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.

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.

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.

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.

Embedded-cluster calculations in a numeric atomic orbital density-functional theory framework.

We integrate the all-electron electronic structure code FHI-aims into the general ChemShell package for solid-state embedding quantum and molecular mechanical (QM/MM) calculations. A major undertaking in this integration is the implementation of pseudopotential functionality into FHI-aims to describe cations at the QM/MM boundary through effective core potentials and therewith prevent spurious overpolarization of the electronic density. Based on numeric atomic orbital basis sets, FHI-aims offers particularly efficient access to exact exchange and second order perturbation theory, rendering the established QM/MM setup an ideal tool for hybrid and double-hybrid level density functional theory calculations of solid systems.

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.

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.

The Quixote project: Collaborative and Open Quantum Chemistry data management in the Internet age.

Computational Quantum Chemistry has developed into a powerful, efficient, reliable and increasingly routine tool for exploring the structure and properties of small to medium sized molecules. Many thousands of calculations are performed every day, some offering results which approach experimental accuracy. However, in contrast to other disciplines, such as crystallography, or bioinformatics, where standard formats and well-known, unified databases exist, this QC data is generally destined to remain locally held in files which are not designed to be machine-readable.

Acceleration of the GAMESS-UK electronic structure package on graphical processing units.

The approach used to calculate the two-electron integral by many electronic structure packages including generalized atomic and molecular electronic structure system-UK has been designed for CPU-based compute units. We redesigned the two-electron compute algorithm for acceleration on a graphical processing unit (GPU). We report the acceleration strategy and illustrate it on the (ss|ss) type integrals.

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.

An embedded cluster study of the formation of water on interstellar dust grains.

The formation of water in the interstellar medium from hydrogen and oxygen atoms on a pristine olivine surface (forsterite (010)) is investigated with an embedded cluster approach. The 55-atom quantum cluster is described at the density functional level while the remaining 1629 atoms of the surface cluster are described with atomistic potentials. Transition states are most easily calculated with our modified implementation of the climbing-image nudged elastic band method in ChemShell.

Multiscale methods for macromolecular simulations.

In this article we review the key modeling tools available for simulating biomolecular systems. We consider recent developments and representative applications of mixed quantum mechanics/molecular mechanics (QM/MM), elastic network models (ENMs), coarse-grained molecular dynamics, and grid-based tools for calculating interactions between essentially rigid protein assemblies. We consider how the different length scales can be coupled, both in a sequential fashion (e.

Superlinearly converging dimer method for transition state search.

Algorithmic improvements of the dimer method [G. Henkelman and H. Jonsson, J.

Exploiting QM/MM Capabilities in Geometry Optimization: A Microiterative Approach Using Electrostatic Embedding.

We present a microiterative adiabatic scheme for quantum mechanical/molecular mechanical (QM/MM) energy minimization that fully optimizes the MM part in each QM macroiteration. This scheme is applicable not only to mechanical embedding but also to electrostatic and polarized embedding. The electrostatic QM/MM interactions in the microiterations are calculated from electrostatic potential charges fitted on the fly to the QM density.

Point defects in ZnO.

We have investigated intrinsic point defects in ZnO and extended this study to Li, Cu and Al impurity centres. Atomic and electronic structures as well as defect energies have been obtained for the main oxidation states of all defects using our embedded cluster hybrid quantum mechanical/molecular mechanical approach to the treatment of localised states in ionic solids. With these calculations we were able to explain the nature of a number of experimentally observed phenomena.

On the performance of molecular dynamics applications on current high-end systems.

The effective exploitation of current high performance computing (HPC) platforms in molecular simulation relies on the ability of the present generation of parallel molecular dynamics code to make effective utilisation of these platforms and their components, including CPUs and memory. In this paper, we investigate the efficiency and scaling of a series of popular molecular dynamics codes on the UK's national HPC resources, an IBM p690+ cluster and an SGI Altix 3700. Focusing primarily on the AMBER, DL_POLY and NAMD simulation codes, we demonstrate the major performance and scalability advantages that arise through a distributed, rather than a replicated data approach.

Supramolecular chemistry of halogens: complementary features of inorganic (M-X) and organic (C-X') halogens applied to M-X...X'-C halogen bond formation.

Electronic differences between inorganic (M-X) and organic (C-X) halogens in conjunction with the anisotropic charge distribution associated with terminal halogens have been exploited in supramolecular synthesis based upon intermolecular M-X...

Hydrogen bonding and perhalometallate ions: a supramolecular synthetic strategy for new inorganic materials.

A synthetic strategy for constructing ionic hydrogen-bonded materials by combining perhalometallate anions with cations able to serve as hydrogen bond donors is presented. The approach is based on identification of well defined hydrogen bond acceptor sites on the anions by a combination of experimental and theoretical approaches. Selective population of these sites by hydrogen bond donors has the potential to afford organized crystalline arrays in one, two, or three dimensions.