Understanding electronic properties of water: a theoretical approach to the calculation of the adiabatic band gap of liquid water

Tese de doutoramento em Química (Química-Física), apresentada à Universidade de Lisboa através da Faculdade de Ciências, 2008Electronic properties of condensed phase water are not very well understood. They are, however, of fundamental importance for a molecular level understanding of the properties of water as well as the role of water, both as participant and medium where chemical reactions occur. It is generally accepted that bulk water can be described as a lone pair amorphous insulator or a large gap lone-pair amorphous semiconductor and the condensed phase ionization potential de_ned as a vertical quantity. A usually accepted value is 8.7 _ 0.5 eV. However, a de_nition of condensed phase properties such as the condensed phase ionization potential is not straightforward and ultimately dependent our understanding of the elementary mechanisms for ionization/excitation in condensed phase water. A longstanding issue is the concearns the fact that hydrated electrons are produced by photoabsorption at _6.5 eV. It has recently been pointed out that the ability of water to reorganize about charged (and neutral) molecules, as well as the reactive nature of electronically excited water molecules, should be taken into account in explaining observed aqueous anion thermochemical and photochemical properties. Moreover, it has been shown that an adiabatic route for accessing the conduction band of liquid water can be de_ned and that the bottom of the conduction band is characterized by the reorganization of the water molecules around the H3O+ cation and OH radical as well as by the presence of a delocalized or quasi-free electron. A _6.9 eV value was proposed by J.V. Coe [Int. Rev. Phys. Chem. 20, 33, 2001], based on known aqueous anion thermochemical and photochemical properties,The present work presents a theoretical estimate for two key reference quantities required for the quantitative estimate of the adiabatic band gap of pure liquidwater as de_ned by J.V. Coe: the hydration energy of the hydroxyl radical andthe electron a_nity of liquid water. The hydration of the hydroxyl radical wasinvestigated by microsolvation modeling and statistical mechanics Monte Carlosimulation. The electron electronic density of states and a_nity of liquid water wasinvestigated trough a sequential Quantum Mechanical / Monte Carlo methodology.Finally, as the adiabatic approach for a de_nition of a band gap for pure liquidwater is based on macroscopic quantities, a molecular level veri_cation of the adiabatic picture was also undertaken

On the Zwitterionic Nature of Gas-Phase Peptides and Protein Ions

Determining the total number of charged residues corresponding to a given value of net charge for peptides and proteins in gas phase is crucial for the interpretation of mass-spectrometry data, yet it is far from being understood. Here we show that a novel computational protocol based on force field and massive density functional calculations is able to reproduce the experimental facets of well investigated systems, such as angiotensin II, bradykinin, and tryptophan-cage. The protocol takes into account all of the possible protomers compatible with a given charge state. Our calculations predict that the low charge states are zwitterions, because the stabilization due to intramolecular hydrogen bonding and salt-bridges can compensate for the thermodynamic penalty deriving from deprotonation of acid residues. In contrast, high charge states may or may not be zwitterions because internal solvation might not compensate for the energy cost of charge separation

Enhanced Stability of the Model Mini-protein in Amino Acid Ionic Liquids and Their Aqueous Solutions

Using molecular dynamics simulations, the structure of model mini-protein was thoroughly characterized in the imidazolium-based amino acid ionic liquids and their aqueous solutions. We report that the mini-protein is more stable when AAIL is added as a cosolvent. Complete substitution of water by organic cations and anions further results in hindered conformational flexibility of the mini-protein. This observation suggests that AAILs are able to defend proteins from thermally induced denaturation. We show by means of radial distributions that the mini-protein is efficiently solvated by both solvents due to agood mutual miscibility. However, amino acid based anions prevail in the first coordination sphere of the mini-protein

Polarizability Plays a Decisive Role in Modulating Association Between Molecular Cations and Anions

Electrostatic interactions involving proteins depend not just on the ionic charges involved but also on their chemical identities. Here we examine the origins of incompletely understood differences in the strength of association of different pairs of monovalent molecular ions that are relevant to protein-protein and protein-ligand interactions. Cationic analogues of the basic amino acid side chains are simulated along with oxyanionic analogues of cation-exchange (CEX) ligands and acidic amino acids. Experimentally observed association trends with respect to the cations, but not anions, are captured by a non-polarizable model. A polarizable model proves decisive in capturing experimentally-suggested trends with respect to both cations and anions. Crucially, relative to a non-polarizable model, polarizability changes the free energy surface for ion-pair association, altering configurational sampling itself. An effective continuum correction to account for electronic polarizability can also capture the experimentally-suggested trends, but at the expense of fidelity to the underlying free energy surface

Development and Investigation of the Fluorescence of Cyclopropenium Ions

The work presented herein employs cyclopropenium ions as a central design element towards the goal of developing fluorescent, superbasic and boronium-substituted compounds. A novel guanidine-cyclopropenimine proton sponge with exceptional basicity is reported that was further utilized to develop a stable tetracoordinate boronium-substituted proton sponge. A large focus of this thesis was also placed on the development of the recently discovered fluorescence of cyclopropenium ions leading to a new class of small molecule organic fluorophores. Among this new platform of fluorescent compounds, a specific fluorophore featured an impressive photophysical profile that bodes well for future applications in fluorescent imaging techniques. Insight into the structure, electronics, bonding and photophysical properties of these derivatives is offered

Soluut-solvent vastasmõjude eksperimentaalne uurimine ja modelleerimine

Väitekirja elektrooniline versioon ei sisalda publikatsiooneEnamik praktilist tähtsust omavatest keemilistest protsessidest toimub vedelikes – mitte ainult tööstuslik süntees ja laborikeemia, vaid ka bioloogilised protsessid nagu rakkude hingamine toimuvad molekulaarsel tasemel keerulise koostisega lahustes. Neist protsessidest arusaamine ja molekulide käitumise ennustamine lahustes on tähtis arvukate uurimisvaldkondade jaoks, meditsiinist ja farmakoloogiast naftakeemiani. Kahjuks on ainete omaduste ennustamine vedelikes arvutuskeemia jaoks üks keerulisemaid ülesandeid. Käesolevas töös hinnati olemasolevate arvutusmetoodikate sobivust vesiniksideme tekke kirjeldamiseks orgaanilistes lahustites ning molekulide jaotuse kirjeldamiseks kahe vedeliku vahel (sisuliselt vedelik-vedelik ekstraktsiooni modelleerimiseks). Peamine kasutatud arvutusmeetod oli COSMO-RS (Conductor-like Screening Model for Real Solvents), valitud oma erakordse sobivuse tõttu kontsentreeritud ja mitmekomponendiliste lahuste omaduste ennustamiseks ja molekulaardisainiks. Töö käigus leiti, et vesiniksidemed neutraalsete molekulide vahel on kirjeldatavad suhteliselt hästi, kuid vaadeldud arvutusmetoodikad pole piisavalt täpsed negatiivselt laetud vesiniksidemega komplekside modelleerimiseks. Vedelik-vedelik ekstraktsiooni tulemuste ennustamine COSMO-RS meetodiga oli üldjuhul edukas. Saadud tulemustele (nii lõpp- kui vahepealsetele parameetritele) saadi täpsuse hinanngud. Peale selle arendati uus metodoloogia tundmatute ühendite jaotuse ennustamiseks kahe mitteseguneva vedeliku vahel ilma vajaduseta ühendeid identifitseerida. See lihtsustab parima lahusti valikut ainete isoleerimiseks või puhastamiseks, vähendades töö- ja kemikaalide kulu ning jäätmete kogust.The majority of practically relevant chemical processes occur in liquids. Those are not limited to industrial synthesis and laboratory chemistry – biological processes such as cellular respiration on molecular level take place in complex solutions. Understanding and being able to predict the behaviour of molecules in solutions is essential for numerous branches of science, ranging from medicine and pharmacology to petroleum chemistry. However, predicting the behavior of chemical compounds in liquids, especially in many-component solutions, is one of the most challenging tasks for computational chemistry. In this work existing computational methodologies were tested for suitability for describing hydrogen bond formation in organic solvents and distribution of organic compounds between liquids (essentially modeling of liquid-liquid extraction). The main computational method in this work is COSMO-RS (Conductor-like Screening Model for Real Solvents), chosen for its unequalled ability to predict properties of concentrated and multicomponent solutions and usability in molecular design. It was found that properties of hydrogen bonds between uncharged molecules can be predicted relatively well, but the tested computational approaches were not accurate enough for description of hydrogen bonds involving negatively charged ions. Modeling of liquid-liquid extraction using COSMO-RS was generally successful. Accuracy of the predictions and intermediate parameters was evaluated and problematic cases identified and discussed. Also, a new methodology was developed for predicting the distribution of unknown compounds between immiscible solutions without need for compound identification. It allows simplifying the solvent selection for compound isolation or purification, reducing the workload, expenses and waste amount