First-principles study of ammonium ions and their hydration in montmorillonites

Density functional theory calculations were performed to investigate the adsorption and hydration of an ammonium ion (NH₄ ⁺) confined in the interlayer space of montmorillonites (MMT). NH₄ ⁺ is trapped in the six-oxygen-ring on the internal surface and forms a strong binding with the surface O atoms. The hydration of NH₄ ⁺ is affected significantly by the surface. Water molecules prefer the surface sites, and do not bind with the NH₄ ⁺ unless enough water molecules are supplied. Moreover, the water molecules involved in NH₄ ⁺ hydration tend to bind with the surface simultaneously. The hydration energy increases with the intercalated water molecules, in contrast to that in gas phase. In addition, the hydration leads to the extension of MMT basal spacing.

Theoretical investigations on the synthesis mechanism of cyanuric acid from NH3 and CO2

In the synthesis of cyanuric acid from NH₃ and CO₂, urea and isocyanic acid OCNH are two pivotal intermediates. Based on density functional theory (DFT) calculations, the synthesis mechanism of cyanuric acid from NH₃ + CO₂ was investigated systematically. Urea can be synthesized from NH₃ and CO₂, and cyanuric acid can be obtained from urea or NH₃ + CO₂. In the stepwise mechanism of cyanuric acid from urea or NH₃ + CO₂, the energy barriers are relatively high, and the condition of high pressure and temperature does not decrease the energy barriers. Our theoretical model shows that cyanuric acid is actually acquired from OCNH via a one-step cycloaddition reaction.

Density functional investigation of CO adsorption on Ni-doped single-walled armchair (5,5) boron nitride nanotubes

The adsorption of CO onto Ni-doped boron nitride nanotubes (BNNTs) was investigated using density functional theory at the B3LYP/LanL2DZ level of theory. The structures of the Ni-doped BNNTs and their CO-adsorbed configurations were obtained. It was found that the strength of adsorption of CO onto Ni-doped perfect BNNTs is higher than that on defective BNNTs. The electronic properties of all of the adsorption configurations of CO on Ni-doped BNNTs are reported.

CO2 adsorption on polar surfaces of ZnO

Physical and chemical adsorption of CO₂ on ZnO surfaces were studied by means of two different implementations of periodic density functional theory. Adsorption energies were computed and compared to values in the literature. In particular, it was found that the calculated equilibrium structure and internuclear distances are in agreement with previous work. CO₂ adsorption was analyzed by inspection of the density of states and electron localization function. Valence bands, band gap and final states of adsorbed CO₂ were investigated and the effect of atomic displacements analyzed. The partial density of states (PDOS) of chemical adsorption of CO₂ on the ZnO(0001) surface show that the p orbitals of CO₂ were mixed with the ZnO valence band state appearing at the top of the valence band and in regions of low-energy conduction band.

Simple benzene derivatives adsorption on defective single-walled carbon nanotubes: a first-principles van der Waals density functional study

We have investigated the interaction between open-ended zig-zag single-walled carbon nanotube (SWCNT) and a few benzene derivatives using the first-principles van der Waals density functional (vdW-DF) method, involving full geometry optimization. Such sp ²-like materials are typically investigated using conventional DFT methods, which significantly underestimate non-local dispersion forces (vdW interactions), therefore affecting interactions between respected molecules. Here, we considered the vdW forces for the interacting molecules that originate from the interacting π electrons of the two systems. The ?0.54 eV adsorption energy reveals that the interaction of benzene with the side wall of the SWCNT is typical of the strong physisorption and comparable with the experimental value for benzene adsorption onto the graphene sheet. It was found that aromatics are physisorbed on the sidewall of perfect SWCNTs, as well as at the edge site of the defective nanotube. Analysis of the electronic structures shows that no orbital hybridization between aromatics and nanotubes occurs in the adsorption process. The results are relevant in order to identify the potential applications of noncovalent functionalized systems.

Microhydration of caesium compounds: Cs,CsOH, CsI and Cs2I2 complexes with one to three H2O molecules of nuclear safety interest

The structure and properties of natural gas hydrates containing hydrocarbons, CO₂, and N₂ molecules were studied by using computational quantum chemistry methods via the density functional theory approach. All host cages involved in I, II, and H types structures where filled with hydrocarbons up to pentanes, CO₂ and N₂ molecules, depending on their size, and the structures of these host–guest systems optimized. Structural properties, vibrational spectra, and density of states were analyzed together with results from atoms-in-a-molecule and natural bond orbitals methods. The inclusion of dispersion terms in the used functional plays a vital role for obtaining reliable information, and thus, B97D functional was shown to be useful for these systems. Results showed remarkable interaction energies, not strongly affected by the type of host cage, with molecules tending to be placed at the center of the cavities when host cages and guest molecules cavities are of similar size, but with molecules approaching hexagonal faces for larger cages. Vibrational properties show remarkable features in certain regions, with shiftings rising from host-guest interactions, and useful patterns in the terahertz region rising from water surface vibrations strongly coupled with guest molecules. Likewise, calculations on crystal systems for the I and H types were carried out using a pseudopotential approach combined with Grimme’s method to take account of dispersion.

Ammonium adsorption on Brønsted acidic centers on low-index vanadium pentoxide surfaces

Vanadium-based catalysts are used in many technological processes, among which the removal of nitrogen oxides (NO_x) from waste gases is one of the most important. The chemical reaction responsible for this selective catalytic reaction (SCR) is based on the reduction of NO_x molecules to N₂, and a possible reductant in this case is pre-adsorbed NH₃. In this paper, NH₃ adsorption on Brønsted OH acid centers on low-index surfaces of V₂O₅ (010, 100, 001) is studied using a theoretical DFT method with a gradient-corrected functional (RPBE) in the embedded cluster approximation model. The results of the calculations show that ammonia molecules are spontaneously stabilized on all low-index surfaces of the investigated catalyst, with adsorption energies ranging from ?0.34 to ?2 eV. Two different mechanisms of ammonia adsorption occur: the predominant mechanism involves the transfer of a proton from a surface OH group and the stabilization of ammonia as an NH₄ ⁺ cation bonded to surface O atom(s), while an alternative mechanism involves the hydrogen bonding of NH₃ to a surface OH moiety. The latter binding mode is present only in cases of stabilization over a doubly coordinated O(2) center at a (100) surface. The results of the calculations indicate that a nondirectional local electrostatic interaction with ammonia approaching a surface predetermines the mode of stabilization, whereas hydrogen-bonding interactions are the main force stabilizing the adsorbed ammonia. Utilizing the geometric features of the hydrogen bonds, the overall strength of these interactions was quantified and qualitatively correlated (R?=?0.93) with the magnitude of the stabilization effect (i.e., the adsorption energy).

The adsorption of NO,NH<Subscript>3</Subscript>, N<Subscript>2</Subscript> on carbon surface: a density functional theory study

To explore the adsorption mechanism of NO, NH₃, N₂ on a carbon surface, and the effect of basic and acidic functional groups, density functional theory was employed to investigate the interactions between these molecules and carbon surfaces. Molecular electrostatic potential, Mulliken population analyses, reduced density gradient, and Mayer bond order analyses were used to clarify the adsorption mechanism. The results indicate that van der Waals interactions are responsible for N₂ physisorption, and N₂ is the least likely to adsorb on a carbon surface. Modification of carbon materials to decorate basic or acidic functional groups could enhance the NH₃ physisorption because of hydrogen bonding or electrostatic interactions, however, NO physisorption on a carbon surface is poor. Zig-zag sites are more reactive than armchair sites when these gas molecules absorb on the edge sites of carbon surface.

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Graphical abstract NH₃, N₂, NO adsortion on carbon surface

     

Cyclo-hexa-peptides at the water/cyclohexane interface: a molecular dynamics simulation

Molecular dynamic (MD) simulations have been performed to study the behaviors of ten kinds of cyclo-hexa-peptides (CHPs) composed of amino acids with the diverse hydrophilic/hydrophobic side chains at the water/cyclohexane interface. All the CHPs take the “horse-saddle” conformations at the interface and the hydrophilicity/hydrophobicity of the side chains influences the backbones’ structural deformations. The orientations and distributions of the CHPs at the interface and the differences of interaction energies (ΔΔE) between the CHPs and the two liquid phases have been determined. RDF analysis shows that the H-bonds were formed between the O_C atoms of the CHPs’ backbones and H_w atoms of water molecules. N atoms of the CHPs’ backbones formed the H-bonds or van der Waals interactions with the water solvent. It was found that there is a parallel relationship between ΔΔE and the lateral diffusion coefficients (D _xy ) of the CHPs at the interface. The movements of water molecules close to the interface are confined to some extent, indicating that the dynamics of the CHPs and interfacial water molecules are strongly coupled.

Responses of CO2 efflux from an alpine meadow soil on the Qinghai Tibetan Plateau to multi-form and low-level N addition

Aims

To assess the effects of atmospheric N deposition on the C budget of an alpine meadow ecosystem on the Qinghai–Tibetan Plateau, it is necessary to explore the responses of soil-atmosphere carbon dioxide (CO₂) exchange to N addition.

Methods

Based on a multi-form, low-level N addition experiment, soil CO₂ effluxes were monitored weekly using the static chamber and gas chromatograph technique. Soil variables and aboveground biomass were measured monthly to examine the key driving factors of soil CO₂ efflux.

Results

The results showed that low-level N input tended to decrease soil moisture, whereas medium-level N input maintained soil moisture. Three-year N additions slightly increased soil inorganic N pools, especially the soil NH ₄ ⁺ -N pool. N applications significantly increased aboveground biomass and soil CO₂ efflux; moreover, this effect was more significant from NH ₄ ⁺ -N than from NO ₃ ^? -N fertilizer. In addition, the soil CO₂ efflux was mainly driven by soil temperature, followed by aboveground biomass and NH ₄ ⁺ -N pool.

Conclusions

These results suggest that chronic atmospheric N deposition will stimulate soil CO₂ efflux in the alpine meadow on the Qinghai–Tibetan Plateau by increasing available N content and promoting plant growth.     

Assessing the quantum mechanical level of theory for prediction of linear and nonlinear optical properties of push-pull organic molecules

In this paper, we assessed the quantum mechanical level of theory for prediction of linear and nonlinear optical (NLO) properties of push-pull organic molecules. The electric dipole moment (μ), mean polarizability (〈α〉) and total static first hyperpolarizability (β_t) were calculated for a set of benzene, styrene, biphenyl and stilbene derivatives using HF, MP2 and DFT (31 different functionals) levels and over 71 distinct basis sets. In addition, we propose two new basis sets, NLO-V and aNLO-V, for NLO properties calculations. As the main outcomes it is shown that long-range corrected DFT functionals such as M062X, ωB97, cam-B3LYP, LC-BLYP and LC-ωPBE work satisfactorily for NLO properties when appropriate basis sets such as those proposed here (NLO-V or aNLO-V) are used. For most molecules with β ranging from 0 to 190 esu, the average absolute deviation was 13.2 esu for NLO-V basis sets, compared to 27.2 esu for the standard 6-31 G(2d) basis set. Therefore, we conclude that the new basis sets proposed here (NLO-V and aNLO-V), together with the cam-B3LYP functional, make an affordable calculation scheme to predict NLO properties of large organic molecules.

Study on the role of SBA-15 in the oxidative dehydrogenation of n-butane over vanadia catalyst using density functional theory

The first step in the mechanism of n-butane oxidative dehydrogenation (ODH) on a V₄O₁₀ cluster and V₄O₁₀ supported SBA-15 is examined using DFT method. The activation and adsorption energies, oxidation state of V atoms are calculated. Over V₄O₁₀ the obtained results indicate that the activation of C-H bond of methylene group can occur at both the terminal and the bridging oxygen atoms with similar barrier (21.5–22.5 kcal mol^?1). The role of SBA-15 (with and without modification by Al) in n-butane adsorption step has been studied in detail. SBA-15 itself has mild effect on the reaction process, but the substitution of silicon atoms by aluminum atoms results in an active supporter for V₂O₅ in ODH reaction. In that, the ratio of Si/Al will decide the direction of initial interaction steps between n-butane and catalyst surface and it will result in the selectivity of the reaction products.

The effect of C-vacancy on hydrogen storage and characterization of H2 modes on Ti functionalized C60 fullerene A first principles study

Density functional theory calculations were performed to examine the effect of a C vacancy on the physisorption of H₂ onto Ti-functionalized C₆₀ fullerene when H₂ is oriented along the x-, y-, and z-axes of the fullerene. The effect of the C vacancy on the physisorption modes of H₂ was investigated as a function of H₂ binding energy within the energy window (?0.2 to ?0.6 eV) targeted by the Department of Energy (DOE), and as functions of a variety of other physicochemical properties. The results indicate that the preferential orientations of H₂ in the defect-free (i.e., no C vacancy) C₆₀TiH₂ complex are along the x- and y-axes of C₆₀ (with adsorption energies of ?0.23 and ?0.21 eV, respectively), making these orientations the most suitable ones for hydrogen storage, in contrast to the results obtained for defect-containing fullerenes. The defect-containing (i.e., containing a C vacancy) C₅₉TiH₂ complex do not exhibit adsorption energies within the targeted energy range. Charge transfer occurs from Ti 3d to C 2p of the fullerene. The binding of H₂ is dominated by the pairwise support–metal interaction energy E(i)^Cn...Ti, and the role of the fullerene is not restricted to supporting the metal. The C vacancy enhances the adsorption energy of Ti, in contrast to that of H₂. A significant reduction in the energy gap of the pristine C₆₀ fullerene is observed when TiH₂ is adsorbed by it. While the C _n fullerene readily participates in nucleophilic processes, the adjacent TiH₂ fragment is available for electrophilic processes.

Impacts of greenwaste biochar on ammonia volatilisation from bauxite processing residue sand

Background and Aims

The objective of this study was to test the suitability of greenwaste biochar to aid nitrogen (N) retention in rehabilitated bauxite-processing residue sand (BRS).

Methods

Bauxite residue sand was collected from the Alcoa of Australia Pinjarra refinery. The pH of BRS was adjusted to values of 5, 7, 8 and 9 and subsequently amended with different rates (1, 5, 10 and 20 %, w/w) of greenwaste biochar. The loss of N via NH₃ volatilization following addition of di-ammonium phosphate (DAP) was determined using an acid trapping method.

Results

At low pH (5), increasing pH rather than adsorption capacity, resulting from biochar addition, caused greater losses of N through volatilization from BRS. In BRS with medium pH (7, 8), increasing adsorption capacity, induced by biochar addition, played the more dominant role in enhancing adsorption of NH ₄ ⁺ -N /NH₃-N and lowering NH₃ volatilization. In the BRS with high pH (9), the majority of NH ₄ ⁺ -N /NH₃-N pools was lost via NH₃ volatilization due to the strong acid-base reaction at this pH.

Conclusions

It is concluded that the interaction of changes in pH and adsorption capacity induced by greenwaste biochar addition affects the availability and dynamics of NH ₄ ⁺ -N/ NH₃-N in BRS amended with DAP.     

Ruthenium hydride-catalyzed regioselective addition of benzaldehyde to dienes leading to β,γ-unsaturated ketones: a DFT study

Density functional theory (DFT) was used to investigate the ruthenium hydride-catalyzed regioselective addition reactions of benzaldehyde to isoprene leading to the branched β,γ-unsaturated ketone. All intermediates and the transition states were optimized completely at the B3LYP/6-31?G(d,p) level (LANL2DZ(f) for Ru, LANL2DZ(d) for P and Cl). Calculated results indicated that three catalysts RuHCl(CO)(PMe₃)₃ (1), RuH₂(CO)(PMe₃)₃ (2), and RuHCl(PMe₃)₃ (3) exhibited different catalysis, and the first was the most excellent. The most favorable reaction pathway included the coordination of 1 to the less substituted olefin of isoprene, a hydrogen transfer reaction from ruthenium to the carbon atom C1, the complexation of benzaldehyde to ruthenium, the carbonyl addition, and the hydride elimination reaction. The carbonyl addition was the rate-determining step. The dominant product was the branched β,γ-unsaturated ketone. Furthermore, the presence of one toluene molecule lowered the activation free energy of the transition state of the carbonyl addition by hydrogen bonds between the protons of toluene and the chlorine, carbonyl oxygen of the ruthenium complex. On the whole, the solvent effect decreased the free energies of the species.

Relative CO2/NH3 Permeabilities of Human RhAG, RhBG and RhCG

Mammalian glycosylated rhesus (Rh) proteins include the erythroid RhAG and the nonerythroid RhBG and RhCG. RhBG and RhCG are expressed in multiple tissues, including hepatocytes and the collecting duct (CD) of the kidney. Here, we expressed human RhAG, RhBG and RhCG in Xenopus oocytes (vs. H₂O-injected control oocytes) and used microelectrodes to monitor the maximum transient change in surface pH (ΔpH_S) caused by exposing the same oocyte to 5 % CO₂/33 mM HCO₃ ^? (an increase) or 0.5 mM NH₃/NH₄ ⁺ (a decrease). Subtracting the respective values for day-matched, H₂O-injected control oocytes yielded channel-specific values (*). $({\Updelta {\text{pH}}_{\text{S}}^{*} })_{{{\text{CO}}_{ 2} }}$ and $({ - \Updelta {\text{pH}}_{\text{S}}^{*} })_{{{\text{NH}}_{ 3} }}$ were each significantly >0 for all channels, indicating that RhBG and RhCG—like RhAG—can carry CO₂ and NH₃. We also investigated the role of a conserved aspartate residue, which was reported to inhibit NH₃ transport. However, surface biotinylation experiments indicate the mutants RhBG_D178N and RhCG_D177N have at most a very low abundance in the oocyte plasma membrane. We demonstrate for the first time that RhBG and RhCG—like RhAG—have significant CO₂ permeability, and we confirm that RhAG, RhBG and RhCG all have significant NH₃ permeability. However, as evidenced by $({\Updelta {\text{pH}}_{\text{S}}^{*} })_{{{\text{CO}}_{ 2} }} /({ - \Updelta {\text{pH}}_{\text{S}}^{*} })_{{{\text{NH}}_{ 3} }}$ values, we could not distinguish among the CO₂/NH₃ permeability ratios for RhAG, RhBG and RhCG. Finally, we propose a mechanism whereby RhBG and RhCG contribute to acid secretion in the CD by enhancing the transport of not only NH₃ but also CO₂ across the membranes of CD cells.