Publications

122 papers

2026(4)

  1. Minimization of Disorder as a Key Design Principle for Natural Sizes of Light Harvesting 2 Complexes

    K. H. Cho, S. J. Jang, Y. M. Rhee

    J. Phys. Chem. Lett. 17, 7028–7038 (2026) · Link

  2. Perspective of Fermi’s golden rule and its generalizations in chemical physics

    S. J. Jang, G. Kim, Y. M. Rhee

    J. Chem. Phys. 164, 230901 (2026) · Link

  3. Effect of Perturbative Vibronic Correction for Spin–Orbit Coupling in Hot Exciton OLED Systems

    H. Choi, S. W. Park, Y. M. Rhee

    J. Phys. Chem. A 130, 758–766 (2026) · Link

  4. Determining the Optimal Heparin Binding Domain Distance in VEGF165 Using Umbrella Sampling Simulations for Optimal Dimeric Aptamer Design

    J. S. Lee, Y. J. Go, Y. M. Rhee

    Int. J. Mol. Sci. 27, 712 (2026) · Link

2025(5)

  1. Hidden Effects of Anharmonic Bath on the Excitation Energy Transfer in the Light Harvesting 2 Complex of Purple Bacteria

    K. H. Cho, S. Jang, Y. M. Rhee

    J. Phys. Chem. Lett. 16, 10473–10482 (2025) · Link

  2. VeloxChem Quantum–Classical Interoperability for Modeling of Complex Molecular Systems

    J. A. de Gracia Triviño, I. E. Brumboiu, ..., Y. M. Rhee, ..., M. S. G. Ahlquist

    J. Phys. Chem. A 129, 7575–7587 (2025) · Link

  3. Influence of Spin-Dependent Polaron Pair Charge Recombination Rates on Singlet Exciton Yields of Fluorescent Organic Light-Emitting Diode Materials

    B. K. Min, J. K. Kang, J. W. Park, S. W. Park, ..., Y. M. Rhee

    J. Phys. Chem. A 129, 3445–3454 (2025) · Link

  4. Fermi’s Golden Rule Rate Expression for Transitions Due to Nonadiabatic Derivative Couplings in the Adiabatic Basis

    S. Jang, B. K. Min, Y. M. Rhee

    J. Chem. Theory Comput. 21, 1850–1864 (2025) · Link

  5. Conformational and vibrational contributions to configurational entropy change of a flexible peptide ligand upon binding: The role of higher-order correlations between backbone and side-chains

    M. Kalathingal, Y. M. Rhee

    Chem. Phys. Lett. 861, 141827 (2025) · Link

2024(8)

  1. Very-Large-Scale GPU-Accelerated Nuclear Gradient of Time-Dependent Density Functional Theory with Tamm–Dancoff Approximation and Range-Separated Hybrid Functionals

    I. Kim, ..., Y. M. Rhee, ..., H. Kim, ..., S. Kim, Y. Cho, ..., S. Lee, D. S. Kim

    J. Chem. Theory Comput. 20, 9018–9031 (2024) · Link

  2. Enhancing the electron pair approximation with measurements on trapped-ion quantum computers

    L. Zhao, Q. Wang, ..., Y. M. Rhee, K. Kim

    npj Quantum Inf. 10, 76 (2024) · Link

  3. Red Fluorescence from Organic Microdots: Leveraging Foldamer-Linked Azobenzene for Enhanced Stability and Intensity in Bioimaging Applications

    L. Zhang, ..., J. Lee, J. Kim, J. Lee, J. Park, ..., H. Kim, Y. M. Rhee, H. Lee, H. Lee

    Small 20, e2401480 (2024) · Link

  4. Dynamic embedding of effective harmonic normal mode vibrations in all-atomistic energy gap fluctuations: Case study of light harvesting 2 complex

    K. H. Cho, S. Jang, Y. M. Rhee

    J. Chem. Phys. 160, 184104 (2024) · Link

  5. Thermodynamic consequences of stapling side-chains on a peptide ligand using a lactam-bridge: A theoretical study on anti-angiogenic peptides targeting VEGF

    M. Kalathingal, Y. M. Rhee

    Proteins 92, 959–974 (2024) · Link

  6. An Ensemble Docking Approach for Analyzing and Designing Aptamer Heterodimers Targeting VEGF165

    Y. J. Go, M. Kalathingal, Y. M. Rhee

    Int. J. Mol. Sci. 25, 4066 (2024) · Link

  7. Potential energy interpolation with target-customized weighting coordinates: application to excited-state dynamics of photoactive yellow protein chromophore in water

    S. S. Kim, Y. M. Rhee

    Phys. Chem. Chem. Phys. 26, 9021–9036 (2024) · Link

  8. Variational quantum eigensolver for closed-shell molecules with non-bosonic corrections

    K. Kim, ..., G. Lee, ..., J. K. Rhee, Y. M. Rhee

    Phys. Chem. Chem. Phys. 26, 8390–8396 (2024) · Link

2023(9)

  1. Electron-Binding Dynamics of the Dipole-Bound State: Correlation Effect on the Autodetachment Dynamics

    D. H. Kang, K. H. Cho, J. Kim, H. J. Eun, Y. M. Rhee, S. K. Kim

    J. Am. Chem. Soc. 145, 25824–25833 (2023) · Link

  2. Effect of choosing coordinate systems on computationally predicting nonradiative transition rates of flexible thermally activated delayed fluorescence molecules

    B. K. Min, D. Kim, D. Kim, D. Kim, D. Kim, Y. M. Rhee

    Bull. Korean Chem. Soc. 44, 989–1003 (2023) · Link

  3. Overcoming the Limitation of Spin Statistics in Organic Light Emitting Diodes (OLEDs): Hot Exciton Mechanism and Its Characterization

    S. W. Park, D. Kim, Y. M. Rhee

    Int. J. Mol. Sci. 24, 12362 (2023) · Link

  4. Modified Fermi’s golden rule rate expressions

    S. Jang, Y. M. Rhee

    J. Chem. Phys. 159, 014101 (2023) · Link

  5. Orbital-optimized pair-correlated electron simulations on trapped-ion quantum computers

    L. Zhao, ..., J. K. Rhee, Y. M. Rhee, ..., J. Kim, S. Johri

    npj Quantum Inf. 9, 60 (2023) · Link

  6. Kohn–Sham time-dependent density functional theory with Tamm–Dancoff approximation on massively parallel GPUs

    I. Kim, ..., Y. M. Rhee, ..., H. Choi, ..., D. S. Kim

    npj Comput. Mater. 9, 81 (2023) · Link

  7. eChem: A Notebook Exploration of Quantum Chemistry

    T. Fransson, ..., I. E. Brumboiu, ..., Y. M. Rhee, P. Norman

    J. Chem. Educ. 100, 1664–1671 (2023) · Link

  8. Elucidating activation and deactivation dynamics of VEGFR-2 transmembrane domain with coarse-grained molecular dynamics simulations

    Y. J. Go, M. Kalathingal, Y. M. Rhee

    PLoS ONE 18, e0281781 (2023) · Link

  9. Molecular mechanism of binding between a therapeutic RNA aptamer and its protein target VEGF: A molecular dynamics study

    M. Kalathingal, Y. M. Rhee

    J. Comput. Chem. 44, 1129–1137 (2023) · Link

2022(3)

  1. Mechanism of Ir(ppy)3 Guest Exciton Formation with the Exciplex-Forming TCTA:TPBI Cohost within a Phosphorescent Organic Light-Emitting Diode Environment

    J. W. Park, K. H. Cho, Y. M. Rhee

    Int. J. Mol. Sci. 23, 5940 (2022) · Link

  2. Nearly 100% Exciton Utilization via Hybridized Inter- and Intramolecular Triplet Exciton Harvesting Channels in Blue Fluorescent Organic Light-Emitting Diodes

    H. Lee, ..., B. K. Min, Y. M. Rhee, Y. K. Kim, T. Kim, J. Y. Lee

    Adv. Opt. Mater. 10, 2200256 (2022) · Link

  3. Two-dimensional electronic spectrum simulation of simple photosynthetic complex models with semi-classical Poisson bracket mapping equation

    H. W. Kim, Y. M. Rhee

    Bull. Korean Chem. Soc. 43, 355–363 (2022) · Link

2021(10)

  1. Analytical gradients for core-excited states in the algebraic diagrammatic construction (ADC) framework

    I. E. Brumboiu, D. R. Rehn, A. Dreuw, Y. M. Rhee, P. Norman

    J. Chem. Phys. 155, 044106 (2021) · Link

  2. Uncovering the Conformational Distribution of a Small Protein with Nanoparticle-Aided Cryo-Electron Microscopy Sampling

    H. Ki, ..., Y. Kim, T. W. Kim, C. Kim, Y. Kim, C. W. Kim, ..., S. J. Lee, Y. Kim, H. M. Kim, ..., Y. M. Rhee, H. Ihee

    J. Phys. Chem. Lett. 12, 6565–6573 (2021) · Link

  3. Three States Involving Vibronic Resonance is a Key to Enhancing Reverse Intersystem Crossing Dynamics of an Organoboron-Based Ultrapure Blue Emitter

    I. Kim, K. H. Cho, ..., D. Kim, Y. M. Rhee, ..., H. Choi, D. S. Kim

    JACS Au 1, 987–997 (2021) · Link

  4. Cooperation between Excitation Energy Transfer and Antisynchronously Coupled Vibrations

    K. H. Cho, Y. M. Rhee

    J. Phys. Chem. B 125, 5601–5610 (2021) · Link

  5. Theoretical Study on the Degree of CO Activation in CO-Coordinated Ni(0) Complexes

    J. Park, M. A. Cho, Y. M. Rhee, Y. Jung

    ACS Omega 6, 7646–7654 (2021) · Link

  6. Excited State Proton Transfer of Quinone Cyanine 9: Implications on the Origin of Super-Photoacidity

    C. Lee, S. Chung, H. Song, Y. M. Rhee, E. Lee, T. Joo

    ChemPhotoChem 5, 186 (2021) · Link

  7. Computational elucidations on the role of vibrations in energy transfer processes of photosynthetic complexes

    K. H. Cho, Y. M. Rhee

    Phys. Chem. Chem. Phys. 23, 26623–26639 (2021) · Link

  8. Considering both small and large scale motions of vascular endothelial growth factor (VEGF) is crucial for reliably predicting its binding affinities to DNA aptamers

    W. Lee, J. W. Park, Y. J. Go, W. J. Kim, Y. M. Rhee

    RSC Adv. 11, 9315–9326 (2021) · Link

  9. Frontiers in Multiscale Modeling of Photoreceptor Proteins

    M. A. Mroginski, ..., S. S. Kim, ..., Y. M. Rhee, ..., I. Schapiro

    Photochem. Photobiol. 97, 243–269 (2021) · Link

  10. Excited State Proton Transfer of Quinone Cyanine 9: Implications on the Origin of Super-Photoacidity

    C. Lee, S. Chung, H. Song, Y. M. Rhee, E. Lee, T. Joo

    ChemPhotoChem 5, 245–252 (2021) · Link

2020(7)

  1. Two-oscillator mapping modification of the Poisson bracket mapping equation formulation of the quantum–classical Liouville equation

    H. W. Kim, Y. M. Rhee

    J. Chem. Phys. 153, 214103 (2020) · Link

  2. Effect of Perturbative Vibronic Correction for Weak Fluorescence in Thermally Activated Delayed Fluorescence Systems

    S. W. Park, J. H. Yang, H. Choi, Y. M. Rhee, D. Kim

    J. Phys. Chem. A 124, 10384–10392 (2020) · Link

  3. Enhancement of Energy Transfer Efficiency with Structural Control of Multichromophore Light-Harvesting Assembly

    I. Oh, H. Lee, T. W. Kim, C. W. Kim, ..., C. Kim, E. H. Choi, Y. M. Rhee, J. Kim, ..., H. Ihee

    Adv. Sci. 7, 2001623 (2020) · Link

  4. Toward monitoring the dissipative vibrational energy flows in open quantum systems by mixed quantum–classical simulations

    C. W. Kim, Y. M. Rhee

    J. Chem. Phys. 152, 244109 (2020) · Link

  5. Protein folding from heterogeneous unfolded state revealed by time-resolved X-ray solution scattering

    T. W. Kim, S. J. Lee, ..., J. G. Kim, ..., C. W. Kim, K. H. Cho, J. Choi, J. H. Lee, ..., Y. M. Rhee, H. Ihee

    Proc. Natl. Acad. Sci. U.S.A. 117, 14996–15005 (2020) · Link

  6. Free energy level correction by Monte Carlo resampling with weighted histogram analysis method

    S. Chung, S. M. Choi, W. Lee, K. H. Cho, Y. M. Rhee

    Chin. J. Chem. Phys. 33, 183–195 (2020) · Link

  7. Spin–Vibronic Model for Quantitative Prediction of Reverse Intersystem Crossing Rate in Thermally Activated Delayed Fluorescence Systems

    I. Kim, ..., H. Choi, ..., D. Kim, Y. M. Rhee, H. S. Lee

    J. Chem. Theory Comput. 16, 621–632 (2020) · Link

2019(6)

  1. Efficiently Transplanting Potential Energy Interpolation Database between Two Systems: Bacteriochlorophyll Case with FMO and LH2 Complexes

    K. H. Cho, S. Chung, Y. M. Rhee

    J. Chem. Inf. Model. 59, 4228–4238 (2019) · Link

  2. Computational Photochemistry

    D. Jacquemin, L. Blancafort, Y. M. Rhee

    ChemPhotoChem 3, 664–665 (2019) · Link

  3. Modeling Charge Flux by Interpolating Atomic Partial Charges

    S. S. Kim, Y. M. Rhee

    J. Chem. Inf. Model. 59, 2837–2849 (2019) · Link

  4. Exploring the Possibility of Excited State Keto-Enolate Transformation of the Oxyluciferin-Luciferase Complex with QM/MM Free Energy Simulations

    S. Chung, S. M. Choi, Y. M. Rhee

    ChemPhotoChem 3, 804–813 (2019) · Link

  5. Quantum Chemistry for Studying Electronic Spectroscopy and Dynamics of Complex Molecular Systems

    H. W. Kim, K. Kim, S. W. Park, Y. M. Rhee

    Molecular Spectroscopy: A Quantum Chemistry Approach, Volume 1, Chapter 3 (2019) · Link

  6. Effect of Underdamped Vibration on Excitation Energy Transfer: Direct Comparison between Two Different Partitioning Schemes

    C. W. Kim, W. Lee, I. Kim, Y. M. Rhee

    J. Phys. Chem. A 123, 1186–1197 (2019) · Link

2018(3)

  1. A proton transfer network that generates deprotonated tyrosine is a key to producing reactive oxygen species in phototoxic KillerRed protein

    W. Lee, I. Kim, Y. M. Rhee

    Phys. Chem. Chem. Phys. 20, 22342–22350 (2018) · Link

  2. Charge–dipole interactions in G-quadruplex thrombin-binding aptamer

    H. W. Kim, Y. M. Rhee, S. K. Shin

    Phys. Chem. Chem. Phys. 20, 21068–21074 (2018) · Link

  3. Excited state energy fluctuations in the Fenna–Matthews–Olson complex from molecular dynamics simulations with interpolated chromophore potentials

    C. W. Kim, B. Choi, Y. M. Rhee

    Phys. Chem. Chem. Phys. 20, 3310–3319 (2018) · Link

2017(1)

  1. Coherent intermolecular proton transfer in the acid–base reaction of excited state pyranine

    W. Heo, N. Uddin, J. W. Park, Y. M. Rhee, C. H. Choi, T. Joo

    Phys. Chem. Chem. Phys. 19, 18243–18251 (2017) · Link

2016(5)

  1. Constructing an Interpolated Potential Energy Surface of a Large Molecule: A Case Study with Bacteriochlorophyll a Model in the Fenna–Matthews–Olson Complex

    C. W. Kim, Y. M. Rhee

    J. Chem. Theory Comput. 12, 5235–5246 (2016) · Link

  2. Electric Field Keeps Chromophore Planar and Produces High Yield Fluorescence in Green Fluorescent Protein

    J. W. Park, Y. M. Rhee

    J. Am. Chem. Soc. 138, 13619–13629 (2016) · Link

  3. How Does Solvation Affect the Binding of Hydrophilic Amino Saccharides to Cucurbit[7]uril with Exceptional Anomeric Selectivity?

    J. Wang, ..., Y. Kim, C. J. Lee, Y. M. Rhee, K. Kim

    Chem. Eur. J. 22, 15791–15799 (2016) · Link

  4. Emission shaping in fluorescent proteins: role of electrostatics and π-stacking

    J. W. Park, Y. M. Rhee

    Phys. Chem. Chem. Phys. 18, 3944–3955 (2016) · Link

  5. Interpolation for molecular dynamics simulations: from ions in gas phase to proteins in solution

    Y. M. Rhee, J. W. Park

    Int. J. Quantum Chem. 116, 573–577 (2016) · Link

2015(6)

  1. Effect of Chromophore Potential Model on the Description of Exciton–Phonon Interactions

    C. W. Kim, J. W. Park, Y. M. Rhee

    J. Phys. Chem. Lett. 6, 2875–2880 (2015) · Link

  2. Highly Sensitive and Selective Biosensors Based on Organic Transistors Functionalized with Cucurbit[6]uril Derivatives

    M. Jang, H. Kim, S. Lee, H. W. Kim, ..., Y. M. Rhee, ..., K. Kim, J. H. Oh

    Adv. Funct. Mater. 25, 4882–4888 (2015) · Link

  3. N-Heterocyclic Carbene Nitric Oxide Radicals

    J. Park, H. Song, Y. Kim, ..., Y. Kim, ..., S. Park, Y. M. Rhee, W. J. Kim, K. Kim, E. Lee

    J. Am. Chem. Soc. 137, 4642–4645 (2015) · Link

  4. On Surface Hopping and Time-Reversal

    J. E. Subotnik, Y. M. Rhee

    J. Phys. Chem. A 119, 990–995 (2015) · Link

  5. A structural remedy toward bright dipolar fluorophores in aqueous media

    S. Singha, D. Kim, ..., J. Y. Kim, ..., J. W. Park, Y. M. Rhee, T. Wang, K. H. Kim, ..., K. H. Ahn

    Chem. Sci. 6, 4335–4342 (2015) · Link

  6. Advances in molecular quantum chemistry contained in the Q-Chem 4 program package

    Y. Shao, ..., Y. M. Rhee, ..., J. Kim, J. Kim, ..., A. J. Sodt

    Mol. Phys. 113, 184–215 (2015) · Link

2014(8)

  1. Diabatic Population Matrix Formalism for Performing Molecular Mechanics Style Simulations with Multiple Electronic States

    J. W. Park, Y. M. Rhee

    J. Chem. Theory Comput. 10, 5238–5253 (2014) · Link

  2. Improving long time behavior of Poisson bracket mapping equation: A mapping variable scaling approach

    H. W. Kim, W. Lee, Y. M. Rhee

    J. Chem. Phys. 141, 124107 (2014) · Link

  3. Towards the Realization of Ab Initio Dynamics at the Speed of Molecular Mechanics: Simulations with Interpolated Diabatic Hamiltonian

    J. W. Park, Y. M. Rhee

    ChemPhysChem 15, 3183–3193 (2014) · Link

  4. Improving long time behavior of Poisson bracket mapping equation: A non-Hamiltonian approach

    H. W. Kim, Y. M. Rhee

    J. Chem. Phys. 140, 184106 (2014) · Link

  5. Poly-cyclodextrin and poly-paclitaxel nano-assembly for anticancer therapy

    R. Namgung, Y. M. Lee, J. Kim, ..., B. H. Lee, I. S. Kim, P. Sokkar, Y. M. Rhee, ..., W. J. Kim

    Nat. Commun. 5, 3702 (2014) · Link

  6. Constructing polyatomic potential energy surfaces by interpolating diabatic Hamiltonian matrices with demonstration on green fluorescent protein chromophore

    J. W. Park, Y. M. Rhee

    J. Chem. Phys. 140, 164112 (2014) · Link

  7. Excitonic Energy Transfer of Cryptophyte Phycocyanin 645 Complex in Physiological Temperature by Reduced Hierarchical Equation of Motion

    W. Lee, Y. M. Rhee

    Bull. Korean Chem. Soc. 35, 858–864 (2014) · Link

  8. Ground-State Elevation Approach To Suppress Side Reactions in Gold-Sensing Systems Based on Alkyne Activation

    H. Seo, ..., K. Lee, K. Kim, ..., Y. M. Rhee, K. H. Ahn

    Org. Lett. 16, 1374–1377 (2014) · Link

2013(5)

  1. Simple Method for Simulating the Mixture of Atomistic and Coarse-Grained Molecular Systems

    P. Sokkar, S. M. Choi, Y. M. Rhee

    J. Chem. Theory Comput. 9, 3728–3739 (2013) · Link

  2. On the pH Dependent Behavior of the Firefly Bioluminescence: Protein Dynamics and Water Content in the Active Pocket

    H. W. Kim, Y. M. Rhee

    J. Phys. Chem. B 117, 7260–7269 (2013) · Link

  3. DNSC: a fluorescent, environmentally sensitive cytidine derivative for the direct detection of GGG triad sequences

    K. T. Kim, H. W. Kim, D. Moon, Y. M. Rhee, B. H. Kim

    Org. Biomol. Chem. 11, 5605 (2013) · Link

  4. Fluorescent peptide indicator displacement assay for monitoring interactions between RNA and RNA binding proteins

    H. S. Jeong, S. M. Choi, H. W. Kim, J. W. Park, H. N. Park, S. Park, ..., Y. M. Rhee, B. H. Kim

    Mol. BioSyst. 9, 948–951 (2013) · Link

  5. Can Adenosine Triarsenate Role as an Energy Carrier?

    J. W. Park, Y. M. Rhee, M. S. Kim

    Bull. Korean Chem. Soc. 34, 361-362 (2013) · Link

2012(6)

  1. Phase Behavior and Conductivity of Sulfonated Block Copolymers Containing Heterocyclic Diazole-Based Ionic Liquids

    O. Kim, S. Y. Kim, H. Ahn, C. W. Kim, Y. M. Rhee, M. J. Park

    Macromolecules 45, 8702–8713 (2012) · Link

  2. Interpolated Mechanics–Molecular Mechanics Study of Internal Rotation Dynamics of the Chromophore Unit in Blue Fluorescent Protein and Its Variants

    J. W. Park, Y. M. Rhee

    J. Phys. Chem. B 116, 11137–11147 (2012) · Link

  3. All-Atom Semiclassical Dynamics Study of Quantum Coherence in Photosynthetic Fenna–Matthews–Olson Complex

    H. W. Kim, A. Kelly, J. W. Park, Y. M. Rhee

    J. Am. Chem. Soc. 134, 11640–11651 (2012) · Link

  4. Molecule-specific determination of atomic polarizabilities with the polarizable atomic multipole model

    H. W. Kim, Y. M. Rhee

    J. Comput. Chem. 33, 1662–1672 (2012) · Link

  5. Behavior of Poisson Bracket Mapping Equation in Studying Excitation Energy Transfer Dynamics of Cryptophyte Phycocyanin 645 Complex

    W. Lee, A. Kelly, Y. M. Rhee

    Bull. Korean Chem. Soc. 33, 933–940 (2012) · Link

  6. Studying Interfacial Reactions of Cholesterol Sulfate in an Unsaturated Phosphatidylglycerol Layer with Ozone Using Field Induced Droplet Ionization Mass Spectrometry

    J. Y. Ko, S. M. Choi, Y. M. Rhee, J. L. Beauchamp, H. I. Kim

    J. Am. Soc. Mass Spectrom. 23, 141–152 (2012) · Link

2011(7)

  1. Characterization of Vinylgold Intermediates: Gold-Mediated Cyclization of Acetylenic Amides

    O. Egorova, H. Seo, Y. Kim, D. Moon, Y. M. Rhee, K. H. Ahn

    Angew. Chem. Int. Ed. 50, 11446–11450 (2011) · Link

  2. Condensed phase molecular dynamics using interpolated potential energy surfaces with application to the resolvation process of coumarin 153

    J. W. Park, H. W. Kim, C. Song, Y. M. Rhee

    J. Chem. Phys. 135, 014107 (2011) · Link

  3. Dynamics on the Electronically Excited State Surface of the Bioluminescent Firefly Luciferase–Oxyluciferin System

    C. Song, Y. M. Rhee

    J. Am. Chem. Soc. 133, 12040–12049 (2011) · Link

  4. Density functional calculations of electronic structure and magnetic properties of the hydrocarbon K picene superconductor near the metal-insulator transition

    M. Kim, B. I. Min, G. Lee, H. J. Kwon, Y. M. Rhee, J. H. Shim

    Phys. Rev. B 83, 214510 (2011) · Link

  5. On the Mechanism of Irreversible Carbon Dioxide Binding with a Frustrated Lewis Pair: Solvent-Assisted Frustration and Transition-State Entropic Encouragement

    H. J. Kwon, H. W. Kim, Y. M. Rhee

    Chem. Eur. J. 17, 6501–6507 (2011) · Link

  6. Mixed Quantum-Classical Description of Excitation Energy Transfer in a Model Fenna−Matthews−Olsen Complex

    A. Kelly, Y. M. Rhee

    J. Phys. Chem. Lett. 2, 808–812 (2011) · Link

  7. Development of force field parameters for oxyluciferin on its electronic ground and excited states

    C. Song, Y. M. Rhee

    Int. J. Quantum Chem. 111, 4091–4105 (2011) · Link

2010(1)

  1. C-Symmetric Cage-like Receptors: Chiral Discrimination of α-Chiral Amines in a Confined Space

    S. Sambasivan, S. Kim, S. M. Choi, Y. M. Rhee, K. H. Ahn

    Org. Lett. 12, 4228–4231 (2010) · Link

2009(3)

  1. Dispersion-Oriented Soft Interaction in a Frustrated Lewis Pair and the Entropic Encouragement Effect in its Formation

    H. W. Kim, Y. M. Rhee

    Chem. Eur. J. 15, 13348–13355 (2009) · Link

  2. 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

    Y. M. Rhee, D. Casanova, M. Head-Gordon

    J. Phys. Chem. A 113, 10564–10576 (2009) · Link

  3. Quartic-Scaling Analytical Gradient of Quasidegenerate Scaled Opposite Spin Second-Order Perturbation Corrections to Single Excitation Configuration Interaction

    Y. M. Rhee, D. Casanova, M. Head-Gordon

    J. Chem. Theory Comput. 5, 1224–1236 (2009) · Link

2008(3)

  1. Quasidegenerate scaled opposite spin second order perturbation corrections to single excitation configuration interaction

    D. Casanova, Y. M. Rhee, M. Head-Gordon

    J. Chem. Phys. 128, 164106 (2008) · Link

  2. 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

    Y. M. Rhee, M. Head-Gordon

    J. Am. Chem. Soc. 130, 3878–3887 (2008) · Link

  3. Solvent Viscosity Dependence of the Protein Folding Dynamics

    Y. M. Rhee, V. S. Pande

    J. Phys. Chem. B 112, 6221–6227 (2008) · Link

2007(3)

  1. Scaled Second-Order Perturbation Corrections to Configuration Interaction Singles: Efficient and Reliable Excitation Energy Methods

    Y. M. Rhee, M. Head-Gordon

    J. Phys. Chem. A 111, 5314–5326 (2007) · Link

  2. Charged polycyclic aromatic hydrocarbon clusters and the galactic extended red emission

    Y. M. Rhee, T. J. Lee, M. S. Gudipati, L. J. Allamandola, M. Head-Gordon

    Proc. Natl. Acad. Sci. U.S.A. 104, 5274–5278 (2007) · Link

  3. An improved algorithm for analytical gradient evaluation in resolution-of-the-identity second-order Møller-Plesset perturbation theory: Application to alanine tetrapeptide conformational analysis

    R. A. DiStasio, R. P. Steele, Y. M. Rhee, Y. Shao, M. Head-Gordon

    J. Comput. Chem. 28, 839–856 (2007) · Link

2006(5)

  1. Advances in methods and algorithms in a modern quantum chemistry program package

    Y. Shao, ..., T. Wang, ..., A. M. Lee, M. S. Lee, ..., Y. M. Rhee, ..., M. Head-Gordon

    Phys. Chem. Chem. Phys. 8, 3172-3191 (2006) · Link

  2. Analytical gradient of restricted second-order Møller–Plesset correlation energy with the resolution of the identity approximation, applied to the TCNE dimer anion complex

    Y. M. Rhee, R. A. DiStasio, R. C. Lochan, M. Head-Gordon

    Chem. Phys. Lett. 426, 197–203 (2006) · Link

  3. Kinetic Definition of Protein Folding Transition State Ensembles and Reaction Coordinates

    C. D. Snow, Y. M. Rhee, V. S. Pande

    Biophys. J. 91, 14–24 (2006) · Link

  4. The Solvation Interface is a Determining Factor in Peptide Conformational Preferences

    E. J. Sorin, Y. M. Rhee, M. R. Shirts, V. S. Pande

    J. Mol. Biol. 356, 248–256 (2006) · Link

  5. On the role of chemical detail in simulating protein folding kinetics

    Y. M. Rhee, V. S. Pande

    Chem. Phys. 323, 66–77 (2006) · Link

2005(4)

  1. Does Water Play a Structural Role in the Folding of Small Nucleic Acids?

    E. J. Sorin, Y. M. Rhee, V. S. Pande

    Biophys. J. 88, 2516–2524 (2005) · Link

  2. One-Dimensional Reaction Coordinate and the Corresponding Potential of Mean Force from Commitment Probability Distribution

    Y. M. Rhee, V. S. Pande

    J. Phys. Chem. B 109, 6780–6786 (2005) · Link

  3. Dimerization of the p53 Oligomerization Domain: Identification of a Folding Nucleus by Molecular Dynamics Simulations

    L. T. Chong, C. D. Snow, Y. M. Rhee, V. S. Pande

    J. Mol. Biol. 345, 869–878 (2005) · Link

  4. How Well Can Simulation Predict Protein Folding Kinetics and Thermodynamics?

    C. D. Snow, E. J. Sorin, Y. M. Rhee, V. S. Pande

    Annu. Rev. Biophys. Biomol. Struct. 34, 43–69 (2005) · Link

2004(2)

  1. Simulations of the role of water in the protein-folding mechanism

    Y. M. Rhee, E. J. Sorin, G. Jayachandran, E. Lindahl, V. S. Pande

    Proc. Natl. Acad. Sci. U.S.A. 101, 6456–6461 (2004) · Link

  2. Does Native State Topology Determine the RNA Folding Mechanism?

    E. J. Sorin, B. J. Nakatani, Y. M. Rhee, G. Jayachandran, V. Vishal, V. S. Pande

    J. Mol. Biol. 337, 789–797 (2004) · Link

2003(3)

  1. Insights into Nucleic Acid Conformational Dynamics from Massively Parallel Stochastic Simulations

    E. J. Sorin, Y. M. Rhee, B. J. Nakatani, V. S. Pande

    Biophys. J. 85, 790–803 (2003) · Link

  2. Multiplexed-Replica Exchange Molecular Dynamics Method for Protein Folding Simulation

    Y. M. Rhee, V. S. Pande

    Biophys. J. 84, 775–786 (2003) · Link

  3. Atomistic protein folding simulations on the submillisecond time scale using worldwide distributed computing

    V. S. Pande, ..., Y. M. Rhee, ..., B. Žagrović

    Biopolymers 68, 91–109 (2003) · Link

2000(1)

  1. Construction of an accurate potential energy surface by interpolation with Cartesian weighting coordinates

    Y. M. Rhee

    J. Chem. Phys. 113, 6021-6024 (2000) · Link

1998(1)

  1. Dynamic isotope effect on the product energy partitioning in CHOH+ → CHO+ + H

    Y. M. Rhee, M. S. Kim

    J. Chem. Phys. 109, 5363–5371 (1998) · Link

1997(3)

  1. Mode-specific energy analysis for rotating-vibrating triatomic molecules in classical trajectory simulation

    Y. M. Rhee, M. S. Kim

    J. Chem. Phys. 107, 1394–1402 (1997) · Link

  2. Potential energy surfaces for polyatomic reactions by interpolation with reaction path weight: CHOH+ → CHO+ + H reaction

    Y. M. Rhee, T. G. Lee, S. C. Park, M. S. Kim

    J. Chem. Phys. 106, 1003–1012 (1997) · Link

  3. Energy partitioning during the exit channel motion for CHOH+ → CHO+ + H

    T. G. Lee, Y. M. Rhee, M. S. Kim, S. C. Park

    Chem. Phys. Lett. 264, 303–308 (1997) · Link