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Selected Publications


List of Publications

Classical racemization of tetrahedral tetracoordinate centers via a planar transition state or an intermediate structure

S Raghunathan, K Yadav, VC Rojisha, T Jaganade, V Prathyusha, S Bikkina, U Lourderaj, UD Priyakumar

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Computational modeling of the catalytic mechanism of hydroxymethylbilane synthase

N Bung, A Roy, UD Priyakumar, G Bulusu

Phys. Chem. Chem. Phys., 2019, in press.

Recent advancements in computing reliable binding free energies in drug discovery projects

NA Murugan, V Poongavanam, UD Priyakumar

in Structure Bioinformatics: Applications in Preclinical Drug Discovery Process (Ed. C. Mohan), Springer, 2019, pp221-246

A probabilistic framework for constructing temporal relations in replica exchange molecular trajectories

A Chattopadhyay, M Zheng, MP Waller, UD Priyakumar

J. Chem. Theory Comput., 2018, 14, 3365-3380

Model molecules to classify CH⋯O hydrogen-bonds

AM Vibhute, UD Priyakumar, A Ravi, KM Sureshan

Chem. Commun., 2018, 54, 4629-4632

pH-mediated gating and formate transport mechanism in the Escherichia coli formate channel

S Padhi, LK Reddy, UD Priyakumar

Molecular Simulation, 2017, 43, 1300-1306

Role of Urea–Aromatic Stacking Interactions in Stabilizing the Aromatic Residues of the Protein in Urea-Induced Denatured State Names

S Goyal, A Chattopadhyay, K Kasavajhala, UD Priyakumar

Journal of the American Chemical Society, 2017, 139 (42), 14931-14946

Temperature Dependence of the Stability of Ion Pair Interactions, and its Implications on the Thermostability of Proteins from Thermophiles Names

S Bikkina, AP Bhati, S Padhi, UD Priyakumar

Journal of Chemical Sciences, 2017, 129 (3), 405-414

Microsecond simulation of human aquaporin 2 reveals structural determinants of water permeability and selectivity

Padhi, S.; Priyakumar, U. D.

Biochimica et Biophysica Acta (BBA)-Biomembranes, 2017, 1859 (1), 10-16

Ligand-induced stabilization of a duplex-like architecture Is crucial for the switching mechanism of the SAM-III riboswitch

Suresh, G.; Srinivasan, H.; Nanda, S.; Priyakumar, U. D.

Biochemistry 2016, 55, 3349-3360

Urea mimics nucleobases by preserving the helical integrity of B-DNA duplexes via hydrogen bonding and stacking interactions

Suresh, G.; Padhi, S.; Patil, I.; Priyakumar, U. D.

Biochemistry 2016, 55, 5653–5664

Structure, interaction, and dynamics of Au/Pd bimetallic nanoalloys dispersed in aqueous ethylpyrrolidone, a monomeric moiety of polyvinylpyrrolidone

Gupta, A.; Boekfa, H.; Sakurai, H.; Ehara, M.; Priyakumar, U. D.

J. Phys. Chem. C 2016, 120, 17454–17464

Nucleobases tagged to gold nanocluster cause a mechanistic crossover in the oxidation of CO

Rai, S.; Ehara, M.; Priyakumar, U. D.

Phys. Chem. Chem. Phys. 2015, 17, 24275-24281

Sumoylation of Sir2 differentially regulates transcriptional silencing in yeast

Hannan, A.; Abraham, N. M.; Goyal, S.; Jamir, I.; Priyakumar, U. D.; Mishra, K.

Nucleic Acids Res. 2015.

Molecular dynamics study of the structure, flexibility and hydrophilicity of PETIM dendrimers: A comparison with PAMAM dendrimers

Kanchi, S.; Suresh, G.; Priyakumar U. D.; Ayappa, K.; Maiti, P.

J. Phys. Chem. B 2015, 119.

Modeling the structure of SARS 3a transmembrane protein using a minimum unfavorable contact approach

Ramakrishna, S.; Padhi, S.; Priyakumar, U. D.

J. Chem. Sci. 2015, 127.

Prediction of the structures of helical membrane proteins based on a minimum unfavorable contacts approach

Padhi, S.; Ramakrishna, S.; Priyakumar, U. D.

J. Comp. Chem. 2015, 36, 539-552.

Dynamics based pharmacophore models for screening potential inhibitors of Mycobacterial cyclopropane synthase

Choudhury, C.; Priyakumar, U. D.; Sastry, G. N.

J. Chem. Inf. Model. 2015.

Dispersion interactions between urea and nucleobases contribute to the destabilization of RNA by urea in aqueous solution

Kasavajhala, K.; Bikkina, S.; Patil, I.; MacKerell, A. D.; Priyakumar, U. D.

J. Phys. Chem. B 2015, 119, 3755-3761.

Small molecule inhibitors of ERK-mediated immediate early gene expression and proliferation of melanoma cells expressing mutated BRaf

Samadani, R.; Zhang, J.; Brophy, A.; Oashi, T.; Priyakumar U. D.; Priyakumar, U. D.; Raman, E. P.; St.John, F. J.; Jung.; K.-Y.; Fletcher, S.; Pozharki, E.; MacKerell, A. D.; Shapiro, P.

Biochem. J. 2015, 467, 425-438.

Double zipper helical assembly of deoxyoligonucleotides: Mutual templating and chiral imprinting to form hybrid DNA ensembles

Narayanaswamy, N.; Suresh, G.; Priyakumar, U. D.; Govindaraju,T.

Chem. Commun. 2015, 51, 5493-5496.

Atomistic detailed mechanism and weak cation-conducting activity of HIV-1 vpu revealed by free energy calculations

Padhi, S.; Burri, R. R.; Jameel, S.; Priyakumar, U. D.

PLoS ONE 2014, DOI: 10.1371/journal.pone.0112983.

Molecular dynamics simulations reveal the HIV-1 vpu transmembrane protein to form stable pentamers

Padhi, S.; Khan, N.; Jameel, S.; Priyakumar, U. D.

PLoS ONE 2013, DOI: 10.1371/journal.pone.0079779. 

Solvent induced helical assembly and reversible chiroptical switching of cyclic dipeptide chiral auxiliary functionalized naphthalenediimides

Manchineella, S; Prathyusha, V.; Priyakumar, U. D.; Govindaraju,T.

Chem. Eur. J. 2013, 19, 16615-16624.

Synthesis and reactivity studies of dicationic dihydrogen complexes bearing sulfur-donor ligands: A combined experimental and computational study

Gandhi, T.; Rajkumar, S.; Prathyusha, V.; Priyakumar, U. D.

Eur.J. Inorg. Chem. 2013, 2013, 1434-1443.

Crenarchaeal chromatin proteins Cren7 and Sul7 compact DNA by inducing rigid bends

Driessen, R.P.C.; Meng, H.; Suresh, G.; Shahapure, R.; Lanzani, G.; Priyakumar, U.D.; White, M.F.; Schiessel, H.; Noort, J.v.; Dame, R.Th.

Nucleic Acids Res. 2013, 41, 196-205.

Inter versus intramolecular cyclization of tripeptides containing tetrahydrofuran amino acids: Density functional theory study on the kinetic control

Kumar, N. V. S.; Priyakumar, U. D.; Singh, H.; Roy, S.; Chakraborty, T. K.

J. Mol. Modell. 2012, 18, 3181-3197.

Impact of 2’-hydroxyl sampling on the conformational properties of RNA: Update of the CHARMM all-atom additive force field for RNA

Denning, E. J.; Priyakumar, U. D.; Nilsson, L.; MacKerell, Jr. A. D.

J. Comp. Chem. 2011, 32, 1929-1943.

Characterization of ERK docking domain inhibitors that induce apoptosis by targeting Rsk-1 and Caspase-9

Boston, S. R.; Deshmukh, R.; Strome, S.; Priyakumar, U. D.; MacKerell, Jr. A. D.; Shapiro, P.

BMC Cancer 2011, 11, 7.

Structural and energetic determinants of thermal stability and hierarchical unfolding pathways of hyperthermophilic proteins, Sac7d and Sso7d

Priyakumar, U. D.; Ramakrishna, S.; Nagarjuna, K. R.; Reddy, S. K.

J. Phys. Chem. B 2010, 114, 1707-1718.

Urea destabilizes RNA by forming stacking interactions and multiple hydrogen bonds with nucleic acid bases

Priyakumar, U. D.; Hyeon, C.; Thirumalai, D.; MacKerell, Jr. A. D. 

J. Am. Chem. Soc. (3-page communication) 2009, 131, 17759-17761.

Molecular modeling of base flipping in DNA  and RNA modification enzymes: Structure, mechanism, function and evolution

Priyakumar, U. D.; MacKerell, Jr. A. D.

Ed. Grosjean, J. Landes Bioscience, Austin, 2009.

Atomic detail investigation of the structure and dynamics of DNA•RNA hybrids: A molecular dynamics study

Priyakumar, U. D.; MacKerell, Jr. A. D.

J. Phys. Chem. B 2008, 112, 1515-1524

NMR imino proton exchange experiments on duplex DNA primarily monitor the opening of purine bases

Priyakumar, U. D.; MacKerell, Jr. A. D.

J. Am. Chem. Soc. (communication) 2006, 128, 678-679

Computational approaches for investigating base flipping in oligonucleotides

Priyakumar, U. D.; MacKerell, Jr. A. D.

Chem. Rev. 2006, 106, 489-505

A lipophilic hexaporphyrin assembly supported on a stannoxane core

Chandrasekhar, V.; Nagendran, S.; Azhakar, R.; Kumar, M. R.; Srinivasan, A.; Ray, K.; Chandrashekar, T. K.; Madhavaiah, C.; Verma, S.; Priyakumar, U. D.; Sastry, G. N

J. Am. Chem. Soc. (communication) 2005, 127, 2410-2411.

Design of neutral hydrocarbons having a planar tetracoordinate carbon

Priyakumar, U. D.; Sastry, G. N.

Indian J. Chem. A (communication) 2004, 43, 455-457.

Facile valence isomerization among bis(silacyclopropenyl), disila(Dewar benzene) and disilabenzvalene

Priyakumar, U. D.; Punnagai, M.; Sastry, G. N.

J. Organomet. Chem. 2004, 689, 1284-1287.

A computational study of cation–π interactions in polycyclic systems: Exploring the dependence on the curvature and electronic factors

Priyakumar, U. D.; Punnagai, M.; Mohan, G. P. K.; Sastry, G. N.

Tetrahedron 2004, 60, 3037-3043.

The design of molecules containing planar tetracoordinate carbon

Priyakumar, U. D.;* Reddy, A. S.; Sastry, G. N.

Tetrahedron Lett. 2004, 45, 2495-2498.

C21H9Z (Z=−3 to +3): a theoretical study on the redox behaviour of C3 symmetric fragment of C60

Priyakumar, U. D.; Sastry, G. N.

J. Mol. Struct. (Theochem) 2004, 674, 69-75.

Basis set and method dependence of the relative energies of C2S2H2 isomers

Vijay, D.; Priyakumar, U. D.; Sastry, G. N.

Chem. Phys. Lett. 2004, 383, 192-197.

On the use of NICS criterion to evaluate aromaticity in heteroaromatics involving III and IV row main group elements

Saieswari, A.; Priyakumar, U. D.; Sastry, G. N.

J. Mol. Struct. (Theochem) 2003, 663, 145-148.

Cation-π interactions of curved polycyclic systems: M+ (M=Li and Na) ion complexation with buckybowls

Sastry, G. N.; Rao, H. S. P.; Priyakumar, U. D.; Bednarek, P.

Tetrahedron Lett. 2003, 44, 6043-6046.

The tricyclo[2.1.0.02,5]pentan-3-one system: A new probe for the study of π-facial selectivity in nucleophilic additions

Mehta, G.; Singh, S. R.; Priyakumar, U. D.; Sastry, G. N.

Tetrahedron Lett. 2003, 44, 3101-3104.

Silaaromaticity in polycyclic systems: A computational study

Dhevi, D. M.; Priyakumar, U. D.; Sastry, G. N.

J. Org. Chem. 2003, 68, 1168-1171

Measures to evaluate heteroaromaticity and their limitations: Story of skeletally substituted benzenes

Priyakumar, U. D.; Sastry, G. N.

Proc. Indian Acad. Sci. 2003, 115, 49-66. 

The effect of bulky group substitution on the skeleton, geometries, relative energies and the reactivities of silabenzene valence isomers

Dhevi, D. M.; Priyakumar, U. D.; Sastry, G. N.

J. Mol. Struct. (Theochem) 2002, 618, 173-179. 

Isomers of disilabenzene (C4Si2H6): A computational study

Priyakumar, U. D.; Saravanan, D.; Sastry, G. N.

Organometallics 2002, 21, 4823-4832

Theoretical study of silabenzene and Its valence isomers

Priyakumar, U. D.; Sastry, G. N.

Organometallics 2002, 21, 1493-1499.

A computational study of the valence isomers of benzene and their group V hetero analogs

Priyakumar, U. D.; Dinadayalane, T. C; Sastry, G. N.

New. J. Chem. 2002, 26, 347-353.

Ring closure synthetic strategies toward buckybowls: benzannulation versus cyclopentannulation

Dinadayalane, T. C.; Priyakumar, U. D.; Sastry, G. N.

J. Chem. Soc., Perkin Trans. 2 2002, 94-101.

The bicyclo[2.1.1]hexan-2-one system: a new probe for the experimental and computational study of electronic effects in π-facial selectivity in nucleophilic additions

Mehta, G.; Singh, S. R.; Gagliardini, V.; Priyakumar, U. D.; Sastry, G. N.

Tetrahedron Lett.  2001, 42, 8527-8530

An ab initio and DFT study of the valence isomers of pyridine

 Priyakumar, U. D.; Dinadayalane, T. C.; Sastry, G. N.

Chem. Phys. Lett. 2001, 337, 361-367

Theory provides a clue to accomplish the synthesis of sumanene, C21H12, the prototypical C3v-buckybowl

Priyakumar, U. D.; Sastry, G. N.

Tetrahedron Lett. 2001, 42, 1379-1381.

Structures, energetics and vibrational spectra of the valence isomers of phosphinine. An ab initio and DFT study

Priyakumar, U. D.; Dinadayalane, T. C.; Sastry, G. N. 

Chem. Phys. Lett. 2001, 336, 343-348.

Theoretical studies on the effect of sequential benzannulation to corannulene.

 Dinadayalane, T. C.; Priyakumar, U. D.; Sastry, G. N.

 J. Mol. Struct. (Theochem) 2001, 543, 1-10.

The role of heteroatom substitution in the rigidity and curvature of buckybowls. A theoretical study

Sastry, G. N.; Priyakumar, U. D. 

J. Chem. Soc., Perkin Trans. 2 2001, 30-40