The electronic structure of Amorphous Carbon Nanodots

We have studied hydrogen-passivated amorphous carbon nanostructures with semiempirical molecular orbital theory in order to provide an understanding of the factors that affect their electronic properties. Amorphous structures were first constructed using periodic calculations in a melt/quench protocol. Pure periodic amorphous carbon structures and their counterparts doped with nitrogen and/or oxygen feature large electronic band gaps. Surprisingly, descriptors such as the elemental composition and the number of sp³-atoms only influence the electronic structure weakly. Instead, the exact topology of the sp²-network in terms of effective conjugation defines the band gap. Amorphous carbon nanodots of different structures and sizes were cut out of the periodic structures. Our calculations predict the occurrence of localized electronic surface states, which give rise to interesting effects such as amphoteric reactivity and predicted optical band gaps in the near-UV/visible range. Optical and electronic gaps display a dependence on particle size similar to that of inorganic colloidal quantum dots

Evaluation and Development of Quantum Chemical Methodologies for Noncovalent Interactions and Supramolecular Thermochemistry

This thesis focuses on the application and development of electronic structure methods for noncovalent interactions in general and the evaluation of multilevel methodologies for an accurate description of supramolecular thermochemistry in particular. Noncovalent interactions are omnipresent in systems of various domains of science, such as supramolecular chemistry, structural biology, and surface science. Within supramolecular chemistry, host-guest complexes are of particular importance due to their diverse applicability in various fields like molecular recognition or self-assembly. The binding situation in a supramolecular complex is often unknown and sampling many different conformations is desired. Therefore, the first part of this thesis is concerned with cost-efficient density functional theory (DFT) and Hartree-Fock (HF) based electronic structure methods for noncovalent interactions, which are about a factor of 50 to 100 faster than calculations in a large basis set. The main errors in a DFT or HF calculation with small atomic orbital basis sets are the missing London dispersion and the basis set superposition error (BSSE). An exemplary benchmark study shows that modern correction strategies clearly outperform plain DFT or HF for energies and geometries of small dimers, large supramolecular complexes, and molecular crystals. Further, the development and evaluation of a minimal basis set Hartree--Fock method with three atom-pairwise corrections for London dispersion, BSSE, and basis set incompleteness (HF-3c) is presented. With nine global parameters, the empiricism of HF-3c is moderate, the method is self-interaction error free, and noiseless analytical frequencies can be obtained. HF-3c provides accurate geometries of organic supramolecular systems and small proteins, and good noncovalent interaction energies. The mean absolute deviations (MADs) for the S22 set of small noncovalently bound dimers and the S12L set of supramolecular host-guest association energies are 0.6 and 4.4 kcal mol-1, respectively. This is excellent compared to dispersion corrected DFT methods whose MADs are in the range of 0.3-0.5 and 2-5 kcal mol-1, respectively. The second part focuses on the application and evaluation of multilevel methodologies for an accurate description of Gibbs free energies of association (Δ Ga) for supramolecular host-guest complexes in solution. First, state-of-the-art dispersion corrected DFT (DFT-D3ATM) is used together with a large quadruple-zeta (QZ) basis set to obtain association energies in the gas phase. A semiempirical method is utilized to compute the thermostatistical corrections from energy to free energy and last, a continuum solvation model is employed. The general procedure is illustrated with a case study on eight typical complexes. The SAMPL4 blind test challenge provides a unique opportunity to test this methodology in a realistic setting. Relative Δ Ga in water are predicted for a cucurbit[7]uril host and 14 guest molecules containing ammonia groups. The HF-3c method was employed to sample possible binding conformations and the final Δ Ga were calculated on the PW6B95-D3ATM/QZ level with HF-3c thermal corrections and COSMO-RS solvation contributions. Compared to other methods theses predictions rank in the top three of all statistical measurements. The MAD and RMSD are only 2.0 and 2.6 kcal mol-1, respectively. Further, the S30L benchmark set is proposed as an extension of the S12L set for association (free) energies of host-guest complexes. Larger systems with up to 200 atoms, more divers interaction motifs, and higher charges are represented by experimentally measured complexes with Δ Ga values in the range from -0.7 to -24.7 kcal mol-1. In order to obtain a theoretical best estimate for Δ Ga different dispersion corrected density functionals, semiempirical methods, and continuum solvation models are tested. The best method combination is similar to the one used for the SAMPL4 bind test and yields an MAD with respect to experiment of only 2.4 kcal mol-1. Inclusion of counterions for the charged systems (S30L-CI) were found to improve the results overall. Synergy between theory and experiment is demonstrated in the last part of this thesis with the application of quantum chemical methods to two specific chemical problems related to supramolecular chemistry. Experimentally, it was found that titanocene(III) catalysts can be stabilized by chloride additives and the calculations reveal that the stabilities of these adducts are determined by the extent of hydrogen bonding between the catalyst and the ammonium cation. 1,1'-Binaphthol based ligands can be used to obtain enantiomerically pure double- and triple-stranded helicates with transition-metal ions in a completely diastereoselective self-assembly process. Electronic circular dichroism spectra of precursors for paracyclophane based ligands have been investigated computationally in order to identify their absolute configuration

Effect of temperature and branching on the nature and stability of alkene cracking intermediates in H-ZSM-5

Catalytic cracking of alkenes takes place at elevated temperatures in the order of 773–833 K. In this work, the nature of the reactive intermediates at typical reaction conditions is studied in H-ZSM-5 using a complementary set of modeling tools. Ab initio static and molecular dynamics simulations are performed on different C4single bond C5 alkene cracking intermediates to identify the reactive species in terms of temperature. At 323 K, the prevalent intermediates are linear alkoxides, alkene π-complexes and tertiary carbenium ions. At a typical cracking temperature of 773 K, however, both secondary and tertiary alkoxides are unlikely to exist in the zeolite channels. Instead, more stable carbenium ion intermediates are found. Branched tertiary carbenium ions are very stable, while linear carbenium ions are predicted to be metastable at high temperature. Our findings confirm that carbenium ions, rather than alkoxides, are reactive intermediates in catalytic alkene cracking at 773 K

The Nature of Interlayer Binding and Stacking of spsp-sp2sp^{2} Hybridized Carbon Layers: A Quantum Monte Carlo Study

$\alpha$-graphyne is a two-dimensional sheet of $sp$-$sp^2$ hybridized carbon atoms in a honeycomb lattice. While the geometrical structure is similar to that of graphene, the hybridized triple bonds give rise to electronic structure that is different from that of graphene. Similar to graphene, $\alpha$-graphyne can be stacked in bilayers with two stable configurations, but the different stackings have very different electronic structures: one is predicted to have gapless parabolic bands and the other a tunable band gap which is attractive for applications. In order to realize applications, it is crucial to understand which stacking is more stable. This is difficult to model, as the stability is a result of weak interlayer van der Waals interactions which are not well captured by density functional theory (DFT). We have used quantum Monte Carlo simulations that accurately include van der Waals interactions to calculate the interlayer binding energy of bilayer graphyne and to determine its most stable stacking mode. Our results show that interlayer bindings of $sp$- and $sp^{2}$-bonded carbon networks are significantly underestimated in a Kohn-Sham DFT approach, even with an exchange-correlation potential corrected to include, in some approximation, van der Waals interactions. Finally, our quantum Monte Carlo calculations reveal that the interlayer binding energy difference between the two stacking modes is only 0.9(4) meV/atom. From this we conclude that the two stable stacking modes of bilayer $\alpha$-graphyne are almost degenerate with each other, and both will occur with about the same probability at room temperature unless there is a synthesis path that prefers one stacking over the other.Comment: 25 pages, 6 figure

Ultra-Fast Semi-Empirical Quantum Chemistry for High-Throughput Computational Campaigns with Sparrow

Semi-empirical quantum chemical approaches are known to compromise accuracy for feasibility of calculations on huge molecules. However, the need for ultrafast calculations in interactive quantum mechanical studies, high-throughput virtual screening, and for data-driven machine learning has shifted the emphasis towards calculation runtimes recently. This comes with new constraints for the software implementation as many fast calculations would suffer from a large overhead of manual setup and other procedures that are comparatively fast when studying a single molecular structure, but which become prohibitively slow for high-throughput demands. In this work, we discuss the effect of various well-established semi-empirical approximations on calculation speed and relate this to data transfer rates from the raw-data source computer to the results visualization front end. For the former, we consider desktop computers, local high performance computing, as well as remote cloud services in order to elucidate the effect on interactive calculations, for web and cloud interfaces in local applications, and in world-wide interactive virtual sessions. The models discussed in this work have been implemented into our open-source software SCINE Sparrow.Comment: 39 pages, 4 figures, 4 table

Problems, successes and challenges for the application of dispersion-corrected density-functional theory combined with dispersion-based implicit solvent models to large-scale hydrophobic self-assembly and polymorphism

© 2015 Taylor & Francis. The recent advent of dispersion-corrected density-functional theory (DFT) methods allows for quantitative modelling of molecular self-assembly processes, and we consider what is required to develop applications to the formation of large self-assembled monolayers (SAMs) on hydrophobic surfaces from organic solution. Focus is on application of the D3 dispersion correction of Grimme combined with the solvent dispersion model of Floris, Tomasi and Pascual-Ahuir to simulate observed scanning-tunnelling microscopy (STM) images of various polymorphs of tetraalkylporphyrin SAMs on highly oriented pyrolytic graphite surfaces. The most significant problem is identified as the need to treat SAM structures that are incommensurate with those of the substrate, providing a challenge to the use of traditional periodic-imaging boundary techniques. Using nearby commensurate lattices introduces non-systematic errors into calculated lattice constants and free energies of SAM formation that are larger than experimental uncertainties and polymorph differences. Developing non-periodic methods for polymorph interface simulation also remains a challenge. Despite these problems, existing methods can be used to interpret STM images and SAM atomic structures, distinguishing between multiple feasible polymorph types. They also provide critical insight into the factors controlling polymorphism. All this stems from a delicate balance that the intermolecular D3 and solvent Floris, Tomasi and Pascual-Ahuir corrections provide. Combined optimised treatments should yield fully quantitative approaches in the future