Proton transfer, electron binding and electronegativity in ammonium-containing systems

Using modern electronic structure methods, the ammonia-hydrogen halide complexes and their anions are characterised to determine the number, type, and properties of their minima, and their electron binding energies. Methodological issues of determining the potential energy surfaces of reactive monomers are addressed in the course of this investigation. The energetic origins of the hydrogen-bonded minima are determined by evaluation of the one-body and two-body terms composing the total energy of the complexes, and a rationale for the drive to proton transfer is presented. It is concluded that the systems have qualitatively similar potential surfaces, and that the balance of the one-body and two-body forces determines the number and depth of minima, while the electron acts as a perturbing agent on the one- or two-body energy, depending upon the nature of the minimum encountered. The halogen-bonded structures of ammonia-hydrogen bromide, iodide, and astatide complexes are shown to be stable, and one may perhaps bind an electron. The concept of the ammonium radical as a pseudo-atom is presented and tested. It is found to show competing pseudo-atomic and molecular properties.Engineering and Physical Sciences Research Council (EPSRC

Structure, solvation, thermodynamics and fragmentation of molecular clusters

Cette thèse vise à étudier en détail le comportement d'agrégats moléculaires complexes et se concentre sur deux aspects principaux. Tout d'abord, la description des isomères de faible énergie des clusters d'ammonium et ammoniac et (H2O)1-7,11,12UH+ à travers l'exploration des surfaces d'énergie potentielle (PES) en utilisant une combinaison d'approches d'optimisation globales et locales. Les propriétés structurelles, de solvatation et thermodynamiques des isomères de basse énergie nouvellement identifiés ont été caractérisées. Par la suite, des simulations dynamiques de la dissociation induite par collision des (H2O)1-7,11,12UH+ et Py2+ ont été réalisées et analysées en termes de : mécanisme de dissociation, répartition d'énergie, spectres de masse et sections efficaces de collision pour complémenter des mesures expérimentales récentes menées sur ces espèces. L'optimisation globale des clusters (H2O)1-10NH4+ et (H2O)1-10NH3 a été réalisée au niveau de théorie SCC-DFTB (pour self-consistent-charge density-functional based tight-binding), pour laquelle des paramètres N-H améliorés ont été proposés, en combinaison avec l'approche d'exploration PTMD (pour parallel-tempering molecular dynamics). Les isomères de basse énergie nouvellement déterminés ont été optimisés au niveau MP2 afin d'évaluer la fiabilité de nos paramètres N-H modifiés. Les structures et les énergies de liaison obtenues avec la méthode SCC-DFTB sont en très bon accord avec les résultats de niveau MP2/Def2TZVP, ce qui démontre la capacité de l'approche SCC-DFTB à décrire la PES de ces espèces moléculaires et représente ainsi une première étape vers la modélisation d'agrégats complexes d'intérêt atmosphérique. L'intérêt porté aux (H2O)1-7,11,12UH+ vise à fournir une description détaillée d'expériences récentes de dissociation induite par collision (CID). Premièrement, les isomères stables des (H2O)1-7,11,12UH+ sont calculés en utilisant la même méthodologie que celle décrite ci-dessus. Ensuite, des simulations dynamiques des collisions entre isomères (H2O)1-7,11,12UH+ et un atome d'argon sont réalisées à énergie de collision constante au niveau SCC-DFTB. La proportion simulée d'agrégats neutres contenant l'uracile par rapport à celle d'agrégats chargés contenant l'uracile, la section efficace de fragmentation ainsi que les spectres de masse sont cohérents avec les données expérimentales ce qui met en évidence la précision de nos simulations. Ces dernières permettent de sonder en details les fragments qui se forment aux temps courts et de rationaliser la localisation du proton en excès sur ces fragments. Cette dernière propriété est fortement influencée par la nature de l'agrégat soumis à la collision. L'analyse de la proportion des fragments en fonction du temps et des spectres de masse démontrent que, jusqu'à 7 molécules d'eau, un mécanisme de dissociation direct alors que pour 11,12 molécules, un mécanisme statistique est plus susceptible d'intervenir. Enfin, des simulations d'expériences CID du Py2+ à différentes énergies de collision, entre 2,5 et 30 eV, sont présentées. Les simulations permettent de comprendre les processus de dissociation mis en jeu. L'accord entre les spectres de masse simulés et mesurés suggère que les principaux processus sont bien pris en compte par cette approche. Il semble que la majeure partie de la dissociation se produise sur une courte échelle de temps (moins de 3 ps). L'analyse de la répartition d'énergie cinétique est utilisée pour obtenir des informations sur les processus de collision/dissociation à l'échelle atomique. Les spectres de masse simulés des clusters parents et dissociés sont obtenus à partir en combinant simulations de dynamique moléculaire et théorie de l'espace des phases pour traiter respectivement la dissociation aux courtes et longues échelles de temps.This thesis aims at studying in details the behavior of complex molecular clusters and focuses on two main aspects. First, the description of low-energy isomers of ammonium/ammonia water clusters and (H2O)1-7,11,12UH+ through an extensive exploration of potential energy surfaces (PES) using a combination of global and local optimization schemes. Structural, solvation and thermodynamics properties of the newly identified low-energy isomers were characterized. Second, the dynamical simulations of collision-induced dissociation of (H2O)1-7,11,12UH+ and Py2+ were carried out to explore collision trajectories, dissociation mechanism, energy partition, mass spectra, and collision cross sections to complement experimental measurements conducted on these species. Global optimization of (H2O)1-10NH4+ and (H2O)1-10NH3 clusters is conducted at the self-consistent-charge density-functional based tight-binding (SCC-DFTB) level of theory, for which improved N-H parameters are proposed, in combination with the parallel-tempering molecular dynamics (PTMD) approach. Low-energy isomers of (H2O)1-10NH4+ and (H2O)1-10NH3 are further optimized at MP2 level in order to evaluate the reliability of our modified N-H parameters. Both structures and binding energies obtained at SCC-DFTB agree with the results at MP2/Def2TZVP level, which demonstrates the ability of SCC-DFTB to describe the PES of molecular species and represents a first step towards the modeling of complex aggregates of atmospheric interest. Focus on (H2O)1-7,11,12UH+ aims at providing a detailed description of recent collision-induced dissociation (CID) experiments. First, stable isomers of (H2O)1-7,11,12UH+ are calculated using the same methodology as described above. Then, dynamical simulations of the collisions between various (H2O)1-7,11,12UH+ isomers and argon is conducted at a constant collision energy at the SCC-DFTB level. Simulated proportion of formed neutral vs. protonated uracil containing clusters, fragmentation cross-section as well as mass spectra are consistent with the experimental data which highlights the accuracy of our simulations. They allow to probe which fragments are formed on the short time scale and rationalize the location of the excess proton on these fragments. This latter property is highly influenced by the nature of the aggregate undergoing the collision. Analyses of proportion of time-dependent fragments and mass spectra demonstrate that, up to 7 water molecules, a shattering mechanism occurs after collision whereas for n=11,12 a statistical mechanism is more likely to participate. Dynamical simulation of CID experiments of Py2+ for different collision energies between 2.5 and 30 eV is also presented. The dynamical simulations allow to understand the dissociation processes. The agreement between the simulated and measured mass spectra suggests that the main processes are captured by this approach. It appears that most of the dissociation occurs on a short timescale (less than 3 ps). Analysis of the kinetic energy partition is used to get insights into the collision/dissociation processes at the atomic scale. The simulated mass spectra of the parent and dissociated products are obtained from the combination of molecular dynamics simulations and phase space theory to address the short and long timescales dissociation, respectively

Quantum Chemical Investigations in Homogeneous Catalysis: Dehydroperoxidation and Asymmetric Reductive Amination

This thesis describes the investigation of homogeneously catalyzed reactions with quantum chemical methods. Two different reactions were studied in this work: the dehydroperoxidation of alkyl hydroperoxides with both vanadium and chromium catalysts and the direct asymmetric reductive amination of ketones with ruthenium. In the first part, the dehydroperoxidation of cyclohexyl and 4-heptyl hydroperoxide to the corresponding ketones with a vanadium dipicolinato complex is investigated. It is found that a radical-free mechanism is feasible and that it proceeds through hydrogen abstraction by the vanadium oxo group. The barrier difference for this process for both substrates is in line with higher experimental selectivities for the non-cyclic hydroperoxide. A mechanistic study on the chromium-catalyzed dehydroperoxidation follows, which shows that a similar mechanism is active for Cr. The better selectivity and activity of this catalyst in comparison with the vanadium system is reproduced as the activation energy for dehydroperoxidation is lower with chromium. Finally, we rule out that the reaction proceeds via an intramolecular hydrogen transfer in an alkoxy/alkylperoxo chromium species, which has been suggested in previous research on the topic. The second part of the thesis explores the mechanism of the direct asymmetric reductive amination of ketones with a ruthenium (S,S)-f-binaphane complex. Acetophenone is used as the model ketone for this reaction. The investigations show that the rate-determining step of the reaction is the proton transfer from a σ-dihydrogen complex to liberate the amine. A thorough analysis of possible isomer/conformer combinations turns out to be crucial for a quantitative understanding of the reaction; following such an analysis, the experimental enantioselectivity is accurately reproduced for a series of catalysts with different halide ligands. These results are supplemented by studies on the chemoselectivity of the reaction. The mechanism is then applied to build a simple model for estimating the bite angle dependency of the reaction’s enantioselectivity. It is predicted that larger bite angles should favor higher enantioselectivity. A search in the CCDC database reveals several promising ligand backbone candidates for an optimized binaphane ligand of which a biaryl motif is finally considered as the most promising candidate

Molecular aggregation of thiols and alcohols: study of non-covalent interactions by microwave spectroscopy

El estudio y comprensión de las interacciones no covalentes a nivel molecular es un campo que está en continuo desarrollo y cobra vital importancia para determinar el comportamiento estructural de muchas moléculas de interés químico, tecnológico o biológico. En esta tésis doctoral se han analizado las interacciones intermoleculares implicadas en la formación de agregados moleculares neutros, tanto dímeros como productos de microsolvatación, en fase gas. Los complejos intermoleculares se han generado mediante expansiones supersónicas pulsadas, caracterizándose posteriormente mediante espectroscopía de rotación. Este trabajo ha utilizado dos técnicas espectroscópicas, incluyendo un espectrómetro de microondas con transformada de Fourier (FTMW) de tipo Balle-Flygare en el rango de frecuencias 8-20 GHz, y un espectrómetro de transformada de Fourier de banda ancha con excitación multifrecuencia (CP-FTMW) cubriendo el rango espectral de 2-8 GHz. Los complejos intermoleculares estudiados han incluido moléculas con grupos alcohol y/o tiol, con objeto de analizar las diferencias entre las interacciones intermoleculares que implican átomos de oxígeno o azufre, en especial el enlace de hidrógeno. Se han estudiado moléculas incluyendo tanto sistemas cíclicos alifáticos (ciclohexanol, ciclohexanotiol) como aromáticos (furfuril alcohol, furfuril mercaptano, tienil alcohol, tienil mercaptano). Los enlaces de hidrógeno analizados han comprendido especialmente interacciones de tipo O-H···O, O-H···S y S-H···S. La formación de los complejos intermoleculares ha revelado en algunos de ellos una gran variedad conformacional, como la observación de seis isómeros del dímero de ciclohexanol. En el caso de los monohidratos se han observado en algunos casos desdoblamientos asociados a movimientos internos de gran amplitud, como la rotación de la molécula de agua en los monohidratos de ciclohexanol y tienil mercaptano. En los casos de moléculas quirales la dimerización ha permitido observar la estabilidad relativa de los diastereoisómeros homo o heteroquirales. El estudio experimental se ha completado con diferentes cálculos teóricos de orbitales moleculares, en especial teoría del funcional de la densidad, a fin de caracterizar las interacciones estructuralmente, energéticamente y mediante análisis topológico de la densidad electrónica. El conjunto de datos experimentales y teóricos permite aumentar la información existente sobre enlaces de hidrógeno con átomos de azufre, generalmente poco estudiados, y su comparación con los análogos oxigenados.The study and understanding of non-covalent interactions at molecular level is a field in continuous development and essential to determine the structural behavior of many molecules of chemical, technological or biological interest. In this PhD thesis, the intermolecular interactions involved in the formation of neutral molecular aggregates, both dimers and microsolvation products, have been analyzed in the gas phase. The intermolecular complexes were generated by pulsed supersonic expansions, and later characterized by rotational spectroscopy. This work has used two spectroscopic techniques, including a Balle-Flygare Fourier-Transform Microwave (FTMW) spectrometer in the 8-20 GHz frequency range, and a broadband Chirped-Pulse Fourier Transform Microwave (CP-FTMW) spectrometer covering the 2-8GHz spectral range. The intermolecular complexes studied have included molecules with alcohol and / or thiol groups, in order to analyze the differences between the intermolecular interactions involving oxygen or sulfur atoms, especially hydrogen bonds. Molecules that comprise both aliphatic (cyclohexanol) and aromatic (furfuryl alcohol, furfuryl mercaptan, thenyl alcohol, thenyl mercaptan) ring systems have been studied. The analyzed hydrogen bonds included especially O-H···O, O-H···S and S-H···S interactions. The formation of intermolecular complexes has revealed a great conformational diversity in some of them, such as the observation of six isomers of the cyclohexanol dimer. With regard to the monohydrates, tunnelling splittings associated with internal large amplitude motions have been observed in some cases, such as the rotation of the water molecule in the monohydrates of cyclohexanol, thenyl alcohol and thenyl mercaptan. In the case of chiral molecules, dimerization has made it possible to observe the relative stability of homo- or heterochiral diastereoisomers. The experimental study has been supported by different theoretical molecular orbital calculations, in particular Density Functional Theory (DFT) calculations, in order to characterize the interactions structurally, energetically and by a topological analysis of electron density. The set of experimental and theoretical data will advance the existing information on hydrogen bonds involving sulfur atoms, generally scarcely studied, and their comparison with the oxygenated analogues.Departamento de Química Física y Química InorgánicaDoctorado en Físic

New Conceptual Understanding of Lewis Acidity, Coordinate Covalent Bonding, and Catalysis

The focus of this dissertation is to correct misconceptions about Lewis acidity, uncover the physical nature of the coordinate covalent bond, and discusses how Lewis acid catalysts influence the rate enhancement of the Diels-Alder reaction. Large-scale quantum computations have been employed to explore many of Lewis\u27 original ideas concerning valency and acid/base behavior. An efficient and practical level of theory able to model Lewis acid adducts accurately was determined by systematic comparison of computed coordinate covalent bond lengths and binding enthalpies of ammonia borane and methyl substituted ammonia trimethylboranes with high-resolution gas-phase experimental work. Of all the levels of theory explored, M06-2X/6-311++G(3df,2p) provided molecular accuracy consistent with more resource intensive QCISD(T)/6 311++G(3df,2p) computations. Coordinate covalent bond strength has traditionally been used to judge the strength of Lewis acidity; however, inconsistencies between predictions from theory and computation, and observations from experiment have arisen, which has resulted in consternation within the scientific community. Consequently, the electronic origin of Lewis acidity was investigated. It has been determined that the coordinate covalent bond dissociation energy is an inadequate index of intrinsic Lewis acid strength, because the strength of the bond is governed not only by the strength of the acid, but also by unique orbital interactions dependent upon the substituents of the acid and base. Boron Lewis acidity is found to depend upon both substituent electronegativity and atomic size. Originally deduced from Pauling\u27s electronegativities, boron\u27s substituents determine acidity by influencing the population of its valence by withdrawing electron density. However, size effects manifest differently than previously considered, where greater σ-bond orbital overlap, rather than π-bond orbital overlap, between boron and larger substituents increase the electron density available to boron, thereby decreasing Lewis acidity. The computed electronegativity and size effects of substituents establish unique periodic trends that provide a novel and clearer understanding of boron Lewis acidity, consistent with first principle predictions. Lastly, it is discovered that the energetics associated with the transition structure converge much slower than what was observed for coordinate covalent bonded ground states. Consequently, it is harder to model activation barriers, as compared to binding energies, to within experimental accuracy, because larger basis sets must be employed. Hyperconjugation within dienophile ground states, initiated by geminal Lewis acid interactions, is found to govern the strength of the coordinate covalent bond between the Lewis acid and the dienophile. A novel interpretation is presented where the strength of the coordinate covalent bond within the Lewis acid activated dienophile is governed by donor-acceptor orbital interactions between the π-density present on the carbonyl group to the σ* orbitals on the Lewis acid, rather than the main donor-acceptor motif between the oxygen lone pair and the empty 2p orbital on the Lewis acid. Moreover, the same hyperconjugation within the dienophile controls the rate enhancement of the Lewis acid catalyzed Diels-Alder reaction, by modulating the energy of the dienophile\u27s lowest unoccupied molecular orbital. A new understanding of Lewis acidity and coordinate covalent bonding has been achieved to better describe and predict the structure and electronic mechanism of organic reactions

Computational Characterization of Carboxyphosphate

Carboxyphosphate (CP) is an important intermediate involved in reactions catalyzed by acetyl-CoA carboxylase, pyruvate carboxylase, N5-Carboxyaminoimidazole ribonucleotide synthetase, propionyl-CoA carboxylase, urea amidolyase, and carbamoyl phosphate synthetase. Despite its important role, properties for CP have never been reported due to its short estimated half-life (t1/2 70 ms). Thus, the high level ab initio methods, MP2 and CCSD(T), along with the DFT functionals: B3LYP, BB1K, M05-2X, M06-2X, and MPW1K were used to investigate the structure and energetics of CP in both vacuum and the PCM continuum solvation model of water. It was found that CP adopts a novel pseudo-cyclic structure featuring an intramolecular charge-assisted hydrogen bond (CAHB) that is reminiscent of chair cyclohexane. This structure is found to be the most stable in both vacuum and implicit solvation for both mono and dianionic charge states. Additionally, the M06-2X/aug-cc-pVTZ level of theory was shown to give consistent agreement with ab initio methods for both geometric and energetic properties. The strengths of the CAHBs observed in mono- and dianionic CP were estimated to be within the range of -17.8 to -25.4 and -15.7 to -20.9 kcal/mol, respectively. This classifies them as short-strong but not low-barrier and makes them the dominant stabilizing feature for these conformations. pKa values were computed to distinguish between different possible protonation states of CP. The predicted pKa values were found to be be -3.43±0.81, 4.04±0.35, and 8.14±1.92 for the first, second and third acid dissociations of CP, respectively, indicating it is most likely to be present as a dianion or trianion in aqueous solution but more work is required to predict its charge state in the enzymatic pocket

Simulations of proton transfer processes using reactive force fields

Within this thesis we presented the development of reactive force fields that are ca- pable to describe the dynamics of proton and hydrogen atom transfer processes. The presented implementation in CHARMM overcomes the limitation that bond break- ing and formation cannot be investigated by conventional classical MD simulations. Derived from high-level ab initio calculations this approach combines the accuracy of such calculations with the speed of MD simulations. The high-quality force fields of the prototype systems are comparable to high-level ab initio calculations in terms of structure and energy barriers. The PESs of proton transfer reactions are extremely sensitive with respect to the chemical environment. Nevertheless one is always able to classify the PT under investigation into symmetric and asymmetric PES. We de- veloped a series of parameter sets that are not only able to describe symmetric and asymmetric correctly but also can accommodate to different locations of energetic minima and barriers. The chosen three-dimensional potential energy functions have shown to be quite flexible and transferable in characterizing PT reactions in quite diverse chemical systems. The morphing transformation of MMPT force field param- eter, starting from one of our prototype systems to develop a new force field for a new molecular system which exhibits a similar topology in the PES along the proton reac- tion coordinates, has been shown to be successfully applicable in various examples. Energy scaling has been employed to investigate the effect on the proton transfer os- cillation in NH+ 4 · · ·NH3. New parameters through morphing have been developed for protonated diglyme, as well as for double proton transfer in 2PY2HP and for as- partic acid and water as model system for PT reactions in the active site of bacterial ferredoxin I. We applied the MMPT force field to investigate the vibrational infrared spectra of proton-bound species and explored the relationship of infrared spectra for protonated water dimer and protonated diglyme. The results for protonated water dimer compared well with other high-level calculations. Besides the further system- atic development of the morphing approach one can also employ the force field in combination with Feynman path integral methods. The MMPT force field could be a viable alternative to lower level quantum mechanical methods because the accuracy of the force field is only limited by the initial determination of the underlying PES for the PT of interest

Determining the dominant degradation mechanisms in Nitrocellulose

Nitrocellulose (NC) is the base component for many modern day propellants and explosives, as well as for everyday items such as printing inks, paint and lacquer coatings. Despite its early beginnings as the first man-made plastic, the decomposition pathways from the bulk material to the products observed from its ambient ageing are still not fully understood. Knowledge of these processes are of critical importance when considering the conservation of NC artefacts, refinement of product formulations, predictions of shelf life and safety improvements. In this study, the dominant degradation pathways of NC were investigated using quantum mechanics (QM) methods to probe the mechanisms leading to the initial cleavage of nitrate groups from the cellulosic backbone. The NC structure was truncated from a polymer chain to monomer, dimer and trimer units. Density functional theory methods (DFT) were used to study the mechanistic detail at individual nitrate sites. Comparison of differently sized units using the quantum theory of atoms in molecules (QTAIM), analysis of the electrostatic potential (ESP) surface and partial charges showed that the most suitable approximation for study of the decomposition reactions was the β-glucopyranose monomer, bi-capped with methoxy groups. The primary thermolytic and hydrolytic denitration routes were explored using transition state (TS) searches and potential energy surface (PES) scans. It was found that the thermolytic behaviour of the NC denitration step matched that of a well studied nitrate ester, pentaerythritol tetranitrate (PETN). The hydrolytic scheme for nitrate cleavage was studied, finding that protonation at the bridging oxygen site was the most likely to lead to denitration. It was not possible to isolate a TS for the hydrolytic reaction, though a number of coordination schemes were tested. Key secondary processes beyond nitrate cleavage were examined to determine the fate of nitrogen in the system and the cause of the transition from a first order reaction rate to autocatalytic decomposition. The energies of reactions in three different decomposition schemes proposed in literature were compared. Ethyl nitrate was used as a test system before extension to the NC monomer. New reaction pathways for decomposition were constructed using the reactions posed in the literature studies. The new schemes revealed that •NO2 was the most likely cause for the experimentally observed autocatalytic rate of degradation