Paul Sherwood

Paul Sherwood
Science and Technology Facilities Council | STFC · Scientific Computing Department

BA, PhD

About

157
Publications
20,220
Reads
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9,279
Citations
Citations since 2016
7 Research Items
4216 Citations
20162017201820192020202120220100200300400500600
20162017201820192020202120220100200300400500600
20162017201820192020202120220100200300400500600
20162017201820192020202120220100200300400500600
Introduction
Visiting Scientist, STFC Daresbury Laboratory, Honorary Professor and Researcher at Department of Chemistry, Lancaster University.
Additional affiliations
November 1989 - present
Science and Technology Facilities Council
Position
  • Head, Applications Division

Publications

Publications (157)
Article
Full-text available
The semiconducting behaviour and optoelectronic response of gallium nitride is governed by point defect processes, which, despite many years of research, remain poorly understood. The key difficulty in the description of the dominant charged defects is determining a consistent position of the corresponding defect levels, which is difficult to deriv...
Article
Full-text available
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 c...
Article
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We have investigated the properties of defects in MnO bulk and at (100) surfaces, as used in catalytic applications, using hybrid-level density functional theory (i.e. inclusion of exact exchange within the exchange-correlation evaluation) in a hybrid QM/MM embedded-cluster approach. Initially, we calculate the formation energy for bulk Mn and O va...
Article
Full-text available
The source of n-type conductivity in undoped transparent conducting oxides has been a topic of debate for several decades. The point defect of most interest in this respect is the oxygen vacancy, but there are many conflicting reports on the shallow versus deep nature of its related electronic states. Here, using a hybrid quantum mechanical/molecul...
Article
Full-text available
The semiconducting behaviour and optoelectronic response of gallium nitride is governed by point defect processes, which are poorly understood. Using hybrid quantum mechanical/molecular mechanical (QM/MM) embedded cluster calculations, we investigate the structure, formation and ionisation energies, and equilibrium concentrations of native point de...
Article
Using hybrid quantum mechanical/molecular mechanical (QM/MM) embedded cluster calculations, we investigate the stabilization of silicon and oxygen dopants in GaN. Formation energies of Si on a Ga site and O on an N site are calculated at two levels of theory using conventional thermochemical and kinetic exchange and correlation density functionals...
Article
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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 exo...
Article
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DOI:https://doi.org/10.1103/PhysRevLett.115.029702
Article
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We report accurate energetics of defects introduced in GaN on doping with divalent metals, focussing on the technologically important case of Mg doping, using a model which takes into consideration both the effect of hole localisation and dipolar polarisation of the host material, and includes a well-defined reference level. Defect formation and io...
Article
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We integrate the all-electron electronic structure code FHI-aims into the general ChemShell package for solid-state embedding (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 pre...
Article
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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...
Article
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The role of defects in materials is one of the long-standing issues in solid-state chemistry and physics. On one hand, intrinsic ionic disorder involving stoichiometric amounts of lattice vacancies and interstitials is known to form in highly ionic crystals. There is a substantial literature on defect formation and the phenomenological limits of do...
Article
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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 explana...
Article
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 a...
Technical Report
Full-text available
The work aims at evaluating the performance of DALTON on different platforms and implementing new strategies to enable the code for petascaling. The activities have been organized into four tasks within PRACE project: (i) Analysis of the current status of the DALTON quantum mechanics (QM) code and identification of bottlenecks, implementation of se...
Article
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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,...
Article
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 str...
Chapter
Computational chemistry covers a wide spectrum of activities ranging from quantum mechanical calculations of the electronic structure of molecules, to classical mechanical simulations of the dynamical properties of many-atom systems, to the mapping of both structure-activity relationships and reaction synthesis steps. Although chemical theory and i...
Article
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A task-farm parallelization framework has been implemented in the ChemShell computational chemistry environment to provid a facility for parallelizing common chemical calculations, including finite-difference Hessian evaluation, the nudged elasti band method for reaction path optimization, and population-based methods for global optimization. The o...
Article
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We performed QM/MM simulations based on density functional theory (DFT) and the density-functional tight binding method (DFTB) to investigate the reaction mechanism of the peptide-bond formation in the ribosome in atomistic detail. We found the key role of the ribosome in the increased availability of mobile ions, the counter-ions to the negatively...
Article
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. T...
Article
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 atomisti...
Article
Interatomic potentials (IP) have demonstrated considerable application in the study of bulk and surfaces of ceria (CeO2), and also the long range component in QM/MM calculations. Despite the development and ability of several IPs to reproduce the structural and dielectric properties of bulk ceria, in the absence of high quality electronic structure...
Article
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 essentiall...
Article
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Density Functional Theory calculations are reported on cage structured BN, AlN, GaN and InN sub- and low nanosize stoichiometric clusters, including two octahedral families of Td and Th symmetry. The structures and energetics are determined, and we observe that BN clusters in particular show high stability with respect to the bulk phase. The cluste...
Article
Hybrid quantum and molecular mechanical calculations have been used to investigate the nucleation and growth of copper clusters on the (0001)-Zn polar surface of ZnO. Our method is based on the embedded molecular cluster approach developed to study point defects in polarizable ionic solids, where we make use of the chemically accurate exchange and...
Article
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 o...
Article
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We present a new and completely parallel method for protein ligand docking. The potential of the docking target structure is obtained directly from the electron density derived through an ab initio computation. A large subregion of the crystal structure of Isocitrate Lyase, was selected as docking target. To allow the full ab initio treatment of...
Article
We used the free-energy perturbation (FEP) method in quantum mechanics/molecular mechanics (QM/MM) calculations to compute the free-energy profile of the hydroxylation reaction in the enzyme p-hydroxybenzoate hydroxylase (PHBH). k statistics were employed to analyze the FEP sampling including estimation of the sampling error. Various approximations...
Article
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 st...
Article
We consider the role that large-scale electronic structure computations can now play in the modelling of the condensed phase. To structure our analysis, we consider four distict ways in which today's scientific targets can be re-scoped to take advantage of advances in computing resources: 1. time to solution-performing the same calculation, with de...
Article
Full-text available
We report a series of computations on the active site in Ti-substituted zeolites, specifically TS-1. Hybrid QM/MM methods based on density functional calculations using the BB1K functional and a valence force field are used to study the processes of hydrolysis of Ti-O-Si linkages and 10 inversion of the TiO4 tetrahedra. The structural features of t...
Article
Brechen und Umklappen: Quantenmechanische/molekülmechanische Rechnungen wurden verwendet, um die Strukturen der aktiven Zentren in Silicalit zu untersuchen, der mit Heteroatomen der Gruppen 4 und 14 dotiert ist. Nach diesen Rechnungen sind tripodale (siehe Bild; Si gelb, O rot, H weiß, Heteroatom blau) oder bipodale Zentren, die durch Hydrolyse und...
Article
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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 s...
Article
Inorganic (M–X) and suitably chosen organic (C–X) halogens exhibit anisotropic electrostatic potentials whose complementary aspects can be exploited to permit supramolecular assembly of molecules or ions based upon attractive M–X…X'–C interactions. Electrostatic potential calculations and crystal syntheses are presented to illustrate this approach...
Article
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...X'-C halogen bonds. The synthesis and crystal structures of a family of compounds trans-[MCl(2)(NC(5)H(4)X...
Article
Full-text available
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 n...
Article
We present a hybrid quantum mechanical/molecular mechanical technique recently developed and implemented in the computational chemistry software environment, ChemShell, aimed at the study of reactions at the surfaces of ionic solids including reconstructed polar surfaces and interfaces. The method follows approaches commonly used for the treatment...
Article
In this paper, we review a series of hybrid QM/MM studies performed on the methanol synthesis catalyst. This work has required development of a new embedded cluster approach suitable for polar surfaces of ionic oxides, which has been implemented in the computer code ChemShell. Five themes have been pursued: simulation of polar oxide surfaces of ZnO...
Article
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 dep...
Article
Full-text available
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 dep...
Article
To study in detail the interaction of copper atoms and clusters in various, potentially important catalytic oxidation states (Cu, Cu(+), and Cu(2+)) on polar surfaces, we have applied a hybrid QM/MM embedding model within the computational chemistry package ChemShell. Using the model, we study specific Cu/ZnO surface sites treated at a high ab init...
Article
A replica path method has been developed and extended for use in complex systems involving hybrid quantum/classical (quantum mechanical/molecular mechanical) coupled potentials. This method involves the definition of a reaction path via replication of a set of macromolecular atoms. An “important” subset of these replicated atoms is restrained with...
Article
In this paper, we review a series of hybrid QM/MM studies performed on the methanol synthesis catalyst. This work has required development of a new embedded cluster approach suitable for polar surfaces of ionic oxides, which has been implemented in the computer code ChemShell. Five themes have been pursued: simulation of polar oxide surfaces of ZnO...
Article
Hydrogenated zinc oxide gives rise to complex vibrational spectra with many prominent features that remain unexplained. Our calculations have unambiguously shown that the presence of vacant oxygen and zinc interstitial surface sites is the only way to rationalize the observed spectra, notably the 1710 cm−1 zinc hydride stretching mode. The large nu...
Article
Full-text available
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 proble...
Article
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 populati...
Conference Paper
Full-text available
Beowulf clusters, on face value, offer the potential of a viable cost effective alternative for the provision of High Performance Computing. In this paper we compare the performance of Beowulf clusters built from commodity "off the shelf" components in the support of major research and production codes, with current high-end hardware such as the IB...
Article
The structures and energetics of the key intermediates in the catalytic conversion of CO2 into methanol (shown in the figure) are investigated. The polarity of the catalytically relevant (000) surface of ZnO gives rise to vacant oxygen sites, which by trapping electrons can promote the reaction. The solid-state embedding method developed is particu...
Article
Struktur und Energetik der Schlüsselintermediate bei der katalytischen Umwandlung von CO2 zu Methanol (siehe Bild) wurden untersucht. Die Polarität der für die Katalyse relevanten (000)-Oberfläche von ZnO führt zu unbesetzten Sauerstoffpositionen, die als Elektronenfallen die Reaktion vorantreiben. Die entwickelte Festphasen-Embedding-Methode eigne...
Article
The similarities and differences between the behavior of carbon-bound and terminal metal-bound halogens and halide ions as potential hydrogen bond acceptors has been extensively investigated through examination of many thousands of interactions present in crystal structures. Halogens in each of these environments are found to engage in hydrogen bon...
Article
Computational chemistry covers a wide spectrum of activities ranging from quantum mechanical calculations of the electronic structure of molecules, to classical mechanical simulations of the dynamical properties of many-atom systems, to the mapping of both structure-activity relationships and reaction synthesis steps. Although chemical theory and i...
Article
A new solid-state embedding approach has been developed which focuses on modelling the surfaces of polar materials. The method is applied to investigate the chemisorption of pre- methanol species on the polar (000-1) surface of zincite (a major phase of zinc oxide having the wurtzite structure). Initial results include the geometries of active site...
Article
An overview is provided of the range of approaches to hybrid QM/MM (quantum mechanics/molecular mechanics) calculations. The factors considered include the choice of QM and MM methods, the construction of the total QM/MM energy ex- pression, the nature of the QM/MM coupling, and the treatment of bonds between QM and MM regions. The practical issues...
Article
Much shorter hydrogen bonds with unexpected directional properties are formed by fluoride ligands in comparison to their heavier halogen congeners (X=Cl, Br, I). Abinitio calculations elucidate the underlying electronic origin of this geometric behavior. The viability of hydrogen bonding is clearly established for all donor–acceptor combinations, D...
Article
Proton-energy differences, ammonia adsorption, and D/H-exchange barriers for methane at selected isolated Brønsted sites in zeolites FAU, MFI, BEA, ERI, and CHA are studied by combined quantum-chemical−classical (QM/MM) calculations in an attempt to understand the factors that determine the reactivity at these Brønsted sites. The barrier of the D/H...
Article
The two basic methods of computational chemistry, namely electronic structure calculations (quantum mechanics, QM) and those based upon force fields (molecular mechanics, MM) are now widely used, in a routine fashion, to model many aspects of the structure and reactivity of macromolecular systems. Energy minimizations based upon quite simple repres...
Article
Quantum-chemical studies of ethene, propene and isobutene chemisorption at an aluminosilicate Brønsted-acid site in the zeolite chabazite are reported. Comparison of the results using different cluster models and a qm/mm (quantum mechanical/molecular mechanical) embedded cluster approach are compared and contrasted. As in previous studies, the acti...
Article
Full-text available
Ab initio determination of the electric field gradient (EFG) tensors at halogen and other centres ena-bled determination of the nuclear quadrupole coupling constants (NQCC) for a diverse set of axially symmetric (C