Publications

  1. J. P. Heindel, R. A. LaCour, T. Head-Gordon (2024). The Role of Charge in Microdroplet Redox Chemistry. Nature Comm. accepted.
  2. E. C.-Y. Yuan*, A. Kumar*, X. Guan, E. D. Hermes, A.P. Rosen, J. Zádor, S. M. Blau, T. Head-Gordon (2024). Deep Learning of ab initio Hessians for Transition State Optimization. *equal contribution. submitted
  3. S. Sami, R. A. LaCour, J. P. Heindel, T. Head-Gordon (2024). Simple and accurate 1-body energy and dipole surfaces for water.  submitted
  4. H. Ghafouri, T. Lazar, A. Del Conte, L. G Tenorio Ku, PED Consortium, P.  Tompa, S. C. E. Tosatto, A. M. Monzon (2024). PED in 2024: improving the community deposition of structural ensembles for intrinsically disordered proteins. Nucleic Acids Research, gkad947 [link]
  5. J. Li*, J. Liang*, Z. Wang, A. L. Ptaszek, X. Liu, B. Ganoe, M. Head-Gordon, T. Head-Gordon (2024). Highly Accurate Prediction of NMR Chemical Shifts from Low-Level Quantum Mechanics Calculations Using Machine Learning.  J. Chem. Theory Comput. 20, 5, 2152–2166 *equal contribution [link]
  6. J. Li, X. Guan, O. Zhang, K. Sun, Y. Wang, D. Bagni, T. Head-Gordon (2024). Leak Proof PDBBind: A Reorganized Dataset of Protein-Ligand Complexes for More Generalizable Binding Affinity Prediction. submitted [link]
  7. J. Li, O. Zhang, F. L. Kearns, M. Haghighatlari, C. Parks, R. E. Amaro, T. Head-Gordon (2024). Mining for Potent Inhibitors through Artificial Intelligence and Physics: A Unified Methodology for Ligand Based and Structure Based Drug Design. Submitted [link]
  8. R. A. LaCour, J. P. Heindel, T. Head-Gordon (2023). Predicting the Raman Spectra of Liquid Water with a Monomer-Field Model. J. Phys. Chem. Lett. 14, 11742–11749 [link]
  9. Z. Zheng, O. Zhang, H. Nguyen, N. Rampal, A. Alawadhi, Z. Rong, T. Head-Gordon, C. Borgs, J. Chayes, O. Yaghi (2023). ChatGPT Research Group for Optimizing Crystallinity of MOFs and COFs. ACS Central Sci., 9, 2161–2170 [link]
  10. W.-Lu Li, Y. Li, J. Li, T. Head-Gordon (2023). How Thermal Fluctuations Influence the Function of the FeMo-cofactor in Nitrogenase Enzymes. Chem Catalysis, 3, 100662 [link]
  11. H. Hao, E. M. Adams, S. Funke, G. Schwaab, M. Havenith, T. Head-Gordon (2023). The Highly Altered State of Proton Transport in Acid Pools in Charged Reverse Micelles. J. Am. Chem. Soc. 145(3), 1826–1834 [link]
  12. X. Guan, J.P. Heindel, T. Ko, C. Yang, T. Head-Gordon (2023). Beyond potential energy surface benchmarking: a complete application of machine learning to chemical reactivity. Nature Comp. Sci., 3, 965–974 [link]
  13. F. Novelli, K. Chen, A. Buchmann, T. Ockelmann, C. Hoberg, T. Head-Gordon, M. Havenith (2023). The birth and evolution of solvated electrons in the water, Proc. Natl. Acad. Sci. 120 (8) e2216480120 [link].
  14. O. Zhang, M. Haghighatlari, J. Li, J. Correia Teixeira, A. Namini, Z.H. Liu, J. Forman-Kay, T. Head-Gordon (2023). Learning to Evolve Structural Ensembles of Unfolded and Disordered Proteins Using Experimental Solution Data. J. Chem. Phys. (ML special issue).  158, 174113 [link]
  15. K. Carter-Fenk, M. Liu, L. Pujal, M. Loipersberger, M. Tsanai, R. M. Vernon, J.D. Forman-Kay, M. Head-Gordon, F. Heidar-Zadeh, T. Head-Gordon (2023). The Energetic Origins of Pi-Pi Contacts in Proteins. J. Am Chem. Soc. 145 (45), 24836–24851. [link]
  16. W.-L. Li, K. Chen, E. Rossomme, M. Head-Gordon, T. Head-Gordon (2023). Greater Transferability and Accuracy of Norm-conserving Pseudopotentials using Nonlinear Core Corrections. Chem Sci. 14, 10934-10943  [link]
  17. J. Li, O. Zhang, S. Lee, A. Namini, Z. H. Liu, J. M. C. Teixeira, J. D. Forman-Kay, T. Head-Gordon (2023).  Learning Correlations between Internal Coordinates to improve 3D Cartesian Coordinates for Proteins. J. Chem. Theory Comput. 19, 14, 4689–4700  [link]
  18. T. Khuu, T. Schleif, A. Mohamed, S. Mitra, J. Valdiviezo, J. P. Heindel, T. Head-Gordon, M. Johnson (2023). Intra-cluster charge migration upon hydration of protonated formic acid by anharmonic analysis of cold ion vibrational spectra.  J. Phys. Chem. A 127, 36, 7501–7509. [link]
  19. Z.H. Liu, O. Zhang, J. M. C. Teixeira, J. Li, T. Head-Gordon, J. D. Forman-Kay (2023). SPyCi-PDB: A modular command-line interface for back-calculating experimental datatypes of protein structures. J. Open Source Software, 8(85), 4861. [link]
  20. T. Ko, J. Heindel, X. Guan, T. Head-Gordon, D. Williams-Young, C. Yang (2023). Using Diffusion Maps to Analyze Reaction Dynamics for a Hydrogen Combustion Benchmark Dataset. J. Chem. Theory Comput. 19, 17, 5872–5885 [link]
  21. E. Rossomme, L. dos Anjos Cunha, W.-L. Li, K. Chen, A. McIsaac, T. Head-Gordon, M. Head-Gordon (2023). The good, the bad, and the ugly: Pseudopotential inconsistency errors in molecular applications of density functional theory. J. Chem. Theory Comput. 19(10), 2827–2841.  [link]
  22. J. Wong, B. Ganoe, X. Liu, T. Neudecker, J. Lee, J. Liang, Z. Wang, J. Li, A. Rettig, T. Head-Gordon, M. Head-Gordon (2023). An in-silico NMR laboratory for nuclear magnetic shieldings computed via finite fields: Exploring Nucleus-specific renormalizations of MP2 and MP3. J. Chem. Phys. 158, 164116  [link]
  23. A. Aldossary, M. Gimferrer, Y. Mao, H. Hao, A. Das, P. Salvador, T. Head-Gordon, M. Head-Gordon (2023). Force Decomposition Analysis: A method to decompose intermolecular forces into physically relevant component contributions. J. Phys. Chem. A 127(7), 1760–1774. [link]
  24. J. Liang, Z. Wang, J. Li, J. Wong, X. Liu, B. Ganoe, T. Head-Gordon, M. Head-Gordon (2023). Efficient Calculation of NMR Shielding Constants Using Composite Method Approximations and Locally Dense Basis Sets. J. Comp. Theo. Chem. 19(2), 514–523 [link]
  25. Z. H. Liu, J. M.C. Teixeira, O. Zhang, T. E. Tsangaris, J. Li, C. C. Gradinaru, T. Head-Gordon, J. D. Forman-Kay (2023). Local Disordered Region Sampling (LDRS) for Ensemble Modeling of Proteins with Experimentally Undetermined or Low Confidence Prediction Segments. Bioinformatics, 39(12):btad739. [link]
  26. J. P. Heindel, H. Hao, R. A. LaCour, T. Head-Gordon (2022). On the Spontaneous Formation of Hydrogen Peroxide in Water Microdroplets. J. Phys. Chem. Lett. 3, 43, 10035–10041. [link]
  27. J. Herbert, M. Head-Gordon, H. P. Hratchian, T. Head-Gordon, R. E. Amaro, A. Aspuru-Guzik, R. Hoffmann, C. A. Parish, C. M. Payne, T. Van Voorhis (2022). Words Matter: On the Debate over Free Speech, Inclusivity, and Academic Excellence. J. Phys. Chem. Lett. 13 (30), 7100–7104.[link]
  28. J. Witek, J. P. Heindel, X. Guan, I. Leven, H. Hao, P. Naullage, R. A. LaCour, S. Sami, M.F.S.J. Menger, D. V. Cofer-Shabica, S. Faraji, E. Epifanovsky, T. Head-Gordon (2022). M-Chem: a Modular Software Package for Molecular Simulation that Spans Scientific Domains. Mol. Phys. (Peter Gill Festschrift), Article: e2129500 [link]
  29. H. Hao, L. R. Pestana, J. Qian, M. Liu, Q. Xu, T. Head-Gordon (2022). Chemical transformations and transport phenomena at interfaces. WIRES: Comp.Mol. Sci.  e1639.[link]
  30. M. Haghighatlari, J. Li, X. Guan, O. Zhang, A.K. Das, C. J. Stein, F. Heidar-Zadeh, M. Liu, M. Head-Gordon, L. Bertels, H. Hao, I. Leven, T. Head-Gordon (2022). NewtonNet: A Newtonian message passing network for deep learning of interatomic potentials and forces. Digital Discovery, 1, 333-343. [link]
  31. W.-L. Li, H. Hao, T. Head-Gordon (2022). Optimizing the solvent reorganization free energy by metal substitution for nanocage catalysis. ACS Catalysis Letter 12 (7), 3782–3788 [link]
  32. H. Hao, I. Leven, T. Head-Gordon (2022).  Can electric fields drive chemistry for an aqueous microdroplet? Nature Comm. 13, Article number: 280 (Editor’s choice) [link]
  33. L. Ruiz Pestana, T. Head-Gordon (2022). Evaporation of Water Nanodroplets on Heated Surfaces: Does Nano Matter? ACS Nano 16 (3), 3563–3572  [link]
  34. A. K. Das, M. Liu, T. Head-Gordon (2022). Development of a Many-Body Force Field for Aqueous Alkali Metal and Halogen Ions: An ALMO-EDA Guided Approach. J. Chem. Theory Comput. 18 (2):953-967.  [link]
  35. J.M.C. Teixeira, Z. H. Liu, A. Namini, J. Li, R. M. Vernon, M. Krzeminski, A. A. Shamandy, O. Zhang, M. Haghighatlari, L. Yu, T. Head-Gordon, J. D. Forman-Kay (2022). IDPConformerGenerator: A Flexible Software Suite for Sampling Conformational Space of Disordered Protein States. J. Phys. Chem. A (editor’s choice) 126(35), 5985–6003 [link]
  36. X. Guan*, A. K. Das* , C.J. Stein* , F. Heidar Zadeh* , L. Bertels* , M. Liu ,  M. Haghighatlari , J. Li , O. Zhang , H. Hao , I. Leven , M. Head-Gordon, T. Head-Gordon (2022). A Benchmark Data Set for Hydrogen Combustion. Scientific Data, 9, Article number: 215. [link]
  37. P. M. Naullage, M. Haghighatlari, A. Namini, J. M. C. Teixeira, J. Li, O. Zhang, C. C. Gradinaru, J. D. Forman-Kay, T. Head-Gordon (2022). Protein Dynamics to Define and Refine Disordered Protein Ensembles. J. Phys. Chem. B (Jose Onuchic Festschrift), 126, 9, 1885–1894. [link]
  38. K. Chen, W.-L. Li, T. Head-Gordon (2021). Linear Combination of Atomic Dipoles to Calculate the Bond and Molecular Dipole Moments of Molecules and Molecular Liquids. J. Phys. Chem. Lett. 12, 12360–12369 [link]
  39. W.-L. Li, T. Head-Gordon (2021). Catalytic Principles from Natural Enzymes and Translational Design Strategies for Synthetic Catalysts. ACS Central Science, 7, 1, 72–80 [link]
  40. X. Wang*, J. Li*, H. D. Ha, J. C. Dahl, T. Head-Gordon, A. P. Alivisatos (2021). AutoDetect-mNP: an unsupervised machine learning algorithm for automated analysis of TEM images of metal nanoparticles. J. Am. Chem. Soc. Au, 1, 3, 316–327 [link] (*equal first author).
  41. E. M. Adams*, H. Hao*, I. Leven, M. Rüttermann, H. Wirtz, M. Havenith, T. Head-Gordon (2021). Proton traffic jam: Effect of nanoconfinement and acid concentration on proton hopping mechanism. Angew. Chem. Int. Ed. 60 (48) (*equal first author).  [link]
  42. W.-L. Li, K. Chen, E. Rossomme, M. Head-Gordon, T. Head-Gordon (2021). Optimized norm-conserving pseudopotentials and basis sets for B97M-V and ωB97X-V for typical main-group elements, 3d transition metals, and noble metals. J. Phys. Chem. Lett. 12(42), 10304–10309 [link]
  43. X. Guan, I. Leven, F. Heidar-Zadeh, T. Head-Gordon (2021). Protein C-GeM: A coarse-grained electron model for fast and accurate protein electrostatics prediction. J. Chem. Inf. Model. 61, 9, 4357–4369. [link]
  44. M. Liu, A. K. Das, J. Lincoff, S. Sasmal, S. Y. Cheng, R. Vernon, J. Forman-Kay, T. Head-Gordon (2021). Configurational entropy of folded proteins and its importance for intrinsically disordered proteins. (Special Issue Frontiers in Protein Structure Research)  Int. J. Mol. Sci. 22(7), 3420; [link]
  45. W.-L. Li, C. N. Lininger,  V. V. Welborn, E. Rossomme, A. T. Bell, M. Head-Gordon, T. Head-Gordon, (2021). Critical Role of Thermal Fluctuations for CO Binding on Electrocatalytic Metal Surfaces. J. Am. Chem. Soc. Au, 1 (10), 1708–1718 [link]
  46. I. Leven, H. Hao, S. Tan, X. Guan, K. A. Penrod, D. Akbarian, B. Evangelisti, M. J. Hossain, M. M. Islam, J. Koski, S. Moore, H. M. Aktulga, A. van Duin, T. Head-Gordon  (2021). Recent advances for improving the accuracy, transferability and efficiency of reactive force fields. J. Chem. Theory Comput. Perspective 17, 6, 3237–3251. [link]
  47. M. Ahmed, M. Blum, E. J. Crumlin, P. L. Geissler, T. Head-Gordon,  D. T. Limmer, K. K. Mandadapu, R. J. Saykally, K. R. Wilson (2021). Molecular properties and chemical transformations near interfaces, J. Phys. Chem. Feature Article,  (Editor’s Choice) 125, 32, 9037–9051 [link]
  48. T. Stauch*, B. Ganoe*, J. Wong*, J. Lee, A. Rettig, J. Liang, J. Li, E. Epifanovsky, T. Head-Gordon, M. Head-Gordon (2021). Molecular Magnetizabilities Computed Via Finite Fields: Assessing Alternatives to MP2 and Revisiting Magnetic Exaltations in Aromatic and Antiaromatic Species. Mol. Phys. 119 (21-22) e1990426[link]
  49. E. Epifanovsky, A. Gilbert, X. Feng, J.H. Lee,  et al. (2021). Software for the frontiers of quantum chemistry: An overview of developments in the Q-Chem 5 package. J. Chem. Phys. 155, 084801.  [link]
  50. C. N. Lininger, W.-L. Li, E. Rossomme, V. V. Welborn, T. Head-Gordon, M. Head-Gordon, A. T. Bell (2021). Challenges for DFT: Calculation of CO adsorption on electrocatalytically relevant metals. Phys. Chem. Chem. Phys. 23, 9394-9406  [link]
  51. Y. Mao, M. Loipersberger, P. R.Horn, A. K. Das, O. N. Demerdash, D. S. Levine, S. P. Veccham, T. Head-Gordon, M. Head-Gordon (2021). From intermolecular Interaction Energies and Observable Shifts to Component Contributions and Back Again: A Tale of Variational Energy Decomposition Analysis.  Ann. Rev. Phys. Chem., 72, 641-666 [link]
  52. D. An, S. Y. Cheng, T. Head-Gordon, L. Lin, J. Lu (2021). Convergence of a stochastic-extended Lagrangian molecular dynamics method for polarizable forcefield simulation. J. Comp. Phys. 438, 110338 [link]
  53. Lazar, E. Martínez-Pérez, F. Quaglia, A. Hatos, L. Chemes, P. Bernado, M. Blackledge, T. Cordeiro, E. Fagerberg, J. Forman-Kay, M. Silvina, N. Garrone, T. Gibson, G. Gomes, C. Gradinaru, T. Head-Gordon, J. Iserte, M. Jensen, E. Lemke, S. Longhi, J. Marchetti, C. Marino-Buslje, N. Mendez, G. Minervini, T. Mittag, A. Monzon, R. Pappu, G. Parisi, S. Ricard-Blum, K. Ruff, T. Saldano, E. Salladini, M. Skepo, D. Svergun, S. Vallet, M. Varadi, A. Rueda, P. Tompa, S. Tosatto, D. Piovesan (2021). PED in 2021: a major update of the Protein Ensemble Database for intrinsically disordered proteins. Nucleic Acids Research,  Database issue, 49 (D1), D404–D411, [link]
  54. V. Vaissier Welborn, W.-L. Li, T. Head-Gordon (2020). Interplay of Encapsulated Water and a Supramolecular Capsule for Catalysis of Reductive Elimination Reaction from Gold. Nature Comm. 11, Article number: 415 [link]
  55. L. Ruiz Pestana, H. Hao, T. Head-Gordon (2020). Diels-Alder Reactions in Water are Determined by Microsolvation. ACS Nano Lett. 20, 1, 606-611 [link].
  56. M. Haghighatlari, J. Li, F. Heidar-Zadeh, Y. Liu, X. Guan, T. Head-Gordon (2020). Learning to Make Chemical Predictions: the Interplay of Feature Representation, Data, and Machine Learning Algorithms. Chem 6, 1527-1542 [link].
  57. F. Sebastiani, T. A. Bender, S. Pezzotti, W.-L. Li, G. Schwaab, R. G. Bergman, K. N. Raymond, F. D. Toste, T. Head-Gordon, M. Havenith (2020). An Isolated Water Droplet in the Aqueous Solution of a Supramolecular Tetrahedral Cage.  Proc. Natl. Acad. Sci. USA, 117 (52) 32954-32961 [link]
  58. S. Tan, I. Leven, D. An, L. Lin, T. Head-Gordon (2020). Stochastic Constrained Extended System Dynamics for Solving Charge Equilibration Models. J. Chem. Theory Comput. 16, 10, 5991–5998 [link]
  59. G.-N. Gomes, M.  Krzeminski, E. W. Martin, T. Mittag, T.  Head-Gordon,  J. D. Forman-Kay, C. C. Gradinaru (2020).  Integrating smFRET, SAXS and NMR data to infer structural ensembles of an intrinsically-disordered protein.  J. Am. Chem. Soc. 142, 37, 15697–15710 [link]
  60. I. Leven , H. Hao, A. K. Das, T. Head-Gordon (2020).  A Reactive Force Field with Coarse-Grained Electrons for Liquid Water. J. Phys. Chem. Lett. 11, 21, 9240–9247.  [link]
  61. J. Lincoff, M. Krzeminski, M. Haghighatlari, J. M.C. Teixeira, G.-N. W. Gomes, C. C. Gardinaru, J. Forman-Kay, T. Head-Gordon (2020). Extended Experimental Inferential Structure Determination Method for Evaluating the Structural Ensembles of Disordered Protein States. Chem. Comm. 3, Article no: 74  [link]
  62. J. Li, K. C. Bennett, Y. Liu, M. V. Martin, T. Head-Gordon (2020).  Accurate Prediction of Chemical Shifts for Aqueous Protein Structure for “Real World” Cases using Machine Learning. Chem. Sci. 11, 3180-3191 [link]
  63. E. C. Rossomme, C. N. Lininger, A. T. Bell, T. Head-Gordon, M. Head-Gordon (2020). Electronic structure calculations permit identification of the driving forces behind frequency shifts in transition metal monocarbonyls. Phys. Chem. Chem. Phys. 22, 781-798 [link].
  64. F. Novelli, L. Ruiz Pestana, K. C. Bennett, F. Sebastiani, E. Adams, N. Stavrias,  T. Ockelmann, A. Colchero, C. Hoberg, G. Schwaab, T. Head-Gordon, M. Havenith (2020). Strong Anisotropy in Liquid Water upon Librational Excitation Using Terahertz Laser Fields. J. Phys. Chem. B 124, 24, 4989–5001 [link].
  65. V. Vaissier Welborn, T. Head-Gordon (2019). Fluctuations of Electric Fields in the Active Site of the Enzyme Ketosteroid Isomerase. J. Am. Chem. Soc. Comm. 141 (32), 12487-12492 [link]
  66. M. Loipersberger, J. Lee, Y. Mao, A. Das, K. Ikeda, J. Thirman, T. Head-Gordon, M. Head-Gordon (2019). 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, 44, 9621-9633. [link]
  67. V. Vaissier Welborn, T. Head-Gordon (2019). Computational Design of Synthetic Enzymes. Chem. Rev. 119 (11), 6613-6630. [link]
  68. T. Head-Gordon and F. Paesani (2019). Water is Not a Dynamic Polydisperse Branched Polymer (Letter to the Editor). Proc. Natl. Acad. Sci. USA, 116 (27) 13169-13170. [link]
  69. I. Leven, T. Head-Gordon (2019). C-GeM: Coarse-Grained Electron Model for Predicting the Electrostatic Potential in Molecules. J. Phys. Chem. Lett. 10, 6820-6826. [link]
  70. S. Liu, J. Li, K. C. Bennett, B. Ganoe, T. Stauch, M. Head-Gordon, D. Ushizema, A. Hexemer, T. Head-Gordon (2019).  A Multi-Resolution 3D-DenseNet for Chemical Shift Prediction in NMR Crystallography. J. Phys. Chem. Lett. 10 (16), 4558-4565 [link]
  71. I. Leven, T. Head-Gordon (2019). Inertial Extended-Lagrangian Scheme for Solving Charge Equilibration Force Fields. Phys. Chem. Chem. Phys. 21, 18652 – 18659 [link]
  72. A. K. Das, L. Urban, I. Leven, M. Loipersberger, A. Aldossary, M. Head-Gordon, T. Head-Gordon (2019). Development of an Advanced Force Field for Water using Variational Energy Decomposition Analysis. J. Chem. Theory Comput. 15 (9), 5001-5013 [link]
  73. Y. Qiu, P. Nerenberg, T. Head-Gordon, L.-P. Wang (2019). Systematic Optimization of Water Models using Liquid/Vapor Surface Tension Data. J. Phys. Chem. B 123 (32), 7061-7073 [link].
  74. J. Lincoff, S. Sasmal, T. Head-Gordon (2019). The Combined Force Field-Sampling Problem in Simulations of Disordered Amyloid-β Peptides. J. Chem. Phys. 150, 104108. [link]
  75. A. Albaugh, M. Tuckerman, and T. Head-Gordon (2019). Combining Iteration-Free Polarization with Large Time Step Stochastic-Isokinetic Integration. J. Chem. Theory Comput., 15 (4), 2195–2205. [link]
  76. J. Dziedzic, T. Head-Gordon, M. Head-Gordon, C.-K. Skylaris (2019). Mutually Polarizable QM/MM Model with In Situ Optimized Localized Basis Functions. J. Chem. Phys. 150 (7), 074103. [link]
  77. V. Vaissier Welborn, L. Ruiz Pestana, T. Head-Gordon (2018). Computational Optimization of Electric Fields for Better Catalysis Design. Nature Catalysis, 1, 649–655. [link]
  78. A. Krylov, T. L. Windus, T. Barnes, E. Marin-Rimoldi, J. Nash, B. Pritchard, D. G. A. Smith, D. Altarawy, P. Saxe, C. Clementi, T. D. Crawford, R. Harrison, S. Jha, V. S. Pande, T. Head-Gordon (2018). Computational Chemistry Software and its Advancement as Illustrated through Three Grand Challenge Cases for Molecular Science. J. Chem. Phys. (Perspective) 149, 180901 [link]
  79. A. K. Das, O. N. Demerdash, T. Head-Gordon (2018). Improvements to the AMOEBA Force Field by Introducing Anisotropic Atomic Polarizability of the Water Molecule. J. Chem. Theory Comput., 14 (12), 6722–6733 [link]
  80. V. Vaissier, S. C. Sharma, K. Schaettle, T. Zhang, T. Head-Gordon (2018). Computational Optimization of Electric Fields for Improving Catalysis of a Designed Kemp Eliminase. ACS Catalysis, 8, 219-227. [link]
  81. P. S. Nerenberg and T. Head-Gordon (2018). New developments in force fields for biomolecular simulations. Curr. Opin. Struct. Bio. 49, 129-138. [link]
  82. L. Ruiz Pestana, L. E. Felberg, T. Head-Gordon (2018). Coexistence of multilayered phases of nanoconfined water: the importance of flexible confining surfaces. ACS Nano 2 (1), 448–454. [link]
  83. V. Vaissier Welborn, T. Head-Gordon (2018). Electrostatics generated by a supramolecular capsule stabilizes the transition state for carbon-carbon reductive elimination from a gold(III) complex. J. Phys. Chem. Lett. 9(14), 3814-3818.  [link]
  84.  L. Ruiz Pestana, O. Marsalek, T. E. Markland, T. Head-Gordon (2018). The quest for accurate liquid water properties from first principles. J. Phys. Chem. Lett. 9 (17), 5009-5016.  [link]
  85. O. N. Demerdash, L.-P. Wang, T. Head-Gordon (2018). Advanced models for water simulations. WIREs Computational Molecular Science 8 (1), e1355 [link]
  86. E. Jurrus, D. Engel, K. Star, K. Monson, J. Brandi, L. E. Felberg, D.H. Brookes, L. Wilson, J. Chen, K. Liles, M. Chun, P. Li, T. Dolinsky, R. Konecny, D. Koes, J. E. Nielsen, T. Head-Gordon, W. Geng, R. Krasny, M. Gunner, G.-W. Wei, M. J. Holst, J. A. McCammon, N. A. Baker (2018). Improvements to the APBS biomolecular solvation software suite. Protein Sci. 27 (1), 112-128. [link]
  87. L. R. Pestana, N. Minnetian, L. Nielsen Lammers, T. Head-Gordon, (2018). Dynamical inversion of the energy landscape promotes non-equilibrium self-assembly of binary mixtures. RSC Chem. Sci. 9, 1640-1646. [link]
  88. S. Belsare, V. Pattni, M. Heyden, and T. Head-Gordon (2018). Solvent entropy contributions to catalytic activity in designed and optimized Kemp Eliminases. J. Phys. Chem. B (Ken Dill Festschrift), 122 (21), 5300-5307. [link]
  89. K. Schaettle, L. R. Pestana, L. Nielsen Lammers, T. Head-Gordon (2018). A structural coarse-grained model for clays using simple iterative Boltzmann inversion, J. Chem. Phys. 148, 222809. [link]
  90. A. Albaugh, A. M. N. Niklasson, T. Head-Gordon (2018). Higher-order Extended Lagrangian Born-Oppenheimer Molecular Dynamics for Classical Polarizable Models. J. Chem. Theory Comput. 14 (2), 499-511. [link]
  91. A. Albaugh and T. Head-Gordon (2017). A New Method for Treating Drude Polarization in Classical Molecular Simulation. J. Chem. Theory Comput. 13 (11), 5207–5216. [link]
  92. A. Bhowmick, S. Sharma, T. Head-Gordon (2017). The importance of the scaffold for de novo enzymes. J. Am. Chem. Soc. 139(16):5793-5800 [link]
  93. L. R. Pestana, K. Kolluri, T. Head-Gordon, and L. Nielsen Lammers (2017). Direct exchange mechanism for interlayer ions in non-swelling clays. Environmental Science & Technology, 51(1), 393-400 [link]
  94. N. Mardirossian, L. Ruiz Pestana, J. C. Womack, C.-K. Skylaris, T. Head-Gordon, M. Head-Gordon (2017). On the use of the rVV10 nonlocal correlation functional in the B97M-V density functional. J. Phys. Chem. Lett. 8 (1), 35–40 [link]
  95. A. Esser*, S. Belsare*, D. Marx, and T. Head-Gordon (2017). Mode specific THz spectra of solvated amino acids using the AMOEBA polarizable force field. Phys. Chem. Chem. Phys. 19, 5579-5590 [link]
  96. A. Albaugh, A. Niklasson, and T. Head-Gordon (2017) Accurate classical polarization solution with no self-consistent field iterations. J. Phys. Chem. Lett. 8, 1714-1723 [link]
  97. V. Vitale, J. Dziedzic, A. Albaugh, A. Niklasson, T. Head-Gordon, C.-K. Skylaris (2017) Performance of extended Lagrangian Schemes for molecular dynamics simulations with classical polarizable force fields and density functional theory. J. Chem. Phys. 146, 124115 [link]
  98. A. C. Carr, L. E. Felberg, V. A. Piunova, J. E. Rice, T. Head-Gordon, W. C. Swope (2017). The effect of hydrophobic core topology and composition on the structure and kinetics of star polymers, a molecular dynamics study. J. Chem. Theory Comput. 121 (13), 2902-2918 [link]
  99. L. E. Felberg, D. H. Brookes, E. Jurrus, N. Baker, and T. Head-Gordon (2017). PB-AM: An open-source, fully analytical linear Poisson-Boltzmann solver. J. Comp. Chem. (Brooks Festschrift) 38 (15), 1275-1282 [link]
  100. L. Ruiz Pestana, N. Mardirossian, M. Head-Gordon, T. Head-Gordon (2017). Ab Initio simulations of liquid water using high quality meta-GGA functionals. Chem. Sci., 8, 3554 – 3565, Edge article [link]
  101. L.-P. Wang, K. A. McKiernan, J. Gomes, K. A. Beauchamp, T. Head-Gordon, J. E. Rice, W. C. Swope, T. J. Martinez, V. S. Pande (2017) Building a more predictive protein force field: a systematic and reproducible route to AMBER-FB15. J. Phys. Chem. BJ. Phys. Chem. B 121 (16), 4023–4039. [link]
  102. Y. Mao, Y. Shao, J. Dziedzic, C.-K. Skylaris, T. Head-Gordon, M. Head-Gordon (2017). Performance of the AMOEBA water model in the vicinity of QM solutes: a diagnosis using energy decomposition analysis. J. Chem. Theory Comput. 13 (5), 1963–1979. [link]
  103. S. Sasmal, J. Lincoff, and T. Head-Gordon (2017). Effect of a paramagnetic spin label on the intrinsically disordered peptide ensemble of amyloid-b.  Biophys. J. 113 (5), 1002-1011. [link]
  104. O. N. Demerdash, Y. Mao, T. Liu, M. Head-Gordon, T. Head-Gordon (2017). 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. [link]
  105. O. N. Demerdash and T. Head-Gordon (2016). Parallel implementation of approximate atomistic models of the AMOEBA polarizable model. Chem. Phys. Lett. 664, 191–198 [link]
  106. J. Lincoff, S. Sasmal, and T. Head-Gordon (2016). Comparing generalized ensemble methods for sampling of systems with many degrees of freedom. J. Chem. Phys. 145(17), 174107  [link]
  107. Y. Mao*,O. N. Demerdash*, M. Head-Gordon, T. Head-Gordon (2016). Assessing water-water and ion-water interactions in the AMOEBA force field using energy decomposition analysis of electronic structure calculations. J. Chem. Theory Comput. 12 (11), 5422–5437 [link]
  108. S. Sasmal, N. Schwierz, and T. Head-Gordon (2016). Mechanism of Nucleation and Growth for Different Monomer Ensemble Additions to Aβ40 Alzheimer’s Disease Fibrils. J. Phys. Chem. B. 120, 12088−12097 [link]
  109. L. E. Felberg, A. Doshi, G. L. Hura, J. Sly, V. A. Plunova, R. Miller, J. E. Rice, W. C. Swope, T. Head-Gordon (2016). Structural transition of nanogel star polymers with pH by controlling PEGMA interactions with acid or base copolymers. Mol. Phys. 114 (21), 3221-3231  [link]
  110. D. H. Brookes and T. Head-Gordon (2016). Experimental inferential structure determination of ensembles for intrinsically disordered proteins J. Am. Chem. Soc. 138(13), 4530-4538 [link]
  111. A. Bhowmick, S. Sharma,  H. Honma, T. Head-Gordon (2016). The role of side chain entropy and mutual information for improving the de novo design of Kemp Eliminases KE07 and KE70. Phys. Chem. Chem. Phys., 18, 19386 [link]
  112. O. N. Demerdash and T. Head-Gordon (2016). Electrostatic embedding schemes for the many-body approximation of classical polarizable models.  J. Chem. Theory Comput. 12 (8), 3884–3893 [link]
  113. Y. Mao, P. R. Horn, N. Mardirossian, C.-K. Skylaris, T. Head-Gordon, M. Head-Gordon (2016). 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. [link]
  114. A. Bhowmick*, D. H. Brookes*, M. S. R. Yost*, H. J. Dyson, J. Forman-Kay, D. Gunter, M. Head-Gordon, G. L. Hura, V. S. Pande, D. E. Wemmer, P. E. Wright, T. Head-Gordon (2016). Finding our way in the dark proteome. J. Am. Chem. Soc. (Perspective) 138 (31), 9730–9742 [link]
  115. A. Albaugh*, R. Bradshaw*, O. N. Demerdash*, J. Dziedzic*, Y. Mao*, D. T. Marguly*, Q. Zeng*, H. A. Boateng, D. Case, P. Eastman, J. Essex, M. Head-Gordon, V. S. Pande, J. Ponder, Y. Shao, J. Swails*, C.-K. Skylaris, I. T. Todorov, M. E. Tuckerman, T. Head-Gordon (2016). Advanced potential energy surfaces and software for molecular simulation. J. Phys. Chem. B (Feature article) 120 (37), 9811–9832. [link]
  116. J. Dziedzic, Y. Mao, Y. Shao, J. Ponder, T. Head-Gordon, M. Head-Gordon, C.-K. Skylaris (2016). TINKTEP: A fully self-consistent QM/polarizable-MM approach based on the AMOEBA force field. J. Chem. Phys. 145, 124106 [link]
  117. A. Albaugh, O. N. Demerdash, and T. Head-Gordon (2015). An efficient and stable hybrid extended lagrangian/self-consistent field scheme for solving classical mutual induction. J. Chem. Phys. 143, 174104 [link]
  118. S. Sharma, T. Armand, K. A. Ball, A. Chen, J. Pelton, D. Wemmer, and T. Head-Gordon (2015). A facile method for expression and purification of 15N-isotope labeled human Alzheimer’s β-amyloid peptides from E. coli for NMR-based structural analysis. Protein Expr. Purif. 116, 82-89 [link]
  119. D. H. Brookes and T. Head-Gordon (2015). The family of oxygen-oxygen radial distribution functions for water. J. Phys. Chem. Lett. 6 (15), 2938-2943 [link]
  120.  M. Laury, L.-P. Wang, V. S. Pande, T. Head-Gordon, J.  Ponder (2015). Revised parameters for the AMOEBA polarizable atomic multipole water model.  J. Phys. Chem. B (Branka Ladanyi Festschrift) 119 (29), 9423-9437 [link]
  121. A. Bhowmick and T. Head-Gordon (2015). A Monte Carlo method for generating side chain structural ensembles. Structure. 23(1):44-55. [link]
  122. L. E. Felberg, D. H. Brookes, J. E. Rice, T. Head-Gordon, and W. Swope (2015). Role of hydrophilicity and length of diblock arms for determining star polymer physical properties. J. Phys. Chem. B (William Jorgensen Festschrift)119 (3), 944–957 [link]
  123. E. Yedvabny, P. S. Nerenberg, C. So, T. Head-Gordon (2015). The disordered structural ensembles of vasopressin and oxytocin and their mutants J. Phys. Chem. B (William Jorgensen Festschrift)119(3):896-905 [link]
  124. O. N. Demerdash, E.-H. Yap and T. Head-Gordon (2014). Advanced potential energy surfaces for condensed phase simulation.  Ann. Rev. Phys. Chem. 65, 149-174 [link]
  125. T. Head-Gordon and J. E. Rice (2014). Tribute to William C. Swope. J. Phys. Chem. B 118 (24) 6357-6359 [link]
  126. K. A. Ball, D. E. Wemmer & T. Head-Gordon (2014). Comparison of structure determination methods for intrinsically disordered amyloid-β peptides J. Phys. Chem. B (William Swope Festschrift) 118 (24), 6405–6416 [link].
  127. T. Vazina, K. A. Ball, H. Lu, T. Head-Gordon, M-M. Poo, D. V. Schaffer (2014). Efficient derivation of cortical glutamatergic neurons from human pluripotent stem cells: A model to study Alzheimer’s disease. Neurobiology of Disesase, 62, 62-72 [link]
  128. E.-H. Yap and T. Head-Gordon (2013). Calculating the biomolecular rate of protein-protein association under crowding conditions  J. Chem. Theory Comput. 9 (5), 2481-2489 [link]
  129. N. Liguori, P. S. Nerenberg, T. Head-Gordon (2013). Reactive Aβ42 N-terminal exposure depends on age-dependent cholesterol asymmetries. Biophys. J. 105 (4), 899-910 [link]
  130. K. A. Ball, A. Phillips, D. E. Wemmer & T. Head-Gordon (2013). Differences in β−strand populations of monomeric Aβ40 and Aβ42. Biophys. J. 104 (12), 2714-2724 (Cover art) [link]
  131. L.-P. Wang, T. Head-Gordon, J. Ponder, P. Ren, J. Chodera, T. Martinez, V. S. Pande (2013) A systematic improvement on the classical molecular model of water. J. Phys. Chem. B. 117 (34), 9956-9972 [link]
  132. D. J. Wales and T. Head-Gordon (2012). Evolution of the potential energy landscape with static pulling force for two model proteins. J. Phys. Chem. B 116 (29), 8394–8411 [link]
  133. T. Head-Gordon, R. M. Lynden-Bell, J. Dowdle, P. J. Rossky (2012). Predicting solubility of hard spheres: How far is the Gaussian approximation valid?  Phys. Chem. Chem. Phys 14 (19), 6996 – 7004. [link]
  134. P. S. Nerenberg, B. Jo, C. So, A. Tripathy, T. Head-Gordon (2012). Optimizing Solute-Water van der Waals Interactions to Reproduce Solvation Free Energies. J. Phys. Chem. B 116 (15), 4524–4534 [link]
  135. R. M. Lynden-Bell, N. Giovambattista, P. G. Debenedetti, T. Head-Gordon, P. J. Rossky (2011). Hydrogen bond strength and network effects on hydration of nonpolar molecules. Phys. Chem. Chem. Phys. 13 (7), 2748 – 2757 [link]
  136. P. S. Nerenberg & T. Head-Gordon (2011). Optimizing protein-solvent force fields to reproduce intrinsic conformational preferences of model peptides. J. Chem. Theory Comput. 7 (4), 1220-1230 [link]
  137. Daniel S. Lambrecht, Gary N. I. Clark, Teresa Head-Gordon, Martin Head-Gordon, (2011). Exploring the Rich Energy Landscape of Sulfate-Water Clusters SO4(2-) (H2O)(n=3-7): An Electronic Structure Approach. The Journal of Physical Chemistry A, 115 (41), 11438-11454. [link]
  138. K. Aurelia Ball, Aaron H. Phillips, Paul S. Nerenberg, Nicolas L. Fawzi, David E. Wemmer, Teresa Head-Gordon, (2011). Homogeneous and Heterogeneous Tertiary Structure Ensembles of Amyloid-β Peptides. Biochemistry, 50 (35), 7612-7628. [link]
  139. Cheng Peng, Teresa Head-Gordon. The Dynamical Mechanism of Auto-Inhibition of AMP-Activated Protein Kinase, (2011). PLoS Computational Biology, 7 (7), e1002082. [link]
  140. Daniel S. Lambrecht, Gary N. I. Clark, Teresa Head-Gordon, Martin Head-Gordon (2011). Simulated Photoelectron Spectra of the Cyanide-Water Anion via Quasiclassical Molecular Dynamics. The Journal of Physical Chemistry A, 115 (23), 5928-5935. [link]
  141. Matthew S. Lin, Teresa Head-Gordon, (2011). Reliable protein structure refinement using a physical energy function, Journal of Computational Chemistry, 32(4), 709-717. [link]
  142. Paul S. Nerenberg, Teresa Head-Gordon (2011). Optimizing Protein−Solvent Force Fields to Reproduce Intrinsic Conformational Preferences of Model Peptides, Journal of Chemical Theory and Computation, 7 (4), 1220-1230. [link]
  143. R. M. Lynden-Bell, N. Giovambattista, P. G. Debenedetti, T. Head-Gordon and P. J. Rossky, (2011). Hydrogen bond strength and network structure effects on hydration of non-polar molecules. Phys. Chem. Chem. Phys, 13, 2748-2757. [link]
  144. Cheng Peng, Liqing Zhang, Teresa Head-Gordon, (2010). Instantaneous Normal Modes as an Unforced Reaction Coordinate for Protein Conformational Transitions, Biophysical Journal, 98(10), 2356-2364 [link]
  145. Eng-Hui Yap, Teresa Head-Gordon, (2010). New and Efficient Poisson−Boltzmann Solver for Interaction of Multiple Proteins, Journal of Chemical Theory and Computation, 6 (7), 2214-2224. [link]
  146. Gary N. I. Clark, Greg L. Hura, Jose Teixeira, Alan K. Soper, and Teresa Head-Gordon (2010). Small-angle scattering and the structure of ambient liquid water. Proc. Nat. Acad. Sci., 107 (32) 14003-14007. [link]
  147. Gary N. I. Clark, Christopher D. Cappa, Jared D. Smith, Richard J. Saykally Teresa Head-Gordon (2010). The structure of ambient water. Molecular Physics: An International Journal at the Interface Between Chemistry and Physics, 108(11), 1415-1433 [link]
  148. Alex J. Sodt, Teresa Head-Gordon (2010). Driving Forces for Transmembrane [alpha]-Helix Oligomerization, Biophysical Journal, 99(1), 227-237. [link]
  149. Alex J. Sodt and Teresa Head-Gordon (2010). An implicit solvent coarse-grained lipid model with correct stress profile J. Chem. Phys. 132, 205103. [link]
  150. Kohn JE, Afonine PV, Ruscio JZ, Adams PD, Head-Gordon T, (2010). Evidence of Functional Protein Dynamics from X-Ray Crystallographic Ensembles. PLoS Comput Biol 6(8). [link]
  151. Jay W. Ponder, Chuanjie Wu, Pengyu Ren, Vijay S. Pande, John D. Chodera, Michael J. Schnieders, Imran Haque, David L. Mobley, Daniel S. Lambrecht, Robert A. DiStasio Jr., Martin Head-Gordon, Gary N. I. Clark, Margaret E. Johnson, Teresa Head-Gordon (2010). Current Status of the AMOEBA Polarizable Force Field. The Journal of Physical Chemistry B,114 (8), 2549-2564. [link]
  152. A. K. Soper, J. Teixeira, and T. Head-Gordon, (2010). Is ambient water inhomogeneous on the nanometer-length scale? PNAS, 107 (12). [link]
  153. J. Z. Ruscio, N. L. Fawzi, and T. Head-Gordon (2010). How hot? Systematic convergence of the replica exchange method using multiple reservoirs. J. Comp. Chem, 31(3), 620-627. [link]
  154. M. E. Johnson, C. Malardier-Jugroot, and T. Head-Gordon (2009). Effects of co-solvents on peptide hydration water structure and dynamics Phys. Chem. Chem. Phys. [link].
  155. C. Malardier-Jugroot, D. T. Bowron, A. K. Soper, M. E. Johnson and T. Head-Gordon (2009). Structure and water dynamics of aqueous peptide solutions in the presence of co-solvents Phys. Chem. Chem. Phys. 12, 382-392 [link]
  156. J. Z. Ruscio, J. E. Kohn, K. A. Ball, T. Head-Gordon (2009). The influence of protein dynamics on the success of computational enzyme design. J. Am. Chem. Soc. 113 ,14111-15. [link]
  157. M. E. Johnson and T. Head-Gordon (2009). Assessing thermodynamic theories of liquid dynamics. J. Chem. Phys. 130 , 214510. [link]
  158. M. E. Johnson, C. Malardier-Jugroot, R. K. Murarka, and T. Head-Gordon (2009). Hydration water dynamics near biological interfaces. J. Phys. Chem. B 113 , 4082–4092. [link]
  159. T. Head-Gordon (2008). Spotlight on “Polypeptide friction and adhesion on hydrophobic and hydrophilic surfaces: a molecular dynamics study” J. Am. Chem. Soc. [link]
  160. C. Malardier-Jugroot, M.E. Johnson, R.K. Murarka, and T. Head-Gordon (2008). Aqueous peptides as experimental models for hydration water dynamics near protein surfaces Phys. Chem. Chem. Phys. 10 , 4303-4308. [link]
  161. N. Lux Fawzi, E. H. Yap, Y. Okabe, K. Kohlstedt, S. P. Brown & T. Head-Gordon (2008). Contrasting disease and non-disease protein aggregation by molecular simulation Acc. Chem. Research 41 , 1037-1047. [link]
  162. N. Lux Fawzi, A. Phillips, J. Z. Ruscio, M. Doucleff, D. E. Wemmer & T. Head-Gordon (2008). Structure and dynamics of the Alzheimer’s Abeta21-30 peptide from the interplay of NMR experiments and simulation J. Am. Chem. Soc. 130 , 6145-6158. [link]
  163. T. Head-Gordon & R. M. Lynden-Bell (2008). Hydrophobic solvation of Gay Berne particles in modified water models. J. Chem. Phys. 128 , 104506-104512. [link]
  164. N. L. Fawzi, K. Kohlstedt, Y. Okabe, and T. Head-Gordon (2008). Protofibril assemblies of the Arctic, Dutch, and Flemish mutants of the Alzheimer’ss Abeta1-40 peptide. Biophys. J. 94 , 2007-2016. [link]
  165. M. S. Lin and T. Head-Gordon (2008). Improved energy selection of native-like loops from protein loop decoys. J. Chem. Theo. Comp. (Cover article) 4 , 515-521. [link]
  166. R. K. Murarka and T. Head-Gordon (2008). Dielectric relaxation of aqueous solutions of amphiphilic and hydrophilic peptides. J. Phys. Chem. B 112 , 179-186. [link]
  167. E.-H. Yap, N. Lux Fawzi & T. Head-Gordon (2008). A coarse-grained α−carbon protein model with anisotropic hydrogen-bonding. Proteins, Struct. Func. Bioinformatics70, 626-638. [link]
  168. R. K. Murarka and T. Head-Gordon (2007). Single particle and collective hydration dynamics of hydrophobic and hydrophilic peptides.  J. Chem. Phys. 126, 215101-215109. [link]
  169. M. S. Lin, N. L. Fawzi, and T. Head-Gordon (2007).  Hydrophobic potential of mean force as a solvent function for protein structure prediction.  Structure 15, 727-740. [link]
  170. M. E. Johnson, T. Head-Gordon, A. A. Louis (2007). Representability problems for coarse-grained water models. J. Chem. Phys. 126, 144509-144519. [link]
  171. C. Malardier-Jugroot and T. Head-Gordon (2007). Separable cooperative and localized translational motions of confined water. Phys. Chem. Chem. Phys. 9, 1962-1971. [link]
  172. T. Head-Gordon and S. Rick (2007). Consequences of chain networks on thermodynamic, dielectric and structural properties for liquid water. Phys. Chem. Chem. Phys. 8, 83-91. [link] Also see discussion in Hot Topics: [link]
  173. N. Lux Fawzi, Y. Okabe, E.-H. Yap & T. Head-Gordon (2007). Fibril stability and elongation studies of the Alzheimer’s Aβ1-40 peptide. J. Mol. Biol. 365, 535-550. [link]
  174. R. M. Lynden-Bell and T. Head-Gordon (2006). Solvation in modified water models:     toward understanding hydrophobic solvation. Mol. Phys. 104, 3593-3605. [link]
  175. T. Head-Gordon and ME Johnson (2006). Tetrahedral structure or chains for liquid water. Proc. Natl. Acad. Sci. 103, 7973-7977. [pdf] Also see Nature Highlight: [link]
  176. I. Lotan and T. Head-Gordon (2006). An analytical electrostatic model for salt screened interactions between multiple proteins. J. Chem. Theory Comp. 2, 541-555 [link]
  177. N. Marianayagam, N. Fawzi & T. Head-Gordon (2005). Protein folding by distributed computing and the denatured state ensemble. Proc. Natl. Acad. Sci. 102, 16684-16689 [pdf]
  178. D. Russo, R. K. Murarka, J. R.D. Copley, T. Head-Gordon (2005). Molecular view of water dynamics near model peptides.  J. Phys. Chem. B 109, 12966-12975 [link]
  179. N. Fawzi, V. Chubukov, L.A. Clark, S. Brown & T. Head-Gordon (2005). Influence of denatured and intermediate states of folding on protein aggregation. Protein Science 14, 993-1003 [link]
  180. D. Russo, R. K. Murarka, G. Hura, E. R. Verschell, J. R.D. Copley, & T. Head-Gordon (2004).  Evidence for anomalous hydration dynamics near a model hydrophobic peptide. J. Phys. Chem. B. 108, 19885-19893 [link]
  181. E. Eskow, B. Bader, R. Byrd, S. Crivelli, T. Head-Gordon, V. Lamberti and R. Schnabel (2004).  An optimization approach to the problem of protein structure prediction. Mathematical Programming 101, 497-514 [pdf]
  182. H. W. Horn, W. C. Swope, J. W. Pitera, J. D. Madura, T. J. Dick, Greg Hura, T. Head-Gordon (2004). Development of an improved four-site water model for biomolecular simulations: TIP4P-Ew. J. Chem. Phys. 120, 9665-9678. [link]
  183. S. Brown & T. Head-Gordon (2004). Intermediates in the folding of proteins L and G. Protein Sci. 13, 958-970. [link]
  184. D. Russo, G. Hura, & T. Head-Gordon (2004). Hydration dynamics near a model protein surface. Biophys. J. 86, 1852-1862  [link]
  185. S. Crivelli & T. Head-Gordon (2004). A new load balancing strategy for the solution of dynamical large tree search problems using a hierarchical approach. IBM R&D Journal 48, 153-160. [link]
  186. S. Brown, N. Fawzi, & T. Head-Gordon (2003). Coarse-grained sequences for protein folding and design. Proc. Natl. Acad. Sci 100, 10712-10717 [pdf]
  187. T. Head-Gordon & S. Brown (2003). Minimalist models for protein folding and design. Curr. Opin. Struct. Biol. 13, 160-167. [pdf]
  188. G. Hura, D. Russo, R.M. Glaeser, M. Krack, M. Parrinello, and T. Head-Gordon (2003). Water structure as a function of temperature from x-ray scattering experiments and ab initio molecular dynamics. Phys. Chem. Chem. Phys. 5, 1981-1991. [link]
  189. S. Brown & T. Head-Gordon (2003). Cool-walking: a new markov chain monte carlo sampling method. J. Comp. Chem. PAK Symposium 24, 68-76.  [pdf]
  190. T. Head-Gordon and G. Hura (2002). Water Structure from scattering experiments and simulation. Chemical Reviews 102, 2651-2670. [link]
  191.   S. J. Zhong, V. Dadarlat, T. Head-Gordon, R. m. Glaeser & K. Downing (2002). Modeling chemical bonding effects for protein electron crystallography. Acta. Cryst. A58, 162-170. [pdf]
  192. J. M. Sorenson & T. Head-Gordon (2002). Protein engineering study of Protein L by Simulation. J. Comp. Biol. 9, 35-54. [pdf]
  193. T. Head-Gordon, G. Hura, J. Sorenson,, R.M. Glaeser (2002). Pure water structure and hydration forces for protein folding, in V. V. Brazhkin. S. V. Buldyrev, V. N. Ryzhov, and H. E. Stanley, eds., New Kinds of Phase Transitions: Transformations in Disordered Substances Kluwer, Dordrecht, V. 8, 403-415.
  194. J. M. Sorenson & T. Head-Gordon (2002). Toward minimalist models of larger proteins: a ubiquitin-like protein. Proteins: Structure, Function, Genetics 46, 368-379. [link]
  195. S. Crivelli, E. Eskow, B. Bader, V. Lamberti, R. Byrd, R. Schnabel & T. Head-Gordon (2002). A physical approach to protein structure prediction. Biophys. J. 82, 36-49. [link]
  196. T. Head-Gordon and J. Wooley (2001). Computational challenges in structural and functional genomics. IBM Systems Journal: Deep Computing in the Life Sciences 40, 265-296. [pdf]
  197. C. P. Hsu, G. R. Fleming, M. Head-Gordon, and T. Head-Gordon (2001). Excitation energy transfer in condensed media. J. Chem. Phys. 114, 3065-3072 [pdf]
  198. J. M. Sorenson & T. Head-Gordon (2000). Matching simulation and experiment: a new simplified model for simulating protein folding. J. Comp. Bio. 7, 469-481.[pdf]
  199. G. Hura, J. Sorenson, R.M. Glaeser & T. Head-Gordon (2000). A high-quality x-ray scattering experiment on liquid water at ambient conditions. J. Chem. Phys. 113, 9140-9148.[link]
  200. J. Sorenson, G. Hura, R.M. Glaeser & T. Head-Gordon (2000). What can x-ray scattering tell us about the radial distribution functions of water? J. Chem. Phys 113, 9149-9161. [link]
  201. A. Azmi, R. H. Byrd, E. Eskow, R. Schnabel, S. Crivelli, T. M. Philip, T. Head-Gordon (2000). Predicting protein tertiary structure using a global optimization algorithm with smoothing. Optimization in Computational Chemistry and Molecular Biology: Local and Global Approaches, C. A. Floudas and P. M. Pardalos, editors (Kluwer Academic Publishers, Netherlands), 1-18.
  202. S. Crivelli, T. M. Philip, R. Byrd, E. Eskow, R. Schnabel, R. C. Yu, T. Head-Gordon (2000). A global optimization strategy for predicting protein tertiary structure: α−helical proteins. Comp. & Chem 24, 489-497 [pdf]
  203. S. Crivelli, T. Head-Gordon, R. H. Byrd, E. Eskow, R. Schnabel (1999). A hierarchical approach for parallelization of a global optimization method for protein structure prediction. Lecture Notes in Computer Science, Euro-Par ’99, P. Amestoy, P. Berger, M. Dayde, I. Duff, V. Fraysse, L. Giraud, D. Ruiz (eds.), pg. 578-585.[]
  204. G. Hura, J. M. Sorenson, R. M. Glaeser & T. Head-Gordon (1999). Solution x-ray scattering as a probe of hydration-dependent structuring of aqueous solutions. Perspectives in Drug Discovery and Design 17, 97-118. [pdf]
  205. J. M. Sorenson & T. Head-Gordon (1999). Redesigning the hydrophobic core of a model β-sheet protein: destabilizing traps through a threading approach. Proteins: Structure, Function, Genetics 37, 582-91.
  206. C. P. Hsu, M. Head-Gordon & T. Head-Gordon (1999). Reaction field cavity optimization: A born-again Born model for ionic hydration. J. Chem. Phys. 111, 9700-9704. [link]
  207. J. M. Sorenson, G. Hura, A, K, Soper, A. Pertsemlidis & T. Head-Gordon (1999). Determining the role of hydration forces in protein folding. Feature Article for J. Phys. Chem. B 103, 5413-5426. [link]
  208. A. Pertsemlidis, A. K. Soper, J. M. Sorenson & T. Head-Gordon (1999). Evidence for microscopic, long-range hydration forces for a hydrophobic amino acid. Proc. Natl. Acad. Sci. 96, 481-486. [pdf]
  209. S. Chang, T. Head-Gordon, R. M. Glaeser & K. Downing (1999). Chemical bonding effects in the determination of protein structures by electron crystallography. Acta. Cryst. A55, 305-313. [pdf]
  210. C. P. Hsu, M. Head-Gordon, & T. Head-Gordon (1999). Electronic reaction field cavity optimization: extension to solvation of molecules Proceedings of the Workshop on Treatment of Electrostatic Interactions in Computer Simulations of Condensed Media (AIP, New York) 96, 350-358.
  211. J. M. Sorenson & T. Head-Gordon (1998). The importance of hydration for the kinetics and thermodynamics of protein folding: simplified lattice models. Fold & Design 3, 523-534.
  212. T. Head-Gordon, J. M. Sorenson, A. Pertsemlidis & R. M. Glaeser (1997). Differences in hydration structure near hydrophobic and hydrophilic amino acid side chains. Biophys. J. 73, 2106-2115[link]
  213. A. Pertsemlidis, A. M. Saxena, A. K. Soper, T. Head-Gordon & R. M. Glaeser (1996). Direct, structural evidence for modified solvent structure within the hydration shell of a hydrophobic amino acid. Proc. Natl. Acad. Sci. 93, 10769-10774. [pdf]
  214. T. Head-Gordon (1995). A new solvent model for hydrophobic association in water. I. Thermodynamics. J. Am. Chem. Soc. 117, 501-507. [link]
  215. R.C. Yu & T. Head-Gordon (1995). Neural network design applied to protein secondary structure prediction. Phys. Rev. E 51, 3619-3627. [link]
  216. T. Head-Gordon (1995). Is water structure around hydrophobic groups clathrate-like? Proc. Natl. Acad. Sci. USA 92, 8308-8312. [pdf]
  217. F.H. Stillinger & T. Head-Gordon (1995). Collective aspects of protein folding illustrated by a toy model. Phys. Rev. E 52, 2872-2877.  [link]
  218. T. Head-Gordon (1994). Toward quantitative protein structure prediction, in The Protein folding problem and tertiary structure prediction. K. M. Merz Jr. & S. M. Le Grand, eds. (Boston, Birkhauser), ch. 15.
  219. H.S. Shang & T. Head-Gordon (1994). Stabilization of helices in glycine  and alanine dipeptides in a reaction field model of solvent. J. Am. Chem. Soc. 116, 1528-1532. [pdf]
  220. T. Head-Gordon (1994). An efficient solvent model for study of hydrophobic phenomena. Chem. Phys. Letts. 227, 215-220 [link]
  221. M. Head-Gordon & T. Head-Gordon (1994). Analytic MP2 frequencies without fifth-order  storage. Theory and application to bifurcated hydrogen bonds in the water hexamer. Chem. Phys. Lett. 220, 122-128 [link]
  222. F.H. Stillinger & T. Head-Gordon (1993). Perturbational view of inherent structures in water. Phys. Rev. E. 47, 2484-2490 [link]
  223. T. Head-Gordon & F.H. Stillinger (1993). Toward optimal neural networks for protein structure prediction. Phys. Rev. E  48 1502-1515 [link]
  224. F.H. Stillinger, T. Head-Gordon & C.L. Hirschfeld (1993). Toy model for protein folding. Phys. Rev. E 48, 1469-1477 [link]
  225. T. Head-Gordon & F.H. Stillinger (1993). Predicting polypeptide and protein structures from amino acid sequence: antlion method applied to melittin. Biopolymers 33, 293-303.
  226. T. Head-Gordon & F.H. Stillinger (1993). An orientational perturbation theory for pure liquid water. J. Chem. Phys. 98, 3313-3327.
  227. T. Head-Gordon, F.H. Stillinger, M.H. Wright, & D.M. Gay (1992). Poly-L-alanine as a universal reference material for understanding protein energies and structures. Proc. Natl. Acad. Sci. USA 89, 11513-17. [pdf]
  228. D.M. Gay, T. Head-Gordon, F. H. Stillinger & M.H. Wright (1992). An application of constrained optimization in protein folding: the poly-l-alanine hypothesis. Forefronts, Cornell Theory Center 8, 4-6.
  229. T. Head-Gordon & F.H. Stillinger (1992). Enthalpy of knotted polypeptides. J. Phys. Chem. 96, 7796-7807.
  230. T. Head-Gordon & C.L. Brooks (1991). Virtual rigid body dynamics. Biopolymers 31, 77-100.
  231. T. Head-Gordon, M. Head-Gordon, M.J. Frisch, C.L. Brooks & J.A. Pople (1991). Theoretical study of blocked glycine and alanine dipeptide analogues. J. Am. Chem. Soc. 113, 5989-5997.
  232. T. Head-Gordon, F.H. Stillinger & J. Arrecis (1991). A strategy for finding classes of minima on a hypersurface: implications for neural network approaches to the protein folding problem. Proc. Natl. Acad. Sci. U.S.A. 88, 11076-11080. [pdf]
  233. T. Head-Gordon, M. Head-Gordon, M.J. Frisch, C.L. Brooks & J.A. Pople (1989). A theoretical study of alanine dipeptide and analogues. Int. J. Quant. Chem.: Quant. Biol. Symp. 16, 311-322.
  234. T. Head-Gordon & C. L. Brooks (1988). Evaluation of simple model descriptions of the diffusional association rate for enzyme-ligand systems. J. Phys. Chem. 93, 490.
  235. T. Head-Gordon & C.L. Brooks (1987). The role of electrostatics in the binding of small ligands to enzymes. J. Phys. Chem. 91, 3342-3349.
  236. A.B. Anderson, T.L. Gordon & M.E. Kenney (1985). Electronic and redox properties of stacked-ring silicon pthalocyanines from molecular orbital theory. J. Am. Chem. Soc. 107, 192-195