2010

Oxygen Binding to [Pd(L)(L0)] (L= NHC, L0 = NHC or PR3, NHC = N-Heterocyclic Carbene). Synthesis and Structure of a Paramagnetic trans-[Pd(NHC)2(η1-O2)2] Complex
Xiaochen Cai, Subhojit Majumdar, George C. Fortman, Catherine S. J. Cazin, Alexandra M. Z. Slawin, Charles Lhermitte, Rajeev Prabhakar, Meaghan E. Germain, Taryn Palluccio, Steven P. Nolan, Elena V. Rybak-Akimova, Manuel Temprado, Burjor Captain, and Carl D. Hoff The Journal of the American Chemical Society, 2010, in press.  

Restricted rotation due to lack of free space within a capsule translates into product selectivity:  Photochemistry of cyclohexyl phenyl ketones within a water-soluble organic capsule
Revathy Kulasekharan, Rajib Choudhury, Rajeev Prabhakar and V. Ramamurthy ChemComm, 2010, in press.

Which One Among Aspartyl Protease, Metallopeptidase, and Artificial Metallopeptidase is the Most Efficient Catalyst in Peptide Hydrolysis?
R Bora, A Barman, X Zhu, M Ozbil, R Prabhakar Journal of Physical Chemistry B 2010,114,10860–10875.

A closed nano-container enables thioketones to phosphoresce at room temperature in aqueous solution
Nithyanandhan Jayaraj, V.S.N. Maddipatla, Rajeev Prabhakar, Steffen Jockusch, N.J. Turo and V. Ramamurthy
Journal of Physical Chemistry B, 2010, 114, 14320–14328.

Elucidation of interactions of Alzheimer Amyloid b-peptides (Ab40 and Ab42) with Insulin Degrading Enzyme (IDE): A molecular dynamics study. Ram Prasad Bora and Rajeev Prabhakar. Biochemistry, 2010, 49 ,3947–3956.

Elucidation of Insulin Degrading Enzyme Catalyzed Site Specific Hydrolytic Cleavage of Amyloid β-Peptide: A Comparative DFT Study. R. Bora, M. Ozbil, R. Prabhakar Journal of Biological Inorganic Chemistry, 2010,15 ,485-495.

Theoretical Insights into the Mechanism of Selective Peptide Bond Hydrolysis Catalyzed by [Pd(H2O)4]2+. A. Kumar, X. Zhu, K. Walsh, R. Prabhakar Inorganic Chemistry, 2010, 49, 38-46.

2009

Translational, rotational and internal dynamics of amyloid beta-peptides (Abeta40 and Abeta42) from molecular dynamics simulations. R. Bora, R. Prabhakar J. Chem. Phys., 2009, 131, 155103-155103.
[selected for online publication in the Virtual Journal of Nanoscale Science and Technology, Nov. 2, 2009]

Computational Insights into Aspartyl Protease Activity of Presenilin 1 (PS1) Generating Alzheimer Amyloid β-Peptides (Aβ40 and Aβ42). R. Singh, A., Barman, and Rajeev Prabhakar Journal of Physical Chemistry B 2009, 113, 2990-2999.

Computational Insights in the Development of Novel Therapeutic Strategies for Alzheimer’s Disease (AD). Rajeev Prabhakar Future Medicinal Chemistry. 2009, 1(1),119-135.

Insights into the Mechanism of Methionine Oxidation Catalyzed by Metal (Cu2+, Zn2+ and Fe3+) - Amyloid Beta (Aβ) Peptide Complexes: A Computational Study. A. Barman, W. Taves, and Rajeev Prabhakar, Journal of Computational Chemistry 2009, 30(9), 1405-1413.

Modeling the self-assembly dynamics of macromolecular protein aggregates underlying neurodegenerative disorders. Z. Zhao, R. Singh, A. Barman, N. F. Johnson, and Rajeev Prabhakar Computational and Theoretical Nanoscience 2009, 6(6),1338-1351(14)

Crystallographic, Spectroscopic, and Computational Analysis of a Flavin-C4a-Oxygen Adduct in Choline Oxidase. A. M. Orville, G. T. Lountos, S. Finnegan, G. Gadda, and Rajeev Prabhakar. Biochemistry 2009, 48, 720-728

Coordination-Mode Control of Bound Nitrile Radical Complex Reactivity: Intercepting End-on Nitrile-Mo(III) Radicals at Low Temperature. M. Germain, M. Temprado, A.  Castonquay, O. Kraytova, E. Rybak-Akimova, Elena, J. Curley, A. Mendiratta, Y-C. Tsai, C. Cummins, Rajeev Prabhakar, J. McDonough and C. Hoff Journal of American Chemical Society 2009, 131 (42), 15412–15423

2008
Crystallographic, Spectroscopic, and Computational Analysis of a Flavin-C4a-Oxygen Adduct in Choline Oxidase. A. M. Orville, G.  T. Lountos, S. Finnegan, G. Gadda, and Rajeev Prabhakar Biochemistry 2008, in press.

Insights into the Mechanism of Methionine Oxidation Catalyzed by Metal (Cu2+, Zn2+ and Fe3+) - Amyloid Beta (Aß) Peptide Complexes: A Computational Study.
A. Barman, W. Taves, and Rajeev Prabhakar, Journal of Computational Chemistry 2008, Published (online).

Modeling the self-assembly dynamics of macromolecular protein aggregates underlying neurodegenerative disorders.
Z. Zhao, R. Singh, A. Barman, N. F. Johnson, and Rajeev Prabhakar Computational and Theoretical Nanoscience 2008, in press.

Comparative Molecular Dynamics Studies of Wild-Type and oxidized forms of Full-Length Alzheimer Amyloid ß-Peptides Aß(1-40) and Aß(1-42).
L. Triguero, R. Singh and Rajeev Prabhakar Journal of Physical Chemistry B 2008, 112, 7123-7131.

A Molecular Dynamics Study to Investigate the Effect of Chemical Substitutions of Methionine35 on the Secondary Structure of the Amyloid Beta (Aß(1-42)) Monomer in Aqueous Solution 
L. Triguero, R. Singh and Rajeev Prabhakar, Journal of Physical Chemistry B 2008,112, 2159-2167.

Insights into the Mechanism of H2O2-based Olefin Epoxidation Catalyzed by the Lacunary [g-(SiO4)W10O32H4]4- and di-V-substituted-g-Keggin [g-1,2 -H2SiV2W10O40]4- Polyoxometalates. A Computational Study
Rajeev Prabhakar, K. Morokuma, Y. V. Geletii, C. L. Hill, D. G. Musaev, Computational Modeling for Homogenous and Enzymatic Catalysis. Ed. D. G. Musaev and K. Morokuma, Wiley-VCH Verlag GmbH & Co. 2008, 1-24.

Computational Insights into the Structural Properties and Catalytic Functions of Selenoprotein Glutathione Peroxidase (GPx)
Rajeev Prabhakar, K. Morokuma, D. G. Musaev, Computational Modeling for Homogenous and Enzymatic Catalysis. Ed. D. G. Musaev and K. Morokuma, Wiley-VCH Verlag GmbH & Co. 2008, 215-229.

2007

Parameter Calibration of Transition metal element for the Spin Polarized Self-Consistent-Charge Density-Functional Tight-Binding (DFTB) Method: Sc, Ti, Fe, Co and Ni.
G. Zheng, H. Witek, P. Bobadova-Parvanova, S. Irle, D. G. Musaev, Rajeev Prabhakar, K. Morokuma, M. Lundberg, M. Elstner, V. Köhler, T. Frauenheim. Journal of Chemical Theory and Computation 2007, 3(4), 1349-1367.

2006

Peroxinitrite Reductase Activity of Selenoprotein Glutathione Peroxidase (GP x): A Density Functional Study
Rajeev Prabhakar, K. Morokuma, and D. G. Musaev Biochemistry 2006, 45 (22), 6967-6977.

Insights into the Mechanism of Selective Olefin Epoxidation Catalyzed by [gama-(SiO 4)W 10O 32H 4] 4-. A Computational Study Rajeev Prabhakar, K. Morokuma, Craig L. Hill and D. G. Musaev Inorganic Chemistry 2006, 45:5703-5709.

Is Protein Surrounding the Active-Site Critical for Hydrogen Peroxide Reduction by Selenoprotein Glutatione Peroxidase (GPx)? An ONIOM Study
Rajeev Prabhakar, T. Vreven, M. J. Frisch, K. Morokuma, and D. G. Musaev
Journal of  Physical Chemistry B 2006, 110, 13608-13613.
 
A DFT Study of the Mechanism of Ni Superoxide Dismutase (NiSOD): Role of the Active Site Cysteine-6 Residue in the Oxidative Half-Reaction
Rajeev Prabhakar, K. Morokuma, and D. G. Musaev Journal of Computational Chemistry 2006, 27:1438-1445.

2005
A Density Functional Theory (DFT) study of the spin forbidden dioxygen activation in Monoamine Oxidase B (MAO B)
Rajeev Prabhakar, M. Li, D. G. Musaev, K. Morokuma, and D. E. Edmondson Flavins and Flavoproteins 2005, 127-131.

Elucidation of the Mechanism of Selenoprotein Glutathione Peroxidase (GPx) Catalyzed Hydrogen Peroxide Reduction by two Glutathione Molecules: A Density Functional Study
Rajeev Prabhakar, T. Vreven, K. Morokuma, and D. G. Musaev Biochemistry 2005, 44(35) 11864-11871.

A Comparative Study of Various Computational Approaches in Calculating the Structure of Pyridoxal 5 ’– Phosphate (PLP) Dependent beta-Lyase Protein. The Importance of Protein Environment
Rajeev Prabhakar , K. Morokuma, and D. G. Musaev Journal of Computational Chemistry 2005, 26(5) 443-446.

2004
Does the Active Site of Mammalian Glutathione Peroxidase (GPx) Contain Water
Molecules? An ONIOM Study
Rajeev Prabhakar, D. G. Musaev, I. V. Khavrutskii, and K. Morokuma Journal of  Physical Chemistry B 2004, 108(34), 12643-12645.

A DFT study of the Mechanism for the biogenesis of cofactor topaquinone (TPQ) in Copper Amine Oxidases (CAOs)
Rajeev Prabhakar and Per E.M. Siegbahn Journal of American Chemical Society 2004, 107(16); 3944 -3953.

Spin transition during H 2O 2 formation in the Oxidative Half-Reaction of Copper amine Oxidases (CAOs)
Rajeev Prabhakar, Per E.M. Siegbahn, Boris F. Minaev and Hans Ågren Journal of Physical Chemistry B 2004, 108, 13882-13892.