786 research outputs found
Strukturanalyse von Glykosylkationen und anderen Intermediaten mittels kryogener Infrarotspektroskopie
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
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
and the dipole-dipole 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
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)
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
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 G, G
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 G 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 BaTiO
We present a first-principles study of the low-temperature rhombohedral phase
of BaTiO using Hubbard-corrected density-functional theory. By employing
density-functional perturbation theory, we compute the onsite Hubbard for
Ti() states and the intersite Hubbard between Ti() and O()
states. We show that applying the onsite Hubbard correction alone to
Ti() states proves detrimental, as it suppresses the Ti()-O()
hybridization and drives the system towards a cubic phase. Conversely, when
both onsite and intersite are considered, the localized character of
the Ti() states is maintained, while also preserving the Ti()-O()
hybridization, restoring the rhombohedral phase of BaTiO. The generalized
PBEsol++ 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++ exhibits reduced accuracy, and the PBEsol+ Raman spectrum
diverges remarkably from experimental data, highlighting the adverse impact of
the correction alone in BaTiO. Our findings underscore the promise of
the extended Hubbard PBEsol++ functional with first-principles and
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
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 MoS revisited: a comprehensive assessment of calculations
Two-dimensional MoS 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 MoS
obtained with , the state-of-the-art in electronic-structure calculations,
are quite scattered, ranging from 2.31 to 2.97 eV. The details of
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
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 results with HSE06 as a starting point including spin-orbit
coupling, a truncated Coulomb potential, and an analytical treatment of the
singularity at
Multiscale QM/MM modelling of catalytic systems with ChemShell
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
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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