Density Functional Theory Cluster Calculations Research Articles

Computational Exploration of a Metal(II) Catecholate-Functionalized UiO-66 Nanoporous Metal–Organic Framework for Effective NOx Capture

Metal–organic frameworks (MOFs) have attracted much attention for the effective capture of contaminants from air. Herein, density functional theory (DFT) calculations and grand canonical Monte Carlo (GCMC) simulations were combined to systematically assess the adsorption performance of the cagelike UiO-66 nanoporous MOF functionalized by metal(II) catecholate [CatM(II), where M(II) = Mg(II), Mn(II), Fe(II), Co(II), Ni(II), Cu(II), Zn(II), Pd(II), and Pt(II)] with respect to NOx potentially present at very low concentration (from the ppm to ppb levels). The adsorption modes and energetics of NOx toward metal(II) catecholate functions were first examined systematically using cluster DFT calculations in order to determine the optimum metal(II) for effective NOx capture. The best CatFe(II) was further incorporated in the crystal structure of UiO-66 and force-field parameters to accurately describe the specific interactions between Fe(II), and both NOx were derived from periodic DFT calculations and further implemented in a GCMC scheme to predict the adsorption isotherms in a whole range of gas pressure. These calculations revealed that UiO-66-CatFe(II) exhibits steep-adsorption isotherms for both NOx, leading to excellent adsorption uptake at very low gas pressure (from 10–9–10–4 bar). This finding complements the portfolio of nanoporous materials that has so far been almost exclusively tested in operation conditions at much higher NOx concentration (>1000 ppm).

Characterization of Chemisorbed Species and Active Adsorption Sites in Mg-Al Mixed Metal Oxides for High-Temperature CO2 Capture.

Mg–Al mixed metal oxides (MMOs), derived from the decomposition of layered double hydroxides (LDHs), have been purposed as adsorbents for CO2 capture of industrial plant emissions. To aid in the design and optimization of these materials for CO2 capture at 200 °C, we have used a combination of solid-state nuclear magnetic resonance (ssNMR) and density functional theory (DFT) to characterize the CO2 gas sorption products and determine the various sorption sites in Mg–Al MMOs. A comparison of the DFT cluster calculations with the observed 13C chemical shifts of the chemisorbed products indicates that mono- and bidentate carbonates are formed at the Mg–O sites with adjacent Al substitution of an Mg atom, while the bicarbonates are formed at Mg–OH sites without adjacent Al substitution. Quantitative 13C NMR shows an increase in the relative amount of strongly basic sites, where the monodentate carbonate product is formed, with increasing Al/Mg molar ratios in the MMOs. This detailed understanding of the various basic Mg–O sites presented in MMOs and the formation of the carbonate, bidentate carbonate, and bicarbonate chemisorbed species yields new insights into the mechanism of CO2 adsorption at 200 °C, which can further aid in the design and capture capacity optimization of the materials.

The Formation of Glycolonitrile (HOCH2CN) from Reactions of C+ with HCN and HNC on Icy Grain Mantles

Abstract Quantum chemical cluster calculations show that reactions of C+ with HCN or HNC embedded in the surface of an icy grain mantle can account for the formation of a recently detected molecule, glycolonitrile, which is considered to be an important precursor to ribonucleic compounds. Reactions of cations deposited on ice mantles with minimal kinetic energy have been found theoretically to result in previously unknown pathways to significant organic compounds in protostellar systems and the interstellar medium. In density functional theory cluster calculations involving up to 24H2O, C+ reacts consistently with HCN embedded in ice to yield the neutral HOCHNC radical with no barrier, along with H3O+ as a byproduct. If HOCHNC then reacts with H, three species can be formed: HOCH2NC (isocyanomethanol), HOCH2CN (glycolonitrile), and HOCHNCH. For the C++ HNC reaction on ice, the HOCHCN and H2OCCN radicals form as intermediates, the first of which is another direct precursor to glycolonitrile via H addition. In addition to characterizing reaction pathways, predictions are provided of the vibrational and electronic spectra of the HCN and HNC starting clusters and the HOCHNC ice-bound intermediate.

Phenol adsorption mechanism on the zinc oxide surface: Experimental, cluster DFT calculations, and molecular dynamics simulations

Pollution by phenols is considered a major environmental issue. Therefore, their removal from wastewaters is of great practical significance and is directly related to human health. Herein, a porous zinc oxide (ZnO) was synthesized by a simple precipitation method and used as an adsorbent for the removal of phenol at different operating conditions. Besides experimental investigations, a comprehensive understanding of the mechanism of phenol adsorption on ZnO surface at the molecular level was achieved by using cluster Density Functional Theory (DFT) and molecular dynamics (MD) simulations. The prepared adsorbent was characterized using a variety of techniques, including X-ray diffraction (XRD), Fourier-transform infrared spectroscopy (FT-IR), as well as the Brunauer Emmett Teller (BET) method. The effects of different variables, such as pH, pHpzc (pH at the point of zero charge), initial concentration, and temperature, were investigated to optimize and understand the adsorption process. Possible controlling mechanism and the potential rate-limiting steps were analyzed using Lagergren's pseudo-first-order and pseudo-second-order models, and the data were found to follow the pseudo-second-order equation. The maximum removal of the phenol molecule was observed at pH = 4 with adsorption capacities of 3.61 and 4.51 mg/g at 30° and 50°, respectively. Furthermore, Cluster DFT calculations and molecular dynamics simulations were used to get deeper mechanistic insights on the adsorption behavior of the phenol molecule onto zinc oxide. DFT results confirmed the predominance of chemisorption while those from MD simulations indicated an increased interaction of ZnO with phenol in the presence of solvent due to water-bridged H-bonds.

Optical, electronic and visible-range photo-electronic properties of boron carbide-indole films

Semiconducting aromatic boron carbide films have been formed by plasma enhanced chemical vapor deposition (PECVD) from closo-1,2-dicarbadodecarborane (orthocarborane) and indole precursors. X-ray photoemission and ellipsometry indicate that the films consist of intact indole moieties bonded to the B sites on orthocarborane icosahedra. The ellipsometry measurements, of the PECVD hydrogenated boron carbide alloyed with indole moieties, indicate indirect and direct band gaps of 1.6 eV and 3.5 eV, respectively, in good agreement with density functional theory cluster calculations. These calculations also indicate that states near the valence band maximum and conduction band minimum are associated with indole and carborane moieties, respectively. The current versus voltage (I(V)) curves, of PECVD hydrogenated boron carbide alloyed with indole moieties to n-type silicon diodes, indicate a photocurrent at zero bias, with an appreciable open-circuit voltage of 1 V. The 4th quadrant conductivity and voltage, at the maximum power point, were 1.66 μA and 0.69 V respectively, under illumination. The frequency- and bias-dependent capacitance versus voltage (C(V)) data yield mean carrier lifetimes from 2.5 ms to 1.5 ms at low and high bias, respectively at 10 kHz, but falling to 0.5 ms, independent of bias voltage, at 100 kHz.

Chemical and electronic structure of composite films deposited by plasma-enhanced chemical vapor deposition from orthocarborane and pyridine source compounds

Semiconducting boron carbide films, with aromatic moieties, were formed by plasma-enhanced chemical vapor deposition (PECVD) using pyridine (C5H5N) and closo-1,2 dicarbadodecaborane (1,2-B10C2H12; ortho-carborane) as source compounds. X-ray photoelectron spectroscopy (XPS), in conjunction with pyridine/orthcarborane cluster density functional theory (DFT) calculations, indicates that such films consist of partially dehydrogenated orthocarboranes coordinated to pyridine moieties at icosahedral B sites. The XPS data also suggest a constant average coordination number of 3–4 pyridines per icosahedral carborane, indicating that higher pyridine content in the film results in greater areas of plasma-polymerized pyridine. Ultraviolet photoelectron spectroscopy (UPS) results and DFT cluster calculations indicate that electronic states near the valence band maximum are associated with pyridine moieties, while states near the conduction band minimum are associated with either carborane or pyridine moieties. Variable angle spectroscopic ellipsometry (VASE), the UPS data and theoretical results also indicate only gradual changes in indirect band gap energies with changing pyridine/orthocarborane stoichiometry, in agreement with previously reported results. The results presented here are consistent with and provide additional insight regarding recent neutron voltaic and photoluminescence results for these materials.

Indium doped SnO2 nanostructures preparation and properties supported by DFT study

Indium doped tin dioxide nanostructures are investigated using experimental and theoretical techniques. XRD, UV-Vis and Raman spectroscopy are used to examine indium doped SnO2 nanostructures with various doping ratios. On the other hand Density functional theory (DFT) is used to check and compare lattice constants, energy gaps and vibrational properties. Large unit cell and previously suggested pyramid clusters of metal dioxides are applied to doped SnO2 and tested to manifest properties of different pure and doping stoichiometries. SnO2 clusters results show oxygen-deficient stoichiometry in agreement with experiment and previous literature. Experimental results of In doped SnO2 show and increase of lattice constants and a decrease of energy gap. The same trend is observed using DFT calculations for energy gap. Theoretical Large unit cell results show nearly the same lattice constant before and after In doping that indicate a change in experimental stoichiometry due to doping. The highest Raman peek at 581 cm−1 encounter blue shifting to 585 cm−1 due to In doping using DFT cluster calculations in comparison with 563–582 cm−1 experimental shift.

Electron Transfer in Cuprates, Pnictides, and Metallic Superconductors

The charge distribution and electronic properties of several materials that become superconductors at a low temperature are examined by using Density Functional Theory cluster calculations. For cuprates, charge transfer occurs between copper atoms only for the cluster with the oxygen vacancy. For pnictides, charge transfer with positive and negative atoms in the FeAs layer is observed in fluorine-doped clusters but not in undoped clusters. For metallic superconductors, alternating positive and negative layers are found in the clusters. These calculated charge distributions are analyzed as a result of electron transfer occurring in the superconducting state involving unsynchronized resonances, as predicted by the RVB theory of Pauling. From this analysis, combinations of chemical elements and their relationship with the superconducting transition temperature are discussed.

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

Removal of Mg from hydrated Ni sulfates has long been a problem in the industrial purification process of hydrated Ni sulfates. In this work, we have investigated this industrial problem using state-of-the-art molecular simulations. Periodic Density Functional Theory (DFT) and cluster DFT calculations are used to study the crystal structures and phase stability of the hexahydrated and heptahydrated Ni and Mg sulfates and their mixed phases. The calculated lattice parameters of MSO4(H2O)n (M=Ni, Mg; n=6, 7) crystals are in good agreement with available experimental data. The relative energy differences of the mixed phase for both hexahydrated and heptahydrated Ni/Mg sulfates obtained from both the periodic and cluster DFT calculations are generally less than kT (25.8meV, T=300K), indicating that a continuous solid solution is formed. We also investigated the Bader charges and electronic structures of the hexahydrated and heptahydrated Ni/Mg sulfates using the periodic DFT calculations. The energy band gaps of the hexahydrated and heptahydrated Ni and Mg sulfates were predicted by first-principles calculations. Large energy band gaps of about ~5.5eV were obtained from the DFT–GGA calculations for hydrated Mg sulfates, and band gaps of about ~5.1eV were obtained by the DFT–GGA+U calculations for hydrated Ni sulfates.

Importance of a Nonlocal Description of Electron–Electron Interactions in Modeling the Dissociative Adsorption of H2 on Cu(100)

Describing the dissociation of molecules on metal surfaces is of major importance in understanding processes such as corrosion or heterogeneous catalysis. Because of its high efficiency and reasonable accuracy, density functional theory (DFT) is the method of choice in this field nowadays, but it can be expected that the semilocal treatment of the exchange-correlation introduces fundamental errors. To understand those errors, it is possible to reduce the complexity of the problem to, for example, describe the dissociation of H2 on Cu(100). In this work, we model this process for an embedded, metallic cluster comparing coupled cluster, configuration interaction, and semilocal DFT calculations. We calculate a two-dimensional potential energy surface (PES) and identify the minimum energy pathway (MEP) for dissociation, the transition state, and also the dissociation minimum. Compared to DFT calculations, the interactions between the molecule and the surface are far more long ranged in explicitly correlated m...

Structure of Mo2Cx and Mo4Cx Molybdenum Carbide Nanoparticles and Their Anchoring Sites on ZSM-5 Zeolites

Mo carbide nanoparticles supported on ZSM-5 zeolites are promising catalysts for methane dehydroaromatization. For this and other applications, it is important to identify the structure and anchoring sites of Mo carbide nanoparticles. In this work, structures of Mo2Cx (x = 1, 2, 3, 4, and 6) and Mo4Cx (x = 2, 4, 6, and 8) nanoparticles are identified using a genetic algorithm with density functional theory (DFT) calculations. The ZSM-5 anchoring sites are determined by evaluating infrared vibrational spectra for surface OH groups before and after Mo deposition. The spectroscopic results demonstrate that initial Mo oxide species preferentially anchors on framework Al sites and partially on Si sites on the external surface of the zeolite. In addition, Mo oxide deposition causes some dealumination, and a small fraction of Mo oxide species anchor on extraframework Al sites. Anchoring modes of Mo carbide nanoparticles are evaluated with DFT cluster calculations and with hybrid quantum mechanical and molecular ...

Quantum mechanical calculations on cellulose–water interactions: structures, energetics, vibrational frequencies and NMR chemical shifts for surfaces of Iα and Iβ cellulose

Periodic and molecular cluster density functional theory calculations were performed on the Iα (001), Iα (021), Iβ (100), and Iβ (110) surfaces of cellulose with and without explicit H2O molecules of hydration. The energy-minimized H-bonding structures, water adsorption energies, vibrational spectra, and 13C NMR chemical shifts are discussed. The H-bonded structures and water adsorption energies (ΔEads) are used to distinguish hydrophobic and hydrophilic cellulose–water interactions. O–H stretching vibrational modes are assigned for hydrated and dry cellulose surfaces. Calculations of the 13C NMR chemical shifts for the C4 and C6 surface atoms demonstrate that these δ13C4 and δ13C6 values can be upfield shifted from the bulk values as observed without rotation of the hydroxymethyl groups from the bulk tg conformation to the gt conformation as previously assumed.

External Surface of Zeolite Imidazolate Frameworks Viewed Ab Initio: Multifunctionality at the Organic−Inorganic Interface

The external surface sites of zinc based zeolite imidazolate frameworks (ZIFs) is investigated by cluster density functional theory calculations, which reveal a great variety of sites. Their stabil...

Adsorption and Diffusion of Light Gases in ZIF-68 and ZIF-70: A Simulation Study

We have computed the adsorption and diffusion of CO2, N2, CH4, and H2 in zeolitic imidazolate framework (ZIF) materials ZIF-68 and ZIF-70 from atomistic simulations. These simulations were performed using geometries obtained from density functional theory (DFT) optimization of the experimental crystal structure of ZIF-68 and on four structures of ZIF-70, one based on the experimental crystal structure and three having different imidazole/nitroimidazole substitution ratios. The framework charges for charge−quadrupole interaction (CQI) terms in our simulations were parametrized with charges obtained from Bader charge decomposition (periodic DFT calculations) and ChelpG charges (cluster DFT calculations). The adsorption and diffusion of the quadrupolar fluids can be dramatically different when using the Bader and ChelpG charges. Agreement between simulations and experiments for the N2 adsorption isotherms in ZIF-68 and 70 is very good when CQI terms are included. In contrast, simulations overpredict the amou...

The importance of charge–quadrupole interactions for H2 adsorption and diffusion in CuBTC

We have assessed the effects of charge–quadrupole interactions (CQIs) between the framework atoms of copper(II) benzene-1,3,5-tricarboxylate (CuBTC) and adsorbed H2 molecules on equilibrium adsorption properties and self- and transport diffusivities. We have also compared charges computed from periodic density functional theory (DFT) on the fully periodic CuBTC structure with charges derived from DFT calculations on cluster models of CuBTC. Our results indicate that carboxylate group atom charges computed from plane wave periodic DFT with the Bader charge analysis formalism are not consistent with the charges computed from the ChelpG method from Gaussian-based DFT cluster calculations. The charges derived from Bader analysis seem to be too large. Adsorption isotherms computed from Monte Carlo simulations and diffusivities computed from molecular dynamics simulations indicate that CQIs have a substantial impact on equilibrium and transport properties of H2 adsorbed in CuBTC at 77 K. Conversely, both adsorption isotherms and diffusivities were shown to be essentially unaffected by CQIs at 298 K.

Anionic Oligomerization of Ethylene over Ga/ZSM-5 Zeolite: A Theoretical Study

Reaction mechanisms for the oligomerization of ethylene on extraframework gallium sites in Ga/ZSM-5 zeolite are studied by density functional theory cluster calculations. The nature of the transition states and intermediates is analyzed by topological analysis of the electron density distribution functions in the framework of the quantum theory of atoms in molecules. Interaction of olefins with the stable intermediate [Ga3+(H−)(C2H5−)]+ of the catalytic ethane dehydrogenation and with the initial extraframework Ga+ site are considered. For the [Ga3+(H−)(C2H5−)]+ site, interaction of ethylene with the hydride ion is a facile process. Addition of ethylene to the Ga−alkyl fragment and oligomer chain growth are rather difficult and compete with ethylene desorption via the β-H transfer reaction. A novel, alternative, and more facile reaction path for the oligomerization of olefins is proposed. This mechanism proceeds via interaction of two C2H4 molecules with the extraframework Ga+ cation in ZSM-5 zeolite, res...

A DFT study of the chemisorption of methoxy on clean and low oxygen precovered Ru(0 0 0 1) surfaces

Adsorption of the methoxy radical on clean and on low oxygen precovered Ru(0 0 0 1) metallic surfaces has been studied by density-functional theory cluster calculations. Methoxy is predicted to be preferentially chemisorbed on both hollow sites (hcp and fcc) of such surfaces, and adopts an upright orientation ( C 3 ν local symmetry). Such prediction is supported by the good agreement found between the calculated vibrational frequencies and the experimentally observed RAIRS spectra. Regarding the charge transfer process between the adsorbate and the surface, our results suggest that the bonding is dominantly polar covalent which arises from a charge donation from the ruthenium surface to the radical, and the co-adsorbed electronegative oxygens deplete slightly the surface electron density. However, the major difference is not induced through much O–Ru bonding, but indirectly, by lowering the valence d-band center of the system. This results in a lower adsorption energy for methoxy than on the clean Ru(0 0 0 1) surface, in accordance with experimental data. Further, accordingly to the present calculations, the radical is expected to dissociate or desorb more easily on the modified surface but with no participation from the co-adsorbed oxygen atoms.

Theoretical Modeling of Formic Acid (HCOOH), Formate (HCOO−), and Ammonium ( \documentclass{aastex} \usepackage{amsbsy} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{bm} \usepackage{mathrsfs} \usepackage{pifont} \usepackage{stmaryrd} \usepackage{textcomp} \usepackage{portland,xspace} \usepackage{amsmath,amsxtra} \usepackage[OT2,OT1]{fontenc} \newcommand\cyr{ \renewcommand\rmdefault{wncyr} \renewcommand\sfdefault{wncyss} \renewcommand\encodingdefault{OT2} \normalfont \selectfont} \DeclareTextFontCommand{\textcyr}{\cyr} \pagestyle{empty} \DeclareMathSizes{10}{9}{7}{6} \begin{document} \landscape $\mathrm{NH}\,^{+}_{4}$ \end{document} ) Vibrational Spectra in Astrophysical Ices

Ions embedded in icy grain mantles are thought to account for various observed infrared spectroscopic features, particularly in certain young stellar objects. The dissociation of formic acid (HCOOH) in astrophysical ices to form the formate ion (HCOO(-)) was modeled with density functional theory cluster calculations. Like isocyanic acid (HOCN), HCOOH was found to spontaneously deprotonate when sufficient water is present to stabilize charge transfer complexes. Both ammonia and water can serve as proton acceptors, yielding ammonium (NH4(+)) and hydronium (H3O(+)) counterions. Computed frequencies of weak infrared features produced by stretching and bending modes in both HCOO(-) and HCOOH were compared with experimental and astronomical data. Our results confirm laboratory assignments that a band at 1381 cm(exp -1) can be attributed to the CH bend in either HCOO(-) or HCOOH, but a band at 1349 cm(exp -1) corresponds to CO stretching in HCOO(-). Another feature at 1710 cm(exp -1) (5.85 m) can possibly be assigned to a CO stretching mode in HCOOH, as suggested by experiment, but the agreement is less satisfactory. In addition, we examine and analyze spectroscopic features associated with NH+4, both as a counterion to HCOO(-) or OCN(-) and in isolation, in order to compare with experimental and astronomical data in the 7 m region.

Study of Rhamnose Radicals in the Solid State Adopting a Density Functional Theory Cluster Approach

A theoretical study is performed on the radiation-induced radicals in crystalline alpha-l-rhamnose, using density functional theory (DFT) calculations. Irrespective of earlier structural assignments, a host of possible radical models is examined in search for a structure that accurately reproduces experimental electron paramagnetic resonance (EPR) properties. A cluster approach is followed, incorporating all hydrogen bond interactions between radical and crystalline environment. Hyperfine coupling tensors as well as g tensors are determined and a comparison is made with available experimental data. Three carbon-centered hydroxyalkyl radicals are validated, in accordance with experimental suggestions for their structure. The occurrence of a carbon-centered oxygen anion radical for one of the radical species is rejected on theoretical grounds, and instead an altered hydroxyalkyl structure is suggested. Our cluster calculations are able to determine g and hyperfine tensors for the oxygen-centered alkoxy radical in rhamnose, in accordance with one of the two measurements for this species. For all radical models, quantitative agreement with experimental hyperfine tensors is obtained by performing full cluster DFT calculations. The inclusion of the molecular environment for the determination of this EPR property proved to be essential.

Radiation-induced radicals in α- d-glucose: Comparing DFT cluster calculations with magnetic resonance experiments

Using density functional theory (DFT) calculations, an enhanced theoretical examination was made of the radiation-induced radicals in α- d-glucose. For the carbon-centred radicals in this sugar, the effect of the model space on the radical geometry as well as on the calculated radical hyperfine coupling tensors was examined. The findings were compared with previously published tensors, as determined by electron paramagnetic resonance (EPR) experiments and single molecule DFT calculations. A cluster approach was adopted, in which intermolecular interactions (predominantly hydrogen bonds) between the radical species and its environment were explicitly incorporated. This substantially improved the correspondence with experimental findings in comparison with single molecule calculations of an earlier examination. In a direct comparison between both computational methods for the glucose radicals, it was shown that the extent of the model space plays an important part in the determination of the radical geometry. Furthermore, the model space also has an impact on the calculated hyperfine coupling tensors. Full cluster EPR calculations, in which the paramagnetic properties are calculated for the entire model space of the cluster, give an excellent agreement with the experimental EPR measurements.