Complete List of Publications

66. Kim, C.W.; Rhee, Y.M.* "Constructing an Interpolated Potential Energy Surface of a Large Molecule: A Case Study with Bacteriochlorophyll a Model in the Fenna-Matthews-Olson Complex," J. Chem. Theory Comput. 12, 5235 (2016).

65. Park, J.W.; Rhee, Y.M.* "Electric Field Keeps Chromophore Planar and Produces High Yield Fluorescence in GFP," J. Am. Chem. Soc. 138, 13619 (2016).

64. Wang, J.; Jang, Y.; Khedkar, J.K.; Koo, J.Y.; Kim, Y.; Lee, C.J.; Rhee, Y.M.*; Kim, K.* "How Does Solvation Affect the Binding of Hydrophilic Amino Saccharides to Cucurbit[7]uril with Exceptional Anomeric Selectivity?" Chem. Eur. J. 22, 15791 (2016).

63. Park, J.W.; Rhee, Y.M.* "Emission Shaping in Fluorescent Proteins: Role of Electrostatics and pi-Stacking," Phys. Chem. Chem. Phys. 18, 3944 (2016).

62. Rhee, Y.M.*; Park, J.W. "Interpolation for Molecular Dynamics Simulations: From Ions in Gas Phase to Proteins in Solution," Int. J. Quantum Chem. 116, 573 (2016).

61. Jang, M.; Kim, H.; Lee, S.; Kim, H.W.; Khedkar, J.K.; Rhee, Y.M.; Hwang, I.*; Kim, K.*; Oh, J.H.* "Highly Sensitive and Selective Biosensors Based on Organic Transistors Functionalized with Cucurbit[6]uril Derivatives," Adv. Funct. Mater. 25, 4882 (2015).

60. Kim, C.W.; Park, J.W.; Rhee, Y.M.* "Effect of Chromophore Potential Model on the Description of Exciton-Phonon Interactions," J. Phys. Chem. Lett. 6, 2875 (2015).

59. Singha, S.; Kim, D.; Roy, B.; Sambasivan, S.; Moon, H.; Rao, A.S.; Kim, J.Y.; Joo, T.*; Park, J.W.; Rhee, Y.M.*; Wang, T.; Kim, K.H.*; Shin, Y.H.; Jung, J.; Ahn, K.H.* "A structural remedy toward bright dipolar fluorophores in aqueous media," Chem. Sci. 6, 4335 (2015).

58. Park, J.; Song. H.; Kim, Y.; Eun, B.; Kim Y.; Bae, D.Y.; Park, S.; Rhee, Y.M.; Kim, W.J.; Kim, K.; Lee, E.* "N-Heterocyclic carbene nitric oxide radicals," J. Am. Chem. Soc. 137, 4642 (2015).

57. Subotnik, J.E.*; Rhee, Y.M. "On surface hopping and time-reversal," J. Phys. Chem. A 119, 990 (2015).

56. Shao, Y et al. "Advances in molecular quantum chemistry contained in the Q-Chem 4 program package," Mol. Phys. 113, 184 (2015).

55. Park, J.W.; Rhee, Y.M.* "Diabatic population matrix formalism for performing molecular mechanics style simulations with multiple electronic states," J. Chem. Theory Comput. 10, 5238 (2014).

54. Kim, H.W.; Lee, W.-G.; Rhee, Y.M.* "Improving long time behavior of Poisson bracket mapping equation: a mapping variable scaling approach," J. Chem. Phys. 141, 124107 (2014).

53. Park, J.W.; Rhee, Y.M.* "Towards the realization of ab initio dynamics at the speed of molecular mechanics: Simulations with interpolated diabatic Hamiltonian," ChemPhysChem 15, 3183 (2014).

52. Namgung, R.; Lee, Y.M.; Kim, J.; Jang, Y.; Lee, B.-H.; Kim, I.-S.; Sokkar, P.; Rhee, Y.M.; Hoffman, A.S.; Kim, W.J.* "Poly-cyclodextrin and poly-paclitaxel nano-assembly for anticancer therapy," Nat. Commun. 5, 3702 (2014).

51. Kim, H.W.; Rhee, Y.M.* "Improving long time behavior of Poisson bracket mapping equation: a non-Hamiltonian approach," J. Chem. Phys. 140, 184106 (2014).

50. Park, J.W.; Rhee, Y.M.* "Constructing polyatomic potential energy surfaces by interpolating diabatic Hamiltonian matrices with demonstration on green fluorescent protein chromophore," J. Chem. Phys. 140, 164112 (2014).

49. Seo, H.; Jun, M.E.; Ranganathan, K.; Lee, K.-H.; Kim, K.-T.; Lim, W.; Rhee, Y.M.; Ahn, K.H.* "Ground-State Elevation Approach to Suppress Side Reactions in Gold-Sensing Systems Based on Alkyne Activation," Org. Lett. 16, 1374 (2014).

48. Lee, W.-G.; Rhee, Y.M.* "Excitonic Energy Transfer of Cryptophyte Phycocyanin 645 Complex in Physiological Temperature by Reduced Hierarchical Equation of Motion," Bull. Kor. Chem. Soc. 35, 858 (2014).

47. Sokkar, P.; Choi, S.M.; Rhee, Y.M.* "Simple Method for Simulating the Mixture of Atomistic and Coarse-Grained Molecular Systems," J. Chem. Theory Comput. 9, 3728 (2013).

46. Kim, K.T.; Kim, H.W.; Moon, D.H.; Rhee, Y.M.; Kim, B.H.* "DNS C: A Fluorescent, Environmentally Sensitive Cytidine Derivative for the Direct Detection of GGG Triad Sequences," Org. Biomol. Chem. 11, 5605 (2013).

45. Kim, H.W.; Rhee, Y.M.* "On the pH Dependent Behavior of the Firefly Bioluminescence: Protein Dynamics and Water Content in the Active Pocket," J. Phys. Chem. B 117, 7260 (2013).

44. Jeong, H.S.; Choi, S.M.; Kim, H.W.; Park, J.W.; Park, H.N.; Park, S.M.; Jang, S.K.; Rhee, Y.M.; Kim, B.H.* "Fluorescent Peptide Indicator Displacement Assay for Monitoring Interactions Between RNA and RNA Binding Proteins," Mol. Biosyst. 9, 948 (2013).

43. Park, J.W.*; Rhee, Y.M.; Kim, M.S. "Can Adenosine Triarsenate Role as an Energy Carrier?" Bull. Kor. Chem. Soc. 34, 361 (2013).

42. Kim, O.; Kim, S.Y.; Ahn, H.; Kim, C.W.; Rhee, Y.M.; Park, M.J.* "Phase Behavior and Conductivity of Sulfonated Block Copolymers Containing Heterocyclic Diazole-Based Ionic Liquids," Macromolecules 45, 8702 (2012).

41. Park, J.W.; Rhee, Y.M.* "Interpolated Mechanics–Molecular Mechanics Study of Internal Rotation Dynamics of the Chromophore Unit in Blue Fluorescent Protein and Its Variants," J. Phys. Chem. B 116, 11137 (2012).

40. Kim, H.W.; Kelly, A.; Park, J.W.; Rhee, Y.M.* "All-Atom Semiclassical Dynamics Study of Quantum Coherence in Photosynthetic Fenna-Matthews-Olson Complex," J. Am. Chem. Soc. 134, 11640 (2012).

39. Kim, H.W.; Rhee, Y.M.* "Molecule-Specific Determination of Atomic Polarizabilities with the Polarizable Atomic Multipole Model," J. Comput. Chem. 33, 1662 (2012).

38. Lee, W.-G.; Kelly, A.; Rhee, Y.M.* "Behavior of Poisson Bracket Mapping Equation in Studying Excitation Energy Transfer Dynamics of Cryptophyte Phycocyanin 645 Complex," Bull. Kor. Chem. Soc. 33, 933 (2012).

37. Ko, J.Y.; Choi, S.M.; Rhee, Y.M; Beauchamp, J.L.; Kim, H.I.* "Studying interfacial reactions of cholesterol sulfate in an unsaturated phosphatidylglycerol layer with ozone using field induced droplet ionization mass spectrometry," J. Am. Soc. Mass Spect. 23, 141 (2012).

36. Egorova, O.A.; Seo, H.; Kim, Y.; Moon, D.; Rhee, Y.M.; Ahn, K.H.* "Characterization of Vinylgold Intermediates: Gold-Mediated Cyclization of Acetylenic Amides," Angew. Chem. Int. Ed. 50, 11446 (2011).

35. Song, C.-I.; Rhee, Y.M.* "Dynamics on the electronically excited state surface of the bioluminescent firefly luciferase-oxyluciferin system," J. Am. Chem. Soc. 133, 12040 (2011).

34. Park, J.W.; Kim, H.W.; Song, C.-I.; Rhee, Y.M.* "Condensed phase molecular dynamics using interpolated potential energy surfaces with application to the resolvation process of coumarin 153," J. Chem. Phys. 135, 014107 (2011).

33. Kim, M.J.; Min, B.I.*; Lee, G.; Kwon, H.J; Rhee, Y.M.; Shim, J.H.* "Density functional calculations of the electronic structure and magnetic properties of the hydrocarbon K3picene superconductor near the metal-insulator transition," Phys. Rev. B 83, 214510 (2011).

32. Kelly, A.; Rhee, Y.M.* "Mixed Quantum-Classical Description of Excitation Energy Transfer in a Model Fenna-Matthews-Olsen Complex," J. Phys. Chem. Lett. 2, 808 (2011).

31. Kwon, H.J.; Kim, H.W.; Rhee, Y.M.* "On the Mechanism of Irreversible Carbon Dioxide Binding with a Frustrated Lewis Pair: Solvent-assisted Frustration and Transition State Entropic Encouragement," Chem. Eur. J. 17, 6501 (2011).

30. Song, C.-I.; Rhee, Y.M.* "Development of Force Field Parameters for Oxyluciferin on its Electronic Ground and Excited States," Int. J. Quantum Chem. 111, 4091 (2011).

29. Sambasivan, S.; Kim, S.-G.; Choi, S.M.; Rhee, Y.M.; Ahn, K.H.* "C3-symmetric Cage-like Receptors: Chiral Discrimination of alpha-Chiral Amines in a Confined Space," Org. Lett. 12, 4228 (2010).

28. Kim, H.W.; Rhee, Y.M.* "Dispersion-Oriented Soft Interaction in a Frustrated Lewis Pair and the Entropic Encouragement Effect in its Formation," Chem. Eur. J. 15, 13348 (2009).

Post-doctoral Publications (UC Berkeley)

27. Rhee, Y.M.; Casanova, D.; Head-Gordon, M.* "Performance of Quasi-Degenerate Scaled Opposite Spin Perturbation Corrections to Single Excitation Configuration Interaction for Excited State Structures and Excitation Energies with Application to the Stokes Shift of 9-Methyl-9,10-dihydro-9-silaphenanthrene," J. Phys. Chem. A 113, 10564 (2009).

26. Rhee, Y.M.; Casanova, D.; Head-Gordon, M.* "Quartic-scaling analytical gradient of quasidegenerate scaled opposite spin second-order perturbation corrections to single excitation configuration interaction," J. Chem. Theory Comput. 5, 1224 (2009).

25. Casanova, D.; Rhee, Y.M.; Head-Gordon, M. "Quasidegenerate scaled opposite spin second order perturbation corrections to single excitation configuration interaction," J. Chem. Phys. 128, 164106 (2008).

24. Rhee, Y.M.; Head-Gordon, M. "A delicate electronic balance between metal and ligand in [Cu-P-Cu-P] diamondoids: Oxidation state dependent plasticity and the formation of a singlet diradicaloid," J. Am. Chem. Soc. 130, 3878 (2008).

23. Rhee, Y.M.; Head-Gordon, M. "Scaled second-order perturbation corrections to configuration interaction singles: Efficient and reliable excitation energy methods," J. Phys. Chem. A 111, 5314 (2007).

22. Rhee, Y.M.; Lee, T.J.; Gudipati, M.S.; Allamandola, L.J.; Head-Gordon, M. "Charged polycyclic aromatic hydrocarbon clusters and the galactic extended red emission," Proc. Natl. Acad. Sci. USA 104, 5274 (2007).

21. Distasio Jr., R.A.; Steele, R.P.; Rhee, Y.M.; Shao, Y.H.; Head-Gordon, M. "An improved algorithm for analytical gradient evaluation in resolution-of-the-identity second-order Moller-Plesset perturbation theory: Application to alanine tetrapeptide conformational analysis," J. Comput. Chem. 28, 839 (2007).

20. Shao, Y; Molnar, L.F.; Jung, Y.; Kussmann, J.; Ochsenfeld, C.; Brown, S.T.; Gilbert, A.T.B.; Slipchenko, L.V.; Levchenko, S.V.; O'Neill, D.P.; DiStasio Jr., R.A.; Lochan, R.C.; Wang, T.; Beran, G.J.O.; Besley, N.A.; Herbert, J.M.; Lin, C.Y.; Van Voorhis, T.; Chien, S.H.; Sodt, A.; Steele, R.P.; Rassolov, V.A.; Maslen, P.E.; Korambath, P.P.; Adamson, R.D.; Austin, B.; Baker, J.; Byrd, E.F.C.; Dachsel, H.; Doerksen, R.J.; Dreuw, A.; Dunietz, B.D.; Dutoi, A.D.; Furlani, T.R.; Gwaltney, S.R.; Heyden, A.; Hirata, S.; Hsu, C.P.; Kedziora, G.; Khalliulin, R.Z.; Klunzinger, P.; Lee, A.M.; Lee, M.S.; Liang, W.; Lotan, I.; Nair, N.; Peters, B.; Proynov, E.I.; Pieniazek, P.A.; Rhee, Y.M.; Ritchie, J.; Rosta, E.; Sherrill, C.D.; Simmonett, A.C.; Subotnik, J.E.; Woodcock, H.L.; Zhang, W.; Bell, A.T.; Chakraborty, A.K.; Chipman, D.M.; Keil, F.J.; Warshel, A.; Hehre, W.J.; Schaefer, H.F.; Kong, J.; Krylov, A.I.; Gill, P.M.W.; Head-Gordon, M. "Advances in methods and algorithms in a modern quantum chemistry program package," Phys. Chem. Chem. Phys. 8, 3172 (2006).

19. Rhee, Y.M.; DiStasio Jr., R.A.; Lochan, R.C.; Head-Gordon, M. "Analytical gradient of restricted second-order Moller-Plesset correlation energy with the resolution of the identity approximation, applied to the TCNE dimer anion complex," Chem. Phys. Lett. 426, 197 (2006).

Graduate School Publications (Stanford and SNU)

18. Rhee, Y.M.; Pande, V.S. "Solvent viscosity dependence of the protein folding dynamics," J. Phys. Chem. B 112, 6221 (2008).

17. Snow, C.D.; Rhee, Y.M.; Pande, V.S. "Kinetic definition of protein folding transition state ensembles and reaction coordinates," Biophys. J. 91, 14 (2006).

16. Rhee, Y.M.; Pande, V.S. "On the role of chemical detail in simulating protein folding kinetics," Chem. Phys. 323, 66 (2006).

15. Sorin, E.J.; Rhee, Y.M.; Shirts, M.R.; Pande, V.S. "The solvation interface is a determining factor in peptide conformational preferences," J. Mol. Biol. 356, 248 (2006).

14. Snow, C.D.; Sorin, E.J.; Rhee, Y.M.; Pande, V.S. "How well can simulation predict protein folding kinetics and thermodynamics?" Annu. Rev. Biophys. Biomol. Struct. 34 , 43 (2005).

13. Rhee, Y.M.; Pande, V.S. "One-dimensional reaction coordinate and the corresponding potential of mean force from commitment probability distribution," J. Phys. Chem. B 109, 6780 (2005).

12. Sorin, E.J.; Rhee, Y.M.; Pande, V.S. "Does water play a structural role in the folding of small nucleic acids?" Biophys. J. 88, 2516, (2005).

11. Chong, L.T.; Snow, C.D.; Rhee, Y.M.; Pande, V.S. "Dimerization of the p53 oligomerization domain: Identification of a folding nucleus by molecular dynamics simulations," J. Mol. Biol. 345, 869 (2005).

10. Rhee, Y.M.; Sorin, E.J.; Jayachandran, G.; Lindahl, E.; Pande, V.S. "Simulations of the role of water in the protein-folding mechanism," Proc. Natl. Acad. Sci. USA 101, 6456 (2004).

9. Sorin, E.J.; Nakatani, B.J.; Rhee, Y.M.; Jayachandran, G.; Vishal, V.; Pande, V.S. "Does native state topology determine the RNA folding mechanism?" J. Mol. Biol. 337, 789 (2004).

8. Sorin, E.J.; Rhee, Y.M.; Nakatani, B.J.; Pande, V.S. "Insights into nucleic acid conformational dynamics from massively parallel stochastic simulations," Biophys. J. 85, 790 (2003).

7. Rhee, Y.M.; Pande, V.S. "Multiplexed-replica exchange molecular dynamics method for protein folding simulation," Biophys. J. 84, 775 (2003).

6. Pande, V.S.; Baker, I.; Chapman, J.; Elmer, S.P.; Khaliq, S.; Larson, S.M.; Rhee, Y.M.; Shirts, M.R.; Snow, C.D.; Sorin, E.J.; Zagrovic, B. "Atomistic protein folding simulations on the submillisecond time scale using worldwide distributed computing," Biopolymers 68, 91 (2003).

5. Rhee, Y.M. "Construction of an accurate potential energy surface by interpolation with Cartesian weighting coordinates," J. Chem. Phys. 113, 6021 (2000).

4. Rhee, Y.M.; Kim, M.S. "Dynamic isotope effect on the product energy partitioning in CH2OH+ → CHO+ + H2," J. Chem. Phys. 109, 5363 (1998).

3. Rhee, Y.M.; Kim, M.S. "Mode-specific energy analysis for rotating-vibrating triatomic molecules in classical trajectory simulation," J. Chem. Phys. 107, 1394 (1997).

2. Lee, T.G.; Rhee, Y.M.; Kim, M.S.; Park, S.C. "Energy partitioning during the exit channel motion for CH2OH+ → CHO+ + H2," Chem. Phys. Lett. 264 303 (1997).

1. Rhee, Y.M.; Lee, T.G.; Park, S.C.; Kim, M.S. "Potential energy surfaces for polyatomic reactions by interpolation with reaction path weight: CH2OH+ → CHO+ + H2 reaction," J. Chem. Phys. 106, 1003 (1997).