Decoherence models for discrete-time quantum walks and their application to neutral atom experiments

We discuss decoherence in discrete-time quantum walks in terms of a phenomenological model that distinguishes spin and spatial decoherence. We identify the dominating mechanisms that affect quantum-walk experiments realized with neutral atoms walking in an optical lattice. From the measured spatial distributions, we determine with good precision the amount of decoherence per step, which provides a quantitative indication of the quality of our quantum walks. In particular, we find that spin decoherence is the main mechanism responsible for the loss of coherence in our experiment. We also find that the sole observation of ballistic-instead of diffusive-expansion in position space is not a good indicator of the range of coherent delocalization. We provide further physical insight by distinguishing the effects of short- and long-time spin dephasing mechanisms. We introduce the concept of coherence length in the discrete-time quantum walk, which quantifies the range of spatial coherences. Unexpectedly, we find that quasi-stationary dephasing does not modify the local properties of the quantum walk, but instead affects spatial coherences. For a visual representation of decoherence phenomena in phase space, we have developed a formalism based on a discrete analogue of the Wigner function. We show that the effects of spin and spatial decoherence differ dramatically in momentum space.

Coarse Graining to Invesitigate Peptide-Lipid Interactions

Experimental characterization of molecular details is challenging, and although single molecule experiments have gained prominence, oligomer characterization remains largely unexplored. The ability to monitor the time evolution of individual molecules while they self assemble is essential in providing mechanistic insights about biological events. Molecular dynamics (MD) simulations can fill the gap in knowledge between single molecule experiments and ensemble studies like NMR, and are increasingly used to gain a better understanding of microscopic properties. Coarse-grained (CG) models aid in both exploring longer length and time scale molecular phenomena, and narrowing down the key interactions responsible for significant system characteristics. Over the past decade, CG techniques have made a significant impact in understanding physicochemical processes. However, the realm of peptide-lipid interfacial interactions, primarily binding, partitioning and folding of amphipathic peptides, remains largely unexplored compared to peptide folding in solution. The main drawback of existing CG models is the inability to capture environmentally sensitive changes in dipolar interactions, which are indigenous to protein folding, and lipid dynamics. We have used the Drude oscillator approach to incorporate structural polarization and dipolar interactions in CG beads to develop a minimalistic peptide model, WEPPROM (Water Explicit Polarizable PROtein Model), and a lipid model WEPMEM (Water Explicit Polarizable MEmbrane Model). The addition of backbone dipolar interactions in a CG model for peptides enabled us to achieve alpha-beta secondary structure content de novo, without any added bias. As a prelude to studying amphipathic peptide-lipid membrane interactions, the balance between hydrophobicity and backbone dipolar interactions in driving ordered peptide aggregation in water and at a hydrophobic-hydrophilic interface, was explored. We found that backbone dipole interactions play a crucial role in driving ordered peptide aggregation, both in water and at hydrophobic-hydrophilic interfaces; while hydrophobicity is more relevant for aggregation in water. A zwitterionic (POPC: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) and an anionic lipid (POPS: 1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine) are used as model lipids for WEPMEM. The addition of head group dipolar interactions in lipids significantly improved structural, dynamic and dielectric properties of the model bilayer. Using WEPMEM and WEPPROM, we studied membrane-induced peptide folding of a cationic antimicrobial peptide with anticancer activity, SVS-1. We found that membrane-induced peptide folding is driven by both (a) cooperativity in peptide self interaction and (b) cooperativity in membrane-peptide interactions. The dipolar interactions between the peptide and the lipid head-groups contribute to stabilizing folded conformations. The role of monovalent ion size and peptide concentration in driving lipid domain formation in anionic/zwitterionic lipid mixtures was also investigated. Our study suggest monovalent ion size to be a crucial determinant of interaction with lipid head groups, and hence domain formation in lipid mixtures. This study reinforces the role of dipole interactions in protein folding, lipid membrane properties, membrane induced peptide folding and lipid domain formation. Therefore, the models developed in this thesis can be used to explore a multitude of biomolecular processes, both at longer time-scales and larger system sizes.

Modyfikacja aglikonu Josamycyny z wykorzystaniem regioselektywnej substytucji nukleofilowej typu SN1’ i dipolarnej cykloaddycji Huisgena

Wydział Chemii: Zakład Syntezy i Struktury Związków Organicznych

Síntese de compostos multiporfirínicos covalentes

Nesta tese descreve-se a síntese de compostos multiporfirínicos covalentes bem como a avaliação da potencial utilização destes compostos como quimiossensores de iões metálicos e para a construção de estruturas supramoleculares com fulerenos. No capítulo 1 desta tese é feita uma introdução à química, propriedades e aplicações das porfirinas e sistemas multiporfirínicos. Relativamente aos sistemas multiporfirínicos é feita uma revisão bibliográfica acerca das estratégias de síntese e abordagem geral à química supramolecular de sistemas porfirina-fulereno. No capítulo 2 são apresentados os resultados referentes à síntese e caracterização dos vários sistemas multiporfirínicos desenvolvidos neste trabalho. De um modo geral, a síntese desses compostos envolveu reações de substituição aromática nucleofílica. Para esse efeito foi necessário preparar porfirinas de partida contendo grupos nucleofílicos nas posições meso (-C6H4OH e -C6H4NH2). Os sistemas multiporfirínicos foram obtidos por reações entre as porfirinas de partida e hexafluorobenzeno ou 5,10,15,20tetraquis(pentafluorofenil)porfirina. Descreve-se também a síntese de uma díade porfirina-C60 e de uma pentíade contendo quatro unidades de porfirina e uma de C60, envolvendo reações de cicloadição 1,3-dipolar e de substituição aromática nucleofílica. Os estudos efetuados ao nível da aplicação de alguns dos novos sistemas multiporfirínicos sintetizados e de um dos seus precursores, a 5-[4(pentafluorofeniloxi)fenil]-10,15,20-trifenilporfirina, como sensores de iões metálicos encontram-se descritos no capítulo 3. Neste capítulo, a título introdutório, é feita uma breve abordagem aos quimiossensores colorimétricos e de fluorescência, apresentando também alguns exemplos de porfirinas como quimiossensores de iões metálicos já descritos na literatura científica. A caracterização fotofísica dos compostos em estudo também é descrita neste capítulo. Os compostos estudados mostraram capacidade de interagir com vários iões metálicos, verificando-se um aumento da seletividade para o ião Hg2+ com o aumento do número de unidades porfirínicas constituintes dos sistemas multiporfirínicos. Os resultados referentes aos estudos de complexação de alguns dos sistemas multiporfirínicos sintetizados com fulerenos encontram-se descritos no capítulo 4. Neste capítulo descreve-se também a caracterização fotofísica dos compostos em estudo. Os estudos realizados com os sistemas multiporfirínicos mostraram uma fraca interação com os fulerenos C60 e C70. No entanto, os valores das constantes de afinidade obtidos com 1-metil-2-(4piridil)[60]fulero[c]pirrolidina mostraram que os sistemas multiporfirínicos apresentam capacidade para formar complexos com este derivado de C60 por coordenação axial e por interações π-π. No capítulo 5 é discutido o trabalho que envolveu o desenvolvimento de novos métodos na síntese de derivados tetrapirrólicos do tipo pirrolo[3,4-b]porfirinas contendo um grupo NH livre no anel exocíclico. A estratégia de síntese requereu a preparação de uma clorina fundida com um anel pirrolina seguida da redução do anel pirrolina. Deste modo obteve-se uma nova clorina fundida com um anel pirrolidina contendo um grupo NH livre. Esta nova clorina foi usada na preparação de uma díade clorina-porfirina por reação de N-arilação com 5,10,15,20-tetraquis(pentafluorofenil)porfirina. A estrutura cristalina da nova díade foi resolvida por difração de raios-X de cristal único. A estrutura dos compostos sintetizados foi estabelecida recorrendo a diversas técnicas espectroscópicas nomeadamente ressonância magnética nuclear (RMN de 1H, 13C e 19F), espectrometria de massa e espectrofotometria de UVvis. No último capítulo desta tese descrevem-se, pormenorizadamente, todas as experiências efetuadas, incluindo os métodos de síntese, purificação e caracterização estrutural dos diversos compostos sintetizados bem como as medições espectrofotométricas e espectrofluorimétricas.

(SP,SP)-(–)-(E)-1,2-Bis(methyl­phenyl­phosphino­yl)ethene

The title compound, C(16)H(18)O(2)P(2), possesses two stereogenic P atoms and shows a distorted s-cis conformation of each O=P-C=C moiety. This has been suggested on the basis of the stereochemical result of 1,3-dipolar cyclo-additions with nitro-nes and is now confirmed by the present crystal structure analysis. There are two crystallographically independent molecules in the asymmetric unit.

Dielectric properties of thermosetting material nanocomposites

The dieletric relaxation properties of thermosetting material nanocomposites based on spherosilicate nanoplatforms were studied from room temperature to 170 degrees C, varying the frequency from 10 to 1000 KHz. Permittivity (epsilon'), dielectric loss (epsilon ''), and activation energy (E-a) were calculated. The results of dielectric relaxation were confirmed by those of the final properties. The dielectric loss amplitude decreases with increasing ODPG content until about 70-73 wt % and slightly increases at higher ODPG content. This means that the increasing of the ODPG content in the composite samples decreases the number of pendants groups and/or increases crosslink densitv, causing decreased motion of organic tethers, and subsequently decreasing of the dipolar mobility. The results of apparent activation energy, fracture toughness and tensile modulus mechanical properties show the same profile with respect to ODPG content, in the sense that they exhibit maxima around 70 wt % ODPG. For the ODPG/MDA composites, this formulation of 70 wt % ODPG containing excess of amine is not composition where the highest crosslinked density is reached. This implies that the best mechanical properties and E-a are provided by some degree of chain flexibility. (c) 2007 Wiley Periodicals, Inc.

Diversity in Catalytic Reactions of Propargylic Diazoesters

Abstract Title of Document: Diversity in Catalytic Reactions of Propargylic Diazoesters Huang Qiu, Doctor of Philosophy, 2016 Directed By: Professor Michael P. Doyle, Department of Chemistry and Biochemistry Propargylic aryldiazoesters, which possess multiple reactive functional groups in a single molecule, were expected to undergo divergent reaction pathways as a function of catalysts. A variety of transition metal complexes including rhodium(II), palladium(II), silver(I), mercury(II), copper(I and II), and cationic gold (I) complexes have been examined to be effective in the catalytic domino reactions of propargylic aryldiazoesters. An unexpected Lewis acid catalyzed pathway was also discovered by using FeCl3 as the catalyst. Under the catalysis of selected gold catalysts, propargylic aryldiazoesters exist in equilibrium with 1-aryl-1,2-dien-1-yl diazoacetate allenes that are rapidly formed at room temperature through 1,3-acyloxy migration. The newly formed allenes further undergo a metal-free rearrangement in which the terminal nitrogen of the diazo functional group adds to the central carbon of the allene initiating a sequence of bond forming reactions resulting in the production of 1,5-dihydro-4H-pyrazol-4-ones in good yields. These 1,5-dihydro-4H-pyrazol-4-ones undergo intramolecular 1,3-acyl migration to form an equilibrium mixture or quantitatively transfer the acyl group to an external nucleophile with formation of 4-hydroxypyrazoles. In the presence of a pyridine-N-oxide, both E- and Z-1,3-dienyl aryldiazoacetates are formed in high combined yields by Au(I)-catalyzed rearrangement of propargyl arylyldiazoacetates at short reaction times. Under thermal reactions the E-isomers form the products from intramolecular [4+2]-cycloaddition with H‡298 = 15.6 kcal/mol and S‡298= -27.3 cal/ (mol•degree). The Z-isomer is inert to [4+2]-cycloaddition under these conditions. The Hammett relationships from aryl-substituted diazo esters ( = +0.89) and aryl-substituted dienes ( = -1.65) are consistent with the dipolar nature of this transformation. An unexpected reaction for the synthesis of seven-membered conjugated 1,4-diketones from propargylic diazoesters with unsaturated imines was disclosed. To undergo this process vinyl gold carbene intermediates generated by 1,2-acyloxy migration of propargylic aryldiazoesters undergo a formal [4+3]-cycloaddition, and the resulting aryldiazoesters tethered dihydroazepines undergo an intricate metal-free process to form observed seven-membered conjugated 1,4-diketones with moderate to high yields.

Asymmetric Syntheses of Analogs of Kainic Acid

Kainic acid has been used for nearly 50 years as a tool in neuroscience due to its pronounced neuroexcitatory properties. However, the significant price increase of kainic acid resulting from the disruption in the supply from its natural source, the alga Digenea Simplex, as well as inefficient synthesis of kainic acid, call for the exploration of functional mimics of kainic acid that can be synthesized in a simpler way. Aza kainoids analog could be one of them. The unsubstituted aza analog of kainoids has demonstrates its ability as an ionotropic glutamate receptor agonist and showed affinity in the chloride dependent glutamate (GluCl) binding site. This opened a question of the importance of the presence of one nitrogen or both nitrogens in the aza kainoid analogs for binding to glutamate receptors. Therefore, two different pyrrolidine analogs of kainic acid, trans-4-(carboxymethyl)pyrrolidine-3-carboxylic acid and trans-2-carboxy-3-pyrrolidineacetic acid, were synthesized through multi-step sequences. The lack of the affinity of both pyrrolidine analogs in GluCl binding site indicated that both nitrogens in aza kainoid analogs are involved in hydrogen bonding with receptors, significantly enhancing their affinity in GluCl binding site. Another potential functional mimic of kainic acid is isoxazolidine analogs of kainoids whose skeleton can be constituted directly via a 1, 3 dipolar cycloaddition as the key step. The difficulty in synthesizing N-unsubstituted isoxazolidines when applying such common protecting groups as alkyl, phenyl and benzyl groups, and the requirement of a desired enantioselectivity due to the three chiral ceneters in kainic acid, pose great challenges. Hence, several different protected nitrones were studied to establish that diphenylmethine nitrone may be a good candidate as the dipole in that the generated isoxazolidines can be deprotected in mild conditions with high yields. Our investigations also indicated that the exo/endo selectivity of the 1, 3 dipolar cycloaddition can be controlled by Lewis acids, and that the application of a directing group in dipolarophiles can accomplish a satisfied enantioselectivity. Those results demonstrated the synthesis of isoxazoldines analogs of kainic acid is very promising.

High-precision force sensing using a single trapped ion

We introduce quantum sensing schemes for measuring very weak forces with a single trapped ion. They use the spin-motional coupling induced by the laser-ion interaction to transfer the relevant force information to the spin-degree of freedom. Therefore, the force estimation is carried out simply by observing the Ramsey-type oscillations of the ion spin states. Three quantum probes are considered, which are represented by systems obeying the Jaynes-Cummings, quantum Rabi (in 1D) and Jahn-Teller (in 2D) models. By using dynamical decoupling schemes in the Jaynes-Cummings and Jahn-Teller models, our force sensing protocols can be made robust to the spin dephasing caused by the thermal and magnetic field fluctuations. In the quantum-Rabi probe, the residual spin-phonon coupling vanishes, which makes this sensing protocol naturally robust to thermally-induced spin dephasing. We show that the proposed techniques can be used to sense the axial and transverse components of the force with a sensitivity beyond the yN/\wurzel{Hz}range, i.e. in the xN/\wurzel{Hz}(xennonewton, 10^−27). The Jahn-Teller protocol, in particular, can be used to implement a two-channel vector spectrum analyzer for measuring ultra-low voltages.

Multifarious tumor-oriented small molecules: development of synthetic methodologies and application for diagnostic platforms

Cancer represents one of the most relevant and widespread diseases in the modern age. In this context, integrin receptors are important for the interactions of cells with extracellular matrix and for the development of both inflammation and carcinogenic phenomena. There are many tricks to improve the bioactivity and receptor selectivity of exogenous ligands; one of these is to integrate the amino acid sequence into a cyclic peptide to restrict its conformational space. Another approach is to develop small peptidomimetic molecules in order to enhance the molecular stability and open the way to versatile synthetic strategies. Starting from isoxazoline-based peptidomimetic molecules we recently reported, in this thesis we are going to present the synthesis of new integrin ligands obtained by modifying or introducing appendages on already reported structures. Initially, we are going to introduce the synthesis of linear and cyclic α-dehydro-β-amino acids as scaffolds for the preparation of bioactive peptidomimetics. Subsequently, we are going to present the construction of small molecule ligands (SMLs) based delivery systems performed starting from a polyfunctionalised isoxazoline scaffold, whose potency towards αVβ3 and α5β1 integrins has already been established by our research group. In the light of these results and due to the necessity to understand the behaviour of a single enantiomer of the isoxazoline-based compounds, the research group decided to synthesise the enantiopure heterocycle using a 1,3-dipolar cycloaddiction approach. Subsequently, we are going to introduce the synthesis of a Reporting Drug Delivery System composed by a carrier, a first spacer, a linker, a self-immolative system, a second spacer and a latent fluorophore. The last part of this work will describe the results obtained during the internship abroad in Prof. Aggarwal’s laboratory at the University of Bristol. The project was focused on the Mycapolyol A synthesis.