DFT Cluster Model Research Articles

DFT Investigation of the catalytic conversion of acetic acid to acetone on the zeolite H-ZSM5

Biomaterials processing has become increasingly important in the chemical industry. Identification and optimization of processes to facilitate biomass conversion is therefore recognized as being of great importance. Carboxylic acids derived from biomaterials are important building blocks that can be used in a wide variety of industrial applications. As such, methods to process them in an efficient and cost-effective manner are highly desirable. In this study we report the use of theoretical methods to explore the catalytic conversion of acetic acid to acetone on the zeolite H-ZSM5. We have employed a 46T DFT cluster model to explore mechanistic proposals reported in the literature. We investigate the relative energetics associated with the formation of the proposed intermediates, including acyl-zeolite complexes, enols, acylium cations, ketenes, anhydrides, and beta-keto acids, that could potentially connect acetic acid to the desired product, acetone. This assessment would allow us to identify the most probable mechanism connecting the reactant to products. We predict a low energy pathway starting with the generation of a surface acyl, followed by an anhydride, with the rate determining step involving methyl group migration. The reaction is predicted to be bi-molecular and involves C-C bond formation, in line with proposals based on isotopic labelling experiments.

Cluster model DFT study of lactic acid dehydration over Fe and Sn-BEA zeolite

Cluster model DFT study of lactic acid dehydration over Fe and Sn-BEA zeolite

Cu2+ in Keggin anion – Influence of copper position on electronic structure/redox properties of heteropolyacids. DFT cluster model study

Heteropolyacids systems (HPAs) exhibit a wide range of molecular sizes, compositions and architectures. Modification of those parameters leads to the creation of a structure that presents diverse chemical and catalytic features. In this paper, the theoretical description of electronic structure of tungsten and molybdenum heteropolyacids modified by copper Cu2+ ion (Cu-HPA) has been presented. The obtained results showed that the Cu2+ cation introduced into the Keggin anion, into the position of the central ion or addenda atom(s), influences the acid-base properties of the active centers that are present in the system. In addition, the impact of copper ions on the density of states and character of frontier orbitals has been presented.

Phosphoramidate hydrolysis catalyzed by human histidine triad nucleotide binding protein 1 (hHint1): a cluster-model DFT computational study.

As a member of the histidine triad (HIT) protein superfamily, human histidine triad nucleotide binding protein 1 (hHint1) serves as an efficient enzyme in the hydrolysis of phosphoramidate. In particular, hHint1 has been utilized to activate nucleotide prodrugs (proTides). Understanding the mechanism of hHint1 will aid in the future design of proTides. Density functional theory (DFT) computations on a 228-atom cluster active-site model were performed to investigate the hydrolysis mechanism of a phosphoramidate substrate. The overall proposed mechanism included the key involvement of the histidine triad as a proton shuttle. Protonated methylphosphoramidate was first formed by proton transfer of protonated His114 species. A penta-coordinated phosphoryl intermediate, protonated methylphosphorodiamidate, was generated by a nucleophilic attack of His112. After the release of amine and the generation of a phosphorylated histidine intermediate, the nucleophilic attack of an active-site water produced a hydrolyzed intermediate that subsequently transferred a proton back to His114. A rate-determining fully associative pathway with a free energy of activation of 21.7 kcal mol-1 formed the penta-coordinated phosphoryl intermediate. A non-rate determining associative-interchange transition state was involved in the formation of transient tetra-coordinated phosphoryl intermediate. The overall hydrolysis was favorable by -16.1 kcal mol-1.

Electronic Structure of Ti3+–Ethylene Complexes in Microporous Aluminophosphate Materials. A Combined EPR and DFT Study Elucidating the Role of SOMO Orbitals in Metal–Olefin π Complexes

The interaction of tetrahedrally coordinated Ti3+ ions generated in the framework of TiAlPO-5 microporous materials with 12,13C2H4 leads to the formation of side-on η2 {Ti3+—C2H4} complexes with a unique 5-fold coordination of titanium, supported by four oxygen donor ligands of the framework. The detailed electronic and magnetic structure of this adduct is obtained by the combination of advanced EPR techniques (HYSCORE and SMART-HYSCORE) in conjunction with periodic and cluster model DFT calculations. The binding of C2H4 results from the σ overlap of low lying C2H4 filled π orbitals with the 3dz2 empty orbital of titanium, enhanced by a small contribution due the π overlap between the semioccupied 3dyz orbital of titanium and the empty π* orbital of ethylene. The spin density repartition over the ethylene molecule, obtained experimentally, allows probing directly the entity of the metal-to-substrate π*-back-donation, highlighting an asymmetry in the spin density delocalization. This interesting feature is supported by parallel theoretical calculations, which cast the role of the oxygen donor ligands in driving this bonding asymmetry. As a consequence, the interesting structural feature of potential and actual inequality in the electronic spin states (α,β) on the two ethylene carbon atoms of the π coordinated ethylene molecule is produced. The underlying electronic effects associated with the π coordination of ethylene to an early transition metal in paramagnetic state are thus revealed with an unprecedented accuracy for the first time.

DFT cluster model study of Mo[sbnd]V[sbnd]O-type mixed-metal oxides

Cluster models of the proposed active site of MoVO mixed-metal oxides (MMOs) have been explored computationally using density functional methods. Besides the density functional approximation, the size of the cluster models, the number of reduced metal centers, and the effect of the crystal environment on anionic cluster models have been examined. We studied the electronic structure of the MMO and, as a model reaction, the hydrogenation of a surface vanadyl group as well as the subsequent formation of a water molecule. For an adequate description of the electronic structure and the resulting reaction energies, it is necessary to use a density functional that accounts, at least partially, for the self-interaction error, e.g., the hybrid functional PBE0. To predict adequate reaction energies, one has to employ cluster models featuring at least two layers of the MoVO structure, so that inter-layer interactions can be modeled.

Structural, electronic, and vibrational properties of acetylene on Pd(100) doped with Sn or Pb: A DFT cluster model study

Some structural, electronic, and vibrational properties of the acetylene (C2H2) molecule adsorbed at various sites on the Pd(100) surface doped with Sn or Pb are determined theoretically. The calculations were performed using the B3LYP hybrid density functional, and the Sn- or Pb-doped Pd(100) surfaces were represented by a cluster model approach. It is found that the geometry of the C2H2 molecule adsorbed in di- σ configurations is highly perturbed with respect to the structure of acetylene in the gas phase. By contrast, the geometry of acetylene adsorbed in π configurations on the doped surfaces shows a much smaller distortion. Apart from calculating the properties of the adsorbed C2H2 molecule, the effect of the dopants, i.e. Sn and Pb atoms, on these properties is established by comparing the properties of acetylene adsorbed on the Sn- or Pb-doped Pd(100) surfaces with its properties on the monometallic Pd(100) surface. The results indicate that the geometry of the adsorbed C2H2 molecule is similar on the doped and monometallic Pd(100) surfaces.

Tautomerization in the UDP-Galactopyranose Mutase Mechanism: A DFT-Cluster and QM/MM Investigation

UDP-galactopyranose mutase (UGM) is a key flavoenzyme involved in cell wall biosynthesis of a variety of pathogenic bacteria and hence, integral to their survival. It catalyzes the interconversion of UDP-galactopyranose (UDP-Galp) and UDP-galactofuranose (UDP-Galf); interconversion of the galactose moieties six- and five-membered ring forms. We have synergistically applied both density functional theory (DFT)-cluster and ONIOM quantum mechanics/molecular mechanics (QM/MM) hybrid calculations to elucidate the mechanism of this important enzyme and to provide insight into its uncommon mechanism. It is shown that the flavin must initially be in its fully reduced form. Furthermore, it requires an N5(FAD)-H proton, which, through a series of tautomerizations, is transferred onto the ring oxygen of the substrate's Galp moiety to facilitate ring-opening with concomitant Schiff base formation. Conversely, Galf formation is achieved via a series of tautomerizations involving proton transfer from the galactose's -O4(Gal)H group ultimately onto the flavin's N5(FAD) center. With the DFT-cluster model, the overall rate-limiting step with a barrier of 120.0 kJ mol(-1) is the interconversion of two Galf-flavin tautomers: one containing a C4(FAD)-OH group and the other a tetrahedral protonated-N5(FAD) center. In contrast, in the QM/MM model a considerably more extensive chemical model was used that included all of the residues surrounding the active site, and modeled both their steric and electrostatic effects. In this approach, the overall rate-limiting step with a barrier of 99.2 kJ mol(-1) occurs during conformational rearrangement of the Schiff base linear galactose-flavin complex. This appears due to the lack of suitable functional groups to facilitate the rearrangement.

Electronic structure of MoO 2. DFT periodic and cluster model studies

Electronic properties of MoO 2 bulk and (0 1 1) surface are discussed. It is found that Fermi level is located within the band dominated by d molybdenum orbitals, thereby reflecting the metallic character of the system. Results for (0 1 1)MoO 2 surface indicate that the surface retains the metallic character of the bulk. Depending on the thickness of the slab used to model the surface (1-layer or 2-layers) the electronic structure and properties change. In the 2-layer slab, bands close to the Fermi level originate both from regular six-fold coordinated Mo(6) centers as well as from five-fold coordinated Mo(5) centers occurring due to surface formation. In the 1-layer slab, peaks right below the Fermi level are dominated by the surface centers that are six-fold coordinated Mo(6) but also centers which are effectively four-fold coordinated Mo(4). This has a profound effect on the reactivity as was tested by a probe reaction of H 2 adsorption, which did not interact with the surface described by the 2-layer slab, but underwent dissociation on the 1-layer slab. The Mo–Mo pairs with bonds of approximately single character, characteristic for the bulk structure, are also present on the surface, both on 1-layer and 2-layer slabs. The local properties of (0 1 1)MoO 2 surface are very similar to other transition metal oxides. Metal–oxygen bonds are of a mixed ionic and covalent nature and the nucleophilicity of oxygen increases with the increase of coordination numbers of the corresponding oxygen atoms.

An Energetic Comparison of Different Models for the Oxygen Evolving Complex of Photosystem II

The computed total energy from a cluster model DFT calculation is used to discriminate between different suggested models for the oxygen evolving complex of photosystem II. The comparison between different structures rules out several suggestions. Only one suggested structure remains.

Mechanisms for pyrrole adsorption on the Si(1 1 1)7 × 7 surface: A DFT cluster model study

The chemisorption and decomposition of pyrrole (C 4H 4NH) on the reconstructed Si(1 1 1)7 × 7 surface have been investigated by means of hybrid density functional B3LYP method in combination with the cluster model approach. Three chemisorption mechanisms, N–H dissociative adsorption, [4 + 2] cycloaddition, C–H and N–H dissociative adsorption of pyrrole onto a rest atom–adatom pair site, have been considered comparatively. It is shown that the dissociaton of C 4H 4NH occurs readily on either the adatom site (Si a) or the rest atom site (Si r), giving rise to C 4H 4N and H adspecies, and forming N adsP a and N adsP r products respectively. The calculations showed that the C α adsorption process is barrierless and favorable over the N adsorption one. Through compare and analysis the three chemisorption mechanisms, N–H dissociative adsorption on a rest atom–adatom pair of the Si(1 1 1)7 × 7 surface is the most favorable, whereas C–H and N–H dissociative adsorption on a rest atom–adatom pair is the most difficult.

The reactivity of CO2 with K atoms adsorbed on MgO powders

In this combined quantum chemical and EPR study we have investigated the formation of CO(2)(-) radicals by contact of CO(2) molecules with a K precovered MgO surface. K atoms have been deposited on polycrystalline MgO samples, and then exposed to CO(2). The typical EPR signal of the isolated K atoms disappears when the reaction with CO(2) takes place and a new paramagnetic species attributed to CO(2)(-) is observed. DFT cluster model calculations show that there is a spontaneous electron transfer from the adsorbed K atom to the CO(2) molecule, with formation of K(+)CO(2)(-) surface complexes. These species have the same electronic characteristics and spin distribution of gas-phase M(+)CO(2)(-) (M = Li, Na, K) molecules, but are stabilized by the presence of the ionic surface. The most stable MgO sites where the adsorption of CO(2) occurs and the computed EPR properties are discussed.

Formation of CO2− Radical Anions from CO2 Adsorption on an Electron-Rich MgO Surface: A Combined ab Initio and Pulse EPR Study

We report the results of DFT cluster model calculations on the formation of carboxylate radical anions, CO2−, by reaction of CO2 with an electron rich MgO surface. The theoretical results are used in conjunction with new pulse electron paramagnetic resonance (EPR) experiments to interpret recently reported experimental data obtained with continuous wave EPR (CW-EPR) (Chiesa, M.; Giamello, E. Chem. Eur. J. 2007, 13, 1261). Three cases have been considered: (1) interaction of CO2 with oxide anions at low-coordinated sites and formation of surface carbonates, CO32−; (2) interaction of CO2 with “free” electrons trapped at low-coordinated sites of the MgO surface with formation of adsorbed CO2−; and (3) interaction of CO2 with (H+)(e−) centers and formation of CO2− species bound near an adsorbed proton (OH group). CO2 prefers to form surface carbonates and only once most or all the low-coordinated O sites of the surface have reacted it will interact with trapped electrons to form CO2−. Several adsorption sites...

A theoretical study of cis–trans isomerisation in H-ZSM5: probing the impact of cluster size and zeolite framework on energetics and structure

In this study the results from a series of calculations are reported that probe the influence of the QM cluster size and the extended framework treatment in ONIOM calculations. This is done by comparing the differences in the structures and energetics obtained during simulations of cis-trans isomerisation of butene in H-ZSM-5 at varying level of accuracy. Seven different models have been employed; 3T, 5T and 10T DFT cluster models, and to more effectively encode the extended framework of ZSM-5; 3T:46T, 5T:46T, 10T:46T DFT:MM ONIOM models, and a 46T DFT cluster model. The results show that irrespective of the exact QM cluster size, relatively small gasphase clusters show clear limitations due to the neglect of the extended framework. In particular, the structural and electronic implications of using the different zeolite models have been rigorously assessed using the multivariate statistical method principal components analysis (PCA).

Cluster Model DFT Study of CO Adsorption to Gallium Ions in Ga/HZSM-5

Cluster model DFT calculations of CO adsorption on various possible forms of gallium in Ga/HZSM-5 zeolites have been performed. CO was found to only weakly interact with Ga+, (GaO)+, and (Ga(OH)2-nHn)+ (n = 1, 2) cationic clusters. The resulting shifts of the CO stretching frequency (ΔνCO) are only very small. On the other hand, CO coordination to small mononuclear and binuclear Ga3+ hydride/hydroxide/oxide species results in positive shifts in the stretching frequency in the range ΔνCO = 20−40 cm-1. Larger shifts (ΔνCO = 70−90 cm-1) are associated with CO coordination to Ga ions at the corners of small three-dimensional Ga−oxide clusters. The experimentally observed changes in the infrared spectrum of adsorbed CO over Ga/HZSM-5 zeolites upon reductive and oxidative treatments are interpreted with these insights. Possibilities for the formation of such polynuclear oxide species in the zeolite micropore space are discussed. On the basis of recent literature insights, we suggest that large shifts derive fro...

Vibrational Stark tuning rates from periodic DFT calculations: CO/Pt(1 1 1)

DFT periodic calculations have been used to study the influence of an external electric field on the adsorption of CO on Pt(1 1 1). Particular attention has been focused on the determination of the CO and metal-CO vibrational Stark tuning rates. Stark tuning rates have been calculated at various CO coverages; a linear dependence between the CO Stark tuning rate and the CO surface coverage has been found. We have calculated a value of 68.94 cm −1/(V/Å) for the zero-coverage limit CO Stark tuning rate, in good agreement with the experimental value of 75 ± 9 cm −1/(V/Å). Like the CO Stark tuning rate, the metal-CO vibrational Stark tuning rate also increases as CO surface coverage decreases. In addition, we have found (at 0.25 ML) that the CO Stark tuning rate is similar at different adsorption sites, being only slightly larger at high-coordinated sites. CO vibrational Stark tuning rates of 45.58, 47.96, 47.61 and 48.49 cm −1/(V/Å) have been calculated for ontop, bridge, hcp and fcc hollow sites, respectively. Calculations at high coverage using a (2 × 2)-3CO model yield a CO Stark tuning rate of 21.08 and 25.93 cm −1/(V/Å) for ontop and three-fold hollow CO, respectively. These results show that the CO Stark tuning rate for CO adsorbed at high coordinated sites is only slightly larger than that at ontop sites. This result is in contradiction with experiments, which reported larger CO Stark tuning rates at high-coordinates sites than at ontop sites. Furthermore, the calculated metal-CO stretch is larger for ontop sites than for high-coordinated sites; this result is in disagreement with previous DFT cluster model calculations. Unfortunately, there is not experimental information available to support either result. Finally, we have also studied the CO adsorption site preference dependence on electric fields. We have found that CO adsorbs preferentially at high coordinated sites at more negative fields, and at ontop sites at more positive fields, in agreement with previous experiments and DFT cluster model calculations.

Partially Hydroxylated Polycrystalline Ionic Oxides: A New Route toward Electron-Rich Surfaces

Charge traps at the surface of oxide materials play a fundamental role in various chemical processes, such as the activation of supported metal clusters. In this study, combining electron paramagnetic resonance with cluster model DFT calculations, we show that excess electrons at the surface of MgO, CaO, and SrO polycrystalline materials can be generated by preparing weakly hydroxylated surfaces followed by deposition of small amounts of alkali metals. The residual OH groups present on specific sites of the partially dehydroxylated surface act as stable traps for electrons donated by the alkali metal (Na in this case) which forms a Na+ ion distant from the trapped electron. This process results in the formation of thermally stable (H+)(e-) color centers at the surface of the oxide. The procedure could be of interest for the stabilization and activation of supported metal nanoparticles with potential use in catalysis.

Oxygen vacancies and peroxo groups on regular and low-coordinated sites of MgO, CaO, SrO, and BaO surfaces

The formation of an oxygen vacancy and the simultaneous re-adsorption of an oxygen atom on regular and low-coordinated (LC) sites (edges and corners) of the surface of alkaline-earth oxides with cubic rock salt structure, MgO, CaO, SrO, and BaO, has been investigated using DFT cluster model calculations. The process corresponds to the formation of a surface Frenkel defect when the vacancy formation energy is partially compensated by the energy gained in the formation of a peroxo group. The structural and electronic properties of vacancies and peroxo groups along the series of alkaline-earth oxides have been analyzed. We found that the role of low-coordinated sites on the surface chemistry of alkaline-earth oxides is of crucial importance for MgO, but decreases for the heavier members. For instance, on BaO the formation of a peroxo group is practically site-insensitive. This is not the case of the vacancy formation, which is always favored on the low-coordinated sites.

Nature of the Chemical Bond between Metal Atoms and Oxide Surfaces: New Evidences from Spin Density Studies of K Atoms on Alkaline Earth Oxides

We have studied the interaction of K atoms with the surface of polycrystalline alkaline-earth metal oxides (MgO, CaO, SrO) by means of CW- and Pulsed-EPR, UV-Vis-NIR spectroscopies and DFT cluster model calculations. The K adsorption site is proposed to be an anionic reverse corner formed at the intersection of two steps, where K binds by more than 1 eV, resulting in thermally stable species up to about 400 K. The bonding has small covalent and large polarization contributions, and the K atom remains neutral, with one unpaired electron in the valence shell. The interaction results in strong modifications of the K electronic wave function which are directly reflected by the hyperfine coupling constant, (K)a(iso). This is found to be a very efficient "probe" to measure the degree of metal-oxide interaction which directly depends on the substrate basicity. These results provide an original and general model of the early stages of the metal-support interaction in the case of ionic oxides.

Reactivity of low-coordinated MgO anions towards CO: A DFT study of (C nO n+1 ) 2− polymeric species

The reactivity of low-coordinated anions of MgO towards CO has been studied by means of ab initio cluster model DFT calculations. Differently from MgO terraces, where the O 2− anions are totally unreactive, oxide anions at step, edge and corner sites exhibit a very high basicity and reactivity towards CO. The reaction: [O LC(CO) n−1 ] 2− (s) + CO (g) → [O LC(CO) n ] 2− (s) leads to the formation of polymeric (C n O n+1 ) 2− species, where n goes from 1 to 5. The reaction is non-activated and exothermic; only the formation of the tetramer appears to be nearly thermoneutral. The formation of the hexamer ( n = 6) is thermodynamically unfavorable. For each value of n, several isomers have been considered. The vibrational properties of the [O LC(CO) n ] 2− surface complexes have been computed and used to interpret the low-temperature infrared spectra obtained in the group of Zecchina [G. Spoto, E.N. Gribov, G. Ricchiardi, A. Damin, D. Scarano, S. Bordiga, C. Lamberti, A. Zecchina, Prog. Surf. Sci. 76 (2004) 71].