Kinetic model construction using chemoinformatics

Kinetic models of chemical processes not only provide an alternative to costly experiments; they also have the potential to accelerate the pace of innovation in developing new chemical processes or in improving existing ones. Kinetic models are most powerful when they reflect the underlying chemistry by incorporating elementary pathways between individual molecules. The downside of this high level of detail is that the complexity and size of the models also steadily increase, such that the models eventually become too difficult to be manually constructed. Instead, computers are programmed to automate the construction of these models, and make use of graph theory to translate chemical entities such as molecules and reactions into computer-understandable representations. This work studies the use of automated methods to construct kinetic models. More particularly, the need to account for the three-dimensional arrangement of atoms in molecules and reactions of kinetic models is investigated and illustrated by two case studies. First of all, the thermal rearrangement of two monoterpenoids, cis- and trans-2-pinanol, is studied. A kinetic model that accounts for the differences in reactivity and selectivity of both pinanol diastereomers is proposed. Secondly, a kinetic model for the pyrolysis of the fuel “JP-10” is constructed and highlights the use of state-of-the-art techniques for the automated estimation of thermochemistry of polycyclic molecules. A new code is developed for the automated construction of kinetic models and takes advantage of the advances made in the field of chemo-informatics to tackle fundamental issues of previous approaches. Novel algorithms are developed for three important aspects of automated construction of kinetic models: the estimation of symmetry of molecules and reactions, the incorporation of stereochemistry in kinetic models, and the estimation of thermochemical and kinetic data using scalable structure-property methods. Finally, the application of the code is illustrated by the automated construction of a kinetic model for alkylsulfide pyrolysis

Investigating the role of curvature on the formation and thermal transformations of soot

In this work, the role of curved polycyclic aromatic hydrocarbons (cPAH) on the initial formation mechanism and thermal transformations of soot was explored. Experimental and computational techniques were used to probe the integration, presence and impact of internal pentagonal rings on the nucleation mechanism of these particulates. A significant charge polarisation was found to occur when an internal pentagonal ring pyramidalises the aromatic network. Phase contrast transmission electron microscopy allowed for the extent of conjugation and degree of curvature to be determined in early soot nanoparticulates with 15 aromatic rings and two pentagons being the median species. The dipole moment of such a species was calculated to be 5.32 debye. The polarity was found to be persistent at flame temperatures with inversion and fluctuations being minimal. Homogeneous nucleation was considered with homodimerisation energies with one or two internal pentagonal rings within cPAH found to be comparable in energy to flat PAH (fPAH) homodimers of similar weight, with more pentagons reducing the binding energy. Ion-induced nucleation was considered with binding energies calculated between chemi-ions and cPAH suggesting small stable clusters at flame temperatures. However, physical and ion-induced nucleation of cPAH were found to be insufficient alone to explain the formation of soot. The impact of curvature on the reactivity of PAH were then studied. Strong crosslinks between σ-radicals and cPAH were found to form at their rim due to decreased aromaticity. Partially saturated rim-based pentagonal rings were also found to form localised π-radicals that allow stacked and bonded complexes to form, suggesting a covalently stabilised soot nucleation. Finally, the curved geometry of highly annealed soot, otherwise known as non-graphitising carbon, was explored using annealed molecular dynamics simulations and a discrete mesh analysis method. Analysis of the angular defect of the meshes revealed an excess of negative curvature. The coexistence of curved and layered ribbon-like structures was found to be possible due to the presence of a small number of non-sp² defects such as screw dislocations and free edges, which will impact the synthesis of novel carbon materials and the oxidation of thermally annealed soot. The incorporation of curvature and pentagonal rings is therefore considered critical for understanding the properties, formation and destruction of combustion generated carbonaceous particles and other carbon materials.This project is supported by the National Research Foundation (NRF), Prime Minister’s Office, Singapore under its Campus for Research Excellence and Technological Enterprise (CREATE) programme

Interstellar Dust Analogues: Structure, Survivability and Physical Processes

El principal objetivo de la tesis es establecer relaciones entre la estructura microscópica o atomı́stica de análogos de polvo cósmico con una serie de propiedades quimico-fı́sicas de interés astrofı́sico. En primer lugar, se ha estudiado la relación entre la estructura de diferentes arquetipos de carbono amorfo hidrogenado (HAC) y sus propiedades espectroscópicas en el infrarojo y ultravioleta, por métodos teóricos y experimentales. En segundo lugar, se han determinado experimentalmente los tiempos de vida de los enlaces carbono-hidrógeno de los mencionados análogos en entornos astrofı́sicos, como las nubes moleculares densas, mediante el procesado con electrónes de muestras de HAC. Finalmente, y usando silicatos como análogos de polvo cósmico, se han estudiado rutas de sı́ntesis de agua en entornos astrofı́sicos.Departamento de Química Física y Química InorgánicaDoctorado en Químic

On-surface fabrication of functional molecular nanomaterials

Polyzyklische organische Moleküle und deren Derivate sind eine Klasse von Nanostrukturen, die wegen diverser möglicher Anwendungen in molekularer und organischer Elektronik viel Aufmerksamkeit in der Wissenschaft erregt haben. Um ihre einzigartigen Eigenschaften in vollem Umfang auszunutzen, muss man das Verhalten von molekularen Systemen auf der Nanoskala verstehen und eine Reihe von Herstellungsverfahren entwickeln. In dieser Arbeit werden molekulare Nanostrukturen durch den Bottom-Up-Ansatz der Oberflächensynthese erzeugt. Als Untersuchungsmethode gilt Rastertunnelmikroskopie (STM) bei tiefen Temperaturen und im Ultrahochvakuum als Werkzeug der Wahl. Drei verschiedene molekulare Systeme werden ausführlich erforscht, mit dem Ziel organische Nanostrukturen mit gewünschten Eigenschaften und atomarer Präzision zu erzeugen. Im ersten Teil dieser Arbeit wird eine Cyclodehydrierungsreaktion erfolgreich für die Synthese von asymmetrischen Starphen verwendet. Es wird dann gezeigt, dass dieses Molekül als unimolekulares NAND-Logikgatter fungieren kann. Dabei wird die Positionierungsänderung der elektronischen Resonanz nach der Zufügung einzelner Goldatome an die Inputs des Moleküls gemessen. Eine Kombination aus atomarer und molekularer Lateralmanipulation mithilfe der Spitze des Rastertunnelmikroskops sowie Rastertunnelspektroskopie wird verwendet, um dieses Verhalten zu demonstrieren. Die steuerbare Verschiebung von molekularen Resonanzen entsteht wegen der asymmetrischen Form des Starphens und wurde theoretisch vorhergesagt. Molekulare Drähte werden im zweiten Teil der Arbeit durch die oberflächenassistierte Ullmann-Kupplung hergestellt. Ihr Baustein besteht aus abwechselnden Donor- und Akzeptorgruppen und wurde speziell vorgesehen, um leitfähige flexible molekulare Drähte herzustellen. Die Leitfähigkeit wird durch Ziehen einzelner Drähten von der Oberflächen mit der STM-Spitze gemessen. Theoretische Berechnungen der komplexen Bandstruktur der molekularen Drähte bestätigen die experimentellen Ergebnisse und unterstützen dabei die Wichtigkeit der Balance zwischen Akzeptor- und Donorgruppen für die Leitfähigkeit der Drähte. Basierend auf diesen Resultaten werden neue Strukturen zur Herstellung vorgeschlagen. Der letzte Teil befasst sich schließlich mit einer unimolekularen Reaktion, die zur Erzeugung einer anomalen Kombination von Pentagon- und Heptagonringen in einem einzelnen organischen Molekül führt. Solche 5-7-Einheiten sind analog zu Stone-Wales-Defekten in Graphen und können elektronische Eigenschaften beachtlich ändern. Die exakte intramolekulare Struktur der Reaktionsprodukte wird durch hochauflösende STM-Bildgebung mit funktionalisierter Spitze eindeutig zugeordnet und zusätzlich durch DFT-Rechnungen bestätigt.Polycyclic organic molecules and their derivatives present the class of nanostructures that are currently in the focus of scientific research due to their perspectives for the versatile applications in molecular and organic electronics. To exploit their unique properties to full extent, one has to understand the behavior of molecular systems at the nanoscale and to develop a set of fabrication methods. In this work, molecular nanostructures are fabricated using the bottom-up on-surface synthesis approach, which allows precision of the desired products and control over their properties through careful precursors design. To study the reaction flow and the properties of the formed structures, scanning tunneling microscopy (STM) at low temperature and in ultra-high vacuum is the tool of choice. In this work, three molecular systems are studied in detail, with the focus of fabricating atomically precise nanostructures with tailored properties. A cyclodehydrogenation reaction is successfully applied to synthesize an asymmetric starphene molecule in the first part of the work. It is then shown that this molecule can function as a unimolecular NAND logic gate with its response to the attached single Au atoms measured as the position of the electronic resonance. A combination of the atomic and molecular lateral manipulation with the STM tip and scanning tunneling spectroscopy (STS) is used to demonstrate this behavior. The effect of the controllable shifting of the molecular resonances is due to the asymmetric shape of the starphene molecule and was initially predicted theoretically. More complex structures, molecular wires, are presented in the second part of the work by using the surface-assisted Ullmann coupling reaction. The monomer unit, consisting of the alternant donor and acceptor parts, was specifically designed to achieve highly-conductive flexible molecular wires. The conductance is measured by pulling the single wires with the STM tip off the surface. Theoretical calculations of the complex band structure of the wires confirm the obtained results and support the discussion of the importance of the balance between the strength of acceptor and donor units for the conductance of the resultant wires. Based on this, some model structures are proposed. Finally, the last part deals with a unimolecular reaction to create an anomalous combination of pentagon and heptagon rings in a single organic molecule. Such 5-7 moieties are analogous to the Stone-Wales defects in graphene and may significantly alter the electronic properties. The precise intramolecular structure of the reaction products is unambiguously assigned by high-resolution STM imaging with functionalized tips and further confirmed by DFT calculations

Modelling the optical, kinetic, and thermodynamic properties of soot precursor molecules

This thesis investigates the optical, kinetic, and thermodynamic properties of soot precursor molecules, namely polyaromatic hydrocarbons (PAHs), by applying \textit{ab initio} quantum chemical methods. In particular, density functional theory (DFT) is applied to study the properties of several different types of PAHs, including curved PAHs, localized $\pi$-radical PAHs, and cross-linked PAHs. These studies help model the gas phase chemistry that leads to the formation of these different types of PAHs, and also help assess their relevance to the formation of soot. The optical band gaps (OBGs) of curved, cross-linked, and radical PAHs are computed using a DFT method corroborated with UV/Visible spectroscopy measurements. Curved PAHs are shown to increase the OBG due to hybridisation changes. In contrast, $\pi$-radical character was found to decrease the band gap. Crosslinks are observed to minimally impact the OBG of the monomers. The effect of $\sigma$-radicals on the OBG was also shown to be negligible. The results suggest that curved and $\pi$-radical PAHs of moderate size can also explain the optical properties of flames. The persistence of the polarity of curved aromatics in flame conditions is investigated by using DFT to calculate their barriers and rates of inversion. Curved PAHs above 11--15 ($\approx$ 0.8 nm) rings in size were seen to be unable to invert at flame temperatures. This is seen to be a function of the number of pentagons, and hence curvature. \textit{Ab initio} quantum molecular dynamics of a 1 nm curved PAH and C\textsubscript{3}H\textsubscript{3}\textsuperscript{+} chemi-ion suggest molecular dipole fluctuations of 10--20\%, with the chemi-ion and PAH being bound for the entire simulation. This suggests curved PAHs are persistently polar at 1500~K and can bind substantially to ions in flames. The kinetics of seven-member ring formation in PAHs containing a five-member ring is investigated. Seven-member ring formation by the hydrogen-abstraction-acetylene-addition (HACA) mechanism is studied for two different PAHs, one closed shell and one resonance-stabilised-radical (RSR) PAH. The seven-member ring forms more quickly for the RSR PAH. Seven-member ring formation by four different bay closure processes is also studied. The rate constants determined for the pathways are then used in kinetic simulations in 0D homogeneous reactors. The hydrogen abstraction based pathway is seen to dominate until higher temperatures, where the carbene pathway takes over. The results suggest that seven-member ring formation in PAHs containing a five-member ring is possible at flame temperatures. The impact of localized $\pi$-radicals on soot formation is explored by developing a simple mechanism for their formation and computing their relative concentrations under flame conditions using 0D homogeneous reactor simulations. It is seen that flame temperatures at the onset of nucleation (1400--1500~K) promote the formation of localized $\pi$-radicals on rim-based pentagonal rings, whilst lower temperatures favor fully saturated rings, and higher temperatures favor the $\sigma$-radical. A kinetic Monte Carlo study indicates that multiple localized $\pi$-radicals can form on a single PAH suggesting localized $\pi$-radicals on rim-based pentagonal rings could be important to understanding the mechanism of soot formation. The rate and equilibrium constants of cross-linking reactions between PAHs of various reactive edge types is computed. The forward rate constants confirms that reactions involving aryl $\sigma$-radicals are generally fast, but the reactions between aryl $\sigma$-radicals and localized $\pi$-radicals were notably faster than others. Computed equilibrium constants showed that reactions involving $\sigma$ and $\pi$-radical PAHs are the most favorable at flame temperatures. Calculations for larger PAHs showed that the formation of bonded-and-stacked structures results in substantially enhanced equilibrium constants for the reaction of two large localized $\pi$-radicals. This suggests that combined physical and chemical interactions between larger $\pi$-radical PAHs could be important in flame environments.Johnson Matthey National Research Foundation of Singapor

Composition, structure and chemistry of interstellar dust

The observational constraints on the composition of the interstellar dust are analyzed. The dust in the diffuse interstellar medium consists of a mixture of stardust (amorphous silicates, amorphous carbon, polycyclic aromatic hydrocarbons, and graphite) and interstellar medium dust (organic refractory material). Stardust seems to dominate in the local diffuse interstellar medium. Inside molecular clouds, however, icy grain mantles are also important. The structural differences between crystalline and amorphous materials, which lead to differences in the optical properties, are discussed. The astrophysical consequences are briefly examined. The physical principles of grain surface chemistry are discussed and applied to the formation of molecular hydrogen and icy grain mantles inside dense molecular clouds. Transformation of these icy grain mantles into the organic refractory dust component observed in the diffuse interstellar medium requires ultraviolet sources inside molecular clouds as well as radical diffusion promoted by transient heating of the mantle. The latter process also returns a considerable fraction of the molecules in the grain mantle to the gas phase

Scanning probe microscopy of graphene and self-assembled molecules

Trasferimento di CVD grafene su silicio. Misure con AFM e STM. Deposizioni molecole autoassemblanti

From building blocks to 2D networks

The aim of this work is to further the understanding of the important parameters in the formation process of 2D nanostructures and therewith pioneer for novel applications. Such 2D nanostructures can be composed of specially designed organic molecules, which are adsorbed on various surfaces. In order to study true 2D structures, monolayers were deposited. Their properties have been investigated by scanning tunneling microscopy (STM) under ultra-high vacuum (UHV) conditions as well as under ambient conditions. The latter is a highly dynamic environment, where several parameters come into play. Complementary surface analysis techniques such as low-energy electron diffraction (LEED), X-Ray photo-emission spectroscopy (XPS), and Raman spectroscopy were used when necessary to characterize these novel molecular networks. In order to conduct this type of experiments, high technical requirements have to be fulfilled, in particular for UHV experiments. Thus, the focus is on a drift-stable STM, which lays the foundation for high resolution STM topographs. Under ambient conditions, the liquid-solid STM can be easily upgraded by an injection add-on due to the highly flexible design. This special extension allows for adding extra solvent without impairing the high resolution of the STM data. Besides the device, also the quality of the tip is of pivotal importance. In order to meet the high requirements for STM tips, an in vacuo ion-sputtering and electron-beam annealing device was realized for the post-preparation of scanning probes within one device. This two-step cleaning process consists of an ion-sputtering step and subsequent thermal annealing of the probe. One study using this STM setup concerned the incorporation dynamics of coronene (COR) guest molecules into pre-existent pores of a rigid 2D supramolecular host networks of trimesic acid (TMA) as well as the larger analogous benzenetribenzoic acid (BTB) at the liquid-solid interface. By means of the injection add-on the additional solution containing the guest molecules was applied to the surface. At the same time the incorporation process was monitored by the STM. The incorporation dynamics into geometrically perfectly matched pores of trimesic acid as well as into the substantially larger pores of benzentribenzoic acid exhibit a clearly different behavior. For the BTB network instantaneous incorporation within the temporal resolution of the experiment was observed; for the TMA network, however, intermediate adsorption states of COR could be visualized before the final adsorption state was reached. A further issue addressed in this work is the generation of metal-organic frameworks (MOFs) under ultra-high vacuum conditions. A suitable building block therefore is an aromatic trithiol, i.e. 1,3,5-tris(4-mercaptophenyl)benzene (TMB). To understand the specific role of the substrate, the surface-mediated reaction has been studied on Cu(111) as well as on Ag(111). Room temperature deposition on both substrates results in densely packed trigonal structures. Yet, heating the Cu(111) with the TMB molecules to moderate temperature (150 °C) yields two different porous metal coordinated networks, depending on the initial surface coverage. For Ag(111) the first structural change occurs after annealing the sample at 300 °C. Here, several disordered structures with partially covalent disulfur bridges were identified. Proceeding further in the scope of increasing interaction strength between the building blocks, covalent organic frameworks (COFs) were studied under ultra-high vacuum conditions as well as under ambient conditions. For this purpose, a promising strategy is covalent coupling through radical addition reactions of appropriate monomers, i.e. halogenated aromatic molecules such as 1,3,5-tris(4-bromophenyl)benzene (TBPB) and 1,3,5-tris(4- iodophenyl)benzene (TIPB). Besides the correct choice of a catalytic surface, the activation energy for the scission of the carbon-halogen bonds is an essential parameter. In the case of ultra-high vacuum experiments, the influence of substrate temperature, material, and crystallographic orientation on the coupling reaction was studied. For reactive Cu(111) and Ag(110) surfaces room temperature deposition of TBPB already leads to a homolysis of the C-Br bond and subsequent formation of proto-polymers. Applying additional heat facilitates the transformation of proto-polymers into 2D covalent networks. In contrast, for Ag(111) just a variety of self-assembled and rather poorly ordered structures composed of intact molecules has emerged. The deposition onto substrates held at 80 K has never resulted in proto-polymers. For ambient conditions, the polymerization reaction of 1,3,5-tri(4-iodophenyl)benzene (TIPB) on Au(111) was studied by STM after drop-casting the monomer onto the substrate held either at room temperature or at 100 °C. For room temperature deposition only poorly ordered non-covalent arrangements were observed. In accordance with the established UHV protocol for halogenated coupling reaction, a covalent aryl-aryl coupling was accomplished for high temperature deposition. Interestingly, these covalent aggregates were not directly adsorbed on the Au(111) surface, but attached on top of a chemisorbed monolayer comprised of iodine and partially dehalogenated TIPB molecules. For a detailed analysis of the processes, the temperature dependent dehalogenation reaction was monitored by X-ray photoelectron spectroscopy under ultra-high vacuum conditions