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UM Chemistry/CROMIUM

Computational Research on Materials Institute at the University of Memphis (CROMIUM) was established in 1998 to promote computational research at the University of Memphis. CROMIUM currently includes faculty members in chemistry, physics, and engineering. CROMIUM faculty teach courses that provide a graduate concentration in computational chemistry for both the M.S. and Ph.D. degrees and in computational physics for the M.S. degree.

Research

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Focus: Develop and apply advanced computational methods to investigate materials from diverse sources, including biopolymers, synthetic polymers, and crystalline and non-crystalline nanomaterials and mesomaterials

Computational Methods: quantum mechanics, molecular mechanics, coupled quantum-mechanics/molecular-mechanics, molecular dynamics, Monte Carlo, and meso-scale modeling

Research Areas: computational structural biology, rational drug design, protein modeling, heterogenous catalyst materials, enzyme active-site biocatalysis, photochromic materials, polymer materials, soft-condensed matters, high dielectric materials, non-linear optics, and diffusion and transport phenomena

Faculty

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  • Abby Parrill, Professor of Chemistry
    Computational bioorganic chemistry; protein modeling and rational ligand design
  • Henry Kurtz, Professor of Chemistry and Dean, College of Arts and Sciences
    High-k Dielectric materials, atom transport, NLO materials, defects in semiconductor materials
  • Yongmei Wang, Professor of Chemistry
    Computational studies of polymer materials, protein structure and dynamics, protein/protein interactions
  • Charles Edwin Webster, Associate Professor of Chemistry and Director of CROMIUM
    Inorganic materials and heterogeneous catalysts, computational bioinorganic chemistry
  • Mohamed Laradji, Associate Professor of Physics
    Computational studies of polymers, lipid membranes, and nanocomposites
  • Donald Bashford, Adjunct Professor of Chemistry and Associate Member, Department of Structural Biology, St. Jude Children's Research Hospital
  • Don Franceschetti, University Professor of Physics and Chemistry
  • John Hochstein, Professor and Chair, Department of Mechanical Engineering
    Computational fluid dynamics applied to surface tension and flow dynamics with free surfaces
  • Nathan DeYonker, Research Scientist, Webster Group
    Computational inorganic chemistry
  • Alexandra Kikonyogo, Postdoctoral Associate, Parrill Group

Students

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  • James Barr, Ph.D. student, Webster group
  • Brittany Burton, Ph.D. student, Wang group
  • Elise Chaffin, Ph.D. student, Wang group
  • Clayton Davis, M.S. student, Laradji group
  • Jeffery Haugen, Ph.D. student, Wang group
  • Katie Leigh, Ph.D. student, Webster group
  • Roger Letterman, Ph.D. student, Webster group
  • Jacob McMillan, Ph.D. student, Parrill group
  • Louis Montedonico, Ph.D. student, Parrill group
  • Lauren Ragle, Ph.D. student, Parrill group
  • Timothy Robbins, Ph.D. student, Wang group

Resources

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The CROMIUM User’s Guide is available for on-campus users.

Please see here for a FAQ on computer related issues.

Courses

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  • CHEM 4415/6415, Computational Chemistry
  • CHEM 7111/8111, Systematic Inorganic Chemistry
  • CHEM 7411/8411, Electronic Structure and Symmetry
  • CHEM 7711/8711, Approximate Chemical Modeling Methods
  • CHEM 7712/8712, Computational Chemistry Programming
  • CHEM 7713/8713, Advanced Solid State Physics and Chemistry
  • PHYS 7200/8200, Quantum Mechanics I
  • PHYS 7201/8201, Quantum Mechanics II
  • PHYS 7385, Methods of Computational Physics
  • PHYS 7520/8520, Statistical Mechanics

Awards and Grants

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  • Parrill and Webster, 2012, National Science Foundation REU Grant
  • Wu, Lanston, and Webster, 2012, Visualization Cluster--Technology Access for Education and Research
  • Wang, Zhao, Fujiwara, Laradji, and Mishra, 2011, National Science Foundation Grant--Tennessee Solar Conversion and Storage Using Outreach, Research, and Education
  • Webster, 2010, National Science Foundation Career Grant
  • Wang, 2009, ORAU/ORNL High Performance Computing Grant Program
  • Parrill, 2009, NIH ARRA Supplements
  • Parrill, 2009, The University of Memphis, Faculty Research Grant
  • Burkey and Webster, 2009, National Science Foundation Grant
  • Parrill and Webster, 2009, National Science Foundation REU Grant
  • Webster, 2008, Conoco Phillips Contract
  • Parrill, 2008, Elsa Pardee Foundation Grant
  • Wang, 2007, National Science Foundation Grant
  • Webster, 2007, Advanced Technology Materials, Inc. Contract
  • Webster, 2007, The University of Memphis, Faculty Research Grant
  • Fells and Parrill, 2007, American Heart Association Predoctoral Fellowship
  • Parrill, 2007, National Science Foundation MRI Grant
  • Parrill, 2007, National Institutes of Health Diversity Supplement
  • Parrill, 2007, The University of Memphis, Atkins Professorship
  • Wang, 2007, American Chemical Society Petroleum Research Fund Grant
  • Wang, 2006, The University of Memphis, Donovan Travel Award
  • Parrill, 2006-2011, National Institutes of Health Grant
  • Parrill (co-investigator), 2006, National Science Foundation MRI grant
  • Parrill, 2006-2008, University of Tennessee Health Science Center Subcontract (National Institutes of Health Grant)
  • Wang, 2006, National Institutes of Health Grant
  • Wang, 2005, The University of Memphis, Faculty Research Grant
  • Marino, 2004, U.S. Department of Energy Grant
  • Ermler, 2003, U.S. Department of Energy Grant
  • Marino, 2003, U.S. Department of Energy Grant
  • Ermler, 2003, National Science Foundation Intergovernmental Personnel Assignment
  • Ermler, 2002, U.S. Department of Energy Grant
  • Kurtz, 2002, Air Force Research Laboratory Grant
  • Ermler, 2002, National Science Foundation Intergovernmental Personnel Assignment
  • Cundari, 2002, U.S. Department of Energy Grant
  • Cundari, 2002, National Science Foundation Grant
  • Parrill, 2001, The University of Memphis, Sigma Xi Chapter Research Paper Award
  • Cundari, 2001, National Science Foundation Grant
  • Ermler, 2001, National Science Foundation Intergovernmental Personnel Assignment
  • Cundari, 2000, National Science Foundation Grants
  • Cundari, 2000, U.S. Department of Energy Grant
  • Parrill, 2000-2005, University of Tennessee Health Science Center Subcontract (National Institutes of Health Grant)
  • Parrill, 2000-2003, American Heart Association Grant
  • Parrill, 2000, The University of Memphis, College of Arts and Sciences Early Career Research Award
  • Parrill, 1999-2002, National Institutes of Health Grant

Recent Publications

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2006 publications:
  • Hu, X.; Wang, Y. Molecular dynamic simulations of N-terminal receiver domain of NtrC reveal intrinsic conformational flexibility in the inactive state, J. Biomolec. Struct. & Dynamic. (in press).
  • Tsukahara, T.; Tsukahara, R.; Yasuda, S.; Makarova, N.; Valentine, W.J.; Allison, P.; Yuan, H.; Baker, D.L.; Li, Z.; Bittman, R.; Parrill, A.; Tigyi, G. Different Residues Mediate Recognition of 1-O-oleyl-lysophosphatidic Acid and Rosiglitazone in the Ligand Binding Domain of PPARg1, J. Biol. Chem. (2006) 281(6), 3398-3407.
  • Durgam, G.; Tsukahara, R.; Makarova, N.; Fujiwara, Y.; Pigg, K.R.; Baker, D.L.; Sardar, V.M.; Parrill, A.L.; Tigyi, G.; Miller, D.D. Synthesis and Pharmacological Evaluation of Second-Generation Phosphatidic Acid Derivatives as Lysophosphatidic Acid Receptor Ligands, Bioorg. Med. Chem. Letters, (2006) 16(3), 633-640.
  • Laradji, M.; Sunil Kumar, P. B. Anomalously Slow Domain Growth in Fluid Membranes with Asymmetric Transbilayer Lipid Distribution, Phys. Rev. E (in press)
  • Sunil Kumar, P. B.; Laradji, M. Phase separation in two-component fluid vesicles, Proc. Mathematical Biology: Recent Trends, Eds. P. Chandra and B.V.R. Kum, pp. 44-55 (2006)
2005 publications:
  • Labello, N. P.; Ferreira, A. M.; Kurtz, H. A. An Augmented Effective Core Potential Basis Set for the Calculation of Molecular Polarizabilities, J. Comp. Chem. (2005) 26, 1464-1471.
  • Laradji, M.; Sunil Kumar, P. B. Domain growth, budding, and fission in phase-separating self-assembled fluid membranes, J. Chem. Phys. (2005) 123, 224902
  • Hore, M. J. A.; Laradji, M. Effects of nanoscale rods on the kinetics of phase-separating multi-component fluids, Mater. Res. Soc. Symp. Proc. (2005) 856E, BB7.7, 1-6
  • Fujiwara, Y.; Sardar, V.; Tokumura, A.; Baker, D.; Murakami-Murofushi, K.; Parrill, A.; Tigyi, G. Identification of Residues Responsible for Ligand Recognition and Regioisomeric Selectivity of LPA Receptors Expressed in Mammalian Cells, J. Biol. Chem. (2005) 280(41), 35038-35050.
  • Parrill, A.L. Structural Characteristics of Lysophosphatidic Acid Biological Targets, Biochem. Soc. Trans. (2005) 33(pt 6), 1366-1369.
  • Jo, E.; Sanna, M. G.; Gonzalez-Cabrera, P. J.; Thangada, S.; Tigyi, G.; Osborne, D. A.; Hla, T.; Parrill, A. L.; Rosen, H. S1P1-selective in vivo-active agonists from high throughput screening: Off-the-shelf chemical probes of receptor interactions, signaling and fate. Chemistry & Biology (2005) 12, 703-715.
  • Inagaki, Y.; Pham, T.C.T.; Fujiwara, Y.; Kohno, T.; Osborne, D.A.; Igarashi, Y.; Tigyi, G.; Parrill, A.L. Sphingosine-1-Phosphate Analog Recognition and Selectivity at S1P4 within the Endothelial Differentiation Gene Family of Receptors. Biochem. J. (2005) 12, 703-715.
  • Yuan, H.; Parrill, A. L. "Cluster Analysis and Three-dimensional QSAR Studies of HIV-1 Integrase Inhibitors", J. Mol. Graphics Model. (2005) 23, 317-328.
  • Jiang, W.; Khan, S.; Wang, Y. Retention behaviors of block copolymers in liquid chromatography at the critical condition." Macromolecules (2005), 38, 7514-7520.
  • Ziebarth, J.; Orelli, S.; Wang, Y.; The adsorption and partitioning of self-avoiding walk chains into pores from a bulk theta solution. Polymer (2005), 46, 10450-10456.
  • Wang, Y.; Jernigan, R. L.; Comparison of tRNA motions in the free and ribosomal bound structures. Biophysics (2005), 89, 3399-3409.
  • Hu, X.; Wang, Y.; Molecular dynamic simulations of N-terminal receiver domain of NtrC reveal intrinsic conformational flexibility in the inactive state. J. Biomolec. Struct. & Dynamic. (in press).
  • Jo, E.; Sanna, M.G.; Gonzalez-Cabrera, P.J.; Thangada, S.; Tigyi, G.; Osborne, D.A.; Hla, T.; Parrill, A.L.; Rosen, H. S1P1-selective in vivo-active agonists from high throughput screening: Off-the-shelf chemical probes of receptor interactions, signaling and fate, Chemistry & Biology (2005), in press.
  • Inagaki, Y.; Pham, T.C.T.; Fujiwara, Y.; Kohno, T.; Osborne, D.A.; Igarashi, Y.; Tigyi, G.; Parrill, A.L. Sphingosine-1-Phosphate Analog Recognition and Selectivity at S1P4 within the Endothelial Differentiation Gene Family of Receptors, Biochem. J. (2005), in press.
  • Yuan, H.; Parrill, A. Cluster Analysis and three-dimensional QSAR studies of HIV-1 integrase inhibitors, Journal of Molecular Graphics and Modelling (2005), 23, 317-328.
2004 publications:
  • Kumar, N.; Tomar, A.; Parrill, A.L.; Khurana, S. Functional dissection and molecular characterization of calcium-sensitive actin-capping and actin-depolymerizing sites in villin, J. Biol. Chem. (2004), 279(43), 45036-45046.
  • Holdsworth, G.; Osborne, D.A.; Pham, T.C.T.; Fells, J. I.; Hutchinson, G.; Milligan, G.; Parrill, A.L., A single amino acid determines preference between phospholipids and reveals length restriction for activation of the S1P4 receptor, BMC Biochemistry (2004), 5:12.
  • Parrill, Abby L.; Sardar, Vineet M.; Yuan, Hongbin. Sphingosine 1-phosphate and lysophosphatidic acid receptors: agonist and antagonist binding and progress toward development of receptor-specific ligands. Seminars in Cell & Developmental Biology (2004), 15(5), 467-476.
  • Teraoka, Iwao; Wang, Yongmei. Computer simulation studies on overlapping polymer chains confined in narrow channels. Polymer (2004), 45(11), 3835-3843.
  • Wang, Yongmei. Confinement free energy and chain conformations of homopolymers confined between two repulsive walls. Journal of Chemical Physics (2004), 121(8), 3898-3904.
  • Jiang, Wenhua; Wang, Yongmei. Thermodynamics and partitioning of homopolymers into a slit-A grand canonical Monte Carlo simulation study. Journal of Chemical Physics (2004), 121(8), 3905-3913.
  • Wang, Yongmei; Rader, A. J.; Bahar, Ivet; Jernigan, Robert L. Global Ribosome Motions Revealed with Elastic Network Model. Journal of Structural Biology (2004), 147(3), 302-314.
  • Wang, Yongmei; Howard, Derek; Gong, Yingchuan. Partitioning of Polymers into Pores with Surface Interactions at Dilute Solution Limit. Polymer (2004), 45, 313-320.
  • Wilburn, Jeremy P.; Ciobanu, Madalina; Buss, N.I.; Franceschetti, Donald R.; Lowy, Daniel A. Miniaturized Reference Electrodes with Stainless Steel Internal Reference Elements. Analytica Chimica Acta (2004), 511(1), 83-89.
  • Ferreira, Antonio M.; Moore, Bob M.; Krishnamurthy, Mathangi. Theoretical Analysis of the NMR and Electronic Structure of Novel D8–THC Derivatives. Theochem (2004), 674(1-3), 131-138.
  • Laradji, Mohamed; Hore, M.J.A. Nanospheres in Phase-Separating Multicomponent Fluids: A Three-Dimensional Dissipative Particle Dynamics Simulation. Journal of Chemical Physics (2004), 121, 10641-10647.
  • Laradji, Mohamed. A Monte Carlo Study of Fluctuating Polymer-Grafted Membranes, Journal of Chemical Physics (2004), 121(3), 1591-1600.
  • Laradji, Mohamed; Kumar, P. B. Sunil. Dynamics of Domain Growth in Self-Assembled Fluid Vesicles. Physical Review Letters (2004) , 93(19), 198105/1-198105/4.
  • Laradji, Mohamed. A Langevin Dynamics Study of Mobile Filler Particles in Phase-Separating Binary Systems. Journal of Chemical Physics (2004), 120(19), 9330-9334.
2003 publications:
  • Parrill, A. L.. HIV-1 Integrase Inhibition: Binding sites, Structure Activity Relationships and Future Perspectives. Current Medicinal Chemistry (2003), 10(18), 1811-1824.
  • Virag, Tamas; Elrod, Don B.; Liliom, Karoly; Sardar, Vineet M.; Parrill, Abby L.; Yokoyama, Kazuaki; Durgam, Gangadhar; Deng, Wenlin; Miller, Duane D.; Tigyi, Gabor. Fatty Alcohol Phosphates are Subtype-selective Agonists and Antagonists of Lysophosphatidic Acid Receptors. Molecular Pharmacology (2003), 63(5), 1032-1042.
  • Tigyi, Gabor; Parrill, Abby L. Molecular Mechanisms of Lysophosphatidic Acid Action. Progress in Lipid Research (2003), 42(6), 498-526.
  • Nadipuram, Asha K.; Krishnamurthy, Mathangi; Ferreira, Antonio M.; Li, Wei; Moore, Bob M. Synthesis and Testing of Novel Classical Cannabinoids: Exploring the Side Chain Ligand Binding Pocket of the CB1 and CB2 Receptors. Bioorganic & Medicinal Chemistry (2003), 11(14), 3121-3132.
  • Krishnamurthy, Mathangi; Ferreira, Antonio M.; Moore, Bob M. Synthesis and Testing of Novel Phenyl Substituted Side-chain Analogues of Classical Cannabinoids. Bioorganic & Medicinal Chemistry Letters (2003), 13(20), 3487-3490.
  • Laradji, Mohamed; MacNevin, Grant. Phase Separation Dynamics in Binary Fluids Containing Quenched or Mobile Filler Particles. Journal of Chemical Physics (2003), 119(4), 2275-2283.

Department of Chemistry, The University of Memphis | 213 Smith Chemistry Bldg, Memphis, Tennessee 38152-3550
phone 901.678.2621 | fax 901.678.3447