Literature DB >> 25242489

Low-energy spectrum of iron-sulfur clusters directly from many-particle quantum mechanics.

Sandeep Sharma1, Kantharuban Sivalingam2, Frank Neese2, Garnet Kin-Lic Chan1.   

Abstract

Iron-sulfur clusters are a universal biological motif. They carry out electron transfer, redox chemistry and even oxygen sensing, in diverse processes including nitrogen fixation, respiration and photosynthesis. Their low-lying electronic states are key to their remarkable reactivity, but they cannot be directly observed. Here, we present the first ever quantum calculation of the electronic levels of [2Fe-2S] and [4Fe-4S] clusters free from any model assumptions. Our results highlight the limitations of long-standing models of their electronic structure. In particular, we demonstrate that the widely used Heisenberg double exchange model underestimates the number of states by one to two orders of magnitude, which can conclusively be traced to the absence of Fe dd excitations, thought to be important in these clusters. Furthermore, the electronic energy levels of even the same spin are dense on the scale of vibrational fluctuations and this provides a natural explanation for the ubiquity of these clusters in catalysis in nature.

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Year:  2014        PMID: 25242489     DOI: 10.1038/nchem.2041

Source DB:  PubMed          Journal:  Nat Chem        ISSN: 1755-4330            Impact factor:   24.427


  21 in total

Review 1.  Synthetic analogues of the active sites of iron-sulfur proteins.

Authors:  P Venkateswara Rao; R H Holm
Journal:  Chem Rev       Date:  2004-02       Impact factor: 60.622

2.  The density matrix renormalization group in quantum chemistry.

Authors:  Garnet Kin-Lic Chan; Sandeep Sharma
Journal:  Annu Rev Phys Chem       Date:  2011       Impact factor: 12.703

3.  Convergence behavior of the density-matrix renormalization group algorithm for optimized orbital orderings.

Authors:  Gerrit Moritz; Bernd Artur Hess; Markus Reiher
Journal:  J Chem Phys       Date:  2005-01-08       Impact factor: 3.488

Review 4.  Structure, function, and formation of biological iron-sulfur clusters.

Authors:  Deborah C Johnson; Dennis R Dean; Archer D Smith; Michael K Johnson
Journal:  Annu Rev Biochem       Date:  2005       Impact factor: 23.643

5.  On the spin and symmetry adaptation of the density matrix renormalization group method.

Authors:  Dominika Zgid; Marcel Nooijen
Journal:  J Chem Phys       Date:  2008-01-07       Impact factor: 3.488

6.  Entangled quantum electronic wavefunctions of the Mn₄CaO₅ cluster in photosystem II.

Authors:  Yuki Kurashige; Garnet Kin-Lic Chan; Takeshi Yanai
Journal:  Nat Chem       Date:  2013-06-09       Impact factor: 24.427

7.  Synthetic analogs of the active sites of iron-sulfur proteins. II. Synthesis and structure of the tetra(mercapto-m 3 -sulfido-iron) clusters, (Fe 4 S 4 (SR) 4 ) 2- .

Authors:  B A Averill; T Herskovitz; R H Holm; J A Ibers
Journal:  J Am Chem Soc       Date:  1973-05-30       Impact factor: 15.419

Review 8.  Iron-sulfur clusters: nature's modular, multipurpose structures.

Authors:  H Beinert; R H Holm; E Münck
Journal:  Science       Date:  1997-08-01       Impact factor: 47.728

9.  Spin-adapted density matrix renormalization group algorithms for quantum chemistry.

Authors:  Sandeep Sharma; Garnet Kin-Lic Chan
Journal:  J Chem Phys       Date:  2012-03-28       Impact factor: 3.488

10.  High-performance ab initio density matrix renormalization group method: applicability to large-scale multireference problems for metal compounds.

Authors:  Yuki Kurashige; Takeshi Yanai
Journal:  J Chem Phys       Date:  2009-06-21       Impact factor: 3.488

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  33 in total

Review 1.  Metal Ion Modeling Using Classical Mechanics.

Authors:  Pengfei Li; Kenneth M Merz
Journal:  Chem Rev       Date:  2017-01-03       Impact factor: 60.622

2.  Cluster-Dependent Charge-Transfer Dynamics in Iron-Sulfur Proteins.

Authors:  Ziliang Mao; Shu-Hao Liou; Nimesh Khadka; Francis E Jenney; David B Goodin; Lance C Seefeldt; Michael W W Adams; Stephen P Cramer; Delmar S Larsen
Journal:  Biochemistry       Date:  2018-01-24       Impact factor: 3.162

3.  Charge Transfer between [4Fe4S] Proteins and DNA Is Unidirectional: Implications for Biomolecular Signaling.

Authors:  Ruijie D Teo; Benjamin J G Rousseau; Elizabeth R Smithwick; Rosa Di Felice; David N Beratan; Agostino Migliore
Journal:  Chem       Date:  2018-10-25       Impact factor: 22.804

4.  Perspective: Quantum mechanical methods in biochemistry and biophysics.

Authors:  Qiang Cui
Journal:  J Chem Phys       Date:  2016-10-14       Impact factor: 3.488

5.  Exploring the applicability of density functional tight binding to transition metal ions. Parameterization for nickel with the spin-polarized DFTB3 model.

Authors:  Milena Vujović; Mioy Huynh; Sebastian Steiner; Pablo Garcia-Fernandez; Marcus Elstner; Qiang Cui; Maja Gruden
Journal:  J Comput Chem       Date:  2018-10-09       Impact factor: 3.376

6.  Computational Approach to Molecular Catalysis by 3d Transition Metals: Challenges and Opportunities.

Authors:  Konstantinos D Vogiatzis; Mikhail V Polynski; Justin K Kirkland; Jacob Townsend; Ali Hashemi; Chong Liu; Evgeny A Pidko
Journal:  Chem Rev       Date:  2018-10-30       Impact factor: 60.622

Review 7.  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

8.  Electronic landscape of the P-cluster of nitrogenase as revealed through many-electron quantum wavefunction simulations.

Authors:  Zhendong Li; Sheng Guo; Qiming Sun; Garnet Kin-Lic Chan
Journal:  Nat Chem       Date:  2019-09-30       Impact factor: 24.427

9.  Electron Redistribution within the Nitrogenase Active Site FeMo-Cofactor During Reductive Elimination of H2 to Achieve N≡N Triple-Bond Activation.

Authors:  Dmitriy A Lukoyanov; Zhi-Yong Yang; Dennis R Dean; Lance C Seefeldt; Simone Raugei; Brian M Hoffman
Journal:  J Am Chem Soc       Date:  2020-12-16       Impact factor: 15.419

10.  Ultrafast Charge-Transfer Dynamics in the Iron-Sulfur Complex of Rhodobacter capsulatus Ferredoxin VI.

Authors:  Ziliang Mao; Elizabeth C Carroll; Peter W Kim; Stephen P Cramer; Delmar S Larsen
Journal:  J Phys Chem Lett       Date:  2017-09-07       Impact factor: 6.475

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