Proton transfer or hemibonding? The structure and stability of radical cation clusters

The basin hopping search algorithm in conjunction with second-order Moller-Plesset perturbation theory is used to determine the lowest energy structures of the radical cation clusters (NH_3)_n^+, (H_2O)_n^+, (HF)_n^+, (PH_3)_n^+, (H_2S)_n^+ and (HCl)_n^+, where n=2-4. The energies of the most stable structures are subsequently evaluated using coupled cluster theory in conjunction with the aug-cc-pVTZ basis set. These cationic clusters can adopt two distinct structural types, with some clusters showing an unusual type of bonding, often referred to as hemibonding, while other clusters undergo proton transfer to give an ion and radical. It is found that proton transfer based structures are preferred by the (NH_3)_n+, (H_2O)_n^+, and (HF)_n^+ clusters while hemibonded structures are favoured by (PH_3)_n^+, (H_2S)_n^+ and (HCl)_n^+. These trends can be attributed to the relative strengths of the molecules and molecular cations as Brønsted bases and acids, respectively, and the strength of the interaction between the ion and radical in the ion-radical clusters

Relative energetics of acetyl-histidine protomers with and without Zn²⁺ and a benchmark of energy methods

We studied acetylhistidine (AcH), bare or microsolvated with a zinc cation by simulations in isolation. First, a global search for minima of the potential energy surface combining both, empirical and first-principles methods, is performed individually for either one of five possible protonation states. Comparing the most stable structures between tautomeric forms of negatively charged AcH shows a clear preference for conformers with the neutral imidazole ring protonated at the N-epsilon-2 atom. When adding a zinc cation to the system, the situation is reversed and N-delta-1-protonated structures are energetically more favorable. Obtained minima structures then served as basis for a benchmark study to examine the goodness of commonly applied levels of theory, i.e. force fields, semi-empirical methods, density-functional approximations (DFA), and wavefunction-based methods with respect to high-level coupled-cluster calculations, i.e. the DLPNO-CCSD(T) method. All tested force fields and semi-empirical methods show a poor performance in reproducing the energy hierarchies of conformers, in particular of systems involving the zinc cation. Meta-GGA, hybrid, double hybrid DFAs, and the MP2 method are able to describe the energetics of the reference method within chemical accuracy, i.e. with a mean absolute error of less than 1kcal/mol. Best performance is found for the double hybrid DFA B3LYP+XYG3 with a mean absolute error of 0.7 kcal/mol and a maximum error of 1.8 kcal/mol. While MP2 performs similarly as B3LYP+XYG3, computational costs, i.e. timings, are increased by a factor of 4 in comparison due to the large basis sets required for accurate results

Computation of Atmospheric Concentrations of Molecular Clusters from ab initio Thermochemistry

The computational study of the formation and growth of atmospheric aerosols requires an accurate Gibbs free energy surface, which can be obtained from gas phase electronic structure and vibrational frequency calculations. These quantities are valid for those atmospheric clusters whose geometries correspond to a minimum on their potential energy surfaces. The Gibbs free energy of the minimum energy structure can be used to predict atmospheric concentrations of the cluster under a variety of conditions such as temperature and pressure. We present a computationally inexpensive procedure built on a genetic algorithm-based configurational sampling followed by a series of increasingly accurate screening calculations. The procedure starts by generating and evolving the geometries of a large set of configurations using semi-empirical models then refines the resulting unique structures at a series of high-level ab initio levels of theory. Finally, thermodynamic corrections are computed for the resulting set of minimum-energy structures and used to compute the Gibbs free energies of formation, equilibrium constants, and atmospheric concentrations. We present the application of this procedure to the study of hydrated glycine clusters under ambient conditions

Computation of Atmospheric Concentrations of Molecular Clusters from \u3cem\u3eab initio\u3c/em\u3e Thermochemistry

The computational study of the formation and growth of atmospheric aerosols requires an accurate Gibbs free energy surface, which can be obtained from gas phase electronic structure and vibrational frequency calculations. These quantities are valid for those atmospheric clusters whose geometries correspond to a minimum on their potential energy surfaces. The Gibbs free energy of the minimum energy structure can be used to predict atmospheric concentrations of the cluster under a variety of conditions such as temperature and pressure. We present a computationally inexpensive procedure built on a genetic algorithm-based configurational sampling followed by a series of increasingly accurate screening calculations. The procedure starts by generating and evolving the geometries of a large set of configurations using semi-empirical models then refines the resulting unique structures at a series of high-level ab initio levels of theory. Finally, thermodynamic corrections are computed for the resulting set of minimum-energy structures and used to compute the Gibbs free energies of formation, equilibrium constants, and atmospheric concentrations. We present the application of this procedure to the study of hydrated glycine clusters under ambient conditions

Investigation of the Structures and Energy Landscapes of Thiocyanate-Water Clusters

The Basin Hopping search method is used to find the global minima (GM) and map the energy landscapes of thiocyanate-water clusters, (SCN−)(H2O)n with 3–50 water molecules, with empirical potentials describing the ion-water and water-water interactions. (It should be noted that beyond n = 23, the lowest energy structures were only found in 1 out of 8 searches so they are unlikely to be the true GM but are indicative low energy structures.) As for pure water clusters, the low energy isomers of thiocyanate-water clusters show a preponderance of fused water cubes and pentagonal prisms, with the weakly solvated thiocyanate ion lying on the surface, replacing two water molecules along an edge of a water polyhedron and with the sulfur atom in lower coordinated sites than nitrogen. However, by comparison with Density Functional Theory (DFT) calculations, the empirical potential is found to overestimate the strength of the thiocyanate-water interaction, especially O–H⋯S, with low energy DFT structures having lower coordinate N and (especially) S atoms than for the empirical potential. In the case of these finite ion-water clusters, the chaotropic (“disorder-making”) thiocyanate ion weakens the water cluster structure but the water molecule arrangement is not significantly changed

Determining Molecular Physicochemical Properties Using Differential Mobility Spectrometry

This thesis aims to explore the usage of differential mobility spectrometry (DMS) and quantum chemical calculations to separate and identify drug compounds, as well as the use of machine learning (ML) to predict physicochemical properties such as the collision cross section (CCS) and single solvent binding energies (BEs) using experimental DMS data. Chapter 3 shows the ability of DMS to separate derivatized amphetamines and methamphetamine isomers and uses calculated BEs to identify the separated isomers by their DMS behavior. Chapter 4 demonstrates the separation of (+)-ephedrine and (+)-pseudoephedrine as well as three groups of sulfonamide isomers using a variety of gas modifiers within the DMS. CCS are used to describe behavior in pure N2 gas, while BEs are used to predict the ordering of the separation voltage at the compensation voltage minima (SV at CVmin) values within different isomeric groups. By making use of data gathered by Walker et al.1 ML models were generated for prediction of CCS as well as H2O and MeOH BEs and tested using the isomers studied in this chapter. In order to demonstrate the need for the model to train on similar compounds to those being tested, several of the test compounds were moved into the training set of the ML model and the change in predictivity observed. In the final chapter of this work, chapter 5, the CCS ML database was expanded using a sizable number of compounds with varied structure and functionalities in order to increase the predictivity of the ML model for new compounds. The effectiveness of incorporating additional compounds was evaluated by the creation of learning curves for the ML training and test sets. These projects ultimately show the capability of DMS in making separations of isomeric compounds, as well as its potential for use in the prediction of CCSs and BEs through ML modelling

Computational and Spectroscopic Investigations of Intermolecular Interactions in Clusters

In this thesis, the study of intermolecular interactions within cluster systems is presented. Covalently and non-covalently bound clusters possess oftentimes unique and unexpected properties which can be tuned by adjustment of size, composition, and geometry to target desired properties for use in nanotechnologies. Additionally, clusters present a computationally tractable model of bulk systems such as reactive sites on bulk heterogeneous catalysts. Infrared spectra have been collected of various clusters and theoretical computations have been conducted to interpret spectra and provide predictions for other properties to guide future works. Investigations of the forces binding cluster species together are conducted to provide insight into the fundamental underpinning of molecular properties with applications in the field of nanomaterial design. A variety of clusters have been studied here. Computational studies of size-dependency in nitrous oxide reactions with rhodium sulphide clusters have been conducted. Barriers to competing N2O desorption and decomposition have been ascertained and compared with and without thermal corrections. Inclusion of the sulphur atom is found to alter which reaction pathway is preferred, as seen by comparison with analogous studies on pure rhodium clusters. Infrared multiple photon dissociation (IRMPD) spectroscopy is utilized to probe the additional clusters; a series of palladium coordination complexes and a series of clusters containing icosahedral [B12X12]2─ (X = H, halogen) cages complexed with a cationic transition metal atom, a cationic amine, or a neutral polar cyclohexane-based compound. This IRMPD technique successfully produced infrared spectra for these species in the gas phase and unique properties were observed for each cluster upon IR induced dissociation. Density functional theory calculations determined geometries, dissociation thresholds, and interpreted IR spectra. Additional theoretical tools quantified molecular orbital interactions and topographical parameters of the electron density

Computational Catalysis of Homogenous and Heterogeneous Systems: New Insights into the Activation of Small Molecules

Esta Tesis Doctoral se ubica en el contexto del estudio teórico y computacional de catalizadores, tanto homogéneos como heterogéneos, para la fijación de moléculas pequeñas, en concreto N2, O2, CO, NH3, HCOOH e hidrosilanos, empleando DFT. Estos procesos presentan un gran interés en investigación química, ya que un conocimiento en profundidad de los mismos facilitaría el diseño racional de nuevos catalizadores más activos y respetuosos con el medio ambiente. A continuación se presenta un resumen de los procesos estudiados.En el campo de la catálisis homogénea, se estudiaron cuatro procesos químicos diferentes, catalizados por complejos organometálicos de Rh e Ir:i) Fijación de amoniaco mediante complejos de Ir con ligandos de tipo pincer. En particular, se estudiaron los factores cinéticos y termodinámicos que afectan a laactividad del catalizador. Para ello, se emplearon diferentes métodos para el estudio del enlace químico, como IQA y la ELF.ii) La sililación de enlaces C–H aromáticos mediante un complejo bien definido de Ir(III)– NHC. Se propuso un mecanismo de reacción completo mediante cálculoscomputacionales. Asimismo, se realizaron una serie de experimentos que apoyan dicho mecanismo. Los resultados obtenidos revelaron el papel clave de los grupos directorespresentes en el sustrato en el control de la selectividad del proceso.iii) El empleo de hidrógeno molecular como vector energético. En particular, se estudió el proceso de deshidrogenación de ácido fórmico para generar H2 catalizado por uncompuesto de Rh–NHO muy activo. Los estudios computacionales permitieron proponer un mecanismo de reacción plausible, que está de acuerdo con las barreras energéticas determinadas experimentalmente.iv) La alcoxicarbonilación de alcoholes y aminas con CO para preparar carbamatos. El proceso está catalizado por un complejo de Rh y requiere le acción de un oxidante(KHSO5). El estudio teórico realizado permitió proponer un mecanismo de reacción y determinar el papel clave del oxidante.Con respecto a la catálisis heterogénea, se abordó la propuesta de nuevos descriptores de la actividad catalítica basados en las propiedades magnéticas del catalizador y los reactivos. Los diferentes procesos estudiados se resumen a continuación:v) Las reacciones de reducción de oxígeno (ORR) y de evolución de oxígeno (OER) catalizadas por materiales basados en perovskitas. En concreto, es analizaron laspropiedades magnéticas de diferentes catalizadores derivados de LaMnO3. Los resultados mostraron la importancia de tener en cuenta la entropía electrónica y la fasemagnética del catalizador. Basándonos en estos resultados, se propusieron una serie dereglas para el diseño de nuevos catalizadores heterogéneos derivados de óxidosmetálicos magnéticos para ORR y OER. Finalmente, estas reglas se emplearon en eldiseño de un nuevo catalizador para OER basado en la perovskita LaFeO3.vi) Los principios previamente presentados se ampliaron al estudio de procesos de fijación de N2 catalizados por nitruros de Mo. Los resultados muestran la validez de la aplicación del momento magnético del molibdeno como descriptor de la actividad catalítica.<br /

Exploration of Free Energy Surface and Thermal Effects on Relative Population and Infrared Spectrum of the Be6B11− Fluxional Cluster

The starting point to understanding cluster properties is the putative global minimum and all the nearby local energy minima; however, locating them is computationally expensive and difficult. The relative populations and spectroscopic properties that are a function of temperature can be approximately computed by employing statistical thermodynamics. Here, we investigate entropy-driven isomers distribution on Be6B11− clusters and the effect of temperature on their infrared spectroscopy and relative populations. We identify the vibration modes possessed by the cluster that significantly contribute to the zero-point energy. A couple of steps are considered for computing the temperature-dependent relative population: First, using a genetic algorithm coupled to density functional theory, we performed an extensive and systematic exploration of the potential/free energy surface of Be6B11− clusters to locate the putative global minimum and elucidate the low-energy structures. Second, the relative populations’ temperature effects are determined by considering the thermodynamic properties and Boltzmann factors. The temperature-dependent relative populations show that the entropies and temperature are essential for determining the global minimum. We compute the temperature-dependent total infrared spectra employing the Boltzmann factor weighted sums of each isomer’s infrared spectrum and find that at finite temperature, the total infrared spectrum is composed of an admixture of infrared spectra that corresponds to the lowest energy structure and its isomers located at high energies. The methodology and results describe the thermal effects in the relative population and the infrared spectra