Computational analyses on the structure-function relation in ion channels

Ion channels are protein molecules, embedded in the lipid bilayer of the cell membranes. They act as powerful sensing elements switching chemicalphysical stimuli into ion-fluxes. At a glance, ion channels are water-filled pores, which can open and close in response to different stimuli (gating), and one once open select the permeating ion species (selectivity). They play a crucial role in several physiological functions, like nerve transmission, muscular contraction, and secretion. Besides, ion channels can be used in technological applications for different purpose (sensing of organic molecules, DNA sequencing). As a result, there is remarkable interest in understanding the molecular determinants of the channel functioning. Nowadays, both the functional and the structural characteristics of ion channels can be experimentally solved. The purpose of this thesis was to investigate the structure-function relation in ion channels, by computational techniques. Most of the analyses focused on the mechanisms of ion conduction, and the numerical methodologies to compute the channel conductance. The standard techniques for atomistic simulation of complex molecular systems (Molecular Dynamics) cannot be routinely used to calculate ion fluxes in membrane channels, because of the high computational resources needed. The main step forward of the PhD research activity was the development of a computational algorithm for the calculation of ion fluxes in protein channels. The algorithm - based on the electrodiffusion theory - is computational inexpensive, and was used for an extensive analysis on the molecular determinants of the channel conductance. The first record of ion-fluxes through a single protein channel dates back to 1976, and since then measuring the single channel conductance has become a standard experimental procedure. Chapter 1 introduces ion channels, and the experimental techniques used to measure the channel currents. The abundance of functional data (channel currents) does not match with an equal abundance of structural data. The bacterial potassium channel KcsA was the first selective ion channels to be experimentally solved (1998), and after KcsA the structures of four different potassium channels were revealed. These experimental data inspired a new era in ion channel modeling. Once the atomic structures of channels are known, it is possible to define mathematical models based on physical descriptions of the molecular systems. These physically based models can provide an atomic description of ion channel functioning, and predict the effect of structural changes. Chapter 2 introduces the computation methods used throughout the thesis to model ion channels functioning at the atomic level. In Chapter 3 and Chapter 4 the ion conduction through potassium channels is analyzed, by an approach based on the Poisson-Nernst-Planck electrodiffusion theory. In the electrodiffusion theory ion conduction is modeled by the drift-diffusion equations, thus describing the ion distributions by continuum functions. The numerical solver of the Poisson- Nernst-Planck equations was tested in the KcsA potassium channel (Chapter 3), and then used to analyze how the atomic structure of the intracellular vestibule of potassium channels affects the conductance (Chapter 4). As a major result, a correlation between the channel conductance and the potassium concentration in the intracellular vestibule emerged. The atomic structure of the channel modulates the potassium concentration in the vestibule, thus its conductance. This mechanism explains the phenotype of the BK potassium channels, a sub-family of potassium channels with high single channel conductance. The functional role of the intracellular vestibule is also the subject of Chapter 5, where the affinity of the potassium channels hEag1 (involved in tumour-cell proliferation) and hErg (important in the cardiac cycle) for several pharmaceutical drugs was compared. Both experimental measurements and molecular modeling were used in order to identify differences in the blocking mechanism of the two channels, which could be exploited in the synthesis of selective blockers. The experimental data pointed out the different role of residue mutations in the blockage of hEag1 and hErg, and the molecular modeling provided a possible explanation based on different binding sites in the intracellular vestibule. Modeling ion channels at the molecular levels relates the functioning of a channel to its atomic structure (Chapters 3-5), and can also be useful to predict the structure of ion channels (Chapter 6-7). In Chapter 6 the structure of the KcsA potassium channel depleted from potassium ions is analyzed by molecular dynamics simulations. Recently, a surprisingly high osmotic permeability of the KcsA channel was experimentally measured. All the available crystallographic structure of KcsA refers to a channel occupied by potassium ions. To conduct water molecules potassium ions must be expelled from KcsA. The structure of the potassium-depleted KcsA channel and the mechanism of water permeation are still unknown, and have been investigated by numerical simulations. Molecular dynamics of KcsA identified a possible atomic structure of the potassium-depleted KcsA channel, and a mechanism for water permeation. The depletion from potassium ions is an extreme situation for potassium channels, unlikely in physiological conditions. However, the simulation of such an extreme condition could help to identify the structural conformations, so the functional states, accessible to potassium ion channels. The last chapter of the thesis deals with the atomic structure of the !- Hemolysin channel. !-Hemolysin is the major determinant of the Staphylococcus Aureus toxicity, and is also the prototype channel for a possible usage in technological applications. The atomic structure of !- Hemolysin was revealed by X-Ray crystallography, but several experimental evidences suggest the presence of an alternative atomic structure. This alternative structure was predicted, combining experimental measurements of single channel currents and numerical simulations. This thesis is organized in two parts, in the first part an overview on ion channels and on the numerical methods adopted throughout the thesis is provided, while the second part describes the research projects tackled in the course of the PhD programme. The aim of the research activity was to relate the functional characteristics of ion channels to their atomic structure. In presenting the different research projects, the role of numerical simulations to analyze the structure-function relation in ion channels is highlighted.

Advanced lithium and lithium-ion rechargeable batteries for automotive applications

The worldwide demand for a clean and low-fuel-consuming transport promotes the development of safe, high energy and power electrochemical storage and conversion systems. Lithium-ion batteries (LIBs) are considered today the best technology for this application as demonstrated by the recent interest of automotive industry in hybrid (HEV) and electric vehicles (EV) based on LIBs. This thesis work, starting from the synthesis and characterization of electrode materials and the use of non-conventional electrolytes, demonstrates that LIBs with novel and safe electrolytes and electrode materials meet the targets of specific energy and power established by U.S.A. Department of Energy (DOE) for automotive application in HEV and EV. In chapter 2 is reported the origin of all chemicals used, the description of the instruments used for synthesis and chemical-physical characterizations, the electrodes preparation, the batteries configuration and the electrochemical characterization procedure of electrodes and batteries. Since the electrolyte is the main critical point of a battery, in particular in large- format modules, in chapter 3 we focused on the characterization of innovative and safe electrolytes based on ionic liquids (characterized by high boiling/decomposition points, thermal and electrochemical stability and appreciable conductivity) and mixtures of ionic liquid with conventional electrolyte. In chapter 4 is discussed the microwave accelerated sol–gel synthesis of the carbon- coated lithium iron phosphate (LiFePO 4 -C), an excellent cathode material for LIBs thanks to its intrinsic safety and tolerance to abusive conditions, which showed excellent electrochemical performance in terms of specific capacity and stability. In chapter 5 are presented the chemical-physical and electrochemical characterizations of graphite and titanium-based anode materials in different electrolytes. We also characterized a new anodic material, amorphous SnCo alloy, synthetized with a nanowire morphology that showed to strongly enhance the electrochemical stability of the material during galvanostatic full charge/discharge cycling. Finally, in chapter 6, are reported different types of batteries, assembled using the LiFePO 4 -C cathode material, different anode materials and electrolytes, characterized by deep galvanostatic charge/discharge cycles at different C-rates and by test procedures of the DOE protocol for evaluating pulse power capability and available energy. First, we tested a battery with the innovative cathode material LiFePO 4 -C and conventional graphite anode and carbonate-based electrolyte (EC DMC LiPF 6 1M) that demonstrated to surpass easily the target for power-assist HEV application. Given that the big concern of conventional lithium-ion batteries is the flammability of highly volatile organic carbonate- based electrolytes, we made safe batteries with electrolytes based on ionic liquid (IL). In order to use graphite anode in IL electrolyte we added to the IL 10% w/w of vinylene carbonate (VC) that produces a stable SEI (solid electrolyte interphase) and prevents the graphite exfoliation phenomenon. Then we assembled batteries with LiFePO 4 -C cathode, graphite anode and PYR 14 TFSI 0.4m LiTFSI with 10% w/w of VC that overcame the DOE targets for HEV application and were stable for over 275 cycles. We also assembled and characterized ―high safety‖ batteries with electrolytes based on pure IL, PYR 14 TFSI with 0.4m LiTFSI as lithium salt, and on mixture of this IL and standard electrolyte (PYR 14 TFSI 50% w/w and EC DMC LiPF 6 50% w/w), using titanium-based anodes (TiO 2 and Li 4 Ti 5 O 12 ) that are commonly considered safer than graphite in abusive conditions. The batteries bearing the pure ionic liquid did not satisfy the targets for HEV application, but the batteries with Li 4 Ti 5 O 12 anode and 50-50 mixture electrolyte were able to surpass the targets. We also assembled and characterized a lithium battery (with lithium metal anode) with a polymeric electrolyte based on poly-ethilenoxide (PEO 20 – LiCF 3 SO 3 +10%ZrO 2 ), which satisfied the targets for EV application and showed a very impressive cycling stability. In conclusion, we developed three lithium-ion batteries of different chemistries that demonstrated to be suitable for application in power-assist hybrid vehicles: graphite/EC DMC LiPF 6 /LiFePO 4 -C, graphite/PYR 14 TFSI 0.4m LiTFSI with 10% VC/LiFePO 4 -C and Li 4 T i5 O 12 /PYR 14 TFSI 50%-EC DMC LiPF 6 50%/LiFePO 4 -C. We also demonstrated that an all solid-state polymer lithium battery as Li/PEO 20 –LiCF 3 SO 3 +10%ZrO 2 /LiFePO 4 -C is suitable for application on electric vehicles. Furthermore we developed a promising anodic material alternative to the graphite, based on SnCo amorphous alloy.

Photo- and redox-active supramolecular systems containing metal complexes

The aim of this Ph.D. project has been the photophysical and photochemical characterization of new photo- and redox-active supramolecular systems. In particular we studied two different classes of compounds: metal complexes and dendrimers. Two different families of bis-cyclometalated neutral Ir(III) complexes are presented and their photophysical properties are discussed. The first family of complexes contains two 2-phenylpyridyl (ppy) or 2-(4,6-difluorophenyl)pyridyl (F2ppy) cyclometalated ligands and an ancillary ligand constituted by a phenol-oxazoline (phox), which can be substituted in the third position with a fluorine group (Fphox). In the second part of this study, we present another family of bis-cyclometalated Ir(III) complexes in which the ancillary ligand could be a chiral or an achiral bis-oxazoline (box). We report on their structural, electrochemical, photophysical, and photochemical properties. Complexes containing phox and Fphox ancillary ligands show blue luminescence with very high quantum yield, while complexes with box ligands do not show particularly interesting photophysical properties. Surprisingly these complexes give an unexpected photoreaction when irradiated with UV light in presence of dioxygen. This photoreaction originates a stable, strong blue emitting and particularly interesting photoproduct. Three successive generations of a family of polyethyleneglycol (PEG)-coated Pd(II) tetrabenzoporphyrin (PdTBP)-based dendritic nanoprobes are presented, and their ability to sensitize singlet oxygen and inflict cellular photodamage are discussed. It was found that the size of the dendrimer has practically no effect on the singlet oxygen sensitization efficiency, that approximate the unity, in spite of the strong attenuation of the triplet quenching rate with an increase in the dendrimer generation. Nevertheless, when compared against a commonly used singlet oxygen sensitizer, as Photofrin, the phosphorescent probes were found to be non-phototoxic. The lack of phototoxicity is presumably due to the inability of PEGylated probes to associate with cell surfaces and/or penetrate cellular membranes. The results suggest that protected phosphorescent probes can be safely used for oxygen measurements in biological systems in vivo. A new family of two photoswitchable (G0(Azo) and G1(Azo)) dendrimers with an azobenzene core, two cyclam units as coordination sites for metal ions, and luminescent naphthalene units at the periphery have been characterized and their coordination abilities have been studied. Because of their proximity, the various functional groups of the dendrimer may interact, so that the properties of the dendrimers are different from those exhibited by the separated functional units. Both the naphthalene fluorescence and the azobenzene photoisomerization can be observed in the dendrimer, but it has been shown that (i) the fluorescent excited state of the naphthalene units is substantially quenched by excimer and exciplex formation and by energy transfer to the azobenzene units, and (ii) in the latter case the fluorescence quenching is accompanied by the photosensitized isomerization of the trans → cis, and, with higher efficiency, the cis → trans reaction. Complexation of these dendrimers, both trans and cis isomers, with Zn(II) ions shows that complexes of 1:1 and 2:1 metal per dendrimer stoichiometry are formed showing different photophysical and photochemical properties compared to the corresponding free ligands. Practically unitary efficiency of the sensitized isomerization of trans → cis and cis → trans reaction is observed, as well as a slight increase in the naphthalene monomer emission. These results are consistent with the coordination of the cyclam amine units with Zn(II), which prevents exciplex formation. No indication of a concomitant coordination of both cyclam to a single metal ion has been obtained both for trans and cis isomer.

Hybrid portable systems for bio-nanosensors

The promising development in the routine nanofabrication and the increasing knowledge of the working principles of new classes of highly sensitive, label-free and possibly cost-effective bio-nanosensors for the detection of molecules in liquid environment, has rapidly increased the possibility to develop portable sensor devices that could have a great impact on many application fields, such as health-care, environment and food production, thanks to the intrinsic ability of these biosensors to detect, monitor and study events at the nanoscale. Moreover, there is a growing demand for low-cost, compact readout structures able to perform accurate preliminary tests on biosensors and/or to perform routine tests with respect to experimental conditions avoiding skilled personnel and bulky laboratory instruments. This thesis focuses on analysing, designing and testing novel implementation of bio-nanosensors in layered hybrid systems where microfluidic devices and microelectronic systems are fused in compact printed circuit board (PCB) technology. In particular the manuscript presents hybrid systems in two validating cases using nanopore and nanowire technology, demonstrating new features not covered by state of the art technologies and based on the use of two custom integrated circuits (ICs). As far as the nanopores interface system is concerned, an automatic setup has been developed for the concurrent formation of bilayer lipid membranes combined with a custom parallel readout electronic system creating a complete portable platform for nanopores or ion channels studies. On the other hand, referring to the nanowire readout hybrid interface, two systems enabling to perform parallel, real-time, complex impedance measurements based on lock-in technique, as well as impedance spectroscopy measurements have been developed. This feature enable to experimentally investigate the possibility to enrich informations on the bio-nanosensors concurrently acquiring impedance magnitude and phase thus investigating capacitive contributions of bioanalytical interactions on biosensor surface.

Towards eco-friendly batteries: concepts for lithium and sodium ion batteries

Several possibilities are arising aiming the development of “greener”, more sustainable energy storage systems. One point is the completely water-based processing of battery electrodes, thus being able to renounce the use of toxic solvents in the preparation process. Despite its advantage of lower cost and eco-friendlyness, there is the need of similar mechanical and electrochemichal behavior for boosting this preparation mode. Another point – accompanying the water-based processing - is the replacement of solvent-based polymer binders by water-based ones. These binders can be based on fluorinated, crude-oil based polymers on the one side, but also on naturally abundant and economic friendly biopolymers. The most common anode materials, graphite and lithium titanate (LTO), have been subjected a water-based preparation route with different binder systems. LTO is a promising anode material for lithium ion batteries (LIBs), as it shows excellent safety characteristics, does not form a significant SEI and its volume change upon intercalation of lithium ions is negligible. Unfortunately, this material suffers from a rather low electric conductivity - that is why an intensive study on improved current collector surfaces for LTO electrodes was performed. In order to go one step ahead towards sustainable energy storage, anode and cathode active materials for a sodium ion battery were synthesized. Anode active material resulted in a successful product which was then subjected to further electrochemical tests. In this PhD work the development of “greener” energy storage possibilities is tested under several aspects. The ecological impact of raw materials and required battery components is examined in detail.