Publications

2021

  1. Chemical kinetic basis of synergistic blending for research octane number, Gina M. Fioroni, Mohammed J. Rahimi, Charles K. Westbrook, Scott W. Wagnon, William J. Pitz, Seonah Kim and Robert L. McCormick, Fuel 307, 121865 (2022) [Online Article] (In Press)
  2. A comprehensive experimental and kinetic modeling study of di-isobutylene isomers: Part 1, Nitin Lokachari, Goutham Kukkadapu, Hwasup Song, Guillaume Vanhove, Guillaume Dayma, Zeynep Serinyel, Kuiwen Zhang, Roland Dauphin, Brian Etz, Seonah Kim, Mathias Steglich, Andras Bodi, Gina Fioroni, Patrick Hemberger, Sergey S. Matveev, Alexander A. Konnov, Philippe Dagaut, Scott W Wagnon, William J. Pitz, Henry J. Curran, Combustion and Flame (submitted) (In Press)
  3. Connecting cation site location to alkane dehydrogenation activity in Ni/BEA catalysts, Carrie A. Farberow; Evan C. Wegener; Anurag Kumar; Jacob Miller; Daniel P. Dupuis; Seonah Kim; Daniel A. Ruddy, J. of Catalysis (revision submitted) (In Press)
  4. Predicting catalytic pyrolysis aromatic selectivity from Pyrolysis Vapor Composition using Mass Spectra Coupled with Statistical Analysis, Anne K. Strace, David D. Lee, Kristen T. Hietala, Yeonjoon Kim, Seonah Kim, Anne E. Harman-Ware and Daniel L. Carpenter, ACS Sustainable Chem. Eng. (in revision) (In Press)
  5. Elucidating the chemical pathways of soot precursor formation during combustion of 1- and 2-phenylethanol, Brian D. Etz, Gina M. Fioroni, Richard A. Messerly, Mohammad J. Rahimi, Peter C. St. John, David J. Robichaud, Earl D. Christensen, Brian P. Beekley, Charles S. McEnally, Lisa D. Pfefferle, Yuan Xuan, Shubham Vyas, Robert S. Paton, Robert L. McCormick, Seonah Kim, Proc. Comb. Inst. 2021 [Online Article] (In Press)
  6. The importance of engineered and learned molecular representations in predicting organic reactivity, selectivity and chemical properties, Liliana Gallegos, Guilian Luchini, Peter C. St. John, Seonah Kim, Robert S. Paton, Accounts of Chemical Research (2021) [Online Article] (In Press)
  7. Understanding how chemical structure affects ignition-delay-time φ-sensitivity, Richard A. Messerly, Jon H. Luecke, Peter C. St. John, Brian D. Etz, Yeonjoon Kim, Bradley T. Zigler, Robert L. McCormick, Seonah Kim, Combustion & Flame, 225, 377-387 (2021) [Online Article]

2020

  1. A perspective on biomass-derived biofuels: from catalyst design principles to fuel properties, Yeonjoon Kim, Anna E. Thomas, David J. Robichaud, Kristiina Iisa, Peter C. St. John, Brian D. Etz, Gina M. Fioroni, Abhijit Dutta, Robert L. McCormick, Calvin Mukarakate, Seonah Kim, J. Haz. Mat., 400, 5, 123198 (2020). [Online Article]
  2. In-situ hydrogenation of bio-oil/bio-oil phenolic compounds with secondary alcohols over a synthesized mesoporous Ni/CeO2 catalyst, Hoda Shafaghat, Yiu Fai Tsang, Jong-Ki Jeon, Ji Man Kim, Youri Park, Yeonjoon Kim, Seonah Kim, Young-Kwon Park, Chemical Engineering Journal, 382, 122912 (2020) [Online Article]
  3. Integrating Experimental and Computational Studies Unravels the Ga Species Responsible for Enhancing Alkene Production during Catalytic Upgrading of Biomass Pyrolysis Vapors over Ga/ZSM-5, Kristiina Iisa, Yeonjoon Kim, Kellene A. Orton, David J. Robichaud, Rui Katahira, Michael J. Watson, Mark R. Nimlos, Joshua A. Schaidle, Calvin Mukarakate, and Seonah Kim, Green Chem., 22, 2403-2418 (2020) (cover page, 2020 Green Chemistry Hot Articles) [Online Article]
  4. Investigation of structural effects of aromatic compounds on sooting tendency with mechanistic insight into ethylphenol isomers, Yeonjoon Kim, Brian D. Etz, Peter C. St. John, Gina M. Fioroni, Richard A. Messerly, Shubham Vyas, Brain P. Beekley, Facheng Guo, Charles S. McEnally, Lisa D. Pfefferle, Robert L. McCormick, Seonah Kim, Proc. Comb. Inst. 2020 (in press). [Online Article] (In Press)
  5. Isotopic Studies for Tracking Biogenic Carbon during Co-processing of Biomass and Vacuum Gas Oil, Calvin Mukarakate, Kellene Orton, Yeonjoon Kim, Stefano Dell’Orco, Carrie A Farberow, Seonah Kim, Michael J Watson, Robert Baldwin and Kim Magrini, ACS Sustainable Chem. Eng., 8, 7, 2652-2664 (2020) [Online Article]
  6. Prediction of gas-phase homolytic bond dissociation energies at near chemical accuracy with sub-second computational cost, Peter C. St. John, Yanfei Guan, Yeonjoon Kim, Seonah Kim, Robert S. Paton, 10.26434/chemrxiv.10052048 (2019) and Nature Comm., 11, 2328 (2020). [Online Article]
  7. Prediction of Hydroxymethylfurfural Yield in Glucose Conversion through Investigation of Lewis Acid and Organic Solvent Effects, Yeonjoon Kim, Ashutosh Mittal, David J. Robichaud, Heidi M. Pilath, Brian D. Etz, Peter C. St. John, David K. Johnson, and Seonah Kim, ACS Catalysis, 10, 24, 14707-14721 (2020). [Online Article]
  8. Quantum chemical calculations for over 200,000 organic radical species and 40,000 associated closed-shell molecules, Peter St. John, Yanfei Guan, Yeonjoon Kim, Brian D. Etz, Seonah Kim, Robert S. Paton, Scientific Data, 7, 244 (2020). [Online Article]
  9. Reactive Molecular Dynamics Simulations and Quantum Chemistry Calculations To Investigate Soot-Relevant Reaction Pathways for Hexylamine Isomers, Hyunguk Kwon, Brian D. Etz, Matthew J. Montgomery, Richard Messerly, Sharmin Shabnam, Shubham Vyas, Adri C. T. van Duin, Charles S. McEnally, Lisa D. Pfefferle, Seonah Kim, and Yuan Xuan, J. Phys. Chem. A, 124, 4290-4304 (2020) [Online Article]
  10. Towards quantitative prediction of ignition-delay-time sensitivity on fuel-to-air equivalence-ratio, Richard A. Messerly, Mohammad J. Rahimi, Peter C. St. John, Jon H. Luecke, Ji-Woong Park, Nabila A. Huq, Thomas D. Foust, Tianfeng Lu, Bradley T. Zigler, Robert L. McCormick, Seonah Kim, Combustion and Flame, 214, 103-115 (2020). [Online Article]

2019

  1. Development of a data-derived sooting index including oxygen-containing fuel components, Peter St. John, Seonah Kim, Robert L. McCormick, Energy & Fuels, 33, 10, 10290-10296 (2019) [Online Article]
  2. Experimental and theoretical insight into the soot tendencies of the methylcyclohexene isomers, Seonah Kim, Gina M. Fioroni, Ji-Woong Park, David J. Robichaud, Dhrubajyoti D. Das, Peter C. St. John, Tianfeng Lu, Charles S. McEnally, Lisa D. Pfefferle, Robert S. Paton, Thomas D. Foust, Robert L. McCormick, Proc. Comb. Inst., 37, 1, 1083-1090 (2019). [Online Article]
  3. Performance-Advantaged Ether Diesel Bioblendstock Production by a priori Design, Nabila A. Huq, Xiangchen Huo, Glenn R. Hafenstine, Stephen M. Tifft, Jim Stunkel, Earl D. Christensen, Gina M. Fioroni, Lisa Fouts, Robert L. McCormick, Matthew R. Wiatrowski, Mary J. Biddy, Teresa L. Alleman, Raynella M. Connatser, Michael D. Kass, Patrick A. Cherry, Charles S. McEnally, Lisa D. Pfefferle, Peter St. John, Seonah Kim, Derek R. Vardon, 116 (52) 26421-26430, PNAS (2019). [Online Article]
  4. Small ester combustion chemistry: Computational kinetics and experimental study of methyl acetate and ethyl acetate, Ahfaz Ahmed, William J.Pitz, Carlo Cavallotti, Marco Mehl, Nitin Lokachari, Elna J.K. Nilsson, Jui-Yang Wang, Alexander A. Konnov, Scott W. Wagnon, Bingjie Chen, Zhandong Wang, Seonah Kim, Henry J. Curran, Stephen J. Klippenstein, William L. Roberts, S. Mani Sarathy, Proc. Comb. Inst., 37, 1, 419-428 (2019) [Online Article]
  5. Sooting tendencies of co-optima test gasolines and their surrogates, Charles S. McEnally, Yuan Xuan, Peter C. St. John, Dhrubajyoti D. Das, Abhishek Jain, Seonah Kim, Thomas A. Kwan, Lance K. Tan, Junqing Zhu, Lisa D. Pfefferle, Proc. Comb. Inst., 37, 1, 961-968 (2019) [Online Article]
  6. Tailoring Diesel Bioblendstock from Integrated Catalytic Upgrading of Carboxylic Acids: A “Fuel Property First” Approach, Xiangchen Huo, Nabila A. Huq, Jim Stunkel, Nicholas S. Cleveland, Anne K. Starace, Amy E. Settle, Allyson M. York, Robert S. Nelson, David G. Brandner, Lisa Fouts, Peter C. St. John, Earl D. Christensen, Jon Luecke, J. Hunter Mack, Charles S. McEnally, Patrick A. Cherry, Lisa D. Pfefferle, Timothy J. Strathmann, Davinia Salvachúa, Seonah Kim, Robert L. McCormick, Gregg T. Beckham, Derek R. Vardon, Green Chem. 21, 5813-5827 (2019) [Online Article]
  7. Theoretical Determination of Size Effects in Zeolite-catalyzed Alcohol Dehydration, Larissa Y. Kunz, Lintao Bu, Brandon C. Knott, Cong Liu, Mark R. Nimlos, Rajeev S. Assary, Larry A. Curtiss, David J. Robichaud, and Seonah Kim, Catalysts, 9, 700 (2019). [Online Article]

2018

  1. Advancing Catalytic Fast Pyrolysis through Integrated Multiscale Modeling and Experimentation: Challenges, Progress and Perspectives, Peter N. Ciesielski, M. Brennan Pecha, Vivek S. Bharadwaj, Calvin Mukarakate, G. Jeremy Leong, Branden Kappes, Michael F. Crowley, Seonah Kim, Thomas D. Foust, Mark R. Nimlos, Wiley Interdisciplinary Reviews: Energy and Environment, (2018) (DOI: 10.1002/wene.297). [Online Article]
  2. Consideration of the Aluminum Distribution in Zeolites in Theoretical and Experimental Catalysis Research, Brandon C. Knott, Claire T. Nimlos, David J. Robichaud, Mark R. Nimlos, Seonah Kim, Rajamani Gounder, ACS Catal., 8, 770-784 (2018) [Online Article]
  3. Different Behaviors of a Substrate in P450 Decarboxylase and Hydroxylase Reveal Reactivity-Enabling Actors, Vivek S. Bharadwaj, Seonah Kim, Michael T. Guarnieri, Michael F. Crowley, Scientific Reports, 8, 12826 (2018). [Online Article]
  4. Diffusion of aromatic hydrocarbons in hierarchical mesoporous H-ZSM-5, Lintao Bu, Mark R. Nimlos, David J. Robichaud, Seonah Kim†, Catalysis Today, 312, 73-81 (2018) [Online Article]
  5. Experimental and theoretical study of oxidative stability of alkylated furans used as gasoline blend components, Earl Christensen, Gina M. Fioroni, Seonah Kim, Lisa Fouts, Erica Gjersing, Robert S. Paton, and Robert L. McCormick, Fuel, 576-585(2018). [Online Article]
  6. Improving Biomass Pyrolysis Economics by Integrating Vapor and Liquid Phase Upgrading, Kristiina Iisa, Michael J. Watson, Jeroen ten Dam, Abhijit Dutta, Robert M. Baldwin, Calvin Mukarakate, Seonah Kim, David J. Robichaud and Mark R. Nimlos, Green Chem. 20, 567 (2018). [Online Article]
  7. Measuring and Predicting Sooting Tendencies of Oxygenates, Alkanes, Alkenes, Cycloalkanes, and Aromatics on a Unified Scale, Dhruhajyoti D. Das, Peter St. John, Charles S. McEnally, Seonah Kim, Lisa D. Pfefferle, Combustion and Flame, 190, 349-364 (2018). [Online Article]
  8. Sooting tendencies of aromatic hydrocarbons with oxygen- containing side-chains, Brian P. Beekley, Charles S. McEnally, Peter C. St. John, Seonah Kim, Abhishek Jain, Hyunguk Kwon, Yuan Xuan, Lisa D. Pfefferle, ESSCI (Eastern States Section of the Combustion Institute) Spring 2018, Proceedings of the Combustion Institute. [Online Article]
  9. Structural and molecular dynamics studies of a C1-oxidizing lytic polysaccharide monooxygenase from Heterobasidion irregulare reveal amino acids important for substrate recognition, Bing Liu, Abhishek A. Kognole, Miao Wu, Bjørge Westereng, Michael F. Crowley, Seonah Kim, Maria Dimarogona, Christina M. Payne, Mats Sandgren, The FEBS Journal, 285, 2225-2242 (2018). [Online Article]

2017

  1. A quantitative model for the prediction of sooting tendency from molecular structure, Peter C. St John, Paul Kairys, Dhrubajyoti D. Das, Charles S. McEnally, Lisa D. Pfefferle, David J. Robichaud, Mark R. Nimlos, Bradley T. Zigler, Robert L. McCormick, Thomas D. Foust, Yannick J. Bomble, and Seonah Kim†, Energy & Fuels, 31 (9), 9983-9990 (2017). [Online Article]
  2. Diffusion of biomass pyrolysis products in H-ZSM-5 by molecular dynamics simulations, Lintao Bu, Mark R. Nimlos, David J. Robichaud, and Seonah Kim†, J. Phys. Chem. C, 121, 500-510 (2017). (Selected Special Issue as part of The Journal of Physical Chemistry virtual special issue “Mark S. Gordon Festschrift”) [Online Article]
  3. Exploring low-temperature dehydrogenation at ionic Cu sites in beta zeolite to enable alkane recycle in dimethyl ether homologation, Carrie A. Farberow, Singfoong Cheah, Seonah Kim, Jeffrey T. Miller, James R. Gallagher, Jesse Hensley, Joshua A. Schaidle and Daniel A. Ruddy, ACS Catal., 7(5), 3662-3667 (2017). [Online Article]
  4. Through-Space Ultrafast Photoinduced Electron Transfer Dynamics of a C70-Encapsulated Bisporphyrin Covalent Organic Polyhedron in a Low-Dielectric Medium, Michael Ortiz, Sung Cho, Jens Niklas, Seonah Kim, Oleg G. Poluektov, Wei Zhang, Garry Rumbles, Jaehong Park, JACS, 139. 4286-4289 (2017). [Online Article]
  5. Understanding Trends in Autoignition of Biofuels: Homologous Series of Oxygenated C5 Molecules, Lintao Bu, Peter N. Ciesielski, David J. Robichaud, Seonah Kim, Robert L. McCormick, Thomas D. Foust, and Mark R. Nimlos, J. Phys. Chem. A, 127, 121, 5475-5486 (2017). [Online Article]

2016

  1. Furan production from glycolaldehyde over HZSM-5, Seonah Kim, Tabitha J. Evans, Calvin Mukarakate, Lintao Bu, Gregg T. Beckham, Mark R. Nimlos, Robert S. Paton and David J. Robichaud, ACS Sustainable Chem. Eng., 4(5), 2615-2623 (2016). [Online Article]

2015

  1. Carbocation Stability in H-ZSM-5 at High Temperature, Glen A. Ferguson, Lei Cheng, Lintao Bu, Seonah Kim, David J. Robichaud, Mark R. Nimlos, Larry A. Curtiss, Gregg T. Beckham, J. Phys. Chem. A. 119, 11397-11405 (2015). [Online Article]
  2. Ethanol Dehydration in HZSM-5 studied by Density Functional Theory: Evidence for Concerted Process, Seonah Kim†, David J. Robichaud, Gregg T. Beckham, Robert S. Paton, and Mark R. Nimlos†, J. Phys. Chem. A 119 (15), 3604-3614 (2015). [Online Article]

2014

  1. A Mechanistic Investigation of Acid-Catalyzed Cleavage of Aryl-Ether Linkages: Implications for Lignin Depolymerization in Acidic Environments, Matthew R. Sturgeon*, Seonah Kim*, Kelsey Lawrence, Robert S. Paton, Stephen C. Chmely, Mark Nimlos, Thomas D. Foust, Gregg T. Beckham, ACS Sustainable Chem. Eng., 2, 472-485 (2014) (* denotes equal author contributions). [Online Article]
  2. Crystal structure of glycoside hydrolase family 127 β-l-arabinofuranosidase from Bifidobacterium longum, Tasuku Ito*, Kyo Saikawa*, Seonah Kim*, Kiyotaka Fujita, Akihiro Ishiwata, Sophon Kaeothip, Takatoshi Arakawa, Takyoshi Wakagi, Gregg T. Beckhame, Yukishige Ito, Shinya Fushinobu, Biochem. Biophys. Res. Commun. 447, 32-37 (2014) (* denotes equal author contributions). [Online Article]
  3. Quantum Mechanical Calculations suggest that Lytic Polysaccharide Monooxygenases employ a Copper-oxyl, Oxygen-rebound Mechanism, Seonah Kim, Mats Sandgren, Jerry Ståhlberg, Robert S. Paton, Gregg T. Beckham, PNAS 111, 149-154 (2014) [Online Article]
  4. Structural and electronic snapshots during the transition from a Cu(II) to Cu(I) metal center of a lytic polysaccharide monooxygenase by X-ray photo-reduction, Mikael Gudmundsson*, Seonah Kim*, Miao Wu*, Takuya Ishida, Majid Hadadd Momeni, Gustav Vaaje-Kolstad, Daniel Lundberg, Antoine Royant, Jerry Ståhlberg, Vincent G.H. Eijsink, Gregg T. Beckham, and Mats Sandgren, JBC 289, 18782-18792 (2014) (* denotes equal author contributions). [Online Article]

2013

  1. Aromatic Claisen Rearrangements of O-Phrenylated Tyrosine and Model Prenyl Aryl Ethers: Computational Study of the Role of Water on Acceleration of Claisen Rearrangements, Silvia Osuna, Seonah Kim, Guillaume Bollot, K. N. Houk, Eur. J. Org. Chem. 2823-2831 (2013). [Online Article]
  2. Crystal structure and computational characterization of the lytic polysaccharide monooxygenase GH61D from the basidiomycota fungus Phanerochaete chrysosporium, Miao Wu, Gregg T. Beckham, Anna M. Larsson, Takuya Ishida, Seonah Kim, Christina M. Payne, Michael E. Himmel, Michael F. Crowley, Svein J. Horn, Bjorge Westereng, Kiyohiko Igarashi, Masahiro Samejima, Jerry Stahlberg, Vincent G. H. Eijsink, Mats Sandgren, J. Biol. Chem. 288, 12828-12839 (2013). [Online Article]
  3. Diels-Alder Reactivities of Strained and Unstrained Cycloalkenes with Normal and Inverse-Electron-Demand Dienes: Activation Barriers and Distortion/Interaction Analysis, Fang Liu, Robert S. Paton, Seonah Kim, Yong Liang, K. N. Houk, JACS 135(41), 156442-15649 (2013). [Online Article]
  4. Mechanistic study of a Ru-xantphos catalyst for tandem alcohol dehydrogenation and reductive aryl-ether cleavage, Stephen C. Chmely*, Seonah Kim*, Peter N. Ciesielski, Gonzalo Jimenez-Oses, Robert S. Paton, Gregg T. Beckham, ACS Catal. 3, 963-974 (2013) (* denotes equal author contributions) [Online Article]

2012

  1. A Synthetic Recursive “+1” Pathway for Carbon Chain Elongation, Ryan J. Marcheschi, Han Li, Kechun Zhang, E.lizabeth L. Noey, Seonah Kim, Asha Chaubey, K. N. Houk, and James C. Liao, ACS Chem. Biol. 7, 689-697 (2012). [Online Article]

2011

  1. Computational Design of New Protein Catalysts, Gert Kiss, Scott A. Johnson, Geoffrey Nosrati, Nihan Celebi-Olcum, Seonah Kim, Robert S. Paton, K. N. Houk, Book Chapter for Modeling of Molecular Properties, Chapter 16, Wiley-VCH Verlag GmbH & Co. (2011). [Online Article]
  2. Computational Study of Bond Dissociation Enthalpies for a Large Range of Native and Modified Lignins, Seonah Kim, Stephen C. Chmely Mark R. Nimlos, Yannick J. Bomble, Thomas D. Foust, R. S. Paton, and Gregg T. Beckham, J. Phys. Chem. Lett. 2, 2846-2852 (2011). [Online Article]
  3. Experimental Diels-Alder Reactivities of Cycloalkenones and Cyclic Dienes Explained through Transition-State Distortion Energies, R. S. Paton, Seonah Kim, Audrey G. Ross, Samuel J. Danishefsky, and K. N. Houk, Angew. Chem. Int. Ed. 50, 10366-10368 (2011). [Online Article]
  4. Facilitation Scientific Discovery using Scientific Workflows on the Grid, Jianwu Wang, Prakashan Korambath, Seonah Kim, Scott A. Johnson, Kejian Jin, Daniel Crawl, Ilkay Atintas, Shava Smallen, Bill Labate, and K. N. Houk, Book Chapter for Guide to e-Science: Computer Communications and Networks, Part 4, 353-382 (2011) [Online Article]

2010

  1. Theoretical Enzyme Design using the Kepler Scientific Workflows on the Grid, Jianwu Wang, Prakashan Korambath, Seonah Kim, Scott A. Johnson, Kejian Jin, Daniel Crawl, Ilkay Atintas, Shava Smallen, Bill Labate, and K. N. Houk, Procedia Computer Science, 1, 1, 1175-1184, ICCS 2010 (2010). [Online Article]

2009

  1. Bad Seeds Sprout Perilous Dynamics: Stochastic Thermostat Induced Synchronization of Molecular Dynamics Trajectories in Biomolecules, Daniel J. Sindhikara, Seonah Kim, Art Voter, and Adrian E. Roitberg, J. Chem. Theory Chem. 5(6), 1624-1631 (2009). [Online Article]
  2. Crystal Structure Prediction (CSP) of Flexible Molecules using Parallel Genetic Algorithms with a Standard Force Field, Seonah Kim, Anita M. Orendt, Marta B. Ferraro, and Julio C. Facelli, J. Comput. Chem. 30, 1973-1985 (2009). [Online Article]
  3. Theoretical Studies of Short Polyproline Systems: Recalibration of a Molecular Ruler, Elena Dolghih, Wilfredo Ortiz, Seonah Kim, Brent P. Krueger, Jeffrey L. Krause, and Adrian E. Roitberg, J. Phys. Chem. A 113, 4639-4646 (2009). [Online Article]

2008

  1. Crystal Structure Prediction of Flexible Molecules with Genetic Algorithms and Standard Force Field, Julio C. Facelli, Seonah Kim, Anita M. Orendt, Marta B. Ferraro, Ian Pimienta and Victor Bazterra, Aca Cryst., A64, C226 (2008). [Online Article]
  2. Simulation Temperature Jumps for Protein Folding, Seonah Kim and Adrian Roitberg, J. Phys. Chem. B 112, 1525-1532 (2008). [Online Article]

Denotes corresponding author.