First-Principles Study of Antisite Defect Configurations in ZnGa2O4:Cr Persistent Phosphors.

Zinc gallate doped with chromium is a recently developed near-infrared emitting persistent phosphor, which is now extensively studied for in vivo bioimaging and security applications. The precise mechanism of this persistent luminescence relies on defects, in particular, on antisite defects and antisite pairs. A theoretical model combining the solid host, the dopant, and/or antisite defects is constructed to elucidate the mutual interactions in these complex materials. Energies of formation as well as dopant, and defect energies are calculated through density-functional theory simulations of large periodic supercells. The calculations support the chromium substitution on the slightly distorted octahedrally coordinated gallium site, and additional energy levels are introduced in the band gap of the host. Antisite pairs are found to be energetically favored over isolated antisites due to significant charge compensation as shown by calculated Hirshfeld-I charges. Significant structural distortions are found around all antisite defects. The local Cr surrounding is mainly distorted due to a ZnGa antisite. The stability analysis reveals that the distance between both antisites dominates the overall stability picture of the material containing the Cr dopant and an antisite pair. The findings are further rationalized using calculated densities of states and Hirshfeld-I charges.

Understanding Intrinsic Light Absorption Properties of UiO-66 Frameworks: A Combined Theoretical and Experimental Study.

A combined theoretical and experimental study is performed in order to elucidate the effects of linker functional groups on the photoabsorption properties of UiO-66-X materials. This study, in which both mono- and difunctionalized linkers (with X = OH, NH2, or SH) are investigated, aims to obtain a more complete picture of the choice of functionalization. Static time-dependent density functional theory calculations combined with molecular dynamics simulations are performed on the linkers, and the results are compared to experimental UV/vis spectra in order to understand the electronic effects governing the absorption spectra. The disubstituted linkers show larger shifts than the monosubstituted variants, making them promising candidates for further study as photocatalysts. Next, the interaction between the linker and the inorganic part of the framework is theoretically investigated using a cluster model. The proposed ligand-to-metal-charge transfer is theoretically observed and is influenced by the differences in functionalization. Finally, the computed electronic properties of the periodic UiO-66 materials reveal that the band gap can be altered by linker functionalization and ranges from 4.0 down to 2.2 eV. Study of the periodic density of states allows the band gap modulations of the framework to be explained in terms of a functionalization-induced band in the band gap of the original UiO-66 host.

Advances in theory and their application within the field of zeolite chemistry.

Zeolites are versatile and fascinating materials which are vital for a wide range of industries, due to their unique structural and chemical properties, which are the basis of applications in gas separation, ion exchange and catalysis. Given their economic impact, there is a powerful incentive for smart design of new materials with enhanced functionalities to obtain the best material for a given application. Over the last decades, theoretical modeling has matured to a level that model guided design has become within reach. Major hurdles have been overcome to reach this point and almost all contemporary methods in computational materials chemistry are actively used in the field of modeling zeolite chemistry and applications. Integration of complementary modeling approaches is necessary to obtain reliable predictions and rationalizations from theory. A close synergy between experimentalists and theoreticians has led to a deep understanding of the complexity of the system at hand, but also allowed the identification of shortcomings in current theoretical approaches. Inspired by the importance of zeolite characterization which can now be performed at the single atom and single molecule level from experiment, computational spectroscopy has grown in importance in the last decade. In this review most of the currently available modeling tools are introduced and illustrated on the most challenging problems in zeolite science. Directions for future model developments will be given.

First principle chemical kinetics in zeolites: the methanol-to-olefin process as a case study.

To optimally design next generation catalysts a thorough understanding of the chemical phenomena at the molecular scale is a prerequisite. Apart from qualitative knowledge on the reaction mechanism, it is also essential to be able to predict accurate rate constants. Molecular modeling has become a ubiquitous tool within the field of heterogeneous catalysis. Herein, we review current computational procedures to determine chemical kinetics from first principles, thus by using no experimental input and by modeling the catalyst and reacting species at the molecular level. Therefore, we use the methanol-to-olefin (MTO) process as a case study to illustrate the various theoretical concepts. This process is a showcase example where rational design of the catalyst was for a long time performed on the basis of trial and error, due to insufficient knowledge of the mechanism. For theoreticians the MTO process is particularly challenging as the catalyst has an inherent supramolecular nature, for which not only the Brønsted acidic site is important but also organic species, trapped in the zeolite pores, must be essentially present during active catalyst operation. All these aspects give rise to specific challenges for theoretical modeling. It is shown that present computational techniques have matured to a level where accurate enthalpy barriers and rate constants can be predicted for reactions occurring at a single active site. The comparison with experimental data such as apparent kinetic data for well-defined elementary reactions has become feasible as current computational techniques also allow predicting adsorption enthalpies with reasonable accuracy. Real catalysts are truly heterogeneous in a space- and time-like manner. Future theory developments should focus on extending our view towards phenomena occurring at longer length and time scales and integrating information from various scales towards a unified understanding of the catalyst. Within this respect molecular dynamics methods complemented with additional techniques to simulate rare events are now gradually making their entrance within zeolite catalysis. Recent applications have already given a flavor of the benefit of such techniques to simulate chemical reactions in complex molecular environments.

Exploring the vibrational fingerprint of the electronic excitation energy via molecular dynamics.

A Fourier-based method is presented to relate changes of the molecular structure during a molecular dynamics simulation with fluctuations in the electronic excitation energy. The method implies sampling of the ground state potential energy surface. Subsequently, the power spectrum of the velocities is compared with the power spectrum of the excitation energy computed using time-dependent density functional theory. Peaks in both spectra are compared, and motions exhibiting a linear or quadratic behavior can be distinguished. The quadratically active motions are mainly responsible for the changes in the excitation energy and hence cause shifts between the dynamic and static values of the spectral property. Moreover, information about the potential energy surface of various excited states can be obtained. The procedure is illustrated with three case studies. The first electronic excitation is explored in detail and dominant vibrational motions responsible for changes in the excitation energy are identified for ethylene, biphenyl, and hexamethylbenzene. The proposed method is also extended to other low-energy excitations. Finally, the vibrational fingerprint of the excitation energy of a more complex molecule, in particular the azo dye ethyl orange in a water environment, is analyzed.

Identification of intermediates in zeolite-catalyzed reactions by in situ UV/Vis microspectroscopy and a complementary set of molecular simulations.

The optical absorption properties of (poly)aromatic hydrocarbons occluded in a nanoporous environment were investigated by theoretical and experimental methods. The carbonaceous species are an essential part of a working catalyst for the methanol-to-olefins (MTO) process. In situ UV/Vis microscopy measurements on methanol conversion over the acidic solid catalysts H-SAPO-34 and H-SSZ-13 revealed the growth of various broad absorption bands around 400, 480, and 580 nm. The cationic nature of the involved species was determined by interaction of ammonia with the methanol-treated samples. To determine which organic species contribute to the various bands, a systematic series of aromatics was analyzed by means of time-dependent density functional theory (TDDFT) calculations. Static gas-phase simulations revealed the influence of structurally different hydrocarbons on the absorption spectra, whereas the influence of the zeolitic framework was examined by using supramolecular models within a quantum mechanics/molecular mechanics framework. To fully understand the origin of the main absorption peaks, a molecular dynamics (MD) study on the organic species trapped in the inorganic host was essential. During such simulation the flexibility is fully taken into account and the effect on the UV/Vis spectra is determined by performing TDDFT calculations on various snapshots of the MD run. This procedure allows an energy absorption scale to be provided and the various absorption bands determined from in situ UV/Vis spectra to be assigned to structurally different species.

Enthalpy and entropy barriers explain the effects of topology on the kinetics of zeolite-catalyzed reactions.

The methylation of ethene, propene, and trans-2-butene on zeolites H-ZSM-58 (DDR), H-ZSM-22 (TON), and H-ZSM-5 (MFI) is studied to elucidate the particular influence of topology on the kinetics of zeolite-catalyzed reactions. H-ZSM-58 and H-ZSM-22 are found to display overall lower methylation rates compared to H-ZSM-5 and also different trends in methylation rates with increasing alkene size. These variations may be rationalized based on a decomposition of the free-energy barriers into enthalpic and entropic contributions, which reveals that the lower methylation rates on H-ZSM-58 and H-ZSM-22 have virtually opposite reasons. On H-ZSM-58, the lower methylation rates are caused by higher enthalpy barriers, owing to inefficient stabilization of the reaction intermediates in the large cage-like pores. On the other hand, on H-ZSM-22, the methylation rates mostly suffer from higher entropy barriers, because excessive entropy losses are incurred inside the narrow-channel structure. These results show that the kinetics of crucial elementary steps hinge on the balance between proper stabilization of the reaction intermediates inside the zeolite pores and the resulting entropy losses. These fundamental insights into their inner workings are indispensable for ultimately selecting or designing better zeolite catalysts.

Unraveling the reaction mechanisms governing methanol-to-olefins catalysis by theory and experiment.

The conversion of methanol to olefins (MTO) over a heterogeneous nanoporous catalyst material is a highly complex process involving a cascade of elementary reactions. The elucidation of the reaction mechanisms leading to either the desired production of ethene and/or propene or undesired deactivation has challenged researchers for many decades. Clearly, catalyst choice, in particular topology and acidity, as well as the specific process conditions determine the overall MTO activity and selectivity; however, the subtle balances between these factors remain not fully understood. In this review, an overview of proposed reaction mechanisms for the MTO process is given, focusing on the archetypal MTO catalysts, H-ZSM-5 and H-SAPO-34. The presence of organic species, that is, the so-called hydrocarbon pool, in the inorganic framework forms the starting point for the majority of the mechanistic routes. The combination of theory and experiment enables a detailed description of reaction mechanisms and corresponding reaction intermediates. The identification of such intermediates occurs by different spectroscopic techniques, for which theory and experiment also complement each other. Depending on the catalyst topology, reaction mechanisms proposed thus far involve aromatic or aliphatic intermediates. Ab initio simulations taking into account the zeolitic environment can nowadays be used to obtain reliable reaction barriers and chemical kinetics of individual reactions. As a result, computational chemistry and by extension computational spectroscopy have matured to the level at which reliable theoretical data can be obtained, supplying information that is very hard to acquire experimentally. Special emphasis is given to theoretical developments that open new perspectives and possibilities that aid to unravel a process as complex as methanol conversion over an acidic porous material.

Polycaprolactone and polycaprolactone/chitosan nanofibres functionalised with the pH-sensitive dye Nitrazine Yellow.

Nanofibres functionalised with pH-sensitive dyes could greatly contribute to the development of stimuli-responsive materials. However, the application of biocompatible polymers is vital to allow for their use in (bio)medical applications. Therefore, this paper focuses on the development and characterisation of pH-sensitive polycaprolactone (PCL) nanofibrous structures and PCL/chitosan nanofibrous blends with 20% chitosan. Electrospinning with added Nitrazine Yellow molecules proved to be an excellent method resulting in pH-responsive non-wovens. Unlike the slow and broad response of PCL nanofibres (time lag of more than 3h), the use of blends with chitosan led to an increased sensitivity and significantly reduced response time (time lag of 5 min). These important effects are attributed to the increased hydrophilic nature of the nanofibres containing chitosan. Computational calculations indicated stronger interactions, mainly based on electrostatic interactions, of the dye with chitosan (ΔG of -132.3 kJ/mol) compared to the long-range interactions with PCL (ΔG of -35.6 kJ/mol), thus underpinning our experimental observations. In conclusion, because of the unique characteristics of chitosan, the use of PCL/chitosan blends in pH-sensitive biocompatible nanofibrous sensors is crucial.

Investigating the halochromic properties of azo dyes in an aqueous environment by using a combined experimental and theoretical approach.

The halochromism in solution of a prototypical example of an azo dye, ethyl orange, was investigated by using a combined theoretical and experimental approach. Experimental UV/Vis and Raman spectroscopy pointed towards a structural change of the azo dye with changing pH value (in the range pH 5-3). The pH-sensitive behavior was modeled through a series of ab initio computations on the neutral and various singly and doubly protonated structures. For this purpose, contemporary DFT functionals (B3LYP, CAM-B3LYP, and M06) were used in combination with implicit modeling of the water solvent environment. Static calculations were successful in assigning the most-probable protonation site. However, to fully understand the origin of the main absorption peaks, a molecular dynamics simulation study in a water molecular environment was used in combination with time-dependent DFT (TD-DFT) calculations to deduce average UV/Vis spectra that take into account the flexibility of the dye and the explicit interactions with the surrounding water molecules. This procedure allowed us to achieve a remarkable agreement between the theoretical and experimental UV/Vis spectrum and enabled us to fully unravel the pH-sensitive behavior of ethyl orange in aqueous environment.

Competitive reactions of organophosphorus radicals on coke surfaces.

The efficacy of organophosphorus radicals as anticoking agents was subjected to a computational study in which a representative set of radicals derived from industrially relevant organophosphorus additives was used to explore competitive reaction pathways on the graphene-like coke surface formed during thermal cracking. The aim was to investigate the nature of the competing reactions of different organophosphorus radicals on coke surfaces, and elucidate their mode of attack and inhibiting effect on the forming coke layer by use of contemporary computational methods. Density functional calculations on benzene and a larger polyaromatic hydrocarbon, namely, ovalene, showed that organophosphorus radicals have a high propensity to add to the periphery of the coke surface, inhibiting methyl radical induced hydrogen abstraction, which is known to be a key step in coke growth. Low addition barriers reported for a phosphatidyl radical suggest competitive aptitude against coke formation. Moreover, organophosphorus additives bearing aromatic substituents, which were shown to interact with the coke surface through dispersive π-π stacking interactions, are suggested to play a nontrivial role in hindering further stacking among coke surfaces. This may be the underlying rationale behind experimental observation of softer coke in the presence of organophosphorus radicals. The ultimate goal is to provide information that will be useful in building single-event microkinetic models. This study presents pertinent information on potential reactions that could be taken up in these models.

Theoretical simulations elucidate the role of naphthalenic species during methanol conversion within H-SAPO-34.

The role of naphthalenic species during the methanol-to-olefins (MTO) process in a silicoaluminophosphate zeolitic material exhibiting the chabazite topology (H-SAPO-34) has been studied from first principles. These species could either act as active olefin-eliminating compounds or as precursors for deactivating species. Results incorporating van der Waals contributions for finite large clusters point out that successive methylation steps of naphthalenic compounds are feasible. The calculated intrinsic activation barrier is relatively independent of the number of methyl groups already attached on the aromatic compound and is approximately 140 kJ mol(-1). The influence of the composition of the catalyst and hence the acidic strength on the intrinsic chemical kinetics was investigated in detail through comparison with the isostructural high-silicon material. Apparent chemical kinetics, starting from adsorbed methanol on the acid site, were also computed. The initiation steps of the side-chain route starting from a trimethylated naphthalenium ion were also examined. The actual side-chain methylation exhibits a high barrier and hence this mechanism involving methylated naphthalenes is not expected to be an active ethene-eliminating route in H-SAPO-34.

Validation of DFT-based methods for predicting qualitative thermochemistry of large polyaromatics.

We present a validation of computationally efficient density functional-based methods for the reproduction of relative bond dissociation energies of large polyaromatic hydrocarbons. Through the calculation of intrinsic radical stabilities and the computation of spin densities, the extent of delocalization of the unpaired electron in the benzylic radicals is examined. We focus on the influence of the level of theory choice applied for the geometry optimization and the role of van der Waals corrections on thermochemical properties. The dispersion effects mainly influence the energetics, causing a small upward shift of the bond dissociation energies. The long-range corrected CAM-B3LYP functional does not improve the traditional B3LYP results for the geometry description of the large delocalized radicals, however a non-negligible influence was encountered when applied for the energetics. It is reported that the f polarization functions present in the 6-311+G(3df,2p) basis set lead to an erroneous trend when combined with the B2PLYP functional for the computation of the single point energies.

First principle kinetic studies of zeolite-catalyzed methylation reactions.

Methylations of ethene, propene, and butene by methanol over the acidic microporous H-ZSM-5 catalyst are studied by means of state of the art computational techniques, to derive Arrhenius plots and rate constants from first principles that can directly be compared with the experimental data. For these key elementary reactions in the methanol to hydrocarbons (MTH) process, direct kinetic data became available only recently [J. Catal.2005, 224, 115-123; J. Catal.2005, 234, 385-400]. At 350 °C, apparent activation energies of 103, 69, and 45 kJ/mol and rate constants of 2.6 × 10(-4), 4.5 × 10(-3), and 1.3 × 10(-2) mol/(g h mbar) for ethene, propene, and butene were derived, giving following relative ratios for methylation k(ethene)/k(propene)/k(butene) = 1:17:50. In this work, rate constants including pre-exponential factors are calculated which give very good agreement with the experimental data: apparent activation energies of 94, 62, and 37 kJ/mol for ethene, propene, and butene are found, and relative ratios of methylation k(ethene)/k(propene)/k(butene) = 1:23:763. The entropies of gas phase alkenes are underestimated in the harmonic oscillator approximation due to the occurrence of internal rotations. These low vibrational modes were substituted by manually constructed partition functions. Overall, the absolute reaction rates can be calculated with near chemical accuracy, and qualitative trends are very well reproduced. In addition, the proposed scheme is computationally very efficient and constitutes significant progress in kinetic modeling of reactions in heterogeneous catalysis.

TAMkin: a versatile package for vibrational analysis and chemical kinetics.

TAMkin is a program for the calculation and analysis of normal modes, thermochemical properties and chemical reaction rates. At present, the output from the frequently applied software programs ADF, CHARMM, CPMD, CP2K, Gaussian, Q-Chem, and VASP can be analyzed. The normal-mode analysis can be performed using a broad variety of advanced models, including the standard full Hessian, the Mobile Block Hessian, the Partial Hessian Vibrational approach, the Vibrational Subsystem Analysis with or without mass matrix correction, the Elastic Network Model, and other combinations. TAMkin is readily extensible because of its modular structure. Chemical kinetics of unimolecular and bimolecular reactions can be analyzed in a straightforward way using conventional transition state theory, including tunneling corrections and internal rotor refinements. A sensitivity analysis can also be performed, providing important insight into the theoretical error margins on the kinetic parameters. Two extensive examples demonstrate the capabilities of TAMkin: the conformational change of the biological system adenylate kinase is studied, as well as the reaction kinetics of the addition of ethene to the ethyl radical. The important feature of batch processing large amounts of data is highlighted by performing an extended level of theory study, which TAMkin can automate significantly.

Opposite regiospecific ring opening of 2-(cyanomethyl)aziridines by hydrogen bromide and benzyl bromide: experimental study and theoretical rationalization.

Ring opening of 1-arylmethyl-2-(cyanomethyl)aziridines with HBr afforded 3-(arylmethyl)amino-4-bromobutyronitriles via regiospecific ring opening at the unsubstituted aziridine carbon. Previous experimental and theoretical reports show treatment of the same compounds with benzyl bromide to furnish 4-amino-3-bromobutanenitriles through ring opening at the substituted aziridine carbon. To gain insights into the regioselective preference with HBr, reaction paths have been analyzed with computational methods. The effect of solvation was taken into account by the use of explicit solvent molecules. Geometries were determined at the B3LYP/6-31++G(d,p) level of theory, and a Grimme-type correction term was included for long-range dispersion interactions; relative energies were refined with the meta-hybrid MPW1B95 functional. Activation barriers confirm preference for ring opening at the unsubstituted ring carbon for HBr. HBr versus benzyl bromide ring opening was analyzed through comparison of the electronic structure of corresponding aziridinium intermediates. Although the electrostatic picture fails to explain the opposite regiospecific nature of the reaction, frontier molecular orbital analysis of LUMOs and nucleophilic Fukui functions show a clear preference of attack for the substituted aziridine carbon in the benzyl bromide case and for the unsubstituted aziridine carbon in the HBr case, successfully rationalizing the experimentally observed regioselectivity.

Bond dissociation energies of organophosphorus compounds: an assessment of contemporary ab initio procedures.

Thermodynamic properties of phosphorus-containing compounds were investigated using high-level ab initio computations. An extended set of contemporary density functional theory (DFT) procedures was assessed for their ability to accurately predict bond dissociation energies of a set of phosphoranyl radicals. The results of meta- and double-hybrids as well as more recent methods, in particular M05, M05-2X, M06, and M06-2X, were compared with benchmark G3(MP2)-RAD values. Standard heats of formation, entropies, and heat capacities of a set of ten organophosphorus compounds were determined and the low-cost BMK functional was found to provide results consistent with available experimental data. In addition, bond dissociation enthalpies (BDEs) were computed using the BMK, M05-2X, and SCS-ROMP2 procedure. The three methods give the same stability trend. The BDEs of the phosphorus(III) molecules were found to be lower than their phosphorus(V) counterparts. Overall, the following ordering is found: BDE(P-OPh) < BDE(P-CH(3)) < BDE(P-Ph) < BDE(P-OCH(3)).

Levofloxacin ozonation in water: rate determining process parameters and reaction pathway elucidation.

Ozonation of the quinolone antibiotic levofloxacin was investigated with focus on both the levofloxacin degradation rate and degradation product formation. Degradation was about 2 times faster at pH 10 compared to pH 3 and 7 explained by direct ozonation at the unprotonated N4('), one of the tertiary amines of the piperazinyl substituent. H2O2 concentration (2-100 microM) had only limited effect. Liquid chromatography - high resolution mass spectrometry revealed degradation at the piperazinyl substituent and the quinolone moiety, with the relative importance of both pathways being strongly affected by changes in pH. Levofloxacin N-oxide concentrations reached up to 40% of the initial levofloxacin concentration during ozonation at pH 10. Degradation at the quinolone moiety resulted in isatin and anthranilic acid type metabolites, probably formed through reaction with hydroxyl radicals. Ab initio molecular orbital calculations predicted radical attack mainly at C2 of the quinolone moiety. This is the carbon atom with the largest Fukui function. Reaction with ozone is expected to mainly occur at N(4)('), characterized by the largest negative charge.

Bond dissociation enthalpies of large aromatic carbon-centered radicals.

Carbon-hydrogen bond dissociation enthalpy (BDE) values are computed for the class of benzylic radicals. An extended and representative set of large methylated polyaromatics has been submitted to an accurate computational study using various levels of theory. The hybrid B3P86 as well as two contemporary functionals (BMK and M05-2X) are applied. For a selection of species, the suitability of the DFT methods is validated through comparison with high-level G3(MP2)-RAD and SCS-ROMP2 results. The influence of the polyaromatic environment on the BDE results is thoroughly discussed. The results are compared with other hydrocarbon radical types in order to obtain a generalized radical stability scale. In order to complete this investigation, also carbon-carbon BDE values have been calculated, giving information about the influence of the local environment on removing the methyl group from the polyaromatic.

A DFT-based investigation of hydrogen abstraction reactions from methylated polycyclic aromatic hydrocarbons.

The growth of polycyclic aromatic hydrocarbons (PAHs) is in many areas of combustion and pyrolysis of hydrocarbons an inconvenient side effect that warrants an extensive investigation of the underlying reaction mechanism, which is known to be a cascade of radical reactions. Herein, the focus lies on one of the key reaction classes within the coke formation process: hydrogen abstraction reactions induced by a methyl radical from methylated benzenoid species. It has been shown previously that hydrogen abstractions determine the global PAH formation rate. In particular, the influence of the polyaromatic environment on the thermodynamic and kinetic properties is the subject of a thorough exploration. Reaction enthalpies at 298 K, reaction barriers at 0 K, rate constants, and kinetic parameters (within the temperature interval 700-1100 K) are calculated by using B3LYP/6-31+G(d,p) geometries and BMK/6-311+G(3df,2p) single-point energies. This level of theory has been validated with available experimental data for the abstraction at toluene. The enhanced stability of the product benzylic radicals and its influence on the reaction enthalpies is highlighted. Corrections for tunneling effects and hindered (or free) rotations of the methyl group are taken into account. The largest spreading in thermochemical and kinetic data is observed in the series of linear acenes, and a normal reactivity-enthalpy relationship is obtained. The abstraction of a methyl hydrogen atom at one of the center rings of large methylated acenes is largely preferred. Geometrical and electronic aspects lie at the basis of this striking feature. Comparison with hydrogen abstractions leading to arylic radicals is also made.