Conselho Nacional de Pesquisa e Desenvolvimento Científico e Tecnológico - CNPq / Repeatedly in the field of Quantum Information Science (QIS) it’s essentially required of physical systems the quantification concerning its quantum phenomena, such as Quantum Coherence (QC) relying in quantum superposition states. Hereafter several quantifiers of QC have been proposed over the years through distance measures in quantum state spaces, called distinguishability measures, playing an important role in QIS correlation phenomena such as Discord and Entanglement with Quantum Cryptography implementation, as example. The aim of this dissertation is to extend the research of QC, published by Jonas Maziero in an article, performing an in-depth analysis regarding the control of local and non-local aspects of Hilbert-Schmidt Coherence (HSC) in multipartite systems and its relations with others QC quantifiers, as well as an analisys of a possible Hilbert-Schmidt Distance (HSD) implication in QC functions over the Non-Monotonicity under Tensor Products (NMuTP) inequality and of limitations between Coherence of state populations and energy. Starting from the generic multipartite state of level quantum energy systems (qudit), defined from the Bloch parameterization, calculations of QC functions concerning its particular cases are considered for 1-qubit, 2-qubit, 1-qutrit and two copies of 1-qubit adopting HSD. Writing the HSC function for the latter case in terms of its local and non-local parts and from the result of 1-qubit it is possible, by manipulating the difference between local populations, to infer a non-local implication in the HSC for that system, in contrast to what has been seen by adopting distinct dissimilarity measures for this function, named l1- Norm Distance and Relative Entropy Distance, cases where there are no implications and where there is a direct consequence with their local populations instead of the previously difference between them, respectively. Notwithstanding, HSD usage provides a description of an awkward relation in QIS towards NMuTP, and a possible implication of that kind of relation in QIS emergent phenomena such as QC function. / Reiteradamente no contexto da Ciência da Informação Quântica (CIQ) é essencialmente necessária a quantificação de sistemas físicos com respeito aos seus fenómenos quânticos, tais como a Coerência Quântica (CQ) intrínseca a estados com superposição quântica. Doravante algumas funções quantificadoras de CQ foram atribuídas ao longo dos anos através de medidas de distância em espaços de estados quânticos, denominadas medidas de dissimilaridade, desempenhando papel importante em fenômenos de correlação na CIQ, tal como Discórdia e Emaranhamento com implementação em Criptografia Quântica, por exemplo. O objetivo desta dissertação é estender a pesquisa dedicada a CQ, publicada em artigo por Jonas Maziero, efetuando uma análise aprofundada com respeito ao controle dos aspectos local e não-local da Coerência de Hilbert-Schmidt (CHS) em sistemas multipartidos e suas relações com outras funções quantificadoras de CQ, bem como a investigação de uma possível implicação da Distância de Hilbert-Schmidt (DHS) na função CQ frente a relação da Não-Monotonicidade sobre o Produto Tensorial (NMsPT) e de limitações entre Coerência e populações de estados e energia. Partindo do estado multipartido genérico de sistemas quânticos com níveis de energia (qudit), definido a partir da parametrização de Bloch, calculamos a função CQ para seus respectivos casos particulares 1-qubit, 2-qubit, 1-qutrit e duas cópias de 1-qubit adotando a DHS. Escrevendo a função CHS para este último caso em termos de suas partes local e não-local e do resultado para 1-qubit é possível, manipulando a diferença entre as populações locais, inferir uma implicação não-local na CHS para este sistema, em contraste ao que se observa adotando distintas medidas de dissimilaridade para esta função, denominadas Distância Norma-l1 e Distância Entropia Relativa, nos casos em que não há implicação e onde há consequência direta com suas populações locais do que anteriormente a diferença entre elas, respectivamente. Não obstante, o emprego da DHS proporciona o caráter de uma estranha relação na CIQ através da NMsPT, e uma possível implicação desta relação em fenômenos emergentes da CIQ tal qual a função CQ.

Orientador: Antonio Vidiella Barranco / Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Fisica Gleb Wataghin / Made available in DSpace on 2018-08-04T01:43:39Z (GMT). No. of bitstreams: 1 Soares_AntonioAugusto_M.pdf: 2924266 bytes, checksum: 4d4a9d494dd74748d57e8bd6dbe14108 (MD5) Previous issue date: 2002 / Resumo: Não informado / Abstract: Not informed / Mestrado / Física / Mestre em Física

This thesis is an attempt at studying quantum coherence effects coupled via plasmons. After introducing the quantum coherence in atomic systems in Chapter 1, we utilize it in Chapter 2 to demonstrate a new technique of detection of motion of single atoms or irons inside an optical cavity. By taking into account the interaction of coherences with surface plasmonic waves excited in metal nanoparticles, we provide a theoretical model along with experimental data in Chapter 3 to describe the modification of Raman spectra near metal nanoparticles. We show in chapter 4 that starting from two emitters, coupled via a plasmonic field, the symmetry breaking occurs, making detectable the simultaneous existence of the fast super-radiance and the slow sub-radiance emission of dye fluorescence near a plasmonic surface. In Chapter 5, we study the photon statistics of a group of emitters coupled via plasmons and by the use of quantum regression theorem, we provide a theoretical model to fully investigate the dependence of photon bunching and anti-bunching effects to the interaction between atoms, fields and surrounding mediums.

Optical response of an active medium can substantially be modified when coherent superpositions of states are excited, that is, when systems display quantum coherence and interference. This has led to fascinating applications in atomic and molecular systems. Examples include coherent population trapping, lasing without inversion, electromagnetically induced transparency, cooperative spontaneous emission, and quantum entanglement. We study quantum coherence effects in several quantum optical systems and find interesting applications. We show that quantum coherence can lead to transient Raman lasing and lasing without inversion in short wavelength spectral regions--extreme ultraviolet and x-ray--without the requirement of incoherent pumping. For example, we demonstrate transient Raman lasing at 58.4 nm in Helium atom and transient lasing without inversion at 6.1 nm in Helium-like Boron (triply-ionized Boron). We also investigate dynamical properties of a collective superradiant state prepared by absorption of a single photon when the size of the sample is larger than the radiation wavelength. We show that for large number of atoms such a state, to a good approximation, decays exponentially with a rate proportional to the number of atoms. We also find that the collective frequency shift resulting from repeated emission and reabsorption of short-lived virtual photons is proportional to the number of species in the sample. Furthermore, we examine how a position-dependent excitation phase affects the evolution of entanglement between two dipole-coupled qubits. It turns out that the coherence induced by position-dependent excitation phase slows down the otherwise fast decay of the two-qubit entanglement. We also show that it is possible to entangle two spatially separated and uncoupled qubits via interaction with correlated photons in a cavity quantum electrodynamics setup. Finally, we analyze how quantum coherence can be used to generate continuous-variable entanglement in quantum-beat lasers in steady state and propose possible implementation in quantum lithography.

Μια σχετικά νέα περιοχή έντονης ερευνητικής δραστηριότητας ασχολείται με τη μελέτη των οπτικών ιδιοτήτων κβαντικών συστημάτων (ατόμων/μορίων και ημιαγώγιμων κβαντικών τελειών) συζευγμένων με πλασμονικές (μεταλλικές) νανοδομές. Τα ισχυρά πεδία και ο έντονος περιορισμός του φωτός που σχετίζονται με τους πλασμονικούς συντονισμούς οδηγούν σε ισχυρή αλληλεπίδραση μεταξύ των ηλεκτρομαγνητικών πεδίων και των κβαντικών συστημάτων κοντά σε πλασμονικές νανοδομές. Επιπλέον, χρησιμοποιώντας τα κβαντικά συστήματα μπορεί να επιτευχθεί εξωτερικός έλεγχος των οπτικών ιδιοτήτων της υβριδικής φωτονικής δομής. Στη διδακτορική διατριβή μελετάται θεωρητικά και υπολογιστικά η οπτική απόκριση συμπλεγμάτων κβαντικών συστημάτων με μεταλλικές νανοδομές, δίνοντας έμφαση σε μη-γραμμικές και κβαντικές οπτικές διαδικασίες. Στα συστήματα αυτά τα επιφανειακά πλασμόνια των μεταλλικών νανοδομών επηρεάζουν σημαντικά, τόσο το ηλεκτρομαγνητικό πεδίο που αλληλεπιδρούν τα κβαντικά συστήματα, όσο και το ρυθμό αυθόρμητης εκπομπής των κβαντικών συστημάτων. Μελετάμε απλές και πολύπλοκες μεταλλικές νανοδομές, όπως μια μεταλλική νανοσφαίρα και μια διδιάστατη διάταξη διηλεκτρικών νανοσφαιρών επικαλυμμένων με μέταλλο (μεταλλικοί νανοφλοιοί). Τα κβαντικά συστήματα είναι άτομα/μόρια και κυρίως ημιαγώγιμες κβαντικές τελείες και περιγράφονται από συστήματα δύο, τριών και τεσσάρων ενεργειακών επιπέδων. Δείχνουμε ότι, φαινόμενα όπως δημιουργία κβαντικής συμβολής στην αυθόρμητη εκπομπή, σύμφωνη ελεγχόμενη αναστροφή πληθυσμού, οπτική διαφάνεια και κέρδος χωρίς αναστροφή πληθυσμού, δημιουργία αργού φωτός, τροποποιημένη οπτική μη-γραμμικότητα Kerr και μίξη τεσσάρων κυμάτων, όπως και φαινόμενα ελέγχου μέσω φάσης, εμφανίζονται στα κβαντικά συστήματα και τροποποιούνται σημαντικά λόγω της ύπαρξης της μεταλλικής νανοδομής. / A relatively new area of active research involves the study of the optical properties of quantum systems (atoms/molecules and semiconductor quantum dots) coupled to plasmonic (metallic) nanostructures. The large fields and the strong light confinement associated with the plasmonic resonances enable strong interaction between the electromagnetic field and quantum systems near plasmonic nanostructures. In addition, using the quantum system one may achieve external control of the optical properties of the hybrid photonic structure. In this thesis we analyze both theoretically and computationally the optical response of hybrid nanosystems comprised of quantum emitters and plasmonic nanostructures. We put emphasis on the study of nonlinear and quantum optical processes. In these systems the spontaneous decay rate and the electromagnetic field that interacts with the quantum emitter is significantly modified by the surface plasmons of the plasmonic nanostructures. We study cases of both simple and more involved plasmonic nanostructures. An example of a simple plasmonic nanostructure considered in this thesis is a metallic nanosphere, while a more involved one is a two-dimensional array of metal-coated dielectric nanospheres. The quantum systems are atoms/molecules and especially semiconductor quantum dots and are described by two-level, three-level or four-level systems. We find that several coherent optical phenomena that happen in the quantum systems can be strongly influenced by the presence of the plasmonic nanostructure. Specifically, we show that effects such as quantum interference in spontaneous emission, controlled population inversion, optical transparency and gain without inversion, slow light, enhanced nonlinear optical Kerr effect and four-wave mixing as well as phase-dependent absorption and dispersion profiles can be created and modified.

The author of this thesis concentrates his attention on quantum optical properties of some artificial electromagnetic media, such as quantum coherent atomic vapors (various multilevel electromagnetically induced transparency vapors) and negative refractive index materials, and suggests some possible ways to manipulate wave propagations inside the artificial electromagnetic materials based on quantum coherence and quantum vacuum effects. In Chapters 1 and 2, the author reviews the previous papers on quantum coherence as well as the relevant work such as electromagnetically induced transparency (EIT), atomic population trapping and their various applications. The basic concepts of quantum coherence (atomic phase coherence, quantum interferences within atomic energy levels) and quantum vacuum are introduced, and the theoretical formulations for treating wave propagations in quantum coherent media are presented. In Chapter 3, the author considers three topics on the manipulation of light propagations via quantum coherence and quantum interferences: i) the evolutional optical behaviors (turn-on dynamics) of a four-level N-configuration atomic system is studied and the tunable optical behavior that depends on the intensity ratio of the signal field to the control field is considered. Some typical photonic logic gates (e.g. NOT and NOR gates) are designed based on the tunable four-level optical responses of the N-configuration atomic system; ii) the destructive and constructive quantum interferences between two control transitions (driven by the control fields) in a tripod-type four-level system is suggested. The double-control quantum interferences can be utilized to realize some photonic devices such as the logic-gate devices, e.g., NOT, OR, NOR and EXNOR gates; iii) some new quantum coherent schemes (using EIT and dressed-state mixed-parity transitions) for realizing negative refractive indices are proposed. The most remarkable characteristic (and advantage) of the present scenarios is such that the isotropic left-handed media (with microscopic structure units at the atomic level) in the optical frequency band can be achieved. Quantum vacuum (the ground state of quantized fields) can exhibit many interesting effects. In Chapter 4, we investigate two quantum-vacuum effects in artificial materials: i) the anisotropic distribution of quantum-vacuum momentum density in a moving electromagnetic medium; ii) the angular momentum transfer between quantum vacuum and anisotropic medium. Such quantum-vacuum macroscopic mechanical effects could be detected by current technology, e.g., the so-called fiber optical sensor that can measure motion with nanoscale sensitivity. We expect that these vacuum effects could be utilized to develop sensitive sensor techniques or to design new quantum optical and photonic devices.In Chapter 5, the author suggests some interesting effects due to the combination of quantum coherence and quantum vacuum, i.e., the quantum coherent effects, in which the quantum-vacuum fluctuation field is involved. Two topics are addressed: i) spontaneous emission inhibition due to quantum interference in a three-level system; ii) quantum light-induced guiding potentials for coherent manipulation of atomic matter waves (containing multilevel atoms). These quantum guiding potentials could be utilized to cool and trap atoms, and may be used for the development of new techniques of atom fibers and atom chips, where the coherent manipulation of atomic matter waves is needed.In Chapter 6, we conclude this thesis with some remarks, briefly discuss new work that deserves further consideration in the future, and present a guide to the previously published papers by us. / QC 20100810

Au cours de la dernière décennie, un important effort a été fait dans le domaine des conducteurs électroniques de basse dimensionnalité afin de réaliser une électronique à électrons uniques. Une idée particulièrement attractive étant de pouvoir contrôler complétement la phase d’un électron unique volant pour transporter et manipuler de l’information quantique dans le but de construire un qubit volant. L’injection contrôlée d’électrons uniques dans un système électronique bidimensionnel balistique peut être fait grâce à une source d’électrons uniques basée sur des pulses de tensions lorentziens sub-nanosecondes. Une telle source peut aussi être utilisée pour mettre en évidence de nouveaux phénomènes d’interférences électroniques. Lorsqu’un pulse de tension court est injecté dans un interféromètre électronique, de nouveaux effets d’interférences sont attendus du fait de l’interaction du pulse avec les électrons de la mer de Fermi. Pour la réalisation de cette expérience, il est important de connaître avec précision la vitesse de propagation du paquet d’onde électronique créé par le pulse.Dans cette thèse, nous présentons des mesures résolues en temps d’un pulse de tension court (<100 ps) injecté dans un fil quantique 1D formé dans gaz d’électron bidimensionnel qui nous ont permis de déterminer sa vitesse de propagation. Nous montrons que le pulse se propage bien plus vite que la vitesse de Fermi d’un système sans interaction. La vitesse de propagation est augmentée par les interactions électron-électron. Pour un fil quantique contenant un grand nombre de modes, la vitesse mesurée est en excellent accord avec la vitesse d’un plasmon dans un système 2D en présence de grilles métalliques. En modifiant le potentiel de confinement électrostatique et donc l’intensité des interactions, nous montrons qu’il est possible de contrôler la vitesse de propagation. Nous avons ensuite étudié un interféromètre électronique à deux chemins basé sur deux fils couplés par une barrière tunnel. Nos mesures préliminaires font ressortir une signature qui peut être attribuée à des oscillations tunnel cohérentes des électrons injectés dans ce système. Dans un future proche, cet interféromètre pourrait être utilisé pour mettre en évidence ces nouveaux effets spectaculaires dus à l’interaction du pulse avec les électrons de la mer de Fermi. / Over the past decade, an important effort has been made in the field of low dimensional electronic conductors towards single electron electronics with the goal to gain full control of the phase of a single electron in a solid-state system. A particular appealing idea is to use a single flying electron itself to carry and manipulate the quantum information, the so-called solid state flying qubit. On demand single electron injection into such a ballistic two-dimensional electron system can be realized by employing the recently developed single electron source based on sub-nanosecond lorentzian voltage pulses. Such a source could also be used to reveal interesting new physics. When a short voltage pulse is injected in an electronic interferometer, novel interference effects are expected due to the interference of the pulse with the surrounding Fermi sea. For the realization of such experiments it is important to know with high accuracy the propagation velocity of the electron wave packet created by the pulse.In this thesis, we present time resolved measurements of a short voltage pulse (<100 ps) injected into a 1D quantum wire formed in a two-dimensional electron gas and determine its propagation speed. We show that the voltage pulse propagates much faster than the Fermi velocity of a non-interacting system. The propagation speed is enhanced due to electron interactions within the quantum wire. For a quantum wire containing a large number of modes, the measured propagation velocity agrees very well with the 2D plasmon velocity for a gated two-dimensional electron gas. Increasing the confinement potential allows to control the strength of the electron interactions and hence the propagation speed. We then have studied an electronic two-path interferometer based on two tunnel-coupled wires. Our preliminary measurements show a signature that can be attributed to the coherent tunneling of the electrons injected into this system. In the near future, this system could be used to reveal these new striking effects due to the interaction of the voltage pulse with the Fermi sea.

Cette thèse se place dans le domaine du transport quantique cohérent, et vise à développer un formalisme adapté à la modélisation d'expériences réalisées dans les canaux de bord de l'effet Hall quantique entier. Ce formalisme repose sur les analogies entre ces expériences et celles de l'optique quantique photonique.Le manuscrit commence par une introduction au contexte de la thèse qui propose un tour d'horizon des enjeux, des outils et des succès de l'optique quantique électronique.La première partie du travail traite des propriétés de cohérence mono-électronique et introduit la notion clé d'excès de cohérence à un électron. Plusieurs représentations sont proposées et analysées, permettant d’accéder aux informations physiques contenues dans la fonction de cohérence. Les états émis par des sources à électrons utilisées par plusieurs groupes expérimentaux sont ensuite analysés sous cet angle.Les effets à deux électrons sont au cœur de la seconde partie. L'excès de cohérence à deux électrons est défini en prenant en compte les effets de corrélation classique et d'échange quantique. Les conséquences de l'anti-symétrie fermionique sont également analysées en détail, montrant une redondance dans les informations encodées dans la cohérence à deux électrons. Enfin, un degré de cohérence normalisé est introduit pour étudier plus directement les effets d'indiscernabilité et d'anti-bunching.La mesure et la manipulation de la cohérence électronique par interférométrie sont abordées dans la troisième partie. Dans un premier temps, le lien entre les fonctions de cohérence électronique et les quantités directement accessibles dans les expériences est établi, ce qui justifie le besoin de protocoles plus complexes. La mesure d'excès de cohérence à un électron est alors envisagée par interférométrie Mach-Zehnder à un électron, puis par interférométrie Hong-Ou-Mandel à deux électrons, ce qui suggère une interprétation plus simple d'un protocole de tomographie électronique établi en 2011. Un protocole de mesure de l'excès de cohérence à deux électrons est ensuite proposé par interférométrie de type Franson, étendant les idées relatives à la mesure de cohérence à un électron par un interféromètre de Mach-Zehnder. Enfin, une vision complémentaire est apportée sur l'interféromètre de Franson, en utilisant celui-ci cette fois pour générer une cohérence à deux électrons non locale. / This thesis deals with coherent quantum transport and aims at developing a formalism well suited to model experiments conducted in edge channels of integer quantum Hall effect. This formalism relies on analogies between these experiments and photon quantum optics ones.The manuscript begins with an introduction to the context of the thesis and an overview of issues, tools and successes of electron quantum optics.The first part of the work addresses the question of single electron coherence properties and introduces the key notion of excess of single electron coherence. Several representations are proposed and analyzed, giving access to physical informations encoded in the coherence function. The quantum states emitted by experimentally demonstrated electron sources are then analyzed under this perspective.Two electron effects are at the heart of the second part. The excess of two-electron coherence is defined taking into account both classical correction and quantum exchange effects. A detailed analysis of consequences of fermionic anti-symmetry is provided and shows that information encoded into two-electron coherence is redundant. Last, a normalized degree of coherence is introduced in view of a more direct study of indistinguishability and anti-bunching.The issue of measuring and manipulating electronic coherence by interferometry is addressed in the third part. First the relation between electronic coherence functions and directly measurable quantities in experiments is established, justifying the need for more involved measurement protocols. The measure of the excess of single electron coherence is envisioned through single electron Mach-Zehnder interferometry and two-electron Hong-Ou-Mandel interferometry, suggesting a simpler interpretation of a tomography protocol established in 2011. A protocol for measuring the excess of two-electron coherence is then proposed by Franson-like interferometry, which generalizes the ideas used for measuring single electron coherence with a Mach-Zehnder interferometer. Last, a complementary point of view on Franson interferometer is given, by using it to generate a non-local two-electron coherence.

La notion de cohérence, intimement liée à celle de dualité onde-corpuscule, joue un rôle central en mécanique quantique. Lorsque la cohérence quantique s'étend sur plusieurs particules au sein d'un système, la description en termes d'objets individuels devient impossible en raison des corrélations quantiques (ou intrication) qui se développent. Dans ce manuscrit, nous étudions les systèmes à l'équilibre, pour lesquels nous montrons que les fluctuations cohérentes viennent s'ajouter aux fluctuations prédites par des identités thermodynamiques valides pour les systèmes classiques. Au zéro absolu, les fluctuations cohérentes sont les seules à subsister, et nous étudions dans ce cas leur lien avec l'entropie d'intrication. Nous montrons en particulier qu'une hypothèse de température effective modulée spatialement rend compte de la structure de l'intrication au sein d'un système à N corps, et montrons comment cette température peut être extraite des corrélations usuelles. Nos résultats permettent par ailleurs une compréhension affinée des transitions de phase quantiques. Nous montrons par exemple que la transition entre un isolant de Mott bosonique et un superfluide donne lieu à une singularité de l'entropie d'intrication induite par les fluctuations d'amplitude de la phase du condensat. Nous identifions enfin une longueur de corrélation pilotant les lois d'échelles des fluctuations cohérentes au sein de l'éventail critique avoisinant une transition de phase quantique du second ordre, et proposons une ouverture vers les potentielles applications métrologiques de ces fluctuations cohérentes exceptionnellement fortes en nous appuyant sur l'exemple du modèle d'Ising. / The notion of coherence, intimately related to the notion of wave-particle duality, plays a central role in quantum mechanics. When quantum coherence extends over several particles inside a system, the description in terms of individual objects becomes impossible, due to the development of quantum correlations (or entanglement). In this manuscript, we focus on equilibrium systems, for which we show that coherent fluctuations add up to the fluctuations predicted by thermodynamic identities, valid for classical systems only. In the ground state, coherent fluctuations are the only ones to subsist, an in this case we study their relationship with entanglement entropy. We show in particular that an hypothesis of effective temperature, spatially modulated, captures the structure of entanglement in a many-body system, and we show how this temperature can be reconstructed from usual correlation functions. Our results also enable for a refined understanding of quantum phase transitions. We show in particular that the phase transition between a bosonic Mott insulator and a superfluid gives rise to a singularity of entanglement entropy induced by amplitude fluctuations of the phase of the condensate. We finally identify a coherence length governing the scaling behaviour of coherent fluctuations inside the quantum critical region in the finite-temperature vicinity of a quantum critical point, and open novel perspectives for the metrological advantage offered by the exceptional coherence which develops close to quantum critical points, based on the example of the quantum Ising model.

This thesis titled, “Nature of Local Interactions at cisPro-Aro Peptide Sequences in Proteins: Evidences for van der Waals type Interactions. Design and Synthesis of Novel Covalent Surrogates for the Peptide Hydrogen Bond”, describes two important studies. The first is to gain a thorough understanding of the nature of interactions that govern cisPro stability at Pro-Aro sequences, which described in the first four chapters. The final chapter describes the synthesis of novel 4-carbon covalent surrogates for the peptide H-bonding interaction. Chapter 1: Local Interactions Governing cisPro Stability: Refining the Model Peptides Chapter 1 Section A: Understanding the role of inter-side chain CH•••Aro interaction in cis-trans isomerization at Pro-Aro and Aro-Pro Sequences. This chapter is divided into two sections. In the first section an exhaustive overview of earlier investigations into the nature of local interactions at Xaa-cisPro-Aro and Aro-cisPro-Xaa peptide sequences, by various groups, are discussed. Most studies have found evidence for the close assemblage between side chains of residues flanking cisPro motifs, when at least one of them is an aromatic group. An electronic C-H•••π nature has been proposed for these assemblies and they are proposed to influence the cisPro stability. We highlight those features in these studies that indicate that these interactions are not always electronically tunable, are insensitive to presence of strong chaotropes in the solvent and occur at protein sequences lacking Pro or cisPro; all of which contradict the electronic C-H•••π model for these inter-side chain assemblages and their perceived influence on cisPro stability. Chapter 1 Section B: Investigation of the Nature of H Xaa•••Aro interaction at Xaa-Pro-Pro-Phe-sequences In Section B, we design and synthesize Pro-Aro containing short peptide models to investigate the nature of local C-H•••Aro interactions in them. We synthesize a series of homologous Pro-Pro-Aro containing peptides (modeled based on earlier studies) and investigate the relative populations of its four Xaa-Pro rotamers using extensive 1D and 2D NMR techniques including TOCSY, HSQC and ROESY. We find several drawbacks that make this a relatively deficient model. Firstly, their relative populations of the rotamers (the most important data for current investigation) cannot be determined with high fidelity as they are dependent on the solvent polarity, solute concentration and chemical shift degeneracy of crucial NMR signals for the rotamers. Importantly, the populations of a few rotamers are influenced by strong 13-membered ring backbone H-bonds. Notably, some of the cisPro rotamers do not even contain the inter-side chain assembly, whose nature is under investigation. Design of novel models – unconstrained by H-bonds We design the Acyl-Pro-Pro-Aro-OMe peptides that lack the possibility of forming the 13-membered ring H-bonded structures. Thorough 1D and 2D NMR analyses of these models reveal that strong Type VI β-turn type 10-membered ring H-bonds are formed in the rotamers of these models – hence precluding their applications for current study. Interestingly, the relative rotamer populations are strongly influenced by solvent polarity and are entirely different from those of the corresponding C-terminal amide models. We further discover that the Pro-Pro-Aro motif is not essential to express the inter-side chain interactions – Ala-Pro-Aro are sufficient. Formation of the 10-membered H-bonding interactions, however, are not precluded. Chapter 2: Design and Synthesis of Acyl-Pro-Phe-OMe: Novel models to investigate the role of HαXaa•••Aro interactions on Xaa-cisPro-Aro stability. Chapter 2 Section A: Design, Synthesis and Conformational Analysis of Ibu-Pro-Phe-OMe Chapter 2 is divided into two sections. In Section A, we replace the amino acid at the N-terminal of the putative Pro residue with simple isosteric isobutyryl group, the resulting minimalist dipeptide model shows the exclusive influence of desired inter-side chain interactions in the cisPro rotamer. Solvent polarity and temperature coefficient studies reveal that absence of any intramolecular H-bonding or Oπ* interactions in it. 1D and 2D NMR analyses clearly indicate the close proximity between the side chains of Ibu and Phe exclusively in the cisPro rotamer. The Kc/t value decreases upon mutation of Phe to Ala. All these features favor the Ibu-Pro-Phe-OMe as an ideal minimalistic model for investigating the nature of Ibu•••Ph assemblages in the cisPro rotamer. Chapter 2 Section B: Investigation of CH•••Aro /Alp•••Alp interactions in Ibu-cisPro-Xaa-OMe In Section B, the 1D and 2D NMR analyses of the complete set of the aliphatic and aromatic analogues Ibu-Pro-Xaa-OMe were investigated. DMSO-d6 was found to be the best solvent for mimicking both the folded and the unfolded local environments of these short peptide sequences. The HαIbu•••Aro assemblage is observed in Aro analogues, but cannot be electronically tuned. The aliphatic analogues also surprisingly contain the HαIbu•••Alp interactions! The Kc/t values (cisPro %) increase in the aliphatic analogues too, where the aliphatic side chain is long. Increase in cisPro stability is not due to ring current effects or intramolecular H-bonds or Oπ* interactions. It seems to be due to van der Waals type interactions between the involved side chains, either of which need not be aromatic in nature. Chapter 3: Nature of Inter-Side Chain Interactions at Acyl-cisPro-Aro Sequences: Evidence for van der Waals Interactions Chapter 3 Section A: Investigation of nature of inter-side chain interactions in R-CO-cisPro-Phe-OMe Chapter 3 has two sections. Section A describes the systematic design and synthesis of Acyl-Pro-Phe-OMe homologues where first the steric bulk and hence the surface area of the aliphatic side chain of the acyl group is varied. Interaction of the phenyl ring of Phe seems to occur with the Cα-Cβ σ-bond of the acyl group. Branching at either Cα or Cβ seems to destabilize the cisPro rotamer. Aliphatic•••Aromatic interactions overwhelm the cisPro rotamer population to be greater than that of transPro. In the analogues where the acidity of the acyl Cα-H bond is increased, the Kc/t does not increase correspondingly. The Δδ(trans-cis) ppm shifts of HαAcyl protons are dependent exclusively on its acidity rather than on the Kc/t values. In carbamyl-Pro, which entirely lack the HαAcyl proton, the Kc/t values are significantly high and improve as the aliphatic surface on the alkoxy group increases. Introduction of benzyloxy carbamyl group at Pro renders almost the same Kc/t values as that of ethyloxy carbamate. All these data contradict the C-H•••π interaction model and strongly support a van der Waals type interaction between the Acyl (preceding cisPro) group’s Xα-Yβ σ-bond and the Aro or Alp side chains (succeeding cisPro). Chapter 3 Section B: Evidence for the Van der Waals nature of Inter Side Chain (Acyl•••S.C.Aro/Alp) interactions- Determination of Interactions energies In Section B, a thorough investigation of both aliphatic•••aliphatic and aliphatic•••aromatic interactions on the background of homologous Acyl-Pro-Aro/Alp-OMe peptide models is undertaken. These models uniquely allow the delineation of contribution of the van der Waals interactions and the ring current effects to the cis/trans isomerization in these peptides. We see that the energy of the van der Waals component of these aliphatic•••aliphatic and aliphatic…aromatic interactions increase linearly with increase in Kc/t, in both DMSO-d6 and D2O. On other hand, energy from the ring current effects largely remains invariant. The Acyl•••Aro/Alp interactions are not hydrophobic and are facilitated by conformational effects. Chapter 4: Crystallographic evidence for van der Waals interaction-mediated stabilization of cisPro conformers Chapter 4 Section A: Systematic crystallization and crystal structure analyses of homologous Xaa-cisPro-Alp and Xaa-cisPro-Aro rotamers: Evidence for van der Waals interactions Chapter 4 has two sections, both of which present crystallographic evidence for the van der Waals nature of the Xaa•••Aro interactions at Xaa-cisPro-Aro sequences. Section A describes the unique crystal structures of five of the Acyl-Pro-Alp-OMe analogues that have been synthesized in the current study. All of them remarkably crystallize with two features: 1) the Acyl-Pro peptide bond adopts the cisPro rotamer in all; and 2) the aliphatic side chains of the acyl group and the Alp side chain are involved in van der Waals type interactions. The cisPro rotamers of even the bulkiest motifs, namely Ibu-Pro-Val-OMe, Piv-Pro-Ile-OMe and Piv-Pro-Leu-OMe crystallize, stabilized by van der Waals packing between aliphatic groups of the acyl and the Leu/Ile/Val side chains. Where the side chains are not long enough to make sub-van der Waals contacts with each other, their acyl C′-Cα σ-bond rotations are restricted due to Oσ* interactions involving the charge on the acyl carbonyl O. Where this occurs, the short space between the acyl and Alp side chains are filled in by aliphatic groups from neighbouring molecules at sub van der Waals distances. The Pro, Alp and χ1(Alp) dihedral angles are restricted to narrow range of values, irrespective of the length of Alp side chain, indicating that this backbone conformation is a conformational minimum when i+3i backbone H-bond is removed, with Pro at the i+1st position. This is further substantiated in Piv-Pro-Gly-OMe, which crystallizes in trans-Pro form, but still adopts similar backbone dihedral angles in spite of lacking any Alp side chain for interactions with the acyl group. Three of the Acyl-Pro-Aro-OMe models also crystallize in cisPro rotamer forms – both exhibit van der Waals type contacts between the Acyl group and backbone of Phe, rather than the aromatic ring of Phe. The phenyl ring of Phe may or may not form intramolecular Ph•••Pro inter-side chain contacts – which is not a pre-requisite for cisPro stabilization. No C-H••• interactions are observed anywhere in these peptides – van der Waals type contacts alone predominate in all cases. There are no abnormal distortions in bond angles or lengths even in the most sterically hindered cases, signifying that the conformations of these cisPro rotamers involving aliphatic•••aliphatic type contacts are natural minima. Chapter 4 Section B: Mining the PDB for Statistical Evidence of van der Waals interactions Section B of chapter 4 describes the data mining and statistical analyses of Xaa-cisPro-Phe, Xaa-cisPro-Val and Xaa-cisProLeu sequences in the PDB. The PEARL program was used to mine the PDB data. The overall frequency of 5.3% for appearance of cisPro among all Xaa-Pro peptide bonds, improves when Xaa is Phe or Tyr. However, several anomalies highlight the need for refining the analyses set to only those sequences where the side chains of Xaa and Aro/Alp face each other. In this refined set, clearly, inter side chain Xaa•••Alp/Aro contacts take precedence over even Aro•••Pro interactions at Aro-cisPro sequences (where Xaa is Aro). The Phe and the Leu side chains induce similar conformational effects on the preceding Xaa-Pro backbone. So does Val. Strong aliphatic•••aliphatic inter side chain contacts at van der Waals distances are observed to flank cisPro in several proteins. Substitution at the Cα of Xaa governs the proximity of the approaching side chain of Alp / Aro residue. The Cα-H of Xaa steers away from the Aro side chain at Xaa-Pro-Phe sequences, as the Aro group gets closer to it – implying the absence of ordered C-H••• contacts between them. There is consistent parallel alignment between Cα-Cβ -bond of Xaa and the C -C bond of the approaching side chain of Alp or Aro group – clearly highlighting the presence of van der Waals type interactions between them. All these evidences clearly point towards the van der Waals nature of local interactions at cisPro-Aro/Alp peptide sequences. Chapter 5: A novel 4-carbon covalent surrogate model for peptide H-Bond Chapter 5 describes the design and synthesis of novel 4-carbon covalent surrogates for the peptide H-bond (HBS). These surrogates would allow the unique constraining of two peptide strands in their extended conformations. The covalent HBS contain four orthogonal functional groups for independent extension at all of the four ends – similar to an endogenous inter-strand peptide H-bond. The synthesis of the surrogate is achieved by directly using natural chiral amino acid derivatives, beginning from amino alcohols obtained from reduction of desired amino acids. Suitably N-protected alcohols undergo oxidation to aldehyde followed by Grignard addition of allyl magnesium bromide, TBDMS protection of the homoallylic alcohol and reductive ozonolysis of the olefin to get a primary alcohol which is subject to Fukuyama-Mitsunobu reaction with desire protected peptide. The residue preferences that produce strongest inter-strand H-bonds were explored. The designed 4-carbon covalent HBS was incorporated using this methodology in a Gramicidin-S analogue, its first structural mimic containing only a single turn motif. This HBS model will have wide applications for constraining peptides in a number of secondary structures.