Theory of chemical bonds in metalloenzymes III: Full geometry optimization and vibration analysis of ferredoxin‐type [2Fe–2S] cluster

Shoji, Mitsuo; Koizumi, Kenichi; Taniguchi, Tadatsugu; Kitagawa, Yasutaka; Yamanaka, Shusuke; Okumura, Mitsutaka; Yamaguchi, Kizashi

doi:10.1002/qua.21016

Cited by 34 publications

(39 citation statements)

References 61 publications

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“…For instance, approximate spin projection corrections are up to , 0.1 Å for the Fe -Fe distance of [2Fe -2S] clusters for calculations at the BP86/BSIV [96] level and the B3LYP level using a double-z basis set [60]. However, there is no automated method for adding either projection correction into geometry optimisation, and the corrections are rather small.…”

Section: Further Improvementsmentioning

confidence: 99%

Density functional theory calculations of redox properties of iron–sulphur protein analogues

Ichiye

2011

Molecular Simulation

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A central issue in understanding redox properties of iron-sulphur (Fe-S) proteins is determining the factors that tune the reduction potentials of the Fe-S clusters. Studies of redox site analogues play an important role, particularly because individual factors can be examined independently of the environment by combining calculations and experiments of carefully designed ligands for the analogues. For iron-sulphur analogues, our study has shown that broken-symmetry density functional theory gives good energetics when the geometry is optimised using B3LYP with a double-z basis set with polarisation functions, and the energies of these geometries are calculated using B3LYP with additional diffuse functions added to the sulphurs. A comparison of our calculated energies for redox site analogues in the gas phase against electron detachment energies measured by a combination of electrospray ionisation and photoelectron spectroscopy (EI-PES) by Wang and co-workers has been essential because the comparison is for exactly the same molecule with no approximation for the environment. Overall, the correlation of our B3LYP/ 6-31(þþ) S G**//B3LYP/6-31G** detachment energies with EI-PES experiments is excellent for a wide variety of analogues. Moreover, our calculations at this level have provided insight into a wide variety of properties of iron-sulphur proteins.Dr Shuqiang Niu is a computational chemist interested in exploring complex electronic structures, physical properties, and reaction mechanisms of chemical and biological molecules using quantum mechanical and hybrid quantum mechanics/molecular mechanics methods. He received his B.S. and M.S. degrees in physical chemistry from Nankai University. After teaching for two years at Nankai University, he joined Professor R. Gleiter's group at Heidelberg University, Germany, and completed his Ph.D. degree in computational and organic chemistry in 1994. He then did postdoctoral work with Professor Michael Hall at Texas A&M University (1994 -1999) and with Dr Jeffrey Nichols at Pacific Northwest National Laboratories (1999 -2000) developing and applying computational methodologies for investigations of catalytic reactions and enzymatic mechanisms. He joined Professor Toshiko Ichiye's group at Washington State University in 2000 and then moved to Georgetown University with her in 2003. His current research primarily focuses on the simulation and prediction of redox properties of iron-sulfur proteins. Health. Her research involves computational and theoretical studies of biological macromolecules and other condensed matter systems at a molecular level. One major research interest is in understanding properties of electron transfer proteins utilising both quantum mechanical calculations of redox site analogs and classical mechanical calculations of the proteins. Another major interest is in understanding the underlying molecular basis of the unusual properties of water and in developing models of water for liquid state computer simulations using molecular multipole expansions.

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Section: Further Improvementsmentioning

confidence: 99%

Density functional theory calculations of redox properties of iron–sulphur protein analogues

Ichiye

2011

Molecular Simulation

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“…23 A large literature has developed on this and related broken-symmetry approaches. [24][25][26][27][28][29][30][31][32][33] Broken-symmetry solutions have also been studied in other contexts, and it has often been found that it is important to allow the orbitals to break symmetry in order to get a qualitatively correct description of the system. [33][34][35][36][37][38][39][40][41][42] The energies of the broken-symmetry states are often used without correcting for their spin character.…”

Section: Introductionmentioning

confidence: 99%

Density Functional Theory in Transition-Metal Chemistry: Relative Energies of Low-Lying States of Iron Compounds and the Effect of Spatial Symmetry Breaking

Sorkin

Iron

Truhlar

2008

J. Chem. Theory Comput.

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Abstract:The ground and lower excited states of Fe 2 , Fe 2 -, and FeO + were studied using a number of density functional theory (DFT) methods. Specific attention was paid to the relative state energies, the internuclear distances (r e ), and the harmonic vibrational frequencies (ω e ). A number of factors influencing the calculated values of these properties were examined. These include basis sets, the nature of the density functional chosen, the percentage of HartreeFock exchange in the density functional, and constraints on orbital symmetry. A number of different types of generalized gradient approximation (GGA) density functionals (straight GGA, hybrid GGA, meta-GGA, and hybrid meta-GGA) were examined, and it was found that the best results were obtained with hybrid GGA or hybrid meta-GGA functionals that contain nonzero fractions of HF exchange; specifically, the best overall results were obtained with B3LYP, M05, and M06, closely followed by B1LYP. One significant observation was the effect of enforcing symmetry on the orbitals. When a degenerate orbital (π or δ) is partially occupied in the 4 Φ excited state of FeO + , reducing the enforced symmetry (from C 6v to C 4v to C 2v ) results in a lower energy since these degenerate orbitals are split in the lower symmetries. The results obtained were compared to higher level ab initio results from the literature and to recent PBE+U plane wave results by Kulik et al. (Phys. Rev. Lett. 2006, 97, 103001). It was found that some of the improvements that were afforded by the semiempirical +U correction can also be accomplished by improving the form of the DFT functional and, in one case, by not enforcing high symmetry on the orbitals.

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“…Computationally this implies severe limitations in terms of system size and coupling to molecular dynamics (MD). A well established compromise in terms of cost versus accuracy are spin-projection schemes (11, 12) that rely on an approximate purification of the spin state (13) by carrying out independent total energy calculations for several uncoupled spin configurations (14,15). Such approaches allow the calculation of the exchange coupling constant J directly and have been proven to perform particularly well for binuclear homovalent clusters in static calculations (16, 17).…”

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confidence: 99%

Dynamical magnetostructural properties of Anabaena ferredoxin

Schreiner

Nair

Pollet

et al. 2007

Proc. Natl. Acad. Sci. U.S.A.

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A mixed quantum/classical investigation of the dynamical magnetostructural properties, that is, ''magnetodynamics,'' of oxidized Anabaena PCC7119 ferredoxin is carried out at room temperature in two distinct conformational states. This protein hosts a [2Fe-2S] cluster in which two iron centers are antiferromagnetically coupled to an overall low-spin electronic ground state that has a genuine multireference character. To study the magnetodynamics of this prosthetic group, an approximate spin projection method is formulated in the framework of density functional theory that allows for multideterminant ab initio molecular dynamics simulations to be carried out efficiently. By using this scheme, the influence of both thermal fluctuations and conformational motion on the structure of the [2Fe-2S] cluster and on the dynamics of the antiferromagnetic coupling constant, J(t), has been investigated. In addition to demonstrating how sensitively the shape of the [2Fe-2S] core itself is affected by hydrogen bonding, the analyses reveal a complex dynamical coupling of J to both local vibrations and large-amplitude motion. It is shown that this interplay can be understood in terms of specific vibrational modes and distinct hydrogen-bonding patterns between the iron-sulfur cluster and the protein backbone, respectively. This implies going beyond the Goodenough-Kanamori rules for angular magnetostructural correlations of oxidized iron-sulfur prosthetic groups.exchange coupling ͉ extended broken-symmetry ͉ hydrogen bonding ͉ iron-sulfur protein ͉ multideterminant hybrid molecular dynamics I ron-sulfur clusters are among the most ubiquitous, functionally versatile, and ancient prosthetic groups in proteins (1-4). One of the major classes of mobile electron carriers in contemporary biology is ferredoxin (Fd). Its fourfold cysteine-coordinated [2Fe-2S] core mediates electron transfer from photosystem I to ferredoxin-NADP ϩ -oxidoreductase, which reduces NADP ϩ to NADPH. A particularly interesting system is Fd from cyanobacterium Anabaena PCC7119 whose crystal structure was recently obtained at 1.3 and 1.17 Å resolution in the oxidized and the reduced forms (5), respectively. Most interestingly, it was found that two alternative conformations of Cys-46 exist, which is one of the four cysteinyl ligands of the [2Fe-2S] cluster (5). In the oxidized state Cys-46 adopts the so-called CO-in conformation, where the peptide oxygen points in the direction of the cluster, whereas, on reduction, the backbone flips to the CO-out conformation.Spin Coupling in Iron-Sulfur Clusters. In the ground state of the oxidized form of bioinorganic [mFe-nS] clusters, the Fe 3ϩ metal centers are typically in a local high-spin d 5 configuration [i.e., S Fe ϭ 5/2 for ferric Fe(III) centers], whereas they themselves are antiferromagnetically coupled to yield an overall low-spin state due to dominant superexchange interactions (6). In particular, the electronic ground state of [2Fe-2S] clusters in Fd has genuine multireference character and makes computational ...

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Theory of chemical bonds in metalloenzymes III: Full geometry optimization and vibration analysis of ferredoxin‐type [2Fe–2S] cluster

Cited by 34 publications

References 61 publications

Density functional theory calculations of redox properties of iron–sulphur protein analogues

Density functional theory calculations of redox properties of iron–sulphur protein analogues

Density Functional Theory in Transition-Metal Chemistry: Relative Energies of Low-Lying States of Iron Compounds and the Effect of Spatial Symmetry Breaking

Dynamical magnetostructural properties of Anabaena ferredoxin

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