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Department of Chemistry
N. Sukumar
Department of Chemistry,
Director, Center for Informatics,
School of Natural Sciences
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Education Details
Ph.D. Chemistry, State University of New York at Stony Brook, 1984
M.Sc. Chemistry, Indian Institute of Technology, Kanpur, 1979
B.Sc.(Hons.), St.Xavier's College, Calcutta, 1976
Professional Experience
Research Associate Professor, Rensselaer Polytechnic Institute, Troy (2004-2011); Alexander von Humboldt Fellow, University of Bonn, Germany (1993-1995, 1997), Visiting faculty at the Institute of Mathematical Sciences, Chennai (2009-2010), and Panjab University, Chandigarh (1989-1991); Visiting Scientist at the Wadsworth Institute, Albany, NY (2003); CSIR pool officer at the Indian Institute of Technology, Madras (1992-1993); postdoctoral appointments at Marquette University, Milwaukee (1998), the University of New Orleans (1985-1987) and the University of Southern California, Los Angeles (1984-1985).
Research Interests:
Quantum Chemistry and Density Functional Theory
Drug Design, Cheminformatics and BioInformatics
Geometric Phase and Nonadiabatic Couplings

My research uses computational and cheminformatic methods for the discovery of molecules with specific chemical and biological properties, and the development of cheminformatics software. I am co-developer of the RECON, PROTEIN RECON, PEST and DIXEL program packages for generating accurate molecular properties and descriptors for QSAR and QSPR (Quantitative Structure-Activity/Property Relationships). These tools enable macromolecules and large chemical databases to be rapidly scanned for desirable combinations of chemical, physiological and materials properties, to enable prediction and interpretation of protein-ligand binding, protein similarity classification, as well as drugs and materials design.

Current directions include the design of polymers with specific dielectric properties, mapping the network topology of chemical spaces, and development of algorithms for de novo proteomic analysis. Broader goals include establishment of an inter-disciplinary informatics research center encompassing chemical and systems biology, bioinformatics, cheminformatics, materials informatics, statistical modeling, risk assessment and management, as well as network studies and its applications to ecology and for studies of human consciousness, music cognition and art appreciation. Other personal research interests include the quantum theory of nonadiabatic couplings, density functional theory and manifestations of the geometric phase in molecular systems.
Select Publications:
Abdur Rahim, Pinaki Saha, Kunal Kumar, N. Sukumar, Bani KantaSarma, "Reciprocal carbonyl–carbonyl interactions in small molecules and proteins", Nature Comm. (Accepted, In press, 2017). DOI: 10.1038/s41467-017-00081-x

Pinaki Saha, Amol B. Rahane, Vijay Kumar, and N. Sukumar, “Electronic Origin of the Stability of Transition Metal Doped B14 Drum Shaped Boron Clusters and Their Assembly in to a Nanotube”. J. Phys. Chem. C, 121(20), 10728–10742 (2017). DOI: 10.1021/acs.jpcc.6b10838

Ke Wu, N. Sukumar, Nicholas A. Lanzillo, Chenchen Wang, Ramamurthy (Rampi) Ramprasad, Rui Ma, Aaron F. Baldwin, Greg Sotzing, Curt Breneman, “Prediction of polymer properties using Infinite Chain Descriptors (ICD) and Machine Learning: Towards optimized dielectric polymeric materials”, J. Polymer Sci.B: Polymer Phys.54, 2082–2091(2016). DOI: 10.1002/polb.24117

Ganesh Prabhu,Sudeepto Bhattacharya,MichaelP.Krein, N. Sukumar, “Investigation of similarity and diversity threshold networks generated from diversity-oriented and focused chemical libraries”, J. Math. Chem. 54(10), 1916-1941 (2016). DOI: 10.1007/s10910-016-0657-0

Pinaki Saha, Amol B. Rahane, Vijay Kumar, N. Sukumar, Analysis of the electron density features of small boron ring clusters and the effects of doping,PhysicaScripta91, 053005 (2016). DOI: 10.1088/0031-8949/91/5/053005

N. Sukumar, M. P. Krein, G. Prabhu, S. Bhattacharya, S. Sen, Network Measures for Chemical Library Design, Drug Development Research 75: 402–411 (2014)

N. Sukumar, Ganesh Prabhu and Pinaki Saha, Applications of Genetic Algorithms in QSAR/QSPR modeling, Applications of Metaheuristics in Process Engineering, Eds: Jayaraman Valadi, Patrick Siarry (Springer, 2014) pp.315-324.

Pilania, G., Wang, C., Wu, K.; Sukumar, N., Breneman, C., Sotzing, G. A., Ramprasad, "New Group IV Chemical Motifs for Improved Dielectric Permittivity of Polyethylene" J. Chem. Inf. Model. 53(4):879-886 (2013)

N. Sukumar, Michael Krein, Qiong Luo and Curt Breneman, “MQSPR modeling in materials informatics: a way to shorten design cycles?”, J. Materials Sci. 47(21), 7703-7715 (2012). DOI: 10.1007/s10853-012-6639-0. [2011 Impact Factor = 2.015].

N. Sukumar and Michael P. Krein, “Graphs and networks in chemical and biological informatics: past, present and future”, Future Med. Chem. 4(16), 2039-2047 (2012). DOI: 10.4155/FMC.12.128. [2011 Impact Factor = 2.522].

N. Sukumar, Michael P. Krein and Mark J. Embrechts, "Predictive Cheminformatics in Drug Discovery: Statistical Modeling for Analysis of Micro-Array and Gene Expression Data" in "Biocomputing and Drug Discovery" Richard S. Larson, Ed. (Humana Press, in press, 2012).

N. Sukumar, "The atom in a molecule as a mereological construct in chemistry" Found. Chem. ISSN: 1386-4238, Nov. 2012. DOI 10.1007/s10698-012-9171-z.

N. Sukumar and Michael P. Krein, "Exploration of the Topology of Chemical Spaces with Network Measures" J. Phys. Chem. A, 115 (45), 12905-12918 (2011). DOI:10.1021/jp204022u

N. Sukumar, Sourav Das, Michael Krein, Rahul Godawat, Inna Vitol, Shekhar Garde, Kristin P. Bennett and Curt M. Breneman, "Molecular Descriptors for Biological Systems"" in "Computational Approaches in Cheminformatics and Bioinformatics" Rajarshi Guha and Andreas Bender, Eds. (Wiley, Hoboken, NJ, 2012), pp.107-144.

N. Sukumar, Ed. "A matter of density: Exploring the Electron Density Concept in the Chemical, Biological, and Materials Sciences" (Wiley, Hoboken, NJ, in press 2012).

N. Sukumar and Sourav Das, "Current Trends in Virtual High Throughput Screening Using Ligand-Based and Structure-Based Methods" in "Combinatorial Chemistry & High Throughput Screening" B. Kundu, Ed. 14, (Bentham, in press, 2011).

N. Sukumar, "The Chemist's Concept of Molecular Structure" Found. Chem. 11 (1), 7-20 (2009). DOI: 10.1007/s10698-008-9060-7

N. Sukumar, Michael Krein and Curt M. Breneman, "Bio- and Chem-Informatics: Where do the twain meet?" Curr. Opinion Drug Disc. Devel. 11(3) 311-319 (2008). PMID:18428084

N. Sukumar and Curt M. Breneman, "QTAIM in Drug Discovery and Protein Modeling" in "The Quantum Theory of Atoms in Molecules: From Solid State to DNA and Drug Design" C.F. Matta & R.J. Boyd, Eds. (Wiley-VCH, 2007), pp.471-498. DOI: 10.1002/9783527610709.ch18

Pankaj Kulshrestha, N. Sukumar, Jane S. Murray, Rossman F. Giese and Troy D. Wood, "Computational Prediction of Antibody Binding Sites on Tetracycline Antibiotics: Electrostatic Potentials and Average Local Ionization Energies on Molecular Surfaces" J. Phys. Chem. A, 113 (4), 756-766 (2009). DOI: 10.1021/jp8089165

C. Matthew Sundling, N. Sukumar, Hongmei Zhang, Mark J. Embrechts and Curt M. Breneman, "Wavelets in chemistry and cheminformatics" Rev. Comput. Chem. 22, 295-329 (2006).

Scott Oloff, Shuxing Zhang, N. Sukumar, Curt Breneman and Alexander Tropsha, "Chemometric Analysis of Ligand Receptor Complementarity: Identifying Complementary Ligands Based on Receptor Information (CoLiBRI)" J. Chem. Inf. Model. 46 (2), 844 - 851 (2006).

Minghu Song, Curt M. Breneman and N. Sukumar, "Three-Dimensional Quantitative Structure-Activity Relationship Analyses of Piperidine-based CCR5 Receptor Antagonists" Bioorg. Med. Chem. 12, 489-499 (2004).

Curt M. Breneman, C. Matthew Sundling, N. Sukumar, Lingling Shen, William P. Katt and Mark J. Embrechts, "New developments in PEST shape/property hybrid descriptors"J. Comput.-Aided Mol. Design, 17, 231-240, (2003).

Christopher E. Whitehead, Curt M. Breneman, N. Sukumar and M. D. Ryan, "Transferable Atom Equivalent Multi-Centered Multipole Expansion Method" J. Comp. Chem. 24, 512-529 (2003).

N. Tugcu, M.H. Song, C.M. Breneman, N. Sukumar, K.P. Bennett, and S.M. Cramer, "Prediction of the effect of mobile-phase salt type on protein retention and selectivity in anion exchange systems" Analyt. Chem. 75, 3563-3572 (2003).

Minghu Song, Curt M. Breneman, Jinbo Bi, N. Sukumar, Kristin P. Bennett, Steven Cramer and Nihal Tugcu, "Prediction of Protein Retention Times in Anion-exchange Chromatography Systems using Support Vector Regression" J. Chem. Inf. Comput. Sci. 42, 1347-1357 (2002).

Cecilia B. Mazza, N. Sukumar, Curt M. Breneman and Steven Cramer, "Prediction of Protein Retention in Ion-Exchange Systems Using Molecular Descriptors Obtained from Crystal Structure" Analyt. Chem. 73, 5457-5461 (2001).

Chutian Shu, N. Sukumar and C. P. Ursenbach, "Adsorption of O2 on TiO2(110): A theoretical study" J. Chem. Phys. 110, 10539-10544 (1999).

N. Sukumar and S. D. Peyerimhoff, "Nonadiabatic coupling of the 1A" and 2A" states of Ozone in the vicinity of their conical intersection and construction of Diabatic States" Mol. Phys. 95, 61-70 (1998).

P. Raveendran, N. Sukumar and T. K. K. Srinivasan, "Temperature Dependence of Phonon-Assisted Luminescence Intensity in GdTb(MoO4)3 Evidence for change in Electron-Lattice Coupling near Tc" Phys. Rev. B 55, 4978-4982 (1997).

Harjinder Singh, N. Sukumar and B. M. Deb, "Atom as a Complex System: One- and Two-Dimensional Cellular Automata Simulations" Int. J. Quantum Chem. 60, 21-28 (1996).

N. Sukumar, "Density Functional Theory of Born Couplings" Int. J. Quantum Chem. 56, 423-432 (1995).

Thomas Neuheuser, N. Sukumar and S. D. Peyerimhoff, "Nonadiabatic Coupling of the 1A' and 2A' States of Ozone" Chem. Phys. 194, 45-64 (1995).

N. Sukumar, "Cellular Automaton Simulation of Solitonic Structures in the Su-Schrieffer-Heeger Hamiltonian" in "New Challenges in Comp. Quantum Chem."

R.Broer, P.J.C.Aerts and P.S.Bagus, Eds., Univ.Groningen, pp.270-277 (1993). B. M. Deb, Ranbir Singh and N. Sukumar, "A Universal Density Criterion for Correlating the Radii and other Properties of Atoms and Ions" J. Molec. Struct. (Theochem) 259, 121-139 (1992).

N. Sukumar and B. M. Deb, "Phase Associated with the Single-Particle Density of Many-Electron Systems" Intl. J. Quantum Chem. 40, 501-510 (1991).
Latest Book:

Student’s Ph.D. Thesis:
Ganesh Prabhu, “Diversity Oriented Synthesis of a Molecular Library, Analysis of Molecular Diversity through Network/Graph Measures and Correlation with Biological Activity Profile(s), Ph.D. Dissertation,Shiv Nadar University, 2017.
Teaching (courses taught):
General Chemistry
Physical Chemistry
Quantum Chemistry
Computer Science
Molecular Structure and Spectroscopy
Molecular Reaction Dynamics
Chemical Principles
Chemical Equilibrium
Chemical Binding
Drugs and Natural Remedies
Research Methodology
Chemistry of color and Art
Informatics and Medicinal Chemistry
Informatics and Drug Discovery
Molecules of Love, Lust and Passion
Teaching Responsibilities (2012-2017):
CCC401: Drugs and Natural remedies
CCC403: Art & Science of Color
CCC501: Scientific Epistemology & Consciousness
CCC415: Molecules of Love, Lust and Passion
CHY111: Chemical Principles
CHY211: Chemical Equilibrium
CHY311: Chemical Binding
CHY332: Informatics and Medicinal Chemistry
CHY512: Advanced Molecular Spectroscopy
CHY522: Informatics and Drug Discovery
CHY600: Research Methodologies
CHY622: Computational Chemistry
National & International Recognition:
Alexander von Humboldt Fellow (1993-1995, 1997)
Associate of the Photographic Society of America, 2016
Executive Summary:
In addition to research interests in theoretical chemistry, cheminformatics and related inter-disciplinary areas, Sukumar is an award-winning fine art photographer. He has been published in photographic books and magazines, exhibited in photographic and art galleries in USA and Canada, and presented photographic programs at conferences in USA and India.

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