APPLICATION AND DEVELOPMENT OF THE LINEAR COMBINATION OF ATOMIC ORBITALS B-SPLINE DENSITY FUNCTIONAL THEORY METHOD FOR THE MOLECULAR ELECTRONIC CONTINUUM

2004/2005Lo scopo della presente tesi è l'applicazione e lo sviluppo del metodo LCAO B-spline DFT, basato sulla Combinazione Lineare degli Orbitali Atomici (LCAO), sulla Teoria del Funzionale Densità (DFT) e sull'impiego delle funzioni di base Bspline, per lo studio della fotoionizzazione molecolare. Nel Capitolo 1 viene considerata una breve introduzione al processo di fotoionizzazione e alla teoria della fotoionizzazione molecolare. Nel Capitolo 2 vengono presentati i metodi computazionali utilizzati durante il presente lavoro di tesi. I risultati ottenuti sono presentati nei successivi Capitoli della tesi. Il lavoro è suddiviso in tre parti. Nella prima parte (Capitoli 3-6) il metodo LCAO B-spline DFT è applicato allo studio del Dicroismo Circolare nella Distribuzione Angolare (CDAD) dei fotoelettroni emessi da molecole chirali, ionizzate da luce circolarmente polarizzata di definita elicità. Un primo studio computazionale sull'effetto CDAD è focalizzato su una serie di derivati chirali dell'ossirano, con lo scopo di identificare tendenze lungo la serie molecolare. I risultati evidenziano una inaspettata sensibilità da parte del dicroismo circolare verso cambiamenti nella struttura elettronica molecolare. Inoltre i valori calcolati sottolineano come lintensità dell'effetto CD AD è da attribuire non tanto alla chiralità dello stato iniziale, ma bensì alla capacità della funzione d'onda del fotoelettrone (completamente delocalizzata su tutta la molecola) di sondare l'asimmetria nel potenziale molecolare effettivo. Il metodo LCAO B-spline DFT è quindi applicato allo studio del dicroismo circolare nella distribuzione angolare dei fotoelettroni emessi dai livelli di core e di valenza degli enantiomeri della canfora. I risultati sono confrontati con i valori calcolati attraverso l'approccio Continuum Multiple Scattering: i due metodi teorici mostrano un sostanziale accordo nei risultati. Inoltre, un confronto dei risultati calcolati con i dati sperimentali disponibili mostra un accordo sostanziale se non addirittura quantitativo. E' inoltre presentato uno studio teorico e sperimentale sul dicroismo circolare nella distribuzione angolare dei fotoelettroni emessi dai livelli di valenza del 3- idrossitetraidrofurano, il quale è una molecola relativamente flessibile. Questo lavoro mette luce su nuove caratteristiche del dicroismo in fotoemissione, il quale appare molto sensibile a fattori di tipo conformazionale. L'influenza degli effetti conformazionali sui parametri dinamici di fotoionizzazione, con particolare attenzione all'effetto CDAD, è quindi investigata in dettaglio. Il metodo LCAO E-spline DFf è applicato ai conformeri della molecola (1R,2R)-1,2-dibromo-1,2-dicloro-1,2-difluoroetano. Il parametro dicroico mostra una significativa sensibilità verso il conformero della molecola. Ciò suggerisce che il profilo energetico del parametro dicroico potrebbe essere utilizzato come un fingerprint dei conformeri di una molecola chirale. Il metodo computazionale è anche applicato alla rotazione del metile nella molecola (S)-ossirano, in modo da verificare l'assunzione che la rotazione del metile non influisca in maniera significativa sui valori calcolati dell'effetto CDAD. Si verifica invece come la rotazione del gruppo metile provochi variazioni inaspettate e drammatiche sul profilo del parametro dicroico. La seconda parte del lavoro (Capitolo 7) riguarda l'investigazione teorica sulla correttezza dell'assunzione che il Eranching Ratio nella ionizzazione dei livelli di core di siti atomici chimicamente diversi dello stesso elemento, segua il rapporto statistico. Il metodo LCAO E-spline DFT è stato impiegato per calcolare in maniera accurata le sezioni d'urto associate alla ionizzazione degli orbitali ls dei carboni per un set di molecole organiche scelte. I risultati mostrano che deviazioni nella sezione d'urto inducono forti andamenti non statistici da parte dei Eranching Ratios relativi alla ionizzazione dei livelli core, fino a diversi e V sopra la soglia di ionizzazione. La parte finale della tesi (Capitolo 8) riguarda il problema delle shape resonances. La razionalizzazione delle strutture risonanti, spesso presenti nello spettro molecolare del continuo, è un problema ampiamente discusso. Nel presente lavoro una nuova metodologia per localizzare e caratterizzare in termini molecolari le shape resonances viene proposta. Partendo da un sistema modello, è stato sviluppato un metodo per caratterizzare le risonanze in termini di contributo da parte degli orbitali virtuali di valenza. Il metodo sviluppato è quindi esteso al caso molecolare ed applicato alla localizzazione e caratterizzazione delle shape resonances che appaiono nella fotoionizzazione dei livelli crg di core e di valenza di N1.XVIII Ciclo1977Versione digitalizzata della tesi di dottorato cartacea

Density functional theory based molecular dynamics study of solution composition effects on the solvation shell of metal ions

We present an ab initio molecular dynamics study of the alkali metal ions Li+, Na+, K+ and Cs+, and of the alkaline earth metal ions Mg2+ and Ca2+ in both pure water and electrolyte solutions containing the counterions Cl- and SO42-. Simulations were conducted using different density functional theory methods (PBE, BLYP and revPBE), with and without the inclusion of dispersion interactions (-D3). Analysis of the ion-water structure and interaction strength, water exchange between the first and second hydration shell, and hydrogen bond network and low-frequency reorientation dynamics around the metal ions have been used to characterise the influence of solution composition on the ionic solvation shell. Counterions affect the properties of the hydration shell not only when they are directly coordinated to the metal ion, but also when they are at the second coordination shell. Chloride ions reduce the sodium hydration shell and expand the calcium hydration shell by stabilizing under-coordinated hydrated Na(H2O)5+ complexes and over-coordinated Ca(H2O)72+. The same behaviour is observed in CaSO4(aq), where Ca2+ and SO42- form almost exclusively solvent-shared ion pairs. Water exchange between the first and second hydration shell around Ca2+ in CaSO4(aq) is drastically decelerated compared with the simulations of the hydrated metal ion (single Ca2+, no counterions). Velocity autocorrelation function analysis, used to probe the strength of the local ion-water interaction, shows a smoother decay of Mg2+ in MgCl2(aq), which is a clear indication of a looser inter-hexahedral vibration in the presence of chloride ions located in the second coordination shell of Mg2+. The hydrogen bond statistics and orientational dynamics in the ionic solvation shell show that the influence on the water-water network cannot only be ascribed to the specific cation-water interaction, but also to the subtle interplay between the level of hydration of the ions, and the interactions between ions, especially those of opposite charge. As many reactive processes involving solvated metal ions occur in environments that are far from pure water but rich in ions, this computational study shows how the solution composition can result in significant differences in behaviour and function of the ionic solvation shell

Sulfate and molybdate incorporation at the calcite–water interface: insights from ab initio molecular dynamics

Sulfur and molybdenum trace impurities in speleothems (stalagmites and stalactites) can provide long and continuous records of volcanic activity, which are important for past climatic and environmental reconstructions. However, the chemistry governing the incorporation of the trace element-bearing species into the calcium carbonate phases forming speleothems is not well understood. Our previous work has shown that substitution of tetrahedral oxyanions [XO4]2– (X = S and Mo) replacing [CO3]2– in CaCO3 bulk phases (except perhaps for vaterite) is thermodynamically unfavorable with respect to the formation of competing phases, due to the larger size and different shape of the [XO4]2– tetrahedral anions in comparison with the flat [CO3]2– anions, which implied that most of the incorporation would happen at the surface rather than at the bulk of the mineral. Here, we present an ab initio molecular dynamics study, exploring the incorporation of these impurities at the mineral–water interface. We show that the oxyanion substitution at the aqueous calcite (10.4) surface is clearly favored over bulk incorporation, due to the lower structural strain on the calcium carbonate solid. Incorporation at surface step sites is even more favorable for both oxyanions, thanks to the additional interface space afforded by the surface line defect to accommodate the tetrahedral anion. Differences between sulfate and molybdate substitutions can be mostly explained by the size of the anions. The molybdate oxyanion is more difficult to incorporate in the calcite bulk than the smaller sulfate oxyanion. However, when molybdate is substituted at the surface, the elastic cost is avoided because the oxyanion protrudes out of the surface and gains stability via the interaction with water at the interface, which in balance results in more favorable surface substitution for molybdate than for sulfate. The detailed molecular-level insights provided by our calculations will be useful to understand the chemical basis of S- and Mo-based speleothem records

Hydrogen-bond structure and low-frequency dynamics of electrolyte solutions: Hydration numbers from ab Initio water reorientation dynamics and dielectric relaxation spectroscopy

We present an atomistic simulation scheme for the determination of the hydration number (h) of aqueous electrolyte solutions based on the calculation of the water dipole reorientation dynamics. In this methodology, the time evolution of an aqueous electrolyte solution generated from ab initio molecular dynamics simulations is used to compute the reorientation time of different water subpopulations. The value of h is determined by considering whether the reorientation time of the water subpopulations is retarded with respect to bulk-like behavior. The application of this computational protocol to magnesium chloride (MgCl2 ) solutions at different concentrations (0.6-2.8 mol kg-1 ) gives h values in excellent agreement with experimental hydration numbers obtained using GHz-to-THz dielectric relaxation spectroscopy. This methodology is attractive because it is based on a well-defined criterion for the definition of hydration number and provides a link with the molecular-level processes responsible for affecting bulk solution behavior. Analysis of the ab initio molecular dynamics trajectories using radial distribution functions, hydrogen bonding statistics, vibrational density of states, water-water hydrogen bonding lifetimes, and water dipole reorientation reveals that MgCl2 has a considerable influence on the hydrogen bond network compared with bulk water. These effects have been assigned to the specific strong Mg-water interaction rather than the Cl-water interaction

Properties of water confined in hydroxyapatite nanopores as derived from molecular dynamics simulations

Bone tissue is characterized by nanopores inside the collagen-apatite matrix where fluid can exist and flow. The description of the fluid flow within the bone has however mostly relied on a macroscopic continuum mechanical treatment of the system, and, for this reason, the role of these nanopores has been largely overlooked. However, neglecting the nanoscopic behaviour of fluid within the bone volume could result in large errors in the overall description of the dynamics of fluid. In this work, we have investigated the nanoscopic origin of fluid motion by conducting atomistic molecular dynamics simulations of water confined between two parallel surfaces of hydroxyapatite (HAP), which is the main mineral phase of mammalian bone. The polarizable core–shell interatomic potential model used in this work to simulate the HAP–water system has been extensively assessed with respect to ab initio calculations and experimental data. The structural (pair distribution functions), dynamical (self-diffusion coefficients) and transport (shear viscosity coefficients) properties of confined water have been computed as a function of the size of the nanopore and the temperature of the system. Analysis of the results shows that the dynamical and transport properties of water are significantly affected by the confinement, which is explained in terms of the layering of water on the surface of HAP as a consequence of the molecular interactions between the water molecules and the calcium and phosphate ions at the surface. Using molecular dynamics simulations, we have also computed the slip length of water on the surface of HAP, the value of which has never been reported before

Anisotropic diffusion of water molecules in hydroxyapatite nanopores

Funded by EPSRC Grant EP/K000128/1

Disease-specific and general health-related quality of life in newly diagnosed prostate cancer patients: The Pros-IT CNR study

Background: The National Research Council (CNR) prostate cancer monitoring project in Italy (Pros-IT CNR) is an observational, prospective, ongoing, multicentre study aiming to monitor a sample of Italian males diagnosed as new cases of prostate cancer. The present study aims to present data on the quality of life at time prostate cancer is diagnosed. Methods: One thousand seven hundred five patients were enrolled. Quality of life is evaluated at the time cancer was diagnosed and at subsequent assessments via the Italian version of the University of California Los Angeles-Prostate Cancer Index (UCLA-PCI) and the Short Form Health Survey (SF-12). Results: At diagnosis, lower scores on the physical component of the SF-12 were associated to older ages, obesity and the presence of 3+ moderate/severe comorbidities. Lower scores on the mental component were associated to younger ages, the presence of 3+ moderate/severe comorbidities and a T-score higher than one. Urinary and bowel functions according to UCLA-PCI were generally good. Almost 5% of the sample reported using at least one safety pad daily to control urinary loss; less than 3% reported moderate/severe problems attributable to bowel functions, and sexual function was a moderate/severe problem for 26.7%. Diabetes, 3+ moderate/severe comorbidities, T2 or T3-T4 categories and a Gleason score of eight or more were significantly associated with lower sexual function scores at diagnosis. Conclusions: Data collected by the Pros-IT CNR study have clarified the baseline status of newly diagnosed prostate cancer patients. A comprehensive assessment of quality of life will allow to objectively evaluate outcomes of different profile of care

Bridging atomistic simulations and thermodynamic hydration models of aqueous electrolyte solutions

Chemical thermodynamic models of solvent and solute activities predict the equilibrium behavior of aqueous solutions. However, these models are semi-empirical. They represent micro-scale ion and solvent behaviors controlling the macroscopic properties using small numbers of parameters whose values are obtained by fitting to activities and other partial derivatives of the Gibbs energy measured for the bulk solutions. We have conducted atomistic simulations of aqueous electrolyte solutions (MgCl2 and CaCl2) to determine the parameters of thermodynamic hydration models. We have implemented a cooperative hydration model to categorize the water molecules in electrolyte solutions into different subpopulations. The value of the electrolyte-specific parameter, k, was determined from the ion-affected subpopulation with the lowest absolute value of the free energy of removing the water molecule. The other equilibrium constant parameter, K1, associated with the first degree of hydration, was computed from the free energy of hydration of hydrated clusters. The hydration number, h, was determined from a reorientation dynamic analysis of the water subpopulations compared to bulk-like behavior. The reparameterized models [R. H. Stokes and R. H. Robinson, J. Solution Chem. 2, 173 (1973) and Balomenos et al., Fluid Phase Equilib. 243, 29 (2006)] using the computed values of the parameters lead to the osmotic coefficients of MgCl2 solutions that are consistent with measurements. Such an approach removes the dependence on the availability of experimental data and could lead to aqueous thermodynamic models capable of estimating the values of solute and solvent activities as well as thermal and volumetric properties for a wide range of compositions and concentrations