Electronic structures of 4d transition metal monoxides by density functional theory

Bond distances, dissociation energies, ionization potentials and electron affinities of 4d transition metal monoxides from YO to CdO and their positive and negative ions were studied by use of density functional methods B3LYP, BLYP, B3PW91, BPW91, B3P86, BP86, SVWN, MPW1PW91 and PBE1PBE. It was found that calculated properties are highly dependent on the functionals employed, especially for dissociation energy. For most neutral species, pure density functionals BLYP, BPW91 and BP86 have good performance in predicting dissociation energy than hybrid density functionals B3LYP, B3PW91 and B3P86. In addition, BLYP gives the largest bond distance compared with other density functional methods, while SVWN gives shortest bond distance, largest dissociation energy and electron affinity. For the ground state, the spin multiplicity of the charged species can be obtained by +/- 1 of their corresponding neutral species.

Active site structure of NO decomposition on perovskite(-like) oxides: An investigation from experiment and density functional theory

Active site structure for NO decomposition carried out on perovskite-like oxides were discussed based on the N-2 yield measured from LaSrNi1-x,AlxO4 with different B-site cations and from La2-ySryCuO4 with different crystal phases. Results show that the active site contains two oxygen vacancies, two transition metals, and one lattice-oxygen, with the oxygen vacancy locating on the apex of MO6 octahedron, and the lattice oxygen locating between the two transition metals (i.e., M-O-M plane). Density functional theory (DFT) analysis to the structure shows that this new active site is the most active structure for NO adsorbing, and hence, for NO decomposition. The similar trend of the relative energies that are required for the formation of oxygen vacancies with f form (calculated from DFT), the amount of oxygen vacancies, and the activities (N-2 yield) certifies this result further.

Electronic structures of hafnium dimer and trimer by density functional theory

Equilibrium geometries, vibrational frequencies and dissociation energies of hafnium dimer and trimer were studied by density functional methods B3LYP, BLYP, B3PW91, BHLYP, BP86, B3P86, mPW1PW91 and PBE1PBE. The results indicate that singlet is the ground state both for hafnium dimer and for trimer. For hafnium dimer, the calculated bond distance is less sensitive to the methods used. Except at BHLYP level, the calculated vibrational frequency is comparable to the experimental value. For hafnium trimer, equilateral triangle with D-3h symmetry is slightly favored compared with isosceles triangle with C-2v, symmetry except at BHLYP level. This conclusion is in agreement with experiment in which the ground state of Hf-3 is fluxional and low-spin or closed shell is preferred.

Experimental and density functional theory study of the vibrational properties of 2-mercaptobenzimidazole in interaction with gold

The vibrational properties of the 2-mercaptobenzimidazole (MBI) molecule in interaction with gold were examined by a combined approach of FTIR measurements and density functional theory (DFT). A complete assignment of the 42 normal modes of MBI has been performed on the basis of DFT calculations at the B3PW91 level in complement to the Raman and FTIR spectra. Calculations demonstrated that, on the deprotonated MBI molecule, the negative charge is localized on the sulfur atom, favoring the formation of a gold-sulfur bond upon reaction of MBI with gold. This was confirmed by the very good agreement between the calculated spectrum and the experimental spectra of different gold-MBI compounds, indicating that the vibrational properties of adsorbed MBI are chiefly determined by the coordination through the sulfur atom. © 2006 American Chemical Society.

Can density functional theory (DFT) be used as an aid to a deeper understanding of tandem mass spectrometric fragmentation pathways?

Prediction of tandem mass spectrometric (MS/MS) fragmentation for non-peptidic molecules based on structure is of immense interest to the mass spectrometrist. If a reliable approach to MS/MS prediction could be achieved its impact within the pharmaceutical industry could be immense. Many publications have stressed that the fragmentation of a molecular ion or protonated molecule is a complex process that depends on many parameters, making prediction difficult. Commercial prediction software relies on a collection of general heuristic rules of fragmentation, which involve cleaving every bond in the structure to produce a list of 'expected' masses which can be compared with the experimental data. These approaches do not take into account the thermodynamic or molecular orbital effects that impact on the molecule at the point of protonation which could influence the potential sites of bond cleavage based on the structural motif. A series of compounds have been studied by examining the experimentally derived high-resolution MS/MS data and comparing it with the in silico modelling of the neutral and protonated structures. The effect that protonation at specific sites can have on the bond lengths has also been determined. We have calculated the thermodynamically most stable protonated species and have observed how that information can help predict the cleavage site for that ion. The data have shown that this use of in silico techniques could be a possible way to predict MS/MS spectra. Copyright (C) 2009 John Wiley & Sons, Ltd.

General rules for predicting where a catalytic reaction should occur on metal surfaces: A density functional theory study of C-H and C-O bond breaking/making on flat, stepped, and kinked metal surfaces

To predict where a catalytic reaction should occur is a fundamental issue scientifically. Technologically, it is also important because it can facilitate the catalyst's design. However, to date, the understanding of this issue is rather limited. In this work, two types of reactions, CH4 CH3 + H and CO C + 0 on two transition metal surfaces, were chosen as model systems aiming to address in general where a catalytic reaction should occur. The dissociations of CH4 - CH3 + H and CO --> C + O and their reverse reactions on flat, stepped, and kinked Rh and Pd surfaces were studied in detail. We find the following: First, for the CH4 Ch(3) + H reaction, the dissociation barrier is reduced by similar to0.3 eV on steps and kinks as compared to that on flat surfaces. On the other hand, there is essentially no difference in barrier for the association reaction of CH3 + H on the flat surfaces and the defects. Second, for the CO C + 0 reaction, the dissociation barrier decreases dramatically (more than 0.8 eV on Rh and Pd) on steps and kinks as compared to that on flat surfaces. In contrast to the CH3 + H reaction, the C + 0 association reaction also preferentially occurs on steps and kinks. We also present a detailed analysis of the reaction barriers in which each barrier is decomposed quantitatively into a local electronic effect and a geometrical effect. Our DFT calculations show that surface defects such as steps and kinks can largely facilitate bond breaking, while whether the surface defects could promote bond formation depends on the individual reaction as well as the particular metal. The physical origin of these trends is identified and discussed. On the basis of our results, we arrive at some simple rules with respect to where a reaction should occur: (i) defects such as steps are always favored for dissociation reactions as compared to flat surfaces; and (ii) the reaction site of the association reactions is largely related to the magnitude of the bonding competition effect, which is determined by the reactant and metal valency. Reactions with high valency reactants are more likely to occur on defects (more structure-sensitive), as compared to reactions with low valency reactants. Moreover, the reactions on late transition metals are more likely to proceed on defects than those on the early transition metals.

A Density Functional Theory Study on the Active Center of Fe-Only Hydrogenase: Characterization and Electronic Structure of the Redox States

We have carried out extensive density functional theory (DFT) calculations for possible redox states of the active center in Fe-only hydrogenases. The active center is modeled by [(H(CH(3))S)(CO)(CN(-))Fe(p)(mu-DTN)(mu-CO)Fe(d)(CO)(CN(-))(L)](z) (z is the net charge in the complex; Fe(p)= the proximal Fe, Fe(d) = the distal Fe, DTN = (-SCH(2)NHCH(2)S-), L is the ligand that bonds with the Fed at the trans position to the bridging CO). Structures of possible redox states are optimized, and CO stretching frequencies are calculated. By a detailed comparison of all the calculated structures and the vibrational frequencies with the available experimental data, we find that (i) the fully oxidized, inactive state is an Fe(II)-Fe(II) state with a hydroxyl (OH(-)) group bonded at the Fe(d), (ii) the oxidized, active state is an Fe(II)-Fe(l) complex which is consistent with the assignment of Cao and Hall (J. Am. Chem. Soc. 2001, 123, 3734), and (iii) the fully reduced state is a mixture with the major component being a protonated Fe(l)-Fe(l) complex and the other component being its self-arranged form, Fe(II)-Fe(II) hydride, Our calculations also show that the exogenous CO can strongly bond with the Fe(II)-Fe(l) species, but cannot bond with the Fe(l)-Fe(l) complex. This result is consistent with experiments that CO tends to inhibit the oxidized, active state, but not the fully reduced state. The electronic structures of all the redox states have been analyzed. It is found that a frontier orbital which is a mixing state between the e(g) of Fe and the 2pi of the bridging CO plays a key role concerning the reactivity of Fe-only hydrogenases: (1) it is unoccupied in the fully oxidized, inactive state, half-occupied in the oxidized, active state, and fully occupied in the fully reduced state; (ii) the e(g)-2pi orbital is a bonding state, and this is the key reason for stability of the low oxidation states, such as Fe(l)-Fe(l) complexes; and (iii) in the e(g)-2pi orbital more charge accumulates between the bridging CO and the Fe(d) than between the bridging CO and the Fe(p), and the occupation increase in this orbital will enhance the bonding between the bridging CO and the Fe(d), leading to the bridging-CO shift toward the Fe(d).

An insight into alkali promotion: a density functional theory study of CO dissociation on K/Rh(111)

The important role of alkali additives in heterogeneous catalysis is, to a large extent, related to the high promotion effect they have on many fundamental reactions. The wide application of alkali additives in industry does not, however, reflect a thorough understanding of the mechanism of their promotional abilities. To investigate the physical origin of the alkali promotion effect, we have studied CO dissociation on clean Rh(111) and K-covered Rh(111) surfaces using density functional theory. By varying the position of potassium atoms relative to a dissociating CO, we have mapped out the importance of different K effects on the CO dissociation reactions. The K-induced changes in the reaction pathways and reaction barriers have been determined; in particular, a large reduction of the CO dissociation barrier has been identified. A thorough analysis of this promotion effect allows us to rationalize both the electronic and the geometrical factors that govern alkali promotion effect: (i) The extent of barrier reductions depends strongly on how close K is to the dissociating CO. (ii) Direct K-O bonding that is in a very short range plays a crucial role in reducing the barrier. (iii) K can have a rather long-range effect on the TS structure, which could reduce slightly the barriers.

Understanding the dehydrogenation mechanism of tetrahydrocarbazole over palladium using a combined experimental and density functional theory approach

The mechanism of the dehydrogenation of tetrahydrocarbazole to carbazole over palladium has been examined for the first time. By use of a combination of deuterium exchange experiments and density functional theory calculations, a detailed reaction profile for the aromatization of tetrahydrocarbazole has been identified and validated by experiment. As with many dehydrogenation reactions, the initial hydrogen abstraction is found to have the highest reaction barrier. Tetrahydrocarbazole has four hydrogens which can, in principle, be cleaved initially; however, the theory and experiment show that the reaction is dominated by the cleavage of the carbon hydrogens at the carbon atoms in positions 1 and 4. The two pathways originating from these two C-H bond cleavage processes are found to have similar reaction energy profiles and both contribute to the overall reaction.

Au on (111) and (110) surfaces of CeO2: A density-functional theory study

The atomic structures of gold supported on (111) and (110) surfaces of CeO2 have been studied using density-functional theory calculations. A single Au atom is placed on three adsorption sites on the surfaces; the stoichiometric surfaces, an oxygen vacancy and a Ce-vacancy. It is found that (i) the Au adsorption energies are in the following order: E-ad(Ce-vacancy) > E-ad(O-vacancy) > E-ad(stoichiometric surface); and (ii) the Au atom adsorption on the Ce-vacancy activates O atoms nearby. One 0 atom is less stable than that in O-2 in the gas phase and another O atom is much easier to remove compared to that of the stoichiometric surfaces. These results suggest that the Au adsorption on Ce-vacancies not only creates an O-vacancy but also activates an O atom nearby. This provides a piece of direct evidence that Au adsorption on a Ce-vacancy may be responsible for some unique catalytic properties of Au/CeO2. (C) 2008 Elsevier B.V. All rights reserved.