Bulk and Surface Contributions to Ionisation Potentials of Metal Oxides.

Determining the absolute band edge positions in solid materials is crucial for optimising their performance in wide-ranging applications including photocatalysis and electronic devices. However, obtaining absolute energies is challenging, as seen in CeO2 , where experimental measurements show substantial discrepancies in the ionisation potential (IP). Here, we have combined several theoretical approaches, from classical electrostatics to quantum mechanics, to elucidate the bulk and surface contributions to the IP of metal oxides. We have determined a theoretical bulk contribution to the IP of stoichiometric CeO2 of only 5.38 eV, while surface orientation results in intrinsic IP variations ranging from 4.2 eV to 8.2 eV. Highly tuneable IPs were also found in TiO2 , ZrO2 , and HfO2 , in which surface polarisation plays a pivotal role in long-range energy level shifting. Our analysis, in addition to rationalising the observed range of experimental results, provides a firm basis for future interpretations of experimental and computational studies of oxide band structures.

Computational infrared and Raman spectra by hybrid QM/MM techniques: a study on molecular and catalytic material systems.

Vibrational spectroscopy is one of the most well-established and important techniques for characterizing chemical systems. To aid the interpretation of experimental infrared and Raman spectra, we report on recent theoretical developments in the ChemShell computational chemistry environment for modelling vibrational signatures. The hybrid quantum mechanical and molecular mechanical approach is employed, using density functional theory for the electronic structure calculations and classical forcefields for the environment. Computational vibrational intensities at chemical active sites are reported using electrostatic and fully polarizable embedding environments to achieve more realistic vibrational signatures for materials and molecular systems, including solvated molecules, proteins, zeolites and metal oxide surfaces, providing useful insight into the effect of the chemical environment on the signatures obtained from experiment. This work has been enabled by the efficient task-farming parallelism implemented in ChemShell for high-performance computing platforms.  This article is part of a discussion meeting issue 'Supercomputing simulations of advanced materials'.

Multiscale QM/MM modelling of catalytic systems with ChemShell.

Hybrid quantum mechanical/molecular mechanical (QM/MM) methods are a powerful computational tool for the investigation of all forms of catalysis, as they allow for an accurate description of reactions occurring at catalytic sites in the context of a complicated electrostatic environment. The scriptable computational chemistry environment ChemShell is a leading software package for QM/MM calculations, providing a flexible, high performance framework for modelling both biomolecular and materials catalysis. We present an overview of recent applications of ChemShell to problems in catalysis and review new functionality introduced into the redeveloped Python-based version of ChemShell to support catalytic modelling. These include a fully guided workflow for biomolecular QM/MM modelling, starting from an experimental structure, a periodic QM/MM embedding scheme to support modelling of metallic materials, and a comprehensive set of tutorials for biomolecular and materials modelling.

Toward a Consistent Prediction of Defect Chemistry in CeO2.

Polarizable shell-model potentials are widely used for atomic-scale modeling of charged defects in solids using the Mott-Littleton approach and hybrid Quantum Mechanical/Molecular Mechanical (QM/MM) embedded-cluster techniques. However, at the pure MM level of theory, the calculated defect energetics may not satisfy the requirement of quantitative predictions and are limited to only certain charged states. Here, we proposed a novel interatomic potential development scheme that unifies the predictions of all relevant charged defects in CeO2 based on the Mott-Littleton approach and QM/MM electronic-structure calculations. The predicted formation energies of oxygen vacancies accompanied by different excess electron localization patterns at the MM level of theory reach the accuracy of density functional theory (DFT) calculations using hybrid functionals. The new potential also accurately reproduces a wide range of physical properties of CeO2, showing excellent agreement with experimental and other computational studies. These findings provide opportunities for accurate large-scale modeling of the partial reduction and nonstoichiometry in CeO2, as well as a prototype for developing robust interatomic potentials for other defective crystals.

Influence of Solvent on Selective Catalytic Reduction of Nitrogen Oxides with Ammonia over Cu-CHA Zeolite.

The copper-exchanged zeolite Cu-CHA has received considerable attention in recent years, owing to its application in the selective catalytic reduction (SCR) of NOx species. Here, we study the NH3-SCR reaction mechanism on Cu-CHA using the hybrid quantum mechanical/molecular mechanical (QM/MM) technique and investigate the effects of solvent on the reactivity of active Cu species. To this end, a comparison is made between water- and ammonia-solvated and bare Cu species. The results show the promoting effect of solvent on the oxidation component of the NH3-SCR cycle since the formation of important nitrate species is found to be energetically more favorable on the solvated Cu sites than in the absence of solvent molecules. Conversely, both solvent molecules are predicted to inhibit the reduction component of the NH3-SCR cycle. Diffuse reflectance infrared fourier-transform spectroscopy (DRIFTS) experiments exploiting (concentration) modulation excitation spectroscopy (MES) and phase-sensitive detection (PSD) identified spectroscopic signatures of Cu-nitrate and Cu-nitrosamine (H2NNO), important species which had not been previously observed experimentally. This is further supported by the QM/MM-calculated harmonic vibrational analysis. Additional insights are provided into the reactivity of solvated active sites and the formation of key intermediates including their formation energies and vibrational spectroscopic signatures, allowing the development of a detailed understanding of the reaction mechanism. We demonstrate the role of solvated active sites and their influence on the energetics of important species that must be explicitly considered for an accurate understanding of NH3-SCR kinetics.

The Interplay of Interstitial and Substitutional Copper in Zinc Oxide.

Cu impurities are reported to have significant effects on the electrical and optical properties of bulk ZnO. In this work, we study the defect properties of Cu in ZnO using hybrid quantum mechanical/molecular mechanical (QM/MM)-embedded cluster calculations based on a multi-region approach that allows us to model defects at the true dilute limit, with polarization effects described in an accurate and consistent manner. We compute the electronic structure, energetics, and geometries of Cu impurities, including substitutional and interstitial configurations, and analyze their effects on the electronic structure. Under ambient conditions, CuZn is the dominant defect in the d9 state and remains electronically passive. We find that, however, as we approach typical vacuum conditions, the interstitial Cu defect becomes significant and can act as an electron trap.

QM/MM Simulations of Protein Crystal Reactivity Guided by MSOX Crystallography: A Copper Nitrite Reductase Case Study.

The recently developed multiple structures from one crystal (MSOX) serial crystallography method can be used to provide multiple snapshots of the progress of enzymatic reactions taking place within a protein crystal. Such MSOX snapshots can be used as a reference for combined quantum mechanical/molecular mechanical (QM/MM) simulations of enzyme reactivity within the crystal. QM/MM calculations are used to identify details of reference states that cannot be directly observed by X-ray diffraction experiments, such as protonation and oxidation states. These reference states are then used as known fixed endpoints for the modeling of reaction paths. We investigate the mechanism of nitrite reduction in an Achromobacter cycloclastes copper nitrite reductase crystal using MSOX-guided QM/MM calculations, identifying the change in nitrite binding orientation with a change in copper oxidation state, and determining the reaction path to the final NO-bound MSOX structure. The results are compared with QM/MM simulations performed in a solvated environment.

Open-Source, Python-Based Redevelopment of the ChemShell Multiscale QM/MM Environment.

ChemShell is a scriptable computational chemistry environment with an emphasis on multiscale simulation of complex systems using combined quantum mechanical and molecular mechanical (QM/MM) methods. Motivated by a scientific need to efficiently and accurately model chemical reactions on surfaces and within microporous solids on massively parallel computing systems, we present a major redevelopment of the ChemShell code, which provides a modern platform for advanced QM/MM embedding models. The new version of ChemShell has been re-engineered from the ground up with a new QM/MM driver module, an improved parallelization framework, new interfaces to high performance QM and MM programs, and a user interface written in the Python programming language. The redeveloped package is capable of performing QM/MM calculations on systems of significantly increased size, which we illustrate with benchmarks on zirconium dioxide nanoparticles of over 160000 atoms.

A QM/MM Study of Nitrite Binding Modes in a Three-Domain Heme-Cu Nitrite Reductase.

Copper-containing nitrite reductases (CuNiRs) play a key role in the global nitrogen cycle by reducing nitrite (NO2-) to nitric oxide, a reaction that involves one electron and two protons. In typical two-domain CuNiRs, the electron is acquired from an external electron-donating partner. The recently characterised Rastonia picketti (RpNiR) system is a three-domain CuNiR, where the cupredoxin domain is tethered to a heme c domain that can function as the electron donor. The nitrite reduction starts with the binding of NO2- to the T2Cu centre, but very little is known about how NO2- binds to native RpNiR. A recent crystallographic study of an RpNiR mutant suggests that NO2- may bind via nitrogen rather than through the bidentate oxygen mode typically observed in two-domain CuNiRs. In this work we have used combined quantum mechanical/molecular mechanical (QM/MM) methods to model the binding mode of NO2- with native RpNiR in order to determine whether the N-bound or O-bound orientation is preferred. Our results indicate that binding via nitrogen or oxygen is possible for the oxidised Cu(II) state of the T2Cu centre, but in the reduced Cu(I) state the N-binding mode is energetically preferred.

Enzyme catalysis captured using multiple structures from one crystal at varying temperatures.

High-resolution crystal structures of enzymes in relevant redox states have transformed our understanding of enzyme catalysis. Recent developments have demonstrated that X-rays can be used, via the generation of solvated electrons, to drive reactions in crystals at cryogenic temperatures (100 K) to generate 'structural movies' of enzyme reactions. However, a serious limitation at these temperatures is that protein conformational motion can be significantly supressed. Here, the recently developed MSOX (multiple serial structures from one crystal) approach has been applied to nitrite-bound copper nitrite reductase at room temperature and at 190 K, close to the glass transition. During both series of multiple structures, nitrite was initially observed in a 'top-hat' geometry, which was rapidly transformed to a 'side-on' configuration before conversion to side-on NO, followed by dissociation of NO and substitution by water to reform the resting state. Density functional theory calculations indicate that the top-hat orientation corresponds to the oxidized type 2 copper site, while the side-on orientation is consistent with the reduced state. It is demonstrated that substrate-to-product conversion within the crystal occurs at a lower radiation dose at 190 K, allowing more of the enzyme catalytic cycle to be captured at high resolution than in the previous 100 K experiment. At room temperature the reaction was very rapid, but it remained possible to generate and characterize several structural states. These experiments open up the possibility of obtaining MSOX structural movies at multiple temperatures (MSOX-VT), providing an unparallelled level of structural information during catalysis for redox enzymes.

Active-site protein dynamics and solvent accessibility in native Achromobacter cycloclastes copper nitrite reductase.

Microbial nitrite reductases are denitrifying enzymes that are a major component of the global nitrogen cycle. Multiple structures measured from one crystal (MSOX data) of copper nitrite reductase at 240 K, together with molecular-dynamics simulations, have revealed protein dynamics at the type 2 copper site that are significant for its catalytic properties and for the entry and exit of solvent or ligands to and from the active site. Molecular-dynamics simulations were performed using different protonation states of the key catalytic residues (AspCAT and HisCAT) involved in the nitrite-reduction mechanism of this enzyme. Taken together, the crystal structures and simulations show that the AspCAT protonation state strongly influences the active-site solvent accessibility, while the dynamics of the active-site 'capping residue' (IleCAT), a determinant of ligand binding, are influenced both by temperature and by the protonation state of AspCAT. A previously unobserved conformation of IleCAT is seen in the elevated temperature series compared with 100 K structures. DFT calculations also show that the loss of a bound water ligand at the active site during the MSOX series is consistent with reduction of the type 2 Cu atom.

Modelling the chemistry of Mn-doped MgO for bulk and (100) surfaces.

We have investigated the energetic properties of Mn-doped MgO bulk and (100) surfaces using a QM/MM embedding computational method, calculating the formation energy for doped systems, as well as for surface defects, and the subsequent effect on chemical reactivity. Low-concentration Mn doping is endothermic for isovalent species in the bulk but exothermic for higher oxidation states under p-type conditions, and compensated by electrons going to the Fermi level rather than cation vacancies. The highest occupied dopant Mn 3d states are positioned in the MgO band gap, about 4.2 eV below the vacuum level. Surface Mn-doping is more favourable than subsurface doping, and marginally exothermic on a (100) surface at high O2 pressures. For both types of isovalent Mn-doped (100) surfaces, the formation energy for catalytically important oxygen defects is less than for pristine MgO, with F0 and F2+-centres favoured in n- and p-type conditions, respectively. In addition, F+-centres are stabilised by favourable exchange coupling between the Mn 3d states and the vacancy-localised electrons, as verified through calculation of the vertical ionisation potential. The adsorption of CO2 on to the pristine and defective (100) surface is used as a probe of chemical reactivity, with isovalent subsurface Mn dopants mildly affecting reactivity, whereas isovalent surface-positioned Mn strongly alters the chemical interactions between the substrate and adsorbate. The differing chemical reactivity, when compared to pristine MgO, justifies further detailed investigations for more varied oxidation states and dopant species.

Band alignment of rutile and anatase TiO2.

The most widely used oxide for photocatalytic applications owing to its low cost and high activity is TiO2. The discovery of the photolysis of water on the surface of TiO2 in 1972 launched four decades of intensive research into the underlying chemical and physical processes involved. Despite much collected evidence, a thoroughly convincing explanation of why mixed-phase samples of anatase and rutile outperform the individual polymorphs has remained elusive. One long-standing controversy is the energetic alignment of the band edges of the rutile and anatase polymorphs of TiO2 (ref. ). We demonstrate, through a combination of state-of-the-art materials simulation techniques and X-ray photoemission experiments, that a type-II, staggered, band alignment of ~ 0.4 eV exists between anatase and rutile with anatase possessing the higher electron affinity, or work function. Our results help to explain the robust separation of photoexcited charge carriers between the two phases and highlight a route to improved photocatalysts.

Activation of carbon dioxide over zinc oxide by localised electrons.

The unique mechanism of activation of carbon dioxide over zinc oxide is unravelled using advanced quantum mechanical methods. The key process is the CO(2) chemisorption catalysed by a highly localized electron carrier trapped at a vacant oxygen interstitial surface site. At the top of the reaction barrier CO(2) pulls the electron from the vacancy and thus becomes active.

DL-FIND: an open-source geometry optimizer for atomistic simulations.

Geometry optimization, including searching for transition states, accounts for most of the CPU time spent in quantum chemistry, computational surface science, and solid-state physics, and also plays an important role in simulations employing classical force fields. We have implemented a geometry optimizer, called DL-FIND, to be included in atomistic simulation codes. It can optimize structures in Cartesian coordinates, redundant internal coordinates, hybrid-delocalized internal coordinates, and also functions of more variables independent of atomic structures. The implementation of the optimization algorithms is independent of the coordinate transformation used. Steepest descent, conjugate gradient, quasi-Newton, and L-BFGS algorithms as well as damped molecular dynamics are available as minimization methods. The partitioned rational function optimization algorithm, a modified version of the dimer method and the nudged elastic band approach provide capabilities for transition-state search. Penalty function, gradient projection, and Lagrange-Newton methods are implemented for conical intersection optimizations. Various stochastic search methods, including a genetic algorithm, are available for global or local minimization and can be run as parallel algorithms. The code is released under the open-source GNU LGPL license. Some selected applications of DL-FIND are surveyed.

Combining insights from solid-state NMR and first principles calculation: applications to the 19F NMR of octafluoronaphthalene.

Advances in solid-state NMR methodology and computational chemistry are applied to the (19)F NMR of solid octafluoronaphthalene. It is demonstrated experimentally, and confirmed by density functional theory (DFT) calculations, that the spectral resolution in the magic-angle spinning spectrum is limited by the anisotropy of the bulk magnetic susceptibility (ABMS). This leads to the unusual observation that the resolution improves as the sample is diluted. DFT calculations provide assignments of each of the peaks in the (19)F spectrum, but the predictions are close to the limits of accuracy and correlation information from 2-D NMR is invaluable in confirming the assignments. The effects of non-Gaussian lineshapes on the use of 2-D NMR for mapping correlations of spectral frequencies (e.g. due to the ABMS) are also discussed.

Assessment of a Coulomb-attenuated exchange-correlation energy functional.

The recently proposed CAM-B3LYP exchange-correlation energy functional, based on a partitioning of the r operator in the exchange interaction into long- and short-range components, is assessed for the determination of molecular thermochemistry, structures, and second order response properties. Rydberg and charge transfer excitation energies and static electronic polarisabilities are notably improved over the standard B3LYP functional; classical reaction barriers also improve. Ionisation potentials, bond lengths, NMR shielding constants and indirect spin-spin coupling constants are comparable with the two functionals. CAM-B3LYP atomisation energies and diatomic harmonic vibrational wavenumbers are less accurate than those of B3LYP. Future research directions are outlined.

Semiempirical hybrid functional with improved performance in an extensive chemical assessment.

It is demonstrated that there is still scope for improvement in the quality of conventional, semiempirical hybrid exchange-correlation functionals in density-functional theory. A new functional, denoted B97-3, is determined from a fit to eight chemical properties (316 data points). For a series of 25 chemical assessments (850 data points) including 17 assessments and 10 chemical properties absent from the fitting data, B97-3 provides the lowest or joint-lowest mean absolute error on 15 occasions, compared to 6, 5, and 4 occasions for B3LYP, PBE0, and B97-2, respectively [A. D. Becke, J. Chem. Phys. 98, 5648 (1993); M. Ernzerhof and G. E. Scuseria, J. Chem. Phys. 110, 5029 (1999); C. Adamo and V. Barone, J. Chem. Phys. 110, 6158 (1999); P. J. Wilson, T. J. Bradley, and D. J. Tozer, J. Chem. Phys. 115, 9233 (2001)]. Mean absolute errors from B97-3 are, on average, 21%, 18%, and 12% smaller than from these three functionals. The most notable improvements are obtained for classical reaction barriers, where the error reductions are 60%, 54%, and 27%.

A semiempirical generalized gradient approximation exchange-correlation functional.

We describe our attempts to improve upon the quality of the KT1 and KT2 generalized gradient approximation (GGA) exchange-correlation functionals [T. W. Keal and D. J. Tozer, J. Chem. Phys. 119, 3015 (2003)], through the introduction of additional gradient-corrected exchange and correlation terms. A GGA functional, denoted KT3, is presented, which maintains the high quality main-group nuclear magnetic resonance shielding constants obtained with KT1 and KT2; results are 2-3 times more accurate than conventional GGA and hybrid functionals. For the extensive range of systems considered in this study, KT3 also provides atomization energies, ionization potentials, electron affinities, proton affinities, bond angles, and electronic polarizabilities that are comparable to, or that surpass, those of the best present-day GGAs. Furthermore, it provides equilibrium molecular bond lengths and diatomic harmonic vibrational wave numbers that are as accurate as those from the best hybrid functionals. Further improvements are required in the description of classical chemical reaction barriers.