Publications

(Last Updated: 8/27/2025)

Google Scholar: https://goo.gl/ysuwAa

47. Submitted. ChemRxiv: 10.26434/chemrxiv-2025-jmzwn

Combining Geometry and Topology for Accurate Protein Solubility Prediction

Sabari N. Kumar, Olivia Harman, Su-min Song, Yeonjoon Kim, Robert S. Paton, Seonah Kim

46. In revision.

Cr-Promoted Pt@Fe2-xCrxO3 Hematite-Type Catalysts for Efficient Base-Free HMF Oxidation under Mild Conditions

Santhana Krishnan Perumal, Hyejin Yu, Hyeonsu Je, Hangil Lee*, Yeonjoon Kim*, Hyun Sung Kim* (* Co-corresponding authors)

45. J. Korean Chem. Soc. 2025, 69, 165.

Investigating Chemical Interpretability in Graph Neural Networks via Atom-wise Shapley Additive Explanations

Hyeonsu Je, JaeHun Kim, Yeonjoon Kim*

44. Chem. Eur. J. 2025, 31, e202500316.

Machine learning-based design of metallocene catalysts for controlled olefin copolymerization

Yongjun Kim*, Yeonjoon Kim*, Hyeonsu Kim, Sungwoo Kang, Jaewook Kim, Kyunghoon Lee, Wook Jeong, Won Jong Lee, Ho Ryu, Kyungwoo Kim, Woo Youn Kim (* Equal contribution)

43. Digital Discovery, 2025, 4, 1492.

Enhancing Predictive Models for Solubility in Multicomponent Solvent Systems using Semi-Supervised Graph Neural Networks

Hojin Jung, Christopher D. Stubbs, Sabari Kumar, Raúl Pérez-Soto, Su-min Song, Yeonjoon Kim*, Seonah Kim* (* Co-corresponding authors)

42. Bull. Korean Chem. Soc., 2025, 46, 526.

Dielectric Environment Effects on Rylene-based Organic Fluorophores: A Quantum Mechanical Study

Larissa Kupriyanova, Banyu Firdaus Soeriawidjaja, Juyoung Hwang, Myeongkee Park, Minseok Kwak*, Yeonjoon Kim* (* Co-corresponding authors)

41. ChemistryOpen, 2025, 14, e202500001.

One-Pot Gram-Scale Synthesis of Cynandione A and Detailed Mechanistic Insights into its Regioselectivity

Jun Sung Kang, Jin Yi Jung, Chan Jae Cho, Seoungwoo Kang, Yeonjoon Kim*, Jae Hyun Kim* (* Co-corresponding authors)

40. Digital Discovery, 2025, 4, 424.
Predicting homopolymer and copolymer solubility through machine learning

Christopher D. Stubbs, Yeonjoon Kim, Ethan C. Quinn, Raúl Pérez-Soto, Eugene Y.-X. Chen, Seonah Kim

39. J. Phys. Chem. A, 2024, 128, 8220.

High-Pressure Rate Rules for Ether Alkylperoxy Radical Isomerization

Samah Y. Mohamed, Yeonjoon Kim, Gina Fioroni, Seonah Kim, Robert L. McCormick

38. Green Chem. 2024, 26, 10247.

Designing Green Chemicals by Predicting Vaporization Properties Using Explainable Graph Attention Networks

Yeonjoon Kim*, Jaeyoung Cho*, Hojin Jung, Lydia E. Meyer, Gina M. Fioroni, Keunhong Jeong, Robert L. McCormick, Peter C. St. John, Seonah Kim  (* Equal contribution)

37. Small. 2024, 20, 2405559.

Unveiling Ru(bpy)32+-Encapsulated Zeolite Y as Photocatalyst: Harnessing Photocatalytic Singlet Oxygen Generation for Mustard Gas Simulant Detoxification

Sumin Kim, Yeonjoon Kim*, Hyun Sung Kim* (* Co-corresponding authors)

36. Proc. Combust. Inst., 2024, 40, 105669.

Sooting Tendency of Substituted Aromatic Oxygenates: The Role of Functional Groups and Positional Isomerism in Vanillin Isomers

Hojin Jung, Jaeyoung Cho, Yeonjoon Kim, Zhanhong Xiang, Sabari Kumar, Piper Barnard, Charles S. McEnally, Lisa D. Pfefferle, Seonah Kim

35. Combust. Flame, 2024, 267, 113568.

An Experimental and Chemical Kinetic Modeling Study of 4-Butoxyheptane Combustion

Sean P. Cooper, Nimal Naser, Tanusree Chatterjee, Yeonjoon Kim, Goutham Kukkadapu, Gina M. Fioroni, Seonah Kim, Olivier Mathieu, Eric L. Petersen, William J. Pitz, Robert McCormick

34. JACS Au, 2024, 4, 2246.

Simple and efficient enantioselective α-deuteration method of α-amino acids without external chiral sources

Soojun Park, Jae Hyun Kim, Dongjun Kim, Yeonjoon Kim, Seonah Kim, Sanghee Kim

33. ACS Appl. Mater. Interfaces, 2024, 16, 7353.

Synergistic Interaction between Ruthenium Catalysts and Grafted Niobium on SBA-15 for 2,5-Furandicarboxylic Acid Production using 5-Hydroxymethylfurfural

Santhana Krishnan Perumal, Sangyeob Lee, Hyejin Yu, Jaeseong Heo, Myung Jong Kang, Yeonjoon Kim, Myeongkee Park, Hangil Lee, Hyun Sung Kim

32. Chem. Sci. 2024, 15, 923.

Designing solvent systems using self-evolving solubility databases and graph neural networks

Yeonjoon Kim, Hojin Jung, Sabari Kumar, Robert S. Paton, Seonah Kim

31. Digital Discovery, 2023, 2, 1900.

Expansion of Bond Dissociation Prediction with Machine Learning to Medicinally and Environmentally Relevant Chemical Space

Shree Sowndarya S. V., Yeonjoon Kim, Seonah Kim, Peter C. St. John, Robert S. Paton

30. Combust. Flame, 2023, 258, 113071.

Effect of the β-hydroxy group on ester reactivity: combustion kinetics of methyl hexanoate and methyl 3-hydroxyhexanoate

Samah Y. Mohamed, Nimal Naser, Gina Fioroni, Jon Luecke, Yeonjoon Kim, Peter C. St. John, Robert McCormick, Seonah Kim

29. ACS Sustainable Chem. Eng., 2023, 11, 11912.

A Machine Learning Model for Predicting Composition of Catalytic Co-processing Products from Molecular Beam Mass Spectra

Mohammed A. Jabed*, Yeonjoon Kim*, Clark Yarbrough, Anne Harman-Ware, Jessica Olstad, Reinhard Seiser, Cheyenne Paeper, Anne Starace, Seonah Kim (* Equal contribution)

28. SAE Technical Paper No. 2023-32-0052.

Designing high-performance fuels through graph neural networks for predicting cetane number of multicomponent surrogate mixtures

Yeonjoon Kim*, Sabari Kumar*, Jaeyoung Cho, Nimal Naser, Wonjong Ko, Peter C. St. John, Robert L. McCormick, Seonah Kim (* Equal contribution)

27. Org. Biomol. Chem. 2023, 21, 1868.

Short and scalable synthesis of cynandione A

Seoungwoo Kang, Yeonjoon Kim, Seonah Kim, Ju Young Ko, Jae Hyun Kim

26. Proc. Combust. Inst. 2023, 39, 4939.

Enhancing φ-sensitivity of ignition delay times through dilution of fuel-air mixture

Jaeyoung Cho, Jon Luecke, Mohammad J Rahimi, Yeonjoon Kim, Bradley T Zigler, Seonah Kim

25. Proc. Combust. Inst. 2023, 39, 4969.

Physics-informed graph neural networks for predicting cetane number with systematic data quality analysis

Source code: https://github.com/BioE-KimLab/CNpred, Web-based prediction tool: https://cn.ml.nrel.gov

Yeonjoon Kim*, Jaeyoung Cho*, Nimal Naser, Sabari Kumar, Keunhong Jeong, Robert L. McCormick, Peter C. St. John, Seonah Kim (* Equal contribution)

24. Sustain. Energy Fuels, 2022, 6, 3975.

Bioderived ether design for low emission and high reactivity transport fuels

Jaeyoung Cho*, Yeonjoon Kim*, Brian D. Etz, Gina M. Fioroni, Nimal Naser, Junqing Zhu, Zhanhong Xiang, Cameron Hays, Juan V. Alegre-Requena, Peter C. St. John, Bradley Zigler, Charles McEnally, Lisa Pfefferle, Robert L. McCormick, Seonah Kim (* Equal contribution)

23. Chem. Eng. J., 2022, 446, 136965.

Toward rational design of supported vanadia catalysts of lignin conversion to phenol

Yeonjoon Kim, Mohammed A. Jabed, David M. Price, Dmitri Kilin, Seonah Kim

22. ACS Sustainable Chem. Eng., 2022, 10, 234.

Predicting Catalytic Pyrolysis Aromatic Selectivity from Pyrolysis Vapor Composition Using Mass Spectra Coupled with Statistical Analysis

Anne K. Starace, David D. Lee, Kristen T. Hietala, Yeonjoon Kim, Seonah Kim, Anne E. Harman-Ware, Daniel L. Carpenter

21. Proc. Combust. Inst., 2021, 38, 1143.

Investigation of structural effects of aromatic compounds on sooting tendency with mechanistic insight into ethylphenol isomers

Yeonjoon Kim*, Brian D. Etz*, Gina M. Fioroni, Cameron K. Hays, Peter C. St. John, Richard A. Messerly, Shubham Vyas, Brian P. Beekley, Facheng Guo, Charles S. McEnally, Lisa D. Pfefferle, Robert L. McCormick, Seonah Kim (* Equal contribution)

20. Combust. Flame, 2021, 225, 377.

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

19. ACS Catalysis, 2020, 10, 14707.

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, Seonah Kim (* Equal contribution)

18. Scientific Data, 2020, 7, 244.

Quantum chemical calculations for over 200,000 organic radical species and 40,000 associated closed-shell molecules

Peter C. St. John, Yanfei Guan, Yeonjoon Kim, Brian D. Etz, Seonah Kim, Robert S. Paton

17. J. Hazard. Mater., 2020, 400, 123198.

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 (* Equal contribution)

16. Nature Communications., 2020, 11, 2328.

Prediction of organic homolytic bond dissociation enthalpies at near chemical accuracy with sub-second computational cost

Peter C. St. John, Yanfei Guan, Yeonjoon Kim, Seonah Kim, Robert S. Paton

15. Chem. Eng. J., 2020, 382, 122912.

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, Yeonjoon Kim, Seonah Kim, Young-Kwon Park

14. ACS Sustainable Chem. Eng., 2020, 8, 2652.

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 M. Baldwin, Kimberly A. Magrini

13. Phys. Chem. Chem. Phys., 2020, 22, 5057.

Graph theory-based reaction pathway searches and DFT calculations for the mechanism studies of free radical-initiated peptide sequencing mass spectrometry (FRIPS MS): a model gas-phase reaction of GGR tri-peptide

Jae-ung Lee*, Yeonjoon Kim*, Woo Youn Kim, Han Bin Oh (* Equal contribution)

12. Green Chem., 2020, 22, 2403.

Ga/ZSM-5 catalyst improves hydrocarbon yields and increases alkene selectivity during catalytic fast pyrolysis of biomass with co-fed hydrogen

Kristiina Iisa, Yeonjoon Kim, Kellene A. Orton, David J. Robichaud, Rui Katahira, Michael J. Watson, Evan C. Wegener, Mark R. Nimlos, Joshua A. Schaidle, Calvin Mukarakate, Seonah Kim

11. J. Phys. Chem. A, 2019, 123, 4796.

Performance of ACE-Reaction on 26 Organic Reactions for Fully Automated Reaction Network Construction and Microkinetic Analysis

Jin Woo Kim*, Yeonjoon Kim*, Kyung Yup Baek, Kyunghoon Lee, Woo Youn Kim (* Equal contribution)

10. Science Advances, 2018, 4, eaau1956.

Poly(amide-imide) materials for transparent and flexible displays

Sun Dal Kim, Byungyong Lee, Taejoon Byun, Im Sik Chung, Jongmin Park, Isaac Shin, Nam Young Ahn, Myungeun Seo, Yunho Lee, Yeonjoon Kim, Woo Youn Kim, Hyukyun Kwon, Hanul Moon, Seunghyup Yoo, Sang Youl Kim

9. Chem. Eur. J., 2018, 24, 12354.

Feasibility of activation energy prediction of gas-phase reactions via machine learning

Sunghwan Choi, Yeonjoon Kim, Jin Woo Kim, Zeehyo Kim, Woo Youn Kim

8. Phys. Chem. Chem. Phys., 2018, 20, 8185.

Efficient structural elucidation of microhydrated biomolecules through the interrogation of hydrogen bond networks

Yeonjoon Kim, Jaewook Kim, Kyung Yup Baek, Woo Youn Kim

7. Chem. Sci., 2018, 9, 825.

Efficient prediction of reaction paths through molecular graph and reaction network analysis

Yeonjoon Kim, Jin Woo Kim, Zeehyo Kim, Woo Youn Kim

The code has been released in the Amsterdam Density Functional (ADF) package - https://www.scm.com/doc/acerxn/index.html 

6. ChemCatChem, 2016, 8, 2450.

Enhancing the Activity of Platinum‐Based Nanocrystal Catalysts for Organic Synthesis through Electronic Structure Modification

Minjune Kim*, Yena Kim*, Yeonjoon Kim*, Yongmin Kwon, Kyungrok Ham, Woo Youn Kim, Sang Woo Han (* Equal contribution)

5. Carbon, 2016, 98, 404.

Computational searching for new stable graphyne structures and their electronic properties

Hahn Kim, Yeonjoon Kim, Jaewook Kim, Woo Youn Kim

4. Bull. Korean Chem. Soc., 2015, 36, 1769.
Universal Structure Conversion Method for Organic Molecules: From Atomic Connectivity to Three‐Dimensional Geometry

Yeonjoon Kim, Woo Youn Kim

The algorithm in this paper has been implemented in RDKit, an open-source cheminformatics library -

https://github.com/rdkit/rdkit/pull/5557

3. Org. Lett., 2014, 16, 5490.

Bicyclic bridgehead phosphoramidite (briphos) ligands with tunable π-acceptor ability and catalytic activity in the rhodium-catalyzed conjugate additions

Ansoo Lee, Seihwan Ahn, Kyungjun Kang, Min-Seob Seo, Yeonjoon Kim, Woo Youn Kim, Hyunwoo Kim

2. J. Chem. Theory Comput., 2014, 10, 2419.

Efficient basin-hopping sampling of reaction intermediates through molecular fragmentation and graph theory

Yeonjoon Kim, Sunghwan Choi, Woo Youn Kim

1. Chem. Commun., 2014, 50, 9454.

The facet-dependent enhanced catalytic activity of Pd nanocrystals

Minjune Kim*, Yeonjoon Kim*, Jong Wook Hong, Seihwan Ahn, Woo Youn Kim, Sang Woo Han (* Equal contribution)