Complete List of Publications


80. W. Ouyang and J. E. Subotnik. "The dynamics of charge transfer with and without a barrier: A very simplified model of cyclic voltammetry"
J. Chem. Phys. 146, 174103 (2017) [PDF]           link



79. W. Dou and J. E. Subotnik. "Universality of electronic friction: Equivalence of von Oppen's nonequilibrium Green's function approach and the Head-Gordon-Tully model at equilibrium "
Phys. Rev. B. 96, 104305 (2017) [PDF]           link



78. Tianyi Liu, Annemarie L. Exarhos, Ethan C. Alguire, Feng Gao, Elmira Salami-Ranjbaran, Kevin Cheng, Tiezheng Jia, Joseph E. Subotnik, Patrick J. Walsh, James M. Kikkawa, and Zahra Fakhraai "Birefringent Stable Glass with Predominantly Isotropic Molecular Orientation"
Phys. Rev. Lett. 119, 095502 (2017) [PDF]           link



77. W. Dou, G. Miao, and J. E. Subotnik. "Born-Oppenheimer Dynamics, Electronic Friction, and the Inclusion of Electron-Electron Interactions"
Phys. Rev. Lett. 119, 046001 (2017) [PDF]     [Supplementary Info]       link



76. Z. Jin and J. E. Subotnik. "Localized diabatization applied to excitons in molecular crystals"
J. Chem. Phys. 146, 244110 (2017) [PDF]       link



75. W. Dou and J. E. Subotnik. "A Generalized Surface Hopping Algorithm To Model Nonadiabatic Dynamics near Metal Surfaces: The Case of Multiple Electronic Orbitals"
J. Chem. Theor. Comp. 13, 2430-2439 (2017) [PDF]       link



74. G. Medders, E. Alguire, A. Jain, and J. E. Subotnik. "Ultrafast Electronic Relaxation through a Conical Intersection: Nonadiabatic Dynamics Disentangled through an Oscillator Strength-Based Diabatization Framework"
J. Phys. Chem. A 121, 1425-1434 (2017) [PDF]       link



73. D. B. Straus, S. H. Parra, N. Iotov, J. Gebhardt, A. M. Rappe, J. E. Subotnik, J. M. Kikkawa, and C. R. Kagan. "Direct Observation of Electron-Phonon Coupling and Slow Vibrational Relaxation in Organic- Inorganic Hybrid Perovskites"
JACS Comm. 138, 13798-13801 (2016) [PDF]       link



72. A. Jain, E. Alguire and J.E. Subotnik. "An Efficient, Augmented Surface Hopping Algorithm That Includes Decoherence for Use in Large-Scale Simulations"
J. Chem. Theor. Comp. 12, 5256-5268 (2016) [PDF]       link



71. W. Ouyang, W. Dou, A. Jain and J.E. Subotnik. "Dynamics of Barrier Crossings for the Generalized Anderson Holstein Model: Beyond Electronic Friction and Conventional Surface Hopping"
J. Chem. Theor. Comp. 12, 4178-4183 (2016) [PDF]       link



70. W. Dou and J.E. Subotnik. "A many-body states picture of electronic friction: The case of multiple orbitals and multiple electronic states."
J. Chem. Phys. 145, 054102 (2016) [PDF]       link



69. W. Dou and J.E. Subotnik. "Electronic friction near metal surfaces: a case where molecule-metal couplings depend on nuclear coordinates."
J. Chem. Phys. 146, 092304 (2016) [PDF]       link



68. Q. Ou and J.E. Subotnik. "Comparison between GW and Wave-Function-Based Approaches: Calculating the Ionization Potential and Electron Affinity for 1D Hubbard Chains."
J. Phys. Chem. A. 120, 4514-4525 (2016) [PDF]       link       TYPO's



67. J. E. Subotnik, A. Jain, B. Landry, A. Petit, W. Ouyang and N. Bellonzi "Understanding the Surface Hopping View of Electronic Transitions and Decoherence."
Annual Reviews of Physical Chemistry 67, 387-417 (2016)       link       !!       surprise


66. N. Bellonzi, A. Jain and J. E. Subotnik. "An assessment of mean-field mixed semiclassical approaches: equilibrium populations and algorithm stability"
J. Chem. Phys. 144, 154110 (2016) [PDF]       link


65. W. Dou, A. Nitzan, and J.E. Subotnik. "Molecular electronic states near metal surfaces at equilibrium using potential of mean force and numerical renormalization group methods: Hysteresis revisited."
J. Chem. Phys. 144, 074109 (2016) [PDF]       link


64. W. Dou and J.E. Subotnik. "A broadened classical master equation approach for nonadiabatic dynamics at metal surfaces: Beyond the weak molecule-metal coupling limit."
J. Chem. Phys. 144 024116 ( 2016) [PDF]       link



63. A. Jain and J.E. Subotnik. "Does nonadiabatic transition state theory make sense without decoherence?"
J. Phys. Chem. Lett. 6 4809-4814( 2015) [PDF]       link



62. A. Jain and J.E. Subotnik. "Surface hopping, transition state theory and decoherence 2: Thermal rate constants and detailed balance."
J. Chem. Phys. 143, 134107 (2015) [PDF]       link



61. A. Jain, M. F. Herman, W. Ouyang and J. E. Subotnik "Surface hopping, transition state theory and decoherence 1: Scattering theory and time-reversibility."
J. Chem. Phys. 143, 134106 (2015) [PDF]       link



60. W. Ouyang, J. Saven, and J. E. Subotnik. "A Surface Hopping View of Electrochemistry: Non-Equilibrium Electronic Transport through an Ionic Solution with a Classical Master Equation"
J. Phys. Chem. C. 119, 20833-20844 (2015) [PDF]       link



59. A.S. Petit and J.E. Subotnik. "Appraisal of Surface Hopping as a Tool for Modeling Condensed Phase Linear Absorption Spectra."
JCTC 11, 4328-4341 (2015) [PDF]       link



58. W. Dou, A. Nitzan, and J.E. Subotnik. "Frictional effects near a metal surfaces"
J. Chem. Phys. 143, 054103 (2015) [PDF]       link



57. W. Dou, A. Nitzan, and J.E. Subotnik. "Surface hopping with a manifold of electronic states. III. Transients, broadening, and the Marcus picture."
J. Chem. Phys. 142, 234106 (2015) [PDF]       link
ERRATUM:     [PDF]       link



56. J.E. Subotnik, E. C. Alguire, Q. Ou, B. R. Landry, and S. Fatehi. "The Requisite Electronic Structure Theory To Describe Photoexcited Nonadiabatic Dynamics: Nonadiabatic Derivative Couplings and Diabatic Electronic Couplings."
Acc. Chem. Res. 48 1340-1350 (2015) [PDF]       link



55. B. R. Landry and J. E. Subotnik. "Surface hopping outperforms secular Redfield theory when reorganization energies range from small to moderate (and nuclei are classical)."
J. Chem. Phys. 142, 104102 (2015) [PDF]       link



54. W. Dou, A. Nitzan, and J.E. Subotnik "Surface hopping with a manifold of electronic states. II. Application to the many- body Anderson-Holstein model "
J. Chem. Phys., 142, 084110 (2015) [PDF]       link



53. W. Ouyang, W. Dou, and J. E. Subotnik. "Surface hopping with a manifold of electronic states. I. Incorporating surface-leaking to capture lifetimes."
J. Chem. Phys., 142, 084109 (2015) [PDF]       link



52. Q. Ou, G. D. Bellchambers, F. Furche, and J. E. Subotnik. "First order derivative couplings between excited states from adiabatic TDDFT response theory."
J. Chem. Phys. 142, 064114 (2015) [PDF]       Link


51. J. E. Subotnik and Y. M. Rhee, "On Surface Hopping and Time-Reversal."
J. Phys. Chem. A.119, 990-995 (2015) PDF       Link


50. E. Alguire, J. E. Subotnik, N. Damrauer, " Exploring Non-Condon Effects in a Covalent Tetracene Dimer: How Important Are Vibrations in Determining the Electronic Coupling for Singlet Fission
J. Phys. Chem. A., 119, 299-311 (2015) PDF       link



49. B. Veldkamp, X. Liu, M. Wasielewski, J. E. Subotnik and M. A. Ratner, "Molecular Excited States: Accurate Calculation of Relative Energies and Electronic Coupling Between Charge Transfer and Non-Charge Transfer States"
J. Phys. Chem. A., 119, 253-262 (2015) PDF       link



48. Y. Shao, et al. "Advances in molecular quantum chemistry contained in the Q-Chem 4 program package"
Mol. Phys. 113, 184-215 (2015) [PDF]       link



47. A. S. Petit and J. E. Subotnik. "How to model time-dependent differential absorbance spectra with surface hopping trajectories: Applications to ultrafast pump-probe"
J. Chem. Phys 141, , 154108 (2014) [PDF]       link



46. B. R. Landry and J. E. Subotnik. "Quantifying the Lifetime of Triplet Energy Transfer Processes in Organic Chromophores: A Case Study of 4-(2-Naphthylmethyl)benzaldehyde."
J. Chem. Theory. Comp. 10, 4253 (2014) [PDF]       link


45. Samanta, Beames, Lester and Subotnik. Quantum dynamical investigation of the simplest Criegee intermediate CH2OO and its O–O photodissociation channels.
J. Chem. Phys., 141, 134303 (2014) [PDF]       link


44. Ou, Alguire, and Subotnik. "Derivative Couplings between Time-Dependent Density Functional Theory Excited States in the Random-Phase Approximation Based on Pseudo-Wavefunctions: Behavior around Conical Intersections."
J. Phys. Chem. B 119, 7150-7161 (2015) [PDF]       link


43. Alguire, Ou, and Subotnik. "Calculating Derivative Couplings between Time-Dependent Hartree−Fock Excited States with Pseudo-Wavefunctions"
J. Phys. Chem. B 119, 7140-7149 (2015) [PDF]       link


42. Ou, Fatehi, Alguire, Shao and Subotnik. "Derivative couplings between TDDFT excited states obtained by direct differentiation in the Tamm-Dancoff approximation."
J. Chem. Phys. 141, , 024114 (2014) [PDF]       link


41. Petit and Subotnik. "How to calculate linear absorption spectra with lifetime broadening using fewest switches surface hopping trajectories: A simple generalization of ground-state Kubo theory."
J. Chem. Phys. 141, 014107 (2014) [PDF]       link


40. Ouyang and Subotnik. "Estimating the entropy and quantifying the impurity of a swarm of surface-hopping trajectories: A new perspective on decoherence."
J. Chem. Phys. 140, 204102 (2014) [PDF]       link


39. Falk, Landry and Subotnik. Can Surface Hopping sans Decoherence Recover Marcus Theory? Understanding the Role of Friction in a Surface Hopping View of Electron Transfer.
J. Phys. Chem. B, 118, 8108-8117 (2014) [PDF]       link


38. Liu and Subotnik. The Variationally Orbital-Adapted Configuration Interaction Singles (VOA-CIS) Approach to Electronically Excited States.
J. Chem. Theor. Comp., 10, 1004-1020 (2014) [PDF]       link
data files: geom_new.tar.gz

37. Alguire, Fatehi, Shao and Subotnik. "Analysis of Localized Diabatic States beyond the Condon Approximation for Excitation Energy-Transfer Processes."
J. Phys. Chem. A, 118, 11891-11900 (2014) [PDF]       link


36. Landry, Falk, and Subotnik. "Communication: The correct interpretation of surface hopping trajectories: How to calculate electronic Properties."
J. Chem. Phys. 139, 211101 (2013) [PDF]       link


35. Subotnik, Ouyang and Landry. "Can we derive Tully's surface-hopping algorithm from the semiclassical quantum Liouville equation? Almost, but only with decoherence."
J. Chem. Phys. 139, 214107 (2013) [PDF]       link
data files: JCP_139_214107.archive.tar.gz


34. Ou and Subotnik. "Electronic Relaxation in Benzaldehyde Evaluated via TD-DFT and Localized Diabatization: Intersystem Crossings, Conical Intersections, and Phosphorescence."
J. Phys. Chem. C. 117, , 19839-19849 (2013) [PDF]     TYPO's - [pdf]       link


33. Fatehi, Alguire, and Subotnik. "Derivative couplings and analytic gradients for diabatic states, with an implementation for Boys-localized configuration-interaction singles."
J. Chem. Phys. 139, 124112 (2013) [PDF]       link


32. Liu, Ou, Alguire and Subotnik. "Communication: An inexpensive, variational, almost black-box, almost size- consistent correction to configuration interaction singles for valence excited states."
J. Chem. Phys. 138, 221105 (2013) [PDF]       link


31. Alguire and Subotnik. "Optimal Diabatic States Based on Solvation Parameters."
J. Chem. Phys. 137, 194108 (2012) [PDF]       link


30. Landry and Subotnik. "How to recover Marcus theory with fewest switches surface hopping: Add just a touch of decoherence."
J. Chem. Phys. 137, 22A513 (2012) [PDF]     --TYPOs--       link


29. Fatehi and Subotnik. "Derivative Couplings with Built-In Electron-Translation Factors: Application to Benzene."
J. Phys. Chem. Lett. 3, 2039-2043 (2012) [PDF]       link


28. Liu, Fatehi, Shao, Veldkamp and Subotnik. "Communication: Adjusting charge transfer state energies for configuration interaction singles: Without any parameterization and with minimal cost."
J. Chem. Phys. 136, 161101 (2012) [PDF]       link


27. Landry and Subotnik. "Communication: Standard Surface Hopping Predicts Incorrect Scaling for Marcus’ Golden-Rule Rate: The Decoherence Problem Cannot Be Ignored."
J. Chem. Phys. 135, 191101 (2011) [PDF]       link


26. Fatehi, Alguire, Shao and Subotnik. "Analytical Derivative Couplings Between Configuration Interaction Singles States with Built-in Translation Factors for Translational Invariance."
J. Chem. Phys. 135, 234105 (2011) [PDF]     link




25. Subotnik. "Fewest-Switches Surface Hopping and Decoherence in Multiple Dimensions."
J. Phys. Chem. A 115, 12083-12096 (2011) [PDF]       link
There is a typo here, in Eq. 32, just as in Ref. 30 above:     --TYPOs--

24. Subotnik. "Communication: Configuration interaction singles has a large systematic bias against charge-transfer states."
J. Chem. Phys. 135, 071104 (2011) [PDF]       link


23. Alguire and Subotnik. "Diabatic couplings for charge recombination via Boys localization and spin-flip cofiguration interaction singles."
J. Chem. Phys. 135, 044114 (2011) [PDF]       link


22. Shenvi, Subotnik and Yang. "Phase-Corrected Surface Hopping: Correcting the phase evolution of the electronic wavefunction."
J. Chem. Phys. 135, 024101 (2011) [PDF]       link


21. Subotnik and Shenvi. "Decoherence and surface hopping: when can averaging over initial conditions help capture the effects of wave packet separation?"
J. Chem. Phys. 134, 244114 (2011) [PDF]       link


20. Shenvi, Subotnik and Yang. "Simultaneous-trajectory surface hopping: A parameter-free algorithm for implementing deocherence in nonadiabatic dynamics."
J. Chem. Phys. 134, 144102 (2011) [PDF]       link



19. Subotnik and Shenvi. "A New Approach to Decoherence and Momentum Rescaling in the Surface Hopping Algorithm."
J. Chem. Phys. 134, 024105 (2011) [PDF]       link



18. Vura-Weis, Newton, Wasielewski and Subotnik. "Characterizing the Locality of Diabatic States for Electronic Excitation Transfer by Decomposing the Diabatic Coupling."
J. Phys. Chem. C. 114, 20449-20460 (2010) [PDF]       link



17. Subotnik. "Augmented Ehrenfest Dynamics Yields a Rate for Surface Hopping."
J. Chem. Phys. 132, 134112 (2010) [PDF]       link



16. Subotnik, Cave, Steele and Shenvi. "The Initial and Final States of Electron and Energy Transfer Processes: Diabatic States as Motivated by System-Solvent Interactions."
J. Chem. Phys. 130, , 234102 (2016) [PDF]     --TYPOs--       link


Postdoctoral Publications (Tel-Aviv and Northwestern):


15. Hermann, Solomon, Subotnik, Mujica and Ratner. "Ghost Transmission: How large basis sets can make electron transport calculations worse."
J. Chem. Phys. 132, , 024103 (2010) [PDF]       link


14. Subotnik, Vura-Weis, Sodt, and Ratner. "Predicting Accurate Electronic Excitation Transfer Rates via Marcus Theory with Boys or Edmiston-Ruedenberg Localization."
J. Phys. Chem. A. 114, 8665-8675 (2010) [PDF]     TYPO's [PDF]       link



13. Subotnik, Hansen, Ratner and Nitzan. "Nonequilibrium Steady State Transport via the Reduced Density Matrix."
J. Chem. Phys. 130, 144105 (2010) [PDF]       link


12. Subotnik, Yeganeh, Cave and Ratner. "Constructing Diabatic States from Adiabatic States: Extending Generalized Mulliken Hush to Multiple Charge Centers with Boys Localization."
J. Chem. Phys. 129, 244101 (2008) [PDF]     TYPO's- [PDF]       link


11. Subotnik and Nitzan. "Multibody Scattering, Correlation, Molecular Conduction and the 0.7 Anomaly."
J. Chem. Phys. 129, 144107 (2008) [PDF]       link


Graduate School Publications (Berkeley)

10. Subotnik and Head-Gordon. "Exploring The Accuracy of Relative Molecular Energies With Local Correlation Theory."
J. Phys.: Cond. Matt. 20, 294221 (2008) [PDF]       link


9. Subotnik, Sodt and Head-Gordon. "The Limits of Local Correlation Theory: Electronic Delocalization and Chemically Smooth Potential Energy Surfaces."
J. Chem. Phys. 128, 034103 (2008) [PDF]       link


8. Subotnik, Sodt and Head-Gordon. "Localized Orbital Theory and Ammonia Triborane."
PCCP 9, 5522-5530 (2007) [PDF]     TYPO's [PDF]       link


7. Sodt, Subotnik and Head-Gordon. "Linear scaling density fitting."
J. Chem. Phys. 125, 194109 (2006) [PDF]       link



6. Subotnik, Sodt, Head-Gordon. "A Near Linear Scaling Smooth Coupled Cluster Algorithm For Electronic Structure."
J. Chem. Phys. 125, 074116 (2006) [PDF]       link



5. Y. Shao et al. "Advances in methods and algorithms in a modern quantum chemistry program package."
PCCP 8, 3172-3191 (2006) [PDF]       link


4. Subotnik, Dutoi and Head-Gordon. "Fast localized orthonormal virtual orbitals which depend smoothly on nuclear coordinates."
J. Chem. Phys. 123, 114108 (2005) [PDF]       link



3. Subotnik, Head-Gordon. "A local correlation model that yields intrinsically smooth potential energy surfaces."
J. Chem. Phys. 123, 064108 (2005) [PDF]       link



2. Subotnik, Head-Gordon. "A localized basis that allows fast and accurate second order MP2 calculations."
J. Chem. Phys. 122, 034109 (2005) [PDF]       link



1. Subotnik, Shao, Liang, Head-Gordon. "An Efficient method for Calculating Maxima of Homogeneous Functions of Orthogonal Matrices: Applications to Localized Orbitals."
J. Chem. Phys. 121, 9220-9229 (2004) [PDF]       link