Curly arrows, electron flow, and reaction mechanisms from the perspective of the bonding evolution theory

Despite the usefulness of curly arrows in chemistry, their relationship with real electron density flows is still imprecise, and even their direct connection to quantum chemistry is still controversial. The paradigmatic description – from first principles – of the mechanistic aspects of a given chemical process is based mainly on the relative energies and geometrical changes at the stationary points of the potential energy surface along the reaction pathway; however, it is not sufficient to describe chemical systems in terms of bonding aspects. Probing the electron density distribution during a chemical reaction can provide important insights, enabling us to understand and control chemical reactions. This aim has required an extension of the relationships between the concepts of traditional chemistry and those of quantum mechanics. Bonding evolution theory (BET), which combines the topological analysis of the electron localization function (ELF) and Thom’s catastrophe theory (CT), provides a powerful method that offers insight into the molecular mechanism of chemical rearrangements. In agreement with the laws of physical and aspects of quantum theory, BET can be considered an appropriate tool to tackle chemical reactivity with a wide range of possible applications. In this work, BET is applied to address a long-standing problem: the ability to monitor the flow of electron density. BET analysis shows a connection between quantum mechanics and bond making/forming processes. Likewise, the present approach retrieves the classical curly arrows used to describe the rearrangements of chemical bonds and provides detailed physical grounds for this type of representation. We demonstrate this procedure using the test set of prototypical examples of thermal ring apertures, and the degenerated Cope rearrangement of semibullvalene

Bonding Interactions in Congested Molecules: A Study of the Interatomic Forces and the Molecular Electrostatic Potential

Chemistry and Polymer Scienc

Challenges in simulating light-induced processes in DNA

© 2016 by the authors; licensee MDPI, Basel, Switzerland. In this contribution, we give a perspective on the main challenges in performing theoretical simulations of photoinduced phenomena within DNA and its molecular building blocks. We distinguish the different tasks that should be involved in the simulation of a complete DNA strand subject to UV irradiation: (i) stationary quantum chemical computations; (ii) the explicit description of the initial excitation of DNA with light; (iii) modeling the nonadiabatic excited state dynamics; (iv) simulation of the detected experimental observable; and (v) the subsequent analysis of the respective results. We succinctly describe the methods that are currently employed in each of these steps. While for each of them, there are different approaches with different degrees of accuracy, no feasible method exists to tackle all problems at once. Depending on the technique or combination of several ones, it can be problematic to describe the stacking of nucleobases, bond breaking and formation, quantum interferences and tunneling or even simply to characterize the involved wavefunctions. It is therefore argued that more method development and/or the combination of different techniques are urgently required. It is essential also to exercise these new developments in further studies on DNA and subsystems thereof, ideally comprising simulations of all of the different components that occur in the corresponding experiments

Evaluating common QTAIM and NCI interpretations of the electron density concentration through IQA interaction energies and 1D cross-sections of the electron and deformation density distributions

Nine kinds of inter- and intramolecular interactions were investigated by exploring the topology of electron density in the interatomic regions using standard protocols of QTAIM, IQA and NCI techniques as well as in-house developed cross-sections of the electron and deformation density distributions. The first four methods provide the properties of the resultant density distribution in a molecular system whereas the later illustrates the process, inflow or outflow of density from fragments to the interatomic region of an interaction on its formation in a molecular system. We used (i) the QTAIM-defined atomic interaction line, AIL (presence or absence), (ii) IQA-defined interaction energy, EA;B int , and its components, classical VA;B cl and exchange–correlation VA;B XC term, (iii) NCI-defined isosurfaces to identify local regions of accumulated (k2 0) density relative to immediate environment, and (iv) deformation density for which Dq(r) > 0 indicates an inflow or otherwise an outflow of density on the interaction formation to explore the nature of the interactions. We found (i) AILs for highly attractive and repulsive interactions, regardless whether an inflow (Dq(r) > 0) or outflow of density into the interatomic region, (ii) no correlation between the signs of k2 and EA;B int ; both, highly repulsive and attractive, interactions might have locally depleted density and vice versa, (iii) locally accumulated density (k2 < 0) does not imply that this is the result of an inflow (Dq(r) > 0) of density and this equally applies to attractive and repulsive interactions either with or without an AIL. Results obtained demonstrate that the molecular environment can change the character of an interaction radically, from (i) attractive to repulsive, (ii) k2 0, or (iii) Dq(r) > 0 to Dq(r) < 0; hence, none of the topological indices used here, either separately or combined, can be used to definitely predict the (de)stabilizing nature of an interaction except highly repulsive ones for which the absence of AIL, interatomic density depletion and outflow of density on interaction formation are observed.The National Research Foundation of South Africa (Grant Number 87777) and the University of Pretoria.http://www.elsevier.com/locate/comptchb2016Chemistr

Understanding the Interaction of CO and O2 with MgO(001) and Supported Metal Atoms: Towards Single-Atom Catalysis

This thesis contributes to the fundamental understanding of the interactions of a single gold atom supported by a defective and defect-free MgO(001) surface in a mixed CO/O2 atmosphere. Using cluster models and point charge embedding within a density functional theory framework, the CO oxidation reaction for a single gold atom is simulated on differently charged oxygen vacancies of MgO(001) to rationalise its experimentally observed lack of catalytic activity. The results show, that only the F0 colour centre promotes the electron redistribution towards an adsorbed oxygen molecule and sufficiently weakens the oxygen bond, as required for a sustainable catalytic cycle. The moderate adsorption energy of the gold atom, however, cannot prevent the insertion of oxygen atoms into the vacancy, which remains after the formation of the first CO2 molecule. The surface becomes invariably repaired, which set the focus on the chemistry on a defect-free MgO(001) surface. To contribute towards the field of heterogeneous single-atom catalysis, various analysis tools are used to shed light on the binding situation of supported group 11 metal atoms to the defect-free substrate and both CO and O2 molecules. Cooperative effects are found to enhance the stability of CO upon co-adsorption with O2 for all three metal centres. The results gives further insights to the lack of catalytic activity with respect to the CO oxidation under thermal conditions as a competition between OC-O2 bond activation and surface diffusion leading to metal atom agglomeration. For the simulation of surface dynamics, an accurate description of the potential energy surface is achieved for CO on a defect-free MgO(001) surface by parametrizing a reactive bond order force field to a new set of ab initio data. Theoretical investigation of the non-reactive scattering of CO from the surface are done by performing quasi-classical scattering dynamic simulations. The scattering behaviour for several incidence energies and different initial ro-vibrational states of impinging CO is evaluated, which illustrates the role of surface atom motion on energy transfer processes. The analysis of time of flight spectra and scattering angle distributions reveals two different scattering channels, which become particularly noticeable at low incidence energies due to the weak interaction potential of CO with MgO(001). The scattering process is strongly influenced by the anisotropy of the potential energy surface for CO impinging in upwards and downwards alignment. Eventually, the observations are in agreement with the established Baule model especially for the distinct scattering features at low incident energies.Die Arbeit vertieft das Wissen über die Wechselwirkungen zwischen einzelnen Goldatomen auf defekthaltigen und defektfreien MgO(001)-Oberflächen in einer gemischten CO/O2 Atmosphäre. Mit Hilfe der Cluster-Einbettungs-Methode und der Dichtefunktionaltheorie wird die Oxidationsreaktion von CO auf einen einzelnen Goldatom simuliert, welches verschieden geladenen Sauerstoff-Fehlstellen der Oberfläche besetzt, um experimentelle Ergebnisse nachzuvollziehen. Es zeigt sich, dass nur die neutral geladenen F0-Fehlstellen durch Elektronenumlagerung in Richtung adsorbierten Sauerstoff-Molekülen in der Lage sind, die Sauerstoffbindung soweit zu schwächen, um eine katalytische Reaktion zu ermöglichen. Dennoch ist die moderate Bindungsenergie eines Goldatoms auf der Fehlstelle nicht ausreichend um die Einlagerung eines einzelnen Sauerstoffatoms zu verhindern, das nach der Bildung des ersten CO2 Moleküls auf der Oberfläche zurückbleibt. Dies führt zur unwiderruflichen Reparatur der Oberflächendefekte. Deswegen verschiebt sich der Fokus auf die Chemie der defektfreien MgO(001)-Oberfläche. Es werden verschiedene Analysemethoden verwendet, um die Bindungsverhältnisse der Metalle der 11. Gruppe mit CO als auch O2 zu verstehen und weitere Einblicke aud den Gebiet der heterogenen Einzelatom-Katalyse zu bekommen. Die gemeinsame Anlagerung von CO und O2 auf allen drei Metallzentren verstärkt die jeweilige Adsorptionsstärke durch kooperative Effekte. Das Ausbleiben einer katalytischen Oxidation von CO unter thermischen Bedingungen wird durch die Ergebnisse unterstützt, vor allem wegen des Widerspruchs, sowohl gleichzeitig einen Bindungsbruch zu ermöglichen, ohne dabei die Metallatome zu größeren Clustern zusammenzuführen. Für die Simulation von Oberflächenprozesse wurde eine präzise Beschreibung des Potentials von CO auf defektfreien MgO(001)-Oberflächen unter Einbezug reaktiver Kraftfelder entwickelt. Es sind quasi-klassische Streusimulationen von CO durchgeführt und dessen Streuverhalten bei verschiedenen Einschlagsenergien und Rotationsschwingungszuständen untersucht worden. Besonderes Augenmerk fällt dabei auf die Bewegungsmöglichkeit der Oberflächenatome. Die Spektren der Flugzeit und Verteilung der Streuwinkel deuten auf zwei verschiedene Streukanäle hin, welche sich vor allem bei schwachen Einschlagsenergien deutlich hervorheben. Dies ist im Einklang mit der schwachen Natur der Gas-Oberflächen-Wechselwirkung. Der Streuprozess hängt deutlich von der Orientierung des Kohlenmonoxids beim Einschlag ab, was an der Anisotropie der Potentialenergiefläche ersichtlich wird. Die Beobachtungen, vor allem bei kleinen Einschlagsenergien, stimmen mit den Vorhersagen des etablierten Baule-Modells überein

Computational Modelling of Excited State Decay in Polyatomic Molecules

The introduction of general numerical methods in the form of widely available software can have a dramatic effect on the development of a scientific field. In electronic structure theory, for example, general-purpose programs (such as Gaussian, ADF, MOLPRO,. . . ) combined with better computational resources have in part led to molecular electronic structure calculations becoming a ubiquitous tool in chemical research. Similarly, quantum dynamics methods based on coupled time-evolving Gaussian basis sets and molecular potential energy surfaces calculated on-the-fly hold out similar promise in the study of non-adiabatic processes, because of their generality and freedom from ad hoc assumptions. Therefore, the aim of this thesis is to investigate the convergence and applicability of quantum dynamics calculations with a fully variational coupled Gaussian basis set description, termed variational Multi-Con guration Gaussian (vMCG). It is suggested that the vMCG approach provides a way to balance accuracy against computational cost for molecules of comparable size by choosing the number of coupled Gaussian product basis functions and a middle way forward between grid-based and trajectory surface hopping approaches to non-adiabatic molecular quantum dynamics calculations. In order to prove the suitability of vMCG we show its application to three problems of chemical interest: the study of fulvene excited state decay, the prediction of a coherent control mechanism for the same system and the benchmarking of an electronic population dynamics model for electronic transitions when occurring through a conical intersection. In the long term, the development of vMCG is expected to have a major impact, allowing nonadiabatic dynamics simulations to be made not only by theoreticians, but also by non-specialists and experimentalists in both industry and academia.Chapter 1: Modelling Excited State Decay [Diagrams appear here. To view, please open pdf attachment] This chapter introduces and reviews the current state-of-the-art modelling of non-adiabatic processes in molecular systems. This is a challenging topic since the simulation must treat simultaneously the motion of the nuclei and the electrons, which are coupled together. It is concluded that a wide range of methodologies are available. However, when looking for a general tool for the study of non-adiabatic processes, quantum dynamics methods based on coupled time-evolving Gaussian basis sets such as the Direct Dynamics variational Multi-Con guration Gaussian (DD-vMCG) wavepacket method, as well as to other related methods - such as Ab Initio Multiple Spawning (AIMS, FMS)[1, 2] and Multi-Con gurational Ehrenfest (MCE)[3, 4] - seem to be an especially suitable choice because of their generality and freedom from ad hoc assumptions. Chapter 2: variational Gaussian nuclear wavepackets [Diagrams appear here. To view, please open pdf attachment] This chapter describes three possible time-evolving Gaussian basis sets for use in non-adiabatic quantum dynamics based on the Direct Dynamics variational Multi-Con guration Gaussian (DD-vMCG) wavepacket method. These general model representations are compared using model calculations in a simple harmonic oscillator and describing their connections to other work. It is suggested that the fully variational nuclear wavefunction, termed vMCG (variational Multi-Con guration Gaussian) is a very convenient formulation leading towards a realistic sampling of the phase space without the initial conditions (i.e. initial disposition and momentum) being so important when using a su cient amount of coupled Gaussian basis functions. Chapter 3: Fulvene S1/S0 Excited State Decay [Diagrams appear here. To view, please open pdf attachment] The vMCG (variational Multi-Con guration Gaussian) approach described in Chapter 2 is benchmarked in a realistic system by modelling the radiationless decay from an electronic excited state through an extended conical intersection seam. As a benchmark system, we model the radiationless decay of fulvene from its rst electronic excited state and monitor two associated properties: the spatial extent to which the conical intersection seam is sampled and the timescale and stepwise nature of the population transfer. We illustrate how the use of a fully variational nuclear wavefunction provides a way to balance accuracy against computational cost for molecules of comparable size by choosing the number of coupled Gaussian product basis functions. Chapter 4: Controlling Fulvene S1/S0 Decay [Diagrams appear here. To view, please open pdf attachment] Direct quantum dynamics simulations using the vMCG (variational Multi- Con guration Gaussian) approach were performed in order to model the control of the stepwise population transfer in fulvene. As shown in Chapter 3, ultra-fast internal conversion takes place centred on the higher-energy planar/sloped region of the S1/S0 conical intersection seam. Therefore, two possible schemes for controlling whether stepwise population transfer occurs or not | either altering the initial geometry distribution or the initial momentum composition of the photo-excited wavepacket - were explored. In both cases, decay took place instead in the lower-energy twisted/peaked region of the crossing seam, switching o the stepwise population transfer. This absence of re-crossing is a direct consequence of the change in the position on the intersection at which decay occurs and its consequences should provide an experimentally observable fingerprint of this system. Chapter 5: A population transfer model for intramolecular electron transfer [Diagrams appear here. To view, please open pdf attachment] The aim of this chapter is to further prove the applicability of the vMCG (variational Multi-Con guration Gaussian) approach by benchmarking an approximate population dynamics model in Jahn-Teller systems. The socalled Density Matrix Non-Equilibrium Fermi Golden Rule (DM-NFGR) can be seen as a simpli ed version of vMCG, in which the nite Gaussian basis set and on-the-fly evaluation of the nuclear Hamiltonian are eliminated via use of the density matrix formalism and a perturbational treatment of the equations. This has three clear advantages: firstly, it allows us to extend the maximum molecular size considerably; secondly, we can relate the population dynamics to an analytical time-dependent rate expression; and finally, temperature effects can be included in the simulations. Benchmark calculations for the 2,6-bis(methylene) adamantyl (BMA) radical cation support the reliability of the results

Mixed Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulations of Biological Systems in Ground and Electronically Excited States

The current state of the art of Quantum Mechanical/molecular mechanical (QM/MM) molecular dynamics approaches in ground and electronically excited states and their applications to biological problems is reviewed. For a complete description of quantum phenomena, the quantum nature of both electrons and nuclei has to be taken into account. Most of the current QM/MM applications are based on adiabatic dynamics in the electronic ground state. However, for dynamics in electronically excited states, the coupling between states, which is mediated via the nuclear motion, can be sizable, and nonadiabatic effects have to be taken into account. Configuration Interaction Singles (CIS) is a popular method in QM/MM applications due to its computational expedience that allows for the treatment of several hundred atoms. Since the 1990s, the Modified Neglect of Differential Overlap (MNDO) method has been further extended to a d orbital basis. This MNDO/d extension allows for the treatment of heavier elements. By using feature selection algorithms348 to identify the most appropriate subset of relevant variables that describe a certain phenomenon, the high-dimensionality of QM/MM data can be reduced and used for further analysis with causal inference algorithms to establish unique cause-effect relationships

Semiclassical roots of universality in many-body quantum chaos

Quantum chaos of many-body (MB) systems has been swiftly developing into a vibrant research area at the interface between various disciplines, ranging from statistical physics to condensed matter to quantum information and to cosmology. In quantum systems with a classical limit, advanced semiclassical methods provide the crucial link between classically chaotic dynamics and corresponding universal features at the quantum level. Recently, single-particle (SP) techniques dealing with ergodic wave interference in the usual semiclassical limit have begun to be transformed into the field theoretical domain of N-particle systems in the analogous semiclassical limit , thereby accounting for genuine MB quantum interference. This semiclassical MB theory provides a unified framework for understanding random-matrix correlations of both SP and MB quantum chaotic systems. Certain braided bundles of classical orbits, and of mean field modes, govern interference, respectively, and provide the key to the foundation of universality. Case studies presented include an MB version of Gutzwiller’s trace formula for the spectral density and out-of-time-order correlators along with brief remarks on where further progress may be forthcoming