Publications



Accordion Group

Open All Tabs
  • Publications, 2025 - 2020

    2025

    In silico, in vitro, and ex vivo studies of antioxidant properties of manganese(II) complexes: influence of coumarin-based ligands. Samuel Rocha; Bruna Barriquel Segat; Lucas Menezes; Rodrigo Cervo; Roberta Cargnelutti; Sreerag N. Moorkkannur; Rajeev Prabhakar; Adolfo Horn Jr.; Christiane Fernandes. Inorganic Chemistry, 2025, Submitted

    Consequences of heterogeneity of organic molecules in water: Enhanced photodimerization of olefins. Vaitheesh Jeyapalan; Brijesh Mishra; Sreerag N. Moorkkannur; Rajeev Prabhakar; Narayanasami Sathyamurthy; Vaidhyanathan Ramamurthy. Langmuir, 2025, Submitted

    Experimental and Computational Insights into Denitrosylation of S-Nitrosoglutathione Catalyzed by a Water Soluble Copper(II) Complex. Bruna Barriquel Segat; Adolfo Horn Jr; Bruno Szpoganicz; Lino Meurer; Roberta Cargnelutti; Rodrigo Cervo; Sreerag N. Moorkkannur; Rajeev Prabhakar; Lucas Cézar Pinheiro and Christiane Fernandes. JACS, 2025, Under second review.

    Development of a Quadruple-Conjugated Carbon Dot Nanomodel for Targeted Glioma Therapy. Emel Kirbas Cilingir, Sajini D. Hettiarachchi, Parth Rathee, Yiqun Zhou, Braulio CLB Ferreira, Lukun Wang, Annu Joji, Carlos M. Gonzalez, Maria J. Moreno Hollweg, Mehrdad Shiri, Kun Wang, Rajeev Prabhakar, Steven Vanni, Roger M. Leblanc, Regina M. Graham, Communications Chemistry, 2025, Under second review.

    Hydrolytic Degradation of Key Plastic Pollutants by a Discrete Metal-Oxo Cluster: A Combined Experimental and Theoretical Study. Leonardo F. Serafim; Francisco de Azambuja; Parth Rathee; Lukun Wang; Tatjana N. Parac-Vogt and Rajeev Prabhakar. The Journal of Physical Chemistry B, 2025,129, 21, 5268–5283.  https://doi.org/10.1021/acs.jpcb.5c01255

    Book Chapter: Insights into the Development of Artificial Metalloenzymes. Sreerag N. Moorkkannur, Parth Rathee, Jiawen Yang, Lukun Wang and Rajeev Prabhakar. Topics in Organometallic Chemistry.2025   https://doi.org/10.1007/3418_2025_123

    2024 

    Enantioselective Regiospecific Addition of Propargyltrichlorosilane to Aldehydes Catalyzed by Biisoquinoline N, N’-Dioxide. Noble Brako, Sreerag Moorkkannur Narayanan, Amber Burns, Layla Auter, Valentino Cesiliano, Rajeev Prabhakar and Norito Takenaka. Beilstein Journal of Organic Chemistry, 2024, 20, 3069–3076. https://doi.org/10.3762/bjoc.20.255

    Experimental and theoretical investigation of cyclohexane halogenation catalysed by mono- and trinuclear Cu(II) complexes in the presence of trichloroisocyanuric acid as oxidant. Monica M. de Souza, Christiane Fernandes, Sreerag N. Moorkkannur, Rajeev Prabhakar, Guillot Régis, Frédéric Avenier and Adolfo Horn. Journal of Molecular Structure 2025, 1321:139958. DOI: https://doi.org/10.1016/j.molstruc.2024.139958

    A multipurpose metallophore and its copper complexes with diverse catalytic antioxidant properties to deal with metal and oxidative stress disorders:  A combined experimental, theoretical and in vitro study. Lucas Menezes, Raquel Sampaio,  Lino Meurer, Bruno Szpoganicz, Rodrigo Cervo, Roberta Cargnelutti, Lukun Wang, Jiawen Yang, Rajeev Prabhakar, Christiane Fernandes and Adolfo Horn. Inorganic Chemistry, 2024, 63, 32, 14827–14850. DOI: https://doi.org/10.1021/acs.inorgchem.4c00232

    Tuneable redox-responsive albumin-hitchhiking drug delivery to tumour for cancer treatment. Shiwei Fu, Ajay Zheng, Lukun Wang, Jiuyan Chen, Bowen Zhao, Xiao Zhang, Victoria A. A. McKenzie, Zixin Yang, Roger M. Leblanc, Rajeev Prabhakar and Fuwu Zhang. Journal of Materials Chemistry B, 2024, 12, 6563-6569. DOI: https://doi.org/10.1039/D4TB00751D

    Modeling of orange carbon dots-CO2 interaction and its effects on photosynthesis and productivity in maize and green beans. Milenković, Ivana; Zhou, Yiqun; Borišev, Milan; Serafim, Leonardo;  Chen, Jiuyan; ElMetwally, Ahmed; Spasić, Sladjana; Algarra, Manuel; Martinez de Yuso, M.V.; Prabhakar, Rajeev; Leblanc, Roger; Radotic, Ksenija. Journal of Environmental Informatics, 2024, 43(2), DOI: https://doi.org/10.3808/jei.202400511.

    Structural studies of catalytic peptides using molecular dynamics simulations. Parth Rathee, Sreerag N. Moorkkannur, and Rajeev Prabhakar. Methods in Enzymology, 2024, 697, 151-180. DOI: https://doi.org/10.1016/bs.mie.2024.01.019.

    2023 

    Application of Molecular Dynamic Simulations in Modeling the Excited State Behavior of Confined Molecules.; Dipendra Khadka; Vindi M Jayasinghe-Arachchige; Rajeev Prabhakar and Vaidhyanathan Ramamurthy. Photochemical & Photobiological Sciences, 2023, 22:2781–2798. DOI: https://doi.org/10.1007/s43630-023-00486-2  

    Discovery of SARS-CoV-2 inhibitors featuring novel histidine α-nitrile motif. Nilu V. Gone, Ghalib Mohammed, Jessy Thomas, Parth Rathee, Rajeev Prabhakar, Kiran K. Bokara, Gangadhar J. Sanjayan. Chemistry and Biodiversity, 2023, 20, e202300957. DOI: https://doi.org/10.1002/cbdv.202300957

    Feature article: Distinct Chemical Factors in Hydrolytic Reactions Catalyzed by Metalloenzymes and Metal Complexes. Serafim, Leonardo; Jayasinghe-Arachchige Vindi; Wang, Lukun; Rathee, Parth; Yang, Jiawen; Sreerag N. Moorkkannur; and Prabhakar, Rajeev. Chem Commun, 2023, 59, 8911-8928. DOI: https://doi.org/10.1039/D3CC01380D.

    Elucidating the Roles of Distinct Chemical Factors in the Hydrolytic Activities of Hetero- and Homonuclear Synthetic Analogues of Binuclear Metalloenzymes. Jayasinghe-Arachchige, Vindi; Serafim, Leonardo; Hu, Qiaoyu; Ozen, Cihan; Sreerag N. Moorkkannur; Schenk, Gerhard; Prabhakar, Rajeev. ACS Catalysis, 2023, 13, 3131–3147. DOI: https://pubs.acs.org/doi/10.1021/acscatal.2c05758

    In vitro anti-Leishmania activity of new isomeric cobalt(II)complexes and in silico insights: mitochondria impairment and apoptosis-like cell death of the parasite. Samuel M. Rocha , Adolfo Horn Jr, Aline R. de M. L. Terra, Lara M. Rezende, Felipe F. Moreira, Renato A. DaMatta, Fernando R. Xavier, Rodrigo Cervo, Roberta Cargnelutti, Sreerag N. Moorkkannur, Graysen Owenby, Rajeev Prabhakar, Sérgio H. Seabra, Christiane Fernandes. Journal of Inorganic Biochemistry, 2023, 240, 112088. DOI:https://doi.org/10.1016/j.jinorgbio.2022.112088

    Deconvoluting Amyloid Aggregation Using Photoluminescence Lifetime: a hidden binding site revealed. Bo Jiang, Utana Umezaki, Andrea Augustine, Vindi M. Jayasinghe‐Arachchige, Leonardo F. Serafim, Kevin M. Wyss, Rajeev Prabhakar, Angel A. Martí. Chemical Science, 2023, 14, 1072-1081. DOI: https://doi.org/10.1039/D2SC05418C (Also contributed cover art for the issue).

    2022   

    Promiscuous Catalytic Activity of a Binuclear Metallohydrolase: Peptide and Phosphoester Hydrolyses. Leonardo F. Serafim, Vindi M. Jayasinghe-Arachchige, Lukun Wang, and Rajeev Prabhakar. Journal of Chemical Information and Modeling, 2022, 62, 10, 2466–2480. DOI: https://doi.org/10.1021/acs.jcim.2c00214 

    Organic Host Encapsulation Effects on Nitrosobenzene Monomer-Dimer Distribution and C-NO Bond Rotation in Aqueous Solution. Varadharajan, Ramkumar ; Kelley, Sarah; Jayasinghe-Arachchige, Vindi ; Prabhakar, Rajeev; Ramamurthy, Vaidhyanathan; Blackstock, Silas. ACS Org. Inorg. Au 2022, 2, 2, 175–185. DOI: https://doi.org/10.1021/acsorginorgau.1c00043

    Structure-Activity Relationship of Carbon Nitride Dots in Inhibiting Tau Aggregation. Yiqun Zhou, Nabin Kandel, Mattia Bartoli, Leonardo Farias Serafim, Ahmed E. El Metwally, Sophia M. Falkenberg, Xavier E. Paredes, Christopher J. Nelson, Nathan Smith, Elisa Padovano, Wei Zhang, Keenan J. Mintz, Braulio C.L.B. Ferreira, Emel Kirbas Cilingir, Jiuyan Chen, Sujit K. Shah, Rajeev Prabhakar, Alberto Tagliaferro, Chunyu Wang and Roger Leblanc. Carbon, 2022, 193, 1-16. DOI: https://doi.org/10.1016/j.carbon.2022.03.021 

    Peptide hydrogel with self-healing and redox-responsive properties. Areetha D’Souza, Liam R. Marshall, Jennifer Yoon, Alona Kulesha, Siddarth Chandrasekaran, Dona I.U. Edirisinghe, Parth Rathee, Rajeev Prabhakar and Olga Makhlynets. Nano Convergence, 2022, 9(1), 1-8. DOI: https://doi.org/10.1186/s40580-022-00309-7 

    2021 

    Interacctions of Urea-based Inhibitors with Prostate-Specific Membrane Antigen (PSMA) for Boron Neutron Capture Therapy (BNCT). Qiaoyu Hu, Kevin Padron, Daiki Hara, Junwei Shi, Alan Pollack, Rajeev Prabhakar and Wensi Tao. ACS Omega, 2021, 6, 49, 33354–33369. DOI: https://doi.org/10.1021/acsomega.1c03554 

    Remediation of Environmentally Hazardous Organophosphates by Artificial Metalloenzymes. Leonardo F. Serafim, Lukun Wang, Parth Rathee, Jiawen Yang, Hannah Sofia Frenk Knaul and Rajeev Prabhakar. Current Opinion in Green and Sustainable Chemistry, 2021, 32, 100529. DOI: https://doi.org/10.1016/j.cogsc.2021.100529

    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, 2021, 143, 2025. DOI: https://doi.org/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. Information and Modeling, 2021, 61, 2, 764. DOI: https://doi.org/10.1021/acs.jcim.0c00797 

    2020 

    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.

    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.

  • Publications, 2019 - 2010

    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-Protein Interactions at Chemically Distinct Binding Sites. Thomas J. Paul, Tatjana Parac-Vogt, David Quiñonero, Rajeev Prabhakar. The Journal of Physical Chemistry B. 2018, 122 (29), 7219–7232. DOI: 10.1021/acs.jpcb.8b02931 (Link)

    Hydrolysis of Chemically Distinct Sites of Human Serum Albumin (HAS) by Polyoxometalate (POM): A Hybrid QM/MM (ONIOM) Study. Vindi M. Jayasinghe-Arachchige, Qiaoyu Hu, Gaurav Sharma, Thomas J. Paul, Marcus Lundberg, David Quiñonero, Tatjana N. Parac-Vogt and Rajeev Prabhakar. Journal of Computational Chemistry. 2018. DOI: 10.1002/jcc.25528 (Link)

    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-β Fibillar Aggregrates. Amir Aliyan, Thomas J. Paul, Christopher Pennington, Gaurav Sharma, Rajeev Prabhakar, Angel Martí. Chem. 2017, 3, 898-912. DOI: http://dx.doi.org/10.1016/j.chempr.2017.09.011 (Link)

    Structural and Mechanistic Insights into Development of Chemical Tools to Control Individual and Inter-related Pathological Features in Alzheimer’s Disease. Hyuck Jin Lee, Kyle J. Korshavn, Younwoo Nam, Juhye Kang, Thomas J. Paul, Richard A. Kerr, Il Seung Youn, Mehmet Ozbil, Kwang S. Kim, Brandon T. Ruotolo, Rajeev Prabhakar, Ayyalusamy Ramamoorthy and Mi Hee Lim. Chemistry - A European Journal. 2017, 23, 2706-15 DOI: 10.1002/chem.201605401 (Link)

    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, 1079-1088. DOI: 10.1021/acs.jcim.6b00781 (Link)

    CD11b Activation Suppresses TLR-Dependent Inflammation and Autoimmunity in Systemic Lupus Erythematosus. Faridi M, Khan S, Zhao W, Zhang K, Kumar V, Armstrong A R, Moore E, Dorschner J M, Schnaith A M, Purmalek M, Carmona-Rivera C, Irizarry-Caro J, Zhang T, Day R, Stoub D, Hoffman V, Jehangir S, Bhargava P, Lopez A, Torroella-Kouri M, Isaac B, Altintas M A, Cimbaluk D, Zloza A, Prabhakar R, Deep S, Jolly M, Koh K H, Lee H W, Reichner J, Bradshaw E, Chen J, Moita L, Yuen P, Tsai W, Niewold T, Vazquez-Padron R, Kaplan M, and Gupta V. The Journal of clinical investigation 127.4, 2017: 1271-1283.  DOI: 10.1172/JCI88442 (Link)

    2016

    Cooperative Self-assembly of a Quaternary Complex Formed by Two Cucurbit[7]uril Hosts, Cyclobis(paraquat-p-phenylene) and a “Designer” Guest. Mohammad Hossein Tootoonchi, Gaurav Sharma, Jonathan Calles, Rajeev Prabhakar and Angel E. Kaifer. Angewandte Chemie. 2016, 55, 1-6. DOI: 10.1002/anie.201606038R1 (Link)

    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-2016-0292 (Link)

    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, 1-10. (Link)

    2015

    A Compact Molecule for Redirecting Amyloid-ß Peptides into Nontoxic, Off-pathway Aggregates. Younwoo Nam, Richard A. Kerr, Jeffrey S. Derrick, Hyuck Jin Lee, Kristy L. Peck, Mehmet Ozbil, Kyle J. Korshavn, Ayyalusamy Ramamoorthy, Rajeev Prabhakar, Jason Shearer, Brandon T. Ruotolo, Mi Hee Lim. , Journal of American Chemical Society, 2015, 137 (46), 14785–14797. (Link)

    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-sh-Buforin: Influence of the ATCUN charge and stereochemistry on antimicrobial activity. M. Daben Libardo, Thomas J. Paul, Rajeev Prabhakar, Alfredo Angeles-Boza. Biochimie, 2015, 113, 143-155.  (Link) 

    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), 192-200. (Link) 

    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, 1509-1520. (Link) 

    Computational Insights into Substrate and Site Specificities, Catalytic Mechanism and Protonation States of the Catalytic Asp Dyad of ß-Secretase (BACE1). Arghya Barman and Rajeev  Prabhakar. Scientifica, 2014, doi:10.1155/2014/598728  (Link)

    Peptide Hydrolysis by Metal-Cyclen Complexes and Their Analogues: Insights from Theoretical Studies. Tingting Zhang, Xiaoxia Zhu, Rajeev Prabhakar. Organometallics, 2014, 33(8), 1925–1935. (Link) 

    Mechanistic Insights into Metal (Pd2+, Co2+ and Zn2+) - Beta Cyclodextrin Catalyzed Peptide Hydrolysis: A QM/MM Approach. Tingting Zhang, Xiaoxia Zhu, Rajeev Prabhakar. Journal of Physical Chemistry B, 2014, 118(15), 4106–4114. (Link)

    2013

    Pb(II)-promoted Amide Cleavage: Mechanistic Comparison to a Zn(II) Analog. Eric S. Elton, Tingting Zhang, Rajeev Prabhakar, Atta M. Arif, and Lisa M. Berreau. Inorganic Chemistry, 2013, 52(19), 11480-11492.(Link) 

    Unraveling the Photoluminescence Response of Light-Switching Ruthenium(II) Complexes Bound to Amyloid-β. Nathan Cook, Mehmet Ozbil, Christina Katsampes, Rajeev Prabhakar, Angel Martí. Journal of American Chemical Society, 2013, 135(29), 10810-10816.(Link)* Highlighted in Chemical and Engineering News & Rice university News and Media & e-Veritas

    Elucidating the Catalytic Mechanism of β-secretase (BACE1): A Quantum Mechanics/Molecular Mechanics (QM/MM) Approach. Arghya Barman and Rajeev Prabhakar. Journal of Molecular Graphics and Modelling, 2013, 40, 1-9.(Link)

    Experimental and Computational Evidence of Metal-O2 Activation in a Copper Amine Oxidase. Yi Liu, Arnab Mukherjee, Nadav Nahumi, Mehmet Ozbil, Doreen Brown, Alfredo M. Angeles-Boza, David M. Dooley,  Rajeev Prabhakar, and Justine P. Roth. Journal of Physical Chemistry B, 2013, 117(1), 218-229.(Link)

    Hydrocarbons Depending on the Chain Length and Head Group Adopt Different Conformations Within a Water-soluble Nanocapsule: 1H NMR and Molecular Dynamics Studies. Rajib Choudhury, Arghya Barman, Rajeev Prabhakar and V. Ramamurthy. Journal of Physical Chemistry B, 2013, 117(1), 398-407.(Link)

    2012

    Perspective: Computational Insights into Dynamics of Protein Aggregation and Enzyme-Substrate Interactions. Mehmet Ozbil, Arghya Barman, Ram Prasad Bora and Rajeev Prabhakar. Journal of Physical Chemistry Letters, 2012, 3, 3460-3469.  (Link)

    Protonation States of the Catalytic Dyad of β-Secretase (BACE1) in the Presence of Chemically Diverse Inhibitors: A Molecular Docking Study. Arghya Barman and Rajeev Prabhakar. Journal of Chemical Information and Modeling, 2012, 52(5), 1275-1287.  (Link)


    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)

    Dimerization of the Full-Length Alzheimer Amyloid β-peptide (Aβ42) in Explicit Aqueous Solution: A Molecular Dynamics Study. Xiaoxia Zhu, Ram Prasad Bora, Arghya Barman, Rajiv Singh, and Rajeev Prabhakar. Journal of Physical Chemistry B, 2012, 116(15), 4405-4416. (Link)

    2011

    Mechanism of Peptide Hydrolysis by Co-catalytic Metal Centers Containing Leucine Aminopeptidase Enzyme: A DFT Approach. Xiaoxia Zhu, Arghya Barman, Mehmet Ozbil, Tingting Zhang, Shanghao Li, and Rajeev Prabhakar. Journal of Biological Inorganic Chemistry, 2011, 17(2), 209-222. (Link)

    Loss of Cleavage at β’-Site Contributes to the Apparent Increase of Aβ Secretion by BACE1-GPI Proccessing of APP. Kulandaivelu S. Vetrivel, Arghya Barman, Ying Chen, Phuong D. Nguyen, Steven L. Wagner, Rajeev Prabhakar, and Gopal Thinakaran. Journal of Biological Chemistry, 2011, 286, 26166-26177. (Link)

    Computational Modeling of Substrate Specificity and Catalysis of the ß-Secretase (BACE1) Enzyme. Arghya Barman, Stephan Schuerer and Rajeev Prabhakar. Biochemistry, 2011, 50, 4337-4349.  (Link)

    Cotinine Reduces Amyloid-β Aggregation and Improves Alzheimer’s Disease Mice. Valentina Echeverria, Ross Zeitlin, Sarah Burgess, Sagar Patel, Arghya Barman, Garima Thakur, Hideyo Inouye, Magorzota Mamcarz, Li Wang, Steven D. Buckingham, Daniel A Kirschner, Takashi Mori, Roger M. Leblanc, Rajeev Prabhakar, David Sattelle, and Gary W. Arendash. Journal of Alzheimer’s Disease, 2011, 24, 817-835 [chosen for a press release]. (Link)

    Oxygen Binding to [Pd(L)(L’)] (L = NHC, L’ = NHC or PR3, NHC = N-Heterocyclic Carbene ). Synthesis and Structure of a Paramagnetic trans-[Pd(NHC)2(1-O2)2] Complex Cai, Xiaochen; Majumdar, Subhojit; Fortman, George; Cazin, Catherine; Slawin, Alexandra; Lhermitte, Charles; Prabhakar, Rajeev; Germain, Meaghan; Palluccio, Taryn; Nolan, Steven; Rybak-Akimova, Elena; Temprado, Manuel; Captain, Burjor; Hoff, Carl Journal of American Chemical Society, 2011, 133(5), 1290-1293. (Link)

    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 Chemical Communications, 2011, 47, 2841-2843. (Link)

    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-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. Ram Prasad Bora, Mehmet Ozbil, Rajeev 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.

  • Publications, 2009 - 2000

    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

    Comparative Molecular Dynamics Studies of Wild-Type and oxidized forms of Full-Length Alzheimer Amyloid β-Peptides Aβ(1-40) and Aβ(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 (Aβ(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)W10O 32H 4] 4-. A Computational Study Rajeev Prabhakar, K. Morokuma, Craig L. Hill and D. G. Musaev Inorganic Chemistry 2006, 45:5703-5709.

    s 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 J. Phys. Chem.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 J. Comp. Chem., 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 Comp.Chem., 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 J. Phys.Chem.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 J. Am. Chem. Soc., 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 J. Phys. Chem.B, 2004, 108, 13882-13892.

    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, 173-178.

    A Comparison of the Mechanism for the Reductive Half-Reaction Between Pea Seedling and Other Copper Amine Oxidases (CAO's). Rajeev Prabhakar and Per E.M. Siegbahn J. Comp. Chem., 2003, 24, 1599-1609.

    A Theoretical study of the Mechanism for the Oxidative Half-Reaction of Copper Amine Oxidases (CAO). Rajeev Prabhakar and Per E.M. Siegbahn J. Phys. Chem.B, 2003, 107, 3944-3953.

    2002

    Activation of Triplet Dioxygen by Glucose Oxidase: Spin-Orbit Coupling in the Superoxide Ion. Rajeev Prabhakar, Per E.M. Siegbahn, Boris F. Minaev and Hans Ågren J. Phys. Chem. B, 2002, 106(14), 3742-3750.

    2001

    A theoretical study of the Mechanisms of the Reductive Half-Reaction of Pea seedling amine Oxidase (PSAO). Rajeev Prabhakar and Per E.M. Siegbahn J. Phys. Chem. B, 2001, 105(19), 4400-4408.

    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, 461-470.

Top