Literature DB >> 23204948

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

Qian Peng1, Jeffrey W Pavlik, W Robert Scheidt, Olaf Wiest.   

Abstract

Nuclear Resonance Vibrational Spectroscopy (NRVS) is a sensitive vibrational probe for biologically important heme complexes. The exquisite sensitivity of the NRVS data to the electronic structure provides detailed insights into the nature of these interesting compounds, but requires highly accurate computational methods for the mode assignments. To determine the best combinations of density functionals and basis sets, a series of benchmark DFT calculations on the previously characterized complex [Fe(OEP)NO] (OEP(2-)=octaethylporphyrinatio dianion) were performed. A test set of 21 methodology combinations including 8 functionals (BP86, mPWPW91, B3LYP, PBE1PBE, M062X, M06L, LC-BP86 and ωB97X-D) and 5 basis set (VTZ, TZVP, Lanl2DZ for iron and 6-31G*, 6-31+G* for other atoms) was carried out to calculate electronic structures and vibrational frequencies. We also implemented the conversion of frequency calculations into orientation-selective mode composition factors (e(2)), which can used to simulate the Vibrational Density Of States (VDOS) using Gaussian normal distribution functions. These use a series of user-friendly scripts for their application to NRVS. The structures as well as the isotropic and anisotropic NRVS of [Fe(OEP)NO] obtained with the M06L functional with a variety of basis sets are found to best reproduce the available experimental data, followed by B3LYP/LanL2DZ calculations. Other density functionals and basis sets do not produce the same level of accuracy. The noticeably worse agreement between theory and experiment for the out-plane NRVS compared with the excellent performance of the M06L functional for the in-plane prediction is attributed to deficiencies of the physical model rather than the computational methodology.

Entities:  

Year:  2011        PMID: 23204948      PMCID: PMC3507453          DOI: 10.1021/ct2006456

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


  41 in total

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2.  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

Review 3.  Nuclear resonance vibrational spectroscopy--NRVS.

Authors:  W Robert Scheidt; Stephen M Durbin; J Timothy Sage
Journal:  J Inorg Biochem       Date:  2005-01       Impact factor: 4.155

4.  Probing vibrational anisotropy with nuclear resonance vibrational spectroscopy.

Authors:  Jeffrey W Pavlik; Alexander Barabanschikov; Allen G Oliver; E Ercan Alp; Wolfgang Sturhahn; Jiyong Zhao; J Timothy Sage; W Robert Scheidt
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5.  Single-atom test of all-atom empirical potentials: Fe in myoglobin.

Authors:  Brajesh K Rai; Earl W Prohofsky; Stephen M Durbin
Journal:  J Phys Chem B       Date:  2005-10-13       Impact factor: 2.991

6.  Anisotropic nuclear inelastic scattering of an iron(II) molecular crystal.

Authors:  H Paulsen; R Benda; C Herta; V Schünemann; A I Chumakov; L Duelund; H Winkler; H Toftlund; A X Trautwein
Journal:  Phys Rev Lett       Date:  2001-02-12       Impact factor: 9.161

7.  Vibrational assignments of six-coordinate ferrous heme nitrosyls: new insight from nuclear resonance vibrational spectroscopy.

Authors:  Florian Paulat; Timothy C Berto; Serena DeBeer George; Lauren Goodrich; V K K Praneeth; Corinne D Sulok; Nicolai Lehnert
Journal:  Inorg Chem       Date:  2008-12-15       Impact factor: 5.165

8.  Direct determination of the complete set of iron normal modes in a porphyrin-imidazole model for carbonmonoxy-heme proteins: [Fe(TPP)(CO)(1-MeIm)].

Authors:  Brajesh K Rai; Stephen M Durbin; Earl W Prohofsky; J Timothy Sage; Mary K Ellison; Arne Roth; W Robert Scheidt; Wolfgang Sturhahn; E Ercan Alp
Journal:  J Am Chem Soc       Date:  2003-06-11       Impact factor: 15.419

9.  Quantitative vibrational dynamics of iron in nitrosyl porphyrins.

Authors:  Bogdan M Leu; Marek Z Zgierski; Graeme R A Wyllie; W Robert Scheidt; Wolfgang Sturhahn; E Ercan Alp; Stephen M Durbin; J Timothy Sage
Journal:  J Am Chem Soc       Date:  2004-04-07       Impact factor: 15.419

10.  Dynamics of Rhodobacter capsulatus [2FE-2S] ferredoxin VI and Aquifex aeolicus ferredoxin 5 via nuclear resonance vibrational spectroscopy (NRVS) and resonance Raman spectroscopy.

Authors:  Yuming Xiao; Ming-Liang Tan; Toshiko Ichiye; Hongxin Wang; Yisong Guo; Matt C Smith; Jacques Meyer; Wolfgang Sturhahn; Ercan E Alp; Jiyong Zhao; Yoshitaka Yoda; Stephen P Cramer
Journal:  Biochemistry       Date:  2008-06-24       Impact factor: 3.162

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  10 in total

1.  Probing heme vibrational anisotropy: an imidazole orientation effect?

Authors:  Qian Peng; Ming Li; Chuanjiang Hu; Jeffrey W Pavlik; Allen G Oliver; E Ercan Alp; Michael Y Hu; Jiyong Zhao; J Timothy Sage; W Robert Scheidt
Journal:  Inorg Chem       Date:  2013-09-10       Impact factor: 5.165

Review 2.  What Can Be Learned from Nuclear Resonance Vibrational Spectroscopy: Vibrational Dynamics and Hemes.

Authors:  W Robert Scheidt; Jianfeng Li; J Timothy Sage
Journal:  Chem Rev       Date:  2017-09-18       Impact factor: 60.622

3.  Effects of imidazole deprotonation on vibrational spectra of high-spin iron(II) porphyrinates.

Authors:  Chuanjiang Hu; Qian Peng; Nathan J Silvernail; Alexander Barabanschikov; Jiyong Zhao; E Ercan Alp; Wolfgang Sturhahn; J Timothy Sage; W Robert Scheidt
Journal:  Inorg Chem       Date:  2013-03-07       Impact factor: 5.165

4.  Quantitative vibrational dynamics of the metal site in a tin porphyrin: an IR, NRVS, and DFT study.

Authors:  Bogdan M Leu; Marek Z Zgierski; Christian Bischoff; Ming Li; Michael Y Hu; Jiyong Zhao; Steve W Martin; Esen Ercan Alp; W Robert Scheidt
Journal:  Inorg Chem       Date:  2013-08-20       Impact factor: 5.165

5.  3D Motions of Iron in Six-Coordinate {FeNO}(7) Hemes by Nuclear Resonance Vibration Spectroscopy.

Authors:  Qian Peng; Jeffrey W Pavlik; Nathan J Silvernail; E Ercan Alp; Michael Y Hu; Jiyong Zhao; J Timothy Sage; W Robert Scheidt
Journal:  Chemistry       Date:  2016-03-21       Impact factor: 5.236

6.  Vibrational probes and determinants of the S = 0 ⇌ S = 2 spin crossover in five-coordinate [Fe(TPP)(CN)]-.

Authors:  Jianfeng Li; Qian Peng; Alexander Barabanschikov; Jeffrey W Pavlik; E Ercan Alp; Wolfgang Sturhahn; Jiyong Zhao; J Timothy Sage; W Robert Scheidt
Journal:  Inorg Chem       Date:  2012-10-19       Impact factor: 5.165

7.  Recent advances in biosynthetic modeling of nitric oxide reductases and insights gained from nuclear resonance vibrational and other spectroscopic studies.

Authors:  Saumen Chakraborty; Julian Reed; J Timothy Sage; Nicole C Branagan; Igor D Petrik; Kyle D Miner; Michael Y Hu; Jiyong Zhao; E Ercan Alp; Yi Lu
Journal:  Inorg Chem       Date:  2015-08-14       Impact factor: 5.165

8.  Hydride bridge in [NiFe]-hydrogenase observed by nuclear resonance vibrational spectroscopy.

Authors:  Hideaki Ogata; Tobias Krämer; Hongxin Wang; David Schilter; Vladimir Pelmenschikov; Maurice van Gastel; Frank Neese; Thomas B Rauchfuss; Leland B Gee; Aubrey D Scott; Yoshitaka Yoda; Yoshihito Tanaka; Wolfgang Lubitz; Stephen P Cramer
Journal:  Nat Commun       Date:  2015-08-10       Impact factor: 14.919

9.  Anisotropic iron motion in nitrosyl iron porphyrinates: natural and synthetic hemes.

Authors:  Jeffrey W Pavlik; Qian Peng; Nathan J Silvernail; E Ercan Alp; Michael Y Hu; Jiyong Zhao; J Timothy Sage; W Robert Scheidt
Journal:  Inorg Chem       Date:  2014-02-14       Impact factor: 5.165

10.  Comprehensive Fe-ligand vibration identification in {FeNO}6 hemes.

Authors:  Jianfeng Li; Qian Peng; Allen G Oliver; E Ercan Alp; Michael Y Hu; Jiyong Zhao; J Timothy Sage; W Robert Scheidt
Journal:  J Am Chem Soc       Date:  2014-12-18       Impact factor: 15.419

  10 in total

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