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The 3,3-disubstitued 3-silaheterocyclohexane with an electronegative substituent at silicon, 3-fluoro-3-methyl-3-silatetrahydropyran 1, was synthesized, and its molecular structure and conformational properties studied by gas-phase electron diffraction (GED) and low temperature C-13 and F-19 NMR spectroscopy. Quantum-chemical calculations were carried out both for the isolated species and Hcomplexes in gas and in polar medium. The predominance of the 1-FeqMeax conformer (1-F-eq:1-F-ax ratio of 65:35, Delta G degrees = 0.37 kcal/mol) determined from GED is close to the theoretically estimated conformational equilibrium, especially at the DFT level. In solution, low temperature NMR spectroscopy showed no decoalescence of the signals in C-13 (down to 95 K) and F-19 NMR spectra (down to 123 K). However, the calculated F-19 chemical shift of -173.6 ppm for the 1-FeqMeax conformer practically coincides with the experimentally observed value (-173 to -175 ppm) as distinct from that for the 1-FaxMeeq conformer (-188.8 ppm), suggesting compound 1 to be anancomeric in solution, in compliance with its theoretical and experimental preference in the gas phase.
To enhance the spin-orbit interaction in graphene by a proximity effect without compromising the quasi-free-standing dispersion of the Dirac cones means balancing the opposing demands for strong and weak graphene-substrate interaction. So far, only the intercalation of Au under graphene/Ni(111) has proven successful, which was unexpected since graphene prefers a large separation (similar to 3.3 angstrom) from a Au monolayer in equilibrium. Here, we investigate this system and find the solution in a nanoscale effect. We reveal that the Au largely intercalates as nanoclusters. Our density functional theory calculations show that the graphene is periodically stapled to the Ni substrate, and this attraction presses graphene and Au nanoclusters together. This, in turn, causes a Rashba effect of the giant magnitude observed in experiment. Our findings show that nanopatterning of the substrate can be efficiently used for engineering of spin-orbit effects in graphene.
Biological carbon dioxide (CO2) reduction is an important step by which organisms form valuable energy-richer molecules required for further metabolic processes. The Mo-dependent formate dehydrogenase (FDH) from Rhodobacter capsulatus catalyzes reversible formate oxidation to CO2 at a bis-molybdopterin guanine dinucleotide (bis-MGD) cofactor. To elucidate potential substrate binding sites relevant for the mechanism, we studied herein the interaction with the inhibitory molecules azide and cyanate, which are isoelectronic to CO2 and charged as formate. We employed infrared (IR) spectroscopy in combination with density functional theory (DFT) and inhibition kinetics. One distinct inhibitory molecule was found to bind to either a non-competitive or a competitive binding site in the secondary coordination sphere of the active site. Site-directed mutagenesis of key amino acid residues in the vicinity of the bis-MGD cofactor revealed changes in both non-competitive and competitive binding, whereby the inhibitor is in case of the latter interaction presumably bound between the cofactor and the adjacent Arg587.
Electrochemical fluorination in anhydrous HF, also known as the Simons process, is a widely used industrial method for fluorination of organic compounds. Its mechanism, being not so well understood, has long been debated and is believed to involve higher valent nickel fluorides formed on the nickel-plated anode during the process. One of these is speculated to be Ni2F5, which was previously reported in the literature and assigned via infrared spectroscopy, but its crystal structure is not yet known. We have identified known crystal structures of compounds with similar stoichiometries as Ni2F5 and utilized them as a starting point for our periodic DFT investigations, applying the PBE+U method. Ni2F5 as the most stable polymorph was found to be of the same crystal structure as another mixed valent fluoride, Cr2F5. The calculated lattice parameters are a = 7.24 angstrom, b = 7.40 angstrom, c = 7.08 angstrom and beta = 118.9 degrees with an antiferromagnetic ordering of the nickel magnetic moments.
Aluminum oxide is an Earth-abundant geological material, and its interaction with water is of crucial importance for geochemical and environmental processes. Some aluminum oxide surfaces are also known to be useful in heterogeneous catalysis, while the surface chemistry of aqueous oxide interfaces determines the corrosion, growth and dissolution of such materials. In this doctoral work, we looked mainly at the (0001) surface of α-Al 2 O 3 and its reactivity towards water. In particular, a great focus of this work is dedicated to simulate and address the vibrational spectra of water adsorbed on the α-alumina(0001) surface in various conditions and at different coverages. In fact, the main source of comparison and inspiration for this work comes from the collaboration with the “Interfacial Molecular Spectroscopy” group led by Dr. R. Kramer Campen at the Fritz-Haber Institute of the MPG in Berlin. The expertise of our project partners in surface-sensitive Vibrational Sum Frequency (VSF) generation spectroscopy was crucial to develop and adapt specific simulation schemes used in this work. Methodologically, the main approach employed in this thesis is Ab Initio Molecular Dynamics (AIMD) based on periodic Density Functional Theory (DFT) using the PBE functional with D2 dispersion correction. The analysis of vibrational frequencies from both a static and a dynamic, finite-temperature perspective offers the ability to investigate the water / aluminum oxide interface in close connection to experiment.
The first project presented in this work considers the characterization of dissociatively adsorbed deuterated water on the Al-terminated (0001) surface. This particular structure is known from both experiment and theory to be the thermodynamically most stable surface termination of α-alumina in Ultra-High Vacuum (UHV) conditions. Based on experiments performed by our colleagues at FHI, different adsorption sites and products have been proposed and identified for D 2 O. While previous theoretical investigations only looked at vibrational frequencies of dissociated OD groups by staticNormal Modes Analysis (NMA), we rather employed a more sophisticated approach to directly assess vibrational spectra (like IR and VSF) at finite temperature from AIMD. In this work, we have employed a recent implementation which makes use of velocity-velocity autocorrelation functions to simulate such spectral responses of O-H(D) bonds. This approach allows for an efficient and qualitatively accurate estimation of Vibrational Densities of States (VDOS) as well as IR and VSF spectra, which are then tested against experimental spectra from our collaborators.
In order to extend previous work on unimolecularly dissociated water on α-Al 2 O 3 , we then considered a different system, namely, a fully hydroxylated (0001) surface, which results from the reconstruction of the UHV-stable Al-terminated surface at high water contents. This model is then further extended by considering a hydroxylated surface with additional water molecules, forming a two-dimensional layer which serves as a potential template to simulate an aqueous interface in environmental conditions. Again, employing finite-temperature AIMD trajectories at the PBE+D2 level, we investigated the behaviour of both hydroxylated surface (HS) and the water-covered structure derived from it (known as HS+2ML). A full range of spectra, from VDOS to IR and VSF, is then calculated using the same methodology, as described above. This is the main focus of the second project, reported in Chapter 5. In this case, comparison between theoretical spectra and experimental data is definitely good. In particular, we underline the nature of high-frequency resonances observed above 3700 cm −1 in VSF experiments to be associated with surface OH-groups, known as “aluminols” which are a key fingerprint of the fully hydroxylated surface.
In the third and last project, which is presented in Chapter 6, the extension of VSF spectroscopy experiments to the time-resolved regime offered us the opportunity to investigate vibrational energy relaxation at the α-alumina / water interface. Specifically, using again DFT-based AIMD simulations, we simulated vibrational lifetimes for surface aluminols as experimentally detected via pump-probe VSF. We considered the water-covered HS model as a potential candidate to address this problem. The vibrational (IR) excitation and subsequent relaxation is performed by means of a non-equilibrium molecular dynamics scheme. In such a scheme, we specifically looked at the O-H stretching mode of surface aluminols. Afterwards, the analysis of non-equilibrium trajectories allows for an estimation of relaxation times in the order of 2-4 ps which are in overall agreement with measured ones.
The aim of this work has been to provide, within a consistent theoretical framework, a better understanding of vibrational spectroscopy and dynamics for water on the α-alumina(0001) surface,ranging from very low water coverage (similar to the UHV case) up to medium-high coverages, resembling the hydroxylated oxide in environmental moist conditions.
1-(Dimethylamino)-1-phenyl-1-silacyclohexane 1, was synthesized, and its molecular structure and conformational properties studied by gas-phase electron diffraction (GED), low temperature C-13 NMR spectroscopy and quantum-chemical calculations. The predominance of the 1-Ph-ax conformer (1-Ph-eq:1-Ph-ax ratio of 20:80%, Delta G degrees (317 K) = -0.87 kcal/mol) in the gas phase is close to the theoretically estimated conformational equilibrium. In solution, low temperature NMR spectroscopy showed analyzable decoalescence of C-ipso and C(1,5) carbon signals in C-13 NMR spectra at 103 K. Opposite to the gas state in the freon solution employed (CD2Cl2/CHFCl2/CHFCl2 = 1:1:3), which is still liquid at 100 K, the 1-Ph-eq conformer was found to be the preferred one [(1-Ph-eq: 1-Ph-ax = 77%: 23%, K = 77/23 = 2.8; -Delta G degrees = -RT In K (at 103 K) = 0.44 +/- 0.1 kcal/mol]. When comparing 1 with 1-phenyl-1-(X)silacylohexanes (X = H, Me, OMe, F, Cl), studied so far, the trend of predominance of the Ph-ax conformer in the gas phase and of the Ph-eq conformer in solution is confirmed.
In this study we report the structure of supercritical H2O-SiO2 fluid composed of 50 mol% H2O and 50 mol% SiO2 at 3000 K and 2400 K. investigated by means of ab initio molecular dynamics of models comprising 192 and 96 atoms. The density is set constant to 138 g/cm(3), which yields a pressure of 4.3 GPa at 3000 K and 3.6 GPa at 2400 K. Throughout the trajec[ories, water molecules are formed and dissociated via the network modifying reaction 2 SiOH = SiOSi + H2O The calculation of the reaction constant K- [OH](2)/[H2O][O2-] is carried out on the basis of the experimentally relevant Q ' species notation and agrees well with an extrapolation of experimental data to 3000 K. After quench from 3000 K to 2400 K, the degree of polymerization of the silicate network in the 192-atom models increases noticeably within several tens of picoseconds, accompanied by release of molecular H2O. An unexpected opposite trend is observed in smaller 96-atom models, due to a finite size effect, as several uncorrelated models of 192 and 96 atoms indicate. The temperature-dependent slowing down of the H2O-silica interaction dynamics is described on the basis of the bond autocorrelation function. (C) 2016 Elsevier B.V. All rights reserved.
Using optical absorption and Raman spectroscopic measurements, in conjunction with the first-principles calculations, a pressure-induced high-spin (HS)-to-low-spin (LS) state electronic transition of Fe2+ (M2-octahedral site) was resolved around 76-80GPa in a natural triphylite-lithiophilite sample with chemical composition (LiFe0.7082+Mn0.292PO4)-Li-M1-Fe-M2 (theoretical composition (LiFe0.52+Mn0.5PO4)-Li-M1-Fe-M2). The optical absorption spectra at ambient conditions consist of a broad doublet band with two constituents (1) (similar to 9330cm(-1)) and (2) (similar to 7110cm(-1)), resulting from the electronic spin-allowed transition (T2gEg)-T-5-E-5 of octahedral (HSFe2+)-Fe-M2. Both (1) and (2) bands shift non-linearly with pressure to higher energies up to similar to 55GPa. In the optical absorption spectrum measured at similar to 81GPa, the aforementioned HS-related bands disappear, whereas a new broadband with an intensity maximum close to 16,360cm(-1) appears, superimposed on the tail of the high-energy ligand-to-metal O2-Fe2+ charge-transfer absorption edge. We assign this new band to the electronic spin-allowed dd-transition (1)A(1g)(1)T(1g) of LS Fe2+ in octahedral coordination. The high-pressure Raman spectra evidence the Fe2+ HS-to-LS transition mainly from the abrupt shift of the P-O symmetric stretching modes to lower frequencies at similar to 76GPa, the highest pressure achieved in the Raman spectroscopic experiments. Calculations indicated that the presence of Mn-M2(2+) simply shifts the isostructural HS-to-LS transition to higher pressures compared to the triphylite Fe-M2(2+) end-member, in qualitative agreement with our experimental observations.
Hot localised charge carriers on the Si(111)-7x7 surface are modelled by small charged clusters. Such resonances induce non-local desorption, i.e. more than 10 nm away from the injection site, of chlorobenzene in scanning tunnelling microscope experiments. We used such a cluster model to characterise resonance localisation and vibrational activation for positive and negative resonances recently. In this work, we investigate to which extent the model depends on details of the used cluster or quantum chemistry methods and try to identify the smallest possible cluster suitable for a description of the neutral surface and the ion resonances. Furthermore, a detailed analysis for different chemisorption orientations is performed. While some properties, as estimates of the resonance energy or absolute values for atomic changes, show such a dependency, the main findings are very robust with respect to changes in the model and/or the chemisorption geometry. [GRAPHICS] .
Hot localised charge carriers on the Si(111)-7×7 surface are modelled by small charged clusters. Such resonances induce non-local desorption, i.e. more than 10 nm away from the injection site, of chlorobenzene in scanning tunnelling microscope experiments. We used such a cluster model to characterise resonance localisation and vibrational activation for positive and negative resonances recently. In this work, we investigate to which extent the model depends on details of the used cluster or quantum chemistry methods and try to identify the smallest possible cluster suitable for a description of the neutral surface and the ion resonances. Furthermore, a detailed analysis for different chemisorption orientations is performed. While some properties, as estimates of the resonance energy or absolute values for atomic changes, show such a dependency, the main findings are very robust with respect to changes in the model and/or the chemisorption geometry.