DFT insights into competing mechanisms of guaiacol hydrodeoxygenation on a platinum cluster.

In a scenario of declining fossil resources and increasing demand for renewable and sustainable alternatives, biomass is the only source able to offer an easy and gradual transition in the use of current energy technologies based on the exploitation of carbon derivatives. Its conversion to liquid fuels has oriented our study towards the computational mechanistic analysis of the guaiacol catalytic hydrodeoxygenation, which is currently considered one of the most challenging routes for upgrading biomass-derived bio-oils. For this purpose, a subnanometric Pt10 platinum cluster was chosen as the catalyst model, with Pt as a computational reference element for catalytic hydrogenation, and guaiacol as a model compound of bio-oils. DFT calculations revealed that the energy barriers related to the cleavage of C(sp2)-O bonds in the direct deoxygenation mechanism are significantly lower (by an average of 60 kJ mol-1) than those in the deoxygenation-through-hydrogenation mechanism in which C(sp3)-O bond breaking from a saturated ring occurs. Even if the ring hydrogenation is easier in the oxygenated compound, the analysis reveals that the direct deoxygenation mechanism is favoured at all temperatures. Furthermore, the results obtained highlight that, from a thermodynamic perspective, the removal of oxygen groups preferentially occurs by the elimination of the -OCH3 fragment as methanol and then of the -OH fragment as a water molecule.

Growth of sub-nanometric palladium clusters on boron nitride nanotubes: a DFT study.

A QM/MM investigation is reported dealing with the nucleation and growth of small palladium clusters, up to Pd8, on the outer surface of a suitable model of boron nitride nanotubes (BNNTs). It is shown that BNNTs could have a template effect on the cluster growth, which is due to the interplay between Pd-N and Pd-Pd interactions as well as due to the matching of the B3N3 ring and the Pd(111) face arrangement. The values for the cluster adsorption energies reveal a relatively strong physisorption, which suggests that under particular conditions the BNNTs could be used as supports for the preparation of shape-controlled metal clusters.

N-doped carbon networks: alternative materials tracing new routes for activating molecular hydrogen.

The fragmentation of molecular hydrogen on N-doped carbon networks was investigated by using molecular (polyaromatic macrocycles) as well as truncated and periodic (carbon nanotubes) models. The computational study was focused on the ergonicity analysis of the reaction and on the properties of the transition states involved when constellations of three or four pyridinic nitrogen atom defects are present in the carbon network. Calculations show that whenever N-defects are embedded in species characterized by large conjugated π-systems, either in polyaromatic macrocycles or carbon nanotubes, the corresponding H2 bond cleavage is largely exergonic. The fragmentation Gibbs free energy is affected by the final arrangement of the hydrogen atoms on the defect and by the extension of the π-electron cloud, but it is not influenced by the curvature of the system.

Oxygen-assisted hydroxymatairesinol dehydrogenation: a selective secondary-alcohol oxidation over a gold catalyst.

Selective dehydrogenation of the biomass-derived lignan hydroxymatairesinol (HMR) to oxomatairesinol (oxoMAT) was studied over an Au/Al(2)O(3) catalyst. The reaction was carried out in a semi-batch glass reactor at 343 K under two different gas atmospheres, namely produced through synthetic air or nitrogen. The studied reaction is, in fact, an example of secondary-alcohol oxidation over an Au catalyst. Thus, the investigated reaction mechanism of HMR oxidative dehydrogenation is useful for the fundamental understanding of other secondary-alcohol dehydrogenation over Au surfaces. To investigate the elementary catalytic steps ruling both oxygen-free- and oxygen-assisted dehydrogenation of HMR to oxoMAT, the reactions were mimicked in a vacuum over an Au(28) cluster. Adsorption of the involved molecular species--O(2), three different HMR diastereomers (namely, one SRR and two RRR forms), and the oxoMAT derivative--were also studied at the DFT level. In particular, the energetic and structural differences between SRR-HMR and RRR-HMR diastereomers on the Au(28) cluster were analyzed, following different reaction pathways for the HMR dehydrogenation that occur in presence or absence of oxygen. The corresponding mechanisms explain the higher rates of the experimentally observed oxygen-assisted reaction, mostly depending on the involved HMR diastereomer surface conformations. The role of the support was also elucidated, considering a very simple Au(28) charged model that explains the experimentally observed high reactivity of the Au/Al(2)O(3) catalyst.

Alkali-metal azides interacting with metal-organic frameworks.

Interactions between alkali-metal azides and metal-organic framework (MOF) derivatives, namely, the first and third members of the isoreticular MOF (IRMOF) family, IRMOF-1 and IRMOF-3, are studied within the density functional theory (DFT) paradigm. The investigations take into account different models of the selected IRMOFs. The mutual influence between the alkali-metal azides and the π rings or Zn centers of the involved MOF derivatives are studied by considering the interactions both of the alkali-metal cations with model aromatic centers and of the alkali-metal azides with distinct sites of differently sized models of IRMOF-1 and IRMOF-3. Several exchange and correlation functionals are employed to calculate the corresponding interaction energies. Remarkably, it is found that, with increasing alkali-metal atom size, the latter decrease for cations interacting with the π-ring systems and increase for the azides interacting with the MOF fragments. The opposite behavior is explained by stabilization effects on the azide moieties and determined by the Zn atoms, which constitute the inorganic vertices of the IRMOF species. Larger cations can, in fact, coordinate more efficiently to both the aromatic center and the azide anion, and thus stabilizing bridging arrangements of the azide between one alkali-metal and two Zn atoms in an η(2) coordination mode are more favored.

A DFT study of IRMOF-3 catalysed Knoevenagel condensation.

It has been recently reported that IRMOF-3 [Gascon et al., J. Catal, 2009, 261, 75] may behave as a basic catalyst, active in the Knoevenagel condensation. In particular, it has been shown that the basicity of aniline-like amino moieties is enhanced, along with the catalytic activity, when incorporated into MOF structures. The computational study here was aimed at finding possible atomistic explanations of the increased basicity and catalytic activity of the IRMOF-3 embedded aniline groups, experimentally claimed. It was, moreover, aimed at guessing a reaction mechanism for the IRMOF-3 catalysed Knoevenagel condensation of benzaldehyde and ethyl-cyanoacetate. Within the DFT framework we have studied structure and basicity properties of IRMOF-3 and we have analysed the energetics of the catalytic cycle as well as of possible deactivation paths, including it. The increased basicity of IRMOF-3 over other amminic catalysts has been explained via the formation of protonated conjugate derivatives, involving hydrogen-bonds and originating quasi-planar 6-term rings. Several plausible reaction steps have been moreover taken into account and a mechanism for the Knoevenagel condensation, including catalyst deactivation, has been proposed for aniline molecules and embedded aniline moieties. This allowed us to suggest that the increased IRMOF-3 activity, as a basic catalyst, should be mostly related to its water adsorption ability, preserving the properties of the catalytically active amino moieties.

Cation environment of BaCeO3-based protonic conductors II: new computational models.

Quantum chemical calculations have been carried out to simulate Y-doped BaCeO(3) derivatives. Hartree-Fock energy functional was used to study octahedral site environments embedded in a Pmcn orthorhombic framework, showing local arrangement characterized by Ce-O-Ce, Ce-O-Y, and Y-O-Y (Z-O-Ξ) configurations and including or not hydrogen close to the moieties encompassing those configurations. The latter are, in fact, representative of - and, in our modeling approach, were treated as - local arrangements that could be found in Y:BaCeO(3)-doped materials. The geometrical optimizations performed on the structural models and a detailed orbital analysis of these systems allowed us to confirm and deepen new interpretations, concerning experimental findings already reported in the literature. In particular, the bimodal distribution characterizing the Y-O first coordination shell, found by EXAFS analysis, could be attributed to a local clustering of Y atoms showing characteristic Y-O-Y arrangements. Moreover, the local charge analysis, characterizing the models containing or not hydrogen atoms, showed that the moving protons are able to dynamically change the properties of their near environment, in any case, leaving unaltered the global protonic conduction features of the material, irrespective of the kind of cation in a given Z-O-Ξ moiety.

Structural, energetic and kinetic database of catalytic reactions: Benzyl alcohol to benzaldehyde oxidation on MnO x clusters.

Data here reported are connected with the research article "Benzyl Alcohol to Benzaldehyde Oxidation on MnO x Clusters: Unraveling Atomistic Features" Gueci et al. [1]. This work described and discussed structural and energetic results, calculated by Density Functional Theory (DFT). In order to get kinetic information, DFT results were refined by an original approach, which will be shortly described in the following article. The crossed analysis of experimental and computational energetic and kinetic data allowed to (i) reconstruct the complicated lattice that connects the primary and secondary mechanisms of the reaction and (ii) identify alternative process pathways capable of by-passing parasitic mechanisms, decreasing selectivity. On the other hand, the data here presented show what is the basic information necessary to obtain the modeling of a complex process of heterogeneous catalysis. Moreover, they can be used either to verify the validity of the discussion outlined in the original article Gueci et al. [1] or as a starting point to computationally explore alternative routes and the related kinetics of the same oxidation processes, in the aim to further optimize the corresponding experimental approach.

Ultrafast Interface Charge Separation in Carbon Nanodot-Nanotube Hybrids.

Carbon dots are an emerging family of zero-dimensional nanocarbons behaving as tunable light harvesters and photoactivated charge donors. Coupling them to carbon nanotubes, which are well-known electron acceptors with excellent charge transport capabilities, is very promising for several applications. Here, we first devised a route to achieve the stable electrostatic binding of carbon dots to multi- or single-walled carbon nanotubes, as confirmed by several experimental observations. The photoluminescence of carbon dots is strongly quenched when they contact either semiconductive or conductive nanotubes, indicating a strong electronic coupling to both. Theoretical simulations predict a favorable energy level alignment within these complexes, suggesting a photoinduced electron transfer from dots to nanotubes, which is a process of high functional interest. Femtosecond transient absorption confirms indeed an ultrafast (<100 fs) electron transfer independent of nanotubes being conductive or semiconductive in nature, followed by a much slower back electron transfer (≈60 ps) from the nanotube to the carbon dots. The high degree of charge separation and delocalization achieved in these nanohybrids entails significant photocatalytic properties, as we demonstrate by the reduction of silver ions in solution. The results are very promising in view of using these "all-carbon" nanohybrids as efficient light harvesters for applications in artificial photocatalysis and photosynthesis.

DFT studies on catalytic properties of isolated and carbon nanotube supported Pd9 cluster. Part II. Hydro-isomerization of butene isomers.

The processes involved in the butene hydro-isomerization, occurring on a small palladium cluster in the presence of dissociated hydrogen, have been investigated by means of DFT and DFT/MM approaches. This study has been performed both on an isolated (unsupported) Pd(9) cluster and on the same cluster when it is supported on a portion of a single-walled armchair(6,6) carbon nanotube. The study follows another investigation which has already been published concerning the adsorption, fragmentation and diffusion of hydrogen on the same metal cluster. The main aspects involved in the parallel reaction steps of the whole hydro-isomerization mechanisms are not strongly affected by the presence of the support, which does, however, modify the energetics involved, likely due to the presence of strong metal surface interaction (SMSI) effects. Noticeably, a common step corresponding to the diffusion of one hydrogen atom is present. This diffusion step creates a characteristic semihydrogenated surface species along the occurrence of all the reaction pathways. Hence, the semihydrogenated species is a kind of molecular node able to connect the transformation pathways of the different surface species involved in the hydro-isomerization processes. Considering the energetics involved in the processes of both supported and unsupported systems and being aware of the simplification introduced in studying the same systems, it is still possible (i) to emphasize the basis importance of taking account of the support in modeling catalytic properties and (ii) to state that the models proposed here are able to capture the main characteristics of the title reaction.

Cation environment of BaCeO(3)-based protonic conductors: a computational study.

Geometry calculations were performed on pure BaCeO(3) fragments and on Y- and In-doped derivatives. HF and DFT approaches were used to investigate monoclinic and orthorhombic structures. The computational methods, structural models, and electronic structure investigation protocols were tuned taking into consideration and balancing the consistency of the results against the computational cost. The calculated structures and energetics parameter, as well as the detailed orbital analysis performed on the corresponding BaCeO(3) derivatives allowed us to explain experimental findings and to develop a procedure to study the cationic octahedral environment of doped X:BaCeO(3) (X = Y, In) and undoped BaCeO(3) protonic conductors useful to interpret experimental results and hopefully to design new experimental approaches. In detail, distances and angles of the studied materials are easily captured in the frame of the HF paradigm even by using low-level ECP basis sets. While, pure electronic-based approaches, involving the investigation of the Partial Density of States resulting from the C-Squared Population Analysis, show that the dopant species must leave unchanged, or even decrease, the local basicity of the oxygen octahedral environment in order to increase the conductivity of the BaCeO(3) derivatives. Whereas local structural changes that are not related to the basicity above affect to a less, if not null, extent the conductivity of the same derivatives.

Hydrogen Arrangements on Defective Quasi-Molecular BN Fragments.

Considering the ever-increasing interest in metal-free materials, some potential chemical applications of quasi-molecular boron nitride (BN) derivatives were tested. Specifically, the behavior of BN fragments was analyzed when given defects, producing local electron density changes, were introduced by using topological engineering approaches. The inserted structural faults were Schottky-like divacancy (BN-d) defects, assembled in the fragment frame by the subtraction of one pair of B and N atoms or Stone-Wales (SW) defects. This study is aimed at highlighting the role of these important classes of defects in BN materials hypothesizing their future use in H2-based processes, related to either (i) H2 activation or (ii) H2 production, from preadsorbed hydrogenated molecular species on BN sites. Here, it has been observed that BN species, embodying SW defects, are characterized by endothermic H2 adsorption and fragmentation phenomena in order to guess their potential use in processes based on the transformation or production of hydrogen. On the contrary, in the presence of BN-d defects, and for reasons strictly related to local structural changes occurring along with the hydrogen rearrangements on the defective BN fragments, a possible use can be inferred. Precautions must be however taken to decrease the material rigidity that could actually decrease the ability of the BN fragment to flatten. This conversely seems to be a necessary requirement to have strong exothermic effects, following the rearrangements of the H2 molecules.

Y:BaZrO3 perovskite compounds II: designing protonic conduction by using MD models.

The proton dynamics in Y-doped BaZrO(3) derivatives, in particular the different dopant environments within a Pm3m cubic framework, were studied by using classical molecular dynamics (MD) calculations. Single- and double substitution of zirconium by yttrium atoms was considered. The presence of yttrium induced variations in the surrounding oxygen sites, according to their local geometrical arrangements. The differences among such distinct oxygen sites became evident when protons interacted with them and upon changes in the temperature. So, different proton transfer pathways, which had different energy barriers, characterized the topologically different oxygen sites. The experimental proton-hopping activation energy was only reproduced in those structures in which two yttrium atoms formed a Y-O-Y arrangement, which also acted as multilevel protonic traps. Protonic conduction in these materials could be improved by avoiding such yttrium clustering, hence preventing the formation of the protonic traps.

Y:BaZrO3 perovskite compounds I: DFT study on the unprotonated and protonated local structures.

Y-doped BaZrO(3) derivatives were studied by density functional theory (DFT) to investigate the local arrangements of the octahedral sites in Pm3m cubic frameworks. Single- and double substitution of zirconium by yttrium were considered, including in the presence of a nearby oxygen vacancy. Although the structural symmetry of undoped barium zirconate was not modified after yttrium doping, the presence of yttrium induced several differences in the oxygen sites around it, according to the local geometrical arrangement of yttrium in the host matrix. As an example, the differences between such oxygen sites were shown in the presence of a proton. In this case, different stabilization energies characterized the protonated fragments. Only in those structures, in which two yttrium atoms were neighbors (i.e., formed Y-O-Y moieties), were the relative energy differences between the corresponding proton stable sites in agreement with the order of magnitude of the experimental proton-hopping activation energies. The distribution of such energy differences suggested a grouping of the oxygen atoms into three sets, which had peculiar structural features that weren't easily deducible from their topologies. The existence of proton traps was also discussed on the basis of the energy-difference distributions.

Adsorbed CO on group 10 metal fragments: a DFT study.

DFT calculations on the helicopter and cartwheel rotations of one CO molecule adsorbed at the bridge site on metal-surface fragments, characterized by two (M(8)) or three (M(14)) metal-atom layers (M = Ni, Pd, Pt) were performed by the B3LYP[LANL2DZ+6-31 g(d,p)] method, to rationalize the adsorption energetics and the steric hindrance characteristics of surface CO molecules. Potential Energy Surfaces were obtained, either fixing the C-O bond-length or allowing it to change. The behavior of the three metals, as obtained from the study of the configurational space characterizing the CO adsorption on the fragments was explained on the basis of the interaction energies involved in the different CO/M systems. The results, obtained by using the M(14) fragments and varying both the C-O and the CO/M distances, point out that the CO adsorption on the Ni fragment is stabilized by surface-configurations in which the O atom is pointing toward a metal center. At variance, C-O bond elongation and stabilization occur on Pd when the O atom is situated between two palladium atoms. The CO adsorption on Pt displays similar characteristics to those observed on the Pd systems, but with the fundamental difference caused by the destabilization of the Pt-O interactions when the O atom is situated exactly between two Pt atoms. The calculations allowed us to estimate the IR spectroscopy frequency and band-broadening of the adsorbed CO stretching by a statistic analysis on a large set of energy / bond-length computed data. Good agreement with the experimental results was obtained for all the metals, in particular concerning the frequencies. Reliable band-broadenings were also obtained for the CO/Ni and CO/Pt systems, while the lower band-broadening value for the CO/Pd system was related to the small extent of the configurational sampling space.

DFT studies on catalytic properties of isolated and carbon nanotube supported Pd(9) cluster-I: adsorption, fragmentation and diffusion of hydrogen.

The processes of adsorption, fragmentation and diffusion of hydrogen on a small palladium cluster have been investigated by means of DFT and DFT/MM approaches. These studies have been performed by considering a D(3h) symmetry Pd(9) in the isolated state as well as when supported on a portion of single-walled armchair(6,6) carbon nanotube. The hydrogen fragmentation process easily occurs on the bare Pd(9) cluster, involving energy barriers of 25-35 kJ mol(-1) and the drop in spin multiplicity on passing from the reactant to the product. The atomic hydrogen diffuses through the cluster atoms with energy barriers, which do not exceed 20 kJ mol(-1), with some positions clearly identifiable as the most stable. In the case of the palladium supported system, which is a better model to simulate experimental conditions, calculations predict that the hydrogen fragmentation barrier is reduced by ca. 15 kJ mol(-1), with respect to that of the unsupported system, while the energetics of the diffusive process is not significantly affected by the support, if the reduction of the number of sites available in the same palladium cluster, as well as their geometry, are taken into account.

Confined But-2-ene Catalytic Isomerization Inside H-ZSM-5 Models: A DFT Study.

The isomerization of cis-but-2-ene to trans-but-2-ene within a 22T H-ZSM-5 zeolite model, also in the presence of two adsorbed Pd atoms, has been studied by DFT calculations. The results obtained allow us to state that the cis/trans but-2-ene isomerization can easily proceed inside unsupported zeolite cavities. In this case, differently than in the gas phase reaction, the trans-but-2-ene is less stable than the cis-but-2-ene, when adsorbed on the zeolite inner surface. Excluding the adsorption-desorption steps, the isomerization process involves two intermediates and three transition states, whose energy content is always very low with respect to that of reagents and intermediate species. The reaction is in principle allowed also in the presence of two Pd atoms embedded inside the zeolite cavity. However, strong H-Pd interactions seem to cause higher activation energies along the formation of the involved intermediates and transition states. To evaluate the confining effects of the zeolite room on the cis/trans isomerization process, the latter has been also analyzed on protonated (Pd2H(+)) and unprotonated (Pd2) bare palladium fragments at different multiplicity states. The but-2-ene adsorption on the considered systems and the mutual influence occurring between the metal atoms and the hydrogen acidic sites at different multiplicity states have also been taken into consideration.

Comparison of different theory models and basis sets in the calculation of 13C NMR chemical shifts of natural products.

The influence of the calculation method in mimicking experimental (13)C NMR chemical shifts of 15 low-polarity natural products singularly containing 10-20 carbon atoms was investigated by employing different quantum chemistry approaches and basis sets, both in the preliminary geometry optimizations and in the following single-point (13)C GIAO calculations of the NMR chemical shifts. The geometries of the involved species were optimized at the PM3, HF, B3LYP and mPW1PW91 levels whereas the (13)C NMR parameters were determined at the HF, B3LYP and mPW1PW91 levels. Different combinations of basis sets were also tested. The consistency and efficiency of the considered combinations of geometry optimizations and GIAO (13)C NMR calculations were thoroughly checked by the analysis of statistical parameters concerning computed and experimental (13)C NMR chemical shift values.

SCSA code: applications on the cyclopeptide renieramide.

SCSA is an algorithm designed to get information on molecular conformational properties. The most stable conformers are determined by the homemade SCSA code, performing a multistep systematic conformational search, which involves energy and structure quantum chemical optimizations at low-level and high-level. The SCSA method was employed to analyze the conformational space of the in vacuo cyclopeptide renieramide at AM1 and B3LYP/6-31G(d) levels. Calculations at B3LYP level of the GIAO (13)C NMR chemical shifts were also performed on the final conformers. In fact, to validate the conformational search results experimental and calculated (13)C NMR spectra of renieramide were compared. Slight disagreements observed between experimental and calculated spectra could be attributed to solute-solvent interactions, which were not taken into account in the algorithm proposed here.

Structure validation of natural products by quantum-mechanical GIAO calculations of 13C NMR chemical shifts.

Geometry optimization and GIAO (gauge including atomic orbitals) (13)C NMR chemical shift calculations at Hartree-Fock level, using the 6-31G(d) basis set, are proposed as a tool to be applied in the structural characterization of new organic compounds, thus providing useful support in the interpretation of experimental NMR data. Parameters related to linear correlation plots of computed versus experimental (13)C NMR chemical shifts for fourteen low-polar natural products, containing 10-20 carbon atoms, were employed to assess the reliability of the proposed structures. A comparison with the hybrid B3LYP method was carried out to evaluate electron correlation contributions to the calculation of (13)C NMR chemical shifts and, eventually, to extend the applicability of such computational methods to the interpretation of NMR spectra in apolar solutions. The method was tested by studying three examples of revised structure assignments, analyzing how the theoretical (13)C chemical shifts of both correct and incorrect structures matched the experimental data.