Literature DB >> 21258606

The prediction of Fe Mössbauer parameters by the density functional theory: a benchmark study.

Arteum D Bochevarov1, Richard A Friesner, Stephen J Lippard.   

Abstract

We report the performance of eight density functionals (B3LYP, BPW91, OLYP, O3LYP, M06, M06-2X, PBE, and SVWN5) in two Gaussian basis sets (Wachters and Partridge-1 on iron atoms; cc-pVDZ on the rest of atoms) for the prediction of the isomer shift (IS) and the quadrupole splitting (QS) parameters of Mössbauer spectroscopy. Two sources of geometry (density functional theory-optimized and X-ray) are used. Our data set consists of 31 iron-containing compounds (35 signals), the Mössbauer spectra of which were determined at liquid helium temperature and where the X-ray geometries are known. Our results indicate that the larger and uncontracted Partridge-1 basis set produces slightly more accurate linear correlations of electronic density used for the prediction of IS and noticeably more accurate results for the QS parameter. We confirm and discuss the earlier observation of Noodleman and co-workers that different oxidation states of iron produce different IS calibration lines. The B3LYP and O3LYP functionals have the lowest errors for either IS or QS. BPW91, OLYP, PBE, and M06 have a mixed success whereas SVWN5 and M06-2X demonstrate the worst performance. Finally, our calibrations and conclusions regarding the best functional to compute the Mössbauer characteristics are applied to candidate structures for the peroxo and Q intermediates of the enzyme methane monooxygenase hydroxylase (MMOH), and compared to experimental data in the literature.

Entities:  

Year:  2010        PMID: 21258606      PMCID: PMC3023914          DOI: 10.1021/ct100398m

Source DB:  PubMed          Journal:  J Chem Theory Comput        ISSN: 1549-9618            Impact factor:   6.006


  53 in total

1.  Generalized Gradient Approximation Made Simple.

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Journal:  Phys Rev Lett       Date:  1996-10-28       Impact factor: 9.161

2.  (57)Fe Mössbauer isomer shifts of heme protein model systems: electronic structure calculations.

Authors:  Yong Zhang; Junhong Mao; Eric Oldfield
Journal:  J Am Chem Soc       Date:  2002-07-03       Impact factor: 15.419

3.  Atoms, molecules, solids, and surfaces: Applications of the generalized gradient approximation for exchange and correlation.

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Journal:  Phys Rev B Condens Matter       Date:  1992-09-15

4.  Dioxygen activation at non-heme diiron centers: characterization of intermediates in a mutant form of toluene/o-xylene monooxygenase hydroxylase.

Authors:  Leslie J Murray; Ricardo García-Serres; Sunil Naik; Boi Hanh Huynh; Stephen J Lippard
Journal:  J Am Chem Soc       Date:  2006-06-14       Impact factor: 15.419

5.  Density functional theory augmented with an empirical dispersion term. Interaction energies and geometries of 80 noncovalent complexes compared with ab initio quantum mechanics calculations.

Authors:  Petr Jurecka; Jirí Cerný; Pavel Hobza; Dennis R Salahub
Journal:  J Comput Chem       Date:  2007-01-30       Impact factor: 3.376

6.  Basis set exchange: a community database for computational sciences.

Authors:  Karen L Schuchardt; Brett T Didier; Todd Elsethagen; Lisong Sun; Vidhya Gurumoorthi; Jared Chase; Jun Li; Theresa L Windus
Journal:  J Chem Inf Model       Date:  2007-04-12       Impact factor: 4.956

7.  Dioxygen Activation and Methane Hydroxylation by Soluble Methane Monooxygenase: A Tale of Two Irons and Three Proteins A list of abbreviations can be found in Section 7.

Authors:  Maarten Merkx; Daniel A. Kopp; Matthew H. Sazinsky; Jessica L. Blazyk; Jens Müller; Stephen J. Lippard
Journal:  Angew Chem Int Ed Engl       Date:  2001-08-03       Impact factor: 15.336

8.  DFT calculations of comparative energetics and ENDOR/Mössbauer properties for two protonation states of the iron dimer cluster of ribonucleotide reductase intermediate X.

Authors:  Wen-Ge Han; Louis Noodleman
Journal:  Dalton Trans       Date:  2009-06-23       Impact factor: 4.390

9.  Density functional theory calculations on Mössbauer parameters of nonheme iron nitrosyls.

Authors:  Kathrin H Hopmann; Abhik Ghosh; Louis Noodleman
Journal:  Inorg Chem       Date:  2009-10-05       Impact factor: 5.165

10.  Unusual peroxo intermediates in the reaction of dioxygen with carboxylate-bridged diiron(II,II) paddlewheel complexes.

Authors:  Ferman A Chavez; Raymond Y N Ho; Maren Pink; Victor G Young; Sergei V Kryatov; Elena V Rybak-Akimova; Hanspeter Andres; Eckard Münck; Lawrence Que; William B Tolman
Journal:  Angew Chem Int Ed Engl       Date:  2002-01-04       Impact factor: 15.336

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  12 in total

1.  Insights into the different dioxygen activation pathways of methane and toluene monooxygenase hydroxylases.

Authors:  Arteum D Bochevarov; Jianing Li; Woon Ju Song; Richard A Friesner; Stephen J Lippard
Journal:  J Am Chem Soc       Date:  2011-04-25       Impact factor: 15.419

2.  Mössbauer properties of the diferric cluster and the differential iron(II)-binding affinity of the iron sites in protein R2 of class Ia Escherichia coli ribonucleotide reductase: a DFT/electrostatics study.

Authors:  Wen-Ge Han; Gregory M Sandala; Debra Ann Giammona; Donald Bashford; Louis Noodleman
Journal:  Dalton Trans       Date:  2011-08-12       Impact factor: 4.390

3.  Protonation of a peroxodiiron(III) complex and conversion to a diiron(III/IV) intermediate: implications for proton-assisted O-O bond cleavage in nonheme diiron enzymes.

Authors:  Matthew A Cranswick; Katlyn K Meier; Xiaopeng Shan; Audria Stubna; Jószef Kaizer; Mark P Mehn; Eckard Münck; Lawrence Que
Journal:  Inorg Chem       Date:  2012-09-12       Impact factor: 5.165

4.  Calibration of DFT Functionals for the Prediction of Fe Mössbauer Spectral Parameters in Iron-Nitrosyl and Iron-Sulfur Complexes: Accurate Geometries Prove Essential.

Authors:  Gregory M Sandala; Kathrin H Hopmann; Abhik Ghosh; Louis Noodleman
Journal:  J Chem Theory Comput       Date:  2011-10-11       Impact factor: 6.006

5.  Proton-Electron Transfer to the Active Site Is Essential for the Reaction Mechanism of Soluble Δ9-Desaturase.

Authors:  Daniel Bím; Jakub Chalupský; Martin Culka; Edward I Solomon; Lubomír Rulíšek; Martin Srnec
Journal:  J Am Chem Soc       Date:  2020-05-29       Impact factor: 15.419

6.  Iron Complexes of a Proton-Responsive SCS Pincer Ligand with a Sensitive Electronic Structure.

Authors:  Kazimer L Skubi; Reagan X Hooper; Brandon Q Mercado; Melissa M Bollmeyer; Samantha N MacMillan; Kyle M Lancaster; Patrick L Holland
Journal:  Inorg Chem       Date:  2022-01-05       Impact factor: 5.165

7.  Proton-Coupled Electron-Transfer Reactivity Controls Iron versus Sulfur Oxidation in Nonheme Iron-Thiolate Complexes.

Authors:  Jesse B Gordon; Jeremy P McGale; Maxime A Siegler; David P Goldberg
Journal:  Inorg Chem       Date:  2021-04-19       Impact factor: 5.165

8.  On Predicting Mössbauer Parameters of Iron-Containing Molecules with Density-Functional Theory.

Authors:  Mátyás Pápai; György Vankó
Journal:  J Chem Theory Comput       Date:  2013-10-15       Impact factor: 6.006

9.  Density Functional Calculations for Prediction of 57Fe Mössbauer Isomer Shifts and Quadrupole Splittings in β-Diketiminate Complexes.

Authors:  Sean F McWilliams; Emma Brennan-Wydra; K Cory MacLeod; Patrick L Holland
Journal:  ACS Omega       Date:  2017-06-12

10.  The Mössbauer Parameters of the Proximal Cluster of Membrane-Bound Hydrogenase Revisited: A Density Functional Theory Study.

Authors:  Shadan Ghassemi Tabrizi; Vladimir Pelmenschikov; Louis Noodleman; Martin Kaupp
Journal:  J Chem Theory Comput       Date:  2015-12-16       Impact factor: 6.006

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