Recent Publications of the Noodleman Group

  1. Mössbauer Properties of the Diferric Cluster and the Differential Iron(II)-Binding Affinity of the Iron Sites in Protein R2 of Class Ia Escherichia coli Ribonucleotide Reductase: A DFT/Electrostatic Study
    Dalton Transactions, 2011, in press.

  2. Calibration of DFT Functionals for the Prediction of 57Fe Mössbauer Spectral Parameters in Iron–Nitrosyl and Iron–Sulfur Complexes: Accurate Geometries Prove Essential
    Journal of Chemical Theory and Computation, 2011, in press.

  3. Modeling the MoFe Nitrogenase System with Broken Symmetry Density Functional Theory
    Nitrogen Fixation: Methods and Protocols (Methods in Molecular Biology). Edited by M. W. Ribbe, Humana Press (Springer Science + Business Media, LLC), New York, NY, USA. Vol. 766, Chapter 19, pp.293-312, 2011.

  4. Geometric and Electrostatic Study of the [4Fe-4S] Cluster of Adenosine-5´-Phosphosulfate Reductase from Broken Symmetry Density Functional Calculations and Extended X-ray Absorption Fine Structure Spectroscopy
    Inorganic Chemistry, Vol. 50, 6610-6625, 2011.

  5. DFT Calculations for Intermediate and Active States of the Diiron Center with a Tryptophan or Tyrosine Radical in Escherichia coli Ribonucleotide Reductase
    Inorganicl Chemistry, Vol. 50, 2302-2320, 2011.

  6. Density Functional Theory Analysis of Structure, Energetics, and Spectroscopy for the Mn-Fe Active Site of Chlamydia trachomatis Ribonucleotide Reductase in Four Oxidation States
    Inorganicl Chemistry, Vol. 49, 7266-7281, 2010.

  7. Quantum Cluster Size and Solvent Polarity Effects on the Geometries and Mössbauer Properties of the Active Site Model for Ribonucleotide Reductase Intermediate X: A Density Functional Theory Study
    Theoretical Chemistry Accounts, Vol. 125, 305-317, 2010.

  8. Spin Coupling in Roussin’s Red and Black Salts
    Chemistry - A European Journal, Vol. 16, 10397-10408, 2010.

  9. DFT Calculations of Comparative Energetics and ENDOR/Mössbauer Properties for Two Protonation States of the Iron Dimer Cluster of Ribonucleotide Reductase Intermediate X
    Dalton Transactions, 6045-6057, 2009.

  10. Density Functional Theory Calculations on Mössbauer Parameters of Nonheme Iron Nitrosyls
    Inorganic Chemistry, Vol. 48, 9155-9165, 2009.

  11. Structural Model Studies for the Peroxo Intermediate P of Methane Monooxygenase from Broken-Symmetry Density Functional Calculations
    Inorganic Chemistry, Vol. 47, 2975-2986, 2008.

  12. Structural Model Studies for the High-Valent Intermediate Q of Methane Monooxygenase from Broken-Symmetry Density Functional Calculations
    Inorganica Chimica Acta, Vol. 361, 973-986, 2008.

  13. Toward a Chemical Mechanism of Proton Pumping by the B-Type Cytochrome c Oxidases: Application of Density Functional Theory to Cytochrome ba3 of Thermus thermophilus
    Journal of the American Chemical Society, Vol. 130, 15002-15021, 2008.

  14. Ligand-Bound S = 1/ 2 FeMo-Cofactor of Nitrogenase: Hyperfine Interaction Analysis and Implication for the Central Ligand X Identity
    Inorganic Chemistry, vol. 47, 6162-6172, 2008.

  15. Testing if the Interstitial Atom, X, of the Nitrogenase Molybdenum−Iron Cofactor Is N or C: ENDOR, ESEEM, and DFT Studies of the S = 3/2 Resting State in Multiple Environments
    Inorganic Chemistry, vol. 46, 11437-11449, 2007.

  16. Experimental and DFT Studies: Novel Structural Modifications Greatly Enhance the Solvent Sensitivity of Live Cell Imaging Dyes
    Journal of Physical Chemistry A, Vol. 111, 10849-10860, 2007.

  17. Density Functional Theory Study of Fe(IV) d−d Optical Transitions in Active-Site Models of Class I Ribonucleotide Reductase Intermediate X with Vertical Self-Consistent Reaction Field Methods
    Inorganic Chemistry, Vol. 45(21), 8533-8542, 2006.

  18. Structure, Redox, pKa, Spin, A Golden Tetrad for Understanding Metalloenzyme Energetics and Reaction Pathways
    Journal of Biological Inorganic Chemistry, Vol. 11, 674-694, 2006.

  19. DFT Calculations of 57Fe Mössbauer Isomer Shifts and Quadrupole Splittings for Iron Complexes in Polar Dielectric Media: Applications to Methane Monooxygenase and Ribonucleotide Reductase
    Journal of Computational Chemistry, Vol. 27(12), 1292-1306, 2006.

  20. Seven Clues to the Origin and Structure of Class I Ribonucleotide Reductase Intermediate X
    Journal of Inorganic Biochemistry, Vol. 100, 771-779, 2006.

  21. Active Site Structure of Class I Ribonucleotide Reductase Intermediate X: A Density Functional Theory Analysis of Structure, Energetics, and Spectroscopy
    Journal of the American Chemical Society, Vol. 127(45), 15778-15790, 2005.

  22. Density Functional Vertical Self-consistent Reaction Field Theory for Solvatochromism Studies of Solvent Sensitive Dyes
    Journal of Physical Chemistry A, Vol. 108(16), 3545-3555, 2004.

  23. Quantum Chemical Studies of Intermediates and Reaction Pathways in Enzyme and Catalytic Synthetic Systems
    Chemical Reviews, Vol. 104(2), 459-508, 2004.

  24. Density Functional Study of a μ-1,1-Carboxylate Bridged Fe(III)-O-Fe(IV) Model Complex. 2. Comparison with Ribonucleotide Reductase Intermediate X
    Inorganic Chemistry, Vol.43(2), 613-621, 2004.

  25. On the Role of the Conserved Aspartate in the Hydrolysis of the Phosphocysteine Intermediate of the Low Molecular Weight Tyrosine Phosphatase
    Journal of the American Chemical Society, Vol. 126(39):12677-12684, 2004.

  26. Nornicotine Aqueous Aldol Reactions: Synthetic and Theoretical Investigations into the Origins of Catalysis
    Journal of Organic Chemistry, 69(20), 6603-6609, 2004.

  27. A Theoretical Study of the UV/Vis Absorption and Emission Solvatochromic Properties of Solvent-Sensitive Dyes
    ChemPhysChem, Vol. 4(10), 1084-1094, 2003.

  28. DFT Calculations of Isomer Shifts and Quadrupole Splitting Parameters in Synthetic Iron-Oxo Complexes: Applications to Methane Monooxygenase and Ribonucleotide Reductase
    Inorganic Chemistry, Vol. 42, 5244-5251. 2003.

  29. Temperature-Dependent Behavior of Protein-Chromophore Interactions: A Theoretical Study of A Blue Fluorescent Antibody
    ChemPhysChem, Vol. 4(8), 848-855, 2003.

  30. A Density Functional Evaluation of an Fe(III)-Fe(IV) Model Diiron Cluster: Comparisons with Ribonucleotide Reductase Intermediate X
    Inorganic Chemistry, Vol. 42(8), 2751–2758, 2003.

  31. Density Functional Methods Applied to Metalloenzymes
    Coordination Chemistry Reviews, Vol. 238-239, 211-232, 2003.

  32. Density Functional Theory Study of the Intramolecular [2 + 3] Cycloaddition of Azide to Nitriles
    Journal of Organic Chemistry, Vol. 68(23), 9076-9080, 2003.

  33. Density Functional and Reduction Potential Calculations of Fe4S4 Clusters
    Journal of the American Chemical Society, Vol. 125(7), 1923-1936, 2003.

  34. Density Functional and Reduction Potential Calculations of Fe4S4 Clusters
    Journal of Biological Inorganic Chemistry, Vol. 8, 519-526, 2003.

  35. Structural, Spectroscopic, and Redox Consequences of a Central Ligand in the FeMoco of Nitrogenase: A Density Functional Theoretical Study
    Journal of the American Chemical Society, Vol. 125, 8377-8383, 2003.

  36. Density Functional Studies of the Ground and Excited State Potential Energy Curves of Stilbene cis-trans-Isomerization
    ChemPhysChem, Vol. 3, 167-178, 2002.

  37. Metal Substitution in the Active Site of Nitrogenase MFe7S9 (M = Mo4+, V3+, Fe3+)
    Inorganic Chemistry, Vol. 41, 5744-5753, 2002.

  38. Coupled Redox Potentials in Manganese and Iron Superoxide Dismutases from Reaction Kinetics and Density Functional/Electrostatics Calculations
    Inorganic Chemistry, Vol. 41, 205-218, 2002.

  39. A Structural Model for the High-Valent Intermediate Q of Methane Monooxygenase from Broken-Symmetry Density Functional and Electrostatics Calculations
    Journal of the American Chemical Society, Vol. 124, 5890-5894, 2002.

  40. FeMo Cofactor of Nitrogenase: Energetics and Local Interactions in the Protein Environment
    Journal of Biological Inorganic Chemistry, Vol. 7, 735-749, 2002.

  41. Density Functional Calculation of pKa values and Redox Potentials in the Bovine Rieske Iron-Sulfur Protein
    Journal of Biological Inorganic Chemistry, Vol. 7, 632-639, 2002.

  42. Insights into Properties and Energetics of Iron–Sulfur Proteins from Simple Clusters to Nitrogenase
    Current Opinion in Chemical Biology, Vol. 6, 259-273, 2002.

  43. Density Functional Study of the Mechanism of a Tyrosine Phosphatase: I. Intermediate Formation
    Journal of the American Chemical Society, Vol. 124, 10225-10235, 2002.

  44. FeMo Cofactor of Nitrogenase: A Density Functional Study of States MN, MOX, MR, and MI
    Journal of the American Chemical Society, Vol. 123(49), 12392-12410, 2001.

  45. Multiple Reactive Immunization Towards the Hydrolysis of Organophosphorous Nerve Agents: Hapten Design and Synthesis
    Bioorganic and Medicinal Chemistry, Vol. 9, 3185-3195, 2001.

  46. Density Functional Studies of Oxidized and Reduced Methane Monooxygenase. Optimized Geometries and Exchange Coupling of Active Site Clusters
    Inorganic Chemistry, Vol. 40(20), 5251-5266, 2001.

  47. Energetics of Oxidized and Reduced Methane Monooxygenase Active Site Clusters in the Protein Environment
    Inorganic Chemistry, Vol. 40(20), 5267-5278, 2001.

  48. CuZn Superoxide Dismutase Geometry Optimization, Energetics, and Redox Potential Calculations by Density Functional and Electrostatic Methods
    Inorganic Chemistry, Vol. 38(5) 940-950, 1999.

  49. Density Functional and Electrostatic Calculations of Manganese Superoxide Dismutase Active Site Complexes in Protein Environments
    Inorganic Chemistry, Vol. 8(5), 929-939, 1999.

  50. Incorporating Protein Environments in Density Functional Theory: A Self-Consistent Reaction Field Calculation of Redox Potentials of [2Fe2S] Clusters in Ferredoxin and Phthalate Dioxygenase Reductase
    Journal of Physical Chemistry A, Vol. 102(31), 6311-6324, 1998.

  51. Density Functional Calculations of Electronic Structure, Charge Distribution, and Spin Coupling in Manganese-Oxo Dimer Complexes
    Inorganic Chemistry, Vol.36 (6), 1198-1217, 1997.

  52. Calculation of Redox Potentials and pKa Values of Hydrated Transition Metal Cations by a Combined Density Functional and Continuum Dielectric Theory
    Inorganic Chemistry, Vol. 35(16), 4694–4702, 1996.

  53. Density-Functional and Electrostatic Calculations for a Model of a Manganese Superoxide Dismutase Active Site in Aqueous Solution
    Journal of Physical Chemistry, Vol. 100(32), 13498-13505, 1996.