Chemistry

Department of Chemistry, Carnegie Mellon University
Ph.D., Physical Chemistry, University of Chicago, 1989
Summary:

We measure several fundamental electronic properties of molecules such as charge transfer and electronic delocalization using a technique known as Stark spectroscopy. Stark spectroscopy involves applying large electric fields to molecules in films or matrices and analyzing the effects of the field perturbation on the absorption or emission spectrum. We have recently focused on the properties of MEH-PPV and other molecules used to make to organic light emitting diodes (OLED's). Stark spectroscopy reveals the mechanism by which a large applied electric field, such as those present in OLEDs, produces undesirable emission quenching and suggests strategies for minimizing this loss of device efficiency through modifications of the polymer structure.

Emission properties of Single Molecules and Aggregates

Recent years has seen a huge growth in the use of organic conjugated oligomers and polymers in the design of light emitting diodes (OLEDs) and photovoltaic cells. When these molecules are placed in thin films to fabricate devices, they typically form aggregates. These confer several desirable properties for device function such as protection from oxidative damage and enhanced charge transport. However, they also typically shift the wavelength of emission to lower energies and often significantly reduce its intensity. Our group is using microscopy and spectroscopy to investigate the relationships between molecular structure and the brightness and photo-stability of molecules in the solid state, both in isolation (i.e. as single molecules) and as aggregates. We are also developing methods to image aggregation in films at high resolution and to follow the nucleation of aggregates in the solution phase. 

Selected Publications: 
  • "Effects of Solvent Properties on the Spectroscopy and Dynamics of Alkoxy-Substituted PPV Oligomer Aggregates," Woong Young So, Jiyun Hong, Janice J. Kim, Gizelle A. Sherwood, Kelly Chacon-Madrid, James H. Werner, Andrew P. Shreve, and Linda A. PeteanuJ. Phys. Chem. B 116 10504 (2012)
  • "Wavelength Dependence of the Fluorescence Quenching Efficiency of Nearby Dyes by Gold Nanoclusters and Nanoparticles: The Roles of Spectral Overlap and Particle Size," Chowdhury, Sanchari; Wu, Zhikun; Jaquins-Gerstl, Andrea; Liu, Shengpeng; Dembska, Anna; Armitage, Bruce A.; Jin, Rongchao; Peteanu, Linda A.J. Phys. Chem. C 115, 20105 (2011)
  • "Visualizing Core-Shell Structure in Substituted PPV Oligomer Aggregates Using Fluorescence Lifetime Imaging Microscopy (FLIM)," Peteanu, Linda A.; Sherwood, Gizelle A.; Werner, James H.; Shreve, Andrew P.; Smith, Timothy M.; Wildeman, Jurjen, J. Phys. Chem. C 115 15607 (2011)
  • "Fluorescent DNA Nanotags Featuring Covalently Attached Intercalating Dyes: Synthesis, Antibody Conjugation, and Intracellular Imaging," Stadler, Andrea L.; Delos Santos, Junriz O.; Stensrud, Elizabeth S.; Dembska, Anna; Silva, Gloria L.; Liu, Shengpeng; Shank, Nathaniel I.; Kunttas-Tatli, E.; Sobers, Courtney J.; Gramlich, Philipp M. E.; Carell, Thomas; Peteanu, Linda A.; McCartney, Brooke M.; Armitage, Bruce A., Bioconjugate Chem. 22, 1491 (2011)
  • "pH-Responsive Fluorescent Molecular Bottlebrushes Prepared by Atom Transfer Radical Polymerization," Nese, Alper; Lebedeva, Natalia V.; Peteanu, Linda; Sheiko, Sergei, S.; Matyjaszewski, Krzysztof, Macromolecules 44 5905 (2011)
Most Cited Publications
  1. "Vibrationally coherent photochemistry in the femtosecond primary event of vision," Wang, Qing, Robert W. Schoenlein, Linda A. Peteanu, Richard A. Mathies, and Charles V. Shank, Science 266, no. 5184 (1994): 422-424.
  2. "Biodegradable nanogels prepared by atom transfer radical polymerization as potential drug delivery carriers: synthesis, biodegradation, in vitro release, and bioconjugation," Oh, Jung Kwon, Daniel J. Siegwart, Hyung-il Lee, Gizelle Sherwood, Linda Peteanu, Jeffrey O. Hollinger, Kazunori Kataoka, and Krzysztof Matyjaszewski, Journal of the American Chemical Society 129, no. 18 (2007): 5939-5945.
  3. "Light‐induced reversible formation of polymeric micelles," Lee, Hyung‐il, Wei Wu, Jung Kwon Oh, Laura Mueller, Gizelle Sherwood, Linda Peteanu, Tomasz Kowalewski, and Krzysztof Matyjaszewski, Angewandte Chemie 119, no. 14 (2007): 2505-2509.
  4. "Direct observation of fast proton transfer: femtosecond photophysics of 3-hydroxyflavone," Schwartz, Benjamin J., Linda A. Peteanu, and Charles B. Harris, The Journal of Physical Chemistry 96, no. 9 (1992): 3591-3598.
  5. "The electronic spectrum of the amino acid tryptophan in the gas phase," Rizzo, Thomas R., Young D. Park, Linda A. Peteanu, and Donald H. Levy, The Journal of Chemical Physics 84, no. 5 (1986): 2534-2541.
Recent Publications
  1. "A Mono-Cubocotahedral Series of Gold Nanoclusters: Photoluminescense Origin, Large Enhancement, Wide Tunability and Structure-Property Correlation,"  Q Li, M Zhou, WY So, J Huang, M Li, DR Kauffman, M Cotlet, T Higaki, Z Shao, LA Peteanu, and R Jin.  Journal of the American Chemical Society 141.13 (2019)
  2. "WYSo SI Mechanism of Ligand-Controlled Emission in Silicon Nanoparticles,"  ACS Nano (2018)
  3. "Mechanism of Ligand-Controlled Emmision in Silicon Nanoparticles."     So, W.Y., Li, Q., Legaspi, C.M., (...), Jin, R., Peteanu, L.A. ACS Nano 12(7). (2018).
  4. "Rigidity and Polarity Effects on the Electronic Properties of Two Deep Blue Delayed Fluorescence Emitters." Legaspi, C.M., Stubbs, R.E., Wahadoszaman, M., (...), Zheng, Q., Rothberg, L.J. Journal of Physical Chemistry C 122(22). (2018).
  5. "Eliminating Spurious Zero-Efficiency FRET States in Diffusion-Based Single-Molecule Confocal Microscopy." Dey, S.K., Pettersson, J.R., Topacio, A.Z., Das, S.R., Peteanu, L.A. Journal of  Physical Chemistry Letters 9(9). (2018).
Department of Chemistry and Biochemistry, Duquesne University
Ph.D., Computational and Theoretical Organic Chemistry, UCLA, 1990
Summary:

Our research program is driven by significant problems in organic, biochemistry, and physical chemistry. Our research in chemical theory and computation is fully integrated in strong collaboration with successful experimental chemists. We have a full range on interests, starting with the development of fundamental ideas on the theory of chemical bonding, and how this information can be used to understand the fundamentals of Lewis acidity and basicity, organic reaction catalysis, organometallic structures, and the bonding and reactions at surfaces. In the field of biochemistry, we investigate the energetics and mechanisms of phosphoryl transfer reactions, and design new antimicrobial agents to light the increasing risk of drug resistant bacterial fungal infections.

Selected Publications: 
  • "Metalated nitriles: SNi′ cyclizations with a propargylic electrophile," Ping Lu, Venkata S. Pakkala, Jeffrey D. Evanseck, Fraser F. Fleming, Tetrahedron Letters 56, 3216 (2015)
  • "Intramolecular Charge-Assisted Hydrogen Bond Strength in Pseudochair Carboxyphosphate," Sarah E. Kochanek, Traci M. Clymer, Venkata S. Pakkala, Sebastien P. Hebert, Kyle Reeping, Steven M. Firestine, and Jeffrey D. Evanseck, J. Phys. Chem. B 119, 1184 (2015)
  • "Common Hydrogen Bond Interactions in Diverse Phosphoryl Transfer Active Sites," Jean C. Summerton, Gregory M. Martin, Jeffrey D. Evanseck, Michael S. Chapman, PLOS One 9, e108310 (2014)
  • "Hyperconjugation-Mediated Solvent Effects in Phosphoanhydride Bonds," Jean C. Summerton, Jeffrey D. Evanseck, and Michael S. Chapman, J. Phys. Chem. A 116 10209 (2012)
Most Cited Publications
  1. "All-atom empirical potential for molecular modeling and dynamics studies of proteins," A. D. MacKerell Jr., D. Bashford, M. Bellott, R. L. Dunbrack Jr., J. D. Evanseck, M. J. Field, S. Fischer, J. Gao, H. Guo, S. Ha, D. Joseph-McCarthy, L. Kuchnir, K. Kuczera, F. T. K. Lau, C. Mattos, S. Michnick, T. Ngo, D. T. Nguyen, B. Prodhom, W. E. Reiher, B. Roux, M. Schlenkrich, J. C. Smith, R. Stote, J. Straub, M. Watanabe, J. Wiórkiewicz-Kuczera, D. Yin, and M. Karplus, J. Phys. Chem. B. 102, no. 18 (1998)
  2. "Transition structures of hydrocarbon pericyclic reactions," Houk, Kendall N., Yi Li, Jeffrey D. EvanseckAngewandte Chemie International Edition 31, no. 6 (1992)
  3. "Locally accessible conformations of proteins: multiple molecular dynamics simulations of crambin," Caves, Leo SD, Jeffrey D. Evanseck, Martin Karplus.,  Protein Science 7, no. 3 (1998)
  4. "Influence of the heme pocket conformation on the structure and vibrations of the Fe-CO bond in myoglobin: a QM/MM density functional study," Rovira, Carme, Brita Schulze, Markus Eichinger, Jeffrey D. Evanseck, Michele Parrinello,  Biophysical journal 81, no. 1 (2001)
  5. "Density functional theory study of aqueous-phase rate acceleration and endo/exo selectivity of the butadiene and acrolein Diels-Alder reaction," Kong, S., Evanseck, J.D., Journal of the American Chemical Society 122, no. 42 (2000)
Recent Publications
  1. "Chemistry REU Leadership Group: Support for the Chemistry Undergraduate Research Community"  Watkins, L.M., Evanseck, J.DACS Symposium Series 1295, pp. 73-83
  2. "Evolution of an AwESOME Chapter"  Cooper, E., Shaik, S., Bautista, D., (...), Gawalt, E.S., Evanseck, J.D. ACS Symposium Series 1278, pp. 55-71
  3. "Metalated nitriles: SNi′ cyclizations with a propargylic electrophile," Ping Lu, Venkata S. Pakkala, Jeffrey D. Evanseck, Fraser F. Fleming, Tetrahedron Letters 56, 3216 (2015)
  4. "Intramolecular Charge-Assisted Hydrogen Bond Strength in Pseudochair Carboxyphosphate," Sarah E. Kochanek, Traci M. Clymer, Venkata S. Pakkala, Sebastien P. Hebert, Kyle Reeping, Steven M. Firestine, and Jeffrey D. Evanseck, J. Phys. Chem. B 119, 1184 (2015)
  5. "Common Hydrogen Bond Interactions in Diverse Phosphoryl Transfer Active Sites," Jean C. Summerton, Gregory M. Martin, Jeffrey D. Evanseck, Michael S. Chapman, PLOS One 9, e108310 (2014)
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Personal | Department
Department of Chemistry and Biochemistry, Duquesne University
Ph.D., Physical Chemistry, Purdue University, 1985
Summary:

Research in the laboratory consists of the development and application of computational methods in collaboration with experimental research laboratories. Our research interests fall into the areas of computational biophysics and computational material sciences.

Some our current research projects involve, studying the transport mechanism of neurotransmitter sodium symporter proteins, where we are simulating in vivo conditions using molecular dynamics simulations to observe changes in conformation of proteins upon substrate transport. We are researching computer-aided drug design by applying free energy calculations to elucidate intermolecular interactions of various substrates and inhibitors with monoamine transporters. We are investigating conformational properties of polyglutamine peptide systems by applying molecular dynamics, using the metadynmics sampling algorithm, to explore the conformational free energy landscape of polyglutamine peptides in solvent. We are involved in the electronic structure calculations of extended solids, where we are applying computational methods to investigate and predict physicochemical properties of materials. We are also studying smart materials such as hydrogels of PNIPAM.

In the past, we have studied antifreeze proteins at ice/water interfaces and interaction of N-acetylglucosamine with chitnase. The folding of small peptides in salt solution, and structure, function, and dynamics of monoamine transporters have been studied as well.

Dr. Madura is also one of the primary authors to the Brownian dynamics program UHBD, which is used to calculate the diffusion-controlled rate-constants for biomolecular encounters.

Most Cited Publications
  1. "Comparison of simple potential functions for simulating liquid water," William L. Jorgensen, Jayaraman Chandrasekhar, and Jeffry D. Madura, Roger W. Impey and Michael L. Klein, J. Chem. Phys. 79, 926 (1983)
  2. "Optimized intermolecular potential functions for liquid hydrocarbons," William L. Jorgensen, Jeffry D. Madura, Carol J. Swenson, J. Am. Chem. Soc. 106, 6638 (1984)
  3. "Development of an improved four-site water model for biomolecular simulations: TIP4P-Ew," Hans W. Horn, William C. Swope, and Jed W. Pitera, Jeffry D. Madura and Thomas, J. Dick Greg, L. Hura, Teresa Head-Gordon, J. Chem. Phys.120, 9665 (2004)
  4. "Temperature and size dependence for Monte Carlo simulations of TIP4P water," William L. Jorgensen & Jeffry D. MaduraMolecular Physics 56, 1381 (1985)
  5. "Electrostatics and diffusion of molecules in solution: simulations with the University of Houston Brownian Dynamics program," Jeffry D. Madura, James M. Briggs, Rebecca C. Wade, Malcolm E. Davis, Brock A. Luty, Andrew Ilin, Jan Antosiewicz, Michael K. Gilson, Babak Bagheri, L.Ridgway Scott, J.Andrew McCammon, Computer Physics Communications 91, 57 (1995)
Recent Publications
  1. "Polyglutamine Fibrils: New Insights into Antiparallel β-sheet Conformational Preference and Side Chain Structure," David Punihaole, Riley J Workman, Zhenmin Hong, Jeffry D Madura, Sanford A Asher, J. Phys. Chem. B 120, 3012 (2016)
  2. "2-Substituted 3β-Aryltropane Cocaine Analogs Produce Atypical DAT Inhibitor Effects Without Inducing Inward-Facing DAT Conformations," Weimin C. Hong, Theresa A. Kopajtic, Lifen Xu, Stacey A. Lomenzo, Bernandie Jean, Jeffry D. Madura, Christopher K. Surratt, Mark L. Trudell and Jonathan L. Katz, J Pharmacol Exp Ther 356, 624 (2016)
  3. "Human alpha1 Glycine Receptor Allostery as Identified by State-Dependent Crosslinking Studies," Michael Cascio, Rathna J Veeramachaneni, Jeffry MaduraBiophysical Journal 110, 201a (2016)
  4. "Crosslinking/MS Studies of Cholesterol Interactions with Human alpha1 Glycine Receptor," Nicholas Ferraro, Emily Benner, Jeffry Madura, Michael Cascio, Biophysical Journal 110, 355a (2016)
  5. "Computational Investigation of the Transport Mechanism of Neurotransmitter Sodium Symporters using a Physiological Ion Gradient," Emily M Benner, Jeffry D MaduraBiophysical Journal 3, 626a (2016)

Visualizing Molecules in 3D

  • By Aude Marjolin
  • 15 October 2015

Jeffry Madura and student Biran Adams created a software program which allows an individual to view molecular structures in three dimensions by looking through a specially-designed headset.

The project began last year when Madura noticed that there were not many affordable options for people to observe molecules in three dimensions. Madura reached out to the computer science professors and students to help design a solution, and Adams volunteered. According to Madura, Adams’ experience background in programming and algebra was perfect for the task. Madura and Adams developed the idea of using already-existing video game technology to create a virtual world of enlarged molecules. They used the Oculus Rift, a virtual reality headset originally funded through a Kickstarter campaign, and expanded its scope of use.

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