A computational study of H-bonded networks in cyclic water clusters, (H2O)n (n = 3-12).

CONTEXT: We have performed a detailed MM and DFT investigation of neutral water clusters (H2O)n (n = 3-12). Our results show the trend of interaction energies in these clusters as a function of the size of the cluster. They show that the H-bond strength increases with cluster size and that the model of water is better described if two different partial charges are used on the hydrogen, depending on whether hydrogen is H-bonded or not. The average binding enthalpy change due to the formation of H-bonds between water molecules is found to be - 25.9 kJ mol-1 at B3LYP/aug-cc-pVDZ level of theory. We observe the formation of cyclic H-bonded networks through the analysis of frontier orbitals and IR vibrational frequencies spectra. For the water cluster with n = 11, we observe an unusual reduction of the bandgap indicative of a cyclic H-bonded network. METHODS: Calculations were performed with the MMFF94 force field and the B3LYP method using various large basis sets. Molecular orbital diagrams and population analysis were done using standard tools in Gaussian.

Silica nanoparticles and kaolin clay decorated with VO2+ in aerobic oxidative destruction of BTEX contaminants.

The importance of controlled hydrocarbon oxidation has sparked interest in methods that catalyze this process. In this vein, controlled oxidative degradation of BTEX compounds (benzene, toluene, ethylbenzene and xylenes) which are hazardous air and industrial waste water contaminants is very considerable. Accordingly, the reactive VO2+ species was anchored onto silica nanoparticles (VO-SNP) to catalyze the conversion of BTEX into useful compounds. The synthesized heterogeneous VO-SNP catalyst was characterized using different techniques such as FTIR, FETEM, FESEM, XRD, EDX, ICP and XPS. Interestingly, the catalyst performed the activation of the relatively inert C-H bonds of BTEX to produce oxygenated compounds under quite mild and eco-friendly conditions at room temperature with no extra additives. Furthermore, we introduced VO2+ species onto mineral kaolin sheets (VO-kaolin) as a vanadyl decorated natural solid support and the results showed less efficiency compared to VO-SNP.

TEMPO and a co-reductant mediated aerobic epoxidation of olefins using a new magnetically recoverable iron(III) bis(phenol)diamine complex: experimental and computational studies.

A magnetically recoverable catalyst of an iron(III) bis(phenol) diamine complex immobilized onto amine functionalized silica-coated magnetic nanoparticles has been synthesized. The catalyst was characterized using FESEM, TEM and XRD which confirmed the nano structure of the catalyst. The physicochemical techniques of ICP, FT-IR, XPS, EDS and TGA proved the loading of the ligand and metal complex on silica-coated magnetic nanoparticles. Using the prepared heterogeneous catalyst, aerobic epoxidation reactions of different alkenes have been investigated in the presence of SO32- as a reducing agent. Moreover, using TEMPO (2,2,6,6-tetramethyl-1-piperidinyloxy) to discover the mechanism of the aerobic epoxidation of olefins, a new TEMPO-assisted route has been explored. Both of the reaction pathways led to a moderate to high percentage yield of epoxides in water at room temperature. For further understanding mechanistic aspects, density functional theory (DFT) computational studies have been performed. The DFT calculations confirm the suggested mechanism for the title reaction and show the electron density in the vicinity of Fe(II) in the presence of TEMPO as a co-catalyst was more than that in the presence of SO32-.

Miniature physical sphere-in-contact models of heterogeneous catalysts and metal nanoparticles.

CONTEXT: Physical molecular models have played a fundamental role in the understanding of chemical reactions on heterogeneous catalysts and on metal nanoparticles. To date, these physical models have been based on separate models of the metal nanoparticle (NP) or surface and of the substrate and the molecular structure of reactant and product adsorbates and their intermediates. In this paper, we try to provide a new miniature physical molecular model, the sphere-in-contact model of heterogeneous catalysts and metal nanoparticles that can build inexpensive, small and efficient molecular models that can be transported or shipped easily and that depict the chemical reaction as a whole, showing reactants, intermediates, products, the metal nanoparticle bound to the substrate which can give information about a reaction mechanism. These models reveal that there are certain rules with respect to the kind of sites you observe at the metal NP interface with the support by small movement of the nanoparticle. METHODS: We have used in this study physical molecular models using the sphere-in-contact model. This is the first time such physical models are built for heterogeneous catalytic reactions and metal nanoparticles, and they are constructed out of spheres that fuse together when exposed to water.

A Comparison of the Reactivity of the Lattice Nitrogen in Tungsten Substituted Co3 Mo3 N and Ni2 Mo3 N.

The effect of the partial substitution of Mo with W in Co3 Mo3 N and Ni2 Mo3 N on ammonia synthesis activity and lattice nitrogen reactivity has been investigated. This is of interest as the coordination environment of lattice N is changed by this process. When tungsten was introduced into the metal nitrides by substitution of Mo atoms, the catalytic performance was observed to have decreased. As expected, Co3 Mo3 N was reduced to Co6 Mo6 N under a 3 : 1 ratio of H2 /Ar. Co3 Mo2.6 W0.4 N was also shown to lose a large percentage of lattice nitrogen under these conditions. The bulk lattice nitrogen in Ni2 Mo3 N and Ni2 Mo2.8 W0.2 N was unreactive, demonstrating that substitution with tungsten does not have a significant effect on lattice N reactivity. Computational calculations reveal that the vacancy formation energy for Ni2 Mo3 N is more endothermic than Co3 Mo3 N. Furthermore, calculations suggest that the inclusion of W does not have a substantial impact on the surface N vacancy formation energy or the N2 adsorption and activation at the vacancy site.

Mechanism of ammonia synthesis on Fe3Mo3N.

Ammonia (NH3) synthesis is an essential yet energy-demanding industrial process. Hence, there is a need to develop NH3 synthesis catalysts that are highly active under milder conditions. Metal nitrides are promising candidates, with the η-carbide Co3Mo3N having been found to be more active than the industrial Fe-based catalyst. The isostructural Fe3Mo3N catalyst has also been identified as highly active for NH3 synthesis. In the present work, we investigate the catalytic ammonia synthesis mechanisms in Fe3Mo3N, which we compare and contrast with the previously studied Co3Mo3N. We apply plane-wave density functional theory (DFT) to investigate surface N vacancy formation in Fe3Mo3N, and two distinct ammonia synthesis mechanisms. The calculations reveal that whilst N vacancy formation on Fe3Mo3N is more thermodynamically demanding than for Co3Mo3N, the formation energies are comparable, suggesting that surface lattice N vacancies in Fe3Mo3N could facilitate NH3 synthesis. N2 activation was found to be enhanced on Fe3Mo3N compared to Co3Mo3N, for adsorption both at and adjacent to the vacancy. The calculated activation barriers suggest that, as for Co3Mo3N, the associative Mars van Krevelen mechanism affords a much less energy-demanding pathway for ammonia synthesis, especially for initial hydrogenation processes.

A DFT study of the interaction of aspirin, paracetamol and caffeine with one water molecule.

We have studied the interaction of water with three important analgesics, aspirin, paracetamol and caffeine using DFT calculations and FTIR-ATR spectroscopy. In our study, water is used as a probe molecule to reveal the various H-bonding sites on the electrostatic potential energy surface of the analgesics. We find that water forms a strong double H-bond with the COOH group of aspirin and that the oxygen of the ester group can become H-bond acceptors. Paracetamol forms the strongest H-bond with water at the hydroxyl group and weaker H-bonds with the C = O group and the N-H group. Caffeine forms the strongest H-bond with water at the top C = O group and can form additional H-bonds with the bottom C = O group and the nitrogen of the imidazole ring. These studies may help to better understand the solvation of these analgesics in water.

A comparative analysis of the mechanisms of ammonia synthesis on various catalysts using density functional theory.

In this review, we present the recent progress in ammonia synthesis research using density functional theory (DFT) calculations on various industrial catalysts, metal nitrides and nano-cluster-supported catalysts. The mechanism of ammonia synthesis on the industrial Fe catalyst is generally accepted to be a dissociative mechanism. We have recently found, using DFT techniques, that on Co3Mo3N (111) surfaces, an associative mechanism in the synthesis of ammonia can offer a new low-energy pathway that was previously unknown. In particular, we have shown that metal nitrides that are also known to have high activity for ammonia synthesis can readily form nitrogen vacancies which can activate dinitrogen, thereby promoting the associative mechanism. These fundamental studies suggest that a promising route to the discovery of low-temperature ammonia synthesis catalysts will be to identify systems that proceed via the associative mechanism, which is closer to the nitrogen-fixation mechanism occurring in nitrogenases.

Combination of theoretical and in situ experimental investigations of the role of lithium dopant in manganese nitride: a two-stage reagent for ammonia synthesis.

Manganese nitride related materials are of interest as two-stage reagents for ammonia synthesis via nitrogen chemical looping. However, unless they are doped with a co-cation, manganese nitrides are thermochemically stable and a high temperature is required to produce ammonia under reducing conditions, thereby hindering their use as nitrogen transfer materials. Nevertheless, when lithium is used as dopant, ammonia generation can be observed at a reaction temperature as low as 300 °C. In order to develop strategies for the improvement of the reactivity of nitride materials in the context of two-stage reagents, it is necessary to understand the intrinsic role of the dopant in the mechanism of ammonia synthesis. To this end, we have investigated the role of lithium in increasing the manganese nitride reactivity by in situ neutron diffraction studies and N2 and H2 isotopic exchange reactions supplemented by DFT calculations.

Mechanistic aspects of ammonia synthesis on Ta3N5 surfaces in the presence of intrinsic nitrogen vacancies.

A possible dinitrogen activation and the ammonia synthesis mechanism were studied on the (100), (010) and (001) surfaces of Ta3N5 that contain intrinsic nitrogen vacancies. The study suggests that intrinsic nitrogen vacancies can become catalytic centers for the ammonia synthesis reaction on Ta3N5via a Langmuir-Hinshelwood mechanism, which may explain the moderate production of ammonia at high temperatures. In the proposed mechanism, dinitrogen is activated in a peculiar side on a sandwich-like configuration between two surface Ta atoms. Calculation of reaction activation barriers suggests that the mechanism proceeds via moderate barriers but some elementary reaction steps involve the strong adsorption of ammonia which appears to poison the surface catalytic sites on Ta3N5.

An experimental and computational IR and hybrid DFT-D3 study of the conformations of l-lactic and acrylic acid: new insight into the dehydration mechanism of lactic acid to acrylic acid.

We have studied using hybrid Density Functional Theory (DFT) with an aug-cc-pVTZ basis set and D3 dispersion corrections the intra-molecular hydrogen bond of l-lactic acid and l-lactic-acid analogs with the hydroxyl group on the alpha carbon atom substituted by α-XH (where X = S, Se, Te) as well as the conformations of acrylic acid. The results show that there are three types of intramolecular hydrogen bonds that can form only when α-OH is present, whereas other less electronegative functional groups such as -SH, -SeH and -TeH do not exhibit the formation of an intramolecular H-bond. We show that the intra-molecular H-bond formed between the alpha-OH hydrogen and the COOH carbonyl oxygen would enhance the rate of nucleophilic substitution of alpha-OH at the K+ sites in the previously suggested dehydration mechanism of l-lactic to acrylic acids. We find that a temperature range between 190 and 210 °C would be optimum to maximise the rate of nucleophilic substitution of the alpha-OH group at the potassium sites during the dehydration mechanism of l-lactic acid to acrylic acid. Additionally, our hybrid-DFT simulation of the infrared spectrum of the various conformers shows that the lowest energy conformer can be identified by a single vibrational band at 3734 cm-1 whereas for the other conformers, this vibrational band is split with Δν that ranges between 6 cm-1 and 176 cm-1. We also find that the various conformers of acrylic acid can be identified by a double peak for the C[double bond, length as m-dash]O and O-H vibrations, which have Δν' and Δν'' values of 24 and 42 cm-1, respectively. This computational study is useful for spectroscopic experimental efforts that try to identify the various conformers of l-lactic acid and acrylic acid and to gain mechanistic insight into the dehydration mechanism over K substituted NaY zeolites.

Mechanisms of ammonia and hydrazine synthesis on η-Mn3N2-(100) surfaces.

Understanding the mechanism of catalytic reactions is crucial for the future development of catalysts. In this computational study, dispersion-corrected Density Functional Theory (DFT) theory was used to calculate the various mechanistic pathways for ammonia and hydrazine synthesis on η-Mn3N2-(100) surfaces. A simple Lewis structure representation algorithm was used in order to locate various possible NxHy intermediates. Hydrogenation of dinitrogen results in significant activation of the inert triple bond and these intermediates have a significant role in the ammonia and hydrazine synthesis reaction on manganese nitrides via a Langmuir-Hinshelwood mechanism. It is anticipated that these findings are significant in developing new catalysts for hydrazine synthesis using η-Mn3N2(100) catalysts.

The integration of experiment and computational modelling in heterogeneously catalysed ammonia synthesis over metal nitrides.

In this perspective we present recent experimental and computational progress in catalytic ammonia synthesis research on metal nitrides involving a combined approach. On this basis, it suggested that the consideration of nitrogen vacancies in the synthesis of ammonia can offer new low energy pathways that were previously unknown. We have shown that metal nitrides that are also known to have high activity for ammonia synthesis can readily form nitrogen vacancies on their surfaces. These vacancies adsorb dinitrogen much more strongly than the defect-free surfaces and can efficiently activate the strong N-N triple bond. These fundamental studies suggest that heterogeneously catalysed ammonia synthesis over metal nitrides is strongly affected by bulk and surface defects and that further progress in the discovery of low temperature catalysts relies on more careful consideration of nitrogen vacancies. The potential occurrence of an associative pathway in the case of the Co3Mo3N catalytic system provides a possible link with enzymatic catalysis, which will be of importance in the design of heterogeneous catalytic systems operational under process conditions of reduced severity which are necessary for the development of localised facilities for the production of more sustainable "green" ammonia.

On the possibility of an Eley-Rideal mechanism for ammonia synthesis on Mn6N5+x (x = 1)-(111) surfaces.

Recently we reported an Eley-Rideal/Mars-van Krevelen mechanism for ammonia synthesis on cobalt molybdenum nitride (Co3Mo3N). In this mechanism hydrogenation of activated dinitrogen occurs directly from the gas phase in a low barrier step forming a hydrazinylidene intermediate [double bond, length as m-dash]NNH2. In this paper we study whether such a mechanism of ammonia synthesis could occur on the (111) surface of another metal nitride, Mn6N5+x (x = 1), as this would explain the low-T ammonia synthesis activity of Co3Mo3N. We find that although N2 adsorbs more strongly than H2 on the (111) surface, having also examined the (110) and the (100) surface, N2 is not significantly activated when adsorbed in an end-on configuration. The hydrogenation reactions via an Eley-Rideal mechanism are all high barrier processes (>182 kJ mol-1) and therefore an Eley-Rideal mechanism for ammonia synthesis is predicted to not occur on this material unless there are high temperatures. Our study indicates that the fact that an Eley-Rideal/Mars-van Krevelen mechanism occurs on Co3Mo3N is a result of the stronger activation of dinitrogen at nitrogen vacancies when dinitrogen is adsorbed in an end-on configuration.

DFT-D3 study of H2 and N2 chemisorption over cobalt promoted Ta3N5-(100), (010) and (001) surfaces.

The reactants for ammonia synthesis have been studied, employing density functional theory (DFT), with respect to their adsorption on tantalum nitride surfaces. The adsorption of nitrogen was found to be mostly molecular and non-activated with side-on, end-on and tilt configurations. At bridging nitrogen sites (Ta-N-Ta) it results in an azide functional group formation with a formation energy of 205 kJ mol-1. H2 was found also to chemisorb molecularly with an adsorption energy in the range -81 to -91 kJ mol-1. At bridging nitrogen sites it adsorbs dissociatively forming >NH groups with an exothermic formation energy of -175 kJ mol-1 per H2. The nitrogen vacancy formation energies were relatively high compared to other metal nitrides found to be 2.89 eV, 2.32 eV and 1.95 eV for plain, surface co-adsorbed cobalt and sub-surface co-adsorbed cobalt Ta3N5-(010). Co-adsorption of cobalt was found to occur mostly at nitrogen rich sites of the surface with an adsorption energy that ranged between -200 to -400 kJ mol-1. The co-adsorption of cobalt was found to enhance the dissociation of molecular hydrogen on the surface of Ta3N5. The studies offer significant new insight with respect to the chemistry of N2 and H2 with tantalum nitride surfaces in the presence of cobalt promoters.

A Computational Study of the Heterogeneous Synthesis of Hydrazine on Co3Mo3N.

ABSTRACT: Periodic and molecular density functional theory calculations have been applied to elucidate the associative mechanism for hydrazine and ammonia synthesis in the gas phase and hydrazine formation on Co3Mo3N. We find that there are two activation barriers for the associative gas phase mechanism with barriers of 730 and 658 kJ/mol, corresponding to a hydrogenation step from N2 to NNH2 and H2NNH2 to H3NNH3, respectively. The second step of the mechanism is barrierless and an important intermediate, NNH2, can also readily form on Co3Mo3N surfaces via the Eley-Rideal chemisorption of H2 on a pre-adsorbed N2 at nitrogen vacancies. Based on this intermediate a new heterogeneous mechanism for hydrazine synthesis is studied. The highest relative barrier for this heterogeneous catalysed process is 213 kJ/mol for Co3Mo3N containing nitrogen vacancies, clearly pointing towards a low-energy process for the synthesis of hydrazine via a heterogeneous catalysis route.

The sphere-in-contact model of carbon materials.

A sphere-in-contact model is presented that is used to build physical models of carbon materials such as graphite, graphene, carbon nanotubes and fullerene. Unlike other molecular models, these models have correct scale and proportions because the carbon atoms are represented by their atomic radius, in contrast to the more commonly used space-fill models, where carbon atoms are represented by their van der Waals radii. Based on a survey taken among 65 undergraduate chemistry students and 28 PhD/postdoctoral students with a background in molecular modeling, we found misconceptions arising from incorrect visualization of the size and location of the electron density located in carbon materials. Based on analysis of the survey and on a conceptual basis we show that the sphere-in-contact model provides an improved molecular representation of the electron density of carbon materials compared to other molecular models commonly used in science textbooks (i.e., wire-frame, ball-and-stick, space-fill). We therefore suggest that its use in chemistry textbooks along with the ball-and-stick model would significantly enhance the visualization of molecular structures according to their electron density. Graphical Abstract A sphere-in-contact model of C60-fullerene.

Computational inhibition studies of the human proteasome by argyrin-based analogues with subunit specificity.

A computational procedure was developed to study the subunit-specific interactions of the proteasome inhibitors argyrin A and F, with the aim of indentifying the determinants of subunit selectivity. Three-dimensional models of humanized proteasome active sites ß1 , ß2 and ß5 were developed and subsequently used in molecular docking simulations with the argyrin analogues. The subunit selectivity exhibited by each analogue could be explained based on the site-specific interactions and a probability-based specificity parameter derived in this study. A rational approach that involved maximizing site-specific interactions was followed to guide the design of new argyrin analogues as specific inhibitors of the caspase-like (ß1 site) activity.

Impact of co-adsorbed oxygen on crotonaldehyde adsorption over gold nanoclusters: a computational study.

Crotonaldehyde (2-butenal) adsorption over gold sub-nanometer particles, and the influence of co-adsorbed oxygen, has been systematically investigated by computational methods. Using density functional theory, the adsorption energetics of crotonaldehyde on bare and oxidised gold clusters (Au13, d = 0.8 nm) were determined as a function of oxygen coverage and coordination geometry. At low oxygen coverage, sites are available for which crotonaldehyde adsorption is enhanced relative to bare Au clusters by 10 kJ mol(-1). At higher oxygen coverage, crotonaldehyde is forced to adsorb in close proximity to oxygen weakening adsorption by up to 60 kJ mol(-1) relative to bare Au. Bonding geometries, density of states plots and Bader analysis, are used to elucidate crotonaldehyde bonding to gold nanoparticles in terms of partial electron transfer from Au to crotonaldehyde, and note that donation to gold from crotonaldehyde also becomes significant following metal oxidation. At high oxygen coverage we find that all molecular adsorption sites have a neighbouring, destabilising, oxygen adatom so that despite enhanced donation, crotonaldehyde adsorption is always weakened by steric interactions. For a larger cluster (Au38, d = 1.1 nm) crotonaldehyde adsorption is destabilized in this way even at a low oxygen coverage. These findings provide a quantitative framework to underpin the experimentally observed influence of oxygen on the selective oxidation of crotyl alcohol to crotonaldehyde over gold and gold-palladium alloys.