Angeles Pulido

Report on the sixth blind test of organic crystal structure prediction methods

The results of the sixth blind test of organic crystal structure prediction methods are presented and discussed, highlighting progress for salts, hydrates and bulky flexible molecules, as well as on-going challenges.

Functional materials discovery using energy–structure–function maps

Molecular crystals cannot be designed in the same manner as macroscopic objects, because they do not assemble according to simple, intuitive rules. Their structures result from the balance of many weak interactions, rather than from the strong and predictable bonding patterns found in metal–organic frameworks and covalent organic frameworks. Hence, design strategies that assume a topology or other structural blueprint will often fail. Here we combine computational crystal structure prediction and property prediction to build energy–structure–function maps that describe the possible structures and properties that are available to a candidate molecule. Using these maps, we identify a highly porous solid, which has the lowest density reported for a molecular crystal so far. Both the structure of the crystal and its physical properties, such as methane storage capacity and guest-molecule selectivity, are predicted using the molecular structure as the only input. More generally, energy–structure–function maps could be used to guide the experimental discovery of materials with any target function that can be calculated from predicted crystal structures, such as electronic structure or mechanical properties.

Ketonic Decarboxylation Reaction Mechanism: A Combined Experimental and DFT Study

The ketonic decarboxylation of carboxylic acids has been carried out experimentally and studied theoretically by DFT calculations. In the experiments, monoclinic zirconia was identified as a good catalyst, giving high activity and high selectivity when compared with other potential catalysts, such as silica, alumina, or ceria. It was also shown that it could be used for a wide range of substrates, namely, for carboxylic acids with two to eighteen carbon atoms. The reaction mechanism for the ketonic decarboxylation of acetic acid over monoclinic zirconia was investigated by using a periodic DFT slab model. A reaction pathway with the formation of a β-keto acid intermediate was considered, as well as a concerted mechanism, involving simultaneous carbon-carbon bond formation and carbon dioxide elimination. DFT results showed that the mechanism with the β-keto acid was the kinetically favored one and this was further supported by an experiment employing a mixture of isomeric (linear and branched) pentanoic acids.

Combined DFT/CC and IR spectroscopic studies on carbon dioxide adsorption on the zeolite H-FER

Adsorption of carbon dioxide on H-FER zeolite (Si:Al = 8:1) was investigated by means of a combined methodology involving variable-temperature infrared spectroscopy and DFT/CC calculations on periodic zeolite models. The experimentally found value of adsorption enthalpy was ΔH0 = −30 kJ mol−1. According to calculations, adsorption complexes on isolated Si(OH)Al Bronsted acid sites (single sites) involve an adsorption enthalpy in the range of −33 to −36 kJ mol−1, about half of which is due to weak intermolecular interactions between CO2 and the zeolite framework. Calculations show clearly the significant role played by weak intermolecular interactions; adsorption enthalpies calculated with standard GGA type exchange-correlation functionals are about 13 kJ mol−1 underestimated with respect to experimental results. Good agreement was also found between calculated and experimentally observed stretching frequencies for these complexes. Calculations revealed that CO2 adsorption complexes involving two neighbouring Bronsted acid sites (dual sites) can be formed, provided that the dual site has the required geometry. However, no clear evidence of CO2 adsorption complexes on dual sites was experimentally found.

Periodic DFT investigation of the effect of aluminium content on the properties of the acid zeolite H-FER.

Periodic DFT calculations were performed on H-FER models having Si/Al ratios of 71 : 1, 35 : 1 and 8 : 1, in order to investigate the effect of aluminium content on the properties of the zeolite Brønsted acid sites. Relative stability of these sites was found to be dependent on Si/Al ratio, which is the main factor dictating the relative concentration of Brønsted acid sites having different types of local configuration, to the point that some types of acid site are formed only when the aluminium content of the zeolite is relatively high. The number of AlO(4) tetrahedra sharing an oxygen with the SiO(4) tetrahedron involved in the Brønsted acid site determines the Si-O(H)-Al angle, O-H stretching frequency and deprotonation energy (and hence acid strength). For Brønsted acid protons not involved in intra-zeolite H-bonding, a correlation was found between Si-O(H)-Al angle and O-H stretching frequency.

Theoretical investigation of gold clusters supported on graphene sheets

The structure and stabilization of a series of gold (Aun) clusters (where n = 1, 5, 6, 19 and 39) supported on the perfect and defective (vacancy and/or N-doped) graphene sheets were investigated using a periodic DFT model. Much stronger interaction was found between a gold atom and the graphene sheet with a defective structure that is comparable to interaction energies reported for different transition metal oxide supports. Increasing gold particle size does not weaken the interaction with the single vacancy graphene sheet, where the gold clusters are anchored to the carbon surface through only one gold atom and the cluster shape is preserved. Catalytic performance of Au(100) facets in the isolated and graphene-supported Au39 nanoparticle (mean size ∼1 nm) for the O2 dissociation reaction was investigated. Structure of the involved species along the reaction pathway and energy profile were found very much alike, regardless the reaction takes place on the isolated or graphene-supported gold nanoparticle.

Reconstruction of the carbon sp2 network in graphene oxide by low-temperature reaction with CO

Low-temperature (−176 °C) CO adsorption on graphene oxide and partially reduced graphene oxide sheets was investigated in a combined IR spectroscopic and DFT study. The reactivity of the carbon vacancies in the network was observed to be extremely high, causing the CO molecules to dissociate in a barrier-less process that leads to the reconstruction of the sp2graphene network. After the adsorption of CO on the graphene oxide materials, the intensity of the FTIR bands is lower in the case of partially reduced graphene oxide sheets, indicating that there are fewer active sites available for CO interaction.

Computational and Variable‐Temperature Infrared Spectroscopic Studies on Carbon Monoxide Adsorption on Zeolite Ca‐A

Carbon monoxide adsorption on LTA (Linde type 5A) zeolite Ca-A is studied by using a combination of variable-temperature infrared spectroscopy and computational methods involving periodic density functional calculations and the correlation between stretching frequency and bond length of adsorbed CO species (nu(CO)/r(CO) correlation). Based on the agreement between calculated and experimental results, the main adsorption species can be identified as bridged Ca(2+)...CO...Ca(2+) complexes formed on dual-cation sites constituted by a pair of nearby Ca(2+) cations. Two types of such species can be formed: One of them has the two Ca(2+) ions located on six-membered rings of the zeolite framework and is characterized by a C-O stretching frequency in the range of 2174-2179 cm(-1) and an adsorption enthalpy of -31 to -33 kJ mol(-1), whereas the other bridged CO species is formed between a Ca(2+) ion located on an eight-membered ring and another one on a nearby six-membered ring and is characterized by nu(CO) in the range 2183-2188 cm(-1) and an adsorption enthalpy of -46 to -50 kJ mol(-1). Ca(2+)...CO monocarbonyl complexes are also identified, and at a relatively high CO equilibrium pressure, dicarbonyl species can also be formed.

Correlation Between Catalytic Activity and Metal Cation Coordination: NO Decomposition Over Cu/Zeolites

Since Iwamoto’s discovery of an unusually high activity of Cu/zeolites in NO decomposition, there has been an ongoing experimental and theoretical quest to understand the details of the mechanism of this process. Despite this tremendous effort, there are still a number of unsettled questions, including the uncertainty about the nature of the reaction intermediates and about the structure of the active site; either the involvement of only a single extra-framework Cu cation or the concerted effect of two nearby Cu cations, the Cu pair, was proposed. From the vast amount of relevant experimental data available today, it is clear that the activity of the Cu/zeolite catalysts depends on 1) zeolite topology, 2) zeolite composition (Si/Al ratio and Cu loading), and 3) Cu-exchange procedure, including the sample pretreatment. 6,8, 12, 13,15] However, the understanding of the relationship between active site structure (the metal coordination and localization) and catalytic activity is far from complete; it is our goal to increase our knowledge in this respect. The lack of direct experimental evidence about the transition-state structures and about the details of the reaction mechanism justifies the use of quantum chemistry to provide the missing details. However, a reliable description of the reactions catalyzed by transition metals in a complex environment (such as zeolites) represents a major challenge for contemporary computational chemistry since it requires the use of a model that realistically represents the active site (including its environment) and the use of a method that can consistently describe the electronic structure of the system along the reaction path (see the Methods section). Many reaction steps possibly involved in the direct NO decomposition on Cu/zeolites have been investigated previously by employing various models and methods. Several reaction paths proposed in the literature have been compiled (Scheme 1) along with the reaction energies and activation barriers (where available) reported for the elementary reaction steps. Since these energies were obtained at various levels of theory using different types of models for the active site, a direct comparison should be taken with some caution. For example, the reaction energies of 107 and 173 kJmol 1 were reported for reaction step D based on the BP86 functional (using a 1-T cluster model) and based on the B3LYP functional (using a 3-T cluster model), respectively. A majority of the proposed reaction mechanisms start with the interaction of two NO molecules with Cu/zeolite (ZCu) producing ZCuO and N2O (A!B!C). Different routes were proposed for the subsequent conversion of N2O: 1) it can interact with another NO molecule to produce N2 and NO2. One of the G!I!J, A!K!L, or M!L routes can be followed; the rate-determining steps of these reaction routes are characterized with activation barriers of 105, 122, and 126 kJmol 1[20] , respectively. 2) N2O can be reattached to ZCu to release N2 while forming another ZCuO species (process G!H). Note however, that all these reaction paths lead to the production of NO2 and/or ZCuO species. To close the catalytic cycle, the ZCuO needs to be reduced back to ZCu and the NO2 must further react. However, NO2 can readily interact with ZCuO forming ZCuNO3 (process O; DE= 252 kJmol ). It is not clear how to proceed from a stable ZCuNO3 complex towards the products. Another route was proposed following the A!B!C path: a simple reaction mechanism based on the readsorption of N2O on ZCuO (through the O-end) that leads to the formation of N2, O2, and ZCu (D!E!F). An activation barrier for the rate-determining step on this path (the formation of ZCuO2N2) of 152 and 145 kJmol 1 has been reported based on BP86/(1-T cluster) and B3LYP/(3-T cluster) calculations, respectively. Whereas the activation barrier of the D!E!F Scheme 1. A schematic representation of the possible processes taking place during NO removal in zeolites. The reaction energies and activation barriers (denoted by #) are taken from the literature: a) Ref [16] , b) Ref. [17] , c) Ref. [18] , d) Ref. [19] , and e) Ref. [20] . Superscript numbers refer to the spin multiplicity of the adsorption complex.

Computationally-Guided Synthetic Control over Pore Size in Isostructural Porous Organic Cages

The physical properties of 3-D porous solids are defined by their molecular geometry. Hence, precise control of pore size, pore shape, and pore connectivity are needed to tailor them for specific applications. However, for porous molecular crystals, the modification of pore size by adding pore-blocking groups can also affect crystal packing in an unpredictable way. This precludes strategies adopted for isoreticular metal–organic frameworks, where addition of a small group, such as a methyl group, does not affect the basic framework topology. Here, we narrow the pore size of a cage molecule, CC3, in a systematic way by introducing methyl groups into the cage windows. Computational crystal structure prediction was used to anticipate the packing preferences of two homochiral methylated cages, CC14-R and CC15-R, and to assess the structure–energy landscape of a CC15-R/CC3-S cocrystal, designed such that both component cages could be directed to pack with a 3-D, interconnected pore structure. The experimental gas sorption properties of these three cage systems agree well with physical properties predicted by computational energy–structure–function maps.