Paul Sherwood

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.

QUASI: A general purpose implementation of the QM/MM approach and its application to problems in catalysis

Abstract We describe the work of the European project QUASI (Quantum Simulation in Industry, project EP25047) which has sought to develop a flexible QM/MM scheme and to apply it to a range of industrial problems. A number of QM/MM approaches were implemented within the computational chemistry scripting system, ChemShell, which provides the framework for deploying a variety of independent program packages. This software was applied in several large-scale QM/MM studies which addressed the catalytic decomposition of N 2 O by Cu-containing zeolites, the methanol synthesis reaction catalysed by Cu clusters supported on ZnO surfaces, and the modelling of enzyme structure and reactivity.

The GAMESS-UK electronic structure package: algorithms, developments and applications

A description of the ab initio quantum chemistry package GAMESS-UK is presented. The package offers a wide range of quantum mechanical wavefunctions, capable of treating systems ranging from closed-shell molecules through to the species involved in complex reaction mechanisms. The availability of a wide variety of correlation methods provides the necessary functionality to tackle a number of chemically important tasks, ranging from geometry optimization and transition-state location to the treatment of solvation effects and the prediction of excited state spectra. With the availability of relativistic ECPs and the development of ZORA, such calculations may be performed on the entire Periodic Table, including the lanthanides. Emphasis is given to the DFT module, which has been extensively developed in recent years, and a number of other, novel features of the program. The parallelization strategy used in the program is outlined, and detailed speedup results are given. Applications of the code in the areas of enzyme and zeolite catalysis and in spectroscopy are described.

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.

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.g. a coarse-grained or grid model using parameterization from MD simulations), and via concurrent approaches, where the calculations are performed together and together control the progression of the simulation. We suggest how the concurrent coupling approach familiar in the context of QM/MM calculations can be generalized, and describe how this has been done in the CHARMM macromolecular simulation package.

Optimization of quantum mechanical molecular mechanical partitioning schemes: Gaussian delocalization of molecular mechanical charges and the double link atom method

Two new techniques for modeling chemical processes in condensed phases with combined quantum mechanical and molecular mechanical (QM/MM) potentials are introduced and tested on small, model compounds. The first technique, the double link atom (DLA) method, is an extension of the traditional, single link atom (SLA) method to avoid some of the problems with the latter method. These problems are primarily electrostatic, as the SLA method can produce an unphysical overall charge or dipole. The second technique, the delocalized Gaussian MM charge (DGMM) method, is an empirical way to include the delocalized character of the electron density of atoms in the MM region. This can be important for the electrostatic interaction of the QM region with nearby atoms in the MM region, and it can simplify the rules governing which classical interactions are included in the energies and forces. Even for very short distances, the DGMM method does not require the neglect of the MM host in the QM calculation. The DGMM method ...

Superlinearly converging dimer method for transition state search

Algorithmic improvements of the dimer method [G. Henkelman and H. Jonsson, J. Chem. Phys. 111, 7010 (1999)] are described in this paper. Using the limited memory Broyden-Fletcher-Goldfarb-Shanno (L-BFGS) optimizer for the dimer translation greatly improves the convergence compared to the previously used conjugate gradient algorithm. It also saves one energy and gradient calculation per dimer iteration. Extrapolation of the gradient during repeated dimer rotations reduces the computational cost to one gradient calculation per dimer rotation. The L-BFGS algorithm also improves convergence of the rotation. Thus, three to four energy and gradient evaluations are needed per iteration at the beginning of a transition state search, while only two are required close to convergence. Moreover, we apply the dimer method in internal coordinates to reduce coupling between the degrees of freedom. Weighting the coordinates can be used to apply chemical knowledge about the system and restrict the transition state search to only part of the system while minimizing the remainder. These improvements led to an efficient method for the location of transition states without the need to calculate the Hessian. Thus, it is especially useful in large systems with expensive gradient evaluations.

ChemShell—a modular software package for QM/MM simulations

ChemShell is a modular computational chemistry package with a particular focus on hybrid quantum mechanical/molecular mechanical (QM/MM) simulations. A core set of chemical data handling modules and scripted interfaces to a large number of quantum chemistry and molecular modeling packages underpin a flexible QM/MM scheme. ChemShell has been used in the study of small molecules, molecular crystals, biological macromolecules such as enzymes, framework materials including zeolites, ionic solids, and surfaces. We outline the range of QM/MM coupling schemes and supporting functions for system setup, geometry optimization, and transition‐state location (including those from the open‐source DL‐FIND optimization library). We discuss recently implemented features allowing a more efficient treatment of long range electrostatic interactions, X‐ray based quantum refinement of crystal structures, free energy methods, and excited‐state calculations. ChemShell has been ported to a range of parallel computers and we describe a number of options including parallel execution based on the message‐passing capabilities of the interfaced packages and task‐farming for applications in which a number of individual QM, MM, or QM/MM calculations can performed simultaneously. We exemplify each of the features by brief reference to published applications.

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. The approach is applicable to a wide range of metal centers.

Computer simulation of zeolite structure and reactivity using embedded cluster methods

The use of bare cluster models to understand the nature of zeolite–substrate interactions may be improved to take account of the environment of the Bronsted acid site. We consider two models for introducing the electrostatic effects of the zeolite lattice. The first involves generating a specialised correction potential by fitting a non-periodic array of ca. 60 point charges to the difference between the bare cluster and periodic potentials. The second starts by fitting a periodic array of atomic charges to the potential of the infinite lattice and then builds up a classical cluster of ca. 2000 atoms into which the QM cluster is embedded. Such embedded cluster calculations, employing a T3 cluster, with electron correlation at the density functional theory level, are described, to model the interaction of water at a Bronsted acid site. Structures of the water–zeolite complex, and associated vibrational frequencies and 1H NMR shifts are calculated and compared with calculations of bare clusters of varying size and with experimental data. We then describe a mixed quantum mechanical–molecular mechanical (QM–MM) model derived by combining charges from the second model with a standard aluminosilicate force field. We report preliminary results on the effect of embedding on the energetics of a prototypical hydrocarbon cracking reaction; the methyl-shift reaction of a propenium ion coordinated to the acid site.