Rozprawy doktorskie na temat „Theoretical Study - Thermochemistry - Molecules”

Phosphate transfer reactions are catalyzed by a large number of enzymes comprising kinases, mutases and phosphatases. These enzymes play a fundamental role in controlling numerous life processes and it is therefore important to understand the origin of their potent catalytic power. An example is the Ca2+-ATPase. In the E2P-state, this enzyme hydrolyses the phosphorylated amino acid, Asp351, 106 to 107 fold faster than when the model compound, acetyl phosphate, is hydrolyzed in in water.This thesis explores the catalytic power of Ca2+-ATPase using theoretical method based on quantum mechanics. The studies of this protein were made by performing quantum chemical calculations on models of phosphoric monoesters as well as on the explicit reaction pathway of the hydrolysis. The studies show the importance of electrostatic interactions as well as the role of the specific active site residue Glu183, a residue that acts as a base in the catalytic pathway. Furthermore, based on the calculations, the interpretation of the experimental infrared spectrum of the E2P-state of Ca2+-ATPase, could be further elucidated as well as modified.The experimental infrared spectrum of phosphoenol pyruvate in water has also been elucidated through calculations. This molecule is converted into pyruvate in the last step of the glycolytic pathway, a reaction that is catalyzed by pyruvate kinase (PK). These results further enabled the interpretation of the experimental spectrum of the PK's catalytic reaction.These two processes, the transport of Ca2+ into the sarcoplasmatic reticulum against a concentration gradient and the glycolysis, are two important actions of a muscle cell.
At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 2: Epub ahead of print. Paper 3: Submitted. Paper 4: Manuscript. Paper 5: Manuscript.

In this work we have investigated the electronic properties of several types of molecular systems involving a metallic element. Our motivation for such applications on metallic compounds was to obtain an accurate description of close lying electronic states, in which the relativistic effects of heavy atoms are known to be important. Thus various approaches and methods have been employed to treat these effects, including the multi-configurational method, with atomic pseudopotentials and large basis sets. In the first study, we have determined the properties of the low lying electronic states of the diatomic compounds MX, whose combinations in the solid phase produce ionic semi-conductor materials with piezoelectric properties. Based on highly correlated ab initio calculations, we have elucidated the common properties of the low lying electronic states of these diatomic compounds with eight valence electrons, which can be considered as precursors for piezoelectric effects in their solid phase. Based on our electronic structure calculations, we could identify among these diatomic compounds those who could lead to good candidates for piezoelectric effects. As the second application, we have determined the electronic structure and the spectroscopic constants for the ground state of the HZnF molecule and for the low lying electronic states of its diatomic fragments. This application was initiated and motivated by interesting and puzzling results on the close system HZnCl. Comforted by our experience with the previous studies, we used the pseudopotentials approach to obtain an accurate description of the low lying states of ZnH which could be satisfactorily compared with existing data. Next, the ZnF and ZnCl diatomic molecules have been studied with the same ansatz to reveal the properties of so far unknown electronic states. Finally, the potential energy surface of the ground state of HZnF has been determined, and several spectroscopic properties have been deduced

In this thesis, we focus on the structural identification of the interface using surface enhanced Raman spectroscopy (SERS) and inelastic electron tunnelling scattering (IETS). Two different molecular junctions, namely gold/ trans-1,2-bis (4-pyridyl) ethylene/gold junction and gold/4,4'-bipyridine/gold junctions in various conditions were studied and the corresponding configurations were determined. The enhancement in SERS was also studied by employing the time-dependent density functional theory. Furthermore, we studied some properties of the interface, such as the stability of the adsorbates and charge transfer properties of molecular junctions. The decrease in the stability of molecules was found when adsorbed on metallic surface and trapped in metallic junctions. Our studies explained several puzzles and by rational design, more stable molecular devices were obtained.

In this thesis, different organic and organometallic molecules with interest for optoelectronic applications have been studied from a computational standpoint. The work presented in this thesis belongs to the molecular quantum chemistry field and in particular to the investigation of the low- lying electronic excited states involved in the target photophysical processes. Chapter 1 is devoted to the study of the absorption process of several organic dyes with potential application in dye-sensitized solar cells (DSSCs). In particular, the influence of the nature of the π- bridge in donor-acceptor dyes has been investigated. The photophysical properties of the dyes are rationalized based on geometrical characteristics and their electronic structure. The charge transfer nature of the optical state has also been investigated with several computational tools. Solvent effects on the absorption of the dye have also been considered and simulated to give an explanation to experimental observations. Chapter 2 deals with phosphorescent Ir(III) complexes that have interest as triplet emitters for organic light-emitting diodes (OLEDs). All the studies presented in this chapter have been done in collaboration with the experimental group of Prof. Inamur Rahman Laskar at the Birla Institute of Technology and Science (BITS) in Pilani, India, and his coworkers. After our first collaborations, we became interested in Ir(III) complexes exhibiting aggregation induced emission (AIE). This is a very interesting phenomenon where the emission intensity is enhanced in the solid state compared to dilute solution. Systems presenting the AIE are very attractive for a wide range of applications other than OLEDs. In this chapter, a section is devoted exclusively to analyze the evolution of this field and the principal mechanisms proposed to explain this phenomenon. It does not pretend to be a complete review from the literature, but rather a critical assessment with personal thoughts on the subject. As for the results, we were interested to understand how the photophysical properties are influenced by the presence of different ligands on the Ir(III) complexes and by the presence of intermolecular interactions. The absorption and emission of the studied complexes has been characterized and different approaches have been taken to give an explanation to experimental observations from our partners. In Chapter 3 a study on the photophysics of sulfur bridged naphthalene dimers is presented. This work was partially done during a research stay in the group of Prof. Mario Barbatti at the Institut de Chimie Radicalaire in Marseille (France). Herein we were interested in explaining the dependence of the photoluminescence of the aforementioned dimers on the oxidation state of the sulfur atom at the bridge. Experimental work on these compounds and related ones had been previously reported. An explanation for the different luminescence however was not given for the naphthalene dimers. In this chaper we have tackled this problem by characterizing the excited states and crossings between the ground and first excited state PESs.
En aquesta tesi s’han aplicat els mètodes de la química quàntica molecular per estudiar des del punt de vista de la fotofísica, les característiques principals de l’estructura electrònica d’un conjunt de molècules orgàniques i organometàl·liques amb interès per aplicacions optoelectròniques. En particular, s’han estudiat per una part colorants orgànics amb propietats òptiques adients per ser emprats com a sensibilitzadors en cel·les solars sensibilitzades amb colorant (DSSCs en anglès). En una altra direcció, s’han investigat una sèrie de complexos d’Ir(III) amb potencial aplicació com a compostos emissors en díodes orgànics emissors de llum (OLEDs en anglès). Aquests complexos també presenten el fenomen d’emissió induïda per agregació (AIE en anglès), en el que la intensitat d’emissió augmenta en l’estat sòlid en comparació a la feble o inexistent luminiscència mesurada en dissolucions diluïdes. Els sistemes que presenten AIE son molt atractius per un gran varietat d'aplicacions. En aquesta tesi, una secció s’ha dedicat exclusivament a analitzar l’evolució d’aquest camp i dels principals mecanismes proposats per explicar el fenomen de l’AIE, aportant una valoració crítica amb opinions personals sobre el tema en qüestió. Finalment, aquest treball inclou també la investigació computacional de les propietats fotofísiques de dímers de naftalè enllaçats per un pont basat en sofre, amb potencial aplicació en dispositius orgànics fotovoltaics (OPVs en anglès) i OLEDs. En aquest cas estàvem interessats en explicar la dependència de la fotoluminescència dels dímers estudiats amb l’estat d’oxidació de l’àtom de sofre del pont que connecta els monòmers de naftalè. Aquesta qüestió s’ha abordat caracteritzant els estats excitats i els encreuaments entre l’estat fonamental i el primer estat excitat.

Titanium dioxide (TiO2) has been widely used in industry as a photocatalyst due to its superior photoactivity, high photo- and chemical-stability, non-toxicity, abundance, and low cost. Many of its applications in clean energy generation and environmental remediation involve interactions between organic species and TiO2 materials. Such interactions not only depend on the intrinsic properties of TiO2, but also on its surfaces structure. Specifically, the capacity of the TiO2 surface to adsorb organic species is vital for TiO2 photocatalytical performance. Understanding the adsorption properties of organic compounds on various crystalline TiO2 surfaces is essential for further technological development. In this project, theoretical studies initially demonstrated that TiO2 is the most photoactive all Ti-O based materials. A combined photoelectrochemical (PEC) and theoretical study was conducted to understand the adsorption properties of organic molecules on anatase (001) and rutile (111) TiO2 surfaces. PEC measurements can provide quantitative thermodynamic and kinetic information on the adsorption properties of organic species on the TiO2 surface under operational, practical conditions. The theoretical studies provide further information on interactions at the atomic level.
Thesis (PhD Doctorate)
Doctor of Philosophy (PhD)
Griffith School of Environment
Science, Environment, Engineering and Technology
Full Text

Cette thèse présente des recherches théoriques sur la diffusion électronique avec deux molécules polyatomiques d’intérêt pour la pollution atmosphérique, les molécules NO2 et N2O. En ce qui concerne la molécule NO2, nous étudions l’excitation vibrationnelle entre les niveaux les plus bas des états électroniques fondamentaux de cette molécule. Le calcul est effectué par une approche qui combine l’approximation des modes normaux pour les états vibrationnels du NO2, le code de la UK R-matrice pour obtenir la électron-molécule S-matrice pour les géométries fixes de la cible et la « vibrational frame transformation » pour évaluer le matrices de diffusion pour les transitions vibrationnelles. En ce qui nous concerne, la sections efficaces d’excitation vibrationnelle calculée dans cette thèse est rapportée pour la première fois pour la molécule NO2. L’estimation de l’incertitude des résultats est ainsi réalisée pour valider la présente approche théorique. De même, les sections efficaces d’excitation vibrationnelle de la molécule de N2O sont déterminées. Les résultats obtenus sont en accord raisonnable avec les données expérimentales. Les rate coefficient d’excitation vibrationnelle sont obtenus à partir des sections efficaces pour la plage de températures de 10K à 10000 K. La structure rotationnelle des molécules neutres cibles est négligée dans la présente approche, ce qui implique que les sections efficaces et les rate coefficient obtenus doivent être considérés comme une moyenne sur états de rotation initiaux et additionnés sur les états de rotation finaux des niveaux vibrationnels initial et final correspondants. Enfin, l’attachement dissociatif aux électrons (DEA) du NO2 est également étudié dans cette thèse. Ce processus est en concurrence avec l’excitation vibrationnelle dans la plage d’énergie de diffusion en dessous du premier état électronique excité de la cible. La DEA sections efficaces est calculée par la méthode basée sur la théorie de Bardsley-O’Malley développée pour les molécules diatomiques et généralisée aux molécules polyatomiques complexes par Chi Hong Yuen et al. par la suite par rapport aux mesures expérimentales disponibles. Les résultats obtenus pourraient être utilisés dans la modélisation du plasma pour le contrôle et la réduction de la pollution atmosphérique
This thesis presents theoretical investigations on electron scattering with two polyatomic molecules of atmospheric pollution interest, the NO2 and N2O molecules. Regarding the NO2 molecule, we study the vibrational excitation between the lowest levels within the ground electronic states of this molecule. The calculation is carried out by an approach that combines the normal modes approximation for the vibrational states of the NO2, the UK R-matrix code to obtain electron–molecule S-matrix for fixed geometries of the target and the vibrational frame transformation to evaluate the scattering matrices for vibrational transitions. To our knowledge, the vibrational excitation cross section calculated in this thesis is reported for the first time for NO2 molecule. The uncertainty estimation of the results is thus performed to validate the present theoretical approach. Similarly, the vibrational excitation cross sections of N2O molecule are determined. The obtained results are in reasonable agreement with experimental data. The rate coefficient of vibrational excitation are obtained from the cross-sections for temperatures in the 10–10000 K range. The rotational structure of the target neutral molecules is neglected in the present approach, which implies that the obtained cross-sections and rate coefficients should be viewed as averaged over initial rotational states and summed over final rotational states of the corresponding initial and final vibrational levels. Finally, the dissociative electron attachment (DEA) of NO2 are also studied in this thesis. This process competes with vibrational excitation at the scattering energy range below the first electronic excited state of the target. The DEA cross section is calculated by the method based on the Bardsley-O’Malley theory developed for diatomic molecules and generalized to complex polyatomic molecules by Chi Hong Yuen et al. afterwards compared with available experimental measurements. The obtained results could be used in plasma modeling for control and reduction of atmospheric pollution

This work tries to show the significant competence and functionality of density functional theory (DFT) and time-dependent density functional theory (TD-DFT) as theoretical approaches, supporting experimental measurements in various fields of physics from astrophysics to surface science, to study the electronic structure and spectroscopic properties of molecules and clusters: Silicon nanocrystals: Due to their optical properties, silicon nanocrystals have attracted considerable attention in astrophysics. In this work, the optical properties of H-passivated silicon nanocrystals are determined by the energetics of the frontier orbitals and their dependence on the deformation in the relaxed excited state, using DFT and TD-DFT. The Jahn-Teller effect in the lowest excited state results in a distortion toward tetragonal symmetry, contributing significantly to the red shift of the photoluminescence (PL) spectra. Therefore, the deformation in the relaxed excited state consists of a symmetry conserving part and of a symmetry-breaking distortion from Td toward D2d. For nanocrystals up to a diameter of 1.5 nm, we project the deformations at the minima of the excited state potential surface onto the different symmetries, allowing for a discrimination of the respective contributions to the total Stokes shift. The results show a quantitative agreement between the TD-DFT calculations of PL gap and the observed PL energies better than 0.2 eV. It is also seen that the large PL linewidth is the fundamental property of each cluster, not of ensemble average over clusters of different size. 2,3-Benzofluorene: We have presented new theoretical results on the absorption spectroscopy of 2,3-benzofluorene (Bzf) for the transition from the ground state, S0, to the first electronically excited singlet state, S1, to support the measurements of S1(1A´) <- S0(1A´) absorption spectrum of jet-cooled Bzf. The potential energy surfaces (PESs) of the S(n=0,1,2) states of Bzf have been investigated with calculations based on DFT and TD-DFT. At the B3LYP/TZ level of theory, TD-DFT does not deliver a realistic difference between the excited S1 and S2 potential energy surfaces, a problem which can be avoided by introducing a reference geometry (q*) where this difference coincides with the observation. In this geometry, an expression for the Herzberg-Teller corrected intensities of the vibronic bands is proposed, allowing a straightforward assignment of the observed a′ modes below 900 cm−1, including realistic calculated intensities. In spite of the difficulties caused by the small energy difference between the S1 and S2 states, we have obtained a reasonable theoretical absorption spectrum based on a TD-DFT approach applied to the slightly modified molecular geometry. Although the agreement between the theoretical and observed spectra is very good only for vibrational modes with frequencies lower than 900 cm−1, we consider our calculations to be the best approach to an ab initio study realized for Bzf until now since only parametrized force fields had been used before. (Ni–, Pd–, Pt–) Phthalocyanine: We studied the HOMO–LUMO gap shrinking in order to investigate the tip-induced polarization in scanning tunneling spectroscopy (STS) of d8 (Ni, Pd, and Pt) phthalocyanines. By means of DFT, the electronic structure and vibronic properties of single neutral NiPc, PdPc, and PtPc and their singly and doubly ionized cations and anions have been calculated. Interestingly, the position of the HOMO decreases systematically with increasing the atomic number of the central metal atom. The first ionization energies of neutral molecules increase by changing the central metal atom, while the electron affinities remain constant. This causes an increase in the HOMO–LUMO gap. These results show a clear correlation to experimental observations. Furthermore, partitioning of the reorganization energy, corresponding to the photoelectron spectra of the first and second ionizations of studied molecules, into normal mode contributions shows that the major contributions are due to several vibrational modes with a1g symmetry and energies lower than 1600 cm−1. The results reveal that the reorganization energy due to the singly positive ionization in the studied molecules is about one order of magnitude less than other reorganization energies, which makes these metal–phthalocyanines more attractive as electron donor for intramolecular electron transfer in electron acceptor–donor systems.

Dans cette thèse, j'ai étudié théoriquement l'interaction d'atomes et de molécules avec des impulsions laser brèves, intenses et basse-fréquences. En insistant sur la phase spectrale, nous utilisons la génération d'harmoniques d'ordres élevés comme processus auto-sonde pour étudier les dynamiques attoseconde. Nous résolvons l'équation de Schrödinger avec des modèles simples, numériquement ou en utilisant une théorie semi-analytique, nous permettant ainsi d'obtenir des informations approfondies sur les processus physiques mis en jeu, à travers des explications intuitives, tout en gardant une propension prédictive. Avec des outils développés pour analyser nos résultats numériques, nous étudions d'abord la dynamique d'ionisation dans une molécule modèle telle que N2. Puis, en réexaminant les interférences à deux centres, nous mettons au jour un comportement très intéressant, lié à l'habillage de l'état fondamental par le laser, et confirmé par des développements analytiques. Nous prédisons la possibilité d'observer ce phénomène expérimentalement par l'intermédiaire des interférences de chemins quantiques. Enfin, nous étudions les effets de la vibration des noyaux dans les molécules diatomiques en couplant le mouvement des électrons avec celui des noyaux. Nous montrons que pour de telles impulsions laser, l'excitation vibrationnelle de la molécule neutre peut être induite par effet Raman. Nous invalidons alors une théorie non corrélée, nommée Lochfraß, qui base son interprétation sur la dépendance du rendement d'ionisation avec la distance internucléaire. Enfin, nous proposons de prolonger à un modèle analytique standard la notion de potentiel d'ionisation dans les molécules
In this thesis, I studied theoretically atoms and molecules interacting with a short, low-frequency and intense laser pulse, in the typical regime of high-order harmonic generation (HHG). We use HHG as a self-probe process to examine electronic and nuclear dynamics on the attosecond scale with Ångström resolution, insisting on the spectral phase. By using simple models, we are able to solve extensively the time-dependent Schrödinger equation, either numerically or with the Strong Field Approximation (SFA). Our models give us valuable physical insights on the underlying dynamical processes and intuitive explanations while keeping a predictive propensity. With efficient tools developed to analyze our numerical results, we first investigate the ionization dynamics through a shape resonance in a model molecule such as N2. Secondly, we take another look at two-center interferences, and uncover a very interesting behavior which is linked to the dressing of the electronic ground-state by the laser field. It is indeed confirmed by additional developments of molecular SFA. We predict that this behavior can be observed experimentally using quantum path interferences. Finally, we examine the effect of nuclear vibration in diatomic molecules by coupling consistently electronic and nuclear motions. Our results show that with short pulses, nuclear motion in the neutral molecule can be triggered by Raman effect. Thus, we invalidate an uncorrelated theory, so called Lochfraß, which focuses on the dependence of the ionization yield with internuclear distance as an explanation. Lastly, we question the extension within SFA of the notion of ionization potential in molecules

Quand des alumines de transition (gamme et delta) sont prétraitées à hautes températures (au dessus de 400°C) des « défauts » de surface avec une très forte acidité de Lewis sont formés. Leur densité atteint un maximum pour une température de prétraitement de 700°C, puis elle décroit à plus haute température. En combinant des calculs DFT (réactivité et spectroscopie) et des expériences (IR, RMN, DRX et études de réactivité) la structure, la stabilité et la réactivité de ces site envers des petites molécules sondes (N2, H2 et CH4) ont été étudiés en tenant compte de l’hydratation de la surface (densité d’OH, qui décroit en fonction de la température de prétraitement). Cette approche a démontré que i) N2 s’adsorbe sélectivement sur des sites AlIII (coordination), alors que H2 et CH4 sont dissociés sur des sites Al-O, en particulier sur les sites AlIII, avec formation d'espèces Al-H et Al-CH3 et de groupements OH (dissociation hétérolytique), ii) l’hydratation a deux rôles : stabiliser la surface (110) qui contient ces sites AlIII et augmenter la basicité de certains atomes d’oxygène de surface et en conséquence leur réactivité envers H2 et CH4. Cela explique la température optimale de prétraitement de 700°C (la densité de AlIII est augmentée sans changement structural de l’alumine ; au dessus de cette température l’alumine adopte une phase cristalline plus stable, théta et enfin alpha, qui ne présentent pas ces sites AlIII). Finalement, dans le contexte de systèmes catalytiques supportées sur alumine, ces défauts sont proposés comme élément clef pour la génération du site actif de CH3ReO3/alumine-gamma, un catalyseur de métathèse hautement efficace
When pre-treated at high temperatures (above 400 °C), very strong Lewis acid sites (“defect sites”) are formed on transition alumina (gamma and delta) with an optimal site density found for pre-treatment temperatures of ca. 700 °C, before their density decreases with higher thermal treatment. Combining periodic DFT calculations (reaction pathways and spectroscopy) and experiments (IR, NMR, XRD and reactivity studies) the structure, the stability and the reactivity of these sites towards small probe molecules (N2, H2 and CH4) was investigated taking into account hydration of the surface (OH density, which decreases function of thermal pre-treatment). This approach showed that i) N2 adsorbs selectively on AlIII sites (coordination), while H2 and CH4 are dissociated on Al-O sites, in particular on AlIII, to form Al-H and Al-CH3 species, respectively, along with OH-groups (heterolytic splitting). Ii) Hydration has a dual role: stabilizing the (110) surfaces exhibiting these AlIII sites and increasing the basicity of some O atoms and thereby their reactivity towards H2 and CH4, hence the optimal pre-treatment temperature (increasing the AlIII site density without changing the structure of alumina; above 700 °C alumina evolves towards theta and alpha phases, which do not present these sites). Finally, in the context of supported alumina systems, these defect sites are proposed to be the key to generate the active sites of CH3ReO3/gamma-Al2O3, a highly efficient alkene metathesis catalyst

Zeeman deceleration is an experimental technique which allows for the manipulation of open-shell atoms and molecules in a supersonic beam thus producing mK-cold, velocity-tunable beams of particles in selected quantum states. The method relies on the Zeeman interaction between paramagnetic particles and time-varying, inhomogeneous magnetic fields generated by pulsing high currents through an array of solenoid coils. This thesis describes the construction and implementation of a supersonic beam setup including a 12-stage Zeeman decelerator. The Zeeman decelerator follows an original design that makes it possible to replace individual deceleration coils. Using ground-state hydrogen atoms as a test system, it is shown that the transverse acceptance in a Zeeman decelerator can be significantly increased by generating a rather low, temporally varying quadrupole field in one of the solenoid coils. An electron-impact source was constructed and optimised enabling, for the first time, the Zeeman deceleration of metastable helium atoms in the 23S1 state, with an up to 40 % decrease in the kinetic energy of the beam. It is shown that the pulse duration for electron-impact excitation needs to be matched to the acceptance of the decelerator in order to attain a good contrast between the decelerated and undecelerated parts of the beam. Experimental results are rigorously analysed and interpreted using three-dimensional numerical particle trajectory simulations. A phase-space model provides, for the first time, a means to estimate the six-dimensional phase-space acceptance in a Zeeman decelerator and to find optimum parameter sets for improved Zeeman deceleration schemes. The approach also reveals a hitherto unconsidered velocity dependence of the phase stability which is ascribed mainly to the rise and fall times of the current pulses that generate the magnetic fields inside the deceleration coils. In the future, it is planned to combine the Zeeman decelerator with a source of cold atomic and molecular ions to study chemical collisions at low temperatures. A hybrid magnetic guide consisting of permanent magnet assemblies (Halbach arrays) in hexapole configuration and a set of current-carrying wires is proposed and simulated as an interface between these setups. The design promises very efficient velocity selection, a high degree of quantum-state selection and a nearly complete removal of residual carrier gas. Prospects for using magnetic hexapole focusing in front of the Zeeman decelerator are discussed. The work represents a major step towards the study and control of chemical reactivity of paramagnetic species in the low-temperature regime and it will help in the testing of fundamental chemical reaction theories.

Collisions with He+ are an important pathway for the destruction of complex organic molecules in the interstellar medium (ISM). We have carried out dissociative charge transfer reactions of He+ with two oxygen containing organic molecules, ubiquitous in ISM: dimethyl ether (DME, CH3OCH3 ) and methyl formate (MF, HCOOCH3). Since they have a prebiotic relevance, several models were developed to explain how these molecules are formed and destroyed in the ISM. The reactions have been investigated by using the home-built Guided-Ion Beam Mass Spectrometer (GIB-MS) apparatus. Absolute cross sections and branching ratios of the products have been measured as a function of the collision energy in the hyperthermal energy range (i.e. from about 0.1 eV to 7 eV). The presence of the molecular ion was not observed among the products for these reactions, which means that the nascent DME and MF radical cations are formed in a dissociative state. Insights on both the charge transfer processes have been obtained by investigating the nature of the non-adiabatic transitions between the reactant and product potential energy surfaces (PES). The PES has been represented by using a semi-empirical method to model the inter-molecular interactions. To explain the experimental evidence, two excited states of DME and MF radical cations have been invoked: He+ captures an electron from inner valence orbitals of both the organic molecules, having binding energies ~10 eV higher than the HOMO. An improved Landau-Zener-Stückelberg model has been developed to obtain the total integral cross-section to be compared with the experimental results. Inter-molecular interaction and electron densities of the orbitals involved in the reaction turned out to be key points to describe the dynamics of the two studied dissociative charge transfers. A very good agreement is obtained between the experimental and calculated total cross-sections at low collision energy, which is the most relevant range for the interstellar environment. These results represent a significant starting point to estimate rate constants for the total dissociation of DME and MF by collisions with He+ ions in the ISM at low temperatures.

Collisions with He+ are an important pathway for the destruction of complex organic molecules in the interstellar medium (ISM). We have carried out dissociative charge transfer reactions of He+ with two oxygen containing organic molecules, ubiquitous in ISM: dimethyl ether (DME, CH3OCH3 ) and methyl formate (MF, HCOOCH3). Since they have a prebiotic relevance, several models were developed to explain how these molecules are formed and destroyed in the ISM. The reactions have been investigated by using the home-built Guided-Ion Beam Mass Spectrometer (GIB-MS) apparatus. Absolute cross sections and branching ratios of the products have been measured as a function of the collision energy in the hyperthermal energy range (i.e. from about 0.1 eV to 7 eV). The presence of the molecular ion was not observed among the products for these reactions, which means that the nascent DME and MF radical cations are formed in a dissociative state. Insights on both the charge transfer processes have been obtained by investigating the nature of the non-adiabatic transitions between the reactant and product potential energy surfaces (PES). The PES has been represented by using a semi-empirical method to model the inter-molecular interactions. To explain the experimental evidence, two excited states of DME and MF radical cations have been invoked: He+ captures an electron from inner valence orbitals of both the organic molecules, having binding energies ~10 eV higher than the HOMO. An improved Landau-Zener-Stückelberg model has been developed to obtain the total integral cross-section to be compared with the experimental results. Inter-molecular interaction and electron densities of the orbitals involved in the reaction turned out to be key points to describe the dynamics of the two studied dissociative charge transfers. A very good agreement is obtained between the experimental and calculated total cross-sections at low collision energy, which is the most relevant range for the interstellar environment. These results represent a significant starting point to estimate rate constants for the total dissociation of DME and MF by collisions with He+ ions in the ISM at low temperatures.

Esta tesis doctoral se enmarca dentro del estudio de las interacciones no covalentes denominadas "no convencionales", también conocidas como interacciones σ-/π-hole. Su estructura está compuesta por un primer capítulo dedicado al análisis del Estado del arte (Capítulo 1) el cual proporciona una visión general de la química supramolecular “no convencional”, seguido de tres capítulos principales (Capítulos 2 a 4), cada uno dedicado al análisis de una interacción en concreto. Estos capítulos son: Interacciones Tetrel bond (2), Interacciones Pnicogen bond (3) y finalmente Interacciones Aerogen bond (4). El Capítulo 1 recoge una introducción detallada con el objetivo de presentar y focalizar el tema principal de esta investigación. Además de analizar los fundamentos físicos que sustentan la naturaleza de las interacciones σ-/π-hole, se exponen varios ejemplos experimentales con el fin de demostrar el vasto potencial de aplicación de dichas fuerzas no covalentes en campos tales como la química supramolecular, el reconocimiento molecular y la química biológica. Los Capítulos 2 a 4 incluyen varios trabajos derivados de nuestra investigación, los cuales poseen una distribución de secciones común para una lectura más cómoda por parte del lector. En primer lugar, una sección de Introducción donde se detallan los antecedentes relativos al tema de estudio, incluyendo resultados de investigaciones anteriores relacionadas con el tema. La segunda parte consta de la Metodología computacional utilizada, seguida de la sección de Resultados y discusión. Por último, se recogen las principales Conclusiones derivadas de nuestra investigación. El Capítulo 2 se divide en cuatro secciones. En primer lugar, el "redescubrimiento" de la interacción tetrel bond, término propuesto por nuestro grupo de investigación para describir la interacción σ-hole establecida entre compuestos que presentan átomos pertenecientes al grupo de los tetrels y bases de Lewis. En segundo lugar, el análisis de la direccionalidad de interacciones tetrel bond donde participan átomos de carbono con hibridación sp3 en compuestos de tipo ArCX3 (X= H y F), utilizando para ello un estudio teórico, a base de cálculos ab initio de alto nivel, y cristalográfico gracias al CSD (Cambridge Structural Database). Finalmente, la última parte de este capítulo se dedica a estudiar el impacto de las interacciones tetrel bond en dos campos diferentes; la Química Atmosférica y la Química Biológica. El Capítulo 3 se divide en cuatro secciones. En primer lugar, el análisis de la direccionalidad de las interacciones π-hole pnicogen bond que implican al átomo de nitrógeno sp2 presente en el grupo -NO2, utilizando la base de datos CSD (Cambridge Structural Database) y cálculos ab initio de alto nivel. En segundo lugar, la evaluación de la capacidad del anión NO3– de comportarse como un ácido de Lewis al encontrarse en un contexto químico apropiado. De esta manera, es posible establecer interacciones antielectrostáticas utilizando el π-hole generado sobre el átomo de nitrógeno. Dicha hipótesis es confirmada mediante el análisis de las bases de datos CSD y PDB (Protein Data Bank). Finalmente, el último trabajo se centra en el estudio de la interacción entre el σ-hole presente en átomos pertenecientes al grupo de los pnicogens con hibridación sp3 y anillos aromáticos, utilizando la base de datos PDB (Protein Data Bank) como soporte experimental de los resultados obtenidos mediante cálculos ab initio. Dichas interacciones son claves en el mecanismo de acción de fármacos relacionados con el tratamiento de la enfermedad Leishmaniasis. El Capítulo 4 se divide en tres secciones. En primer lugar, se analiza y caracteriza la interacción aerogen bonding que implica a compuestos de Xe(VI) y Xe(IV) como nueva fuerza supramolecular en la que participan el σ-hole presente en el átomo de aerogen y bases de Lewis. Además, se describen también interacciones π-hole presentes en compuestos de Xe(IV), concretamente XeF4 y Xe(OTeF5)4. Por último, la tercera sección del capítulo se centra en la capacidad de los compuestos Xe(VI) y Xe(IV) para interactuar con anillos aromáticos, estableciendo así interacciones aerogen-π. Finalmente, el Capítulo 5 reúne las conclusiones principales derivadas de esta tesis.
This PhD. thesis is devoted to the study of “unconventional” noncovalent interactions, particularly σ-/π-hole interactions. The inner structure is composed by a State of the art (Chapter 1) which gives a general overview of this “non-classical” noncovalent chemistry, followed by three main chapters (Chapters 2 to 4), each one devoted to the analysis of a particular interaction. These chapters are: Tetrel bonding Interactions (2), Pnicogen bonding Interactions (3) and finally Aerogen bonding Interactions (4). Chapter 1 collects a detailed introduction to focalize the main subject of this research, particularly on σ- and π-hole interactions, which are the main goal of this investigation. Their physical nature is explained as well as several experimental examples in order to put onto scene the vast potential of this family of interactions in fields such as supramolecular chemistry, molecular sensing and biological systems. Chapters 2 to 4 are divided into a number of sections, involving several papers derived from our research. In these sections, the reader will find the same distribution for his/her comfort. First, an Introduction part where the background about the main issue is detailed, including previous results related with the topic. The second part gathers the Computational methodology used, followed by the Results and discussion section. Finally, the main Conclusions derived from our investigation are highlighted. Chapter 2 is divided into four sections. First, the "rediscovery" of the tetrel bonding interaction, a term coined by our research group to describe the σ-hole interaction established between tetrel bearing compounds and electron-rich entities. Second, the role of sp3 carbon atoms to act as tetrel bond donors in ArCX3 (X = H and F) compounds is analyzed using a combination of the CSD (Cambridge Structural Database) as a useful source of experimental data and high level ab initio calculations. Finally, the last part of this chapter is devoted to study the impact of tetrel bonding interactions in two different fields; atmospheric chemistry and biological systems. Chapter 3 is divided into four sections. First, the directionality of -hole pnicogen bonding interactions involving the sp2 nitrogen atom present in -NO2 group is analyzed using the CSD (Cambridge Structural Database) and high level ab initio calculations. Second, the ability of the NO3− to behave as a Lewis acid when placed in the appropiate chemical context and establish -hole antielectrostatic interactions with electron-rich guests is studied using both CSD and PDB (Protein Data Bank) databases. Finally, the study of the interaction between sp3 pnicogen atoms and aromatic rings is analysed using the PDB (Protein Data Bank) database to support the results retrieved from ab initio calculations. These particular interactions are key in the mechanism of action of drugs used in the treatment of Leishmaniasis disease. Chapter 4 is divided into three sections. First, aerogen bonding interactions involving Xe(VI) and Xe(IV) compounds are analysed and characterized as a novel supramolecular force involving the σ-hole of the aerogen atom and electron-rich entities. In addition, π-hole bonding interactions involving Xe(IV) compounds are also described focusing on two derivatives; XeF4 and Xe(OTeF5)4. Finally, the last section of the chapter is focused on the ability of Xe(VI) and Xe(IV) compounds to interact with aromatic moieties, thus establishing aerogen- interactions. Finally, Chapter 5 assembles the main conclusions derived from this thesis.
Aquesta tesi doctoral s'emmarca dins de l'estudi de les interaccions no covalents anomenades "no convencionals", també conegudes com interaccions σ-/π-hole. L’estructura general es troba formada per un primer capítol dedicat a l'anàlisi de l'Estat de l'art (Capítol 1) el qual proporciona una visió general de la química supramolecular "no convencional", seguit de tres capítols principals (Capítols 2 a 4), cada un d’ells dedicat a l'anàlisi d'una interacció en particular. Aquests capítols són: Interaccions Tetrel bond (2), Interaccions Pnicogen bond (3) i finalment Interaccions Aerogen bond (4). El Capítol 1 recull una introducció detallada amb l'objectiu de presentar i focalitzar el tema principal d'aquesta investigació. A més dels fonaments físics que componen la naturalesa de les interaccions σ-/π-hole, es recullen diversos exemples experimentals amb la finalitat de demostrar el vast potencial d’aplicació d’aquestes interaccions en camps de recerca com la química supramolecular, el reconeixement molecular i la química biològica. Els Capítols 2 a 4 inclouen diversos treballs derivats de la nostra investigació, els quals posseeixen una distribució de seccions comú per a una lectura més còmoda per part del lector. En primer lloc, una secció d'Introducció on es detallen els antecedents relatius al tema d'estudi, incloent resultats d'anteriors investigacions relacionades amb el tema. La segona part recull la Metodologia computacional utilitzada, seguida de la secció de Resultats i discussió. Finalment, es destaquen les principals Conclusions derivades de la nostra investigació. El Capítol 2 es divideix en quatre seccions. En primer lloc, el "redescobriment" de la interacció tetrel bonding, terme proposat pel nostre grup de recerca per descriure la interacció σ-hole establerta entre compostos que presenten àtoms pertanyents al grup dels tetrels i bases de Lewis. En segon lloc, l’anàlisi de la direccionalitat de les interaccions tetrel bond on participen àtoms de carboni amb hibridació sp3 en composts del tipus ArCX3 (X= H i F), utilitzant una Metodología d’investigació combinada formada per un estudi teòric mitjançant càlculs ab initio d'alt nivell i un estudi cristal·logràfic gràcies al CSD (Cambridge Structural Database). Finalment, la darrera part d'aquest capítol es dedica a estudiar l'impacte de les interaccions tetrel bond en dos camps diferents; la Química Atmosfèrica i la Química Biològica. El Capítol 3 es divideix en quatre seccions. En primer lloc, s'analitza la direccionalitat de les interaccions π-hole pnicogen bond on hi participa l'àtom de nitrogen sp2 present en el grup -NO2, utilitzant la base de dades CSD (Cambridge Structural Database) i càlculs ab initio d'alt nivell. En segon lloc, es va dur a terme una anàlisi de la capacitat del NO3– de comportar-se com un àcid de Lewis al estar localitzat en un contexte químic apropiat. D'aquesta manera, és possible establir interaccions antielectrostàtiques utilitzant el π-hole present a l'àtom de nitrogen. Aquesta hipòtesi va ser confirmada mitjançant l'anàlisi de les bases de dades CSD i PDB (Protein Data Bank). Finalment, l'últim treball es centra en l'estudi de la interacció entre el σ-hole present en àtoms que pertanyen al grup dels pnicogens amb hibridació sp3 i anells aromàtics, utilitzant la base de dades PDB (Protein Data Bank) com a suport experimental dels resultats obtinguts mitjançant càlculs ab initio. Es va poder demostrar que aquestes interaccions són claus en el mecanisme d’acció de fàrmacs relacionats amb el tractament de la malaltia Leishmaniasis. El Capítol 4 es divideix en tres seccions. En primer lloc, s'analitza i caracteritza la interacció aerogen bonding on hi participen compostos de Xe(VI) i Xe(IV) com una nova força supramolecular en la qual participen el σ-hole present a l'àtom d’aerogen i bases de Lewis. A més, es descriuen també interaccions π-hole presents en compostos de Xe(IV), concretament XeF4 i Xe(OTeF5)4. Finalment, la tercera secció del capítol es centra en la capacitat dels compostos Xe(VI) i Xe(IV) per interactuar amb anells aromàtics, establint d’aquesta manera interaccions aerogen-π. Finalment, al Capítol 5 reuneix les conclusions principals derivades d'aquesta tesi.

Developpement d'une technique de calcul des proprietes magnetiques qui combine les avantages des methodes classiques tenant compte de la correlation electronique et qui conserve l'invariance de jauge de la methode des polynomes par un systeme de compensation interne. Calcul des corrections rovibroniques, decrites analytiquement par la methode des perturbation, pour des molecules diatomiques (h::(2), co) pour une comparaison des resultats theoriques et experimentaux

Le travail présenté dans cette thèse se place dans le contexte de la simulation de dommages biologiques. D'abord une étude macroscopique met en question la pertinence des plans de traitement basés sur la dose absorbée et le passage à une étude de micro-dosimétrie permet l'utilisation de paramètres biologiques plus pertinents, tels que les cassures de brins d'ADN. La validité des sections efficaces d'interaction sur lesquelles se basent ces simulations est discutée en plus de détails. Suite à la complexité du milieu biologique, les sections efficaces d'interaction avec l'eau sont souvent utilisées. Nous développons un algorithme qui permet de fournir les sections efficaces d'ionisation pour n'importe quelle cible moléculaire, en utilisant des outils qui permettent de surmonter les difficultés de calcul, ce qui rend notre programme particulièrement intéressant pour les molécules complexes. Nous fournissons des résultats pour l'eau, l'ammoniac, l'acide formique et le tétrahydrofurane
The work presented in this thesis can be placed in the context of biological damage simulation. Webegin with a macroscopic study where we question the relevance of absorbed-dose-based treatmentplanning. Then we move on to a micro-dosimetry study where we suggest the use of morebiologically relevant probes for damage, such as DNA strand breaks. More focus is given to thefundamental considerations on which the simulations are based, particularly the interaction crosssections. Due to the complexity of the biological medium, the interaction cross sections with waterare often used to simulate the behavior of particles. We develop a parallel user-friendly algorithmthat can provide the ionization cross sections for any molecular target, making use of particular toolsthat allow to overcome the computational difficulties, which makes our program particularlyinteresting for complex molecules. We provide preliminary results for water, ammonia, formic acidand Tetrahydrofuran

Developpement d'une approche generale basee sur la formule differentielle de rutherford, avec parametre d'ecran, completee par une formule angulaire parametrique; obtention d'une section efficace differentielle bien adaptee a de nombreuses donnees experimentales et d'une section efficace integree satisfaisante sauf aux tres basses energies de la particule incidente, pour lesquelles on introduit un facteur correctif dependant de deux parametres. Bonne adaptation de ces sections efficaces au code de simulation edifiee au laboratoire pour la modelisation de la structure des traces de particules chargees traversant des tissus vivants

Calcul de la polarisabilité collisionnelle dans la théorie D. I. D à l'ordre 1 des fluctuations du champ pour n::(2), Co::(2), n::(2)o, cl::(2), h::(2) et Co en tenant compte de l'anisotropie propre de la molécule pour obtenir les intensités intégrées Rayleigh dépolarisées, sans négliger les corrélations d'orientation radiales et angulaires : la contribution propre croit avec la longueur de la molécule, mais reste faible par rapport à celle des termes croisé et collisionnel ; la contribution collisionnelle n'est pas toujours prépondérante. Comparaison des mesures aux calculs en tenant compte de nouveaux facteurs d'interférences obtenus par simulation de Monte Carlo.

Ce travail comporte deux parties. La premiere est consacree a l'etude theorique semi-empirique des proprietes electroniques liees aux caracteristiques non-lineaires du second ordre de molecules comportant les cinq types de groupements electroattracteurs suivants: 4h-1-benzopyrane-4-one, 4h-1-benzopyrane-4-thione, (4h-1-benzopyrane-4-ylidene)-malononitrile, 3h-1,2-dithiole-3-one, 3h-1,2-dithiole-3-thione. Apres un rappel des principales techniques de mesures mises en uvre pour caracteriser la non-linearite des molecules etudiees, nous decrivons dans le chapitre suivant les differentes formulations theoriques de l'hyperpolarisabilite quadratique et les methodes quantiques les plus couramment utilisees pour mener a bien ces calculs. La determination, dans le cadre de la methode pm3, des caracteristiques de l'etat fondamental des 17 molecules considerees et l'etude a l'aide de la methode cndo/s-cis des transitions de plus basses energies, permettent en particulier une analyse approfondie du transfert de charge sous excitation ; le caractere complexe de ce dernier, est mis en lumiere par les effets concurrents de transfert donneur-transmetteur-accepteur classique d'une part, interne au groupement electroacttracteur lui-meme d'autre part. Il est cependant possible de preciser, pour chacune des molecules etudiees, la transition a caractere de transfert de charge la plus marquee ; les calculs des hyperpolarisabilites par les methodes a champ fini (pm3/rhf/ff) et somme d'etats (cndo/s-cis/sos) viennent confirmer l'importance de cette transition dans la valeur finale de l'hyperpolarisabilite quadratique, tout en permettant une analyse detaillee des contributions non-negligeables d'un grand nombre d'etats excites. La sensibilite de l'hyperpolarisabilite a de faibles variations de certains parametres geometriques ainsi que les limites des methodes utilisees sont commentees. La seconde partie est dediee aux ameliorations apportees aux calculs des proprietes monoelectroniques dans le cadre du programme semi-empirique vamp et a leur mise en uvre: matrice densite apres interaction de configurations, moments dipolaires (d'etats et de transitions), hyperpolarisabilite quadratique (sos). Les modifications introduites sont testees sur une molecule de reference (paranitroaniline). En particulier, des resultats obtenus sur l'hyperpolarisabilite quadratique font l'objet d'une comparaison critique avec d'autres valeurs theoriques et experimentales

Etude des transitions doubles (simultanees) correspondant a l'absorption d'un seul photon par deux molecules en interaction pour les systemes gazeux comprimes : h::(2) + cf::(4) ou sf::(6), o::(2) ou n::(2) + sf::(6), n::(2) + co::(2). Determination de coefficients d'absorption binaire integres et des profils normalises que l'on compare aux valeurs theoriques calculees en utilisant le moment dipolaire induit et l'intensite de la transition induite en fonction des regles de selection sur les nombres quantiques. Choix des differents parametres caracterisant les deux molecules et leur potentiel d'interaction considere comme isotrope. Mise en evidence du caractere essentiellement binaire des collisions, meme pour des densites de 100 amagat. Variation de la frequence du maximum d'absorption de la transition simultanee avec la densite. Analyse des profils des bandes simultanees a partir de la dynamique de l'interaction : verification du caractere translationnel sauf pour le melange n::(2) + co::(2) pour lequel on applique un modele semi-empirique a deux parametres

Calcul des courbes de potentiel adiabatiques pour les géométries colinéaires et perpendiculaires, à l'aide d'un pseudopotentiel dépendant du moment orbital électronique et d'une approche à deux centres; bon accord avec les calculs ab initio existants. Examen des différentes symétries de ces systèmes dans le formalisme de la théorie des groupes, afin d'étudier les valeurs propres et facteurs propres de l'hamiltonien électronique. Calcul quantique des sections efficaces relatives des transitions de structure fine de Rb induites par collision avec H(2) ou D(2). En tenant compte des niveaux rotationnels moléculaires, obtention d'un très bon accord avec les résultats expérimentaux et interprétation de l'effet isotopique

I. Proposition d'une amelioration de la methode cipsi, qui combine l'approche variationnelle (pour les termes qui contribuent fortement a la solution exacte) et l'approximation perturbative (pour les termes de moindre importance), en introduisant une classe intermediaire. Reexamen de la solution du probleme variationnel pour les matrices de grande dimension; amelioration de la methode classique de davidson. Ii. Comparaison de l'efficacite de differentes variantes d'hamiltoniens effectifs; generalisation du concept sous forme d'hamiltonien effectif intermediaire, examen de sa pertinence et de son efficacite pour resoudre le probleme des etats intrus

Etude approfondie sur la theorie des hamiltoniens effectifs et analyse de leurs applications aux methodes de diabatisation et au traitement des collisions reactives. Propositions pour le calcul des valeurs propres de l'hamiltonien par des methodes de perturbation ou iteratives, pour l'emploi d'hamiltoniens effectifs dans le calcul des surfaces quasi diabatiques et le traitement general des collisions reactives. Application a la reaction cs+h::(2) etudiee par les methodes ab initio pour la geometrie colineaire : surfaces de potentiel, sections efficaces et mecanismes predominants

Modelisation originale de la densite electronique moleculaire par la superposition de densites atomiques spheriques, centrees sur les noyaux a partir de calculs d'orbitales moleculaires, avec trois invariants : la charge totale, le potentiel electrons-noyaux, le moment dipolaire. Description de la methode numerique pour determiner les densites associes aux atomes dans une base d'orbitales gaussiennes. Renseignements obtenus sur les modifications spatiales de la charge electronique par formation de liaisons, sur les facteurs de structure atomiques effectifs, apres transformation de fourier, en tenant compte de l'effet de l'environnement. Extension de la methode a la decomposition de la densite electronique moleculaire en densites composantes, autres qu'atomiques et non necessairement centrees sur les noyaux. Outre les applications a l'etude de la structure et des proprietes electroniques des molecules, proposition d'utilisation au calcul des polarisabilites optiques (lineaires ou non), a l'analyse des donnees cristallographiques obtenues par diffraction de rayon x et a la prevision de la structure des cristaux moleculaires

Calculs numériques, à l'approximation D. I. D, de la diffusion collisionnelle de la lumière par des milieux denses composes de molécules isotropes ou faiblement anisotropes, à l'aide de deux simulations ou l'algorithme de résolution est la méthode de Monte-Carlo. Cas de la première simulation pour les molécules isotropes, avec un modèle réticulaire avec prise en compte des seules interactions entre molécules voisines : intensités collisionnelles des doublets, triplets et quadruplets à différentes températures et densités, facteurs d'interférences Rayleigh et Raman ; bon accord à toutes densités pour les gaz et aux densités élevées pour les liquides. Cas de la deuxième simulation pour des molécules linéaires anisotropes : les corrélations entre axes moléculaires et intermoléculaires sont prépondérantes pour déterminer les taux de dépolarisation Rayleigh de n::(2).

The weakly bound association products of atmospherically relevant radical species (O₂, OH, NO₂, HO₂ and NO) have been studied theoretically using quantum-chemical methods. The thermodynamic stabilities, which are crucial to determining the probability of formation in Earth's atmosphere, were calculated for the hydrotrioxy radical (HOOO) and peroxynitrous acid (HOONO, an isomer of nitric acid) relative to the radical dissociation products. In the case of HOONO, the experimentally determined values were confirmed. For HOOO, the predicted stability was significantly lower than the experimentally determined value; a conclusion that was supported by later experimental work and indicates that HOOO will not form in significant quantities in Earth's atmosphere. The fundamental and multi-quantum vibrational transitions were also predicted for both the HOONO and HOOO systems. The theoretical work on the HOONO system aided the assignment of experimental spectra and was used to correct equilibrium rotational constants. The HOOO system presented a challenge for the methods used here and work to apply other approaches in describing the vibrational modes is ongoing. Second-order vibrational perturbation theory, combined with a correlated quantum-chemical method and a moderately sized basis set, provides a method for accurately predicting fundamental and low-order multi-quantum transition energies and intensities for many systems (HOOO being an exception). Here coupled cluster theory, at a level which treats one- and two-electron correlation with a correction for three-electron correlation, and atomic natural orbitals basis sets were used in the vibrational calculations. To predict the dissociation energies of weakly bound species with the precision required (due to the small energy differences involved), high-order correlation contributions (a full treatment of three-electron correlation and a correction for four-electron correlation) are included, as is extrapolation to the basis set limit. Other contributions, such as that for the zero-point energy, were also considered. For the HOOO system, one-dimensional potential curves along the dissociation and torsional coordinates were constructed with standard single-reference and equation-of-motion coupled-cluster methods. The latter is better able to describe the nature of a system in the bond-breaking region and the complex electronic structure of a species formed from two radical fragments, one doubly degenerate in the ground state: X²[Pi] OH and X³[Sigma] O₂. A possible barrier to dissociation and the torsional potential for HOOO were investigated.
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碩士
國立中正大學
化學所
95
In the first chapter, we have calculated the molecular geometries, association energies and charge distribution of the noble-gas containing anions F−(NgO)n (Ng = He, Ar, Kr; n = 1−6) using the MP2 theory with the Dunning basis set. The geometries of these anions were found to be highly symmetric. The predicted ranges of association energies were 19−39, 37−134, 58−231 kcal/mol for Ng = He, Ar, and Kr, respectively. The stability of these anions was due to the charge-induced formation of the Ng−O bonds. As the size of the system increases, the charge separation along the Ng−O bond decreases, while the fluorine atom remains fully charged. In chapter two, we studied the geometry and stability of a series of noble-gas anions X−NgO (X = F, Cl, OH, HBeO, OBO, CF3O, and etc). The induced NgO bond strengths were similar for different X−. In many cases, the stability of X−NgO depends strongly on the electron affinity of X. In chapter three, the aromatics and their fluorinated derivatives compounds, FNgR (R = phenyl, pyridyl, pyrimidinyl, 1,3,5-triazinyl group; Ng = He, Ar, Kr), have been studied by using ab initio calculation III and DFT theory. The results indicated that as the number of fluorine atoms increases, the FNgR molecules will be less following than the three-body decomposition channel F + Ng + R, while the energy barriers for the exothermic decomposition channel Ng + FR increase. Most aromatic fluorine compounds, FKrR, are predicted to be about 15 kcal/mol lower in energy as compared to the three-body dissociation products F + Kr + R. The energy barriers for the extremely exothermic decomposition channel Kr + FR are about 30 kcal/mol. We believe that some aromatic fluorine compounds such as FKr(2,6-F2-Ph), FKr(2,6-F2-Py) can be synthesized under suitable conditions. In chapter four, we have studied the organometallic complexes [P(2-Py)3M(CO)n(NO)3-n](3-n)+ (M = Cr, Mo, W；n = 1−3) including structures, IR and UV-Vis spectra by using the density functional theory and time-dependent (TD) density functional theory. The calculated structures, IR and UV-Vis spectra are compared to the experimental results. The TD-DFT calculation also indicated that both P(2-Py)3Cr(CO)2(NO)+ and P(2-Py)3Cr(CO)(NO)2 2+ may have a triplet ground state. This is in consistent with the observed NMR spectra and magnetic dipole moment measurements.

碩士
國防大學中正理工學院
應用化學研究所
89
The acidity of gas-phase molecules, without being affected by solvent, can be regard as absolute acidity. After compared the theoretically calculated and experimental measured values, the relative standard deviations as found herein, which are gained through the application of B3LYP/6-311++G(3df,2pd)、B3LYP/6-311+ G(2d,p) and CBS-QB3 provided by the Gaussian 98 package software , are less than 2%. Obviously, the accuracy of the three methods of calculation is more reliable. Carboxylic acids exist in two forms, syn and anti conformers. The result of calculation shows that the calculated value of anti conformer is more closer to the experimental measured value. Because the acidity is affect- ed by the nature of substitution group in the carboxyl group, as a result, the delocalization interaction of electron-withdra- wing and electron-releasing substituents on the π electron in the carboxyl group affected the acidity of carboxylic acids. Fluorine atom has strong electron-withdrawing effect. Molecules are substituited by Fluorine reduce Gibbs energy about at 50-100 kJ/mol and substantially promote the acidity of molecules. Using higher basis set to calculate large molecule is impractic- al in reality. This question has been soved to use single point model. By comparing various calculation methods used in the present research we found that the current method is five to ten times less than B3LYP/6-311++G(3df,2pd). The accuracy of this simple model calculation is also reasonable well compared to B3LYP/6-11++G(3df,2pd).

碩士
國立臺灣師範大學
化學研究所
92
We carried out theoretical studies for two important reactions involving HNCO peptide bond: 1. the methylation of Hydroxamic Acid (RC(=X)NHOH, X=O、R=H) and its derivatives (X=S、R=CH3,Cl,CHCH2) with diazomethane , and 2. the thermal deamination and denitrosation of N-Nitrosoamides . The descriptions are following: Part 1： There are seven possible pathways of methylation of (Z)HAs to generate O-alkylation and N-alkylation products. Path Z7 generating (Z)O,O-dimethylhydroxamates 9 has the lowest energy barrier 17.24 kcal/mol. The reaction between HAs and CH2N2 results in predominant formation of product 9 strictly high-site selective. When the substitutents of CH3, Cl and CHCH2 are added, the energy barrier of pathways and the site selection of product will be affected. The probability for the formation of (Z)N,O-dimethylhydroxamates 6 will be increase. There are six possible pathways in the E-form Has methylation. Path E5、E6 generate (E)O,O-dimethylhydroxamate 24 , with the energy barriers, 22.85 kcal/mol, and 23.06 kcal/mol respectively. The substituents CH3, Cl and CHCH2 have little effect to the site-selectivity of the products except the Cl-substituent changes the rate-determine step. The production of (E)N,O-dimethylhydroxamates 27 has higher energy barrier. Part 2： The similar methylation reaction of thiohydroxamic acid is investigated and the result compared with that of hydroxamic counterparts. We found that the relative energies、structures of transition state and the pathways of reaction were affected by two major factors: the size and the electronegativity of O and S atom. However products of Z and E isomers of SHAs also have high site-selectivity , with N-methyl product obtained at higher barrier, similar to Has counterparts. Part 3： We studied theoretical the thermal decomposition of N-Nitrosoamides and designed two isodesmic reaction to understand the substitutions effects on the stability of the reactant and transition state . We found that the substitution at the different sites (N and C) of N-Nitrosoamides led to very different results. The silyl substituent at C-site even followed different pathway of decomposition. The thermal decomposition of N-Nitrosoamides in acidic condition may undergo deaminative (loss of N2) and denitrosative (loss of NO+) two competitive pathways. According to our result, we may understand how the acidity, temperature and added nucleophilicity affect reaction barriers.

The utilization of energetic strained molecules may be one way to mitigate carbon emissions or better and more economical fuel blends. To investigate candidate molecules, limonene and dicyclopentadiene, both theoretical and experimental procedures were implemented here. Computational quantum chemistry methods were employed to determine the thermodynamic properties and kinetic parameters for the hydrogen-abstraction reactions of limonene by a hydrogen atom. Geometry optimization and energy calculation was conducted for all stable species and transition states using Gaussian 09. The rate constants of the H-abstraction reactions were calculated using conventional transition state theory, as implemented in ChemRate software. The obtained values were fitted over the temperature range of 298 – 2000 K to obtain the modified Arrhenius parameters. Increasing the anti-knock quality of gasoline fuels can enable higher efficiency in spark ignition engines. This study explores blending the anti-knock quality of dicyclopentadiene (DCPD, a by-product of ethylene production from naphtha cracking), with various gasoline fuels. The blends were tested in an ignition quality tester (IQT) and a modified cooperative fuel research (CFR) engine operating under homogenous charge compression ignition (HCCI) and knock limited spark advance (KLSA) conditions. Ethanol is widely used as a gasoline blending component in many markets, due to current fuel regulations. The test results of DCPD-gasoline blends were compared to those of ethanol-gasoline blends. Furthermore, the anti-knock properties of dicyclopentadiene (DCPD) as an additive to primary reference fuels (PRF) and toluene primary reference fuels (TPRF) have been investigated. The research octane number (RON) and motor octane number (MON) were measured using cooperative fuels research (CFR) engine for four different fuel blends. Moreover, the ignition delay times of these mixtures were measured in a high-pressure shock tube at 40 bar and stoichiometric mixtures over a temperature range of [700-1200 K]. Ignition delay measurements were also conducted using rapid compression machine (RCM) at stoichiometric conditions and 20 bar. An ignition quality tester (IQT) compared ignition delay times of iso-octane and DCPD. Furthermore, a chemical kinetic auto-ignition model was designed to simulate the IDT experiments.

碩士
國立暨南國際大學
應用化學系
101
In this investigation, we will introduce and analysis compounds which have been synthesized or non-synthesized by theoretical study. The research have two parts, the first part used theoretical calculation to select the blue phosphorescent host materials of organic light-emitting diodes (OLED). After choosing (4-tolyl)tetraphenylphthalimide (TPPI), tris(4-carbazoyl-9-ylphenyl)amine (TCTA), and 1,2,3,4,5-pentaphenylpyrrole (PPP) as cores, we obtained the influences of HOMO, LUMO, and triplet excited energy by changing positions and numbers of the functional groups. Then we discuss the molecular structure, photoluminescence wavelength, and energy gap of compounds. Finally, we pick the most suitable molecule (TPPI-BPB) for preparing blue phosphorescent host materials. . The second part is investigating the physical properties and transition states of corannulene, Acenaphtho-[3,2,1,8-fghij]dicyclopenta-[pqr,tuv]picene (ADP), Acenaphth- [3,2,1,8-fghij]-as-indaceno-[3,2,1,8,7,6-pqrstuv]picene (AIP), Bowl-aa, Bowl-ba and Bowl-bb which was synthesized by Prof. Y. T. Wu. According the results, the bond distance of bowl shaped molecules are different from the parent of fullerene because of the degree of bending. We found two transition state through the progress of calculation. The shape of corannulene and ADP are planar, AIP, Bowl-aa, Bowl-ba and Bowl-bb are S-shaped. The results are also agreed with the experiments which were measured by Prof. Y. T. Wu.

碩士
國立中正大學
化學暨生物化學研究所
107
In the first chapter, we tried to find the stable noble-gas compounds FNgBNM ( M = 3d transition metal elements ) with high spin states. We started with the stable FNgBNR ( Ng = Xe, Kr, Ar ; R = H, F, CCH, OH, CHCH2,CH3 ) noble gas compounds which we had studied and replace the R groups with 3d and 4d transition metal atoms to design the new types of noble-gas compounds FNgBNM ( Ng = Xe, Kr ). In the first chapter, we used the 3d transition metal atoms ( Sc ~ Zn ). Our results showed that the linear dissociation energies and bending dissociation barriers of FNgBNM are all higher than 10 kcal/mol. We believe that the various FNgBNM molecules are stable at low temperature. In the second chapter, We replaced the 3d transition metal atoms with the 4d transition metal atoms, and have designed the noble-gas compounds FNgBNQ ( Ng = Xe, Kr ; Q = Y ~ Cd ). The linear dissociation energies and bending dissociation barriers of FNgBNQ are all higher than 15 kcal/mol. We believe that FNgBNQ can also exist at low temperature. In the third chapter, we attempted to develop the MC-DFT methods for the noble gas compounds. We increased the number of reference bond energies in the training sets to 39. Our results showed that MPW1B95 functional gives the best performance on predicting bond energies of the noble gas compounds ( MUE ~ 1.8 kcal/mol ) with the aug-cc-pVTZ basis set. The MUE can be further reduced to 1.2 kcal/mol by the MC-DFT scheme.

碩士
國立中正大學
化學暨生物化學研究所
101
This thesis consists of three chapters. In the first chapter, we studied the stable noble-gas molecules or anions containing one nitrogenxenon triple bond. Starting from the two stable anions of NXeO2- and NXeO3-, we replaced some of the O atoms with F atoms. The general formula of these series neutral molecules and anions was NXeOnFm. We used the MP2 and B3LYP theory to predict the structures of NXeOnFm. The results of the calculation illustrated that the N-Xe bond lengths of the NXeOF3, NXeF3, NXeF5, NXeOF4-, NXeOF2-, and NXeF4- were short, and the average N-Xe bond length was 1.80 Å. According to the structural information and the kinetic studies of these molecules, we predicted that these molecules should be kinetically stable at the low temperature. In the second chapter, we investigated the organic noble-gas molecules which contain the Xe-C bonds. We replaced the N atoms of the NXeOnFm molecules by the the isoelectronic CH groups, and we also substituted the O and F atoms by the CH2 and CH3 groups, respectively. The resulting molecules contain Xe-C bonds, such as NXeO2CH2-, NXeOCH2-, NXeF4CH3, NXeO2FCH3-, NXeF3CH3-, CHXeO2-, and CHXeO3- We used the MP2and B3LYP theory to study the geometries and stabilities of these organic noble-gas molecules. The computational results showed that in most cases there were more stable isomers that could be easier generated in the synthesis processes, and thus, it would be difficult to stabilize these molecules in the experiments. Among these molecules, only the NXeO2CH2= anion was found to possess the required thermodynamic and kinetic stabilities, so it could exist at the low temperature. The theoretical studies of the noble-gas molecules containing more than one noble gas atom has been one of the important researche topics in our laboratory. In the third chapter, we studied the F(BFOXeO)nBF2 (n = 1,2,3,4) molecules. We used the ab initio methods and the hybrid DFT functional to predict the structures and stabilities of these molecules. The average Xe-O bonds were about 2.1 Å. For n = 1, the molecule is Xe(OBF2)2, and the average bond energy of the Xe-O bond was 15.0 kcal/mol at the CCSD(T)/aptz level. The decomposition reaction barriers by the B3LYP/apdz and MP2/apdz methods were 54.1 and 69.6 kcal/mol, respectively. It seems to possess the thermodynamic and kinetic stability at the low temperature. For n = 2, 3 and 4, the average bond energy of the Xe-O bond was10.0 kcal/mol. These molecules were also found to enough thermodynamic and kinetic stability, so they could exist at low temperature environment.

碩士
國立中正大學
化學暨生物化學研究所
104
This thesis consists of four chapters. In the first chapter, we tried to find new stable ringed molecules containing noble gas atoms . In previous studies, we had shown that general formula OnXeO2CR1R2 (n = 2, 3; R1,R2 = H, CH3, F, Cl) four-member ringed molecules were not stable because of the ring strain. In the current study, we replaced the O atoms with N atoms, and extended the study to six-member rings. The general formula of these neutral molecules and anions was NgO2N2B2OR2、NgON3B2OR2 ( Ng = Xe、Kr )、( R=H、F ). We used MP2、CCSD(T) and B3LYP theory to predict the structures of these molecules. The results suggested that XeO2N2B2OF2、XeO2N2B2OH2、XeON3B2OF2、XeON3B2OH2all have large ST gaps. Our calculation also showed that the dissociation barriers are high. Our results thus suggested that these molecules could exist at the low temperature. In the second chapter, we studied the stabilities of molecules containing more than one noble gas atom. We used the MP2 and B3LYP theory to predict the structures of R(XeOBeO)nXeR (R = H or F；n = 1, 2) and their stabilities .The calculated results showed that for n = 1, the molecules HXeOBeOXeH、FXeOBeOXeH and FXeOBeOXeF are stable. The noble-gas bond energies of these molecules were 61.2、84.4 and 99.0 kcal/mol, respectively. The dissociation barriers were estimated to be higher than 35 kcal/mol at the CCSD(T)/aug-cc-pVTZ level.However, for n > 1, our calculation indicated that these molecules do not have enough stability even at low temperature. In the third chapter, we studied the mechanisms of the cyclization and dehydrogenation reactions of polyacrylonitrile (PAN). Our results showed that the barrier of cyclization reaction via self-generated CN free radical was about 18 kcal/mol, and the reaction is highly exothermic. Our calculation also showed that the direct dehydrogenation of 4AN needs to overcome barriers over 100 kcal/mol, and the overall reaction was highlyendothermic. We also calculated alternative dehydrogenation pathways at the presence of free radicals. The reactions only required barriers about -1.2 ~ 11 kcal/mol. We conclude that the free radical reactions are much more likely to occur in the dehydrogenation processes. In the fourth chapter, we studied the stabilities of two new type polymers containing more than one noble gas atom. The general formula are (FNgCC-Gly)n and (FNg CH2CCH3)n ( Ng = Kr、Xe ; n=1 ~ 4) The calculated results showed that FNgCC-Gly for Ng = Kr、Xe, the noble-gas bond energies were 28.7、57.2 kcal/mol.With the expansion of the molecular systems (n = 2、3、4) , the noble-gas bond energies were still more than 15、35 kcal/mol, respectively. For (FNg CH2CCH3)n with n > 2, the decomposition reaction would accompanies a radical shift, such that stability substantial declines.

Molecules cooled down to temperatures close to the absolute zero are the subject of the rapidly growing interdisciplinary research field at the border of physics and chemistry. These studies are motivated by possible applications of cold molecules in high-resolution spectroscopy, precision measurements, testing fundamental laws of nature, or in quantum state-controlled chemical reactions. Cold molecules can also be applied for the quantum information processing and quantum simulations of many-body phenomena. The field of cold and ultracold physics was triggered by the first experimental realization of the Bose-Einstein condensate in a dilute gas of rubidium atoms in 1995. The breakthrough required cooling atoms to temperature as low as 200 nanokelvin. Progress made over the last three decades allows nowadays to cool some atoms (mainly alkali metal atoms) to ultralow temperatures by means of laser and evaporative cooling techniques. However, due to the very complex structure of internal states, cooling of molecules is a much more challenging task. Development of efficient and versatile techniques for cooling molecules to ultracold regime (below 1 millikelvin) is one of the key goals of the present research in the field of cold matter. Reaching this goal will allow to observe novel quantum phenomena and practical realization of the above mentioned applications of cold molecules. The main object of the theoretical research reported in this thesis was to explore the possibility of cooling a selected set of molecules and ions by means of photoassociation and sympathetic cooling. Calculations of the interaction potentials and quantum dynamics at ultralow temperatures were performed for systems being investigated experimentally or potentially prospective for future experiments. Regarding the method of sympathetic cooling, the thesis reports results of quantum-dynamical calculations for the LiH + Li, OH + N, and Ba(+) + Rb systems. To evaluate the prospects for sympathetic cooling of lithium hydride by collisions with ultracold lithium atoms we have performed first very accurate calculations of the interaction energy and cross sections for collisions between Li and LiH. The calculated cross sections were then applied in simulations of the sympathetic cooling process in three different molecular traps. The simulations have showed that such a cooling is feasible in a microwave trap but in the electrostatic or alternating gradient field traps it is likely to fail due to substantial molecular losses from the trap. To analyse collision dynamics between open-shell atoms and molecules in external magnetic field we have carried out calculations of cross sections for collisions between the OH radical and the N atom. Results of these calculations have shown that sympathetic cooling of the OH molecules by collisions with nitrogen atoms can be efficient only at rather limited range of collision energies and strengths of the magnetic field, which is a consequence of strong mechanisms leading to inelasticity in this system. Results of the calculations concerning the sympathetic cooling of the Ba(+) ions by collisions with ultracold Rb atoms have proved good prospects for such a process. In the thesis we have also formulated possible optical pathways for efficient photoassociative production of ultracold diatomic strontium molecules in deeply bound rovibrational levels. The effectiveness of the proposed scheme is based on the spin-orbit coupling between two strongly interacting electronic states of the strontium dimer, which paves the way for both photoassociation of cold atoms as well as stabilization of the formed molecules by transfer to the deeply bound rovibrational levels. The proposed scheme of formation of the strontium molecules was possible due to highly accurate ab initio calculations of the potential energy curves for this molecule. Results of these calculations differed significantly from previously published theoretical data and agreed well with the most recent experimental findings. The thesis also includes the analysis of the long-range interactions between open-shell linear molecules and atoms in an S state. Timeliness and importance of this work is mainly due to the interest in such systems for experimental and theoretical studies on the sympathetic cooling of polar molecules. In the thesis we have developed the theory of long-range interactions between a ground-state atom in an S state and a linear molecule in a degenerate state with a nonzero electronic angular momentum. Final formulas for the long-range coefficients that determine the asymptotics of the long-range interaction potentail were expressed in terms of the first and second-order atomic and molecular properties, which gives them a clear physical interpretation. One of the applications of this theory was the OH + N system. The thesis consists of two parts. The first part includes the introduction, outlines the context and the motivation of the present research, and gives a compact description of the obtained results. The second part contains reprints of seven papers published in international scientific journals which describe in details all the obtained results.
Molekuły schłodzone do ultraniskich temperatur, tj. bliskich zera bezwzględnego, stanowią obecnie przedmiot intensywnie rozwijanych, interdyscyplinarnych badań na styku fizyki i chemii. Prace te są motywowane możliwościami zastosowania zimnych cząsteczek w pomiarach spektroskopowych o niespotykanej precyzji, testowaniu fundamentalnych praw fizyki, czy kontroli reakcji chemicznych na poziomie stanów kwantowych reagentów. Zimne cząsteczki mogą także być wykorzystane jako elementy architektury komputerów kwantowych oraz symulatorów kwantowych, służących na przykład do modelowania przejść fazowych. Kamieniem milowym w badaniach nad ultrazimną materią było otrzymanie pierwszego kondensatu Bosego-Einsteina w gazie atomów rubidu w 1995 roku. Wymagało to schłodzenia atomów do temperatur rzędu 200 nanokelwinów. Rozwój technik doświadczalnych opartych na chłodzeniu laserowym i efekcie Dopplera pozwala obecnie na chłodzenie niektórych atomów (głównie metali alkalicznych) do ultraniskich temperatur. Ze względu na skomplikowaną strukturę stanów wewnętrznych, chłodzenie molekuł jest nieporównywalnie trudniejsze niż atomów. Rozwinięcie efektywnych metod chłodzenia molekuł do temperatur poniżej 1 milikelwina stanowi jeden z kluczowych celów prowadzonych obecnie badań nad zimną materią. Osiągnięcie tego celu pozwoli na obserwację nowych zjawisk o czysto kwantowym charakterze oraz realizację w praktyce wyżej wspomnianych zastosowań zimnych cząsteczek. Głównym celem badań teoretycznych przedstawionych w niniejszej pracy była analiza możliwości chłodzenia wybranych molekuł oraz jonów na drodze fotoasocjacji oraz poprzez współchłodzenie (ang. sympathetic cooling) w gazie ultrazimnych atomów. Wybór układów molekularnych, dla których wykonano obliczenia energii oddziaływania i dynamiki zderzeń w ultraniskich temperaturach, był związany z prowadzonymi pracami eksperymentalnymi. W kontekście zastosowania metody współchłodzenia przez termalizację w gazie ultrazimnych atomów w rozprawie przedstawiono wyniki obliczeń kwantowo-dynamicznych dla trzech układów: LiH + Li, OH + N oraz Ba(+) + Rb. Badania możliwości chłodzenie wodorku litu w zderzeniach z atomami litu obejmowały w pierwszej części wykonanie bardzo dokładnych obliczeń potencjału oddziaływania oraz przekrojów czynnych na zderzenia pomiędzy Li i LiH. Obliczone przekroje czynne posłużyły następnie do przeprowadzenia symulacji procesu współchłodzenia molekuł LiH w zderzeniach z atomami Li, testując różne metody pułapkowania molekuł. Pokazano, że najbardziej korzystnym podejściem jest zastosowanie pułapki w postaci wnęki rezonansowej działającej przy częstościach mikrofalowych. Ponadto pokazano, że dla układów o dużej anizotropii potencjału oddziaływania, pułapki oparte o stałe lub przemienne pole elektryczne nie gwarantują pożądanej termalizacji ze względu na szybki spadek ilości pułapkowanych cząsteczek. W ramach projektu dotyczącego analizy dynamiki zderzeń pomiędzy molekułami i atomami otwartopowłokowymi w zewnętrznym polu magnetycznym, wykonano obliczenia przekrojów czynnych na zderzenia pomiędzy rodnikiem OH i atomem N. Wyniki obliczeń pokazały, ze współchłodzenie rodnika OH poprzez zderzenia z atomami azotu może być skuteczne jedynie w stosunkowo niewielkim zakresie energii zderzeń i natężenia pola magnetycznego, co wynika z istnienia silnych mechanizmów prowadzących do zderzeń nieelastycznych w tego typu układach. Wyniki obliczeń dotyczących możliwości chłodzenia jonów Ba(+) w zderzeniach z ultrazimnymi atomami Rb wskazują, że taka metoda powinna być skuteczna a procesy nieelastyczne związane z przeniesieniem ładunku pomiędzy Ba(+) i Rb nie stanowią istotnej przeszkody dla pożądanej termalizacji. W pracy przedstawiono ponadto możliwy schemat tworzenia ultrazimnych molekuł Sr2 w mocno związanych stanach rowibracyjnych, wykorzystując do tego metodę fotoasocjacji. Efektywność zaproponowanej ścieżki opiera się na wykorzystaniu sprzężenia spin-orbita pomiędzy silnie oddziałującymi stanami elektronowymi dimeru strontu. To oddziaływanie umożliwia zarówno wydajną fotoasocjację atomów, jak i skuteczną drogę stabilizacji i tworzenia mocno związanych molekuł Sr2. Proponowany schemat tworzenia cząsteczek Sr2 mógł powstać dzięki wysoce dokładnym obliczeniom ab initio krzywych energii oddziaływania dla tej molekuły, których wyniki istotnie różniły się od uprzednio opublikowanych obliczeń, a jednocześnie były zgodne z najnowszymi danymi eksperymentalnymi. Istotnym problemem poruszonym w rozprawie jest analiza asymptotyki oddziaływania dalekozasięgowego pomiędzy liniowymi molekułami otwartopowłokowymi a atomami w stanie podstawowym o symetrii S. Waga tego zagadnienia wynika z faktu, iż tego typu układy są szeroko rozważane w kontekście zastosowania metody współchłodzenia, a jednocześnie właściwy opis oddziaływania dalekozasięgowego jest kluczowy w badaniach dynamiki kwantowej w niskich temperaturach. W pracy wyprowadzono ogólne wyrażenia na współczynniki van der Waalsa dla oddziaływania atomów w stanie S z molekułą liniową w dowolnym zdegenerowanym stanie elektronowym. Współczynniki te zostały w pełni wyrażone poprzez własności oddziałujących układów (momenty multipolowe, polaryzowalności, itd.), co nadaje im jasną interpretację fizyczną. Jednym z zastosowań tej teorii był wspomniany układ OH + N. Rozprawa składa się z dwóch głównych części. Pierwsza część zawiera wprowadzenie do poruszanej tematyki, nakreślenie celów i motywacji podjętych badań, oraz zwięzłe omówienie stosowanych metod i otrzymanych wyników. Drugą część stanowią kopie siedmiu oryginalnych artykułów naukowych, opublikowanych w czasopismach o międzynarodowym zasięgu, zawierających szczegółowy opis uzyskanych wyników.

碩士
國立中正大學
化學所
97
In chapter one, We have tested several recently developed density functional methods, including M05, M05-2X, M06, M06-2X and double-hybrid density functionals, using the multi-coefficient density functional theory (MC-DFT) approach for the performance on thermochemical kinetics. The results indicated that in most cases, the accuracy can be significantly improved by using more than one basis set, and the same level of accuracy can be reached using less expensive basis set combinations. The three combinations pdz/MG3S, pdz/ptz/apdz, and pc1/pc2/apc1 are especially attractive in this regard. In chapter two, we continued the first chapter, we tested the good methods, including M06-2X, B2K-PLYP and B2T-PLYP methods, using the MC-DFT with more basis set combinations. The tested results showed that the performance of a set of 211 thermochemical kinetics data by the M06-2X method can not be significantly improved, but B2K-PLYP and B2T-PLYP can be reduced 0.2 kcal/mol form using the pdz/ptz/apdz basis set combination to using the pdz/apdz/6-311+G(3df,2pd) and pc1/apc1/6-311+G(3df,2pd) basis set combinations.We further used the thermochemical kinetics data to optimize the ratios of exact exchange energy and the E2 correlation energy on the B2K-PLYP and B2T-PLYP methods, in able to obtain a new MC-B2-PLYP method. The optimized results showed that the mean unsigned errors (MUEs) of the most of the basis set combinations can be reduced 0.1 kcal/mol, and the best result can be using the pc1/apc1/6-311+G(3df,2pd) basis set combinations with 1.29 kcal/mol. In chapter three, we used ab initio and the DFT methods to study the molecules containing XeN multiple bonds. The computed results showed that the Xe-N bond lengths of XeNO2-, XeNOF, XeF2NO-, XeNO2F, XeNO2Li and XeF2NOLi can be very short, there are approximately 1.80 Å. We also calculated the six molecules decomposed to the stable and small molecules, the energy barriers of them have 41.8, 19.6, 27.8, 27.1, 29.7 and 36.2 kcal/mol, respectively. Therefore we think this type of noble-gas (Ng) molecules can be stably existed under the suitable and low temperature conditions. In chapter four, we used EOM-CCSD and TD-B3LYP methods to study the UV-Vis spectra of ClOOCl. The computed results showed that the UV-Vis Spectra of the two methods had approximately the biggest absorption in 225 and 245 nm, respectively. They had the weak absorption at the position of long wave lengths, the results were consistent with the tendency of the experiments. The computed results also showed that the rotation of dihedral angles of ClOOCl had the obvious enhancement at approximately 318 nm; The elongation of the bond of ClO will create the obvious red shift of the absorbing position, possibly to create at the experiment the long wave length absorption reason. We also used ab initio, DFT and the multi-coefficient electronic structure methods to study the relative energies and the barriers of Cl2O2 isomers. The computed results showed that the stability of Cl2O2 isomers were ClClOO> ClClO2>ClOOCl>ClOClO. The energy barriers of Cl2O2 isomers were all higher than the results of Ming-Chang Lin et al, we thought the reason of the difference results were the convergence of basis sets.

博士
國立中正大學
化學暨生物化學研究所
108
This thesis consists of four chapters. In chapter one, we discover the new type stable noble gas containing anions without halogens. In chapter two, we design the stable triplet neutral noble gas containing molecule FNgBCO. In chapter three, we calculate carbon K-edge NEXAFS specta of small organic moleules which contain double bond and aromatic rings and understand the infuence on spectrum by structure. In chapter four, we calculated the carbon and nitrogen K-edge NEXAFS spectra for amide seires molecules with TDDFT method and analyze the corresponding between structures and spectra. In chapter one, we we find the new type stable noble gas containing anions OBONgO、NCONgO、OCNNgO、HBNNgO、FBNNgO and FNgNBOwhere Ng were argon, krypton and Xenon. The linear dissociaiotn energies, barriers of bending dissociation and S-T gap of these noble gas containing anions are more than 23.0, 15.0 and 40.0 kcal/mol respectively. The noble gas containing anions for argon may occure inter-system crossing. By the charge analysis, The OBONgO, NCONgO, OCNNgO, HBNNgO, FBNNgOwere more like ion-dipole complex, but FNgNBO does not possess so much properties of ion-dipole complex. In chapter two, we find the stable triplet neutral noble gas containing molecule FNgBCO where Ng were krypton and Xenon. The linear dissociaiotn energies, barriers of bending dissociation and S-T gap of FNgBCO were larger than 20.3, 15.0 and 16.1 kcal/mol resprectively. The FNgBCO can convert to FNgCBO molecule, but our calculations also showe FNgCBO are stable enougth. In summary, the triplet neutral noble gas containing molecule FNgBCO may be observed at cryogenic conditions. In chapter three, we calculate the carbon K-edge NEXAFS spectra by TDDFT method with B3LYP and LB94 fuctionals for ethyne, ethylene, benzene, benzene derivative, naphthalene, pyridine, pyrimidine and purine moleules. For using TD-B3LYP/6-31+G(d,p) method, although the calculated spectra are needed to shift about 10.0 eV, the corresponding between calculated and experimental spectra are much better. The main excitagtion enregy for 1s →π* transition of containing benzene molecules is located around 285.0 eV which is slightly lower than the main excitagtion enregy of pure doouble bond containing molecule (~ 287.0 eV). The specie of substituent on benzene affect the shifting of excitation energy of main transition but the number of substituent shows influence only on intensity. Increasing the number of benzene rings can not chage the spectrum. From the assignment of pyridne, pyrimidine and purine, the main absorption becomes broad due to the existence of more different carbon atoms in the structure. In chapter four, we calculate the carbon, nitrogen K-edge NEXAFS spectra for amide series molecules. For all amide molecules, the main excitation energies locate around 288.0 and 402.0 eV respectively which correspond to the transition C :1s → peptide π* and N:1s → peptide π*. If the moleule contains both benzene and peptide strctures at the same time, the spectra also showe specific absorption peaks for both structures. The bonding methyl goups also affect the absorption peaks in the region of 289.0 and 402.0 eV.

碩士
東海大學
化學系
99
In this thesis Hartree-Fock (HF) approximation and MP2 method are used to calculate and analyze the electron intracule densities, extracule densities and normal densities of atoms. Some simple molecular topologies of the electron intracule densities and extracule densities, I(R) and E(R), are also calculated by HF method and analyzed. These topologies are found to be inherently more complex than those of the one-electron density. The main topological features of I(R) and E(R) are already present in the densities calculated within the Hartree-Fock (HF) approximation compare with those from correlated wave functions. Results of calculations on several planar molecules show that the positions, number and properties of attractors in I(R) and E(R) are predicted with a surprising fidelity by a native independent-atom model, making it possible to index distinct types of electron pairs present in atoms and molecules. The attractors in I(R) stem from electron pairs of both individual atoms and atomic pairs in the relative electron coordinate; the attractors in E(R) stem from both individual atoms and atomic pairs in the center of electron pair coordinate. The contributions to attractors by such light atom as hydrogen may be present or may not, depending on the other nuclei in the molecular system.

碩士
國立中正大學
化學暨生物化學研究所
103
This thesis consists of five chapters. In chapters 1 and 2, we studied the stability of some metal-containing noble-gas anions. In chapter 3, we studied the stability of transition metal-containing noble-gas anions. In chapter 4, we studied the prebiotic synthesis of glyceraldehyde and dihydroacetone by formose reaction in neutral environment. In addition to the gas-phase study, we also model the solvation effects with two different approaches, micro-solvation and polarizable continuum model (PCM). In chapter 5, we studied the stability of various OSO isomers and their isomerization and dissociation reactions. In Chapter 1, we calculated the geometry and stability of a series of noble-gas anions X−NgO ( X = OBO, OAlO, NCO, OCN, NC, OAg, and etc) by ab initio methods . The anions can induce theformation of the NgO bond by polarization. We found that the stability of X−NgO depended strongly on the electron affinity of the neutral species X. Usually the X with higher electron affinity can form more stable X−NgO anions. The calculated results showed that the OMO−NgO ( Ng=Ar , Kr, Xe ; M=Al , B) anions which has high dissociation energy may be experimentally detectable in low-temperature conditions. In Chapter 2, we have calculated the molecular geometries, bond energies, and charge distribution of the metal-containing noble-gas anions OMO−(NgO )n ( Ng= Ar, Kr, and Xe ; M=Al , B；n =1~2 ). The geometries of these anions were found to be highly symmetric. The calculated results revealed that the OMO−( NgO )n ( Ng= Ar, Kr, and Xe ; M=Al , B；n =1~2 ) anions may be experimentally detectable at low-temperature. We also calculated the OArOMOKr−, OArOMOXe−, and OKrOMOXe− (M=Al , B) anions which has high dissociation energy may be experimentally detectable in low-temperature conditions. In Chapter 3, we have calculated the molecular geometries and the stability of the transition metal-containing noble-gas anions OMOO−ArO (M = Ti, V, Co, Cu). The stable noble-gas anions previously studied were all in singlet states. It is expected that the stable noble-gas anions could exist in different spin states by including 3d transition metal elements. The calculated results showed that the stable anion OVOO−ArO was in singlet state and the stable anion OCoOO−ArO was in the triplet state. We also used various DFT methods to calculate electron affinities of OMOO− (M = Ti, V, Co, Cu) and compared them to experimental results. In Chapter 4, we studied the the prebiotic synthesis of glyceraldehyde and dihydroacetone, which are precursors of ribose, by formose reaction. The possible reaction pathways of synthesis for glyceraldehyde and dihydroacetone from formaldehyde were calculated in the gas phase, in bulk solvent, and with microsolvation by H2O or NH3 molecules. We found that if a reaction step involves a proton transfer, the energy barrier could be significantly reduced by approximately 20 ~ 30 kcal/mol with microsolvation by H2O or NH3. The polarized continuum solvation model (PCM) could sometimes further lower the barrier by 3~5 kcal/mol. So the formose reaction can occurs more readily in comparison with the reactions in the gas phase. In chapter 5, we studied the molecules OSO and SOO which are isoelectronic to the ozone. The high level methods, CASPT2, MRCISD+Q, were used to calculate the relative energies of the cyclic and the open forms of OSO. The first singlet excited state (1A" state) and the ground state (1A' state) potential energy surfaces were calculated. The result showed that when the ground state open-OSO was excited by radiation, it would become open-SOO through the cross section of 1A' and 1A" potential energy surfaces because of the near-degeneracy of ground and excited transition states. However, the reaction open-OSO → cyclic-SOO would not likely to occur through the intersection of the potential energy surfaces. The dissociation energies of reactions open-OSO → SO + O and S + O2 are 149.6 kcal/mol and 145.2 kcal/mol.