Computational and Chemical Analysis of the Oxygen Atom Transfer Process of a Dioxo–Molybdenum Complex Incorporated into a Modified UiO-67 (Zr/Ti)

Crystal structure, stability, and electronic properties of hydrated metal sulfates MSO4(H2O)n (M=Ni, Mg; n=6, 7) and their mixed phases: A first principles study

A review of computational studies on the structures, bonding and reactivity of rhodium σ-alkane complexes in the solid state is presented. These complexes of the general form [(R2P(CH2)nPR2)Rh(alkane)][BArF4] (where ArF = 3,5-(CF3)2C6H3) are formed via solid/gas hydrogenation of alkene precursors, often in single-crystal-to-single-crystal (SC-SC) transformations. Molecular and periodic density functional theory (DFT) calculations complement experimental characterisation techniques (X-ray, solid-state NMR) to provide a detailed picture of the structure and bonding in these species. These σ-alkane complexes exhibit reactivity in the solid state, undergoing fluxional processes, and access different alkane binding modes that link to C-H activation and H/D exchange. The mechanisms of several of these processes have been defined using periodic DFT calculations which provide excellent quantitative agreement with the available experimental activation barriers. A comparison of computed results derived from periodic DFT calculations, where the full solid-state environment is taken into account, with simple model calculations using the isolated molecular cations highlights the importance of modelling the solid state to reproduce the structures of these alkane complexes. The solid-state environment can also have a significant impact on the computed reaction energetics.

Thermodynamic stability is an essential property of crystalline materials, and its accurate calculation requires a reliable description of the thermal motion - phonons - in the crystal. Such information can be obtained from periodic density functional theory (DFT) calculations, but these are costly and in some cases insufficiently accurate for molecular crystals. This deficiency is addressed here by refining a lattice-dynamics model, derived from DFT calculations, against accurate high-resolution X-ray diffraction data. For the first time, a normal-mode refinement is combined with the refinement of aspherical atomic form factors, allowing a comprehensive description and physically meaningful deconvolution of thermal motion and static charge density in the crystal. The small and well diffracting L-alanine system was used. Different lattice-dynamics models, with or without phonon dispersion, and derived from different levels of theory, were tested, and models using spherical and aspherical form factors were compared. The refinements indicate that the vibrational information content in the 23 K data is too small to study lattice dynamics, whereas the 123 K data appear to hold information on the acoustic and lowest-frequency optical phonons. These normal-mode models show slightly larger refinement residuals than their counterparts using atomic displacement parameters, and these features are not removed by considering phonon dispersion in the model. The models refined against the 123 K data, regardless of their sophistication, give calculated heat capacities for L-alanine within less than 1 cal mol-1 K-1 of the calorimetric measurements, in the temperature range 10-300 K. The findings show that the normal-mode refinement method can be combined with an elaborate description of the electron density. It appears to be a promising technique for free-energy determination for crystalline materials at the expense of performing a single-crystal elastic X-ray diffraction determination combined with periodic DFT calculations.

The secondary radiation-induced radicals in lithium formate monohydrate were studied using electron paramagnetic resonance (EPR), electron nuclear double resonance (ENDOR) and ENDOR-induced EPR (EIE) techniques complemented with periodic density functional theory (DFT) calculations. Single crystals of lithium formate monohydrate were X irradiated at 77 K and at room temperature. The main radicals present after irradiation at 77 K are the CO(2)(•-) radical (R1), the recently identified protonated electron-gain product, HCOOH(•-) (R2) (Krivokapić et al., Radiat Res 2014: 181:503-11), and a different geometrical conformation of this latter radical, a species that, up until now, has remained unidentified (R3). The successful quantum chemical modeling of R3 confirmed its structure and also provided a possible mechanism for its formation. After irradiation at 295 K, the crystals were investigated both shortly after irradiation and after storage for eight months at room temperature in ambient environments. After long-term storage the CO(2)(•-) radical had significantly decayed and the EPR spectra were dominated by two minority radicals. Both of these radicals are most likely formate-centered π-radicals, and based on the observed EPR parameters (g- and hyperfine coupling tensors) tentative candidates are the CO(•-) radical and the dimer formed by the CO(2)(•-) radical and a neighboring formate molecule yielding the radical (-)O(2)C·O·(•)CH·O(-).

Methanol adsorption in isomorphously substituted MAPO-34 (M = Mn, Zn, Mg, Si, Ti, or Zr) zeolite clusters was investigated, and periodic density functional theory (DFT) calculations were carried out. All structures are optimized and charactered at B3LYP/LANL2DZ-6-31G** (the LANL2DZ basis set for Mn, Zn, Mg, Ti, and Zr atoms and 6-31G** basis set sequentially for Si, Al, O, C, and H atoms) and generalized gradient approximation and Perder−Burke−Ernzerhof theoretical levels. Both methods demonstrate that the type of metal dopant used plays an active role in methanol protonation. In Mn, Zn, and Mg-AlPO-34, the stable form of methanol is protonated. However, in Si, Ti, and Zr-AlPO-34, methanol is unprotonated and is simply physisorbed. In the protonated mode, the methoxonium cation forms two very strong hydrogen bonds (1.019−1.073 Å) with the negatively charged zeolite. On the other hand, in the physisorbed mode, methanol interacts with the zeolite framework to form an eight-member ring through two hydrogen bonds, one that is short and rather strong (1.392−1.676 Å) and one that is much weaker (1.941−3.036 Å).

Hydrogen-bonding network in anhydrous chitosan from neutron crystallography and periodic density functional theory calculations

We report periodic B3LYP density functional theory calculations for three-dimensional (3D) trans-polyacetylene (t-PA) fibers. Empirical dispersion terms, as proposed by Grimme, are included with an appropriate re-scaling to yield the B3LYP+D* method implemented in CRYSTAL06. The dispersion corrections are critical for obtaining correct unit cell parameters. In our calculations the out-of-phase P2(1)/n structure turns out to be a transition state for the interchain relative translational motion, which lies about 0.35 kcal mol(-1) above the two symmetrically located in-phase P2(1)/a minima. These results provide a possible new explanation for the observed XRD intensities. Our calculations should also be useful for comparison with more costly non-empirical treatments of 3D PA and other pi-conjugated polymers.

BackgroundGoethite is a common and reactive mineral in the environment. The transport of contaminants and anaerobic respiration of microbes are significantly affected by adsorption and reduction reactions involving goethite. An understanding of the mineral-water interface of goethite is critical for determining the molecular-scale mechanisms of adsorption and reduction reactions. In this study, periodic density functional theory (DFT) calculations were performed on the mineral goethite and its (010) surface, using the Vienna Ab Initio Simulation Package (VASP).ResultsCalculations of the bulk mineral structure accurately reproduced the observed crystal structure and vibrational frequencies, suggesting that this computational methodology was suitable for modeling the goethite-water interface. Energy-minimized structures of bare, hydrated (one H2O layer) and solvated (three H2O layers) (010) surfaces were calculated for 1 × 1 and 3 × 3 unit cell slabs. A good correlation between the calculated and observed vibrational frequencies was found for the 1 × 1 solvated surface. However, differences between the 1 × 1 and 3 × 3 slab calculations indicated that larger models may be necessary to simulate the relaxation of water at the interface. Comparison of two hydrated surfaces with molecularly and dissociatively adsorbed H2O showed a significantly lower potential energy for the former.ConclusionSurface Fe-O and (Fe)O-H bond lengths are reported that may be useful in surface complexation models (SCM) of the goethite (010) surface. These bond lengths were found to change significantly as a function of solvation (i.e., addition of two extra H2O layers above the surface), indicating that this parameter should be carefully considered in future SCM studies of metal oxide-water interfaces.

Low-coordinated (LC) ions at the MgO surface (noted Mg2+LC and O2-LC with L = 1-5), located on monatomic and diatomic steps, corners, step divacancies, and kinks, have been modeled thanks to periodic density functional theory (DFT) calculations (VASP). Ions of lowest coordination induce the strongest surface geometry relaxation and the highest surface energies. The hydration energies of these sites and thermodynamic stabilities of the resulting surfaces were studied. The factors controlling the interaction strength between water and the surface are the possibility for the hydroxyl group to adopt a bridging geometry between two Mg2+ cations in concave areas of the surface, such as the bottom of the monatomic step, and at second order the surface atomic coordination, and especially the presence of three-coordinated ions. The Lewis basicity and acidity of O2-LC and Mg2+LC, respectively, increase as their coordination number decreases, which implies the same trend for the Brønsted basicity of the Mg2+-O2- pair toward water. However, this trend can be changed if pairs leading to the formation of bridging OH groups are involved, typically on monatomic steps or in step divacancies where O2C-H and O3C-H are obtained, respectively, instead of the expected O1C-H. Thanks to thermodynamic calculations, the state of the surface as a function of temperature can be determined at a given pressure, unraveling the roles of surface topology and ions coordination.

Scandium doping of black phosphorene for enhanced sensitivity to hydrogen sulfide: Periodic DFT calculations

We present an implementation of a GPU based FFT routine (Graphics Processing Unit based Fast Fourier Transformation) into a CPU based ab initio periodic DFT (Density Functional Theory) calculation code. The FFT calculation in the CPU based DFT codes is the most time-consuming part; for the 128 silicon system, the fraction of time of a CPU FFT calculation amounts to 0.64 of the whole periodic DFT calculation. The replacement of a double precision FFT in the periodic PWscf code with a single precision FFT gives no appreciable differences in both the numerical total energies and the interatomic forces, guaranteeing the use of a single precision GPU based FFT, CUFFT, for the code. The use of the CUFFT reduces the fraction to 0.20 of the whole PWscf code; the replacement speedups a factor of 2.2 for single CPU system. The use of the multi-CPU system with the GPU FFT accelerates by 2.2f, where f is the acceleration factor of the multi-CPU system. The single precision GPU calculation is implementable in any self-consistent electronic structure code, except for the eigensolver part in the DFT codes.

We report a solid-state 17O NMR study of several crystalline carboxylic acids. We found that, while each of these compounds forms discrete hydrogen-bonded dimers in the crystal lattice, their solid-state 17O magic-angle spinning (MAS) NMR spectra display quite different features and different temperature dependencies. We showed that experimentally observed 17O NMR spectral behaviors can be explained as being due to thermal averaging between the two tautomers that are produced as a result of concerted double-hydrogen hopping dynamics within each dimer. In general, the two tautomers have different energies due to intramolecular interactions and crystal packing. From an analysis of variable-temperature 17O MAS NMR spectra, energy asymmetry between the two tautomers was experimentally determined for each of the carboxylic acid compounds studied. The same data analysis also offers an opportunity to simultaneously assess 17O NMR parameters in both low- and high-energy tautomers. We concluded that the periodic plane-wave density functional theory (DFT) calculations can produce reliable 17O NMR parameters (chemical shift and quadrupolar coupling tensors) for both tautomers. The same periodic DFT calculations have also produced reasonable energy asymmetry values for the studied carboxylic acid dimers. We have also observed substantial H/D isotope shifts in solid-state 17O NMR.

Electron paramagnetic resonance (EPR), electron nuclear double resonance (ENDOR), and ENDOR-induced EPR (EIE) measurements on sucrose single crystals at 10 K after in situ X irradiation at this temperature reveal the presence of at least nine different radical species. Nine proton hyperfine coupling tensors were determined from ENDOR angular variations and assigned to six of these species (R1-R6) using EIE. Spectral simulations indicate that four of those (R1-R3 and R6) dominate the EPR absorption. Assisted by periodic density functional theory (DFT) calculations, R1 and R2 are identified as H-abstracted C1- and C5-centered radicals, R3 is tentatively assigned to an H-abstracted C6-centered radical, and R6 is identified as an alkoxy radical where the abstracted hydroxy proton has migrated to a neighboring OH group via intermolecular proton transfer. The latter radical had been characterized and identified in a previous study, but the present DFT calculations provide additional insight into its conformation and particular properties. This study provides the first step in unraveling the formation mechanism of the stable sucrose radicals detected after room-temperature irradiation and contributes to the understanding of the initial stages of radiation damage to solid-state carbohydrates.

Primary free radical formation in trehalose dihydrate single crystals X-irradiated at 10 K was investigated at the same temperature using X-band Electron Paramagnetic Resonance (EPR), Electron Nuclear Double Resonance (ENDOR) and ENDOR-induced EPR (EIE) techniques. The ENDOR results allowed the unambiguous determination of six proton hyperfine coupling (HFC) tensors. Using the EIE technique, these HF interactions were assigned to three different radicals, labeled R1, R2 and R3. The anisotropy of the EPR and EIE spectra indicated that R1 and R2 are alkyl radicals (i.e. carbon-centered) and R3 is an alkoxy radical (i.e. oxygen-centered). The EPR data also revealed the presence of an additional alkoxy radical species, labeled R4. Molecular modeling using periodic Density Functional Theory (DFT) calculations for simulating experimental data suggests that R1 and R2 are the hydrogen-abstracted alkyl species centered at C5' and C5, respectively, while the alkoxy radicals R3 and R4 have the unpaired electron localized mainly at O2 and O4'. Interestingly, the DFT study on R4 demonstrates that the trapping of a transferred proton can significantly influence the conformation of a deprotonated cation. Comparison of these results with those obtained from sucrose single crystals X-irradiated at 10 K indicates that the carbon situated next to the ring oxygen and connected to the CH(2)OH hydroxymethyl group is a better radical trapping site than other positions.

Isolation of RuIII-bda (17-electron specie) complex with an aqua ligand (2-electron donor) is challenging due to violation of the 18-electron rule. Although considerable efforts have been dedicated to mechanistic studies of water oxidation by the Ru-bda family, the structure and initial formation of the RuIII-bda aqua complex are still controversial. Herein, we challenge this often overlooked step by designing a pocket-shape Ru-based complex 1. The computational studies showed that 1 possesses the crucial hydrophobicity at the RuV(O) state as well as similar probability of access of terminal O to solvent water molecules when compared with classic Ru-bda catalysts. Through characterization of single-crystal structures at the RuII and RuIII states, a pseudo seven-coordinate “ready-to-go” aqua ligand with RuIII...O distance of 3.62 Å was observed. This aqua ligand was also found to be part of a formed hydrogen-bonding network, providing a good indication of how the RuIII-OH2 complex is formed.