The local electron attachment energy and the electrostatic potential as descriptors of surface-adsorbate interactions.

Two local reactivity descriptors computed by Kohn-Sham density functional theory (DFT) are used to predict and rationalize interactions of nucleophilic molecules (exemplified by CO and H2O) with transition metal (TM) and oxide surfaces. The descriptors are the electrostatic potential, VS(r), and the local electron attachment energy, ES(r), evaluated on surfaces defined by the 0.001 e Bohr-3 isodensity contour. These descriptors have previously shown excellent abilities to predict regioselectivity and rank molecular as well as nanoparticle reactivities and interaction affinities. In this study, we generalize the descriptors to fit into the framework of periodic DFT computations. We also demonstrate their capabilities to predict local surface propensity for interaction with Lewis bases. It is shown that ES(r) and VS(r) can rationalize the interaction behavior of TM oxides and of fcc TM surfaces, including low-index, stepped and kinked surfaces spanning a wide range of interaction sites with varied coordination environments. Broad future applicability in surface science is envisaged for the descriptors, including heterogeneous catalysis and electrochemistry.

Adsorption of Hydrogen Sulfide, Hydrosulfide and Sulfide at Cu(110) - Polarizability and Cooperativity Effects. First Stages of Formation of a Sulfide Layer.

Understanding the surface site preference for single adsorbates, the interactions between adsorbates, how these interactions affect surface site specificity in adsorption and perturb the electronic states of surfaces is important for rationalizing the structure of interfaces and the growth of surface products. Herein, using density functional theory (DFT) calculations, we investigated the adsorption of H2 S, HS and, S onto Cu(110). The surface site specificity observed for single adsorbates can be largely affected by the presence of other adsorbates, especially S that can affect the adsorption of other species even at distances of 13 Å. The large supercell employed with a surface periodicity of (6×6) allowed us to safely use the Helmholtz method for the determination of the dipole of the surface-adsorbate complex at low adsorbate coverages. We found that the surface perturbation induced by S can be explained by the charge transfer model, H2 S leads to a perturbation of the surface that arises mostly from Pauli exclusion effects, whereas HS shows a mix of charge transfer and Pauli exclusion effects. These effects have a large contribution to the long range adsorbate-adsorbate interactions observed. Further support for the long range adsorbate-adsorbate interactions are the values of the adsorption energies of adsorbate pairs that are larger than the sum of the adsorption energies of the single adsorbates that constitute the pair. This happens even for large distances and thus goes beyond the H-bond contribution for the H-bond capable adsorbate pairs. Exploiting this knowledge we investigated two models for describing the first stages of growth of a layer of S-atoms at the surface: the formation of islands versus the formation of more homogeneous surface distributions of S-atoms. We found that for coverages lower than 0.5 ML the S-atoms prefer to cluster as islands that evolve to stripes along the [1 1‾ 0] direction with increasing coverage. At 0.5 ML a homogeneous distribution of S-atoms becomes more stable than the formation of stripes. For the coverage equivalent to 1 ML, the formation of two half-monolayers of S-atoms that disrupt the Cu-Cu bonds between the first and second layer is more favorable than the formation of 1 ML homogeneous coverage of S-atoms. Here the S-Cu bond distances and geometries are reminiscent of pyrite, covellite, and to some extent chalcocite. The small energy difference of ≈0.1 eV that exists between this structure and the formation of 1 ML suggests that in a real system at finite temperature both structures may coexist leading to a structure with even lower symmetry.

σ-Holes and σ-lumps direct the Lewis basic and acidic interactions of noble metal nanoparticles: introducing regium bonds.

Using local DFT-based probes for electrostatic as well as charge transfer/polarization interactions, we are able to characterize Lewis basic and acidic sites on copper, silver and gold nanoparticles. The predictions obtained using the DFT-probes are compared to the interaction energies of the electron donating (CO, H2O, NH3 and H2S) and the electron accepting (BH3, BF3, HCl [H-down] and Na+) compounds. The probes include the local electron attachment energy [E(r)], the average local ionization energy [I(r)], and the electrostatic potential [V(r)] and are evaluated on isodensity surfaces located at distances corresponding to typical interaction distances. These probes have previously been successful in characterizing molecular interactions. Good correlations are found between Lewis acidity and maxima in V(r), appearing as a consequence of σ-holes, as well as minima in E(r), of the noble metal nanoparticles. Similarly are Lewis basic sites successfully described by surface minima in V(r) and I(r); the former are indicative of σ-lumps, i.e. regions of enhanced σ-density. The investigated probes are anticipated to function as reliable tools in nanoparticle reactivity and interaction characterization, and may act as suitable descriptors in large-scale screenings for materials of specific properties, e.g. in heterogeneous catalysis. Because of the similarity between the noble metal nanoparticle's interactions with Lewis bases and the concepts of halogen and hydrogen bonding, a new class of bonds is introduced - regium bonds - taking place between a σ-hole of a Cu, Ag or Au compound and an electron donor.

Molecular and dissociative adsorption of water and hydrogen sulfide at perfect and defective Cu(110) surfaces.

We performed a density functional theory (DFT) investigation of the molecular and dissociative adsorption of H2O and H2S at perfect and defective Cu(110) surfaces described using supercells with c(6 × 6) periodicity. The defective surface consists of a terrace surrounded by pits. We found considerable differences in adsorption modes and energies for H2O and H2S. At the defective Cu(110) surface, monomers of H2O and H2S preferentially adsorb at the terrace site and molecular adsorption of H2O is significantly more favorable than that of H2S. For dissociative adsorption however, the sulfur species are considerably more stable than the oxygen species. For monolayer (ML) coverages, there are small differences in the molecular adsorption energies for H2O and H2S. However, for the formation of 1 ML of HO and 1 ML of HS from 1 ML of H2O and 1 ML of H2S, respectively, with the release of H2(g), the differences are very large. The formation of 1 ML HO at the perfect Cu(110) surface is endoergic, while at the defective Cu(110) surface it is exoergic by -0.6 eV. For high coverages, H2S forms stacked half-monolayers that interact with each other via a complex hydrogen bond network with a strength per H2S molecule of -0.140 eV per H2S and -0.120 eV per H2S for H2S located in the underlayer and overlayer, respectively. The large distances between hydrogen bonded H2S molecules explain the preference for the formation of the two stacked half-monolayers of H2S instead of a single monolayer as it happens with H2O. Additionally, the formation of 1 ML of HS does not occur because of the spontaneous splitting of some H-S bonds resulting in surface bound HS and S and H2S molecules. Extensive surface reconstruction and relaxation accompanies adsorption of the sulfur adsorbates. Such reconstructions with outwards pull of Cu atoms can be at the origin of the weak adhesion of sulfide films that explains the release of CuS particles from copper sulfide films at copper surfaces. Overall, the surface defects here investigated induce non-linear effects in the molecular and dissociative adsorption energies of different O and S adsorbates.

Searching for the thermodynamic limit--a DFT study of the step-wise water oxidation of the bipyramidal Cu7 cluster.

Oxidative degradation of copper in aqueous environments is a major concern in areas such as catalysis, electronics and construction engineering. A particular challenge is to systematically investigate the details of this process for non-ideal copper surfaces and particles under the conditions found in most real applications. To this end, we have used hybrid density functional theory to study the oxidation of a Cu7 cluster in water solution. Especially, the role of a large water coverage is explored. This has resulted in the conclusion that, under atmospheric H2 pressures, the thermodynamically most favored state of degradation is achieved upon the generation of four H2 molecules (i.e. Cu7 + 8H2O → Cu7(OH)8 + 4H2) in both condensed and gas phases. This state corresponds to an average oxidation state below Cu(I). The calculations suggest that the oxidation reaction is slow at ambient temperatures with the water dissociation as the rate-limiting step. Our findings are expected to have implication for, among other areas, the copper catalyzed water-gas shift reaction, and for the general understanding of copper corrosion in aqueous environments.

Mechanistic insights into copper-catalyzed Sonogashira-Hagihara-type cross-coupling reactions: sub-mol% catalyst loadings and ligand effects.

An efficient catalytic system for Sonogashira-Hagihara-type reactions displaying ligand acceleration in the copper-catalyzed formation of C(sp²)-C(sp) bonds is described. The structure of the ligand plays a key role for the coupling efficiency. Various copper sources show excellent catalytic activity, even in sub-mol% quantities. A wide variety of substituents is tolerated in the substrates. Mechanistic details have been revealed by kinetic measurements and DFT calculations.

Reactivity of metal oxide clusters with hydrogen peroxide and water--a DFT study evaluating the performance of different exchange-correlation functionals.

We have performed a density functional theory (DFT) investigation of the interactions of H2O2, H2O and HO radicals with clusters of ZrO2, TiO2 and Y2O3. Different modes of H2O adsorption onto the clusters were studied. In almost all the cases the dissociative adsorption is more exothermic than molecular adsorption. At the surfaces where H2O has undergone dissociative adsorption, the adsorption of H2O2 and the transition state for its decomposition are mediated by hydrogen bonding with the surface HO groups. Using the functionals B3LYP, B3LYP-D and M06 with clusters of 26 and 8 units of ZrO2, the M06 functional performed better than B3LYP in describing the reaction of decomposition of H2O2 and the adsorption of H2O. Additionally, we investigated clusters of the type (ZrO2)2, (TiO2)2 and (Y2O3) and the performance of the functionals B3LYP, B3LYP-D, B3LYP*, M06, M06-L, PBE0, PBE and PWPW91 in describing H2O2, H2O and HO˙ adsorption and the energy barrier for decomposition of H2O2. The trends obtained for HO˙ adsorption onto the clusters are discussed in terms of the ionization energy of the metal cation present in the oxide. In order to correctly account for the existence of an energy barrier for the decomposition of H2O2, the functional used must include Hartree-Fock exchange. Using minimal cluster models, the best performance in describing the energy barrier for H2O2 decomposition was obtained with the M06 and PBE0 functionals - the average absolute deviations from experiments are 6 kJ mol(-1) and 5 kJ mol(-1) respectively. With the M06 functional and a larger monoclinic (ZrO2)8 cluster model, the performance is in excellent agreement with experimental data. For the different oxides, PBE0 was found to be the most effective functional in terms of performance and computational time cost.

Computational design of a Diels-Alderase from a thermophilic esterase: the importance of dynamics.

A novel computational Diels-Alderase design, based on a relatively rare form of carboxylesterase from Geobacillus stearothermophilus, is presented and theoretically evaluated. The structure was found by mining the PDB for a suitable oxyanion hole-containing structure, followed by a combinatorial approach to find suitable substrates and rational mutations. Four lead designs were selected and thoroughly modeled to obtain realistic estimates of substrate binding and prearrangement. Molecular dynamics simulations and DFT calculations were used to optimize and estimate binding affinity and activation energies. A large quantum chemical model was used to capture the salient interactions in the crucial transition state (TS). Our quantitative estimation of kinetic parameters was validated against four experimentally characterized Diels-Alderases with good results. The final designs in this work are predicted to have rate enhancements of ≈ 10(3)-10(6) and high predicted proficiencies. This work emphasizes the importance of considering protein dynamics in the design approach, and provides a quantitative estimate of the how the TS stabilization observed in most de novo and redesigned enzymes is decreased compared to a minimal, 'ideal' model. The presented design is highly interesting for further optimization and applications since it is based on a thermophilic enzyme (T (opt) = 70 °C).

Envisioning an enzymatic Diels-Alder reaction by in situ acid-base catalyzed diene generation.

We present and evaluate a new and potentially efficient route for enzyme-mediated Diels-Alder reactions, utilizing general acid-base catalysis. The viability of employing the active site of ketosteroid isomerase is demonstrated.

Mechanistic insights into the stepwise Diels-Alder reaction of 4,6-dinitrobenzofuroxan.

The stepwise Diels-Alder reaction between 1-trimethylsiloxy-1,3-butadiene and 4,6-dinitrobenzofuroxan is explored using state-of-the-art computational methods. The results support a stepwise mechanism via a persistent intermediate, however, not the one previously reported (Lakhdar et al., Chem. Eur. J.2007, 16, 5681) but a heterocyclic adduct. The novel DFT functional M062X and the SCS-MP2 method were essential to reproduce a reasonable potential energy surface for this challenging system.

On the formation of hydrogen gas on copper in anoxic water.

Hydrogen gas has been detected in a closed system containing copper and pure anoxic water [P. Szakalos, G. Hultquist, and G. Wikmark, Electrochem. Solid-State Lett. 10, C63 (2007) and G. Hultquist, P. Szakalos, M. Graham, A. Belonoshko, G. Sproule, L. Grasjo, P. Dorogokupets, B. Danilov, T. Aastrup, G. Wikmark, G. Chuah, J. Eriksson, and A. Rosengren, Catal. Lett. 132, 311 (2009)]. Although bulk corrosion into any of the known phases of copper is thermodynamically forbidden, the present paper shows how surface reactions lead to the formation of hydrogen gas in limited amounts. While water cleavage on copper has been reported and investigated before, formation of molecular hydrogen at a single-crystal Cu[100] surface is here explored using density functional theory and transition state theory. It is found that although solvent catalysis seems possible, the fastest route to the formation of molecular hydrogen is the direct combination of hydrogen atoms on the copper surface. The activation free energy (ΔG(s)(‡)(f)) of hydrogen formation in condensed phase is 0.70 eV, which corresponds to a rate constant of 10 s(-1) at 298.15 K, i.e., a relatively rapid process. It is estimated that at least 2.4 ng hydrogen gas could form per cm(2) on a perfect copper surface.

Designing a new Diels-Alderase: a combinatorial, semirational approach including dynamic optimization.

A computationally inexpensive design strategy involving 'semirational' screening for enzymatic catalysis is presented. The protocol is based on well-established computational methods and represents a holistic approach to the catalytic process. The model reaction studied here is the Diels-Alder, for which a successful computational design has recently been published (Siegel, J. B. et al. Science 2010, 329, 309-313). While it is a leap forward in the field of computational design, the focus on designing only a small fraction of the active site gives little control over dynamics. Our approach explicitly incorporates mutagenesis and the analysis of binding events and transition states, and a promising enzyme-substrate candidate is generated with relatively little effort. We estimate catalytic rate accelerations of up to 105.

Theoretical insights into heme-catalyzed oxidation of cyclohexane to adipic acid.

Adipic acid is a key compound in the chemical industry, where it is mainly used in the production of polymers. The conventional process of its generation requires vast amounts of energy and, moreover, produces environmentally deleterious substances. Thus, there is interest in alternative ways to gain adequate amounts of adipic acid. Experimental reports on a one-pot iron-catalyzed conversion of cyclohexane to adipic acid motivated a theoretical investigation based on density functional theory calculations. The process investigated is interesting because it requires less energy than contemporary methods and does not produce environmentally harmful side products. The aim of the present contribution is to gain insight into the mechanism of the iron-catalyzed cyclohexane conversion to provide a basis for the further development of this process. The rate-limiting step of the process is discussed, but considering the accuracy of the calculations, it is difficult to ensure whether the rate-limiting step is in the substrate oxidation or in the generation of the catalytically active species. It is shown that the slowest step in the substrate oxidation is the conversion of cyclohexanol to cyclohexane-1,2-diol. Hydrogen-atom transfer from one of the OH groups of cyclohexane-1,2-diol makes the intradiol cleavage occur spontaneously.

On the mechanism of ruthenium-catalyzed formation of hydrogen from alcohols: a DFT study.

The mechanism of the ruthenium-catalyzed dehydrogenation of methanol has been investigated by using three DFT-based methods. Three pathways were considered in which the ruthenium catalyst was ligated by either two or three phosphine ligands. Dispersion interactions, which are not described by the popular B3LYP functional, were taken into account by using the dispersion-corrected B3LYP-D and M06 density functionals. These interactions were found to be important in the description of reaction steps that involved ligand/substrate/product association with or dissociation from the catalyst. In line with experimental results, the resting state of the catalyst was predicted to be a ruthenium trihydride complex. It is shown that the dehydrogenation reaction preferentially proceeds through pathways in which the catalyst is ligated by two phosphine ligands. The catalytic cycle of the dehydrogenation process involves an intermolecular proton transfer from the methanol substrate to the catalyst followed by the release of dihydrogen. Rate-determining ß-hydride elimination from the resulting methoxide species then regenerates the resting state of the catalyst and completes the catalytic cycle. The overall free-energy barriers of 29.6-31.4 kcal mol(-1) predicted by the three density functionals are in good agreement with the experimentally observed reaction rate of 6 h(-1) at 423 K.

Observed enhancement of the reactivity of a biomimetic diiron complex by the addition of water - mechanistic insights from theoretical modeling.

The biomimetic diiron complex [Fe(III)Fe(IV)(mu-O)(2)(5-Me(3)-TPA)(2)](ClO(4))(3) (TPA = tris(2-pyridylmethyl)amine) has been found to be capable of oxidizing 9,10-dihydroanthracene in a solution of acetonitrile. Addition of water up to 1 M makes the reaction 200 times faster, suggesting that the water molecule in some way activates the catalyst for more efficient substrate oxidation. It is proposed that the enhanced reactivity results from the coordination of a water molecule to the iron(III) half of the complex, converting the bis-mu-oxo structure of the diiron complex to a ring-opened form where one of the bridging oxo groups is transformed into a terminal oxo group on iron(IV). The suggested mechanism is supported by DFT (B3LYP) calculations and transition state theory. Two different computational models of the diiron complex are used to model the hydroxylation of cyclohexane to cyclohexanol. Model has a bis-mu-oxo diiron core (diamond core) while model represents the "open core" analogue with one bridging mu-oxo group, a terminal oxo ligand on iron(IV), and a water molecule coordinated to iron(III). The computational results clearly suggest that the terminal oxo group is more reactive than the bridging oxo group. The free energy of activation is 7.0 kcal mol(-1) lower for the rate limiting step when the oxidant has a terminal oxo group than when both oxo groups are bridging the irons.

Quantifying the effects of the self-interaction error in density functional theory: when do the delocalized states appear? II. Iron-oxo complexes and closed-shell substrate molecules.

Effects of the self-interaction error (SIE) in approximate density functional theory have several times been reported and quantified for the dissociation of charged radicals, charge transfer complexes, polarizabilities, and for transition states of reactions involving main-group molecules. In the present contribution, effects of the SIE in systems composed of a catalytic transition metal complex and a closed-shell substrate molecule are investigated. For this type of system, effects of the SIE have not been reported earlier. It is found that although the best density functionals (e.g., B3LYP) are capable of accurate predictions of structure, thermodynamics, and reactivity of such systems, there are situations and systems for which the magnitude of the SIE can be large, and for which the effects can be severe for the modeling of chemical reactivity. The largest energetic effect reported here is the artificial stabilization of a catalyst-substrate complex by as much as 18 kcal/mol. Also, the disappearance of significant energy barriers for hydrogen atom transfer in certain systems are reported. In line with earlier work, it is found that the magnitude of the SIE is related to the energetics of electron transfer between the metal catalyst and the substrate molecule. It is suggested that these problems might be circumvented by the inclusion of counterions or point charges that would alter the energetics of electron transfer. It is also pointed out that the effects of SIE in the modeling of transition metal reactivity need to be investigated further.

O-O bond cleavage in dinuclear peroxo complexes of iron porphyrins: a quantum chemical study.

To gain insight into the mechanisms of O2 activation and cleavage in metalloenzymes, biomimetic metal complexes have been constructed and experimentally characterized. One such model complex is the dinuclear peroxo complex of iron porphyrins observed at low temperature in a non-coordinating solvent. The present theoretical study examines the O-O bond cleavage in these complexes, experimentally observed to occur either at increased temperature or when a strongly coordinating base is added. Using hybrid density functional theory, it is shown that the O-O bond cleavage always occurs in a state where two low-spin irons (S = +/-1/2) are antiferromagnetically coupled to a diamagnetic state. This state is the ground state when the strong base is present and forms an axial ligand to the free iron positions. In contrast, without the axial ligands, the ground state of the dinuclear peroxo complex has two high-spin irons (S = +/-5/2) coupled antiferromagnetically. Thus, the activation barrier for O-O bond cleavage is higher without the base because it includes also the promotion energy from the ground state to the reacting state. It is further found that this excitation energy, going from 10 unpaired electrons in the high-spin case to 2 in the low-spin case, is unusually difficult to determine accurately from density functional theory because it is extremely sensitive to the amount of exact exchange included in the functional.

Density functional study of the O2 binding to [CuI(TPAR)]+ (TPA = tris(2-pyridylmethyl)amine) in THF and EtCN.

Density functional theory using the B3LYP hybrid functional has been employed to study the formation of [Cu(II)(TPA(H))(O2-)]+ and [Cu(II)(TPA(MeO))(O2-)]+ (TPA = tris(2-pyridylmethyl)amine) in two different solvents, THF and EtCN. The thermodynamics of solvent coordination as well as that of the overall reactions with O2 has been computed. The formations of [Cu(II)(TPA(H))(O2-)]+ in THF and of [Cu(II)(TPA(MeO))(O2-)]+ in both THF and EtCN are found to be initiated from the [Cu(I)(TPA(R))]+ species, that is, the Cu complex possessing an empty coordination site. In contrast, the formation of [Cu(II)(TPA(H))(O2-)]+ in EtCN is found to be initiated from the [Cu(I)(TPA(H))(EtCN)]+ species, that is, one solvent molecule being coordinated to Cu(I). In general, good agreement is found between theoretical and experimental results. The high accuracy of the B3LYP functional in reproducing experimental thermodynamic data for the present type of transition metal complexes is demonstrated by the fact that the differences between measured and computed thermodynamic parameters (DeltaG degree, DeltaH degrees , and -TDeltaS degree, in most cases are less than 2.0 kcal mol(-1). An attempt was made to investigate the kinetics of the formation of [Cu(II)(TPA(H))(O2-)]+ in THF and EtCN. Computed free energies of activation, DeltaG, are in good agreement with experimental results. However, an analysis of the partitioning of the free energy barriers in enthalpic and entropic contributions indicates that the computationally studied reaction pathway might differ from the one observed experimentally.