Periodic Density Functional Study Research Articles

Phosphorene defects for high-quality detection of nitric oxide and carbon monoxide: A periodic density functional study

The electronic and sensing properties of pristine and defect-tuned black phosphorus monolayer for the monitoring of nitric oxide (NO) and carbon monoxide (CO) at two defect concentrations (0.0165 and 0.0073 Å−2) were investigated within the framework of periodic density functional theory (DFT). Several configurations with preserved integrity were found plausible for both molecules at the vacant sites in which the ones with the lowest energy favored top site adsorption. We found that the detection sensitivities of all phosphorene layers correlated well with the electrophilicity of the structures. The performance data showed that the defect-free phosphorene layer could not operate as a reliable conductance-based sensor, but could be considered a satisfactory work function sensor for the analytes at hand. On the contrary, the defect-tuned phosphorene layer would be an excellent detector for both molecules, especially providing a high sensitivity at both concentrations (up to 270.0) and excellent reusability (3.6 ms) for the NO detection without any dependence on external manipulation. Carbon monoxide was better detected (1043.3) at a lower concentration, however. Excellent selectivity was observed for both molecules in dry and humid air atmospheres. The corresponding band structures and density of states were discussed. The analysis of the localized orbital locator (LOL) contour maps indicated that the C–P and N–P bonds behaved van der Waals (vdW) and polar covalent types, respectively. Overall, this paper provides attractive data for the rational design of novel chemosensors for the noxious NO and CO molecules.

Molecular Interactions of MeOH and EtOH with Black Phosphorus Monolayer: A Periodic Density Functional Study

The adsorption properties of black phosphorus monolayer (BPML) nanostructure toward methanol and ethanol were investigated using periodic density functional theory calculations. Despite the subtle in-plane distortions, the integrity of the BPML nanostructure was preserved. All complexes revealed interactions of pure electrostatic nature as evinced by the LOL and QTAIM data. The band gap was slightly enlarged, and both valence and conduction bands moved upward upon the detection of both alcohols. These observations implied that the perfect surface of the semiconductor could be considered a work function sensor for the alcohol molecules. The adsorption energy ranged from –0.13 to –0.36 eV, with ethanol presenting relatively stronger physisorption.

The Interactions Between Chlorides and Zn(001) Surfaces in Zinc/Bromine Flow Battery Electrolytes

Chloride-based supporting electrolytes are conventionally used in zinc/bromine (Zn/Br) and other flow batteries to ensure good conductivity during charge/discharge operation. This work presents preliminary results from experimental and periodic density functional studies of the interactions between chlorides and electrodeposited zinc generated during the charging phase of the Zn/Br system. Scanning electron microscopy and X-ray diffraction analysis show that even relatively low concentrations (0.5 M) of ZnCl2 supporting electrolyte influences zinc electrodeposition behaviour during the charging phase, with a strong preference for the (004) orientation. Molecular modelling carried out in this work provides a foundation for understanding how chlorides present in the supporting electrolyte interact with and alter the electrodeposited zinc surface in Zn/Br flow batteries. Chloride strongly binds above the Zn(001) surface with binding energies of 260–288 kJ mol-1 at 0.11–0.33 ML coverage. Chloride binding lowers the Zn(001) surface uniformity, with higher coverage resulting in lower binding energies. These findings warrant further investigation of the influence and behaviour of supporting electrolytes on the primary electrolyte and at the electrode-electrolyte interface. While this work focuses on Zn/Br systems, the findings are also potentially applicable to other types of RFBs which utilise chloride-containing electrolytes.

On the Electronic Effect of V, Fe, and Ni on MgO(100) and BaO(100) Surface: An Explanation from a Periodic Density Functional

A periodic density functional study of the V, Fe, and Ni sublayer doped MgO(100) and BaO(100) surfaces was carried out using a periodic approach in the context of the GGA approximation. Results suggest that doping atoms accommodate better in the MgO than in BaO because covalent radii of the doping atoms are closer to that of the Mg atom. Sizes of the doping atom, bulk forces, and electronic effects play an important role in the structural changes observed in doped surfaces studied herein. From all the doped studies, Ni doped Ba(100) surface is shown to be a promising material for trapping molecules with partially occupied states.

Location and reactivity of extra-framework cation in the alkali exchanged LTL zeolites: A periodic density functional study

Locations and reactivity of extra-framework alkali cations, Li+, Na+ and K+, in LTL zeolite framework have been investigated by the periodic density functional theory (DFT). The relative stability of six different cation sites, A–F, was systematically studied for all AIs. The calculated results show that the energetically preferable sites for these alkali cations locate inside the cancrinite cage (B), at the center of the nonplanar 8-membered ring (MR) window (C), and at the edge of the nonplanar 8-MR window connected with the 12-MR windows (D). Among the three stable cation sites, only site D is able to directly interact with a CO molecule. The calculated adsorption energy and the C–O stretching frequency decrease when the cation size decreases. The adsorptions of CO on mono-, di-, and nona-cation systems (Si/Al=35, 17, and 3, respectively) are not significantly different because of the large pore size of LTL zeolite and the small occupancy of the adsorbate. In addition, the photonic antenna prototype system representing by proflavine dye-zeolite L has been simulated to investigate the orientation of the adsorbed dye inside the channel of zeolite host. Proflavine dye interacts with K cation locating at the D site, the adsorbed dye is found to be slightly bent and aligned in parallel with the channel of LTL zeolite. This causes changes of photophysical properties of the adsorbed dye compared with its gas phase.

Theoretical Study of Hydrogen Permeation through Mixed NiO–MgO Films Supported on Mo(100): Role of the Oxide–Metal Interface

This work presents a periodic density functional study of the adsorption and permeation of atomic H on Ni-doped MgO oxide thin films supported on a Mo(100) surface. We find that the binding of atomic H is affected by the presence of a metallic support. The chemisorption energies increase considerably when the oxide film is supported. The H permeation through the NiO-MgO oxide was also studied. H migration through the unsupported NiO-MgO oxide is thermodynamically inhibited, while the presence of the metallic Mo makes permeation thermodynamically favored. We attribute the promoting effect to the different character of adsorbed H at the unsupported Ni-doped MgO oxide and at the oxide-Mo interface. In the former case, H forms hydroxyl groups, whereas in the latter case it appears as hydride due to the formation of strong metal-hydrogen bonds. These results illustrate the important role that the oxide-metal interface could play in the mechanism for pure and mixed oxides reduction.

Location and acidity of Brønsted acid sites in isomorphously substituted LTL zeolite: A periodic density functional study

Isomorphously substituted LTL zeolite ([M]-LTL) was studied by the periodic density functional theory. Two different tetrahedral Si atoms of LTL (T1 and T2) were replaced by a series of trivalent atoms (M=Al, B and Ga). The relative energies of the different structural configurations show that the T1 site located at the 12-membered rings is the most favorable site for M substitution. For the [M]-LTL where T1 is substituted, different Brønsted acid sites (O3, O4, and O6) were intensively studied by calculating the deprotonation energy, the O–H vibrational frequency, and the charge of the bridging oxygen, and the adsorption energy of the probe molecules (ethylene, acetonitrile and pyridine) with the [B]-, [Ga]-, and [Al]-LTL models. A direct correlation between those four parameters is observed and the trend of the relative Brønsted acidity for isomorphously substituted systems is predicted as: [B]-LTL<<[Ga]-LTL<[Al]-LTL which is in agreement with the experimental sequence of isomorphously substituted ZSM-5 zeolite.

Computational Studies on SAMs of {Mn6} SMMs on Au(111): Do Properties Change upon Grafting?

Single molecule magnets (SMM) adsorbed on surfaces as magnetic building blocks represent a hot topic of research in the area of molecular magnetism. Indeed, the understanding the properties of molecules on surface is extremely challenging as atomistic structures are not readily available. In this regard, theoretical studies as reliable tool to reproduce and predict the structure and the magnetic ground state of SMMs in the bulk phase and adsorbed on a surface, should be considered very appealing. In this framework, we report a periodic density functional (DF) study on two {Mn6} SMM complexes of general formula [Mn(III)6O2(R-sao)6(O2C-th)2L], where HO2C-th=3-thiophene carboxylic acid, saoH2 = salicylaldoxime, R = H and L = (EtOH)4 (1) or R = Et and L = (EtOH)4(H2O)2 (2), performed to ascertain the structure of their self-assembled monolayers (SAM) on the Au(111) surface. Their magnetic properties in vacuum and in the adsorbed state have also been computed and our results clearly demonstrate that the grafti...

Cluster and Periodic Density Functional Study of Auger Electron Emission from Conducting Carbon Nanotubes

Cluster and Periodic Density Functional Study of Auger Electron Emission from Conducting Carbon Nanotubes

Probing Lewis acidity and reactivity of Sn- and Ti-beta zeolite using industrially important moieties: A periodic density functional study

The Lewis acidic nature and reactivity of two industrially important catalysts, viz., Sn and Ti substituted beta zeolite (T-BEA) are analyzed using a unique combination of structural parameters, energetics and reactivity descriptors. To achieve this purpose, we adsorb the industrially important moieties (L) namely NH 3, H 2O, CH 3OH, CH 3CN on the active sites of T-BEA. The calculations were performed using a periodic density functional method where the valence electrons are described using a plane wave basis set in conjunction with pseudo-potentials for the core electrons. The analysis of the structural properties of these complexes reveals that TO 4 shows typical characteristic splitting 120°/90°, close to bipyramidal geometry as compared to tetrahedral symmetry observed in the bare T-BEA. This is associated with small variations in the framework bond lengths (≥0.08 Å) and a substantially large variation of bond angles (≤10°) in all the ligand-zeolite complexes. Further in both cases of Sn and Ti substituted beta zeolite, ligand interacts at optimum inter-atomic bond distance. Our interaction energies show that adsorption of all ligand moieties is stronger at Sn center than that of Ti. In general, the order of stability of the different T-BEA adducts is NH 3 > H 2O > CH 3OH > CH 3CN. The ligand interaction is associated with the corresponding bond elongation and bond reduction of the adsorbed molecules on catalyst active site, which can be taken as measure of red or blue shifted frequencies. Finally, the global descriptors of reactivity justify the fact that soft acid, Sn-BEA, interacts strongly with soft bases following the Pearson's HSAB principle. However, hard acid, Ti-BEA interacts with soft bases to form a stable Lewis adduct. Furthermore, the HOMO–LUMO gap of all Sn-BEA–L adducts is lower than that of Ti-BEA–L adducts indicating to its higher Lewis acidic nature compared to Ti-BEA.

Si atom adsorption and diffusion on Si(110)-(1×1)and(2×1)

We present a systematic periodic density-functional study of Si adsorption and diffusion on the Si(110)-$(1\ifmmode\times\else\texttimes\fi{}1)$ and $(2\ifmmode\times\else\texttimes\fi{}1)$ surface. The most stable binding configurations on both reconstructions are with a threefold coordinated adatom bridging the gap between two surface zigzag rows. Several of the structures can be stabilized by a lateral shift of the rows or by distortion of a row. The different structures can be identified from their density of states and scanning tunnel microscopy/current image tunneling spectroscopy (STM/CITS) images. Diffusion on the $(1\ifmmode\times\else\texttimes\fi{}1)$ surface is equally likely to proceed along and across zigzag rows. Along rows either simple diffusion or an exchange mechanism can occur, across rows only an exchange mechanism is possible. Diffusion on the $(2\ifmmode\times\else\texttimes\fi{}1)$ reconstruction is easier in the direction along rows than across and proceeds as simple diffusion, not exchange. The mobility of the adatom is higher on the $(2\ifmmode\times\else\texttimes\fi{}1)$ reconstruction.

Application of Hybrid Functionals to the Modeling of NO Adsorption on Cu−SAPO-34 and Co−SAPO-34: A Periodic DFT Study

The structural and chemical properties of Cu- and Co-exchanged silicoaluminophosphates with a chabazite-type structure (SAPO-34) and the adsorption of NO molecules on the extraframework cations have been studied using periodic density functional (DFT) calculations using both convential gradient-corrected exchange-correlation functionals and hybrid functionals mixing exact (i.e., Hartree−Fock) and DFT exchange. To assess the importance of the cation-support interaction, comparative studies of NO adsorption on isolated metal atoms and ions have been performed. We find that whereas the geometrical properties for stoichiometric aluminophosphate (ALPO-34) and protonated silicoaluminophosphate (H−SAPO-34) calculated using both types of functionals are essentially on par, the hybrid functionals predict much wider energy gaps in better agreement with experiment. Significant differences arise for the coordination of extraframework cations in the metal-exchanged silicoaluminophosphates (Cu−SAPO-34 and Co−SAPO-34) and, in particular, for the electronic eigenstates of the cations. The different metal−framework coordination and the differences in the electronic properties lead to markedly different predictions of the chemical reactivities: hybrid functionals predict a weaker binding of molecular adsorbates such as NO. The reduction of the adsorption energy is more pronounced for the magnetic Cu(II) and Co(II) cations than for the nonmagnetic Cu(I) cation. This is a consequence of a much larger exchange splitting of the d states of the cation and also of an enhanced ligand-field splitting due to the binding to the framework. The occupied d states of the transition-metal cations are shifted to larger binding energies, and the empty d states are located in the upper part of the energy gap. Hybrid functionals tend to overestimate the N−O stretching frequency even for the isolated molecule and for gas-phase nitrosyls, whereas conventional functionals predict eigenvalues that are too low. This tendency is also reflected in the vibrational spectra of the Cu(Co)−NO adsorption complexes, whereas the adsorption-induced frequency shifts predicted by both types of functionals are in reasonable agreement with experiment. Significant differences are found in the prediction of the spin states of the adsorption complexes. Altogether, we conclude that conventional gradient-corrected DFT functionals describe these complex materials with good accuracy, whereas the inclusion of exact exchange in the hybrid functionals does not lead to improved performance for the metal-exchanged systems.

Periodic density functional study of Rh and Pd interaction with the (1 0 0)MgO surface

The adsorption geometry and electronic properties of palladium and rhodium atoms deposited on the regular (1 0 0)MgO surface were analyzed by means of periodic DFT calculations using local, gradient-corrected and hybrid (B3LYP) functionals. Spin-polarized computations revealed doublet spin state of Rh atom to be the most stable electronic state for the adsorbed rhodium atom on (1 0 0)MgO. The preferred adsorption site of the metal (Pd and Rh) atoms was found to be the site on top of the surface oxygen atoms. A relatively stable geometry for the adsorption of the Pd and Rh in a bridge position above the two surface oxygens was found as well. The electronic structures suggested partly covalent bonding with contribution from electrostatic attraction between the metal and the oxygen atoms for both optimized structures. Small charge transfer was obtained from the support to the Pd and Rh metal atoms. The calculations showed that rhodium was bound stronger to the substrate probably due to stronger polarization effects.

Modeling the interplay of inter- and intramolecular hydrogen bonding in conformational polymorphs

The predicted stability differences of the conformational polymorphs of oxalyl dihydrazide and ortho-acetamidobenzamide are unrealistically large when the modeling of intermolecular energies is solely based on the isolated-molecule charge density, neglecting charge density polarization. Ab initio calculated crystal electron densities showed qualitative differences depending on the spatial arrangement of molecules in the lattice with the greatest variations observed for polymorphs that differ in the extent of inter- and intramolecular hydrogen bonding. We show that accounting for induction dramatically alters the calculated stability order of the polymorphs and reduces their predicted stability differences to be in better agreement with experiment. Given the challenges in modeling conformational polymorphs with marked differences in hydrogen bonding geometries, we performed an extensive periodic density functional study with a range of exchange-correlation functionals using both atomic and plane wave basis sets. Although such electronic structure methods model the electrostatic and polarization contributions well, the underestimation of dispersion interactions by current exchange-correlation functionals limits their applicability. The use of an empirical dispersion-corrected density functional method consistently reduces the structural deviations between the experimental and energy minimized crystal structures and achieves plausible stability differences. Thus, we have established which types of models may give worthwhile relative energies for crystal structures and other condensed phases of flexible molecules with intra- and intermolecular hydrogen bonding capabilities, advancing the possibility of simulation studies on polymorphic pharmaceuticals.

Methanol and Methoxide Decomposition on Silver

A periodic density functional modeling study of the partial oxidation of methanol to formaldehyde on an Ag(111) surface is presented. Methoxide binds strongly to the surface, preferentially to the highest coordination adsorption sites, while methanol and formaldehyde are weakly adsorbed far from the surface, with no preference for a particular site at low coverage. Energy paths for surface- and oxygen-assisted methanol O−H and methoxide C−H bond scission are compared for various pre-adsorbed oxygen species. Subsurface oxygen stabilizes the adsorbed phase by increasing the binding energy on Ag(111). The effect of subsurface oxygen as compared with the clean surface on the energy barrier of O−H and C−H bond scissions is less dramatic than the effect of onsurface oxygen. In the absence of onsurface oxygen, the O−H and C−H bond scission is hindered by a significant energy barrier, but in the presence of onsurface oxygen, these energy barriers are significantly reduced. Overall, the H transfer reaction in the presence of onsurface oxygen is exothermic from the adsorbed phase, while in the absence of onsurface oxygen, it is endothermic.

A computational study into the (tetrahedral) distortion of TX2α-quartz materials: The effect of changing the chemical composition away from SiO 2

We report a periodic density functional study into the tetrahedral distortion of a range of quartz-like TX 2 materials. The total tetrahedral distortion and its most sizable contribution, the angular part (angular tetrahedral distortion), are found to be strongly dependent on the chemical composition and to increase in the order of BeF 2<SiO 2<CO 2<GeO 2<SiS 2<GeS 2. The bond stretching contribution to the total tetrahedral distortion appears to be significantly smaller and to vary more erratically with changes in the chemical composition. The sulphide materials in the study were found to have tetrahedral distortion values commonly associated in silica with experimentally unrealizable hypothetical frameworks, suggesting that such frameworks might become realizable when stepping away from silica. None of the tetrahedra were found to be strictly regular, in line with the analysis of Smith [Acta. Cryst. 16 (1963) 542–545], demonstrating that regular tetrahedra are in principle possible in quartz but that distortions from ideality are energetically advantageous. The energetic reason for this distortion is still an open question; we propose a simple electrostatic model that explains the ease with which tetrahedra can be distorted in terms of charge transfer and the relative charge on the X (O,S,F) atom.

On the Performance of Au(111) for Ethylene Epoxidation: A Density Functional Study

This work presents a periodic density functional study of the epoxidation mechanism of ethylene on Au(111). It is found that, once atomic oxygen is adsorbed on the surface, partial oxidation to ethylene oxide becomes possible. Calculated transition state theory rate constants for the elementary steps involved in the reaction predict that the selectivity of Au(111) toward epoxide is of approximately 40% in good agreement with recent experimental findings for styrene epoxidation on Au(111).

Adsorption and dissociation of methanol on Au(1 1 1) surface: A first-principles periodic density functional study

The adsorption and dissociation of methanol on Au(111) surface were studied using the first-principles calculations based on density functional theory (DFT) with the generalized gradient approximation (GGA). Adsorption energies, geometric structures, Mulliken charges population, and vibrational frequencies of the various intermediates were computed from full-geometry optimization with a three-layer slab model. The most stable adsorption modes of the species, i.e. CH 3OH, CH 3O, and HCHO were considered in calculation. The possible decomposition pathways were investigated with transition state search methods. The results indicate that methoxyl radical is likely the decomposition intermediate.

Periodic density functional and tight-binding quantum chemical molecular dynamics study of catalytic properties on γ-Al 2O 3 supported Pt catalysts

We investigated the interactions of platinum metal clusters on the γ-alumina using a periodic density functional theory method. Results showed that electron transfer occurs between platinum metal clusters and γ-Al 2O 3. We also investigated NO adsorption properties (NO–Pt 4/γ-Al 2O 3) in order to clarify the support effect on NO activation in terms of the elongation of N–O bond length and NO molecular charge. In our results, the support increases NO activation for three-fold sites but decreases it for on-top and bridge sites. Moreover, the support changes the site preference of NO adsorption. In addition, in order to clarify the support effect at finite temperature, we studied the dynamic behaviors of supported precious metal catalysts by using a tight-binding quantum chemical molecular dynamics program named ‘Colors’.

A periodic density functional study of the location of titanium within TS-1

The thermodynamics of the substitution of titanium within the silicalite framework to form TS-1 has been investigated using periodic density functional theory. In contrast to previous force field and ab initio cluster studies, the favoured tetrahedral sites are found to be T8 and T10 at the level of one titanium per unit cell, which accords with the best information currently available from diffraction studies. At lower concentrations, T4 and T11 are also important sites for substitution. Bond lengths for titanium to neighbouring oxygens are also found to be in good agreement with information from EXAFS. The present work suggests that the titanium distribution in TS-1 is not so greatly at variance with the thermodynamic site preferences as has been proposed on the basis of some previous theoretical studies.