Exploring Potential Energy Surfaces Of Chemical Reactions Using Electronic Structure Methods

This dissertation includes three topics: molecular dynamics in strong laser fields, pKa’s and redox potential calculations of bio–organic molecules, and oxidative damage of the nucleobases. Electronic structure calculations are used to provide a deeper understanding of experimental observations as well as to predict new results. Chapters 2, 3 and 4 investigate the fragmentation and isomerization reactions of small monocations in the presence of strong laser fields. In the presence of intense laser pulses with 800 nm wavelengths, Born-Oppenheimer classical trajectory simulations were performed to investigate the dynamics of methanol monocation on the ground state potential energy surface (Chapter 2). With initially added 75-125 kcal/mol energy and the applied laser fields, 79-81% of the trajectories were seen to produce H atom. H2 loss was found to be the second most frequent dissociation channel (9-13%) and isomerization of CH3OH+ to CH2OH2+ was the third most abundant reaction path (1-3%). Chapter 3 compares the difference in dynamics of the methanol monocation in the presence of 800 nm and 7 µm laser pulses. Randomly oriented methanol cations gained an average of 42 and 81 kcal/mol for 4 cycle 7 µm pulses with intensities of 0.88 × 1014 Wcm-2 and 1.7 × 1014 Wcm-2 respectively, but only 0.5 and 2.0 kcal/mol from 4 cycle 800 nm pulses with the same intensity. Chapter 4 explores the effect of changes in potential energy surface on the isomerization and dissociation reactions driven by the laser field for CH3NH2+, CH3OH+, and CH3F+. The amount of energy absorbed nearly doubled when the laser field was aligned along the C−X axis (X=NH2, OH, and F) and, also when the field intensity was increased from of 0.88 × 1014 to 1.7 ×1014 Wcm-2. Dissociation after isomerization was observed only in CH3F+ (0−6%). The amount of CH3+ + X dissociation for all three molecules increased when the laser field was aligned along C-X bond. Chapters 5-8 detail the development of a computational protocol for computing accurate pKa’s and redox potentials of various bio–organic compounds in aqueous solution. Chapter 5 investigates the effect of explicit water molecules with implicit solvation on the calculated pKa’s and redox potential of nucleobases. Using a few explicit water molecules and an implicit solvation model, the pKa’s and redox potentials of the nucleobases were found to be in good agreement with the experimentally measured values. The methodology is then expanded to calculate the pKa’s of larger sets of organic molecules such as thiols (Chapter 6), selenols (Chapter 7), alcohols, phenols and hydroperoxides (Chapter 8). A survey of a wide range of DFT functionals and basis sets with varying numbers of explicit waters were performed in each of those studies to determine the appropriate computational method and the number of explicit waters needed. At least one explicit water molecule was needed in all cases to reduce some of the errors in implicit solvation model while three explicit waters were required to obtain the chemical accuracy. B97XD/6-31+G(d,p) with three explicit waters in SMD implicit solvation predicted the pKa’s of organic substituted thiols and selenols within 1 pKa units of the experimentally measured values. When three explicit waters were included along with SMD solvation, B3LYP/6-311++G(d,p) was found to perform the best for the alcohols, phenols, and hydroperoxides with very good agreement with the experimentally known pKa values. Chapters 9, 10 and 11 explore some of the pathways of guanine-lysine crosslink formation in aqueous solution in the presence of different oxidizing agents such as benzophenone photosenzetizer, singlet oxygen, and sulfate radical. Various reaction pathways in aqueous solution were investigated by DFT calculations with the SMD solvation model. In some cases, high level quantum chemistry calculations such as CCSD(T), BD(T), and CASSCF calculations were also used to achieve greater accuracy. The barrier heights, enthalpies, pKa’s and reduction potentials were calculated for intermediates to find the lowest energy paths. These chapters provide insight into some of the experimental findings, such as product distributions, the effect of pH, etc

Tautomeric Equilibria Studies by Mass Spectrometry

Tautomerism in organic chemistry has been extensively studied in condensed phase by spectrometric methods, mainly by IR and NMR techniques. Mass spectrometry studies start 40 years ago but just recently it has been recognized the importance of the mass spectral data for the study of tautomerism in the gas phase.
Mass spectrometry can provide valuable information in regard to tautomeric equilibria when studying mass spectra among the members of different families of organic compounds.
The relevance of the mass spectral data resides on several facts but there are two that are of key importance:
1-	Mass spectral fragmentation assignments should be tautomer specific since the corresponding abundances ratios are supposed to be correlated to the keto/enol contents.
2-	Ionization in the ion source is supposed to have no effect on the position of the equilibrium so that the results reflect the tautomers content in the gas phase previous to ionization.
Some of the carbonylic compounds do not exhibit noticeable tautomerism so the fragment abundances assigned to the enol form is very low or not measurable. Since enolization is more noticeable in the case of thio-derivatives (which correlates adequately with the oxygenated analogues), the study of their mass spectra is an interesting choice to reach some degree of generalization. 
In addition, experimental findings are supported by semiempirical theoretical calculations, which probed to be adequate not only for supporting tendency correlations among the members of a compound family but also to calculate heats of tautomerization in gas phase.
Reports using mass spectrometry for tautomerism are becoming less common. One of the reasons is that now it would appear that the interpretation of MS results is not as straightforward as it was once believed, even though in a recent review it was written that: “Mass spectrometry is the most informative and practical method for studying and identifying tautomers in the gas phase” [1]. 
In fact, mass spectrometry seems to be very informative for studying and identifying tautomers, because in this case external factors like solvents, intermolecular interactions, etc., can be excluded by transferring the tautomeric system into gas phase, where the process becomes truly unimolecular [1].
This review covers the study of Tautomerism by Mass Spectrometry in the last four decades. 
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Photochemistry of 1,3-Dicarbonyl Compounds: DNA Photodamage vs. Photoprotection

El objetivo principal de esta tesis es contrastar el papel de dichos compuestos 1,3-dicarbonilicos como agentes que dañan el ADN con respecto a su potencial fotoprotector. Primero, 5,6-dihidropirimidinas han sido derivatizadas utilizando el grupo fotolábil t-Bu cetona con el fin de estudiar la generación de radicales en C5 en un medio no acuoso. Después, el estudio por fotólisis de destello láser en ACN de los derivados 1,3-dicarbonilicos diseñados da lugar a la detección de los supuestos radicales 5,6-dihidropirimidin-5-ilo. Su caracterización muestra especies transitorias de vida larga y están centrados a 400-420 nm o 350-400 nm para los derivados 5,6-dihidrouridina o 5,6-dihidrotimidina, respectivamente. Además, la generación de radicales también se ha evidenciado mediante experimentos de fluorescencia en estado estacionario mediante el uso de una sonda profluorescente (AAA-TEMPO) que atrapa el radical. Por lo tanto, la irradiación de los derivados fotolábiles del ácido nucleico en presencia de AAA-TEMPO produce un aumento de la emisión, de acuerdo con la captura del radical C5 por la sonda paramagnética. La formación del aducto se ha confirmado mediante UPLC-HRMS. Los datos experimentales se han corroborado con cálculos teóricos ab initio CASPT2 // CASSCF. Segundo, otro derivado 1,3-dicarbonílico de la pirimidina se ha investigado. De hecho, el daño 5-formiluracilo (ForU) presenta características interesantes como potencial agente fotosensibilizador intrínseco del ADN. Por lo tanto, los estudios espectroscópicos revelan que ForU tiene una absorción en el rango UVA/UVB y también presenta un estado triplete excitado (3ForU *) con un tiempo de vida algunos micros y con una ET suficientemente alta como para fotosensibilizar la formación de los conocidos dímeros de pirimidina de tipo ciclobutano (CPDs) a través de una transferencia de energía triplete-triplete. Este proceso ha sido confirmado por medio de la síntesis de díadas modelo Thy-Thy y Cyt-Cyt, ya que su irradiación en presencia de ForU ha demostrado que producen CPDs. Asimismo, el estudio en ADN plasmídico permitió establecer la capacidad de ForU para inducir roturas de cadena simple y CPDs. A continuación, se ha desarrollo una nueva estrategia para la fotoprotección de moléculas bioactivas aprovechando la reactividad fotoquímica del tautómero 1,3-dicetona de la avobenzona (AB), un filtro del UVA. Los compuestos seleccionados son dos fármacos antiinflamatorios no esteroideos de uso tópico con propiedades fotosensibilizantes, (S)-ketoprofeno (KP) y diclofenaco (DF). El tautómero dicetona de la AB contiene dos restos fenacilo, que es un grupo protector fotolábil muy establecido. Por lo tanto, un diseño juicioso de una díada profármaco/profiltro permite la fotoliberación del fármaco y de su protector, la AB. La viabilidad de esta liberación controlada de los ingredientes se verificó en diferentes disolventes con carácter dador de H y viscosidad para simular la formulación tópica. Además, los estudios de fotólisis de destello láser en EtOH permiten la caracterización de una especie transitoria a 400-420 nm, la cual ha sido asignada al estado excitado triplete de AB-KP. Finalmente, se ha evaluado la fotoseguridad de la díada fotoactivable AB-KP. Los espectros de absorción transitoria de la díada AB-KP en ciclohexano muestra que la especie observada es el estado excitado triplete del KP y no el de la AB en su forma dicetona. El impacto de la díada sobre la membrana celular se ha abordado mediante irradiación UVA de soluciones de ácido linoleico en presencia de AB-KP y su potencial fototóxico se ha evidenciado mediante espectrofotometría UV-Vis revelando la formación de derivados hidroperóxidos diénicos conjugados del ácido linoleico. Sin embargo, la diada AB-KP no exhibe un potencial fotogenotóxico como lo demuestran los experimentos del ensayo comet, donde a diferencia del KP, la forma redonda noThe main objective of this thesis is to contrast the role of these 1,3-dicarbonyl compounds as DNA damaging agents to their photoprotective potential. Firstly, 5,6-dihydropyrimidines have been derivatized using a tert-butyl ketone photolabile group in order to study the generation of C5-centered radicals in non aqueous media. Then, laser flash photolysis study in acetonitrile of the designed 1,3-dicarbonyl derivatives yields the formation of the purported 5,6-dihydropyrimidin-5-yl radicals. Their characterization shows long lived transient species, which do not decay in the µs range and are centered at 400-420 nm or 350-400 nm for the 5,6-dihydrouridine or 5,6-dihydrothymidine derivatives, respectively. Moreover, radical generation has also been evidenced by steady state fluorescence experiments by using a profluorescent radical trap (AAA-TEMPO). Thus, irradiation of the photolabile nucleic acid derivatives in the presence of AAA-TEMPO results in an increased emission, in agreement with the trapping of C5 radical by the paramagnetic probe. Formation of the resulting adduct has been confirmed by UPLC-HRMS. Experimental data have been corroborated with ab initio CASPT2//CASSCF theoretical calculations. In a second chapter, another 1,3-dicarbonyl derivative of pyrimidine has been investigated. Indeed, 5-formyluracil (ForU) presents interesting features as a potential intrinsic DNA photosensitizing agent. Thus, spectroscopic studies reveal that ForU has not only an absorption in the UVA/UVB range, but also a triplet excited state (3ForU*) with a lifetime of some micros and with an energy high enough to photosensitize the well-known cyclobutane pyrimidine dimers (CPDs) through triplet-triplet energy transfer. This process has been confirmed by means of the synthesis of model Thy-Thy and Cyt-Cyt dyads, which after irradiation in the presence of ForU have been demonstrated to produce CPDs. Finally, the study extended to plasmid DNA allows establishing the ability of ForU to produce single strand breaks and CPDs. Next, the attention has been focused on the development of a new strategy for photoprotection of bioactive molecules taking advantage of the photochemical reactivity of the 1,3-diketo tautomer of the UVA filter avobenzone (AB). The selected bioactive compounds are two photosensitive topical non steroidal anti-inflammatory drugs, (S)-ketoprofen (KP) and diclofenac (DF). In this context, the diketo tautomer of avobenzone contains two phenacyl moieties, which are well-known photoremovable protecting groups. Thus, a judicious design of a pro-drug/pro-filter dyad allows the photorelease of the drug and its protecting shield, avobenzone. The viability of this controlled release of the active ingredients was checked in different solvents of different H donating properties and viscosity to simulate topical formulation.Plus, laser flash photolysis studies in ethanol allow characterization of a transient absorption band at 400-420 nm assigned to the triplet excited state of the dyad by comparison with that of the diketo form of AB. Finally, the photosafety of the photoactivatable AB-KP dyad has been assessed. The transient absorption spectra obtained for AB-KP dyad in cyclohexane showed the triplet excited state of KP and not that of the AB in its diketo form. The impact on the cellular membrane has been addressed by UVA irradiation of linoleic acid solutions in the presence of the dyad. Phototoxic potential of the dyad has been evidenced by UV-Vis spectrophotometry through the formation of the conjugated dienic hydroperoxides derived from linoleic acid. However, AB-KP does not exhibit a photogenotoxic potential as demonstrated by comet assay experiments, where by contrast with KP, the non damaged round shape of the cell is still observed after UVA irradiation.L'objectiu principal d'aquesta tesi és contrastar el paper d'aquests compostos 1,3-dicarbonil com a agents que danyen l'ADN respecte al seu potencial fotoprotector. En primer lloc, 5,6-dihidropirimidines han sigut derivatitzades utilitzant el grup fotolàbil t-Bu cetona amb la finalitat d'estudiar la generació de radicals centrats en C5 en un mitjà no aquós. Després, l'estudi de fotòlisi de flaix làser en acetonitril dels derivats 1,3-dicarbonil dissenyats produeix la formació dels suposats radicals 5,6-dihidropirimidin-5-il. La seua caracterització mostra espècies transitòries de vida llarga i estan centrats a 400-420 nm o 350-400 nm per als derivats 5,6-dihidrouridina o 5,6-dihidrotimidina, respectivament. Per tant, la irradiació dels derivats fotolàbils d'àcid nucleic en presència de AAA-TEMPO dóna com resultat un augment de l'emissió, d'acord amb la captura del radical C5 per la sonda paramagnètica. La formació del adducte resultant s'ha confirmat mitjançant UPLC-HRMS. Així mateix, les dades experimentals s'han corroborat amb càlculs teòrics ab initio CASPT2 // CASSCF. En un segon capítol, un altre derivat 1,3-dicarbonil de la pirimidina ha sigut investigat. De fet, el dany 5-formiluracil (ForU), presenta característiques interessants com a potencial fotosensibilitzador intrínsec de l'ADN. Per tant, els estudis espectroscòpics revelen que ForU té una absorció en el rang UVA/UVB i també presenta un estat triplet excitat (3ForU*) amb un temps de vida d'alguns micros i amb una ET prou alta com per a fotosensibilitzar la formació dels coneguts dímers de pirimidina de tipus ciclobutà (CPDs) a través d'una transferència d'energia triplet-triplet. Aquest procés ha sigut confirmat per mitjà de la síntesi de diades model Thy-Thy i Cyt-Cyt, que després de la irradiació en presència de ForU s'ha demostrat que produeixen CPDs. Finalment, l'estudi en ADN plasmídic ha permès establir la capacitat de ForU per a produir trencaments de cadena simple i CPDs. A continuació, s'ha desenvolupat una nova estratègia per a la fotoprotecció de molècules bioactives aprofitant la reactivitat fotoquímica del tautòmer 1,3-dicetona del filtre de l'UVA Avobenzone (AB). Els compostos seleccionats són dos fàrmacs antiinflamatoris no esteroïdals d'ús tòpic amb propietats fotosensibilizants, (S)-ketoprofè (KP) i diclofenac (DF). En aquest context, el tautòmer dicetona de l'AB conté dues fraccions fenacil, que es un grup protector fotolàbil ben conegut. Per tant, un disseny judiciós d'una diada profàrmac / profiltre permet el fotoalliberament del fàrmac i del seu escut protector, l'AB. La viabilitat d'aquest alliberament controlat dels ingredients actius s'ha verificat en diferents dissolvents de diferent caràcter dador d'hidrogen i viscositat per a simular la formulació tòpica. A més, els estudis de fotòlisi de flaix làser en EtOH permeten la caracterització d'una banda d'absorció transitòria a 400-420 nm, la qual ha sigut assignada a l'estat excitat triplet de AB-KP. Finalment, s'ha avaluat la fotoseguretat de la diada fotoactivable AB-KP. Els espectres d'absorció transitòria de la diada AB-KP en ciclohexà mostres que l'espècie observada és l'estat excitat triplet del KP i no el de la AB en la seua forma dicetònica. L'impacte sobre la membrana cel·lular s'ha abordat mitjançant la irradiació UVA de solucions d'àcid linoleic en presència de AB-KP. El potencial fototòxic de la diada s'ha evidenciat mitjançant espectrofotometria UV-Vis revelant la formació de derivats hidroperòxids diènics conjugats de l'àcid linoleic. No obstant açò, la diada AB-KP no exhibeix un potencial fotogenotòxic com ho demostren els experiments de l'assaig comet, on a diferència del KP, la forma redona no danyada de la cèl·lula encara s'observa després de la irradiació UVA.Aparici Espert, MI. (2018). Photochemistry of 1,3-Dicarbonyl Compounds: DNA Photodamage vs. Photoprotection [Tesis doctoral no publicada]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/105782TESI

DNA/RNA: Building Blocks of Life Under UV Irradiation

International audienceDuring the last 10 years, intense experimental and theoretical work has proven the existence of ultrafast nonradiative decay routes for UV-excited monomeric nucleic acid bases, accounting for their high photostability. This mechanism has been explained by the occurrence of easily accessible conical intersections connecting the first excited ππ* state with the ground state. However, recent studies of substituent and solvent effects indicate that the situation is more complicated than what was initially thought, notably by the presence of dark excited states. Moreover, the actual shape of the excited-state potential energy surface may induce nonexponential dynamics. Further efforts are needed in order to clarify how various environmental factors affect the structural and dynamical aspects of the nucleic acid base excited states

Singlet Oxygen Oxidation of Guanine, 9-Methylguanine and Guanine-Cytosine Base Pair: Dynamics and Kinetics Revealed by Parallel Gas- and Solution-Phase Experiments and Computations

Singlet oxygen (1O2) oxidatively generated damage of DNA gives rise to mutagenesis, carcinogenesis, and cellular death. Guanine is the most susceptible DNA target of 1O2. The related process has been studied over three decades but the mechanism has remained elusive. My thesis research has focused on reaction mechanism, dynamics and kinetics of 1O2 oxidation of guanine, 9-methylguanine and guanine-cytosine base pair, from the gas-phase bare ions, through hydrated clusters, to aqueous solution. Various techniques have been adapted in the work, including 1O2 generation and detection, guided-ion beam tandem mass spectrometry, gas-phase ion-molecule scattering, and on-line spectroscopy and mass spectrometry measurement of solution kinetics. Experimental measurements, corroborated by electronic structure calculations, Rice-Ramsperger-Kassel-Marcus (RRKM) theory and direct dynamics trajectory simulations, have provided insights into the 1O2 oxidation chemistry of guanine. Four projects have been completed, and each of which is described below. In the first project, ion-molecule scattering mass spectrometry was utilized to capture unstable endoperoxides in the collisions of hydrated guanine ions (protonated or deprotonated) with 1O2 at ambient temperature. Theoretical calculations have strongly supported an intermediate structure of 5,8-endoperoxide rather than 4,8-endoperoxide was proposed in literature. Protonation and deprotonation of reactants in the gas phase, vis-à-vis acidic and basic media in solution reactions, lead to different oxidation chemistries starting from initial stage. This project has pieced together reaction mechanisms and dynamics data concerning the early stage of 1O2 induced guanine oxidation, which is missing from conventional condensed-phase studies. In the second experiment of this thesis, gas-phase dry and monohydrated 9-methylguanine (9MG) was utilized as a model compound to examine the early stage oxidation mechanism and dynamics of the guanine nucleoside. Different levels of theory, including Multi-referential CASSCF and CASMP2, were applied for a reliable description of the early-stage reaction potential surface (PES). The oxidation of protonated 9MG is initiated by the formation of a 5,8-endoperoxide via a concerted cycloaddition as protonated guanine. In contrast, the initial stage of deprotonated 9MG oxidation switches to an addition of O2 to the C8 position only. The comparison between the 1O2 oxidation of ionized guanine and 9-methylguanine indicates that the N9-substitution not only affects the reaction mechanism but inhibits the reactivity of guanine toward 1O2. In the third project, a solution-phase kinetic and mechanistic study of 1O2 oxidation of guanine and 9MG was examined at pH 3.0, 7.0 and 10.0, respectively. Oxidation products and the branching ratio were determined, with each structure inferred from collision-induced dissociation (CID) mass spectra. In basic and neutral solutions, the oxidation products of guanine and 9MG are dominated by spiroiminodihydantoin (Sp), whereas in acidic solution guanidinohydantoin (Gh) is the favored product, showing strong pH dependence of oxidation. gem-diol intermediate, which serves as the precursor for the formation of Gh, was detected. On the basis of solution compositions at each pH, first-order rate constants for individual oxidizable species were extracted. That is 3.2 - 3.6 ´ 106 M-1∙s-1 for deprotonated guanine, 1.1 ´ 106 and 4.6 - 4.9 ´ 107 M-1∙s-1 for neutral and deprotonated 9MG, respectively. Guided by density functional theory-calculated reaction potential energy surfaces, transition state theory (TST) was applied to evaluate the kinetics of the 1O2 addition to guanine and 9MG. The comparison of TST predictions with experiment assures that initial 1O2 addition is the rate-limiting for oxidation, and all of the end products evolve from ensuring endoperoxides and/or peroxides which form at an efficiency of £ 2.5% based on previous measurements of the same systems in the gas phase. In the last project, an experimental and trajectory study was reported, focusing on the 1O2 oxidation of gas-phase deprotonated guanine-cytosine base pair [G·C – H]– that is composed of 9HG·[C – H]– and 7HG·[C – H]– (pairing 9H- or 7H-guanine with N1-deprotonated cytosine), and 9HG·[C – H]–_PT and 7HG·[C – H]–_PT (formed by intra-base-pair proton transfer from guanine N1 to the N3 of [C – H]–). Guided-ion-beam mass spectrometry was used to measure the conformer-averaged product and cross section for [G·C – H]– + 1O2. 1O2 collision dynamics with each of the four conformers was simulated at B3LYP/6-31G(d), to explicate conformation-specific reactivities and changes upon and after oxidation. Trajectories showed that 9HG-containing base pairs favor stepwise formation of 4,8-endoperoxide of guanine, whereas 7HG-containing base pairs prefer concerted formation of guanine 5,8-endoperoxide. Oxidation entangles with intra-base-pair proton transfer, and prefers to occur during the time when the base pair adopts a proton-transferred structure. Guided by trajectories, reaction PESs were established using spin-projected density functional theory. PESs indicate that proton-transferred base-pair conformers have lower barriers for oxidation than non-proton-transferred counterparts

Mass Spectrometry of Biomolecules. Part A: Gas-Phase Thermochemical and Structure Determinations of Mononucleotides. Part B: Analysis of Hydrophobic Peptides and Proteins by Matrix -Assisted Laser Desorption /Ionization Time -Of -Flight Mass Spectrometry.

The use of mass spectrometry for thermochemical and structural determinations of mononucleotides is presented in Part A of this work, and the analysis of hydrophobic peptides and proteins are presented in Part B of this work. The goal of Part A is to examine thermochemical and structural properties of (deoxy)nucleoside 5\u27- and 3\u27-monophosphates. Part A consists of three groups of experiments. The first set of experiments utilized the kinetic method with a fast-atom bombardment source and a double focusing sector mass analyzer. Conformational analysis and semi-empirical calculations of mononucleotides were performed for the second set of experiments. The third set of experiments employed hydrogen/deuterium exchange reactions with an electrospray ionization source and a Fourier transform ion cyclotron resonance mass spectrometer. These data are significant because knowledge of the gas-phase thermochemical properties and structures of nucleobases, nucleosides and nucleotides is crucial in understanding gas-phase reactions of oligonucleotides and DNA observed in current mass spectrometric techniques. The goal of Part B was to develop techniques for the mass spectral analysis of hydrophobic peptides and proteins using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS). Hydrophobic peptides are difficult to characterize using mass spectrometric methods because they are often insoluble in aqueous solutions, which are typically required for mass spectral analysis. Two approaches were demonstrated. The first approach used organic solvents to dissolve the analyte and matrix to generate signal from a model hydrophobic peptide. The second approach allows for the simultaneous analysis of both hydrophobic and hydrophilic components of the sample mixture by using surfactants to solubilize the hydrophobic components aqueous solutions. Mixtures of hydrophobic and hydrophilic peptides were characterized using surfactant-aided (SA) MALDI-MS, and it is demonstrated that all components are detectable once the surfactant is included in the sample solution. The applicability of SA-MALDI-MS in peptide mapping experiments is demonstrated on a tryptic digest of myoglobin and cytochrome c (two proteins), and on a tryptic digest of CP 43 and CP 47, two hydrophobic polypeptides from the Photosytem II membrane complex of spinach

New Computational Methods and Developments for Molecular Response Properties in Condensed Matter

In this thesis we are aimed by the purpose of describe three important cases of chemical interest and show how theoretical and computational methods can be useful, even needful to explore and solve very significative applications. The commons theme of this work are represented by the well known Density Functional Theory and the Polarizable Continuum Model used for all the cases reported . As we will able to recall the first is one of the most diffused theoretical approach in computational chemistry studies whenever the electronic structure has to be solved. The second one represents a wide diffuse model which is able to describe with good accuracy molecular interactions in condensed matter. Both of them provide the most common computational configuration in organic, and oreganometallic studies. In this thesis we are going to describe few examples which spread from the study of condensed matters under extremely high pressure to a biological application on DNA nucleobase systems, moving through some typical organometallic problems. Focusing on our issues we are going to present a new computational QM method for the study of structural properties (i.e. equilibrium geometry) of molecular systems under very high pressure. The procedure is based on the Polarizable Continuum Model , usually used to study molecular solutes under standard pressure conditions. The presented development considers two critical items: the definition of the pressure and the elaboration of an analytical code for the calculation of molecular gradient. The method has been developed at HF and DFT levels, with computational costs comparable with those of similar calculations in vacuo. The numerical examples regarding the equilibrium geometries and conformational energies (DFT level) of 1,3-butadiene under high pressure give an indication of the potentialities of the approach and of the problems to which it may be applied. The next argument regards several application in the field of inorganic chemistry. We will shortly describe a computational procedure where we investigate some spectroscopical properties of some luminescence silver complexes. In this, we will describe a time dependent density functional study of several excited states. Moreover we will study the correlation between stretching vibration and Mulliken charges in some rhodium complexes. But most of this section will be dedicate to a very practical application in chemistry that is the chemical reaction path determination. Aimed by unclear experimental evidences provided by the catalytic investigation of an half sandwich Ru(II) complex, we performed a deep exploration of the mechanism through which the pre catalysts operate. Several data obtained by high-resolution MS (ESI) have been explained by a combined ”Density Functional /Polarizable Continuum Model” study. The results reveal that the complexes containing PNH2 operate through a bifunctional mechanism analogous to that proposed for diamines and amino alcohol ligands, but with some new aspects that are important to point out. Finally an efficient computational method has been identified which uses Density Functional Theory, Polarizable Continuum Models with a modified UFF cavity and Boltzmann weighting of tautomers to predict the site-specific and global pKa of DNA nucleobases and their oxidation products. The method has been used to evaluate the acidity of Gh and Sp, two highly mutagenic guanine oxidation products. The trend observed for the pKa values of Gh (9.64 and 8.15) is consistent with the experimentally observed values for guanidine cation (13.7) and hydantoin (9.16). The pKa1(calc) value for deprotonation of Sp cation (Sp+-->Sp) is very close to the experimentally observed pKa1 for 8-oxoG and is consistent with the similarity in their structures. The data suggest that the imide (N7) proton in Sp is considerably more acidic than that in Gh, possibly due to the presence of the through-space electronic e ects of the carbonyl group located at C6. This difference in the acidity of Gh and Sp may be an indication of their potential toxicity and mutagenicity in vivo and remains a fertile area for experimental study