786 research outputs found

    Strukturanalyse von Glykosylkationen und anderen Intermediaten mittels kryogener Infrarotspektroskopie

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    Knowing the structure of reactive intermediates can yield unprecedented insight into organic reaction mechanisms. In particular for glycosyl cations – the reactive intermediates in glycosylations – the stereoselectivity of the reaction could be predicted by knowing the structure of the intermediate. The structure reveals whether an acyl protecting group of the monosaccharide unit interacts with the positively charged anomeric carbon so that it would shield one side from nucleophilic attack and thus steer the stereoselectivity of the reaction. These postulated approaches have been termed neighboring-group and remote participation. However, the short lifetime of reactive intermediates impedes their structural characterization in solution. Hence, for glycosyl cations, the structure remained elusive until very recently. These intermediates are not intrinsically unstable, but well-defined minima on the potential energy surface. Therefore, the ionic intermediates can be generated inside the vacuum of a mass spectrometer, free from nucleophiles or solvent molecules. In this environment, the isolated intermediates are stable and can subsequently be characterized using spectrometric or spectroscopic techniques. Recent advances in instrumentation allow coupling mass spectrometers with infrared lasers for infrared ion spectroscopy. Thus, highly-resolved infrared spectra of the analyte ions can be obtained by using cryogenic infrared spectroscopy in helium nanodroplets. To assign the obtained spectrum to a structure, it can be compared to harmonic frequencies of promising candidate structures calculated using density functional theory. This workflow was successfully used to determine the structure of several glycosyl cations, based on which, a new selective building block for 1,2-cis galactosylations was developed and its stereoselectivity was rationalized. Furthermore, it was determined that c-fragments of RNA dinucleotides are identical to the intermediate of RNA autohydrolysis. Finally, potentially antiaromatic carbocations were investigated

    Universal Pairwise Interatomic van der Waals Potentials Based on Quantum Drude Oscillators

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    Repulsive short-range and attractive long-range van der Waals (vdW) forces have an appreciable role in the behavior of extended molecular systems. When using empirical force fields - the most popular computational methods applied to such systems - vdW forces are typically described by Lennard-Jones-like potentials, which unfortunately have a limited predictive power. Here, we present a universal parameterization of a quantum-mechanical vdW potential, which requires only two free-atom properties - the static dipole polarizability α1\alpha_1 and the dipole-dipole C6C_6 dispersion coefficient. This is achieved by deriving the functional form of the potential from the quantum Drude oscillator (QDO) model, employing scaling laws for the equilibrium distance and the binding energy as well as applying the microscopic law of corresponding states. The vdW-QDO potential is shown to be accurate for vdW binding energy curves, as demonstrated by comparing to ab initio binding curves of 21 noble-gas dimers. The functional form of the vdW-QDO potential has the correct asymptotic behavior both at zero and infinite distances. In addition, it is shown that the damped vdW-QDO potential can accurately describe vdW interactions in dimers consisting of group II elements. Finally, we demonstrate the applicability of the atom-in-molecule vdW-QDO model for predicting accurate dispersion energies for molecular systems. The present work makes an important step towards constructing universal vdW potentials, which could benefit (bio)molecular computational studies

    Functionalization and Subsequent Chemical Reactions of Polypnictogen Ligand Complexes

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    In summary, this dissertation deals with the synthesis and functionalization of polypnictogen ligand complexes. Besides the successful realization of the latter with organic nucleophiles and electrophiles, a conceptually new way for the preparation of phosphines could be found. For the first time, a functionalized phosphorus atom could be removed from the coordination sphere of a transition metal. This finding was transferred to other substituents and the versatility of this method was demonstrated

    Adsorption configurations of Co-phthalocyanine on In2O3(111)

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    Indium oxide offers optical transparency paired with electric conductivity, a combination required in many optoelectronic applications. The most-stable In2O3(111) surface has a large unit cell (1.43 nm lattice constant). It contains a mixture of both bulk-like and undercoordinated O and In atoms and provides an ideal playground to explore the interaction of surfaces with organic molecules of similar size as the unit cell. Non-contact atomic force microscopy (nc-AFM), scanning tunneling microscopy (STM), and density functional theory (DFT) were used to study the adsorption of Co-phthalocyanine (CoPc) on In2O3(111). Isolated CoPc molecules adsorb at two adsorption sites in a 7:3 ratio. The Co atom sits either on top of a surface oxygen ('F configuration') or indium atom ('S configuration'). This subtle change in adsorption site induces bending of the molecules, which is reflected in their electronic structure. According to DFT the lowest unoccupied molecular orbital of the undistorted gas-phase CoPc remains mostly unaffected in the F configuration but is filled by one electron in S configuration. At coverages up to one CoPc molecule per substrate unit cell, a mixture of domains with molecules in F and S configuration are found. Molecules at F sites first condense into a F-(2x2) structure and finally rearrange into a F-(1x1) symmetry with partially overlapping molecules, while S-sited molecules only assume a S-(1x1) superstructure

    Resonant transport in a highly conducting single molecular junction via metal-metal covalent bond

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    Achieving highly transmitting molecular junctions through resonant transport at low bias is key to the next-generation low-power molecular devices. Although, resonant transport in molecular junctions was observed by connecting a molecule between the metal electrodes via chemical anchors by applying a high source-drain bias (> 1V), the conductance was limited to < 0.1 G0_0, G0_0 being the quantum of conductance. Here, we report electronic transport measurements by directly connecting a Ferrocene molecule between Au electrodes at the ambient condition in a mechanically controllable break junction setup (MCBJ), revealing a conductance peak at ~ 0.2 G0_0 in the conductance histogram. A similar experiment was repeated for Ferrocene terminated with amine (-NH2) and cyano (-CN) anchors, where conductance histograms exhibit an extended low conductance feature including the sharp high conductance peak, similar to pristine ferrocene. Statistical analysis of the data along with density functional theory-based transport calculation suggests the possible molecular conformation with a strong hybridization between the Au electrodes and Fe atom of Ferrocene molecule is responsible for a near-perfect transmission in the vicinity of the Fermi energy, leading to the resonant transport at a small applied bias (< 0.5V). Moreover, calculations including Van der Waals/dispersion corrections reveal a covalent like organometallic bonding between Au and the central Fe atom of Ferrocene, having bond energies of ~ 660 meV. Overall, our study not only demonstrates the realization of an air-stable highly transmitting molecular junction, but also provides an important insight about the nature of chemical bonding at the metal/organo-metallic interface.Comment: 23 pages, 6 figures, supplementary include

    Understanding the role of Hubbard corrections in the rhombohedral phase of BaTiO3_3

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    We present a first-principles study of the low-temperature rhombohedral phase of BaTiO3_3 using Hubbard-corrected density-functional theory. By employing density-functional perturbation theory, we compute the onsite Hubbard UU for Ti(3d3d) states and the intersite Hubbard VV between Ti(3d3d) and O(2p2p) states. We show that applying the onsite Hubbard UU correction alone to Ti(3d3d) states proves detrimental, as it suppresses the Ti(3d3d)-O(2p2p) hybridization and drives the system towards a cubic phase. Conversely, when both onsite UU and intersite VV are considered, the localized character of the Ti(3d3d) states is maintained, while also preserving the Ti(3d3d)-O(2p2p) hybridization, restoring the rhombohedral phase of BaTiO3_3. The generalized PBEsol+UU+VV functional yields remarkable agreement with experimental results for the band gap and dielectric constant, while the optimized geometry is slightly less accurate compared to PBEsol. Zone-center phonon frequencies and Raman spectra, being significantly influenced by the underlying geometry, demonstrate better agreement with experiments in the case of PBEsol, while PBEsol+UU+VV exhibits reduced accuracy, and the PBEsol+UU Raman spectrum diverges remarkably from experimental data, highlighting the adverse impact of the UU correction alone in BaTiO3_3. Our findings underscore the promise of the extended Hubbard PBEsol+UU+VV functional with first-principles UU and VV for the investigation of other ferroelectric perovskites with mixed ionic-covalent interactions

    Electronic and Geometric Structure of Copper Single-Metal Sites in Zeolites by Hyperfine Spectroscopy and Quantum Chemical Modelling

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    A Thesis submitted to the Universities of Leipzig and Turin in candidature for a Joint PhD degree by Paolo Cleto Bruzzese Abstract Atomically dispersed transition metal ions in zeolites catalyse a wide range of industrial reactions and are at the centre of intense research interest to design new sustainable synthetic pathways for energy conversion and environment remediation. One of the big challenges in this context is the characterization and location of the active sites. Indeed, mapping their nature with atomic-scale precision occupies a central place in the theory and practice of heterogeneous catalysis. In this thesis, the site-selectivity and sensitivity of Electron Paramagnetic Resonance (EPR) with its pulsed variants are combined with quantum chemical modelling to determine the microscopic structure of monomeric CuII species in zeolites with Chabazite (CHA) topology as a function of the hydration conditions and sample composition. By isotopic labelling of the zeolite framework with 17O and employing 17O ENDOR spectroscopy, the degree of covalency in the Cu-O bond is mapped and the evolution of CuII sites as a function of the hydration conditions is followed. By combining 1H HYSCORE experiments with state-of-the-art quantum chemical modelling, the EPR signature of the redox active hydroxo-CuII species is univocally identified and a quantitative assessment of its electronic and geometric structureis provided as a function of zeolite composition

    Electronic structure of MoS2_2 revisited: a comprehensive assessment of G0W0G_0W_0 calculations

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    Two-dimensional MoS2_2 combines many interesting properties that make the material a top candidate for a variety of applications. It exhibits a high electron mobility comparable to graphene, a direct fundamental band gap, relatively strongly bound excitons, and moderate spin-orbit coupling. For a thorough understanding of all these properties, an accurate description of the electronic structure is mandatory. Surprisingly, published band gaps of MoS2_2 obtained with GWGW, the state-of-the-art in electronic-structure calculations, are quite scattered, ranging from 2.31 to 2.97 eV. The details of G0W0G_0W_0 calculations, such as the underlying geometry, the starting point, the inclusion of spin-orbit coupling, and the treatment of the Coulomb potential can critically determine how accurate the results are. In this manuscript, we employ the linearized augmented planewave + local orbital method to systematically investigate how all these aspects affect the quality of G0W0G_0W_0 calculations, and also provide a summary of literature data. We conclude that the best overall agreement with experiments and coupled-cluster calculations is found for G0W0G_0W_0 results with HSE06 as a starting point including spin-orbit coupling, a truncated Coulomb potential, and an analytical treatment of the singularity at q=0q=0

    Multiscale QM/MM modelling of catalytic systems with ChemShell

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    Hybrid quantum mechanical/molecular mechanical (QM/MM) methods are a powerful computational tool for the investigation of all forms of catalysis, as they allow for an accurate description of reactions occurring at catalytic sites in the context of a complicated electrostatic environment. The scriptable computational chemistry environment ChemShell is a leading software package for QM/MM calculations, providing a flexible, high performance framework for modelling both biomolecular and materials catalysis. We present an overview of recent applications of ChemShell to problems in catalysis and review new functionality introduced into the redeveloped Python-based version of ChemShell to support catalytic modelling. These include a fully guided workflow for biomolecular QM/MM modelling, starting from an experimental structure, a periodic QM/MM embedding scheme to support modelling of metallic materials, and a comprehensive set of tutorials for biomolecular and materials modelling

    Effect of dynamical screening in the Bethe-Salpeter framework: Excitons in crystalline naphthalene

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    Solving the Bethe-Salpeter equation (BSE) for the optical polarization functions is a first principles means to model optical properties of materials including excitonic effects. One almost ubiquitously used approximation neglects the frequency dependence of the screened electron-hole interaction. This is commonly justified by the large difference in magnitude of electronic plasma frequency and exciton binding energy. We incorporated dynamical effects into the screening of the electron-hole interaction in the BSE using two different approximations as well as exact diagonalization of the exciton Hamiltonian. We compare these approaches for a naphthalene organic crystal, for which the difference between exciton binding energy and plasma frequency is only about a factor of ten. Our results show that in this case, corrections due to dynamical screening are about 15\,\% of the exciton binding energy. We analyze the effect of screening dynamics on optical absorption across the visible spectral range and use our data to establish an \emph{effective} screening model as a computationally efficient approach to approximate dynamical effects in complex materials in the future.Comment: 11 pages main text, 5 figures main text, 9 pages supplemental, 6 figures supplementa
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