DommiMOE: An implementation of ligand field molecular mechanics in the molecular operating environment

Deeth, Robert J.; Fey, Natalie; Williams-Hubbard, Benjamin

doi:10.1002/jcc.20137

Cited by 78 publications

(87 citation statements)

References 37 publications

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“…as implemented in the Firefly quantum chemistry package, 45 which is partially based on the GAMESS(US) source code. 46 Bimetallic systems were optimised using ligand field molecular mechanics (LFMM) 47 as implemented in the DommiMOE program, 48 before being annealed at 500 K for 1 ns prior to re-optimisation. Single point energies were determined using the B3LYP-D3(BJ) 44 functional and the def2-TZVP basis set.…”

Section: Molecular Mechanics and Dft Calculationsmentioning

confidence: 99%

Asymmetric triplex metallohelices with high and selective activity against cancer cells

et al. 2014

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Section: Molecular Mechanics and Dft Calculationsmentioning

confidence: 99%

Asymmetric triplex metallohelices with high and selective activity against cancer cells

et al. 2014

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“…While this protocol introduces interactions between the outer, 'surface' water molecules which tends to constrain the tertiary structure, we have shown 41 that the local geometry in the vicinity of the transition metal centre is able to relax fully. The canonical ensemble was employed using the Nose-Poincare-Anderson equations of motion at a temperature of 300 K, a timestep of 2 fs and a temperture relaxation time of 0.1 ps as implemented in DommiMOE, 42 our ligand field extended version of the Molecular Operating Environment (MOE), version 2011.10. 43 All bond lengths to hydrogen atoms were constrained.…”

Section: Computational Detailsmentioning

confidence: 99%

Computational Study of the Structure and Electronic Circular Dichroism Spectroscopy of Blue Copper Proteins

Deeth

Besley

2013

J. Phys. Chem. B

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The calculation of the electronic circular dichroism (CD) spectra of the oxidised form of the blue copper proteins plastocyanin and cucumber basic protein and the relationship between the observed spectral features and the structure of the active site of the protein is investigated.Excitation energies and transition strengths are computed using multi reference configuration interaction, and it is shown that computed spectra based on coordinates from the crystal structure or a single structure optimised in quantum mechanics/molecular mechanics (QM/MM) or ligand field molecular mechanics (LFMM) are qualitatively incorrect. In particular, the rotational strength of the ligand to metal charge transfer band is predicted to be too small or have the incorrect sign. By considering calculations on active site models with modified structures it is shown that the intensity of this band is sensitive to the non-planarity of the histidine and cysteine ligands coordinated to copper. Calculation of the ultraviolet absorption and CD spectra based upon averaging over many structures drawn from a LFMM molecular dynamics simulation are in good agreement with experiment, and superior to analogous calculations based upon structures from a classical molecular dynamics simulation. This provides evidence that the LFMM force field provides an accurate description of the molecular dynamics of these proteins.

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“…19 Therefore, not only the electrostatic and van der Waals interactions but also the description of the ionicity of POMs is a key issue in the development of a force field. Few attempts of MM simulations have been performed using optimized force fields dedicated to inorganic compounds, and either the electrostatic interactions are neglected 20,21 or determined based on potential-derived charges. 17,22 To describe the electrostatic and van der Waals interactions, the nonbonded potential, V nonbonded , needs to be considered and optimized.…”

Section: Introductionmentioning

confidence: 99%

Optimization of a molecular mechanics force field for type‐II polyoxometalates focussing on electrostatic interactions: A case study

Courcot

Bridgeman

2011

J Comput Chem

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In this study, we have focussed on type-II polyanions such as [M(7)O(24)](6-), and we have developed and validated optimized force fields that include electrostatic and van der Waals interactions. These contributions to the total steric energy are described by the nonbonded term, which encompasses all interactions between atoms that are not transmitted through the bonds. A first validation of a stochastic technique based on genetic algorithms was previously made for the optimization of force fields dedicated to type-I polyoxometalates. To describe the new nonbonded term added in the functional, a fixed-charged model was chosen. Therefore, one of the main issues was to analyze that which partial atomic charges could be reliably used to describe these interactions in such inorganic compounds. Based on several computational strategies, molecular mechanics (MM) force field parameters were optimized using different types of atomic charges. Moreover, the influence of the electrostatic and van der Waals buffering constants and 1,4-interactions scaling factors used in the force field were also tested, either being optimized as well or fixed with respect to the values of CHARMM force field. Results show that some atomic charges are not well adapted to CHARMM parameters and lead to unrealistic MM-optimized structures or a MM divergence. As a result, a new scaling factor has been optimized for Quantum Theory of Atoms in Molecules charges and charges derived from the electrostatic potential such as ChelpG. The force fields optimized can be mixed with the CHARMM force field, without changing it, to study for the first time hepta-anions interacting with organic molecules.

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DommiMOE: An implementation of ligand field molecular mechanics in the molecular operating environment

Cited by 78 publications

References 37 publications

Asymmetric triplex metallohelices with high and selective activity against cancer cells

Asymmetric triplex metallohelices with high and selective activity against cancer cells

Computational Study of the Structure and Electronic Circular Dichroism Spectroscopy of Blue Copper Proteins

Optimization of a molecular mechanics force field for type‐II polyoxometalates focussing on electrostatic interactions: A case study

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