Publications by authors named "Maximillian J S Phipps"

5 Publications

  • Page 1 of 1

The ONETEP linear-scaling density functional theory program.

J Chem Phys 2020 May;152(17):174111

Chemistry and Chemical Biology, University of California Merced, Merced, California 95343, USA.

We present an overview of the onetep program for linear-scaling density functional theory (DFT) calculations with large basis set (plane-wave) accuracy on parallel computers. The DFT energy is computed from the density matrix, which is constructed from spatially localized orbitals we call Non-orthogonal Generalized Wannier Functions (NGWFs), expressed in terms of periodic sinc (psinc) functions. During the calculation, both the density matrix and the NGWFs are optimized with localization constraints. By taking advantage of localization, onetep is able to perform calculations including thousands of atoms with computational effort, which scales linearly with the number or atoms. The code has a large and diverse range of capabilities, explored in this paper, including different boundary conditions, various exchange-correlation functionals (with and without exact exchange), finite electronic temperature methods for metallic systems, methods for strongly correlated systems, molecular dynamics, vibrational calculations, time-dependent DFT, electronic transport, core loss spectroscopy, implicit solvation, quantum mechanical (QM)/molecular mechanical and QM-in-QM embedding, density of states calculations, distributed multipole analysis, and methods for partitioning charges and interactions between fragments. Calculations with onetep provide unique insights into large and complex systems that require an accurate atomic-level description, ranging from biomolecular to chemical, to materials, and to physical problems, as we show with a small selection of illustrative examples. onetep has always aimed to be at the cutting edge of method and software developments, and it serves as a platform for developing new methods of electronic structure simulation. We therefore conclude by describing some of the challenges and directions for its future developments and applications.
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http://dx.doi.org/10.1063/5.0004445DOI Listing
May 2020

Mechanism of Os-Catalyzed Oxidative Cyclization of 1,5-Dienes.

J Org Chem 2019 12 13;84(23):15173-15183. Epub 2019 Nov 13.

Department of Chemistry , University of Southampton , Southampton , Hampshire SO17 1BJ , U.K.

The oxidative cyclization of 1,5-dienes by metal-oxo species is a powerful method for stereocontrolled synthesis of tetrahydrofuran diols (THF-diols), structural motifs present in many bioactive natural products. Oxidative cyclization of (2,6)-octa-2,6-diene catalyzed by OsO/NMO has been studied using density functional theory (DFT) calculations (M06-2X/aug-cc-pVDZ/Hay-Wadt VDZ (n+1) ECP), highlighting the remarkable effect of acid on the fate of the first intermediate, an Os(VI) dioxoglycolate. A strong acid promotes cyclization of the Os(VI) dioxoglycolate, or its NMO complex, through protonation of an oxo ligand to give more electrophilic species. By contrast, in the absence of acid, reoxidation may occur to afford the Os(VIII) trioxoglycolate, which is shown to favor conventional "second cycle" dihydroxylation reactivity rather than cyclization. The results of the calculations are consistent with experimental results for reactions of OsO/NMO with 1,5-dienes with acid (oxidative cyclization) and without acid (second cycle osmylation/dihydroxylation). Detailed evaluation of potential catalytic cycles supports oxidation of the cyclized Os(IV) THF-diolate intermediate to the corresponding Os(VI) species followed by slow hydrolysis and, finally, regeneration of OsO.
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http://dx.doi.org/10.1021/acs.joc.9b02174DOI Listing
December 2019

Charge Distributions of Nitro Groups Within Organic Explosive Crystals: Effects on Sensitivity and Modeling.

ACS Omega 2019 May 16;4(5):8614-8625. Epub 2019 May 16.

Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, U.K.

The charge distribution of NO groups within the crystalline polymorphs of energetic materials strongly affects their explosive properties. We use the recently introduced basis-space iterated stockholder atom partitioning of high-quality charge distributions to examine the approximations that can be made in modeling polymorphs and their physical properties, using 1,3,5-trinitroperhydro-1,3,5-triazine, trinitrotoluene, 1-3-5-trinitrobenzene, and hexanitrobenzene as exemplars. The NO charge distribution is strongly affected by the neighboring atoms, the rest of the molecules, and also significantly by the NO torsion angle within the possible variations found in observed crystal structures. Thus, the proposed correlations between the molecular electrostatic properties, such as trigger-bond potential or maxima in the electrostatic potential, and impact sensitivity will be affected by the changes in conformation that occur on crystallization. We establish the relationship between the NO torsion angle and the likelihood of occurrence in observed crystal structures, the conformational energy, and the charge and dipole magnitude on each atom, and how this varies with the neighboring groups. We examine the effect of analytically rotating the atomic multipole moments to model changes in torsion angle and establish that this is a viable approach for crystal structures but is not accurate enough to model the relative lattice energies. This establishes the basis of transferability of the NO charge distribution for realistic nonempirical model intermolecular potentials for simulating energetic materials.
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http://dx.doi.org/10.1021/acsomega.9b00648DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6648017PMC
May 2019

Surfactant Proteins A and D: Trimerized Innate Immunity Proteins with an Affinity for Viral Fusion Proteins.

J Innate Immun 2019 5;11(1):13-28. Epub 2018 Oct 5.

Child Health, Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, United

Innate recognition of viruses is an essential part of the immune response to viral pathogens. This is integral to the maintenance of healthy lungs, which are free from infection and efficient at gaseous exchange. An important component of innate immunity for identifying viruses is the family of C-type collagen-containing lectins, also known as collectins. These secreted, soluble proteins are pattern recognition receptors (PRRs) which recognise pathogen-associated molecular patterns (PAMPs), including viral glycoproteins. These innate immune proteins are composed of trimerized units which oligomerise into higher-order structures and facilitate the clearance of viral pathogens through multiple mechanisms. Similarly, many viral surface proteins form trimeric configurations, despite not showing primary protein sequence similarities across the virus classes and families to which they belong. In this review, we discuss the role of the lung collectins, i.e., surfactant proteins A and D (SP-A and SP-D) in viral recognition. We focus particularly on the structural similarity and complementarity of these trimeric collectins with the trimeric viral fusion proteins with which, we hypothesise, they have elegantly co-evolved. Recombinant versions of these innate immune proteins may have therapeutic potential in a range of infectious and inflammatory lung diseases including anti-viral therapeutics.
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http://dx.doi.org/10.1159/000492974DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6738215PMC
February 2020

Energy decomposition analysis approaches and their evaluation on prototypical protein-drug interaction patterns.

Chem Soc Rev 2015 May 2;44(10):3177-211. Epub 2015 Apr 2.

School of Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, UK.

The partitioning of the energy in ab initio quantum mechanical calculations into its chemical origins (e.g., electrostatics, exchange-repulsion, polarization, and charge transfer) is a relatively recent development; such concepts of isolating chemically meaningful energy components from the interaction energy have been demonstrated by variational and perturbation based energy decomposition analysis approaches. The variational methods are typically derived from the early energy decomposition analysis of Morokuma [Morokuma, J. Chem. Phys., 1971, 55, 1236], and the perturbation approaches from the popular symmetry-adapted perturbation theory scheme [Jeziorski et al., Methods and Techniques in Computational Chemistry: METECC-94, 1993, ch. 13, p. 79]. Since these early works, many developments have taken place aiming to overcome limitations of the original schemes and provide more chemical significance to the energy components, which are not uniquely defined. In this review, after a brief overview of the origins of these methods we examine the theory behind the currently popular variational and perturbation based methods from the point of view of biochemical applications. We also compare and discuss the chemical relevance of energy components produced by these methods on six test sets that comprise model systems that display interactions typical of biomolecules (such as hydrogen bonding and π-π stacking interactions) including various treatments of the dispersion energy.
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http://dx.doi.org/10.1039/c4cs00375fDOI Listing
May 2015
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