Literature DB >> 22039359

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

Gregory M Sandala1, Kathrin H Hopmann, Abhik Ghosh, Louis Noodleman.   

Abstract

Six popular density functionals in conjunction with the conductor-like screening (COSMO) solvation model have been used to obtain linear Mössbauer isomer shift (IS) and quadrupole splitting (QS) parameters for a test set of 20 complexes (with 24 sites) comprised of nonheme nitrosyls (Fe-NO) and non-nitrosyl (Fe-S) complexes. For the first time in an IS analysis, the Fe electron density was calculated both directly at the nucleus, ρ(0)(N), which is the typical procedure, and on a small sphere surrounding the nucleus, ρ(0)(S), which is the new standard algorithm implemented in the ADF software package. We find that both methods yield (near) identical slopes from each linear regression analysis but are shifted with respect to ρ(0) along the x-axis. Therefore, the calculation of the Fe electron density with either method gives calibration fits with equal predictive value. Calibration parameters obtained from the complete test set for OLYP, OPBE, PW91, and BP86 yield correlation coefficients (r(2)) of approximately 0.90, indicating that the calibration fit is of good quality. However, fits obtained from B3LYP and B3LYP* with both Slater-type and Gaussian-type orbitals are generally found to be of poorer quality. For several of the complexes examined in this study, we find that B3LYP and B3LYP* give geometries that possess significantly larger deviations from the experimental structures than OLYP, OPBE, PW91 or BP86. This phenomenon is particularly true for the di- and tetranuclear Fe complexes examined in this study. Previous Mössbauer calibration fit studies using these functionals have usually included mononuclear Fe complexes alone, where these discrepancies are less pronounced. An examination of spin expectation values reveals B3LYP and B3LYP* approach the weak-coupling limit more closely than the GGA exchange-correlation functionals. The high degree of variability in our calculated S(2) values for the Fe-NO complexes highlights their challenging electronic structure. Significant improvements to the isomer shift calibrations are obtained for B3LYP and B3LYP* when geometries obtained with the OLYP functional are used. In addition, greatly improved performance of these functionals is found if the complete test set is grouped separately into Fe-NO and Fe-S complexes. Calibration fits including only Fe-NO complexes are found to be excellent, while those containing the non-nitrosyl Fe-S complexes alone are found to demonstrate less accurate correlations. Similar trends are also found with OLYP, OPBE, PW91, and BP86. Correlations between experimental and calculated QSs were also investigated. Generally, universal and separate Fe-NO and Fe-S fit parameters obtained to determine QSs are found to be of good to excellent quality for every density functional examined, especially if [Fe(4)(NO)(4)(μ(3)-S)(4)](-) is removed from the test set.

Entities:  

Year:  2011        PMID: 22039359      PMCID: PMC3203024          DOI: 10.1021/ct200187d

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


  32 in total

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

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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.  DFT calculations on the spin-crossover complex Fe(salen)(NO): a quest for the best functional.

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Journal:  J Phys Chem B       Date:  2007-10-13       Impact factor: 2.991

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6.  Spin coupling in Roussin's red and black salts.

Authors:  Kathrin H Hopmann; Louis Noodleman; Abhik Ghosh
Journal:  Chemistry       Date:  2010-09-10       Impact factor: 5.236

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Authors:  Alicja Wanat; Thorsten Schneppensieper; Grazyna Stochel; Rudi van Eldik; Eckhard Bill; Karl Wieghardt
Journal:  Inorg Chem       Date:  2002-01-14       Impact factor: 5.165

8.  Nuclear quadrupole moment of 57Fe from microscopic nuclear and atomic calculations.

Authors:  G Martínez-Pinedo; P Schwerdtfeger; E Caurier; K Langanke; W Nazarewicz; T Söhnel
Journal:  Phys Rev Lett       Date:  2001-07-20       Impact factor: 9.161

9.  Broken-symmetry DFT spin densities of iron nitrosyls, including Roussin's red and black salts: striking differences between pure and hybrid functionals.

Authors:  Kathrin H Hopmann; Jeanet Conradie; Abhik Ghosh
Journal:  J Phys Chem B       Date:  2009-07-30       Impact factor: 2.991

10.  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

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  17 in total

Review 1.  Mono- and binuclear non-heme iron chemistry from a theoretical perspective.

Authors:  Tibor András Rokob; Jakub Chalupský; Daniel Bím; Prokopis C Andrikopoulos; Martin Srnec; Lubomír Rulíšek
Journal:  J Biol Inorg Chem       Date:  2016-05-26       Impact factor: 3.358

2.  EPR and (57)Fe ENDOR investigation of 2Fe ferredoxins from Aquifex aeolicus.

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3.  Predicting Nuclear Resonance Vibrational Spectra of [Fe(OEP)(NO)].

Authors:  Qian Peng; Jeffrey W Pavlik; W Robert Scheidt; Olaf Wiest
Journal:  J Chem Theory Comput       Date:  2011-11-29       Impact factor: 6.006

Review 4.  The Spectroscopy of Nitrogenases.

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5.  Robust Production, Crystallization, Structure Determination, and Analysis of [Fe-S] Proteins: Uncovering Control of Electron Shuttling and Gating in the Respiratory Metabolism of Molybdopterin Guanine Dinucleotide Enzymes.

Authors:  Chi-Lin Tsai; John A Tainer
Journal:  Methods Enzymol       Date:  2017-12-19       Impact factor: 1.600

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

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Journal:  J Chem Theory Comput       Date:  2013-10-15       Impact factor: 6.006

7.  Nature of the copper-nitrosyl intermediates of copper nitrite reductases during catalysis.

Authors:  Michael A Hough; Jeanet Conradie; Richard W Strange; Svetlana V Antonyuk; Robert R Eady; Abhik Ghosh; S Samar Hasnain
Journal:  Chem Sci       Date:  2020-10-20       Impact factor: 9.825

8.  Use of Broken-Symmetry Density Functional Theory To Characterize the IspH Oxidized State: Implications for IspH Mechanism and Inhibition.

Authors:  Patrick G Blachly; Gregory M Sandala; Debra Ann Giammona; Tiqing Liu; Donald Bashford; J Andrew McCammon; Louis Noodleman
Journal:  J Chem Theory Comput       Date:  2014-08-13       Impact factor: 6.006

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

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Journal:  J Chem Theory Comput       Date:  2015-12-16       Impact factor: 6.006

10.  Stepwise nitrosylation of the nonheme iron site in an engineered azurin and a molecular basis for nitric oxide signaling mediated by nonheme iron proteins.

Authors:  Shiliang Tian; Ruixi Fan; Therese Albert; Rahul L Khade; Huiguang Dai; Kevin A Harnden; Parisa Hosseinzadeh; Jing Liu; Mark J Nilges; Yong Zhang; Pierre Moënne-Loccoz; Yisong Guo; Yi Lu
Journal:  Chem Sci       Date:  2021-03-31       Impact factor: 9.825

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