Development of parameter sets for semi-empirical MO calculations of transition metal systems: Iron parameters for iron–sulfur proteins

McNamara, Jonathan P.; Sundararajan, Mahesh; Hillier, Ian H.

doi:10.1016/j.jmgm.2005.07.001

Cited by 18 publications

(17 citation statements)

References 48 publications

(117 reference statements)

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“…The aim of any parameter optimisation strategy is to minimise S efficiently and this is achieved using a modified Broyden-Fletcher-Goldfarb-Shanno (BFGS) algorithm. 10,11,24,36 Our error function contains contributions from the different structural parameters (as internal coordinate gradients) as well as interaction energies of the S22 molecular complexes. We require our new semi-empirical models to be capable of accurately predicting interaction energies for structures extracted from experiment and therefore in our fitting function we chose quite large weighting factors for the energy contributions ( Table 1).…”

Section: Parameterisation Strategymentioning

confidence: 99%

Semi-empirical molecular orbital methods including dispersion corrections for the accurate prediction of the full range of intermolecular interactions in biomolecules

McNamara

Hillier

2007

Phys. Chem. Chem. Phys.

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128

176

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Semi-empirical calculations including an empirical dispersive correction are used to calculate intermolecular interaction energies and structures for a large database containing 156 biologically relevant molecules (hydrogen-bonded DNA base pairs, interstrand base pairs, stacked base pairs and amino acid base pairs) for which MP2 and CCSD(T) complete basis set (CBS) limit estimates of the interaction energies are available. The dispersion corrected semi-empirical methods are parameterised against a small training set of 22 complexes having a range of biologically important non-covalent interactions. For the full molecule set (156 complexes), compared to the high-level ab initio database, the mean unsigned errors of the interaction energies at the corrected semi-empirical level are 1.1 (AM1-D) and 1.2 (PM3-D) kcal mol(-1), being a significant improvement over existing AM1 and PM3 methods (8.6 and 8.2 kcal mol(-1)). Importantly, the new semi-empirical methods are capable of describing the diverse range of biological interactions, most notably stacking interactions, which are poorly described by both current AM1 and PM3 methods and by many DFT functionals. The new methods require no more computer time than existing semi-empirical methods and therefore represent an important advance in the study of important biological interactions.

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Section: Parameterisation Strategymentioning

confidence: 99%

Semi-empirical molecular orbital methods including dispersion corrections for the accurate prediction of the full range of intermolecular interactions in biomolecules

McNamara

Hillier

2007

Phys. Chem. Chem. Phys.

Self Cite

128

176

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“…These systems have also provided model compounds for studying physicochemical properties of iron-sulphur proteins. [28][29][30] Additionally, new Fe-based framework derived compounds are potential materials which can replace the expensive Pt-based catalysts in PEMFCs since they are a lower-cost alternative. 31 A relatively recent development in the field of solid state electrolyte materials is that of organic ionic plastic crystals based on choline cations.…”

Section: Introductionmentioning

confidence: 99%

Magnetic ionic plastic crystal: choline[FeCl4]

Pedro

García-Saiz

González

et al. 2013

Phys. Chem. Chem. Phys.

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A novel organic ionic plastic crystal (OIPC) based on a quaternary ammonium cation and a tetrachloroferrate anion has been synthesized with the intention of combining the properties of the ionic plastic crystal and the magnetism originating from the iron incorporated in the anion. The thermal analysis of the obtained OIPC showed a solid-solid phase transition below room temperature and a high melting point above 220 °C, indicating their plastic crystalline behaviour over a wide temperature range, as well as thermal stability up to approximately 200 °C. The magnetization measurements show the presence of three-dimensional antiferromagnetic ordering below 4 K. The results from electrochemical characterization display a solid-state ionic conduction sufficiently high and stable (between 10(-2.7) and 10(-3.6) S cm(-1) from 20 to 180 °C) for electrochemical applications.

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“…44,45,77,78 Details of this algorithm and the modifications for obtaining semiempirical parameters for transition metals have been reported previously. 50,51 Therefore, our approach differs from the optimization of AM1/ sparkle and PM3/sparkle parametrizations which used a combination of Newton-Raphson and simplex optimization methods. 60,63 The chosen error function (S, eq 7; see also Table S1 and Figure S1) for each lanthanide element contained weighted contributions from the internal coordinate gradients for each reference complex and also the relative energy (calculated at the DFT level) of the [Ln(DOTA)(OH 2 )] 1-structures [the square antiprismatic isomer (A) and the inverted antiprismatic isomer (IA)].…”

Section: Construction and Optimization Of The Error Functionmentioning

confidence: 99%

Semiempirical Molecular Orbital Scheme To Study Lanthanide(III) Complexes: PM3 Parameters for Europium, Gadolinium, and Ytterbium

McNamara

Berrigan

Hillier

2007

J. Chem. Theory Comput.

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Semiempirical parameters for europium, gadolinium, and ytterbium have been developed for use in the PM3 method to allow the structure and energetics of complexes containing lanthanide(III) ions to be accurately modeled. At the semiempirical level, the lanthanide(III) ion is represented by a +3 core and has a minimal basis of 6s5d6p (9 atomic orbitals), the 4f electrons being included within the electronic core. Training sets containing up to 19 lanthanide complexes, with data computed at the density functional theory (DFT) level, have been employed for each lanthanide(III) ion. A gradient-based optimization algorithm has been used, and important modifications of the core repulsion function have been highlighted. The derived parameters lead in general to good predictions of the structure of the complexes and demonstrate improvements in the prediction of water binding energies compared to the AM1/sparkle model. For the 28 Eu(III), 28 Gd(III), and 29 Yb(III) complexes optimized at the DFT level, the PM3 average unsigned mean errors for all interatomic distances between the lanthanide(III) ion and the ligand atoms of the first coordination sphere are 0.04, 0.03, and 0.03 Å, respectively. The derived parameters are shown to be comparable to small-basis set DFT calculations in predicting the experimental structures of various lanthanide(III) complexes. The derived parameter sets provide a starting point should greater accuracy for a more restricted range of compounds be required.

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Development of parameter sets for semi-empirical MO calculations of transition metal systems: Iron parameters for iron–sulfur proteins

Cited by 18 publications

References 48 publications

Semi-empirical molecular orbital methods including dispersion corrections for the accurate prediction of the full range of intermolecular interactions in biomolecules

Semi-empirical molecular orbital methods including dispersion corrections for the accurate prediction of the full range of intermolecular interactions in biomolecules

Magnetic ionic plastic crystal: choline[FeCl4]

Semiempirical Molecular Orbital Scheme To Study Lanthanide(III) Complexes: PM3 Parameters for Europium, Gadolinium, and Ytterbium

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