Dataset Information

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

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 ?B97X-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.

SUBMITTER: Peng Q

PROVIDER: S-EPMC3507453 | biostudies-literature | 2012 Jan

REPOSITORIES: biostudies-literature

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

Peng Qian Q Pavlik Jeffrey W JW Scheidt W Robert WR Wiest Olaf O

Journal of chemical theory and computation 20111129 1

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 comple ...[more]

PMID: 23204948

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Project description:This study presents Nuclear Resonance Vibrational Spectroscopy (NRVS) data on the five-coordinate (5C) ferrous heme-nitrosyl complex [Fe(OEP)(NO)] (1, OEP(2-) = octaethylporphyrinato dianion) and the corresponding (15)N(18)O labeled complex. The obtained spectra identify two isotope sensitive features at 522 and 388 cm(-1), which shift to 508 and 381 cm(-1), respectively, upon isotope labeling. These features are assigned to the Fe-NO stretch nu(Fe-NO) and the in-plane Fe-N-O bending mode delta(ip)(Fe-N-O), the latter has been unambiguously assigned for the first time for 1. The obtained NRVS data were simulated using our quantum chemistry centered normal coordinate analysis (QCC-NCA). Since complex 1 can potentially exist in 12 different conformations involving the FeNO and peripheral ethyl orientations, extended density functional theory (DFT) calculations and QCC-NCA simulations were performed to determine how these conformations affect the NRVS properties of [Fe(OEP)NO]. These results show that the properties and force constants of the FeNO unit are hardly affected by the conformational changes involving the ethyl substituents. On the other hand, the NRVS-active porphyrin-based vibrations around 340-360, 300-320, and 250-270 cm(-1) are sensitive to the conformational changes. The spectroscopic changes observed in these regions are due to selective mechanical couplings of one component of E(u)-type (in ideal D(4h) symmetry) porphyrin-based vibrations with the in-plane Fe-N-O bending mode. This leads to the observed variations in Fe(OEP) core mode energies and NRVS intensities without affecting the properties of the FeNO unit. The QCC-NCA simulated NRVS spectra of 1 show excellent agreement with experiment, and indicate that conformer F is likely present in the samples of this complex investigated here. The observed porphyrin-based vibrations in the NRVS spectra of 1 are also assigned based on the QCC-NCA results. The obtained force constants of the Fe-NO and N-O bonds are 2.83-2.94 (based on the DFT functional applied) and about 12.15 mdyn/A, respectively. The electronic structures of 5C ferrous heme-nitrosyls in different model complexes are then analyzed, and variations in their properties based on different porphyrin substituents are explained. Finally, the shortcomings of different DFT functionals in describing the axial FeNO subunit in heme-nitrosyls are elucidated.

Project description:This paper presents oriented single-crystal Nuclear Resonance Vibrational Spectroscopy (NRVS) data for the six-coordinate (6C) ferrous heme-nitrosyl model complex [(57)Fe(TPP)(MI)(NO)] (1; TPP(2-) = tetraphenylporphyrin dianion; MI = 1-methylimidazole). The availability of these data enables for the first time the detailed simulation of the complete NRVS data, including the porphyrin-based vibrations, of a 6C ferrous heme-nitrosyl, using our quantum chemistry centered normal coordinate analysis (QCC-NCA). Importantly, the Fe-NO stretch is split by interaction with a porphyrin-based vibration into two features, observed at 437 and 472 cm(-1). The 437 cm(-1) feature is strongly out-of-plane (oop) polarized and shows a (15)N(18)O isotope shift of 8 cm(-1) and is therefore assigned to nu(Fe-NO). The admixture of Fe-N-O bending character is small. Main contributions to the Fe-N-O bend are observed in the 520-580 cm(-1) region, distributed over a number of in-plane (ip) polarized porphyrin-based vibrations. The main component, assigned to delta(ip)(Fe-N-O), is identified with the feature at 563 cm(-1). The Fe-N-O bend also shows strong mixing with the Fe-NO stretching internal coordinate, as evidenced by the oop NRVS intensity in the 520-580 cm(-1) region. Very accurate normal mode descriptions of nu(Fe-NO) and delta(ip)(Fe-N-O) have been obtained in this study. These results contradict previous interpretations of the vibrational spectra of 6C ferrous heme-nitrosyls where the higher energy feature at approximately 550 cm(-1) had usually been associated with nu(Fe-NO). Furthermore, these results provide key insight into NO binding to ferrous heme active sites in globins and other heme proteins, in particular with respect to (a) the effect of hydrogen bonding to the coordinated NO and (b) changes in heme dynamics upon NO coordination. [Fe(TPP)(MI)(NO)] constitutes an excellent model system for ferrous NO adducts of myoglobin (Mb) mutants where the distal histidine (His64) has been removed. Comparison to the reported vibrational data for wild-type (wt) Mb-NO then shows that the effect of H bonding to the coordinated NO is weak and mostly leads to a polarization of the pi/pi* orbitals of bound NO. In addition, the observation that delta(ip)(Fe-N-O) does not correlate well with nu(N-O) can be traced back to the very mixed nature of this mode. The Fe-N(imidazole) stretching frequency is observed at 149 cm(-1) in [Fe(TPP)(MI)(NO)], and spectral changes upon NO binding to five-coordinate ferrous heme active sites are discussed. The obtained high-quality force constants for the Fe-NO and N-O bonds of 2.57 and 11.55 mdyn/A can further be compared to those of corresponding 5C species, which allows for a quantitative analysis of the sigma trans interaction between the proximal imidazole (His) ligand and NO. This is key for the activation of the NO sensor soluble guanylate cyclase. Finally, DFT methods are calibrated against the experimentally determined vibrational properties of the Fe-N-O subunit in 1. DFT is in fact incapable of reproducing the vibrational energies and normal mode descriptions of the Fe-N-O unit well, and thus, DFT-based predictions of changes in vibrational properties upon heme modification or other perturbations of these 6C complexes have to be treated with caution.

Dataset Information

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

Publications

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

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