpa isolated by 11mua, similar to an array of ultramicroelectrodes. The mixed-SAM was built by the incubation of Au substrate in an ethanolic solution containing both thiols. The redox couple [Fe(CN)6]4-/[Fe(CN)6]3- study demonstrated that pure 3mpa monolayers behaves like the bare gold surface, presenting barely the same parameters of peak current (Ip), peak potential (Ep) and charge transfer resistance (Rct), since it allows the electronic transference to occurs by quantum tunneling effect through the monolayer. On the other hand the 11mua monolayers showed an insulating behavior and a Rct value nearly 250 times greater and, consequently, Ip values significantly less than that for 3mpa. The reductive desorption charges and mass changes obtained with an EQCM for the mixed-SAM indicated the high coverage of gold surface and a adsorption mechanism that depends on the incubation time of the substrate in the thiols solution. The surface configuration with 3mpa domains is reached after 20 hours of immersion. The cyclic voltammetric profile, together with the data from electrochemical impedance spectroscopy , proved the existence of phases segregation in the mixed-SAM with surface regions covered solely by 3mpa (with mean radius of 4.3 µm) surrounded by 11mua with a mean separation of 75.42 µm. The electrochemical behavior of the flavonoid fisetin confirms the rising of differentiated properties with the mixed-SAM, where only one electrochemical process was able to be observed, without irreversible adsorption of the analyte. For 3mpa and bare gold surfaces, two (or more) electrochemical processes were observed together with the blocking of the electrode surface by irreversible adsorption of the reaction product. The utilization of the mixed-SAM with electrochemical sensor for fisetin determination in pure water yielded a detection limit of 1.67 x10-8 mol L-1.

Monocamadas auto-organizadas formadas pela quimissorção de alcanotióis sobre ouro apresentam estruturas bem definidas, organizadas e reprodutíveis. As propriedades de SAMs, aliadas à facilidade de síntese, têm atraído o interesse da comunidade cientifica o que ocasionou um grande avanço na área de nanotecnologia, especialmente em engenharia de superfícies. Neste trabalho, avaliou-se a modificação de um substrato de ouro com uma mistura dos ácidos 3-mercaptopropiônico e 11-mercaptoundecanóico. Com isso procurou-se controlar a configuração da superfície da SAM a fim de se obter um arranjo com ilhas de 3amp circundadas por 11amu, similar a um conjunto de ultramicroeletrodos. A SAM mista foi produzida por incubação de um substrato de ouro em solução etanólica contendo ambos os tiois. O estudo do processo redox do par [Fe(CN)6]4-/[Fe(CN)6]3- demonstrou que monocamadas de 3amp se comportam como a superfície de ouro não modificado, apresentando os mesmos valores de corrente de pico (Ip), potencial de pico (Ep) e resistência de transferência de carga (Rtc), pois permitem que ocorra a transferência eletrônica por efeito de tunelamento quântico dos elétrons através da monocamada. Entretanto monocamadas de 11amu demonstram comportamento isolante, apresentando uma Rtc 250 vezes maior e Ip significativamente menores que a observada para a SAM-3amp. As cargas de dessorção redutiva e variação de massa obtidas com a MECQ para a SAM mista evidenciaram alto recobrimento da superfície e um mecanismo de adsorção que varia com o tempo de incubação do substrato em solução contendo os tiois. Assim, a configuração da superfície com domínios de 3amp bem estabelecidos é alcançada com 20 horas de incubação do substrato. O perfil observado com a voltametria cíclica, aliado aos dados obtidos com a EIE comprova a existência de segregação de fases na SAM mista contendo regiões recobertas pelo 3amp (raio médio de 4,3 µm) circundadas por 11amu (com separação média de 75,42 µm). O estudo do comportamento eletroquímico do fisetin confirma o surgimento de propriedades diferenciadas com a SAM mista, onde observou-se apenas um processo redox sem que o analito permanecesse adsorvido na superfície da SAM. Todavia para a SAM-3amp e ouro não modificado foi observado dois processos redoxes seguido de adsorção irreversível do produto da reação na superfície eletródica. Utilizando a SAM mista como sensor eletroquímico para determinação de fisetin em água alcançou-se um limite de detecção de 1,67 x10-8 mol L-1. / Self-assembled monolayers obtained by chemiosorption of alkanethiols on gold present well-defined, organized and reproducible structures. The unique properties exhibited by such surfaces, allied to the great facility to obtain, have attracted the interest of the scientific community and caused a significant advance in the nanotechnology research, especially in the surface engineering one. In this work, the modification of gold substrate with a mixture of 3-mercaptopropionic acid and 11-mercaptoundecanoic acid was evaluated. The aim was control the surface of the SAMs in order to obtain an island arrangement of 3mpa isolated by 11mua, similar to an array of ultramicroelectrodes. The mixed-SAM was built by the incubation of Au substrate in an ethanolic solution containing both thiols. The redox couple [Fe(CN)6]4-/[Fe(CN)6]3- study demonstrated that pure 3mpa monolayers behaves like the bare gold surface, presenting barely the same parameters of peak current (Ip), peak potential (Ep) and charge transfer resistance (Rct), since it allows the electronic transference to occurs by quantum tunneling effect through the monolayer. On the other hand the 11mua monolayers showed an insulating behavior and a Rct value nearly 250 times greater and, consequently, Ip values significantly less than that for 3mpa. The reductive desorption charges and mass changes obtained with an EQCM for the mixed-SAM indicated the high coverage of gold surface and a adsorption mechanism that depends on the incubation time of the substrate in the thiols solution. The surface configuration with 3mpa domains is reached after 20 hours of immersion. The cyclic voltammetric profile, together with the data from electrochemical impedance spectroscopy , proved the existence of phases segregation in the mixed-SAM with surface regions covered solely by 3mpa (with mean radius of 4.3 µm) surrounded by 11mua with a mean separation of 75.42 µm. The electrochemical behavior of the flavonoid fisetin confirms the rising of differentiated properties with the mixed-SAM, where only one electrochemical process was able to be observed, without irreversible adsorption of the analyte. For 3mpa and bare gold surfaces, two (or more) electrochemical processes were observed together with the blocking of the electrode surface by irreversible adsorption of the reaction product. The utilization of the mixed-SAM with electrochemical sensor for fisetin determination in pure water yielded a detection limit of 1.67 x10-8 mol L-1.

III-V semiconductors have higher charge carrier mobilities than silicon and are used in photovoltaic devices, optical sensors, and emitters. The high injection velocities obtained with III-V channels allow for faster transistors with low power consumption. However, the large-scale implementation in electronic devices is currently limited by the defective interface formed between III-Vs and their oxides. Clean III-V surfaces are highly reactive in air and form amorphous oxides that lead to a high density of dangling bonds. Satisfying these dangling bonds has been associated with an improvement in electrical performance, directing the development of strategies that decrease the surface reactivity (chemical passivation) and the density of surface states that cause power dissipation (electrical passivation). Sulfur bonds easily to III-V surfaces and has been used to chemically and electrically passivate GaAs. In this work, we investigated liquid phase sulfur chemistries in the chemical passivation of clean InSb(100) and In0.53Ga0.47As(100) surfaces terminated by their group V elements. Our strategy consisted of maximizing the number of bonds between sulfur and antimony or arsenic. A long alkane chain thiol, 1-eicosanethiol (ET, 20 carbon atoms), was used to produce a hydrophobic surface and deposit a dense organic layer by taking advantage of the van der Waals interactions between thiol molecules. The first part of the study involved the optimization of the thiol deposition process on InSb. Self-assembled alkanethiol monolayers were formed by immersing clean InSb substrates in ET solutions in ethanol for 20 h. The layers prevented the formation of detectable oxides for 20 min based on the O Auger x-ray photoelectron spectroscopy (XPS) peak. The thiol layer was completely removed by heating the surface to 227 C in vacuum. In the second part of the study, a 20 h ET deposition was performed on In0.53Ga0.47As(100), and re-oxidation was prevented for up to 4 min based on the O 1s XPS peak. The alkanethiolate layer was removed by heating the samples to 350 C in vacuum. The sulfur coverage after 20 min and 20 h ET depositions was increased by performing a second immersion in (NH4)2S without modifying the thickness of the layer. The best process studied consisted of a 20 h immersion in ET solution followed by a short (NH4)2S step, preventing the formation of oxides for up to 9 min. This is due to the presence of available surface sites and weakly bonded molecules in the layer after a long 20 h ET process. The chemical passivation effect is not uniquely influenced by surface termination, roughness, or lattice constant, but is rather a result of a combination of these factors. Future work will involve the fabrication and electrical characterization of III-V devices modified with various chemical passivation strategies.

This thesis details the development of expertise and tools required for the study of amino acids deposited on Au(111), with a primary focus on the design and testing of a Knudsen cell for controlled deposition of L-cysteine and L-methionine. An ultra-high vacuum preparation chamber designed by Dr. Katie Mitchell and built by Torrovap Industries Inc. was installed. This chamber is connected to the existing scanning tunneling microscopy chamber via a gate valve, and both chambers can operate independently. Various instruments such as a mass spectrometer, quartz crystal microbalance, ion source, and sample manipulator were installed on the preparation chamber. Scanning tunneling microscopy was performed on both homemade and commercial Au(111) thin films. High resolution images of "herringbone" reconstruction and individual atoms were obtained on the commercial thin films, and optimal tunneling conditions were determined. A Knudsen cell was designed to be mounted on the preparation chamber. The Knudsen cell operates over the temperature range 300-400K, with temperatures reproducible to ±0.5K, and stable to ±0.1K over a five minute period. Reproducible deposition rates of less than 0.2Ǻ/s were obtained for both L-cysteine and L-methionine. Electron impact mass spectrometry and heat of sublimation measurements were performed to characterize the effusion of L-cysteine and L-methionine from the Knudsen cell. The mass spectrometry results suggest that L-cysteine was decomposing at 403K while L-methionine was stable during effusion. Heats of sublimation of 168.3±33.2kJ/mol and 156.5±10.1kJ/mol were obtained for L-cysteine and L-methionine respectively.

This thesis details the development of expertise and tools required for the study of amino acids deposited on Au(111), with a primary focus on the design and testing of a Knudsen cell for controlled deposition of L-cysteine and L-methionine. An ultra-high vacuum preparation chamber designed by Dr. Katie Mitchell and built by Torrovap Industries Inc. was installed. This chamber is connected to the existing scanning tunneling microscopy chamber via a gate valve, and both chambers can operate independently. Various instruments such as a mass spectrometer, quartz crystal microbalance, ion source, and sample manipulator were installed on the preparation chamber. Scanning tunneling microscopy was performed on both homemade and commercial Au(111) thin films. High resolution images of "herringbone" reconstruction and individual atoms were obtained on the commercial thin films, and optimal tunneling conditions were determined. A Knudsen cell was designed to be mounted on the preparation chamber. The Knudsen cell operates over the temperature range 300-400K, with temperatures reproducible to ±0.5K, and stable to ±0.1K over a five minute period. Reproducible deposition rates of less than 0.2Ǻ/s were obtained for both L-cysteine and L-methionine. Electron impact mass spectrometry and heat of sublimation measurements were performed to characterize the effusion of L-cysteine and L-methionine from the Knudsen cell. The mass spectrometry results suggest that L-cysteine was decomposing at 403K while L-methionine was stable during effusion. Heats of sublimation of 168.3±33.2kJ/mol and 156.5±10.1kJ/mol were obtained for L-cysteine and L-methionine respectively.

Τα αυτό -οργανούμενα μονοστρωματικά συστήματα (self-assembled monolayers, SAMs) παρουσιάζουν μεγάλο τεχνολογικό και βιομηχανικό ενδιαφέρον καθώς προσφέρουν μοναδική ευκαιρία για την κατανόηση των διεπιφανειακών φαινομένων και των διεργασιών που σχετίζονται με αυτά. Ο έλεγχος των ιδιοτήτων διαβροχής και λίπανσης της επιφάνειας , η επιλεκτική ρόφηση διαφόρων ειδών μορίων (π .χ ., μεγάλων βιολογικών μορίων) για το σχηματισμό επιπρόσθετου μονοστρώματος προς μία προεπιλεγμένη δομή (π.χ ., με συγκεκριμένο μοριακό προσανατολισμό), ο σχεδιασμός βιοαισθητήρων αλλά και άλλα παραδείγματα αποτελούν μερικές μόνο από τις πιο διαδεδομένες εφαρμογές των SAMs. Στην παρούσα εργασία εστιάσαμε στο πιο διαδεδομένο σύστημα SAM, αυτό που δημιουργείται κατά τη ρόφηση μορίων αλκανοθειολών σε επιφάνεια χρυσού (R-SH/ Au(111)). Πιο συγκεκριμένα διερευνήσαμε τις δομικές ιδιότητες καθώς και τις ιδιότητες διαμόρφωσης του σχηματιζόμενου μονοστρώματος με τη βοήθεια ενός καινούργιου αλγορίθμου Monte Carlo (MC) που σχεδιάσαμε στο εργαστήριο, βασισμένου σ’ ένα ιδιαίτερα αποδοτικό μίγμα τόσο απλών όσο και πιο σύνθετων (συχνά μη φυσικών) κινήσεων για τη δειγματοληψία απεικονίσεων του συστήματος. Η καινοτομία του αλγόριθμου MC συνίσταται στο ότι, ανεξάρτητα από την αρχική απεικόνιση του συστήματος, έχει την ικανότητα να οδηγεί αποτελεσματικά όλα τα μόρια της αλκανοθειόλης επάνω στο υπόστρωμα του χρυσού με αποτέλεσμα στο τέλος της προσομοίωσης αυτό να χαρακτηρίζεται από 100% επιφανειακή κάλυψη. Κατά τον τρόπο αυτό παρακάμπτεται ένας σημαντικός περιορισμός των προηγούμενων μεθόδων , οι οποίες ουσιαστικά προ-υπέθεταν την αρχική απεικόνιση του συστήματος (στη βάση πειραματικών δεδομένων). Επιπλέον, λαμβάνοντας υπόψη ένα εκτεταμένο σύνολο αντιγράφων του συστήματος καθένα από τα οποία προσομοιώνεται σε μία διαφορετική τιμή της διαμέτρου van der Waals των ατόμων θείου, σss, και επιχειρώντας ανταλλαγές απεικονίσεων μεταξύ συστημάτων με παρακείμενες τιμές σss, ο νέος αλγόριθμος μας επέτρεψε να προσομοιώσουμε αποτελεσματικά πρότυπα συστήματα R-SH/Au(111) για ένα φάσμα τιμών της παραμέτρου σss από 4.25 Å που αντιστοιχεί στο μοριακό μοντέλο των Hautman-Klein [J. Chem. Phys., 1988; 1989] έως 4.97 Å που αντιστοιχεί στο μοριακό μοντέλο των Siepmann-McDonald [Langmuir, 1993]. Η εφαρμογή του αλγορίθμου MC επεκτάθηκε ακολούθως σε συστήματα αλκανοθειολών ροφημένων σε διαφορετικά μεταλλικά υποστρώματα, με σκοπό τη μελέτη της επίδρασης του είδους της μεταλλικής επιφάνειας στις δομικές ιδιότητες των συστημάτων SAMs. Προς την κατεύθυνση αυτή, αρχικά εκτελέστηκαν κβαντομηχανικοί υπολογισμοί ( ab initio calculations) για ένα μόριο μεθανοθειόλης ροφημένου σε επιφάνεια χρυσού, αργύρου ή πλατίνας και τα αποτελέσματα χρησιμοποιήθηκαν για την εξαγωγή ενός κλασσικού δυναμικού για την περιγραφή των αλληλεπιδράσεων μεταξύ θείου -μετάλλου. Με το δυναμικό αυτό διεξήχθησαν στη συνέχεια ατομιστικές προσομοιώσεις MC για διάφορα μοριακά μήκη συστημάτων SAMs R-SH και στη συνέχεια έγινε ανάλυση των δεδομένων, με έμφαση στην εξάρτηση των δομικών ιδιοτήτων του σχηματιζόμενου φιλμ (μοριακός προσανατολισμός, διαμόρφωση αλυσίδων και στατιστική των ατελειών gauche) από τη φύση του μεταλλικού υποστρώματος. Στο τελευταίο στάδιο της διατριβής εστιάσαμε στη μελέτη της θερμοκρασίας υαλώδους μετάπτωσης Tg ισότροπων συστημάτων αλλά και λεπτών υμενίων πολυαιθυλενίου (PE) με τις αλυσίδες εμφυτευμένες σε σκληρή, ενθαλπικά ουδέτερη επιφάνεια και σχετικά μεγάλη πυκνότητα εμφύτευσης. Για το λόγο αυτό επεκτάθηκε η μεθοδολογία προσομοίωσης MC σε χαμηλές θερμοκρασίες (κοντά στο ή ακόμα και χαμηλότερα από το σημείο Tg) χρησιμοποιώντας την πολύ δραστική κίνηση MC αναγεφύρωσης άκρων (end-bridging, EB). Τα δεδομένα της προσομοίωσης για την εξάρτηση της πυκνότητας και της ενθαλπίας από την θερμοκρασία χρησιμοποιήθηκαν για τον υπολογισμό της θερμοκρασίας υαλώδους μετάπτωσης, με το αποτέλεσμα να συμφωνεί σχεδόν επακριβώς με την αντίστοιχη πειραματική τιμή για ημικρυσταλλικό πολυαιθυλένιο στο όριο μηδενικού βαθμού κρυσταλλικότητας (προβλεπόμενη τιμή Tg μεταξύ 220 και 240 Κ). / Self-assembled monolayers (SAMs) find numerous applications in a variety of fields: in the production of thin films from organic materials, in optics and electronics, as means for controlling the hydrophobic or hydrophilic behavior of a surface, as coatings for the protection of surfaces from corrosion, in molecular recognition, and more recently even as biosensors. In an effort to understand the mechanisms and interactions controlling chain organization and packing in these systems and how these affect their macroscopic properties, the present thesis has focused on the development of a Monte Carlo (MC) algorithm, built around a set of simpler but also more complex (sometimes non-physical) moves, for the atomistic simulation of the SAM structures formed by the adsorption of short alkanethiol molecules on a Au(111) surface. The innovation of the MC algorithm is that it is capable of efficiently driving all alkanethiol molecules to the Au(111), thereby leading to full surface coverage, irrespective of the initial setup of the system. This circumvents a significant limitation of previous methods in which the simulation typically starts from optimally packed structures on the substrate that are close to thermal equilibrium. Further, by considering an extended ensemble of configurations each one of which corresponds to a different value of the sulphur-sulphur repulsive core potential, σ ss , and by allowing for configurations to swap between different σ ss values, the new algorithm can adequately simulate model R-SH/ Au(111) systems for values of σ ss ranging from 4.25 Å corresponding to the Hautman-Klein molecular model [J. Chem. Phys., 1988; 1989] to 4.97 Å corresponding to the Siepmann-McDonald model [Langmuir, 1993]. A thorough investigation of the variation of molecular organization and ordering on the Au(111)substrate with chain length is presented. In a parallel study, the MC method was extended to alkanethiol SAM systems on different metal surfaces. This has allowed us to perform a detailed investigation of the substrate’s effect on the structure and conformation of the above systems through atomistic MC simulations based on a first-principles density functional modeling of the sulphur-metal interaction. Ab initio calculations on a methanethiol molecule adsorbed on gold, silver and platinum surfaces were conducted and the data obtained were used to develop an accurate classical force field which served as an input to the new MC algorithm. Emphasis was given primarily to the study of the effect of the substrate on the structural properties of the simulated R-SH SAM systems, like molecular orientation, molecular conformation, and statistics of gauche defects. In the last part of this thesis, and in an attempt to investigate the phenomenon of glass transition ( Tg ), the MC algorithm was employed in simulations with a less complex, than the SAM structures, system, that of amorphous polyethylene (PE). Two sets of simulations were executed: one with a bulk, isotropic sample, and the other with a thin film in which all PE chains were grafted on a hard surface on the one side and exposed to vacuum on the other. In all cases, the simulations were carried out for very long times in order for the autocorrelation function of the chain end-to-end vector to drop practically to zero. For both systems, the value of the glass transition temperature Tg was extracted using volumetric and enhtalpic simulation data and it was found to be between 220 and 240K, i.e., in remarkable agreement with measured data for semicrystalline PE in the limit of zero crystallinity. Additional results about the temperature dependence of the conformational (e.g., the equilibrium mean-square chain end-to-end distance) and structural (e.g., the intermolecular pair distribution function) properties in the two PE systems were also obtained and discussed in detail.

Comme de nombreux colloïdes, des nanoparticules métalliques recouvertes de ligands en suspension s’organisent au-delà d’une fraction volumique seuil et forment ce que l’on appelle un « supracristal ». Ce sont ainsi des systèmes modèles, déjà largement étudiés à partir de suspensions dans des solvants volatils, qui permettent de mieux comprendre l’auto-assemblage de sphères déformables. Les interactions qui conduisent à l’auto-assemblage sont couramment décrites par une compétition entre une attraction de van der Waals entre les cœurs métalliques et une répulsion entre les ligands qui va dépendre de l’affinité entre les ligands et le solvant. Un effet du solvant a déjà été observé sur l’auto-organisation de nano-objets. En mesurant par diffusion de rayons X aux petits angles le facteur de structure de suspensions de nanoparticules d’or greffées, j’ai pu sonder de façon systématique les interactions entre des nanoparticules en suspension avec plusieurs tailles de cœur, des ligands alcane-thiols de longueur différente et dans différents solvants à la fois volatils et non volatils. J’ai ainsi pu mettre en évidence une interaction attractive inattendue dans des alcanes linéaires flexibles et dont l’intensité augmente avec la longueur de l’alcane. Pour corréler les interactions entre particules à leur diagramme de phase, j’ai suivi le processus de cristallisation dans des suspensions en solvant volatil ou partiellement volatil ainsi qu’en émulsion, techniques qui permettent d’augmenter lentement la concentration en nanoparticules. Les interactions attractives induites par le solvant contribuent ainsi à la formation de supracristaux à de très faibles fractions volumiques. A de fortes concentrations, la structure des supracristaux ne dépend pas du solvant utilisé mais, à forte densité de greffage, du rapport R entre la longueur des ligands et le diamètre du cœur d’or. Pour un rapport R voisin de 0.7, la structure finale observée est cubique centrée, la structure à concentration intermédiaire étant cubique à faces centrées. Pour un rapport R deux fois plus petit, une structure originale a été mise en évidence. Il s’agit d’une structure hexagonale de grand paramètre de maille, analysée comme une phase de Frank et Kasper de type MgZn2 ou C14. C’est la première fois qu’une telle phase à empilement local tétraédrique est observée dans un système de sphères monodisperses molles. L’existence de cette phase ainsi que le rôle du rapport R a pu être interprétée en estimant quantitativement la compétition entre l’attraction de van der Waals forte et l’entropie des ligands. / As many colloids, metallic nanoparticles grafted with hydrophobic ligands self-assemble above a volume fraction threshold and thus build superlattices. These model systems, which are widely studied when suspended in volatile oils, enable a better understanding of soft spheres self-assembly.Interactions which lead to self-assembly are commonly described by the combination of van der Waals attraction with interaction between the ligand shells. The shell behavior is controlled by the ligand affinity with the solvent. An effect of the solvent on the self-assembly of nanoparticles has already been observed. Using a small angle X-ray scattering, I measured, through the structure factor, the interactions between gold nanoparticles grafted with alkanethiols in different oils, at various concentrations, for different lengths of ligands and core diameters. I noticed an attractive interaction when using flexible linear alkanes as solvent. It has also been shown that the attraction intensity increases with the solvent length.In order to correlate the interactions between particles to their phase diagram, I studied the crystallization process by concentrating nanoparticles using evaporation in capillaries or Ostwald ripening in emulsions. I showed that attractive interactions induced by the solvent lead to superlattices formation at very low volume fractions.At high concentrations, the superlattice structure depends on the ratio of the ligand length over the gold core diameter. For a ratio around 0.7, the final structure observed is body centered cubic, whereas at lower concentration, it is face centered cubic. When this ratio is halved, an unexpected structure is observed. It is a hexagonal structure with a large lattice parameter. It has been analyzed as a Frank and Kasper’s phase named MgZn2 or C14. It is the first time that this topologically close-packed structure is observed for monodisperse soft spheres. The existence of this phase and the role of the ratio R have been interpreted by considering quantitatively the competition between ligands entropy and the strong van der Waals attraction.