Partial Methane Oxidation to Methanol on Ru-Porphyrins - on the Role of Non-Innocent Ligands and Spin Crossover.

The partial oxidation reaction of CH4 led to the formation of CH3 OH in the presence of Ru-porphyrin oxo complexes (denoted as POR, POR-O and POR-OH where in the case of the last two, oxygen atom and the OH group were attached to the active site, respectively), in which Ru was present on different oxidation states. The simulations were performed based on Density Functional Theory (DFT) with extended geometric and electronic structure analyses of each reaction step. Moreover, the reaction pathways were investigated in different spin states. The Spin Crossover (SCO) phenomenon was found to play an important role in the kinetics of the reaction in the presence of POR and POR-O. Harmonic Oscillator Model of Aromaticity (HOMA) index was applied for different spin states to estimate the aromaticity changes of the pyrrole rings in the Ru-porphyrin complexes. In order to characterize the nature of bonding, the Natural Bond Orbitals (NBO) analysis including the Wiberg Bond Index (WBI) and Natural Population Analysis (NPA) was carried out. Finally, the Non-Covalent Interactions (NCI) index was employed to gain insight into interactions between the components of the reaction. It was found that the non-covalent interactions cannot be neglected in the studied reaction paths.

Effect of Newly Synthesized Structures of Peptides on the Stability of the Monolayers Formed.

The aim of the study was to evaluate the effect of the peptide structure (WKWK)2-KWKWK-NH2, P4 (C12)2-KKKK-NH2, P5 (KWK)2-KWWW-NH2, P6 (KK)2-KWWW-NH2 on their physicochemical properties. The thermogravimetric method (TG/DTG) was used, which made it possible to observe the course of chemical reactions and phase transformations occurring during the heating of solid samples. Based on the DSC curves, the enthalpy of the processes occurring in the peptides was determined. The influence of the chemical structure of this group of compounds on their film-forming properties was determined using the Langmuir-Wilhelmy trough method and was followed by molecular dynamics simulation. Evaluated peptides showed high thermal stability and the first significant mass loss occurred only at about 230 °C and 350 °C. The analysis of the compressibility coefficient of individual peptides indicates that all formed peptide monolayers were in the expanded liquid phase. Their maximum compressibility factor was less than 50.0 mN/m. Its highest value of 42.7 mN/m was achieved in a monolayer made of P4. The results obtained in molecular dynamic simulation indicate that non-polar side chains played an important role in the properties of the P4 monolayer, and the same applies to P5, except that a spherical effect was observed here. A slightly different behavior was observed for the P6 and P2 peptide systems, where the type of amino acids present had an influence. The obtained results indicate that the structure of the peptide affected its physicochemical and layer-forming properties.

Assessment of the Influence of the Selected Range of Visible Light Radiation on the Durability of the Gel with Ascorbic Acid and Its Derivative.

(1) Background: Depending on the type of hydrophilic polymer used, different types of hydrogels may be chemically stable or may degrade and eventually disintegrate, or dissolve upon exposure to sunlight. Many over-the-counter medications are now stored with a limited control of temperature, humidity and lighting. Therefore, in this study, the photostability of a gel made of cross-linked polyacrylic acid (PA), methylcellulose (MC) and aristoflex (AV) was assessed, and the interaction between the polymers used and ascorbic acid and its ethylated derivative was investigated. (2) Methods: The samples were continuously irradiated at constant temperature for six hours. The stability of the substance incorporated into the gels was assessed using a UV-Vis spectrophotometer. FTIR-ATR infrared spectroscopy was used to measure changes during the exposure. (3) Results: Ascorbic acid completely decomposed between the first and second hours of illumination in all samples. The exception is the preparation based on polyacrylic acid with glycerol, in which the decomposition of ascorbic acid slowed down significantly. After six hours of irradiation, the ethylated ascorbic acid derivative decomposed in about 5% for the polyacrylic acid-based gels and aristoflex, and in the methylcellulose gel it decomposed to about 2%. In the case of ascorbic acid, the most stable formulation was a gel based on polyacrylic acid and polyacrylic acid with glycerol, and in the case of the ethyl derivative, a gel based on methylcellulose. (4) Conclusions: The experiment showed significant differences in the decomposition rate of both compounds, resulting from their photostability and the polymer used in the hydrogel.

Sensitivity of Intra- and Intermolecular Interactions of Benzo[h]quinoline from Car-Parrinello Molecular Dynamics and Electronic Structure Inspection.

The O-H...N and O-H...O hydrogen bonds were investigated in 10-hydroxybenzo[h]quinoline (HBQ) and benzo[h]quinoline-2-methylresorcinol complex in vacuo, solvent and crystalline phases. The chosen systems contain analogous donor and acceptor moieties but differently coupled (intra- versus intermolecularly). Car-Parrinello molecular dynamics (CPMD) was employed to shed light onto principle components of interactions responsible for the self-assembly. It was applied to study the dynamics of the hydrogen bonds and vibrational features as well as to provide initial geometries for incorporation of quantum effects and electronic structure studies. The vibrational features were revealed using Fourier transformation of the autocorrelation function of atomic velocity and by inclusion of nuclear quantum effects on the O-H stretching solving vibrational Schrödinger equation a posteriori. The potential of mean force (Pmf) was computed for the whole trajectory to derive the probability density distribution and for the O-H stretching mode from the proton vibrational eigenfunctions and eigenvalues incorporating statistical sampling and nuclear quantum effects. The electronic structure changes of the benzo[h]quinoline-2-methylresorcinol dimer and trimers were studied based on Constrained Density Functional Theory (CDFT) whereas the Electron Localization Function (ELF) method was applied for all systems. It was found that the bridged proton is localized on the donor side in both investigated systems in vacuo. The crystalline phase simulations indicated bridged proton-sharing and transfer events in HBQ. These effects are even more pronounced when nuclear quantization is taken into account, and the quantized Pmf allows the proton to sample the acceptor area more efficiently. The CDFT indicated the charge depletion at the bridged proton for the analyzed dimer and trimers in solvent. The ELF analysis showed the presence of the isolated proton (a signature of the strongest hydrogen bonds) only in some parts of the HBQ crystal simulation. The collected data underline the importance of the intramolecular coupling between the donor and acceptor moieties.

Aminophosphonates and aminophosphonic acids with tetrasubstituted stereogenic center: diastereoselective synthesis from cyclic ketimines.

New chiral tetrasubstituted aminophosphonic acid derivatives of hexahydroquinoxalin-2(1H)-one were synthesised via highly diastereoselective hydrophosphonylation of the corresponding imines with tris(trimethylsilyl) phosphite as phosphorus nucleophile. High asymmetric induction, good yields, mild reaction conditions, and ease of purification of the final products are the key advantages of the presented protocol.

Synergy between TiO2 and Co(x)O(y) sites in electrocatalytic water decomposition.

A computational study of the cooperative effect of a small four-atom Co oxide cluster supported on the TiO2 anatase (100) surface in the electrochemical water splitting reaction is presented. The results have been obtained including explicit solvent water molecules by means of Car-Parrinello MD simulations. Reaction steps in the catalytic cycle determined involve the formation of TiO2 surface hydroxyl groups as well as elementary reaction steps on the Co oxide cluster. Essential is the observation of O-O bond formation at the inter-phase of Co oxide particles and the TiO2 support.

Multiple zeolite structures from one ionic liquid template.

This study reports the use of 1-butyl-3-methyl imidazolium methanesulfonate ionic liquid as a template in the synthesis of zeolites. It is found that the silicon source determines the formation of beta (BEA), mordenite framework inverted (MFI), or analcime (ANA) zeolites. Depending on this source, different preorganized complexes are obtained that drive the formation of the different zeolite structures. In the presence of ethanol, the ionic liquid form preorganized complexes that drive the formation of MFI. In its absence, BEA is obtained. Whereas, the large amount of sodium present when using sodium metasilicate leads to ANA formation. A molecular simulation study of the relative stability of the template-framework system and location of the template provides further insight into the mechanism of synthesis.

Kinetically controlled formation of formamide trimer from first principles.

The formation of formamide trimers was simulated using Car-Parrinello molecular dynamics. A variety of different initial setups were compared to study the effects of spatial arrangement, concentration, and temperature on the trimer product distribution. A total of nine different trimer species were obtained by simulation. Although a triangular initial arrangement of the three monomers is found to favour a less energetically stable chain-like product at high concentration, the more compact global minimum structure is expected to be the most abundant species overall in experiment. This is because there is evidence of a low activation barrier for conversion of the chain-like trimer to the lowest-energy structure. For one, this process is observed upon increasing the length of the trajectories. Furthermore, a slight rise in temperature drastically reduces the number of chain-like trimers. With regard to the intermolecular forces driving the aggregation dynamics, dispersion corrections to the underlying density functional theory description have a strong effect on the product distribution, again favouring the global minimum species. Certain local minimum structures are significantly destabilised relative to the global minimum by dispersion correction while the relative energies of the majority of species are practically unchanged.

The Influence of Ni Addition in the Mechanism of CO2 Electroreduction on Cu Crystals-Mechanistic Insight from DFT Simulations.

We present a DFT analysis of the role of the Cu-Ni synergistic effect for the CO2 reduction to C2H4, in comparison to the pure Cu catalyst. The analysis is focused on the thermodynamic stability of reactive intermediates along the proposed pathway of C2 species formation. We have observed that the potential needed for the reaction decreases with the addition of Ni in the investigated model. In addition, we have observed the differences in the preferred pathway based on the significant differences in stability of the reactive intermediates depending on th Cu:Ni ratio. The results suggest that despite the fact the Cu surface is always exposed, and it is the only one that is able to directly interact with the intermediates, the presence of the Ni in the underlying sections of the crystal is significant enough to change the mechanism of the reaction.

Effect of a Support on the Properties of Zinc Oxide Based Sorbents.

We present the comparative analysis of three Zn-based sorbents for the process of sulphur removal from hot coal gas. The sorbents were prepared by a slurry impregnation of TiO2, SiO2 and Al2O3, resulting in complex, multiphase materials, with the dominant phases of Zn2TiO4, Zn2SiO4 and ZnAl2O4, respectively. We have analyzed the effect of supports on the phase composition, texture, reducibility and H2S sorption. We have found that the phase composition significantly influences the susceptibility of the investigated materials to reduction by hydrogen. Zn2TiO4 have been found to be the easiest to reduce which correlates with its ability to adsorb the largest amount of hydrogen sulphide-up to 4.2 gS/100 g-compared to the other sorbents, which absorb up to 2.2 gS/100 g. In the case of Zn2SiO4 and ZnAl2O4, this effect also correlates with reducibility-these sorbents have been found to be highly resistant to reduction by hydrogen and to absorb much less hydrogen sulphide. In addition, the capacity of ZnAl2O4 for H2S adsorption decreases in the subsequent work cycles-from 2.2 gS/100 g in the first cycle to 0.8 gS/100 g in the third one. Computational analysis on the DFT level has shown that these materials show different thermodynamic stability of sulphur sites within the unit cells of the sorbents. For Zn2TiO4 and Zn2SiO4, the adsorption is favorable in both the first and second layers of the former and only the top layer of the latter, while for zinc aluminate it is not favorable, which is consistent with the experimental findings.

Mixing ReaxFF parameters for transition metal oxides using force-matching method.

We present the development of the method for the refitting the ReaxFF parameters for a system consisting of the mixed transition metal oxides. We have tested several methods allowing to calculate the differences between the vectors of the forces acting on atoms obtained from the reference DFT simulation and the parameters-dependent ReaxFF. We conclude that the footrule method yields the best parameters among the investigated options. We then validate the parameters using the system consisting of the hematite supported (TiO2)n clusters. The results indicate the refitted parameters allow to obtain acceptable geometries of the clusters upon MD simulation on the ReaxFF level, and despite the short timescale lead to the stable structures.

The pathways of the CO2 hydrogenation by NiCu/ZnO from DFT molecular dynamics simulations.

Metal nanoparticles supported on semiconductor surfaces have been proposed as promising nanocatalyst candidates of CO2 conversion to energy carrier molecules such as formic acid or carbon monoxide, which can be used as a feedstock for fuels synthesis. This study is focused on the bimetallic Cu/Ni nanoparticles supported on the ZnO. The respective reaction mechanisms have been studied by means of the Molecular Dynamics with the DFT methodology. The results suggest that on CuNi/ZnO CO2 hydrogenation to formate pathway is more favorable than carboxyl route. These pathways are competitive with the CO2 reduction to CO.

Helping Thy Neighbor: How Cobalt Doping Alters the Electrocatalytic Properties of Hematite.

We present analysis of the indirect role of Co doping on the electrocatalytic activity of α-Fe2O3. Upon substitution of one of the Fe atoms in the hematite surface, we observed a promoting effect of the substitution, upon which the overpotential required for the water-splitting reaction decreased in all substitution sites investigated. The cobalt site itself, however, does not exhibit the improved properties with respect to the undoped hematite. The promoting effect results purely from the altering of the properties of the nearest Fe atoms in the hematite surface. We conclude that the overpotential is reduced upon formation of the structure resembling the O2 molecule strongly interacting with the surface between the Co and Fe sites, and this is consistent with the catalytic activity of the surface vacancies of the hematite.

Insight into the Formation of Nanostructured MFI Sheets and MEL Needles Driven by Molecular Recognition.

Mesoporous and nanostructured zeolite-based catalysts experience prolonged lifetimes due to increased mass transfer and reduced micropore obstruction by coke formation as compared to their bulky microporous counterparts. Diquaternary ammonium structure-directing agents (SDAs) can be used to synthesize hierarchical MFI sheet-like and MEL needle-like zeolites. An explanation of the underlying molecular-level details of the synthesis of these nanostructured zeolites is presented on the basis of non-covalent interactions between the template and zeolite surfaces as well as silicate oligomers studied by means of classical molecular dynamics. Use was made of Si11 and Si33 silicate oligomers that contain structural features of the framework to be formed as originally proposed by the Leuven group. Molecular recognition is driven by a combination of strong electrostatic and weaker dispersion interactions. An analysis of the early stage of zeolite formation is necessary, as the template adsorption energies in the fully formed zeolite crystals cannot explain the preferential growth of the MFI sheets or MEL needles. Specifically, it is found that the differences in dispersion interactions between the SDA alkyl chains and the silicate oligomers are decisive in the formation of particular zeolite structures.

Photoisomerization induced scission of rod-like micelles unravelled with multiscale modeling.

HYPOTHESIS: In photorheological fluids, subtle molecular changes caused by light lead to abrupt macroscopic alterations. Upon UV irradiation of an aqueous cetyltrimethylammonium bromide (CTAB) and trans-ortho-methoxycinnamic acid (trans-OMCA) solution, for instance, the viscosity drops over orders of magnitude. Multiscale modeling allows to elucidate the mechanisms behind these photorheological effects. EXPERIMENTS: We use time-dependent DFT calculations to study the photoisomerization, and a combination of atomistic molecular dynamics (MD) and DFT to probe the influence of both OMCA isomers on the micellar solutions. FINDINGS: The time-dependent DFT calculations show that the isomerization pathway occurs in the first triplet excited state with a minimum energy conformation closest to the after photoisomerization predominant cis configuration. In the MD simulations, with sub-microsecond timescales much shorter than the experimental morphological transition, already a clear difference is observed in the packing of the two OMCA isomers: contrary to trans-OMCA, cis-OMCA exposes notable part of its hydrophobic aromatic rings at the micelle surface. This can explain why trans-OMCA adopts rod-like micellar packing (high viscosity) while cis-OMCA spherical micellar packing (low viscosity). Moreover, lowering of the OMCA co-solute concentration allowed us to perform full simulation of the breakup process of the rod-like micelles which are stable prior to isomerization.

A DFT Study of CO2 Hydrogenation on Faujasite-Supported Ir4 Clusters: on the Role of Water for Selectivity Control.

Reaction mechanisms for the catalytic hydrogenation of CO2 by faujasite-supported Ir4 clusters were studied by periodic DFT calculations. The reaction can proceed through two alternative paths. The thermodynamically favoured path results in the reduction of CO2 to CO, whereas the other, kinetically preferred channel involves CO2 hydrogenation to formic acid under water-free conditions. Both paths are promoted by catalytic amounts of water confined inside the zeolite micropores with a stronger promotion effect for the reduction path. Co-adsorbed water facilitates the cooperation between the zeolite Brønsted acid sites and Ir4 cluster by opening low-energy reaction channels for CO2 conversion.

TiO2-catalyzed synthesis of sugars from formaldehyde in extraterrestrial impacts on the early Earth.

Recent synthetic efforts aimed at reconstructing the beginning of life on our planet point at the plausibility of scenarios fueled by extraterrestrial energy sources. In the current work we show that beyond nucleobases the sugar components of the first informational polymers can be synthesized in this way. We demonstrate that a laser-induced high-energy chemistry combined with TiO2 catalysis readily produces a mixture of pentoses, among them ribose, arabinose and xylose. This chemistry might be highly relevant to the Late Heavy Bombardment period of Earth's history about 4-3.85 billion years ago. In addition, we present an in-depth theoretical analysis of the most challenging step of the reaction pathway, i.e., the TiO2-catalyzed dimerization of formaldehyde leading to glycolaldehyde.

Establishing hierarchy: the chain of events leading to the formation of silicalite-1 nanosheets.

In applying a multi-scale spectroscopic and computational approach, we demonstrate that the synthesis of stacked zeolite silicalite-1 nanosheets, in the presence of a long-tail diquaternary ammonium salt surfactant, proceeds through a pre-organised phase in the condensed state. In situ small-angle X-ray scattering, coupled to paracrystalline theory, and backed by electron microscopy, shows that this phase establishes its meso-scale order within the first five hours of hydrothermal synthesis. Quasi in situ vibrational and solid-state NMR spectroscopy reveal that this meso-shaped architecture already contains some elementary zeolitic features. The key to this coupled organisation at both micro- and meso-scale, is a structure-directing agent that is ambifunctional in shaping silica at the meso-scale whilst involved in molecular recognition at the micro-scale. The latter feature is particularly important and requires the structure-directing agent to reside within the silica matrix already at early stages of the synthesis. From here, molecular recognition directs stabilization of precursor species and their specific embedding into a lattice, as shown by force-field molecular dynamics calculations. These calculations, in line with experiment, further show how it is possible to subtly tune both the zeolite topology and aspect ratio of the condensating crystals, by modifying the headgroup of the structure-directing agent.

The role of Ir4 cluster in enhancing the adsorption of CO2 on selected zeolites - GCMC simulations.

We have investigated the adsorption of CO2 molecules inside the EMT, SAO, SBS, SBT and IWS zeolites with respect to the influence of the Ir4 clusters on the adsorption capabilities of these materials. We have determined that the capabilities of CO2 adsorption depend on the combined effect of the framework topology and the position of the Ir4 cluster. Adsorption intensifies despite the fact that a fraction of the pore volume is occupied by the Ir4 cluster, and thus, the adsorption is more intense than that on empty zeolite. The pore topology however is also playing a crucial role in the effect, as in certain cases it allows the CO2 molecules to order in such a way they fill the most pore space.

Conformation-dependent conductance through a molecular break junction.

Ab initio molecular dynamics simulations have been performed of a gold-1,4-benzenedithiol (BDT)-gold nanojunction under mechanical stress. For three different pulling rates between 10 and 40 m s(-1), it is found that the nanowire always ruptures between the second and third Au atom from the thiol sulfur. Larger rupture forces and longer extensions are required at higher pulling rates and vice versa. The electrical conductance was calculated along a pulling trajectory using the DFT-NEGF method to study the effect of thermal and stress-induced structural changes on the electrical transport properties. While the mechanically induced stretching of the junction is seen to lower the time-averaged conductance, thermal conformational changes are capable of altering the conductance by one order of magnitude. No single geometric quantity could be identified as the main contributor to the conductance fluctuations. Small modulations, however, can be explained in terms of C=C double bond vibrations in the BDT molecule. The dependence of the conductance on different geometric variables has further been investigated systematically by performing constrained geometry optimizations along a number of angle and dihedral coordinates. The largest changes in the conductance are observed when the Au-S-C angle and the Au-S-C-C dihedral are simultaneously constrained.