Molecular Mechanics for Coordination Complexes: The Impact of Adding d-Electron Stabilization Energies

Burton, Veronica J.; Deeth, Robert J.; Kemp, C.; Gilbert, P. J.

doi:10.1021/ja00137a014

Cited by 107 publications

(129 citation statements)

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“…The planar geometry is a function of the low-spin d 8 configuration and arises naturally and automatically from the LFSE inherent in LFMM. 31 However, an equally, if not more, significant feature to consider is the local geometry around guanine N7, in particular, by how much the metal is displaced from the ligand plane. Figure 6) calculated using LFMM and DFT/BP86 were compared.…”

Section: Apart From Cis-diammine-bis(9-ethylguanine)-platinum(ii) (Dementioning

confidence: 99%

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Combined Theoretical and Computational Study of Interstrand DNA Guanine–Guanine Cross-Linking by trans-[Pt(pyridine)₂] Derived from the Photoactivated Prodrug trans,trans,trans-[Pt(N₃)₂(OH)₂(pyridine)₂]

et al. 2012

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Copyright and reuse:The Warwick Research Archive Portal (WRAP) makes the work of researchers of the University of Warwick available open access under the following conditions. Copyright © and all moral rights to the version of the paper presented here belong to the individual author(s) and/or other copyright owners. To the extent reasonable and practicable the material made available in WRAP has been checked for eligibility before being made available.Copies of full items can be used for personal research or study, educational, or not-forprofit purposes without prior permission or charge. Provided that the authors, title and full bibliographic details are credited, a hyperlink and/or URL is given for the original metadata page and the content is not changed in any way. Publisher's statement:This document is the Accepted Manuscript version of a Published Work that appeared in final form in Inorganic Chemistry, © American Chemical Society after peer review and technical editing by the publisher. To access the final edited and published work see http://dx.doi.org/10.1021/ic3005745 A note on versions:The version presented here may differ from the published version or, version of record, if you wish to cite this item you are advised to consult the publisher's version. Please see the 'permanent WRAP url' above for details on accessing the published version and note that access may require a subscription. 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59

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Section: Apart From Cis-diammine-bis(9-ethylguanine)-platinum(ii) (Dementioning

confidence: 99%

“…[31][32][33] Polarizable 34 and solid state 35 versions of LFMM have been implemented and we have estimated that LFMM is up to four orders of magnitude faster than the density functional theory methods which often form the QM part of QM/M simulations.…”

Section: Introductionmentioning

confidence: 99%

Combined Theoretical and Computational Study of Interstrand DNA Guanine–Guanine Cross-Linking by trans-[Pt(pyridine)₂] Derived from the Photoactivated Prodrug trans,trans,trans-[Pt(N₃)₂(OH)₂(pyridine)₂]

et al. 2012

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“…An alternative is ligand field molecular mechanics (LFMM) 25,26 29,30 . The aim of this work is to establish a protocol for generating and subsequently analyzing conformations of a series of platinum(II) species bound to a fragment of Aβ peptide (residues 6-14 -see Figure 1), with the aim of identifying favorable metal-binding modes and peptide conformations.…”

Section: Introductionmentioning

confidence: 99%

Modeling of Platinum-Aryl Interaction with Amyloid-β Peptide

Turner

Platts

Deeth

2016

J. Chem. Theory Comput.

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Ligand field molecular mechanics (LFMM), density functional theory (DFT) and semi-empirical PM7 methods are used to study the binding of two Pt(II)-L systems to an N-terminal fragment of the amyloid-β peptide, where L = 2,2-bipyridyl or 1,10-phenanthroline. Molecular dynamics simulations are used to explore the conformational freedom of the peptide using LFMM combined with AMBER molecular mechanics parameters. We establish a modelling protocol, allowing for identification and analysis of favorable platinum-binding modes and peptide conformations.Preferred binding modes are identified for each ligand investigated; metal coordination occurs via Nε in His residues for both ligands -His6ε-His13ε and His6ε-His14ε for the bipyridyl and phenanthroline ligands, respectively. The observed change in binding mode for the different ligands suggests that the binding mode of these platinum-based structures can be controlled by the choice of ligand. In the bipy systems, Boltzmann population at 310K is dominated by a single conformer, while in the phenanthroline case, three conformations make significant contributions 2 to the ensemble. The relative stability of these conformations is due to the inherent stability of binding platinum via Nε in addition to subtle H-bonding effects.

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“…Our contribution to molecular mechanics for TM centers has been prompted by the observation that for open-shell d n systems, there is an additional important electronic component. 6,[13][14][15][16][17] The d electrons can exert profound structural and energetic effects. For example, d 9 and high-spin d 4 species display large Jahn-Teller distortions, low-spin d 6 complexes are usually sixcoordinate and kinetically inert, and d 8 complexes are generally octahedral when high-spin and square-planar when low-spin.…”

Section: Introductionmentioning

confidence: 99%

“…25 Tchougreeff and coworkers have implemented a similar concept within an effective crystal field (ECF) formalism. 26 -28 The original in-house LFMM implementation, christened Dommino (D-Orbitals in Molecular Mechanics for Inorganics), 16,17 was written in FORTRAN and based around the biosim package of David Osguthorpe. 29 The bond stretch terms were, by default, described by Morse functions to accommodate the large bond length variations encountered in Jahn-Teller-distorted Cu(II) complexes (Ͼ0.5 Å).…”

Section: Introductionmentioning

confidence: 99%

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

Deeth

Fey²,

Williams-Hubbard

2004

J Comput Chem

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The ligand field molecular mechanics (LFMM) model, which incorporates the ligand field stabilization energy (LFSE) directly into the potential energy expression of molecular mechanics (MM), has been implemented in the "chemically aware" molecular operating environment (MOE) software package. The new program, christened DommiMOE, is derived from our original in-house code that has been linked to MOE via its applications programming interface and a number of other routines written in MOE's native scientific vector language (SVL). DommiMOE automates the assignment of atom types and their associated parameters and popular force fields available in MOE such as MMFF94, AMBER, and CHARMM can be easily extended to provide a transition metal simulation capability. Some of the unique features of the LFMM are illustrated using MMFF94 and some simple [MCl)]2- and [Ni(NH3)n]2+ species. These studies also demonstrate how density functional theory calculations, especially on experimentally inaccessible systems, provide important data for designing improved LFMM parameters. DommiMOE treats Jahn-Teller distortions automatically, and can compute the relative energies of different spin states for Ni(II) complexes using a single set of LFMM parameters.

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Molecular Mechanics for Coordination Complexes: The Impact of Adding d-Electron Stabilization Energies

Cited by 107 publications

References 3 publications

Combined Theoretical and Computational Study of Interstrand DNA Guanine–Guanine Cross-Linking by trans-[Pt(pyridine)₂] Derived from the Photoactivated Prodrug trans,trans,trans-[Pt(N₃)₂(OH)₂(pyridine)₂]

Combined Theoretical and Computational Study of Interstrand DNA Guanine–Guanine Cross-Linking by trans-[Pt(pyridine)₂] Derived from the Photoactivated Prodrug trans,trans,trans-[Pt(N₃)₂(OH)₂(pyridine)₂]

Modeling of Platinum-Aryl Interaction with Amyloid-β Peptide

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

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Molecular Mechanics for Coordination Complexes: The Impact of Adding d-Electron Stabilization Energies

Cited by 107 publications

References 3 publications

Combined Theoretical and Computational Study of Interstrand DNA Guanine–Guanine Cross-Linking by trans-[Pt(pyridine)2] Derived from the Photoactivated Prodrug trans,trans,trans-[Pt(N3)2(OH)2(pyridine)2]

Combined Theoretical and Computational Study of Interstrand DNA Guanine–Guanine Cross-Linking by trans-[Pt(pyridine)2] Derived from the Photoactivated Prodrug trans,trans,trans-[Pt(N3)2(OH)2(pyridine)2]

Modeling of Platinum-Aryl Interaction with Amyloid-β Peptide

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

Contact Info

Product

Resources

About

Combined Theoretical and Computational Study of Interstrand DNA Guanine–Guanine Cross-Linking by trans-[Pt(pyridine)₂] Derived from the Photoactivated Prodrug trans,trans,trans-[Pt(N₃)₂(OH)₂(pyridine)₂]

Combined Theoretical and Computational Study of Interstrand DNA Guanine–Guanine Cross-Linking by trans-[Pt(pyridine)₂] Derived from the Photoactivated Prodrug trans,trans,trans-[Pt(N₃)₂(OH)₂(pyridine)₂]