Publications 1999 - present

USD Undergraduate Co-Authors denoted by *  

• Grant, C. V.; Sit, S. -L.; De Angelis, A. A.; Khuong, K. S.; Plesniak, L. A.; Opella, S. J., "An efficient 1H/31P double- resonance solid-state NMR probe that utilizes a scroll coil”, J. Magn. Reson. (in press).

• Herrinton, T. R. , J. Chem.  Ed., 84(9) ,1427 (2007).
• Matsuda, S.; Fillo, J. D.*; Henry, A. A.; Wilkens, S. J.; Dwyer, T. J.;   Wemmer, D. E.; Spraggon, G.; Geierstanger, B. H.; Schultz, P. G.;   Romesberg, F. E.; "Unnatural Base Pair Structure-Activity   Relationships”, J. Am. Chem. Soc. 129, 10466-10473 (2007) . 
• Tahmassebi, D. C.; Williamson, J., "Balancing teaching and research in obtaining a faculty position at a predominantly undergraduate   institution", Chemical Biology, 2(8), 521-524 (2007)
• Chen, J.; Russo, R.; Chao, W.; Margerum, L. D.; Malachowski, M. R.; White, R.*; Thawley, Z.*; Thayer, A.*; Rheingold, A. L.; Zakharov, L. N., "Synthesis, Structure, Redox Properties and Azide Binding for a Series of Biphenyl-Based Cu(II) Complexes," J. Chem. Soc., Dalton Trans., 2571, (2007). 
• Kua, J.; Gyselbrecht, C.R., "Thermodynamics and kinetics of nethylboroxine-amine adduct formation: A computational  study", J. Phys. Chem. A 111, 4759- 4766 (2007). 
• Harned, T.; Kalous, O.; Neuwelt, A.*; Loera, J.*; Neuwelt, E.; Iovine P. M.; Reynolds, C. P., “Sodium Thiosulfate (STS) Administered Six   Hours After Cisplatin Does Not Compromise Anti-Neuroblastoma   Activity”, Proc. Amer. Assoc. Cancer Res., 48, 1172 (2007).
• Tracy A. Mitchell*, Debbie Finocchio, and Jeremy Kua, "Predicting the stability of hypervalent molecules" J. Chem. Educ. 84, 629-634 (2007).
• Jeremy Kua and Keaton Tomlin*, "Computational study of multiple- decker sandwich and rice-ball structures of neutral titanium-benzene clusters" J. Phys. Chem. A  110, 11988-11994 (2006).
• Kirsten W. Loeffler*, Charles A. Koehler*, Nichole M. Paul*, and   David  O. De Haan, "Oligomer Formation in Evaporating Aqueous   Glyoxal and Methyl   Glyoxal Solutions" Environ. Sci. Technol., 40(20)   6318-6323 (2006).
• Cristina M. Sandoval*, Bernhard H. Geierstanger , Satoshi Fujimura,    Calvin Balatbat*, Taylor Williams*, Julio de Unamuno*, Jennifer A.    Whiles-Lillig, Lisa M. Ellerby , H. Michael Ellerby, Patricia Jennings  and Leigh A. Plesniak  "Structural Evaluation of a Novel Pro-apoptotic    Peptide Coupled to CNGRC Tumor Homing Sequence by    NMR"Chemical Biology and Drug Design,  67(6), 383-450 (2006). 
• Peter M. Iovine, Matthew N. Fletcher*, and Shirley Lin.  "Condensation of Arylboroxine Structures on Lewis Basic Copolymers as a Noncovalent Strategy toward Polymer Functionalization" Macromolecules 39(19), 6324-6326 (2006).
• Kua, J.; Fletcher, M. N.*;Iovine, P. M. “Effect of para-substituents and solvent polarity on the formation of triphenylboroxine-amine adducts.”  J. Phys. Chem. A, 110, 8158-8166, (2006). 
• Dwyer, T.J.; Fillo, J.D.* “Assaying alpha-Dicarbonyl Compounds in Wine using a Complementary GC-MS, HPLC and Visible Spectrophotometric Analysis”  J. Chem. Ed., 83(2); 273-276, (2006).
• Wong, C. F.; Kua, J.; Zhang, Y.; Straatsma, T.; McCammon, J. A. “Molecular docking of balanol to snapshots of Protein Kinase A” Protens: Structure, Function, Bioinformatics, (2005) 61, 850-858.
• W. P. Hastings*, C. A. Koehler*, E. L. Bailey* and D. O. De Haan.  “Secondary Organic Aerosol Formation by Glyoxal Hydration and Oligomer Formation: Humidity Effects and Equilibrium Shifts during Analysis,” Environ. Sci. Technol.  39, (22) 8728-8735 (2005) .
• D.L Murphy, M.R. Malachowski, C.F. Campana, S.M. Cohen, "A Chiral, heterometallic metal-organic framework derived from a tris(chelate) coordination compound," Chem. Comm., 5506-5508, 2005. 
• Perttu, Emily K*; Arnold, Matthew*; Iovine, Peter M. "The Synthesis and Characterization of Phenylacetylene Tripodal Compounds Containing Boroxine Cores" Tetrahedron Lett. 2005, 46 (50), 8753-8756.
• Kua, J.; Iovine, P. M. “Formation of para-substituted triphenylboroxines: A computational study”  J. Phys. Chem. A, 2005, 109, 8939-8943.
• C. A. Koehler*, J. D. Fillo*, K. A. Ries, J. T. Sanchez and D. O. De Haan.  “Formation of secondary organic aerosol by reactive condensation of furandiones, aldehydes, and water vapor ontoinorganic aerosol seed particles,” Environ. Sci. Technol.  37, (19) 5064-5072 (2004) doi# 10.1021 es034672b. 
• Zhang, Q.; Dwyer, T. J.; Tsui, V.; Case, D. A.; Cho, J.; Dervan, P. B.; Wemmer, D. E., “NMR Structure of a Cyclic Polyamide-DNA Complex”, J. Am. Chem. Soc., 25, 7958-7966 (2004).
• Sara R. Halper, Mitchell R. Malachowski, Heather M. Delaney and Seth M. Cohen, “Heteroleptic Copper Dipyrromethene Complexes: Synthesis, Structures, and Coordination Polymers,” Inorganic Chemistry, 43, 1242, 2004. 
• Leigh A. Plesniak, Jonathan I. Parducho*, Angie Ziebart*, Bernhard H. Geierstanger, Jennifer Whiles, Guiseppe Melacini, & Patricia A. Jennings.  Orientation and Helical Conformation of a Tissue Specific Hunter-KillePeptide in Micelles. (2004)  Protein Science. 13:1988-96.
• James P. Bolender and F. S. Richardson, “Chirality-Dependent Interactions between Molecular Propeller Structures in Solution.  Chiral Recognition and Discrimination Processes Modulated by Temperature and Incremental Changes in Structural Chirality.” Biophysical Chemistry, 105 (2003) 293 - 322. 
• J. D. Fillo*, C. A. Koehler*, T. P. Nguyen*, D. O. De Haan, B. A. Gilbert and K. P. Flinn.  “Simulating secondary organic aerosol activation by condensation of multiple organics on seed particles,” Environ. Sci. Technol. 37 (20) 4672-4677 (2003)  doi# 10.1021 es034110s.
• M.Sue Lowery and Leigh A. Plesniak.  Some Like It Cold:  A    Computer- Based Laboratory Introduction to Sequence and Tertiary    Structure Comparison of  Cold- Adapted Lactate Dehydrogenases    using Bioinformatics Tools.  (2003) Journal of Chemical Education. 80:   1300-1302  http://jchemed.chem.wisc.edu/ 
• Leigh A. Plesniak and Ellis Bell.  Teaching Proteomics. (2003) 31:127- 30. http://www.bambed.org/  
• Aguirre, G.; Somanathan, R.; Hellberg, L. H.; Dwyer, T. J.; North, R., "N-Alkenyl Amide Rotational Barriers by 2D EXSY NMR", Magn. Reson. Chem. 41, 131 (2003).
• Kua, J., Zhang, Y.; Eslami, A. C.; Butler, J. R*.; McCammon, J. A. “Studying the roles of W86, E202, Y337 in binding of acetylcholine to acetylcholinesterase using a combined molecular dynamics and multiple docking approach” Prot. Sci., (2003) 12, 2675-2684. 
• Mitchell R. Malachowski, “A Day in the Life of CUR,” President’s Column, Council on Undergraduate Research Quarterly, 23, 106, 2003.
• Mitchell R. Malachowski, “A Research Across the Discipline Movement,” chapter in “Undergraduate Research,” edited by Marilyn Kinkead, Jossey-Bass series on higher education, 2003.
• Mitchell R. Malachowski, “Research Across the Curriculum,” President’s Column, Council on Undergraduate Research Quarterly, 23, 152, 2003.
• James P. Bolender and Michel A. Boudrias, “Field Research at the Core of an Interdisciplinary Science Course.” Council for Undergraduate Research – Quarterly, 22 (2002) 180-185. 
• James P. Bolender, Andrew Meyers*, Joseph Cordaro*, and Ryan S. Ries*, " Chiral Recognition Phenomena Probed by Steady-State Luminescence Measurements: Stern-Volmer Analysis of Chiral Discriminatory Behavior " Chirality 14 (2002) 456-464.
• Martha.L. Medina*, Barbara S. Chapman, James P. Bolender and Leigh A. Plesniak.  Transient Vesicle Leakage Initiated by a Synthetic Apoptotic Peptide Derived from the Death Domain of Neurotrophin Receptor, p75NTR.  (2002)  Journal of Peptide Research. 59 (4):  149-158.  
• Leigh A. Plesniak, Yuki Horiuchi, Daniel Sem, David Meinenger, Linda Stiles, Jennifer Shaffer, Patricia A. Jennings, and Joseph A. Adams.  Probing the Nucleotide Binding Domain of Osmoregulator EnvZ Using Fluorescent Nucleotide Derivatives.  (2002) Biochemistry.  41: 876-82.
• Gao, J.; Strassler, C.; Tahmassebi, D.; Kool, E.T.  “Libraries of Composite Polyfluors Built from Fluorescent Deoxyribosides”,  J.  Am. Chem. Soc (Communication). 2002 124(39) 11590-11591.
• O’Neill, B.M.*; Ratto, J.E.*; Good, K.L.*; Tahmassebi, D.C.; Helquist, S.A.; Morales, J.C.; Kool, E.T.  “A Highly Effective Nonpolar Isostere of Deoxyguanosine:  Synthesis, Structure, Stacking, and Base Pairing”,  J. Org. Chem. 2002, 67, 5869-5875.
• Guckian, K. M.; Schweitzer, B. A.; Ren, R. X.-F.; Sheils, C. J.; Tahmassebi, D. C.; Kool, E. T. “Factors Contributing to Aromatic Stacking in Water:  Evaluation in the Context of DNA”, J. Am. Chem. Soc. 2000, 122, 2213. 
• Ronald M. Supkowski, James P. Bolender, Wendy D. Smith, Lewis E.L. Reynolds, and William DeW. Horrocks, Jr. “Lanthanide Ions as Redox Probes of Long-Range Electron Transfer in Proteins.”  Coord. Chem. Rev., 185-186 (1999) 307-319.
• D. O. De Haan, T. Brauers, K. W. Oum, J. Stutz, T. Nordmeyer and B. J. Finlayson-Pitts.  “Heterogeneous chemistry in the troposphere:  experimental approaches and applications to the chemistry of sea salt particles.” International Reviews of Physical Chemistry 18 (3) 343-385 (1999) 
• Mitchell R. Malachowski, Mark Adams*, Nadia Elia*, Arnold Rheingold and Richard Kelly,  “Enforcing Geometrical Constraints on Metal Complexes using Biphenyl-based Ligands:  Spontaneous Reduction of Copper(II) by Sulfur-Containing Ligands,” Journal of the Chemical Society, Dalton Transactions. 2177, 1999.
• Mitchell R. Malachowski, Nancy Mills, “CUR Institutes: A New Model for Supporting Research with Undergraduates,” Journal of Chemical Education, 76, 1320, 1999.      
• Jeremy Kua, Sean W. Hanley*, David O. De Haan, "Thermodynamics and kinetics
  of glyoxal dimer formation:  a computational study" Journal of Physical
  Chemistry A (2008) vol 112, pp. 66-72
• Ashley L. Corrigan*, Sean W. Hanley*, David O. De Haan, "Uptake of glyoxal by organic and inorganic aerosol" Environmental Science & Technology (in
  press, 2008)