Publications

#   denotes equal contributions

*  denotes corresponding author

1. S. Gardner, C. J. Carrano, Y. Mao, F. C. Küpper, A. Cooksy*, "DFT and TD-DFT studies to elucidate the configurational isomers of ferric aerobactin, ferric petrobactin, and their ferric photoproducts", submitted

2. J. T. Kerkhof*, C. J. Breyer, D. K. Smith, Y. Mao*, D. B. Grotjahn, "Sulfonate group improves the solubility and electrocatalytic performance of Ru-based bda- and pda-type water oxidation catalysts under neutral conditions", submitted (DOI: 10.26434/chemrxiv-2024-0h9zw)

3. K. E. Hunter, Y. Mao, A. W. Chin, T. J. Zuehlsdorff*, "Environmentally Driven Symmetry-Breaking Quenches Dual Fluorescence in Proflavine", J. Phys. Chem. Lett. 15, 4623-4632 (2024)

4. X. Pan*, R. Snyder*, J.-N. Wang, C. Lander, C. Wickizer, R. Van, A. Chesney, Y. Xue, Y. Mao*, Y. Mei*, J. Pu*, Y. Shao*, "Training Machine Learning Potentials for Reactive Systems: A Colab Tutorial on Basic Models'', J. Comput. Chem. 45, 638-647 (2024)

5. X. Pan*, R. Van, J. Pu*, K. Nam*, Y. Mao*, Y. Shao*, "Free Energy Profile Decomposition Analysis for QM/MM Simulations of Enzymatic Reactions'', J. Chem. Theory Comput., 19, 8234–8244 (2023)

6. M. S. Chen#, Y. Mao#, A. Snider, P. Gupta, A. Montoya-Castillo, T. J. Zuehlsdorff, C. M. Isborn*, T. E. Markland*, “Elucidating the role of hydrogen bonding in the optical spectroscopy of the solvated green fluorescent protein chromophore: using machine learning to establish the importance of high-level electronic structure”, J. Phys. Chem. Lett. 14, 6610–6619 (2023)

7. A. Aldossary, M. Gimferrer, Y. Mao, H. Hao, A. Das, P. Salvador, T. Head-Gordon, and M. Head-Gordon*, “Force Decomposition Analysis: A method to decompose intermolecular forces into physically relevant component contributions”, J. Phys. Chem. A 127, 1760–1774 (2023)

8. S. Yao, R. Van, X. Pan, J. H. Park, Y. Mao*, J. Pu*, Y. Mei*, and Y. Shao*, “Machine Learning Based Implicit Solvent Model for Aqueous-Solution Alanine Dipeptide Molecular Dynamics Simulations”, RSC Adv. 13, 4565–4577 (2023)

9. P. Eastman*, P. K. Behara, D. L. Dotson, R. Galvelis, J. E. Herr, J. T. Horton, Y. Mao, J. D. Chodera, B. P. Pritchard, Y. Wang, G. De Fabritiis, and T. E. Markland, “SPICE, A Dataset of Drug-like Molecules and Peptides for Training Machine Learning Potentials”, Sci. Data 10, 11 (2023)

1. Z. Pei, Y. Mao*, Y. Shao*, and W. Liang*, “Analytic High-Order Energy Derivatives for Quantum Mechanics/Molecular Mechanics Model with Induced Charges and Dipoles: I. Metal Nanoparticle-Mediated Infrared and Raman Scattering Spectra”, J. Chem. Phys. 157, 164110 (2022)

2. S. D. E. Fried, C. Zheng, Y. Mao, T. E. Markland, and S. G. Boxer, “Solvent Organization and Electrostatics Tuned by Solute Electronic Structure: Amide versus Non-Amide Carbonyls”, J. Phys. Chem. B 126, 5876–5886 (2022)

3. W. Liang*, Z. Pei, Y. Mao*, and Y. Shao*, “Evaluation of Molecular Photophysical and Photochemical Properties Using Linear Response Time-Dependent Density Functional Theory with Classical Embedding: Successes and Challenges”, J. Chem. Phys. (perspective) 156, 210901 (2022)

4. V. Satalkar, E. Benassi*, Y. Mao*, X. Pan, C. Ran, X. Chen, and Y. Shao*, “Computational Investigation of Substituent Effects on the Fluorescence Wavelengths of Oxyluciferin Analogs”, J. Photochemistry & Photobiology, A: Chemistry 431, 114018 (2022)

5. C. Zheng#, Y. Mao#, J. Kozuch, A. O. Atsango, Z. Ji, T. E. Markland, and S. G. Boxer, “A two-directional vibrational probe reveals different electric field orientations in solution and an enzyme active site”, Nat. Chem. 14, 891–897 (2022) (cover by Stanford School of Humanities and Sciences News)

6. L. A. Cunha, D. Hait, R. Kang, Y. Mao, and M. Head-Gordon, “Relativistic Orbital Optimized Density Functional Theory for Accurate Core-Level Spectroscopy”, J. Phys. Chem. Lett. 13, 3438–3449 (2022)

7. J. Yang, Z. Pei, E. C. Leon, C. Wickizer, B. Weng, Y. Mao, Q. Ou, and Y. Shao, “Cavity quantum-electrodynamical time-dependent density functional theory within Gaussian atomic basis. II. Analytic energy gradient”, J. Chem. Phys. 156, 124104 (2022)

8. E. Epivanovsky, A. T. B. Gilbert, X. Feng, J. Lee, Y. Mao, and N. Mardirossian et al., “Software for the frontiers of quantum chemistry: An overview of developments in the Q-Chem 5 package”, J. Chem. Phys. 155, 084801 (2021)

9. Y. Mao, M. Loipersberger, P. R. Horn, A. Das, O. Demerdash, D. S. Levine, S. P. Veccham, T. Head-Gordon, and M. Head-Gordon, “From intermolecular interaction energies and observable shifts to component contributions and back again: A tale of variational energy decomposition analysis", Annu. Rev. Phys. Chem. 72, 641-666 (2021)

10. Z. Pei, Q. Ou*, Y. Mao*, J. Yang, A. de la Lande, F. Plasser*, W. Liang*, Z. Shuai*, and Y. Shao*, “Elucidating the Electronic Structure of a Delayed Fluorescence Emitter via Orbital Interactions, Excitation Energy Components, Charge-Transfer Numbers, and Vibrational Reorganization Energies”, J. Phys. Chem. Lett. 12, 2712–2720 (2021)

11. S. P. Veccham, J. Lee, Y. Mao, P. R. Horn, and M. Head-Gordon, “A Non-Perturbative Pairwise-Additive Analysis of Charge Transfer Contributions to Intermolecular Interaction Energies”, Phys. Chem. Chem. Phys. 28, 928-943 (2021)

12. Y. Mao#*, M. Loipersberger#, K. J. Kron, J. S. Derrick, C. J. Chang, S. M. Sharada, and M. Head-Gordon*, “Consistent Inclusion of Continuum Solvation in Energy Decomposition Analysis: Theory and Application to Molecular CO2 Reduction Catalysts”, Chem. Sci. 12, 1398-1414 (2021)

13. Y. Mao, A. Montoya-Castillo, and T. E. Markland, “Excited state diabatization on the cheap using DFT: Photoinduced electron and hole transfer”, J. Chem. Phys. 153, 244111 (2020)

14. J. Yang, Z. Pei, J. Deng, Y. Mao, Q. Wu, Z. Yang, B. Wang, C. M. Aikens, W. Liang, and Y. Shao, “Analysis and Visualization of Energy Densities. I. Insights from Real-Time Time-Dependent Density Functional Theory Simulations”, Phys. Chem. Chem. Phys. 22, 26838-26851 (2020)

15. Z. Pei, J. Yang, J. Deng, Y. Mao, Q. Wu, Z. Yang, B. Wang, C. M. Aikens, W. Liang, and Y. Shao, “Analysis and Visualization of Energy Densities. II. Insights from Linear-Response Time-Dependent Density Functional Theory Calculations”, Phys. Chem. Chem. Phys. 22, 26852-26864 (2020)

16. Y. Mao*, D. S. Levine, M. Loipersberger, P. R. Horn, and M. Head-Gordon*, “Probing Radical-Molecule Interactions with a Second Generation Energy Decomposition Analysis of DFT Calculations Using Absolutely Localized Molecular Orbitals", Phys. Chem. Chem. Phys. (perspective) 22, 12867-12885 (2020) (selected as PCCP 2020 HOT articles)

17. K. J. Kron, S. J. Gomez, Y. Mao, R. J. Cave, and S. M. Sharada, “Computational analysis of electron transfer kinetics for CO2 reduction with organic photoredox catalysts", J. Phys. Chem. A 124, 5359-5368 (2020)

18. M. Loipersberger#, Y. Mao#, and M. Head-Gordon, “Variational Forward-Backward Charge Transfer Analysis Based on Absolutely Localized Molecular Orbitals: Energetics and Molecular Properties”, J. Chem. Theory Comput. 16, 1073-1089 (2020)

19. Y. Tao, Z. Pei, N. Bellonzi, Y. Mao*, Z. Zou, W. Liang, Z. Yang, and Y. Shao*, “Constructing Spin-Adiabatic States for the Modeling of Spin-Crossing Reactions I. A Shared-Orbital Implementation", Int. J. Quantum Chem. 120, e26123 (2020)

20. Y. Mao, A. Montoya-Castillo, and T. E. Markland, “Accurate and efficient DFT-based diabatization for hole and electron transfer using absolutely localized molecular orbitals", J. Chem. Phys. 151, 164114 (2019)

21. M. Loipersberger, J. Lee, Y. Mao, A. Das, K. Ikeda, J. Thirman, T. Head-Gordon, and M. Head-Gordon, “Energy Decomposition Analysis for Interactions of Radicals: Theory and Implementation at the MP2 Level with Application to Hydration of Halogenated Benzene Cations and Complexes between CO2−• and Pyridine and Imidazole", J. Phys. Chem. A 123, 9621-9633 (2019)

22. Y. Mao and M. Head-Gordon, “Probing Blue-Shifting Hydrogen Bonds with Adiabatic Energy Decomposition and Imidazole", J. Phys. Chem. Lett. 10, 3899-3905 (2019)

23. Y. Mao, M. Head-Gordon, and Y. Shao, “Unraveling Substituent Effects on Frontier Orbitals of Conjugated Molecules Using an Absolutely Localized Molecular Orbital Based Analysis", Chem. Sci. 9, 8598-8607 (2018)

24. W. J. Xie, S. Cha, T. Ohto, W. Mizukami, Y. Mao, M. Wagner, M. Bonn, J. Hunger, and Y. Nagata, “Large Hydrogen Bond Mismatch between TMAO and Urea Promotes Their Hydrophobic Association", Chem 4, 2615-2627 (2018)

25. Y. Mao, Q. Ge, Paul R. Horn, and M. Head-Gordon, “On the Computational Characterization of Charge-Transfer Effects in Non-Covalently Bound Molecular Complexes", J. Chem. Theory Comput. 14, 2401-2417 (2018)

26. Q. Ge, Y. Mao, and M. Head-Gordon, “Energy decomposition analysis for exciplexes using absolutely localized molecular orbitals", J. Chem. Phys. 148, 064105 (2018)

27. O. Demerdash#, Y. Mao#, T. Liu, M. Head-Gordon and T. Head-Gordon, “Assessing many-body contributions to intermolecular interactions of the AMOEBA force field using energy decomposition analysis of electronic structure calculations", J. Chem. Phys. 147, 161721 (2017)

28. Y. Mao#, P. R. Horn#, and M. Head-Gordon, “Energy decomposition analysis in an adiabatic picture", Phys. Chem. Chem. Phys. 19, 5944-5958 (2017)

29. Y. Mao, Y. Shao, J. Dziedzic, C.-K. Skylaris, T. Head-Gordon and M. Head-Gordon, “Performance of the AMOEBA water model in the vicinity of QM solutes: A diagnosis using energy decomposition analysis", J. Chem. Theory Comput. 13, 1963-1979 (2017)

30. Q. Ge, Y. Mao, A. F. White, E. Epifanovsky, K. D. Closser, and M. Head-Gordon, “Simulating the absorption spectra of helium clusters (N=70, 150, 231, 300) using a charge-transfer correction to superposition of fragment single excitations", J. Chem. Phys. 146, 044111 (2017)

31. Y. Mao, P. R. Horn, N. Mardirossian, T. Head-Gordon, C.-K. Skylaris, and M. Head-Gordon, “Approaching the basis set limit for DFT calculations using an environment-adapted minimal basis with perturbation theory: Formulation, proof of concept, and a pilot implementation", J. Chem. Phys. 145, 044109 (2016)

32. Y. Mao#, O. Demerdash#, M. Head-Gordon, and T. Head-Gordon, “Assessing Ion-Water Interactions in the AMOEBA Force Field Using Energy Decomposition Analysis of Electronic Structure Calculations", J. Chem. Theory Comput. 12, 5422-5437 (2016)

33. P. R. Horn, Y. Mao, and M. Head-Gordon, “Probing non-covalent interactions with a second generation energy decomposition analysis using absolutely localized molecular orbitals", Phys. Chem. Chem. Phys. 18, 23067-23079 (2016)

34. P. R. Horn, Y. Mao, and M. Head-Gordon, “Defining the contributions of permanent electrostatics, Pauli repulsion, and dispersion in density functional theory calculations of intermolecular interaction energies", J. Chem. Phys. 144, 114107 (2016)

35. A. Albaugh#, H. A. Boateng#, R. T. Bradshaw#, O. N. Demerdash#, J. Dziedzic#, Y. Mao#, D. T. Margul#, J. Swails#, Q. Zeng#, D. Case, P. Eastman et al., “Advanced Potential Energy Surfaces for Molecular Simulation", J. Phys. Chem. B (feature article) 120, 9811-9832 (2016)

36. J. Dziedzic, Y. Mao, Y. Shao, J. Ponder, T. Head-Gordon, M. Head-Gordon, and C.-K. Skylaris, “TINKTEP: A fully self-consistent, mutually polarizable QM/MM approach based on the AMOEBA force field", J. Chem. Phys. 145, 124106 (2016)

37. D. S. Levine, P. R. Horn, Y. Mao, and M. Head-Gordon, “Variational Energy Decomposition Analysis of Chemical Bonding. 1. Spin-Pure Analysis of Single Bonds", J. Chem. Theory Comput. 12, 4812-4820 (2016)

38. K. D. Closser, Q. Ge, Y. Mao, Y. Shao, and M. Head-Gordon, “Superposition of Fragment Excitations for Excited States of Large Clusters with Application to Helium Clusters", J. Chem. Theory Comput. 11, 5791-5803 (2015)

39. X. Gao, Y. Liu, H. Li, J. Bian, Y. Zhao, Y. Cao, Y. Mao et al., “A cooperative hydrogen bonding system with a CH· · ·O hydrogen bond in ofloxacin", J. Mol. Struct. 1040, 122-128 (2013)