Kinetic modelling of heterogeneous catalytic systems

The importance of heterogeneous catalysis in modern life is evidenced by the fact that numerous products and technologies routinely used nowadays involve catalysts in their synthesis or function. The discovery of catalytic materials is, however, a non-trivial procedure, requiring tedious trial-and-error experimentation. First-principles-based kinetic modelling methods have recently emerged as a promising way to understand catalytic function and aid in materials discovery. In particular, kinetic Monte Carlo (KMC) simulation is increasingly becoming more popular, as it can integrate several sources of complexity encountered in catalytic systems, and has already been used to successfully unravel the underlying physics of several systems of interest. After a short discussion of the different scales involved in catalysis, we summarize the theory behind KMC simulation, and present the latest KMC computational implementations in the field. Early achievements that transformed the way we think about catalysts are subsequently reviewed in connection to latest studies of realistic systems, in an attempt to highlight how the field has evolved over the last few decades. Present challenges and future directions and opportunities in computational catalysis are finally discussed

Simulations of Chemical Catalysis

This dissertation contains simulations of chemical catalysis in both biological and heterogeneous contexts. A mixture of classical, quantum, and hybrid techniques are applied to explore the energy profiles and compare possible chemical mechanisms both within the context of human and bacterial enzymes, as well as exploring surface reactions on a metal catalyst. A brief summary of each project follows. Project 1 — Bacterial Enzyme SpvC The newly discovered SpvC effector protein from Salmonella typhimurium interferes with the host immune response by dephosphorylating mitogen-activated protein kinases (MAPKs) with a -elimination mechanism. The dynamics of the enzyme substrate complex of the SpvC effector is investigated with a 3.2 ns molecular dynamics simulation, which reveals that the phosphorylated peptide substrate is tightly held in the active site by a hydrogen bond network and the lysine general base is positioned for the abstraction of the alpha hydrogen. The catalysis is further modeled with density functional theory (DFT) in a truncated active-site model at the B3LYP/6-31 G(d,p) level of theory. The truncated model suggested the reaction proceeds via a single transition state. After including the enzyme environment in ab initio QM/MM studies, it was found to proceed via an E1cB-like pathway, in which the carbanion intermediate is stabilized by an enzyme oxyanion hole provided by Lys104 and Tyr158 of SpvC. Project 2 — Human Enzyme CDK2 Phosphorylation reactions catalyzed by kinases and phosphatases play an indispensable role in cellular signaling, and their malfunctioning is implicated in many diseases. Ab initio quantum mechanical/molecular mechanical studies are reported for the phosphoryl transfer reaction catalyzed by a cyclin-dependent kinase, CDK2. Our results suggest that an active-site Asp residue, rather than ATP as previously proposed, serves as the general base to activate the Ser nucleophile. The corresponding transition state features a dissociative, metaphosphate-like structure, stabilized by the Mg(II) ion and several hydrogen bonds. The calculated free-energy barrier is consistent with experimental values. Project 3 — Bacterial Enzyme Anthrax Lethal Factor In this dissertation, we report a hybrid quantum mechanical and molecular mechanical study of the catalysis of anthrax lethal factor, an important first step in designing inhibitors to help treat this powerful bacterial toxin. The calculations suggest that the zinc peptidase uses the same general base-general acid mechanism as in thermolysin and carboxypeptidase A, in which a zinc-bound water is activated by Glu687 to nucleophilically attack the scissile carbonyl carbon in the substrate. The catalysis is aided by an oxyanion hole formed by the zinc ion and the side chain of Tyr728, which provide stabilization for the fractionally charged carbonyl oxygen. Project 4 — Methanol Steam Reforming on PdZn alloy Recent experiments suggested that PdZn alloy on ZnO support is a very active and selective catalyst for methanol steam reforming (MSR). Plane-wave density functional theory calculations were carried out on the initial steps of MSR on both PdZn and ZnO surfaces. Our calculations indicate that the dissociation of both methanol and water is highly activated on \ufb02at surfaces of PdZn such as (111) and (100), while the dissociation barriers can be lowered significantly by surface defects, represented here by the (221), (110), and (321) faces of PdZn. The corresponding processes on the polar Zn-terminated ZnO(0001) surfaces are found to have low or null barriers. Implications of these results for both MSR and low temperature mechanisms are discussed

A review of multiscale modeling of metal-catalyzed reactions: Mechanism development for complexity and emergent behavior

We review and provide a perspective on multiscale modeling of catalytic reactions with emphasis on mechanism development and application to complex and emergent systems. We start with an overview of length and time scales, objectives, and challenges in first-principles modeling of reactive systems. Subsequently, we review various methods that ensure thermodynamic consistency of mean-field microkinetic models. Next, we describe estimation of reaction rate constants via quantum mechanical and statistical-mechanical methods as well as semi-empirical methods. Among the latter, we discuss the bond-order conservation method for thermochemistry and activation energy estimation. In addition, we review the newly developed group-additivity method on adsorbate/metal systems and linear free energy or Brønsted-Evans-Polanyi (BEP) relations, and their parameterization using DFT calculations to generate databases of activation energies and reaction free energies. Linear scaling relations, which can enable transfer of reaction energetics among metals, are discussed. Computation-driven catalyst design is reviewed and a new platform for discovery of materials with emergent behavior is introduced. The effect of parameter uncertainty on catalyst design is discussed; it is shown that adsorbate-adsorbate interactions can profoundly impact materials design. Spatiotemporal averaging of microscopic events via the kinetic Monte Carlo method for realistic reaction mechanisms is discussed as an alternative to mean-field modeling. A hierarchical multiscale modeling strategy is proposed as a means of addressing (some of) the complexity of catalytic reactions. Structure-based microkinetic modeling is next reviewed to account for nanoparticle size and shape effects and structure sensitivity of catalytic reactions. It is hypothesized that catalysts with multiple sites of comparable activity can exhibit structure sensitivity that depends strongly on operating conditions. It is shown that two descriptor models are necessary to describe the thermochemistry of adsorbates on nanoparticles. Multiscale and accelerated methods for computing free energies in solution, while accounting explicitly for solvent effects in catalytic reactions, are briefly touched upon with the acid catalyzed dehydration of fructose in water as an example. The above methods are illustrated with several reactions, such as the CO oxidation on Au; the hydrogenation of ethylene and hydrogenolysis of ethane on Pt; the glycerol decomposition to syngas on Pt-based materials; the NH decomposition on single metals and bimetallics; and the dehydration of fructose in water. Finally, we provide a summary and outlook. © 2011 Elsevier Ltd

A study on the effect of lateral interactions on methanation over Fe(100)

In this thesis, the lateral interactions involved in conversion of synthesis gas, a mixture of H2 and CO, to methane over Fe(100) and the effect they have on the kinetics of the process is explored. Understanding the methanation of syngas allows for a better understanding of the initial stages of Fischer-Tropsch synthesis. Density functional theory was used to calculate the energies and properties of simple methanation adsorbates on an Fe(100) surface. All of the parameters were tested and optimized in order to find a balance between efficiency and accuracy. A number of configurations were calculated to investigate nearest neighbour and next nearest neighbour interactions. An energetic break down of the lateral interactions is postulated using the components of the Hamiltonian. The charges associated with the different atoms in each configuration were identified using the Mulliken population analysis and the Bader population analysis. These gave insights into configurations which displayed large electrostatic lateral interactions. Lateral interactions were investigated using larger unit cells than typically utilized in molecular modelling up to now (viz. p(4x4) and p(3x2) unit cells) to enable the estimation of nearest neighbour and next nearest neighbour interactions. When using larger p(4x4) unit cells for CO adsorption on Fe(100), the results showed that the heat of adsorption can differ by as much as 0.24 eV at 0.25 ML. It was concluded that lateral interactions are a function of local coverage (i.e. number of nearest and next nearest neighbours) and not necessarily global coverage. Nearest neighbour interactions are typically repulsive and much larger than next nearest neighbour interactions, which varied between repulsive and attractive interactions. While this is not a unique conclusion it did allow for the creation lateral interaction matrices that vary with temperature. The study has shown that lateral interactions can be broken down into kinetic and potential energy and an inverse relationship exists between these component energies. If this relationship is truly understood, then the total energy can be calculated knowing either kinetic or potential energy instead of both. This would then give additional value to well explored electrostatic interaction models. The lateral interactions were empirically related to nearest neighbour and next nearest neighbour interactions. Two kinetic studies were investigated in this thesis and in both cases, mean field approximations and quasi chemical approximation (QCA) were used and compared to incorporate lateral interactions into the kinetics. The mean field approximation over estimates the lateral interactions and considers global coverage while the QCA approximation considers probability of local combinations. The first kinetic study was a simulated CO TPD experiment on Fe(100). The mean field approximation was an improvement on systems which considered no lateral interactions but did not describe all the aspects observed in the experimental TPD. The prediction by the quasi-chemical approximation shows good agreement for the desorption of associatively bound CO. The deviation observed for the dissociatively adsorbed CO is attributed to the presence of alternative pathways for the adsorbed species (specifically the diffusion of oxygen into the lattice of the solid). A microkinetic model for the methanation of syngas over Fe(100) was also created. The results showed that different methods of lateral interaction incorporation resulted in significantly different coverage profiles and reaction energy profiles. Both methods showed a build-up of oxygen on the surface towards the end of the simulation. The build-up of oxygen on the surface of Fe(100) may indicate that iron-based catalysts need to undergo phase changes to complete the catalytic cycle

Quantum chemical characterization of Biomolecules in the gas phase and on surfaces of metal oxides

During the four years of my PhD study, I performed systematic studies of the conformations of biomolecules ranging from a small amino acid (e.g. glycine) to a medium-sized nucleoside (e.g. 2’-deoxycytidine). To better account for possible effects brought by explicit environments (e.g. radiation, aqueous solution, and so on), we studied biomolecules in different phases, including neutral and charged species, in the gas phase and solid state, and neutral on solid surface. The work being presented in this thesis is original as: (1) A tool which can automatically generate libraries of conformations for a systematic search of the conformational space of a molecule was developed. When combined with tools developed by our colleagues, our toolbox facilitates a combinatorial computational chemical study of some small biomolecules; (2) A new method which can suppress barriers between different local minima on a molecular potential energy surface (PES) was developed, and with this new deformed PES, a lot of other techniques (e.g. Monte Carlo and simulated annealing) could be adopted to search for the global minima structure in a much more efficient way; (3) We performed a highly accurate study of two conformers of glycine up to the coupled-cluster with single and double and perturbative triple excitations (CCSD(T)) with basis sets up to aug-cc-pVQZ level of theory, and we found that the treatment at the CCSD(T) level of theory is necessary to achieve numerical stability of the relative energies with respect to different basis sets at different geometries; (4) Through a thorough search of the conformational space of 2’-deoxycytidine, we found that its conformations in the gas phase are quite different from those in the solid state, and hopefully this finding could correct some of the previous approaches, in which structural information extracted from solid state experiments was used in computational studies of molecules in the gas phase; (5) Adsorptions of hydrogen, methanol and glycine on different types of solid surfaces (conductive and semiconductive) were studied, and catalytic performances of these surfaces on breaking chemical bonds were discussed. The current thesis not only covers the main applications of computational chemistry tools in the conformational study of biomolecules, it also includes discussions on accuracy and methodology which is involved in these studies. We definitely did not intend to solve all of the problems which people have met in their conformational studies of biomolecules. We just hope that the work being presented here was performed in a much more systematic way, and we hope these studies can give people some insights which might be helpful in their further studies

Book of abstracts of the 10th International Chemical and Biological Engineering Conference: CHEMPOR 2008

This book contains the extended abstracts presented at the 10th International Chemical and Biological Engineering Conference - CHEMPOR 2008, held in Braga, Portugal, over 3 days, from the 4th to the 6th of September, 2008. Previous editions took place in Lisboa (1975, 1889, 1998), Braga (1978), Póvoa de Varzim (1981), Coimbra (1985, 2005), Porto (1993), and Aveiro (2001). The conference was jointly organized by the University of Minho, “Ordem dos Engenheiros”, and the IBB - Institute for Biotechnology and Bioengineering with the usual support of the “Sociedade Portuguesa de Química” and, by the first time, of the “Sociedade Portuguesa de Biotecnologia”. Thirty years elapsed since CHEMPOR was held at the University of Minho, organized by T.R. Bott, D. Allen, A. Bridgwater, J.J.B. Romero, L.J.S. Soares and J.D.R.S. Pinheiro. We are fortunate to have Profs. Bott, Soares and Pinheiro in the Honor Committee of this 10th edition, under the high Patronage of his Excellency the President of the Portuguese Republic, Prof. Aníbal Cavaco Silva. The opening ceremony will confer Prof. Bott with a “Long Term Achievement” award acknowledging the important contribution Prof. Bott brought along more than 30 years to the development of the Chemical Engineering science, to the launch of CHEMPOR series and specially to the University of Minho. Prof. Bott’s inaugural lecture will address the importance of effective energy management in processing operations, particularly in the effectiveness of heat recovery and the associated reduction in greenhouse gas emission from combustion processes. The CHEMPOR series traditionally brings together both young and established researchers and end users to discuss recent developments in different areas of Chemical Engineering. The scope of this edition is broadening out by including the Biological Engineering research. One of the major core areas of the conference program is life quality, due to the importance that Chemical and Biological Engineering plays in this area. “Integration of Life Sciences & Engineering” and “Sustainable Process-Product Development through Green Chemistry” are two of the leading themes with papers addressing such important issues. This is complemented with additional leading themes including “Advancing the Chemical and Biological Engineering Fundamentals”, “Multi-Scale and/or Multi-Disciplinary Approach to Process-Product Innovation”, “Systematic Methods and Tools for Managing the Complexity”, and “Educating Chemical and Biological Engineers for Coming Challenges” which define the extended abstracts arrangements along this book. A total of 516 extended abstracts are included in the book, consisting of 7 invited lecturers, 15 keynote, 105 short oral presentations given in 5 parallel sessions, along with 6 slots for viewing 389 poster presentations. Full papers are jointly included in the companion Proceedings in CD-ROM. All papers have been reviewed and we are grateful to the members of scientific and organizing committees for their evaluations. It was an intensive task since 610 submitted abstracts from 45 countries were received. It has been an honor for us to contribute to setting up CHEMPOR 2008 during almost two years. We wish to thank the authors who have contributed to yield a high scientific standard to the program. We are thankful to the sponsors who have contributed decisively to this event. We also extend our gratefulness to all those who, through their dedicated efforts, have assisted us in this task. On behalf of the Scientific and Organizing Committees we wish you that together with an interesting reading, the scientific program and the social moments organized will be memorable for all.Fundação para a Ciência e a Tecnologia (FCT

Chemical vapor deposition of Al, Fe and of the Al13Fe4 approximant intermetallic phase : experiments and multiscale simulations

Films containing intermetallic compounds exhibit properties and combination of properties which are only partially explored. They carry potential solutions to confer multifunctionality to advanced materials required by industrial sectors and to become a source of breakthrough and innovation.Metalorganic chemical vapor deposition (MOCVD) potentially allows conformal deposition on, and functionalization of complex surfaces, with high throughput and moderate cost. For this reason, it is necessary to control the complex chemical reactions and the transport mechanisms involved in a MOCVD process. In this perspective, computational modeling of the process, fed with experimental information from targeted deposition experiments, provides an integrated tool for the investigation and the understanding of the phenomena occurring at different length scales, from the macro- to the nanoscale. The MOCVD of Al-Fe intermetallic compounds is investigated in the present thesis as a paradigm of implementation of such a combined, experimental and theoretical approach. Processing of the approximant phase Al13Fe4 is particularly targeted, due to its potential interest as low-cost and environmentally benign alternative to noble metal catalysts in the chemical industry. The attainment of the targeted Al13Fe4 intermetallic phase passes through the investigation of the MOCVD of unary Al and Fe films. The MOCVD of Al from dimethylethylamine alane (DMEAA) in the range 139oC-241oC results in pure films. Increase of the deposition temperature yields higher film density and decreased roughness. The Aldeposition rate increases to a maximum of 15.5 nm/min at 185oC and then decreases. Macroscopic simulations of the process predictdeposition rates in sufficient agreement with experimental measurements, especially in the range 139oC-227oC. At higher temperatures, competitive gas phase and surface phenomena cannot be captured by the applied model. Multiscale modeling of the process predicts the RMS roughness of the films accurately, thus allowing the control of properties such as electrical resistivity which depend on the microstructure. The MOCVD of Fe from iron pentacarbonyl, Fe(CO)5, is investigated in the range 130oC-250oC for the possibility toobtain fairly pure Fe films with low Oand C contamination. The surface morphology depends strongly on the temperature and changes are observed above 200oC. The Fe deposition rate increases up to 200oC, to a maximum of 60 nm/min, and then decreases. Moreover, the deposition rate decreases sharply with increasing pressure. Computational predictions capture accurately the experimental behavior and they reveal that the decrease athigher temperatures and pressures is attributed to the high gas phase decomposition rate of the precursor and to inhibition of the surface fromCO. The multiscale model calculates RMS roughness in good agreement with experimental data, especially at higher temperatures. Upon investigation of the two processes, aseries of Al-Fe co-depositions performed at 200oC results in Al-rich films with a loose microstructure. They contain no intermetallic phases and they are O-contaminated due to the reaction of the Al with the carbonyl ligands. Sequential deposition of Al and Fe followed by in situ annealing at 575oC for 1 h is applied to bypass the Ocontamination. The process conditions of Fe are modified to 140oC, 40 Torr and 10 min resulting in O-free films with Al:Fe atomic ratio close to the targeted 13:4 one. Characterization techniques including X-ray diffraction, TEM an