Publications

Undergraduates and high school teachers contributing to computational research with me are underlined.
Publications where I am the corresponding author are marked with a * next to my name.

*Kua, J.; Tripoli, L. P. Life, 2024, 14, 933.
"Exploring the Core Formose Cycle: Catalysis and Competition"

*Kua, J.; Miller, N. A. Life, 2022, 12, 1763.
"Preliminary Free Energy Map of Prebiotic Compounds formed from CO2, H2 and H2S"

*Kua, J.; Hernandez, A. L.; Velasquez, D. N. Life, 2021, 11, 1025.
"Thermodynamics of Potential CHO Metabolites in a Reducing Environment"

*Kua, J.; Paradela, T. L. J. Phys. Chem. A, 2020, 124, 10019-10028.
"Early Steps of Glycolonitrile Oligomerization: A Free Energy Map"

*Kua, J.; Miller, A. S.; Wallace, C. E.; Loli, H. ACS Omega, 2019, 4, 22251-22259.
"Role of Acid in the Co-oligomerization of Formaldehyde and Pyrrole"

*Kua, J. J. Phys. Chem. A, 2019, 123, 3840-3850.
"Exploring Free Energy Profiles of Uracil and Cytosine Reactions with Formaldehyde"

Thrush, K. L.; *Kua, J. J. Phys. Chem. A, 2018, 122, 6769-6779.
"Reactions of Glycolonitrile with Ammonia and Water: A Free Energy Map"

*Kua, J.; Loli, H. J. Phys. Chem. A, 2017, 121, 8154-8165.
"Porphinogen Formation from the Co-oligomerization of Formaldehyde and Pyrrole: Free Energy Pathways"

*Kua, J.; Sweet, L. M. J. Phys. Chem. A, 2016, 120, 7577-7588.
"Preliminary Oligomerization in a Glycolic Acid - Glycine Mixture: A Free Energy Map"

*Kua, J.; Thrush, K. L. J. Phys. Chem. B, 2016, 120, 8175-8185.
"HCN, Formamidic Acid and Formamide in Aqueous Solution: A Free Energy Map"

*Kua, J.; Rodriguez, A. A.; Marucci, L. A.; Galloway, M. M.; De Haan, D. O. J. Phys. Chem. A, 2015, 119, 2122-2131.
"Free Energy Map for the Co-oligomerization of Formaldehyde and Ammonia"

*Kua, J.; Avila, J. E.; Lee, C. J.; Smith, W. D. J. Phys. Chem. A, 2013, 117, 12658-12667.
"Mapping the Kinetic and Thermodynamic Energy Landscape of Formaldehyde Oligomerization under Neutral Conditions."

*Kua, J.; Galloway, M. M.; Millage, K. D.; Avila, J. E.; De Haan, D. O. J. Phys. Chem. A, 2013, 117, 2997-3008.
"Glycolaldehyde Monomer and Oligomer Equilibria in Aqueous Solution: Comparing Computational Chemistry and NMR Data."

*Kua, J.; Bada, J. L. Orig. Life Evol. Biosph., 2011, 41, 553-558.
"Primordial Ocean Chemistry and its Compatibility with the RNA World."

*Kua, J.; Krizner, H. E.; De Haan, D. O. J. Phys. Chem. A, 2011, 115, 1667-1675.
"Thermodynamics and kinetics of imidazole formation from glyoxal and methylamine: A computational study."

*Kua, J.; Daly, R. C.; Tomlin, K. M.; van Duin, A. C. T.; Brill, T. B.; Beal, R. W.; Rheingold, A. L. J. Phys. Chem. A, 2009, 113, 11443-11453.
"Self-assembly of SbCl3 and 1,4-dioxane: A cubic structure connected by very weak bonds."

Krizner, H. E.; De Haan, D. O.; *Kua, J. J. Phys. Chem. A, 2009, 113, 6994-7001.
"Thermodynamics and kinetics of methylglyoxal dimer formation: A computational study."

*Kua, J.; Gyselbrecht, C. R. J. Phys. Chem. A, 2008, 112, 9128-9133.
"Favoring heterotrimeric boroxine formation using an internal Lewis base: A computational study."

Iovine, P. M.; Gyselbrecht, C. R., Perrtu, E. K.; Klick, C.; Neuwelt, A.; Loera, J.; DiPasquale, A. G.; Rheingold, A. L.; Kua, J. Dalton Trans. 2008, 3791-3794.
"Hetero-arylboroxines: The first rational synthesis, x-ray crystallographic and computational analysis."

*Kua, J.; Hanley, S. W.; De Haan, D. O. J. Phys. Chem. A, 2008, 112, 66-72.
"Thermodynamics and kinetics of glyoxal dimer formation: A computational study."

*Kua, J.; Gyselbrecht, C. R. J. Phys. Chem. A 2007, 111, 4759-4766.
"Thermodynamics and kinetics of methylboroxine-amine adduct formation: A computational study."

Mitchell, T. A.; Finocchio, D.; *Kua, J. J. Chem. Educ. 2007, 84, 629-634.
"Predicting the Stability of Hypervalent Molecules."

*Kua, J.; Tomlin, K. M. J. Phys. Chem. A 2006, 110, 11988-11994.
"Computational study of multiple-decker sandwich and rice-ball structures of neutral titanium-benzene clusters."

*Kua, J.; Fletcher, M. N.; Iovine, P. M. J. Phys. Chem. A 2006, 110, 8158-8166.
"Effect of para-substituents and solvent polarity on the formation of triphenylboroxine-amine adducts."

Wong, C. F.; Kua, J.; Zhang, Y.; Straatsma, T.; McCammon, J. A. Proteins: Structure, Function, Bioinformatics 2005, 61, 850-858.
"Molecular Docking of Balanol to Dynamics Snapshots of Protein Kinase A."

*Kua, J.; Iovine, P. M. J. Phys. Chem. A 2005, 109, 8938-8943.
"Formation of para-substituted triphenylboroxines: A computational study."

*Kua, J.; Zhang, Y.; Eslami, A. C.; Butler, J. R.; McCammon, J. A. Protein Science 2003, 12, 2675-2684.
"Studying the Roles of W86, E202, Y337 in Binding of Acetylcholine to Acetylcholinesterase using a Combined Molecular Dynamics and Multiple Docking Approach."

Xu, X.; Kua, J.; Periana, R. A.; Goddard III, W. A. Organometallics 2003, 22, 2057-2068.
"Structure, Bonding and Stability of a Catalytica Pt(II) catalyst: A computational study"

Zhang, Y.; Kua, J.; McCammon, J. A. J. Phys. Chem. B 2003, 107, 4459-4463.
"Influence of Structural Fluctuation on Enzyme Reaction Energy Barriers in Combined QM/MM studies"

Zhang, Y.; Kua, J.; McCammon, J. A. J. Am. Chem. Soc. 2002, 124, 10572-10577.
"Role of the catalytic triad and oxyanion hole in Acetylcholinesterase catalysis: an ab initio QM/MMstudy"

*Kua, J.; Zhang, Y.; McCammon, J. A. J. Am. Chem. Soc. 2002, 124, 8260-8267.
"Studying enzyme binding specificity in Acetylcholinesterase using a combined molecular dynamics and multiple docking approach"

Kua, J.; Periana, R. A.; Goddard III, W. A. Organometallics 2002, 21, 511-525.
"Stability and Thermodynamics of the PtCl₂ type catalysts for activating methane to methanol: A computational study"

Kua, J.; Lauhon, L. J.; Ho, W.; Goddard III, W. A. J. Chem. Phys. 2001, 115, 5620-5624.
"Direct Comparison of rates for low temperature diffusion of H and D on Cu(001) from QM calculations and STM experiments."

Goddard III, W. A.; Cagin, T.; Blanco, M.; Vaidehi, N.; Dasgupta, S.; Floriano, W.; Belmares, M.; Kua, J.; Zamanakos, G.; Kashihara, S.; Iotov, M.; Gao, G. Comp. Theor. Poly. Sci. 2001, 11, 329-343.
"Strategies for multiscale modeling and simulation of organic materials: polymers and biopolymers"

Ihee, H.; Kua, J.; Zewail, A. H.; Goddard III, W. A. J. Phys. Chem A 2001, 105, 3623-3632.
"CF₂XCF₂X and CF₂XCF₂ radicals: Ab initio studies and comparison with experiment"

Tang, Y.; Ghirlanda, G.; Vaidehi, N.; Kua, J.; Mainz, D. T.; Goddard III, W. A.; DeGrado, W. F.; Tirrell, D. A. Biochemistry 2001, 40, 2790-2796.
"Stabilization of Leucine Zipper Coiled Coils by introduction of Trifluoroleucine"

Kua, J.; Faglioni, F.; Goddard III, W. A. J. Am. Chem. Soc. 2000, 122, 2309-2321.
"Thermochemistry for hydrocarbon intermediates chemisorbed on metal surfaces..."

Kua, J.; Goddard III, W. A. J. Am. Chem. Soc. 1999, 121, 10928-10941.
"Oxidation of Methanol on 2nd and 3rd row Group VIII Transition Metals: Applications to Direct Methanol Fuel Cells"

Kua, J.; Goddard III, W. A. J. Phys. Chem. B 1998, 102, 9492-9500.
"Chemisorption of Organics on Platinum: 2. Chemisorption of C₂H_x and CH_x on Pt(111)"

Kua, J.; Goddard III, W. A. J. Phys. Chem. B 1998, 102, 9481-9491.
"Chemisorption of Organics on Platinum: 1. The Interstitial Electron Model"

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