2020 Dynamics of Anthracene Excimer Formation within a Water-soluble Nanocavity at Room Temperature. Das, Aritra; Danao, Ashwini; Banerjee, Shubhojit; Mohan Raj, Anthony Raj; Sharma, Gaurav; Prabhakar, Rajeev; Srinivasan, Varadharajan; Ramamurthy, Vaidhyanathan; Sen, Pratik. Journal of the American Chemical Society, 2020, In press. DOI: 10.1021/jacs.0c12169 Degradation of a Main Plastic Pollutant Polyethylene Terephthalate (PET) by Two Distinct Proteases (Neprilysin and Cutinase-Like Enzyme). Qiaoyu Hu, Vindi Jayasinghe-Arachchige, Rajeev Prabhakar. Submitted to Journal of Chemical Information and Modeling, 2020, In press. Encapsulation Effects on Intermolecular Association and Intramolecuar Dynamics of Nitrosobenzenes in Aqueous Solution. Varadharajan, Ramkumar; Ariel Kelley, S.; Jayasinghe-Arachchige, Vindi; Prabhakar, Rajeev; Blackstock, Silas; Ramamurthy, Vaidhyanathan. Journal of the American Chemical Society Communication, 2020, Under Review. Degradation of a Main Plastic Pollutant Polyethylene Terephthalate (PET) by Two Distinct Proteases (Neprilysin and Cutinase-Like Enzyme). Qiaoyu Hu, Vindi Jayasinghe-Arachchige, Rajeev Prabhakar. Submitted to Journal of Chemical Information and Modeling, 2020. Under second review. Clavanin A is a Potent Antibacterial Agent against Multi-Drug Resistant Gram-Negative Pathogens – Insight into its Zn2+-Dependent Activity. Juliano S, Sharma G, Serafim L, Duay S, Chavez M, Comert F, Radulescu A, Cotton M, Mihailescu M, Eric R. May, Greenwood A, Prabhakar R, and Angeles-Boza A. ACS Infectious Diseases, 2020, 6, 5, 1250–1263, DOI: https://doi.org/10.1021/acsinfecdis.0c00051. (Link) Mechanisms of peptide and phosphoester hydrolysis catalyzed by two promiscuous metalloenzymes (insulin degrading enzyme and glycerophosphodiesterase) and their synthetic analogues. Qiaoyu Hu, Vindi M. Jayasinghe-Arachchige, Gaurav Sharma, Leonardo F. Serafim, Thomas J. Paul and Rajeev Prabhakar, WIREs Computational Molecular Science, 2020; e1466, DOI:10.1002/wcms.1466. (Link) Developing Artificial Enzymes using Computers. Advanced Science News. Rajeev Prabhakar. (Link) Heteromeric 3-Stranded Coiled Coils Designed Using a Pb(II)(Cys)3 Template Mediated Strategy. Audrey E Tolbert, Catherine S Ervin, Leela Ruckthong, Thomas J Paul, Vindi M. Jayasinghe-Arachchige, Kosh P. Neupane, Jeanne A Stuckey, Rajeev Prabhakar, and Vincent L Pecoraro. Nature Chemistry. 2020, 0243-6. DOI:10.1038/s41557-020-0423-6. (Link) Highlighted in NEWS at TheU. (Link) Effect of Chemically Distinct Substrates on the Mechanism and Reactivity of a Highly Promiscuous Metallohydrolase. Gaurav Sharma, Vindi M. Jayasinghe-Arachchige, Qiaoyu Hu, Gerhard Schenk and Rajeev Prabhakar. ACS Catalysis, 2020, 10, 3684-3696 DOI: doi.org/10.1021/acscatal.9b04847. (Link) Deconvoluting Amyloid Aggregation using Photoluminescence Lifetime. Bo J, Vindi M. Jayasinghe-Arachchige, Serafim L, Wyss K, Andrea A, Prabhakar R, and Marti A. Angewandte Chemie International Edition, 2020, submitted. 2019 Advances in the Development of Artificial Metalloenzymes (E-book), Ed. Tatjana N. Parac-Vogt , Andrea Erxleben , Gerhard Schenk and Rajeev Prabhakar, Frontiers in Chemistry, 2019, DOI:10.3389/fchem.2019.00599. (Link) Room Temperature Phosphorescence from Encapsulated Pyrene Induced by Xenon. Mohan Raj, A; Sharma, Gaurav; Prabhakar, Rajeev; Ramamurthy, Vaidhyanathan. The Journal of Physical Chemistry A. 2019, 123, 42, 9123-9131. DOI:https://doi.org/10.1021/acs.jpca.9b08354, (link) Space constrained stereoselective geometric isomerization of 1,2-diphenylcyclopropane and stilbenes in an aqueous medium. Raj, A. Mohan; Sharma, Gaurav; Prabhakar, Rajeev; Ramamurthy, Vaidhyanathan. Organic Letters, 2019, 21, 13, 5243-5247. DOI:10.1021/acs.orglett.9b01176. (Link) Ultrafast Solvation Dynamics Reveal the Octa Acid Capsule’s Interior Dryness Depends on the Guest. Das, Aritra; Sharma, Gaurav; Kamatham, Nareshbabu; Prabhakar, Rajeev; Sen, Pratik; Ramamurthy, Vaidhyanathan, The Journal of Physical Chemistry A. 2019, 123, 28, 5928-5936. DOI:10.1021/acs.jpca.9b04626. (Link) Ultrafast Trans → Cis Photoisomerization Dynamics of Alkyl-Substituted Stilbenes in a Supramolecular Capsule. Otolski, Christopher; Raj, A. Mohan; Sharma, Gaurav; Prabhakar, Rajeev; Ramamurthy, Vaidhyanathan; Elles, Christopher. The Journal of Physical Chemistry A. 2019, 123, 24, 5061-5071. DOI:10.1021/acs.jpca.9b03285. (Link) Molecular Dynamics Investigation into the Effect of Zinc(II) on the Structure and Membrane Interactions of the Antimicrobial Peptide Clavanin A. Searle Duay, Gaurav Sharma, Rajeev Prabhakar, Alfredo Angeles-Boza, and Eric May. The Journal of Physical Chemistry B. 2019, 123, 3163-3176. DOI: 10.1021/acs.jpcb.8b11496. (Link) Effects of the Metal Ion on the Mechanism of Phosphodiester Hydrolysis Catalyzed by Metal-Cyclen Complexes. Qiaoyu Hu, Vindi M. Jayasinghe-Arachchige, Joshua Zuchniarz and Rajeev Prabhakar. Frontiers in Chemistry. 2019, 7: 195. DOI: 10.3389/fch-em.2019.00195. (Link). Investigating Coordination Flexibility of Glycerophosphodiesterase (GpdQ) Through Interactions with Mono-, Di-, and Triphosphoester (NPP, BNPP, GPE, and Paraoxon) Substrates. Gaurav Sharma, Qiaoyu Hu, Vindi M. Jayasinghe-Arachchige, Thomas Paul, Gerhard Schenk and Rajeev Prabhakar. Physical Chemistry Chemical Physics. 2019, 21, 5499-5509. DOI: 10.1039/C8CP07031H. (Link) 2018 Investigating Polyoxometalate- Hydrolysis of Chemically Distinct Sites of Human Serum Albumin (HAS) by Polyoxometalate (POM): A Hybrid QM/MM (ONIOM) Study. Vindi M. Jayasinghe- Formation of Catalytically Active Binuclear Center of Glycerophosphodiesterase (GpdQ): A Molecular Dynamics Study. Thomas J. Paul, Gerhard Schenk, Rajeev Prabhakar. The Journal of Physical Chemistry B. 2018, 122 (22), 5797–5808, DOI: 10.1021/acs.jpcb.8b02046 (Link) 2017 Photochemical Identification of Molecular Binding Sites on the Surface of Amyloid- Structural and Mechanistic Insights into Development of Chemical Tools to Control Individual and Inter- Effects of Ligand Environment in Zr(IV) Assisted Peptide Hydrolysis. Zhang, Tingting; Sharma, Gaurav ; Paul, Thomas; Hoffmann, Zachary; Prabhakar, Rajeev. Journal of Chemical Information and Modeling. 2017, 57.5, 1079- CD11b Activation Suppresses TLR- 2016 Cooperative Self- Design of Heparin Based Molecules for Inhibition of Alzheimer Amyloid Beta (Aβ40) Aggregation. Thomas J. Paul, Harvey Kelly, Joshua Zuchniarz, Tahir Ahmed and Rajeev Prabhakar. Canadian Journal of Chemistry. 2016, DOI: 10.1139/cjc- Structural and Mechanical Properties of Amyloid Beta Fibrils: A Combined Experimental and Theoretical Approach. Thomas J. Paul, Zachary Hoffmann, Congzhou Wang, Maruda Shanmugasundaram, Jason DeJoannis, Alexander Shekhtman, Igor K. Lednev, Vamsi K. Yadavalli, and Rajeev Prabhakar. Journal of Physical Chemistry Letters. 2016, 7, 2758–2764. (Link) Mechanisms of Peptide Hydrolysis by Aspartyl and Metalloproteases. Paul T J, Bora R, Ozbil M, Zhang T, Barman, A, Sharma, G, Hoffmann, Z and Prabhakar R. Phys Chem Chem Phys (PCCP), 2016. DOI: 10.1039/C6CP02097F (Link) Structural and Material Properties of Amyloid Fibrils. Dong M, Paul T, Hoffmann Z, Chan K, Hu D, Ai H, and Prabhakar R. ChemPhysChem, 2016, 17, 1- 2015 A Compact Molecule for Redirecting Amyloid- An Extended Polyanion Activation Surface in Insulin Degrading Enzyme. Eun Suk Song, Mehmet Ozbil, Tingting Zhang, Michael Sheetz, David Lee, Danny Tran, Sheng Li, Rajeev Prabhakar, Louis B. Hersh and David W. Rodgers. PLOS ONE, 2015, 10(7): e0133114. (Link) Hybrid peptide ATCUN- Theoretical Insights into the Functioning of Metallopeptidases and Their Synthetic Analogues. Tingting Zhang, Mehmet Ozbil, Arghya Barman, Thomas J. Paul, Ram Prasad Bora, and Rajeev Prabhakar. Accounts of Chemical Research, 2015, 48(2), 192- 2014 Role of hydrogen bonds in molecular packing of photoreactive crystals: templating photodimerization of protonated stilbazoles in crystalline state with a combination of water molecules and chloride ions. Barnali Mondal, Tingting Zhang, Rajeev Prabhakar, Burjor Captain and V. Ramamurthy. Photochemical & Photobiological Sciences, 2014, 13, 1509- Computational Insights into Substrate and Site Specificities, Catalytic Mechanism and Protonation States of the Catalytic Asp Dyad of ß- Peptide Hydrolysis by Metal- Mechanistic Insights into Metal (Pd2+, Co2+ and Zn2+) - 2013 Pb(II)- Unraveling the Photoluminescence Response of Light- Elucidating the Catalytic Mechanism of β- Experimental and Computational Evidence of Metal- Hydrocarbons Depending on the Chain Length and Head Group Adopt Different Conformations Within a Water-
Perspective: Computational Insights into Dynamics of Protein Aggregation and Enzyme-
Disulfide Bridges Remain Intact While Native Insulin converts Into Amyliod Fibrils. Dmitry Kuriuski, Jacqueline Washington, Mehmet Ozbil, Rajeev Prabhakar, Alexander Shektman, and Igor K. Lednev. PLoS ONE, 2012, 7(6), e36989. (Link)
2011
Mechanism of Peptide Hydrolysis by Co-
Loss of Cleavage at β’-
Computational Modeling of Substrate Specificity and Catalysis of the ß-
Cotinine Reduces Amyloid-
Oxygen Binding to [Pd(L)(L’)] (L = NHC, L’ = NHC or PR3, NHC = N-
Restricted rotation due to lack of free space within a capsule translates into product selectivity : Photochemistry of cyclohexyl phenyl ketones within a water-
2010
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 PrabhakarJournal of Physical Chemistry B, 2010,114,10860–10875. (Link)
A closed nano-
Elucidation of interactions of Alzheimer Amyloid b-
Elucidation of Insulin Degrading Enzyme Catalyzed Site Specific Hydrolytic Cleavage of Amyloid β-
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-
2009
Translational, rotational and internal dynamics of amyloid beta-
Computational Insights into Aspartyl Protease Activity of Presenilin 1 (PS1) Generating Alzheimer Amyloid β-
Computational Insights in the Development of Novel Therapeutic Strategies for Alzheimer’s Disease (AD). Rajeev Prabhakar Future Medicinal Chemistry, 2009, 1(1),119-
Insights into the Mechanism of Methionine Oxidation Catalyzed by Metal (Cu2+, Zn2+ and Fe3+) -
Modeling the self-
Crystallographic, Spectroscopic, and Computational Analysis of a Flavin-
Coordination-
2008
Comparative Molecular Dynamics Studies of Wild-
A Molecular Dynamics Study to Investigate the Effect of Chemical Substitutions of Methionine35 on the Secondary Structure of the Amyloid Beta (Aβ(1-
Insights into the Mechanism of H2O2-
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-
2007
Parameter Calibration of Transition metal element for the Spin Polarized Self-
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-
Insights into the Mechanism of Selective Olefin Epoxidation Catalyzed by [gama-
s Protein Surrounding the Active-
A DFT Study of the Mechanism of Ni Superoxide Dismutase (NiSOD): Role of the Active Site Cysteine-
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-
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-
A Comparative Study of Various Computational Approaches in Calculating the Structure of Pyridoxal
5’–Phosphate (PLP) Dependent beta-
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 J. Phys.Chem.B, 2004,108(34), 12643-
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 J. Am. Chem. Soc., 2004, 107(16); 3944 -
Spin transition during H 2O 2 formation in the Oxidative Half-
2003
A Theoretical study of the dioxygen activation by Glucose Oxidase (GO) and Copper Amine Oxidases (CAO). Rajeev Prabhakar, Per E.M. Siegbahn, Boris F. Minaev BIOCHIMICA ET BIOPHYSICA ACTA (BBA) 2003, 1647, 173-
A Comparison of the Mechanism for the Reductive Half-
A Theoretical study of the Mechanism for the Oxidative Half-
2002
Activation of Triplet Dioxygen by Glucose Oxidase: Spin-
2001
A theoretical study of the Mechanisms of the Reductive Half-
Theoretical study of the mechanism for the catalytic cycle of pea seedling amine oxidase (PSAO). Rajeev Prabhakar and Per E.M. Siegbahn J. Inorg. Biochemistry, 2001, 86(1), 382.
2000
A Density functional theory study of a concerted mechanism for proton exchange between amino acid side chains and water. Rajeev Prabhakar, Margareta R. A. Blomberg, Per E. M. Siegbahn Theor. Chem. Acc., 104, 461-