Literature DB >> 16830147

The performance of hybrid DFT for mechanisms involving transition metal complexes in enzymes.

Per E M Siegbahn1.   

Abstract

The accuracy of density functional theory with the B3LYP functional is reviewed for systems of relevance to transition-metal-containing enzymes. Calculated energies are commonly within 3-5 kcal/mol of the correct values; however, some exceptions have appeared in the literature and are discussed here. For example, the binding of NO and that of O(2) to metal centers have for some time been known to be underestimated. Most barriers for chemical reactions are overestimated except those involving hydrogen (or proton) transfer, which instead tend to be underestimated. A minor general improvement of the accuracy can probably be obtained by slightly reducing the amount of exact exchange in the B3LYP functional.

Entities:  

Mesh:

Substances:

Year:  2006        PMID: 16830147     DOI: 10.1007/s00775-006-0137-2

Source DB:  PubMed          Journal:  J Biol Inorg Chem        ISSN: 0949-8257            Impact factor:   3.358


  21 in total

Review 1.  High-level ab initio calculations on the energetics of low-lying spin states of biologically relevant transition metal complexes: a first progress report.

Authors:  Abhik Ghosh; Peter R Taylor
Journal:  Curr Opin Chem Biol       Date:  2003-02       Impact factor: 8.822

2.  Ionization potentials and electron affinities in the Perdew-Zunger self-interaction corrected density-functional theory.

Authors:  Oleg A Vydrov; Gustavo E Scuseria
Journal:  J Chem Phys       Date:  2005-05-08       Impact factor: 3.488

3.  Quantum chemistry applied to the mechanisms of transition metal containing enzymes -- cytochrome c oxidase, a particularly challenging case.

Authors:  Margareta R A Blomberg; Per E M Siegbahn
Journal:  J Comput Chem       Date:  2006-09       Impact factor: 3.376

4.  A localized orbital analysis of the thermochemical errors in hybrid density functional theory: achieving chemical accuracy via a simple empirical correction scheme.

Authors:  Richard A Friesner; Eric H Knoll; Yixiang Cao
Journal:  J Chem Phys       Date:  2006-09-28       Impact factor: 3.488

Review 5.  Mechanisms of metalloenzymes studied by quantum chemical methods.

Authors:  Per E M Siegbahn
Journal:  Q Rev Biophys       Date:  2003-02       Impact factor: 5.318

6.  Crystallographic analysis of oxygenated and deoxygenated states of arthropod hemocyanin shows unusual differences.

Authors:  K A Magnus; B Hazes; H Ton-That; C Bonaventura; J Bonaventura; W G Hol
Journal:  Proteins       Date:  1994-08

7.  Quantifying the effects of the self-interaction error in DFT: when do the delocalized states appear?

Authors:  Marcus Lundberg; Per E M Siegbahn
Journal:  J Chem Phys       Date:  2005-06-08       Impact factor: 3.488

8.  The rate of O2 and CO binding to a copper complex, determined by a "flash-and-trap" technique, exceeds that for hemes.

Authors:  H Christopher Fry; Donald V Scaltrito; Kenneth D Karlin; Gerald J Meyer
Journal:  J Am Chem Soc       Date:  2003-10-01       Impact factor: 15.419

9.  Mechanism for catechol ring-cleavage by non-heme iron extradiol dioxygenases.

Authors:  Per E M Siegbahn; Fredrik Haeffner
Journal:  J Am Chem Soc       Date:  2004-07-28       Impact factor: 15.419

10.  A comparison of the thermodynamics of O[bond]O cleavage for dicopper complexes in enzymes and synthetic systems.

Authors:  Per E M Siegbahn
Journal:  J Biol Inorg Chem       Date:  2003-03-28       Impact factor: 3.358

View more
  30 in total

Review 1.  Recent developments of the quantum chemical cluster approach for modeling enzyme reactions.

Authors:  Per E M Siegbahn; Fahmi Himo
Journal:  J Biol Inorg Chem       Date:  2009-05-13       Impact factor: 3.358

2.  Density functional localized orbital corrections for transition metals.

Authors:  David Rinaldo; Li Tian; Jeremy N Harvey; Richard A Friesner
Journal:  J Chem Phys       Date:  2008-10-28       Impact factor: 3.488

Review 3.  Computational insights into the O2-evolving complex of photosystem II.

Authors:  Eduardo M Sproviero; James P McEvoy; José A Gascón; Gary W Brudvig; Victor S Batista
Journal:  Photosynth Res       Date:  2008-05-16       Impact factor: 3.573

Review 4.  Protein effects in non-heme iron enzyme catalysis: insights from multiscale models.

Authors:  Nathalie Proos Vedin; Marcus Lundberg
Journal:  J Biol Inorg Chem       Date:  2016-06-30       Impact factor: 3.358

5.  Cryoreduction of the NO-adduct of taurine:alpha-ketoglutarate dioxygenase (TauD) yields an elusive {FeNO}(8) species.

Authors:  Shengfa Ye; John C Price; Eric W Barr; Michael T Green; J Martin Bollinger; Carsten Krebs; Frank Neese
Journal:  J Am Chem Soc       Date:  2010-04-07       Impact factor: 15.419

6.  Complexes of arzanol with a Cu2+ ion: a DFT study.

Authors:  Liliana Mammino
Journal:  J Mol Model       Date:  2017-09-12       Impact factor: 1.810

7.  Spectroscopic Evidence for the Two C-H-Cleaving Intermediates of Aspergillus nidulans Isopenicillin N Synthase.

Authors:  Esta Tamanaha; Bo Zhang; Yisong Guo; Wei-Chen Chang; Eric W Barr; Gang Xing; Jennifer St Clair; Shengfa Ye; Frank Neese; J Martin Bollinger; Carsten Krebs
Journal:  J Am Chem Soc       Date:  2016-07-05       Impact factor: 15.419

Review 8.  Why nature really chose phosphate.

Authors:  Shina C L Kamerlin; Pankaz K Sharma; Ram B Prasad; Arieh Warshel
Journal:  Q Rev Biophys       Date:  2013-01-15       Impact factor: 5.318

9.  Investigation of the antioxidant properties of hyperjovinol A through its Cu(II) coordination ability.

Authors:  Liliana Mammino
Journal:  J Mol Model       Date:  2012-12-05       Impact factor: 1.810

Review 10.  Density functional theory.

Authors:  Maylis Orio; Dimitrios A Pantazis; Frank Neese
Journal:  Photosynth Res       Date:  2009 Nov-Dec       Impact factor: 3.573

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.