Literature DB >> 23881496

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

Yuki Kurashige1, Garnet Kin-Lic Chan, Takeshi Yanai.   

Abstract

It is a long-standing goal to understand the reaction mechanisms of catalytic metalloenzymes at an entangled many-electron level, but this is hampered by the exponential complexity of quantum mechanics. Here, by exploiting the special structure of physical quantum states and using the density matrix renormalization group, we compute near-exact many-electron wavefunctions of the Mn4CaO5 cluster of photosystem II, with more than 1 × 10(18) quantum degrees of freedom. This is the first treatment of photosystem II beyond the single-electron picture of density functional theory. Our calculations support recent modifications to the structure determined by X-ray crystallography. We further identify multiple low-lying energy surfaces associated with the structural distortion seen using X-ray crystallography, highlighting multistate reactivity in the chemistry of the cluster. Direct determination of Mn spin-projections from our wavefunctions suggests that current candidates that have been recently distinguished using parameterized spin models should be reassessed. Through entanglement maps, we reveal rich information contained in the wavefunctions on bonding changes in the cycle.

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Year:  2013        PMID: 23881496     DOI: 10.1038/nchem.1677

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


  41 in total

1.  Stoichiometry of proton release from the catalytic center in photosynthetic water oxidation. Reexamination by a glass electrode study at ph 5.5-7.2.

Authors:  E Schlodder; H T Witt
Journal:  J Biol Chem       Date:  1999-10-22       Impact factor: 5.157

2.  Insights into current limitations of density functional theory.

Authors:  Aron J Cohen; Paula Mori-Sánchez; Weitao Yang
Journal:  Science       Date:  2008-08-08       Impact factor: 47.728

3.  The density matrix renormalization group self-consistent field method: orbital optimization with the density matrix renormalization group method in the active space.

Authors:  Dominika Zgid; Marcel Nooijen
Journal:  J Chem Phys       Date:  2008-04-14       Impact factor: 3.488

4.  Orbital optimization in the density matrix renormalization group, with applications to polyenes and beta-carotene.

Authors:  Debashree Ghosh; Johannes Hachmann; Takeshi Yanai; Garnet Kin-Lic Chan
Journal:  J Chem Phys       Date:  2008-04-14       Impact factor: 3.488

Review 5.  P450 enzymes: their structure, reactivity, and selectivity-modeled by QM/MM calculations.

Authors:  Sason Shaik; Shimrit Cohen; Yong Wang; Hui Chen; Devesh Kumar; Walter Thiel
Journal:  Chem Rev       Date:  2010-02-10       Impact factor: 60.622

6.  An energetic comparison of different models for the oxygen evolving complex of photosystem II.

Authors:  Per E M Siegbahn
Journal:  J Am Chem Soc       Date:  2009-12-30       Impact factor: 15.419

7.  Second-order perturbation theory with a density matrix renormalization group self-consistent field reference function: theory and application to the study of chromium dimer.

Authors:  Yuki Kurashige; Takeshi Yanai
Journal:  J Chem Phys       Date:  2011-09-07       Impact factor: 3.488

8.  The effect of backbone constraints: the case of water oxidation by the oxygen-evolving complex in PSII.

Authors:  Per E M Siegbahn
Journal:  Chemphyschem       Date:  2011-09-16       Impact factor: 3.102

9.  Absence of Mn-centered oxidation in the S(2) --> S(3) transition: implications for the mechanism of photosynthetic water oxidation.

Authors:  J Messinger; J H Robblee; U Bergmann; C Fernandez; P Glatzel; H Visser; R M Cinco; K L McFarlane; E Bellacchio; S A Pizarro; S P Cramer; K Sauer; M P Klein; V K Yachandra
Journal:  J Am Chem Soc       Date:  2001-08-15       Impact factor: 15.419

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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  22 in total

1.  Computational chemistry: a multitude of spins.

Authors:  Jeremy N Harvey
Journal:  Nat Chem       Date:  2013-08       Impact factor: 24.427

Review 2.  Metal Ion Modeling Using Classical Mechanics.

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

3.  Supercritical entanglement in local systems: Counterexample to the area law for quantum matter.

Authors:  Ramis Movassagh; Peter W Shor
Journal:  Proc Natl Acad Sci U S A       Date:  2016-11-07       Impact factor: 11.205

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

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

Review 5.  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

6.  Improvement of d-d interactions in density functional tight binding for transition metal ions with a ligand field model: assessment of a DFTB3+U model on nickel coordination compounds.

Authors:  Stepan Stepanovic; Rui Lai; Marcus Elstner; Maja Gruden; Pablo Garcia-Fernandez; Qiang Cui
Journal:  Phys Chem Chem Phys       Date:  2020-12-07       Impact factor: 3.676

7.  The correlation theory of the chemical bond.

Authors:  Szilárd Szalay; Gergely Barcza; Tibor Szilvási; Libor Veis; Örs Legeza
Journal:  Sci Rep       Date:  2017-05-22       Impact factor: 4.379

8.  QM/MM Analysis of Transition States and Transition State Analogues in Metalloenzymes.

Authors:  D Roston; Q Cui
Journal:  Methods Enzymol       Date:  2016-07-01       Impact factor: 1.600

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

Authors:  Sandeep Sharma; Kantharuban Sivalingam; Frank Neese; Garnet Kin-Lic Chan
Journal:  Nat Chem       Date:  2014-08-31       Impact factor: 24.427

10.  Pathway for Mn-cluster oxidation by tyrosine-Z in the S2 state of photosystem II.

Authors:  Daniele Narzi; Daniele Bovi; Leonardo Guidoni
Journal:  Proc Natl Acad Sci U S A       Date:  2014-06-02       Impact factor: 11.205

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