Mannich-Type reactions in the Gas-Phase: the addition of Enol Silanes to cyclic N-Acyliminium Ions

The intrinsic gas-phase reactivity of cyclic N-acyliminium ions in Mannich-type reactions with the parent enol silane, vinyloxytrimethylsilane, has been investigated by double- and triple-stage pentaquadrupole mass spectrometric experiments. Remarkably distinct reactivities are observed for cyclic N-acyliminium ions bearing either endocyclic or exocyclic carbonyl groups. NH-Acyliminium ions with endocyclic carbonyl groups locked in s-trans forms participate in a novel tandem N-acyliminium ion reaction:  the nascent adduct formed by simple addition is unstable and rearranges by intramolecular trimethylsilyl cation shift to the ring nitrogen, and an acetaldehyde enol molecule is eliminated. An NSi(CH3)3-acyliminium ion is formed, and this intermediate ion reacts with a second molecule of vinyloxytrimethylsilane by simple addition to form a stable acyclic adduct. N-Acyl and N,N-diacyliminium ions with endocyclic carbonyl groups, for which the s-cis conformation is favored, react distinctively by mono polar [4+ + 2] cycloaddition yielding stable, ressonance-stabilized cycloadducts. Product ions were isolated via mass-selection and structurally characterized by triple-stage mass spectrometric experiments. B3LYP/6-311G(d,p) calculations corroborate the proposed reaction mechanisms.

The Addition of Allyltrimethylsilane to Cyclic N-Acyliminium Ions Derived from (S)-(+)-Mandelic Acid and Cyclohexyl-Based Chiral Auxiliaries

A adição de aliltrimetilsilano, promovida por TiCl4, a íons N-aciliminios cíclicos de 5- e 6-membros derivados do ácido (S)-(+)-mandélico, (1R,2S)-trans-2-fenil-1-cicloexanol e (1R,2S,5R)-8-fenilmentol ocorreu com baixas a moderadas razões diastereoisoméricas (1:1-6:1) e forneceu as respectivas amidas e carbamatos em bons rendimentos. A melhor diastereosseleção facial foi observada com o uso de (1R,2S,5R)-8-fenilmentol como auxiliar quiral. As amidas e carbamatos 2-substituídos foram convertidos nos alcalóides (S)- e (R)-propil pirrolidina e coniina com eficiente recuperação dos auxiliares quirais.

Exploring the effects of stress history on the drained and undrained cyclic behaviour of granular materials.

This paper presents the results of 3D DEM simulations of granular materials subject to cyclic loading. While both the drained and undrained conditions are considered, the effects of depositional history and consolidation stress history on the stress-strain response are specifically evaluated. It is demonstrated that the different stress histories have a significant effect on soil response and that such effects can be attributed to differences in the initial particle arrangement (fabric).

Intercepting Cyclic Dinucleotide Signaling with Small Molecules

Bacterial infections, especially the ones that are caused by multidrug-resistant strains, are becoming increasingly difficult to treat and put enormous stress on healthcare systems. Recently President Obama announced a new initiative to combat the growing problem of antibiotic resistance. New types of antibiotic drugs are always in need to catch up with the rapid speed of bacterial drug-resistance acquisition. Bacterial second messengers, cyclic dinucleotides, play important roles in signal transduction and therefore are currently generating great buzz in the microbiology community because it is believed that small molecules that inhibit cyclic dinucleotide signaling could become next-generation antibacterial agents. The first identified cyclic dinucleotide, c-di-GMP, has now been shown to regulate a large number of processes, such as virulence, biofilm formation, cell cycle, quorum sensing, etc. Recently, another cyclic dinucleotide, c-di-AMP, has emerged as a regulator of key processes in Gram-positive and mycobacteria. C-di-AMP is now known to regulate DNA damage sensing, fatty acid synthesis, potassium ion transport, cell wall homeostasis and host type I interferon response induction. Due to the central roles that cyclic dinucleotides play in bacteria, we are interested in small molecules that intercept cyclic dinucleotide signaling with the hope that these molecules would help us learn more details about cyclic dinucleotide signaling or could be used to inhibit bacterial viability or virulence. This dissertation documents the development of several small molecule inhibitors of a cyclic dinucleotide synthase (DisA from B. subtilis) and phosphodiesterases (RocR from P. aeruginosa and CdnP from M. tuberculosis). We also demonstrate that an inhibitor of RocR PDE can inhibit bacterial swarming motility, which is a virulence factor.

A SUBSET OF 3´ TO 5´ EXORIBONUCLEASES ARE THE PRIMARY ENZYMES RESPONSIBLE FOR THE DEGRADATION OF PGPG IN CYCLIC DI-GMP SIGNALING

Bis-(3´-5´)-cyclic dimeric guanosine monophosphate, or cyclic di-GMP (c-di-GMP) is a ubiquitous bacterial second messenger that regulates processes such biofilm formation, motility, and virulence. C-di-GMP is synthesized by diguanylate cyclases (DGCs), while phosphodiesterases (PDE-As) end signaling by linearizing c-di-GMP to 5ʹ-phosphoguanylyl-(3ʹ,5ʹ)-guanosine (pGpG), which is then hydrolyzed to two GMPs by previously unidentified enzymes termed PDE-Bs. To identify the PDE-B responsible for pGpG turnover, a screen for pGpG binding proteins in a Vibrio cholerae open reading frame library was conducted to identify potential pGpG binding proteins. This screen led to identification of oligoribonuclease (Orn). Purified Orn binds to pGpG and can cleave pGpG to GMP in vitro. A deletion mutant of orn in Pseudomonas aeruginosa was highly defective in pGpG turnover and accumulated pGpG. Deletion of orn also resulted in accumulation c-di-GMP, likely through pGpG-mediated inhibition of the PDE-As, causing an increase in c-di-GMP-governed auto-aggregation and biofilm. Thus, we found that Orn serves as the primary PDE-B enzyme in P. aeruginosa that removes pGpG, which is necessary to complete the final step in the c-di-GMP degradation pathway. However, not all bacteria that utilize c-di-GMP signaling also have an ortholog of orn, suggesting that other PDE-Bs must be present. Therefore, we asked whether RNases that cleave small oligoribonucleotides in other species could also act as PDE-Bs. NrnA, NrnB, and NrnC can rapidly degrade pGpG to GMP. Furthermore, they can reduce the elevated aggregation and biofilm formation in P. aeruginosa ∆orn. Together, these results indicate that rather than having a single dedicated PDE-B, different bacteria utilize distinct RNases to cleave pGpG and complete c-di-GMP signaling. The ∆orn strain also has a growth defect, indicating changes in other regulatory processes that could be due to pGpG accumulation, c-di-GMP accumulation, or another effect due to loss of Orn. We sought to investigate the genetic pathways responsible for these growth defect phenotypes by use of a transposon suppressor screen, and also investigated transcriptional changes using RNA-Seq. This work identifies that c-di-GMP degradation intersects with RNA degradation at the point of the Orn and the functionally related RNases.

2-categories and cyclic homology

The topic of this thesis is the application of distributive laws between comonads to the theory of cyclic homology. The work herein is based on the three papers 'Cyclic homology arising from adjunctions', 'Factorisations of distributive laws', and 'Hochschild homology, lax codescent,and duplicial structure', to which the current author has contributed. Explicitly, our main aims are: 1) To study how the cyclic homology of associative algebras and of Hopf algebras in the original sense of Connes and Moscovici arises from a distributive law, and to clarify the role of different notions of bimonad in this generalisation. 2) To extend the procedure of twisting the cyclic homology of a unital associative algebra to any duplicial object defined by a distributive law. 3) To study the universality of Bohm and Stefan’s approach to constructing duplicial objects, which we do in terms of a 2-categorical generalisation of Hochschild (co)homology. 4) To characterise those categories whose nerve admits a duplicial structure.

Leader Based Cyclic Pursuit

In this work a system of autonomous agents engaged in cyclic pursuit (under constant bearing (CB) strategy) is considered, for which one informed agent (the leader) also senses and responds to a stationary beacon. Building on the framework proposed in a previous work on beacon-referenced cyclic pursuit, necessary and suffi- cient conditions for the existence of circling equilibria in a system with one informed agent are derived, with discussion of stability and performance. In a physical testbed, the leader (robot) is equipped with a sound sensing apparatus composed of a real time embedded system, estimating direction of arrival of sound by an Interaural Level and Phase Difference Algorithm, using empirically determined phase and level signatures, and breaking front-back ambiguity with appropriate sensor placement. Furthermore a simple framework for implementing and evaluating the performance of control laws with the Robot Operating System (ROS) is proposed, demonstrated, and discussed.

Aerosol transport in a bifurcating tube at cyclic flow

Branching tube flow is a common feature of many fields of science and technology, and occurs both in animate and inanimate systems [1]. The transport of aerosol particles is of particular importance in industrial flow networks but also for the respiratory tree [2]. In this analysis a 3-D numerical study is performed to investigate transport and deposition of aerosol particles in branching tubes. Bifurcation tubes designed according to Hess-Murray law [3] but with different branching angles are analyzed. This study covers cyclic flow conditions at frequencies of 0.25 Hz, 0.50 Hz and 0.75 Hz, Stokes numbers ranging between 0.03 and 0.25, and Reynolds numbers up to 3000.

Tabu search for the cyclic bandwidth problem

International audience

Analysis of cyclic variations during mode switching between spark ignition and controlled auto-ignition combustion operations

© IMechE 2014. Controlled auto-ignition, also known as homogeneous charge compression ignition, has been the subject of extensive research because of their ability to provide simultaneous reductions in fuel consumption and NOx emissions from a gasoline engine. However, due to its limited operation range, switching between controlled auto-ignition and spark ignition combustion is needed to cover the complete operating range of a gasoline engine for passenger car applications. Previous research has shown that the spark ignition -controlled auto-ignition hybrid combustion (SCHC) has the potential to control the ignition timing and heat release process during the mode transition operations. However, it was found that the SCHC is often characterized with large cycle-to-cycle variations. The cyclic variations in the in-cylinder pressure are particularly noticeable in terms of both their peak values and timings while the coefficient of variation in the indicated mean effective pressure is much less. In this work, the cyclic variations in SCHC operations were analyzed by means of in-cylinder pressure and heat release analysis in a single-cylinder gasoline engine equipped with Variable Valve Actuation (VVA) systems. First, characteristics of the in-cylinder pressure traces during the spark ignition-controlled auto-ignition hybrid combustion operation are presented and their heat release processes analyzed. In order to clarify the contribution to heat release and cyclic variation in SCHC, a new method is introduced to identify the occurrence of auto-ignition combustion and its subsequent heat release process. Based on the new method developed, the characteristics of cyclic variations in the maximum rate of pressure rise and different stages of heat release process have been analyzed and discussed.

STRUCTURAL AND FUNCTIONAL STUDIES OF CYCLIC K48-LINKED DIUBIQUITIN

K48-linked di-ubiquitin exists in a dynamic equilibrium between open and closed states. The structure of K48-Ub2 in the closed conformation features a hydrophobic interface formed between the two Ub domains. The same hydrophobic residues at the interface are involved in binding to ubiquitin-associated (UBA) domains. Cyclization of K48-Ub2 should limit the range of conformations available for such interactions. Interestingly, cyclic K48-linked Ub2 (cycUb2) has been found in vivo and can be isolated in vitro to study its structure and dynamics. In this study, a crystal structure of cycUb2 was obtained, and the dynamics of cycUb2 were characterized by solution NMR. The crystal structure of cycUb2, which is in agreement with solution NMR data, is closed with the hydrophobic patches of each Ub domain buried at the interface. Despite its structural constraints, cycUb2 was still able to interact with UBA domains, albeit with lower affinity.

Modulation of GABA and glutamate release by brain-derived neurotrophic factor : role of adenosine A2A receptors

Trabalho Final do Curso de Mestrado Integrado em Medicina, Faculdade de Medicina, Universidade de Lisboa, 2014

[n]cycloparaphenylenes with charges: cyclic conjugation at last

Oligophenylenes (polyphenylenes) are constituted by an array of conjugated benzenes where inter-ring electron delocalization tends to extend over the whole chain (linear conjugation) being intrinsically limited, among other factors, by terminal effects. Alternatively, cyclic conjugation is envisaged as the unlimited free-boundary versionofconjugation which will impact the structure of molecules in rather unknown ways. The cyclic version of oligophenylenes, cycloparaphenylenes ([n]CPPs with n the number of phenyl rings) were first synthesized in 2008 by Beztozzi and Jasti.1 Today the whole [n]CPP series from [5]CPP to [18]CPP has been prepared. [n]CPPs represent ideal models to investigate new insights of the electronic structure of molecules and cyclic conjugation when electrons or charges circulate in a closed circuit without boundaries. Radical cations and dications of [n]CPP from n=5 to n=12 have been prepared and studied by Raman spectroscopy.2 Small [n]CPP dications own their stability to the closed-shell electronic configuration imposed by cyclic conjugation. However, in large [n]CPP dications cyclic conjugation is minimal and these divalent species form open-shell biradicals. The Raman spectra reflect the effect of cyclic conjugation in competition with cyclic strain and biradicaloid aromatic stabilization. Cyclic conjugation provokes the existence of a turning point or V-shape behavior of the frequencies of the G bands as a function of n. In this communication we will show the vibrational spectroscopic fingerprint of this rare form of conjugation. [1] R. Jasti, J. Bhattacharjee, J. B. Neaton, C. R. Bertozzi, “Synthesis, Characterization, and Theory of [9]-, [12]-, and [18]Cycloparaphenylene: Carbon Nanohoop Structures”, J. Am. Chem. Soc. 130 (2008), 17646–17647. [2] M. P. Alvarez, P. M. Burrezo, M. Kertesz, T. Iwamoto, S. Yamago, J. Xia, R. Jasti, J. T. L. Navarrete, M. Taravillo, V. G. Baonza, J. Casado, “Properties of Sizeable [n]CycloParaPhenylenes As Molecular Models of Single-Wall Carbon Nanotubes By Raman Spectroscopy: Structural and Electron-Transfer Responses Under Mechanical Stress”, Angew. Chem. Int. Ed. 53, (2014), 7033−7037.

Progress in understanding of the molecular basis underlying functional diversification of cyclic di-nucleotide turnover proteins

Cyclic di-GMP was the first cyclic di-nucleotide second messenger described, presaging the discovery of additional cyclic di-nucleotide messengers in bacteria and eukaryotes. The GGDEF diguanylate cyclase (DGC) and EAL and HD-GYP phosphodiesterase (PDE) domains conduct the turnover of cyclic di-GMP. These three unrelated domains belong to superfamilies that exhibit significant variations in function, to include both enzymatically active and inactive members with a subset involved in synthesis and degradation of other cyclic di-nucleotides. Here we summarize current knowledge of sequence and structural varitions that underpin the functional diversification of cyclic di-GMP turnover proteins. Moreover, we highlight that superfamily diversification is not restricted to cyclic di-GMP signaling domains, as particular DHH/DHHA1 domain and HD domain proteins have been shown to act as cyclic di-AMP phosphodiesterases. We conclude with a consideration of the current limitations that such diversity of action places on bioinformatic prediction of the roles of GGDEF, EAL and HD-GYP domain proteins.

tRNA anticodon loop modifications ensure protein homeostasis and cell morphogenesis in yeast

Using budding yeast, we investigated a negative interaction network among genes for tRNA modifications previously implicated in anticodon-codon interaction: 5-methoxy-carbonyl-methyl-2-thio-uridine (mcm5s2U34: ELP3, URM1), pseudouridine (Ψ38/39: DEG1) and cyclic N6-threonyl-carbamoyl-adenosine (ct6A37: TCD1). In line with functional cross talk between these modifications, we find that combined removal of either ct6A37 or Ψ38/39 and mcm5U34 or s2U34 results in morphologically altered cells with synthetic growth defects. Phenotypic suppression by tRNA overexpression suggests that these defects are caused by malfunction of tRNALysUUU or tRNAGlnUUG, respectively. Indeed, mRNA translation and synthesis of the Gln-rich prion Rnq1 are severely impaired in the absence of Ψ38/39 and mcm5U34 or s2U34, and this defect can be rescued by overexpression of tRNAGlnUUG. Surprisingly, we find that combined modification defects in the anticodon loops of different tRNAs induce similar cell polarity- and nuclear segregation defects that are accompanied by increased aggregation of cellular proteins. Since conditional expression of an artificial aggregation-prone protein triggered similar cytological aberrancies, protein aggregation is likely responsible for loss of morphogenesis and cytokinesis control in mutants with inappropriate tRNA anticodon loop modifications.