Density Functional Theory

Noodleman, Louis; Lovell, Timothy; Han, Weiwei; Liu, T.; Torres, Rhonda A.; Himo, Fahmi

doi:10.1016/b0-08-043748-6/01067-7

Cited by 39 publications

(67 citation statements)

References 70 publications

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“…We have not included spin projection corrections in the current work since we have estimated that these will make only very small differences in the DFT calculated relative energies of different states. The properties of BS states can be directly connected to the hyperfine properties of corresponding pure spin states using the Wigner Eckart theorem 36-38,67…”

Section: Computational Methodologymentioning

confidence: 99%

DFT Calculations for Intermediate and Active States of the Diiron Center with a Tryptophan or Tyrosine Radical in Escherichia coli Ribonucleotide Reductase

Han

Noodleman

2011

Inorg. Chem.

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Class Ia ribonucleotide reductase (RNR) subunit R2 contains a diiron active site. In this paper, active site models for the intermediate X-Trp48 +· and X-Tyr122 · , the active Fe(III)Fe(III)-Tyr122 · , and the met Fe(III)Fe(III) states of E. coli R2 are studied, using broken-symmetry density functional theory (DFT) incorporated with the conductor like screening (COSMO) solvation model. Different structural isomers and different protonation states have been explored. Calculated geometric, energetic, Mössbauer, hyperfine, and redox properties are compared with available experimental data. Feasible detailed structures of these intermediate and active states are proposed. Asp84 and Trp48 are most likely the main contributing residues to the result that the transient Fe(IV)Fe(IV) state is not observed in wild-type class Ia E. coli R2. Asp84 is proposed to serve as a proton transfer conduit between the diiron cluster and Tyr122 in both the tyrosine radical activation pathway and in the first steps of the catalytic proton coupled electron transfer pathway. Proton coupled and simple redox potential calculations show that the kinetic control of proton transfer to Tyr122 · plays a critical role in preventing reduction from the active Fe(III)Fe(III)-Tyr122 · state to the met state, which is potentially the reason that the Tyr122 · in the active state can be stable over very long period.

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Section: Computational Methodologymentioning

confidence: 99%

DFT Calculations for Intermediate and Active States of the Diiron Center with a Tryptophan or Tyrosine Radical in Escherichia coli Ribonucleotide Reductase

Han

Noodleman

2011

Inorg. Chem.

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“…However, in the case of DFT it is customary to also use the mapping procedure or the corresponding spin projected solution [4,5,73,74]. The use of the unprojected results may obscure some important issues [4,5,28,[56][57][58][75][76][77] and lead to some contradictions [5,28]. Still, the auxiliary nature of the KS orbitals makes this procedure at least controversial [4,5,78].…”

Section: Spin Unrestricted Density Functional Theory: Implications Fomentioning

confidence: 99%

Spin Symmetry Requirements in Density Functional Theory: The Proper Way to Predict Magnetic Coupling Constants in Molecules and Solids

et al. 2006

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Take-down policy If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. Abstract In this paper it is argued that the use of density functional theory (DFT) to solve the exact, non-relativistic, many-electron problem, for magnetic systems requires imposing space and spin symmetry constraints exactly in the same way as it is currently done in ab initio wave function theory. This strong statement is supported on pertinent calculations for selected systems representative of organic diradicals, molecular magnets and antiferromagnetic solids. These calculations include several wave function methods of increasing accuracy and different forms of the exchangecorrelation functional. The comparisons of numerical results carried out always within the same standard Gaussian Type Orbital atomic basis set show that imposing or not the spin and space constraints (restricted or unrestricted formalisms) leads to contradictory results. Therefore, it appears that, in the case of the Heisenberg magnetic constant, the present exchange-correlation functionals may provide reasonable numerical results although for the wrong physical reasons thus evidencing the failure of the current DFT methods to properly describe magnetic systems.

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“…Indeed it fails in describing HT c superconductors and Mott insulators, and in predicting some transition metal compounds properties, whenever the outermost atomic d shell is near half-filled, as for instance, in the high potential iron proteins. 5 Also H 2 molecule in the large distance regime must be included in that list, since the large distance BornOppenheimer energy surface, depending on van der Waals forces, is not well reproduced by the standard functionals, although recently some progress has been made to include these important contributions. 6 Quantum Monte Carlo ͑QMC͒ methods are alternative to the previous ones and until now they have been mainly used in two versions.…”

Section: Introductionmentioning

confidence: 99%

Correlated geminal wave function for molecules: An efficient resonating valence bond approach

Casula

Attaccalite

Sorella

2004

The Journal of Chemical Physics

214

295

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We show that a simple correlated wave function, obtained by applying a Jastrow correlation term to an antisymmetrized geminal power, based upon singlet pairs between electrons, is particularly suited for describing the electronic structure of molecules, yielding a large amount of the correlation energy. The remarkable feature of this approach is that, in principle, several resonating valence bonds can be dealt simultaneously with a single determinant, at a computational cost growing with the number of electrons similar to more conventional methods, such as Hartree-Fock or density functional theory. Moreover we describe an extension of the stochastic reconfiguration method, which was recently introduced for the energy minimization of simple atomic wave functions. Within this extension the atomic positions can be considered as further variational parameters, which can be optimized together with the remaining ones. The method is applied to several molecules from Li(2) to benzene by obtaining total energies, bond lengths and binding energies comparable with much more demanding multiconfiguration schemes.

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Density Functional Theory

Cited by 39 publications

References 70 publications

DFT Calculations for Intermediate and Active States of the Diiron Center with a Tryptophan or Tyrosine Radical in Escherichia coli Ribonucleotide Reductase

DFT Calculations for Intermediate and Active States of the Diiron Center with a Tryptophan or Tyrosine Radical in Escherichia coli Ribonucleotide Reductase

Spin Symmetry Requirements in Density Functional Theory: The Proper Way to Predict Magnetic Coupling Constants in Molecules and Solids

Correlated geminal wave function for molecules: An efficient resonating valence bond approach

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