Density functional theory

Density functional theory (DFT) finds increasing use in applications related to biological systems. Advancements in methodology and implementations have reached a point where predicted properties of reasonable to high quality can be obtained. Thus, DFT studies can complement experimental investigations, or even venture with some confidence into experimentally unexplored territory. In the present contribution, we provide an overview of the properties that can be calculated with DFT, such as geometries, energies, reaction mechanisms, and spectroscopic properties. A wide range of spectroscopic parameters is nowadays accessible with DFT, including quantities related to infrared and optical spectra, X-ray absorption and Mössbauer, as well as all of the magnetic properties connected with electron paramagnetic resonance spectroscopy except relaxation times. We highlight each of these fields of application with selected examples from the recent literature and comment on the capabilities and limitations of current methods.

• Publication year

  2009

• Venue

  Photosynthesis Research

• Publication date

  2009-02-24

• Fields of study

  Medicine, Physics, Chemistry

• Identifiers
  DOI 10.1007/s11120-009-9404-8PMID 19238578PMCID 2777204
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Mössbauer spectroscopy.

  2011cited by this paper
• Prediction of molecular properties and molecular spectroscopy with density functional theory: From fundamental theory to exchange-coupling

  2009cited by this paper
• A new quantum chemical approach to the magnetic properties of oligonuclear transition-metal complexes: application to a model for the tetranuclear manganese cluster of photosystem II.

  2009influential reference
• Efficient, approximate and parallel Hartree–Fock and hybrid DFT calculations. A ‘chain-of-spheres’ algorithm for the Hartree–Fock exchange

  2009cited by this paper
• High Resolution EPR: Applications to Metalloenzymes and Metals in Medicine

  2009cited by this paper
• Ab initio and coupled-perturbed density functional theory estimation of zero-field splittings in MnII transition metal complexes.

  2008cited by this paper
• Electronic structure and spectroscopy of "superoxidized" iron centers in model systems: theoretical and experimental trends.

  2008influential reference
• A systematic density functional study of the zero-field splitting in Mn(II) coordination compounds.

  2008cited by this paper
• Focusing the view on nature's water-splitting catalyst

  2008cited by this paper
• Time-dependent DFT studies of metal core-electron excitations in Mn complexes.

  2008cited by this paper
• Computational insights into the O2-evolving complex of photosystem II

  2008cited by this paper
• Ligation Of The C-Terminus Of The D1 Polypeptide Of Photosystem Ii To The Oxygen Evolving Complex: A Dft-Qm/Mm Study

  2008cited by this paper
• Theoretical studies of O-O bond formation in photosystem II.

  2008cited by this paper
• QM/MM computational studies of substrate water binding to the oxygen-evolving centre of photosystem II

  2008cited by this paper
• Quantum mechanics/molecular mechanics study of the catalytic cycle of water splitting in photosystem II.

  2008cited by this paper
• Geometries of Third-Row Transition-Metal Complexes from Density-Functional Theory.

  2008cited by this paper
• A structure-consistent mechanism for dioxygen formation in photosystem II.

  2008cited by this paper
• Exchange interactions in a Fe5 complex: A theoretical study using density functional theory

  2008cited by this paper
• First-principles calculations of magnetic circular dichroism spectra.

  2008cited by this paper
• Bioinorganic chemistry modeled with the TPSSh density functional.

  2008cited by this paper
• Prediction of iron K-edge absorption spectra using time-dependent density functional theory.

  2008influential reference
• Time-dependent density functional calculations of ligand K-edge X-ray absorption spectra

  2008influential reference
• Advanced aspects of ab initio theoretical optical spectroscopy of transition metal complexes: Multiplets, spin-orbit coupling and resonance Raman intensities

  2007cited by this paper
• Analytic derivatives for perturbatively corrected "double hybrid" density functionals: theory, implementation, and applications.

  2007cited by this paper
• A TDDFT study on the excitation of P700

  2007influential reference
• Calculation of the zero-field splitting tensor on the basis of hybrid density functional and Hartree-Fock theory.

  2007cited by this paper
• Description of the ground-state covalencies of the bis(dithiolato) transition-metal complexes from X-ray absorption spectroscopy and time-dependent density-functional calculations.

  2007cited by this paper
• Polarized X-ray absorption spectroscopy of single-crystal Mn(V) complexes relevant to the oxygen-evolving complex of photosystem II.

  2007cited by this paper
• Performance of modern density functional theory for the prediction of hyperfine structure: meta-GGA and double hybrid functionals

  2007cited by this paper
• Geometries of Second-Row Transition-Metal Complexes from Density-Functional Theory.

  2007cited by this paper
• The performance of hybrid DFT for mechanisms involving transition metal complexes in enzymes

  2006cited by this paper
• O-O bond formation in the S(4) state of the oxygen-evolving complex in photosystem II.

  2006cited by this paper
• Semiempirical GGA‐type density functional constructed with a long‐range dispersion correction

  2006influential reference
• DFT calculations of 57Fe Mössbauer isomer shifts and quadrupole splittings for iron complexes in polar dielectric media: Applications to methane monooxygenase and ribonucleotide reductase

  2006influential reference
• Calculation of excitation energies of open-shell molecules with spatially degenerate ground states. II. Transformed reference via intermediate configuration Kohn-Sham time dependent density functional theory oscillator strengths and magnetic circular dichroism C terms.

  2006cited by this paper
• Where Water Is Oxidized to Dioxygen: Structure of the Photosynthetic Mn4Ca Cluster

  2006cited by this paper
• Importance of direct spin-spin coupling and spin-flip excitations for the zero-field splittings of transition metal complexes: a case study.

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• Semiempirical hybrid density functional with perturbative second-order correlation.

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• First-principles calculations of zero-field splitting parameters.

  2006influential reference
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• QM/MM Methods for Biological Systems

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• Spectroscopic and computational studies on [Ni(tmc)CH3]OTf: implications for Ni-methyl bonding in the A cluster of acetyl-CoA synthase.

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• Spectroscopic and computational studies of the ATP:corrinoid adenosyltransferase (CobA) from Salmonella enterica: insights into the mechanism of adenosylcobalamin biosynthesis.

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• Spectroscopic and computational studies of Ni superoxide dismutase: electronic structure contributions to enzymatic function.

  2005cited by this paper
• Calculation of excitation energies of open-shell molecules with spatially degenerate ground states. I. Transformed reference via an intermediate configuration Kohn-Sham density-functional theory and applications to d1 and d2 systems with octahedral and tetrahedral symmetries.

  2005cited by this paper
• Probing the geometric and electronic structures of the low-temperature azide adduct and the product-inhibited form of oxidized manganese superoxide dismutase.

  2005cited by this paper
• Performance of nonrelativistic and quasi-relativistic hybrid DFT for the prediction of electric and magnetic hyperfine parameters in 57Fe Mössbauer spectra.

  2005cited by this paper
• Toward identification of the compound I reactive intermediate in cytochrome P450 chemistry: a QM/MM study of its EPR and Mössbauer parameters.

  2005cited by this paper
• Dimanganese catalase—spectroscopic parameters from broken-symmetry density functional theory of the superoxidized MnIII/MnIV state

  2005influential reference
• Ab initio calculation of the C/D ratio of magnetic circular dichroism.

  2005cited by this paper
• Theoretical investigations of structure and mechanism of the oxygen-evolving complex in PSII

  2004influential reference
• Quantum chemical studies of intermediates and reaction pathways in selected enzymes and catalytic synthetic systems.

  2004cited by this paper
• Calculation of the A term of magnetic circular dichroism based on time dependent-density functional theory I. Formulation and implementation.

  2004cited by this paper
• Calculating the electron paramagnetic resonance parameters of exchange coupled transition metal complexes using broken symmetry density functional theory: application to a MnIII/MnIV model compound.

  2004cited by this paper
• Definition of corresponding orbitals and the diradical character in broken symmetry DFT calculations on spin coupled systems

  2004cited by this paper
• DFT calculations of isomer shifts and quadrupole splitting parameters in synthetic iron-oxo complexes: applications to methane monooxygenase and ribonucleotide reductase.

  2003cited by this paper
• Quantum chemical calculations of spectroscopic properties of metalloproteins and model compounds: EPR and Mössbauer properties.

  2003cited by this paper
• Mechanisms of metalloenzymes studied by quantum chemical methods

  2003cited by this paper
• Fundamental vibrational frequencies of small polyatomic molecules from density-functional calculations and vibrational perturbation theory

  2003cited by this paper
• Comparative assessment of a new nonempirical density functional: Molecules and hydrogen-bonded complexes

  2003influential reference
• (57)Fe Mössbauer isomer shifts of heme protein model systems: electronic structure calculations.

  2002cited by this paper
• 57Fe Mössbauer isomer shifts of heme protein model systems: Electronic structure calculations

  2002cited by this paper
• Prediction and interpretation of the 57Fe isomer shift in Mössbauer spectra by density functional theory

  2002influential reference
• Recent Advances in Density Functional Methods Part III

  2002cited by this paper
• A Chemist's Guide to Density Functional Theory, by Wolfram Koch and Max C. Holthausen [Review of: Wolfram Koch and Max C. Holthausen. A Chemist's Guide to Density Functional Theory]

  2001cited by this paper
• Molecular and electronic structure of [Mn(V)N(cyclam-acetato)]PF6. A combined experimental and DFT study.

  2001cited by this paper
• Prediction of electron paramagnetic resonance g values using coupled perturbed Hartree–Fock and Kohn–Sham theory

  2001cited by this paper
• Molecular and Electronic Structure of [MnVN(cyclam−acetato)]PF6. A Combined Experimental and DFT Study

  2001cited by this paper
• Theoretical Study of Ligand Superhyperfine Structure. Application to Cu(II) Complexes

  2001cited by this paper
• Mechanisms of EPR Hyperfine Coupling in Transition Metal Complexes

  2000cited by this paper
• Crossed-beam study of Co+(3F4)+propane: experiment and density functional theory

  2000cited by this paper
• Structure and dynamics of biomolecules studied by Mössbauer spectroscopy

  2000cited by this paper
• A Chemist's Guide to Density Functional Theory

  2000cited by this paper
• A Critical Validation of Density Functional and Coupled-Cluster Approaches for the Calculation of EPR Hyperfine Coupling Constants in Transition Metal Complexes

  1999cited by this paper
• Approximation of the exchange-correlation Kohn-Sham potential with a statistical average of different orbital model potentials.

  1999cited by this paper
• Inorganic electronic structure and spectroscopy

  1999cited by this paper
• Solid-State NMR, Crystallographic and Density Functional Theory Investigation of Fe−CO and Fe−CO Analogue Metalloporphyrins and Metalloproteins†

  1999cited by this paper
• An efficient implementation of time-dependent density-functional theory for the calculation of excitation energies of large molecules

  1998cited by this paper
• Molecular excitation energies to high-lying bound states from time-dependent density-functional response theory: Characterization and correction of the time-dependent local density approximation ionization threshold

  1998cited by this paper
• A Multiplet Analysis of Fe K-Edge 1s → 3d Pre-Edge Features of Iron Complexes

  1997cited by this paper
• Improving harmonic vibrational frequencies calculations in density functional theory

  1997cited by this paper
• Auxiliary basis sets for main row atoms and transition metals and their use to approximate Coulomb potentials

  1997cited by this paper
• Generalized Gradient Approximation Made Simple.

  1996influential reference
• Treatment of electronic excitations within the adiabatic approximation of time dependent density functional theory

  1996cited by this paper
• Spin Densities and Spin Coupling in Iron-Sulfur Clusters: A New Analysis of Hyperfine Coupling Constants

  1995cited by this paper
• Integral approximations for LCAO-SCF calculations

  1993cited by this paper
• A New Mixing of Hartree-Fock and Local Density-Functional Theories

  1993cited by this paper
• A local density functional study of the structure and vibrational frequencies of molecular transition-metal compounds

  1992cited by this paper
• Kohn—Sham bond lengths and frequencies calculated with accurate quadrature and large basis sets

  1992cited by this paper
• Density-functional theory of atoms and molecules

  1989cited by this paper
• Density-functional exchange-energy approximation with correct asymptotic behavior.

  1988influential reference
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• Applied Quantum Chemistry

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• Applied Quantum Chemistry

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  1981cited by this paper
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  1978cited by this paper
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