| Year |
Citation |
Score |
| 2024 |
Kim I, Jeong D, Weisburn LP, Alexiu A, Van Voorhis T, Rhee YM, Son WJ, Kim HJ, Yim J, Kim S, Cho Y, Jang I, Lee S, Kim DS. Very-Large-Scale GPU-Accelerated Nuclear Gradient of Time-Dependent Density Functional Theory with Tamm-Dancoff Approximation and Range-Separated Hybrid Functionals. Journal of Chemical Theory and Computation. PMID 39373529 DOI: 10.1021/acs.jctc.4c01003 |
0.618 |
|
| 2024 |
Kim K, Lim S, Shin K, Lee G, Jung Y, Kyoung W, Rhee JK, Rhee YM. Variational quantum eigensolver for closed-shell molecules with non-bosonic corrections. Physical Chemistry Chemical Physics : Pccp. PMID 38406868 DOI: 10.1039/d3cp05570a |
0.515 |
|
| 2021 |
Cho KH, Rhee YM. Computational elucidations on the role of vibrations in energy transfer processes of photosynthetic complexes. Physical Chemistry Chemical Physics : Pccp. PMID 34842245 DOI: 10.1039/d1cp04615b |
0.346 |
|
| 2021 |
Brumboiu IE, Rehn DR, Dreuw A, Rhee YM, Norman P. Analytical gradients for core-excited states in the algebraic diagrammatic construction (ADC) framework. The Journal of Chemical Physics. 155: 044106. PMID 34340367 DOI: 10.1063/5.0058221 |
0.484 |
|
| 2021 |
Ki H, Jo J, Kim Y, Kim TW, Kim C, Kim Y, Kim CW, Muniyappan S, Lee SJ, Kim Y, Kim HM, Yang Y, Rhee YM, Ihee H. Uncovering the Conformational Distribution of a Small Protein with Nanoparticle-Aided Cryo-Electron Microscopy Sampling. The Journal of Physical Chemistry Letters. 6565-6573. PMID 34251825 DOI: 10.1021/acs.jpclett.1c01277 |
0.472 |
|
| 2021 |
Park J, Cho M, Rhee YM, Jung Y. Theoretical Study on the Degree of CO Activation in CO-Coordinated Ni(0) Complexes. Acs Omega. 6: 7646-7654. PMID 33778275 DOI: 10.1021/acsomega.0c06257 |
0.415 |
|
| 2020 |
Mroginski MA, Adam S, Amoyal GS, Barnoy A, Bondar AN, Borin V, Church JR, Domratcheva T, Ensing B, Fanelli F, Ferré N, Filiba O, Pedraza-González L, González R, González-Espinoza CE, ... ... Rhee YM, et al. Frontiers in Multiscale Modelling of Photoreceptor Proteins. Photochemistry and Photobiology. PMID 33369749 DOI: 10.1111/php.13372 |
0.463 |
|
| 2020 |
Kim HW, Rhee YM. Two-oscillator mapping modification of the Poisson bracket mapping equation formulation of the quantum-classical Liouville equation. The Journal of Chemical Physics. 153: 214103. PMID 33291890 DOI: 10.1063/5.0027799 |
0.41 |
|
| 2020 |
Oh I, Lee H, Kim TW, Kim CW, Jun S, Kim C, Choi EH, Rhee YM, Kim J, Jang WD, Ihee H. Enhancement of Energy Transfer Efficiency with Structural Control of Multichromophore Light-Harvesting Assembly. Advanced Science (Weinheim, Baden-Wurttemberg, Germany). 7: 2001623. PMID 33101863 DOI: 10.1002/Advs.202001623 |
0.553 |
|
| 2020 |
Kim CW, Rhee YM. Toward monitoring the dissipative vibrational energy flows in open quantum systems by mixed quantum-classical simulations. The Journal of Chemical Physics. 152: 244109. PMID 32610983 DOI: 10.1063/5.0009867 |
0.571 |
|
| 2020 |
Kim TW, Lee SJ, Jo J, Kim JG, Ki H, Kim CW, Cho KH, Choi J, Lee JH, Wulff M, Rhee YM, Ihee H. Protein folding from heterogeneous unfolded state revealed by time-resolved X-ray solution scattering. Proceedings of the National Academy of Sciences of the United States of America. PMID 32541047 DOI: 10.1073/Pnas.1913442117 |
0.586 |
|
| 2020 |
Chung S, Choi SM, Lee W, Cho KH, Rhee YM. Free energy level correction by Monte Carlo resampling with weighted histogram analysis method Chinese Journal of Chemical Physics. 33: 183-195. DOI: 10.1063/1674-0068/Cjcp2001001 |
0.407 |
|
| 2019 |
Kim I, Jeon SO, Jeong D, Choi H, Son WJ, Kim D, Rhee YM, Lee HS. Spin-Vibronic Model for Quantitative Prediction of Reverse Inter-System Crossing Rate in Thermally Activated Delayed Fluorescence Systems. Journal of Chemical Theory and Computation. PMID 31841330 DOI: 10.1021/Acs.Jctc.9B01014 |
0.302 |
|
| 2019 |
Cho KH, Chung S, Rhee YM. Efficiently transplanting potential energy interpolation database between two systems: bacteriochlorophyll case with FMO and LH2 complexes. Journal of Chemical Information and Modeling. PMID 31487163 DOI: 10.1021/Acs.Jcim.9B00472 |
0.451 |
|
| 2019 |
Kim CW, Lee WG, Kim I, Rhee YM. Effect of Underdamped Vibration on Excitation Energy Transfer: Direct Comparison between Two Different Partitioning Schemes. The Journal of Physical Chemistry. A. PMID 30620598 DOI: 10.1021/Acs.Jpca.8B10977 |
0.526 |
|
| 2018 |
Lee W, Kim I, Rhee YM. A proton transfer network that generates deprotonated tyrosine is a key to producing reactive oxygen species in phototoxic KillerRed protein. Physical Chemistry Chemical Physics : Pccp. PMID 30128469 DOI: 10.1039/C8Cp02939C |
0.349 |
|
| 2018 |
Kim HW, Rhee YM, Shin SK. Charge-dipole interactions in G-quadruplex thrombin-binding aptamer. Physical Chemistry Chemical Physics : Pccp. PMID 30074033 DOI: 10.1039/C8Cp03050B |
0.404 |
|
| 2017 |
Kim CW, Choi B, Rhee YM. Excited state energy fluctuations in the Fenna-Matthews-Olson complex from molecular dynamics simulations with interpolated chromophore potentials. Physical Chemistry Chemical Physics : Pccp. PMID 29186231 DOI: 10.1039/C7Cp06303B |
0.592 |
|
| 2017 |
Heo W, Uddin N, Park JW, Rhee YM, Choi CH, Joo T. Coherent intermolecular proton transfer in the acid-base reaction of excited state pyranine. Physical Chemistry Chemical Physics : Pccp. PMID 28692091 DOI: 10.1039/C7Cp01944K |
0.378 |
|
| 2016 |
Kim CW, Rhee YM. Constructing an Interpolated Potential Energy Surface of a Large Molecule: A Case Study with Bacteriochlorophyll a Model in the Fenna-Matthews-Olson Complex. Journal of Chemical Theory and Computation. PMID 27760297 DOI: 10.1021/Acs.Jctc.6B00647 |
0.603 |
|
| 2016 |
Park JW, Rhee YM. Electric Field Keeps Chromophore Planar and Produces High Yield Fluorescence in GFP. Journal of the American Chemical Society. PMID 27662359 DOI: 10.1021/Jacs.6B06833 |
0.365 |
|
| 2016 |
Park JW, Rhee YM. Emission shaping in fluorescent proteins: role of electrostatics and π-stacking. Physical Chemistry Chemical Physics : Pccp. PMID 26771034 DOI: 10.1039/C5Cp07535A |
0.375 |
|
| 2016 |
Rhee YM, Park JW. Interpolation for molecular dynamics simulations: from ions in gas phase to proteins in solution International Journal of Quantum Chemistry. 116: 573-577. DOI: 10.1002/Qua.25064 |
0.442 |
|
| 2015 |
Kim CW, Park JW, Rhee YM. Effect of Chromophore Potential Model on the Description of Exciton-Phonon Interactions. The Journal of Physical Chemistry Letters. 6: 2875-80. PMID 26267173 DOI: 10.1021/Acs.Jpclett.5B01141 |
0.599 |
|
| 2015 |
Subotnik JE, Rhee YM. On surface hopping and time-reversal. The Journal of Physical Chemistry. A. 119: 990-5. PMID 25635926 DOI: 10.1021/Jp512024W |
0.562 |
|
| 2015 |
Shao Y, Gan Z, Epifanovsky E, Gilbert ATB, Wormit M, Kussmann J, Lange AW, Behn A, Deng J, Feng X, Ghosh D, Goldey M, Horn PR, Jacobson LD, Kaliman I, ... ... Rhee YM, et al. Advances in molecular quantum chemistry contained in the Q-Chem 4 program package Molecular Physics. 113: 184-215. DOI: 10.1080/00268976.2014.952696 |
0.699 |
|
| 2014 |
Park JW, Rhee YM. Diabatic Population Matrix Formalism for Performing Molecular Mechanics Style Simulations with Multiple Electronic States. Journal of Chemical Theory and Computation. 10: 5238-5253. PMID 26583208 DOI: 10.1021/Ct5006856 |
0.415 |
|
| 2014 |
Kim HW, Lee WG, Rhee YM. Improving long time behavior of Poisson bracket mapping equation: a mapping variable scaling approach. The Journal of Chemical Physics. 141: 124107. PMID 25273412 DOI: 10.1063/1.4895962 |
0.467 |
|
| 2014 |
Park JW, Rhee YM. Towards the realization of ab initio dynamics at the speed of molecular mechanics: simulations with interpolated diabatic Hamiltonian. Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry. 15: 3183-93. PMID 25080201 DOI: 10.1002/Cphc.201402226 |
0.428 |
|
| 2014 |
Kim HW, Rhee YM. Improving long time behavior of Poisson bracket mapping equation: a non-Hamiltonian approach. The Journal of Chemical Physics. 140: 184106. PMID 24832252 DOI: 10.1063/1.4874268 |
0.442 |
|
| 2014 |
Park JW, Rhee YM. Constructing polyatomic potential energy surfaces by interpolating diabatic Hamiltonian matrices with demonstration on green fluorescent protein chromophore. The Journal of Chemical Physics. 140: 164112. PMID 24784258 DOI: 10.1063/1.4872155 |
0.453 |
|
| 2014 |
Lee W, Rhee YM. Excitonic Energy Transfer of Cryptophyte Phycocyanin 645 Complex in Physiological Temperature by Reduced Hierarchical Equation of Motion Bulletin of the Korean Chemical Society. 35: 858-864. DOI: 10.5012/Bkcs.2014.35.3.858 |
0.41 |
|
| 2014 |
Kim HW, Rhee YM. Mixed Quantum-Classical Study of the Nonadiabatic Dynamics in Photosynthetic Systems Biophysical Journal. 106: 806a. DOI: 10.1016/J.Bpj.2013.11.4421 |
0.389 |
|
| 2014 |
Park JW, Rhee YM. Interpolation of Potential Energy Surfaces for Nonadiabatic Simulations of Biological Systems Biophysical Journal. 106: 806a. DOI: 10.1016/J.Bpj.2013.11.4420 |
0.476 |
|
| 2014 |
Choi SM, Sokkar P, Rhee YM. Simple Method for Hybrid All-Atom and Coarse-Grained Molecular Dynamics Simulations and Its Applications Biophysical Journal. 106: 413a. DOI: 10.1016/J.Bpj.2013.11.2322 |
0.399 |
|
| 2014 |
Park JW, Rhee YM. Cover Picture: Towards the Realization of Ab Initio Dynamics at the Speed of Molecular Mechanics: Simulations with Interpolated Diabatic Hamiltonian (ChemPhysChem 15/2014) Chemphyschem. 15: 3137-3137. DOI: 10.1002/Cphc.201490071 |
0.385 |
|
| 2013 |
Sokkar P, Choi SM, Rhee YM. Simple Method for Simulating the Mixture of Atomistic and Coarse-Grained Molecular Systems. Journal of Chemical Theory and Computation. 9: 3728-39. PMID 26584124 DOI: 10.1021/Ct400091A |
0.393 |
|
| 2013 |
Kim KT, Kim HW, Moon D, Rhee YM, Kim BH. (DNS)C: a fluorescent, environmentally sensitive cytidine derivative for the direct detection of GGG triad sequences. Organic & Biomolecular Chemistry. 11: 5605-14. PMID 23846401 DOI: 10.1039/C3Ob41222A |
0.386 |
|
| 2013 |
Kim HW, Rhee YM. On the pH dependent behavior of the firefly bioluminescence: protein dynamics and water content in the active pocket. The Journal of Physical Chemistry. B. 117: 7260-9. PMID 23758315 DOI: 10.1021/Jp4024553 |
0.479 |
|
| 2013 |
Jeong HS, Choi SM, Kim HW, Park JW, Park HN, Park SM, Jang SK, Rhee YM, Kim BH. Fluorescent peptide indicator displacement assay for monitoring interactions between RNA and RNA binding proteins. Molecular Biosystems. 9: 948-51. PMID 23255000 DOI: 10.1039/C2Mb25470K |
0.38 |
|
| 2012 |
Park JW, Rhee YM. Interpolated mechanics-molecular mechanics study of internal rotation dynamics of the chromophore unit in blue fluorescent protein and its variants. The Journal of Physical Chemistry. B. 116: 11137-47. PMID 22891786 DOI: 10.1021/Jp306257T |
0.411 |
|
| 2012 |
Kim HW, Kelly A, Park JW, Rhee YM. All-atom semiclassical dynamics study of quantum coherence in photosynthetic Fenna-Matthews-Olson complex. Journal of the American Chemical Society. 134: 11640-51. PMID 22708971 DOI: 10.1021/Ja303025Q |
0.472 |
|
| 2012 |
Woo Kim H, Rhee YM. Molecule-specific determination of atomic polarizabilities with the polarizable atomic multipole model. Journal of Computational Chemistry. 33: 1662-72. PMID 22565616 DOI: 10.1002/Jcc.22985 |
0.333 |
|
| 2012 |
Lee WG, Kelly A, Rhee YM. Behavior of poisson bracket mapping equation in studying excitation energy transfer dynamics of cryptophyte phycocyanin 645 complex Bulletin of the Korean Chemical Society. 33: 933-940. DOI: 10.5012/Bkcs.2012.33.3.933 |
0.401 |
|
| 2011 |
Park JW, Kim HW, Song CI, Rhee YM. Condensed phase molecular dynamics using interpolated potential energy surfaces with application to the resolvation process of coumarin 153. The Journal of Chemical Physics. 135: 014107. PMID 21744888 DOI: 10.1063/1.3605302 |
0.519 |
|
| 2011 |
Song CI, Rhee YM. Dynamics on the electronically excited state surface of the bioluminescent firefly luciferase-oxyluciferin system. Journal of the American Chemical Society. 133: 12040-9. PMID 21728350 DOI: 10.1021/Ja201752P |
0.434 |
|
| 2011 |
Kwon HJ, Kim HW, Rhee YM. On the mechanism of irreversible carbon dioxide binding with a frustrated lewis pair: solvent-assisted frustration and transition-state entropic encouragement. Chemistry (Weinheim An Der Bergstrasse, Germany). 17: 6501-7. PMID 21538604 DOI: 10.1002/Chem.201003483 |
0.453 |
|
| 2011 |
Kelly A, Rhee YM. Mixed quantum-classical description of excitation energy transfer in a model Fenna-Matthews-Olsen complex Journal of Physical Chemistry Letters. 2: 808-812. DOI: 10.1021/Jz200059T |
0.435 |
|
| 2011 |
Song CI, Rhee YM. Development of force field parameters for oxyluciferin on its electronic ground and excited states International Journal of Quantum Chemistry. 111: 4091-4105. DOI: 10.1002/Qua.22957 |
0.404 |
|
| 2009 |
Rhee YM, Casanova D, Head-Gordon M. Quartic-Scaling Analytical Gradient of Quasidegenerate Scaled Opposite Spin Second-Order Perturbation Corrections to Single Excitation Configuration Interaction. Journal of Chemical Theory and Computation. 5: 1224-36. PMID 26609713 DOI: 10.1021/Ct800509Z |
0.55 |
|
| 2009 |
Kim HW, Rhee YM. Dispersion-oriented soft interaction in a frustrated Lewis pair and the entropic encouragement effect in its formation. Chemistry (Weinheim An Der Bergstrasse, Germany). 15: 13348-55. PMID 19918822 DOI: 10.1002/Chem.200902322 |
0.424 |
|
| 2009 |
Rhee YM, 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. The Journal of Physical Chemistry. A. 113: 10564-76. PMID 19736963 DOI: 10.1021/Jp903659U |
0.522 |
|
| 2008 |
Casanova D, Rhee YM, Head-Gordon M. Quasidegenerate scaled opposite spin second order perturbation corrections to single excitation configuration interaction. The Journal of Chemical Physics. 128: 164106. PMID 18447420 DOI: 10.1063/1.2907724 |
0.508 |
|
| 2008 |
Rhee YM, 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. Journal of the American Chemical Society. 130: 3878-87. PMID 18314976 DOI: 10.1021/Ja0764916 |
0.429 |
|
| 2008 |
Rhee YM, Pande VS. Solvent viscosity dependence of the protein folding dynamics. The Journal of Physical Chemistry. B. 112: 6221-7. PMID 18229911 DOI: 10.1021/Jp076301D |
0.574 |
|
| 2007 |
Rhee YM, Head-Gordon M. Scaled second-order perturbation corrections to configuration interaction singles: efficient and reliable excitation energy methods. The Journal of Physical Chemistry. A. 111: 5314-26. PMID 17521172 DOI: 10.1021/Jp068409J |
0.484 |
|
| 2007 |
Rhee YM, Lee TJ, Gudipati MS, Allamandola LJ, Head-Gordon M. Charged polycyclic aromatic hydrocarbon clusters and the galactic extended red emission. Proceedings of the National Academy of Sciences of the United States of America. 104: 5274-8. PMID 17372209 DOI: 10.1073/Pnas.0609396104 |
0.447 |
|
| 2007 |
Distasio RA, Steele RP, Rhee YM, Shao Y, Head-Gordon M. An improved algorithm for analytical gradient evaluation in resolution-of-the-identity second-order Møller-Plesset perturbation theory: application to alanine tetrapeptide conformational analysis. Journal of Computational Chemistry. 28: 839-56. PMID 17219361 DOI: 10.1002/Jcc.20604 |
0.768 |
|
| 2006 |
Shao Y, Molnar LF, Jung Y, Kussmann J, Ochsenfeld C, Brown ST, Gilbert AT, Slipchenko LV, Levchenko SV, O'Neill DP, DiStasio RA, Lochan RC, Wang T, Beran GJ, Besley NA, ... ... Rhee YM, et al. Advances in methods and algorithms in a modern quantum chemistry program package. Physical Chemistry Chemical Physics : Pccp. 8: 3172-91. PMID 16902710 DOI: 10.1039/B517914A |
0.676 |
|
| 2006 |
Snow CD, Rhee YM, Pande VS. Kinetic definition of protein folding transition state ensembles and reaction coordinates. Biophysical Journal. 91: 14-24. PMID 16617068 DOI: 10.1529/Biophysj.105.075689 |
0.735 |
|
| 2006 |
Sorin EJ, Rhee YM, Shirts MR, Pande VS. The solvation interface is a determining factor in peptide conformational preferences. Journal of Molecular Biology. 356: 248-56. PMID 16364361 DOI: 10.1016/J.Jmb.2005.11.058 |
0.772 |
|
| 2006 |
Rhee YM, DiStasio RA, Lochan RC, Head-Gordon M. Analytical gradient of restricted second-order Møller-Plesset correlation energy with the resolution of the identity approximation, applied to the TCNE dimer anion complex Chemical Physics Letters. 426: 197-203. DOI: 10.1016/J.Cplett.2006.05.092 |
0.797 |
|
| 2006 |
Rhee YM, Pande VS. On the role of chemical detail in simulating protein folding kinetics Chemical Physics. 323: 66-77. DOI: 10.1016/J.Chemphys.2005.08.060 |
0.596 |
|
| 2005 |
Rhee YM, Pande VS. One-dimensional reaction coordinate and the corresponding potential of mean force from commitment probability distribution. The Journal of Physical Chemistry. B. 109: 6780-6. PMID 16851763 DOI: 10.1021/Jp045544S |
0.545 |
|
| 2005 |
Snow CD, Sorin EJ, Rhee YM, Pande VS. How well can simulation predict protein folding kinetics and thermodynamics? Annual Review of Biophysics and Biomolecular Structure. 34: 43-69. PMID 15869383 DOI: 10.1146/Annurev.Biophys.34.040204.144447 |
0.791 |
|
| 2005 |
Sorin EJ, Rhee YM, Pande VS. Does water play a structural role in the folding of small nucleic acids? Biophysical Journal. 88: 2516-24. PMID 15681648 DOI: 10.1529/Biophysj.104.055087 |
0.791 |
|
| 2005 |
Chong LT, Snow CD, Rhee YM, Pande VS. Dimerization of the p53 oligomerization domain: identification of a folding nucleus by molecular dynamics simulations. Journal of Molecular Biology. 345: 869-78. PMID 15588832 DOI: 10.1016/J.Jmb.2004.10.083 |
0.802 |
|
| 2004 |
Rhee YM, Sorin EJ, Jayachandran G, Lindahl E, Pande VS. Simulations of the role of water in the protein-folding mechanism. Proceedings of the National Academy of Sciences of the United States of America. 101: 6456-61. PMID 15090647 DOI: 10.1073/Pnas.0307898101 |
0.781 |
|
| 2004 |
Sorin EJ, Nakatani BJ, Rhee YM, Jayachandran G, Vishal V, Pande VS. Does native state topology determine the RNA folding mechanism? Journal of Molecular Biology. 337: 789-97. PMID 15033351 DOI: 10.1016/J.Jmb.2004.02.024 |
0.78 |
|
| 2003 |
Sorin EJ, Rhee YM, Nakatani BJ, Pande VS. Insights into nucleic acid conformational dynamics from massively parallel stochastic simulations. Biophysical Journal. 85: 790-803. PMID 12885628 DOI: 10.1016/S0006-3495(03)74520-2 |
0.798 |
|
| 2003 |
Pande VS, Baker I, Chapman J, Elmer SP, Khaliq S, Larson SM, Rhee YM, Shirts MR, Snow CD, Sorin EJ, Zagrovic B. Atomistic protein folding simulations on the submillisecond time scale using worldwide distributed computing. Biopolymers. 68: 91-109. PMID 12579582 DOI: 10.1002/Bip.10219 |
0.755 |
|
| 2003 |
Rhee YM, Pande VS. Multiplexed-replica exchange molecular dynamics method for protein folding simulation. Biophysical Journal. 84: 775-86. PMID 12547762 DOI: 10.1016/S0006-3495(03)74897-8 |
0.614 |
|
| 2000 |
Rhee YM. Construction of an accurate potential energy surface by interpolation with Cartesian weighting coordinates Journal of Chemical Physics. 113: 6021-6024. DOI: 10.1063/1.1315348 |
0.395 |
|
| 1998 |
Rhee YM, Kim MS. Dynamic isotope effect on the product energy partitioning in CH2OH+→CHO++H2 The Journal of Chemical Physics. 109: 5363-5371. DOI: 10.1063/1.477155 |
0.387 |
|
| 1997 |
Rhee YM, Kim MS. Mode-specific energy analysis for rotating-vibrating triatomic molecules in classical trajectory simulation The Journal of Chemical Physics. 107: 1394-1402. DOI: 10.1063/1.474493 |
0.363 |
|
| 1997 |
Rhee YM, Lee TG, Park SC, Kim MS. Potential energy surfaces for polyatomic reactions by interpolation with reaction path weight: CH2OH+→CHO++H2 reaction The Journal of Chemical Physics. 106: 1003-1012. DOI: 10.1063/1.473184 |
0.356 |
|
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