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2024-02-29T21:39:11ZCryobiophysics: librational dynamics and solvent accessibility in the low-temperature phases of supramolecular aggregatesDocumenti elettronici
https://hdl.handle.net/10955/5440
Titolo: Cryobiophysics: librational dynamics and solvent accessibility in the low-temperature phases of supramolecular aggregatesDocumenti elettronici
Autori: Aloi, Erika; Cipparrone, Gabriella; Bartucci, Rosa
Abstract: Studi biofisici realizzati a temperature criogeniche permettono di investigare proprietà
dinamiche, cinetiche e strutturali di biosistemi che, sebbene presenti, sarebbero
di difficile risoluzione a temperature più alte. Queste proprietà hanno rilevanza
in molti processi fisiologici che influenzano la funzionalità biologica di macromolecole.
I metodi di spettroscopia di risonanza paramagnetica di spin (EPR) sia in
onda continua (cw-EPR) che in regime pulsato (FT-EPR) sono particolarmente
efficienti per la caratterizzazione di aggregati sopramolecolari nello stato congelato.
In questo lavoro sono presentati e discussi esperimenti di cw- e FT-EPR a
9 GHz condotti su diversi biosistemi spin-labellati (membrane lipidiche a doppio
strato, fasi lamellari interdigitate, micelle, membrane naturali e proteine) nelle fasi
a bassa temperatura. È dato particolare risalto allo studio delle proprietà dell’acqua
di idratazione entro una distanza di 0.5 nm dai radicali nitrossidi, alla caratterizzazione
della dinamica a bassa temperatura dei biosistemi e come le condizioni di
idratazione influenzino le proprietà dei biosistemi a bassa temperatura. Sono anche
inclusi i risultati ottenuti dall’analisi di dati di scattering di neutroni per investigare
la dinamica dell’acqua di idratazione nella proteina tau umana, una proteina intrinsecamente
disordinata coinvolta nell’insorgere di patologie neurodegenerative come
la malattia di Alzheimer.
Esperimenti a tre impulsi di modulazione dell’eco di spin elettronico dall’interazione
iperfine con deuterio (D2O-ESEEM) ed esperimenti di cw-EPR sono stati combinati
a T = 77 K per caratterizzare il grado di permeazione dell’acqua e la polarità
dell’ambiente, rispettivamente, nella shell di idratazione più prossima di aggregati
lipidici spin-labellati selettivamente. È stato studiato il comportamento di fase liotropico
di miscele a completa idratazione di lipidi formanti doppi strati (bilayers)
di dipalmitoilfosfatidilcolina (DPPC) con lipidi formanti micelle di dipalmi-toilfosfatidiletanolamina (DPPE) derivati sulla testa polare con poli-etilene glicole
di peso molecolare 2000 Da (PEG:2000-DPPE) o di Liso-palmitoilfosfatidilcolina
(Lyso-PPC), studiando l’intero range di composizione (concentrazioni tra 0 e 100
mol%). Sono stati delineati i profili transmembranali di accessibilità del solvente e
di polarità in liposomi stabilizzati stericamente (SSL), formati da miscele di DPPC
e 2 mol% di PEG:2000-DPPE, e in micelle di polimero-lipidi. Questi profili sono
stati confrontati con quelli registrati per lipidi organizzati in bilayer e in lamelle
con catene interdigitate e per micelle di lipidi a singola catena. Inoltre, misure di
D2O-ESEEM e cw-EPR condotte su steroidi cardiotonici spin-labellati nella pompa
sodio-potassio Na+,K+-ATPase hanno mostrato che il vestibolo che conduce ai siti
di legame di steroidi e cationi è relativamente ampio e ricco di acqua.
Sono stati, poi, combinati spettri cw-EPR e spettri rilevati tramite echo in esperimenti
a due impulsi (spettri ED) per caratterizzare la dinamica di campioni
spin-labellati nello stato congelato nel range di temperatura tra 77 K e 270 K. In
tutti i sistemi modello di membrana analizzati in questo lavoro, costituiti da lipidi
con catene sature o insature o con catene interdigitate, si manifestano moti librazionali
di piccola ampiezza angolare (< 20!) che avvengono sulla scala dei nanosecondi.
Tutti i campioni studiati hanno mostrato un comportamento simile nella dipendenza
in temperatura dell’ampiezza angolare librazionale, manifestando un rapido incremento
in corrispondenza della transizione dinamica che avviene ad una temperatura,
Td, di circa 200 - 220 K. La transizione è associata all’attivazione di moti stocastici
di maggiore ampiezza che fanno sì che i bilayers superino una barriera energetica
con energia di attivazione Ea ⇡ 15 - 30 kJ/mol.
La prima shell di acqua di idratazione che circonda le macromolecole è fondamentale
per l’attivazione della loro funzionalità biologica. È stata, pertanto, caratterizzata
l’influenza dell’idratazione sulla dinamica nello stato congelato di due proteine
con diversa struttura secondaria, cioè ↵ per l’albumina del siero umano e " per la
"-lattoglobulina, e del più comune sistema modello di membrana lipidica costituito
da DPPC. Mentre la dinamica delle proteine è inibita nello stato liofilizzato per attivarsi
progressivamente in presenza di molecole di acqua, nel caso della membrana
lipidica le librazioni di ampiezza significativa si registrano nella regione idrofobica
interna del bilayer anche in assenza di acqua.
Infine, è presentato uno studio della dinamica traslazionale e rotazionale dell’acqua
di idratazione della proteina tau perdeuterata attraverso l’analisi di dati di scattering
di neutroni quasi-elastico, raccolti allo spettrometro TOFTOF alla sorgente di
neutroni Heinz Maier-Leibnitz. Biophysical studies at cryogenic temperatures allow us to unravel dynamic, kinetic,
and structural features of biosystems that are present also at higher temperatures
but difficult to resolve explicitly. These properties impact on functionally
important processes of physiological relevance in biological media. Methods
of electron paramagnetic resonance (EPR) spectroscopy, both in continuous wave
(cw-EPR) and in pulsed, Fourier transform version (FT-EPR), are appropriate to
characterize supramolecular aggregates in the frozen state. In this work, results
from 9 GHz cw- and FT-EPR investigations on differing spin-labelled biosystems
(such as lipid bilayers, interdigitated lamellae, micelles, natural membranes and
proteins) in the low-temperature phases are presented and discussed. Emphasis
is given to investigate the properties of hydration water within 0.5 nm from the
spin-label nitroxide moieties, to characterize the low-temperature dynamics of the
different biosamples, and to highlight the influence of hydration conditions on the
low-temperature properties of the biosystems. Analysis of neutron scattering data
on the intrinsically disordered human tau-protein to investigate the hydration water
motion is also included.
Three-pulse electron spin echo envelope modulation from 2H-hyperfine interaction
with deuterium (D2O-ESEEM) and cw-EPR are jointly employed at 77 K to detect
the extent of solvent permeation and the environmental polarity, respectively, in
the nearest hydration shell of site-specifically spin-labelled self-assembled lipid aggregates.
The lyotropic phase behaviors of fully hydrated mixtures of the bilayer forming
lipid dipalmitoylphosphatidylcholine (DPPC) with either the micelle-forming
lipid poly(ethylene glycol:2000)-phosphatidylethanolamine (PEG:2000-DPPE) or Lyso-
palmitoylphosphatidylcholine (Lyso-PPC) are investigated over the entire composition
range (0 – 100 mol%). The transmembrane water accessibility and polarity profiles of sterically stabilized liposomes (SSL), formed by admixture of DPPC and
2 mol% of PEG:2000-DPPE, and of polymer-lipid micelles have been delineated.
They are compared to those of lipid bilayers and lamellae with interdigitated chains
and those of small, single-chain micelles. Additionally, D2O-ESEEM and cw-EPR
measurements of spin-labelled cardiotonic steroids in Na+,K+-ATPase revealed that
the vestibule leading to steroid-binding and cation binding sites is relatively wide
and water-filled.
Cw-EPR and two-pulse echo detected ED-spectra are used to characterize the
dynamics of spin-labeled samples in the frozen state over the temperature range 77
– 270 K. Rapid librations (in the nanosecond timescale) of small angular amplitude
(< 20!) manifest themselves in all the model membranes of saturated or unsaturated
lipids or with interdigitated chains studied in this work. A feature shared by the investigated
samples is that the temperature dependences of the segmental librational
amplitudes show a rapid increase at the dynamical transition occurring at Td ⇡ 200
- 220 K. The transition is associated with the onset of stochastic motions with the
bilayers crossing low-energy barriers of activation energy Ea ⇡ 15 - 30 kJ/mol.
The hydration water surrounding macromolecules is fundamental in the activation
of their biological functionality. The effects of hydration on the dynamics
of proteins of different structures, namely ↵ for Human Serum Albumin and " for
"-Lactoglobulin, and model membranes of the most common lipid DPPC in cell
membrane in the low-temperature phases have been also addressed. While the protein
dynamics is suppressed in the lyophilized state and is progressively activated in
the presence of water molecules, it is found that segmental librations of considerable
amplitudes are detected in the inner membrane hydrocarbon region even in the dry
state.
Finally, results on the analysis of quasi-elastic neutron scattering data collected
at the Time-Of-Flight spectrometer TOFTOF of the research neutron source Heinz
Maier-Leibnitz on perdeuterated human tau protein are presented, in order to describe
the translational and rotational dynamics of hydration water molecules.
Descrizione: Dottorato di ricerca in Scienze e tecnologie fisiche, chimiche e dei materiali. XXXIII ciclo2021-07-16T00:00:00ZLaser action in liquid crystals: from random to periodic syatems
https://hdl.handle.net/10955/5413
Titolo: Laser action in liquid crystals: from random to periodic syatems
Autori: Ferjani, Sameh; Strangi, Giuseppe; Versace, Carlo
Descrizione: Dipartimenti di Chimica e Fisica, Dottorato di Ricerca in “Science and Technologies of Mesophases and Molecular Materials: Ciclo XX2007-01-01T00:00:00ZTowards more sustainable organic processes : heterocyclizations in non-conventional solvents
https://hdl.handle.net/10955/5404
Titolo: Towards more sustainable organic processes : heterocyclizations in non-conventional solvents
Autori: Maner, Asif S.; Carbone, Vincenzo; Gabriele, Bartolo; Mancuso, Raffaella
Abstract: This thesis reports the synthesis of important heterocyclic derivatives by iodocyclization, carbonylation and cycloisomerization reactions in Non-Conventionl solvents like deep eutectic solvents (DES) and Ionic Liquids (ILs).
In chapter one general aspects of green and sustainable chemistry and introduction to eco-friendly green solvents such as water, DES, ScCO2 and ILs are described. Carbonylation processes, their advantages, types were described along with the application of transition metal catalysis in the carbonylation reactions with mechanistic approaches discussed.
In chapter two, we describe a convenient and general method for the synthesis of substituted thiophenes through heterocyclodehydration and iodocyclization of readily available 1-mercapto-3-alkyn-2-ols in DES as the solvents.
In chapter three we discuss a convenient carbonylative approach to 2-oxazolidinone derivatives carried out in an ionic liquid as the solvent (EmimEtSO4) is presented. It is based on the sequential concatenation of two catalytic cycles, both catalyzed by the same metal species (auto-tandem catalysis).
In chapter four we present iodocyclization reactions to obtain iodinated isobenzofuranones and isochromenones by iodolactonization of 2-alkynyl benzoic acids in ionic liquids. In particular here we have developed divergent syntheses of (E)-3-(iodoalkylidene) isobenzofuran-1(3H)-ones and 4-iodo-1H-isochromen-1-ones by base-free Iodolactonization of 2-alkynylbenzoic acids in ionic liquids.
In chapter five we report the cycloisomerization of readily available 2-alkynylbenzoic acids using an ionic liquid as the reaction medium in the presence of CuCl2 as a simple and inexpensive catalyst. Although in principle two different cyclization pathways can be followed, leading to either 5-exo-dig mode or 6-endo-dig mode, we have found that substrates bearing an aryl group on the triple bond or a terminal triple bond can be selectively converted into the isobenzofuranone derivatives, using N-ethyl-N-methylmorpholinium dicyanamide (Mor1,2N(CN)2) as the solvent. On the other hand, and in a complementary manner, substrates substituted with an alkyl or an alkenyl group on the triple bond selectively led to isochromenones when the reaction was carried out EmimEtSO4 and with excellent recyclability of the catalyst/ionic liquid system.
Descrizione: Ph.D. in Physics, Chemistry and Materials Science and Technology Ciclo XXIX2017-09-19T00:00:00ZImproving oilfield performance enabling horizontal drilling techniques: developments and optimization of standard and special measures for a real case study
https://hdl.handle.net/10955/5403
Titolo: Improving oilfield performance enabling horizontal drilling techniques: developments and optimization of standard and special measures for a real case study
Autori: Al Taie, Amer Abdulhakim; Carbone, Vincenzo; Romagnoli, Raffaele
Abstract: Drilling technique is a crucial issue to pay attention to. Drilling a horizontal
well has a great interest to the oil and gas industry since nowadays it provides
attractive means for improving both production rate and yet the recovery efficiency.
The great improvements in drilling technology make it possible to drill horizontally
no matter how complex are the trajectories and how deep it is suppose to reach.
This study aims at presenting the optimal design aspects of a horizontal well. Design
aspects include the selection of bit and casing sizes, detection of setting depths and
drilling fluid density, casing, hydraulics, well profile, and construction of drill string
simulator.
When many vertical wells exist, an oil field named (Z14 field) should be designated
to have a short radius horizontal well able to increasing the productivity and to
promote the developing of the field itself.
A single build profile with build rate 90 deg/100ft is constructed based on geological
data. A drill string simulator composed of soft-string model and buckling tendency is
constructed to predict torque and drag of string for six operating conditions. These
conditions are pick-up, slack-off, sliding, pick-up with rotation, slack-off with rotation
and drilling with rotation. Results of loads analysis showed that the suggested drill
string can be used without exceeding torsional, tensile and buckling strengths. Analysis of single build profile showed that the torque and drag while drilling
horizontal well could be minimized by drilling with low build rate, employing lighter
pipe, and improving the lubricating capability with oil base mud (low friction forces).
A finite element model was constructed to predict inclination tendency for
multistabilizer rotary BHA in three dimensions, static condition. The bottom hole
assembly was idealized with beam element capable of resisting axial forces, bending
moments about the two principal axes, and twisting moments about its centroidal axis.
Bit and stabilizer were treated as contact point and restricted from movement in all
directions. Each element is loaded with gravity and normal contact forces. Model
validation showed closer agreement between the model and Jiazhi's method (analytic)
for slick, single, and two stabilizers BHA, compared to Akgun results. Predictions
with finite element model showed that for building assembly, the weight on bit had
small effect on bit side force especially in high angle wells. Also inclination tendency (building, dropping) would depend on position of the stabilizer, diameter of drillcollar
behind the bit, and number of stabilizers.
Descrizione: Dottorato di Ricerca in Scienze e Tecnologie Fisiche, Chimiche e dei Materiali. Ciclo XXIX2017-11-13T00:00:00Z