Publications
1. H. Lee Woodcock, Damian Moran, Paul von Rague Schleyer and H.F. Schaefer; The Almost Bottleable Triplet Carbene: 2,6-dibromo-4-tert-butyl-2',6'-bistrifluoromethyl-4'-isopropyldiphenylcarbene; J. Am. Chem. Soc.; 2001; 123(18); 4331.
2. H. Lee Woodcock, Steven S. Wesolowski, Yukio Yamaguchi, and H.F. Schaefer; Systematic Study of the Neutral Radical PH2; J. Chem. Phys. 2001; 105(20); 5037.
3. Ned H. Martin, Justin D. Brown, Kimberly H. Nance, Henry F. Schaefer III, Paul v. R. Schleyer, Zhi-Xiang Wang, and H. Lee Woodcock; Analysis of the Origin of Through-Space NMR (De)shielding by Selected Organic Functional Groups; Org. Lett.;2001; 3(24); 3823.
4. H. Lee Woodcock, H.F. Schaefer, P.R. Schreiner; Problematic energy differences between cumulenes and poly-ynes: Does this point to a systematic improvement of density functional theory? J. Phys. Chem. A 2002; 106(49) 11923-11931.
5. H. Lee Woodcock, Milan Hodoscek, Paul Sherwood, Yong S. Lee, Henry F. Schaefer III, and Bernard R. Brooks; Exploring the QM/MM Replica Path Method: A Pathway Optimization of the Chorismate to Prephenate Claisen Rearrangement Catalyzed by Chorismate; Theor. Chem. Acc. 2003; 109(3); 140-148.
6. Moran D, H. Lee Woodcock, Chen ZF, Schaefer HF, Schleyer PvR; The viability of small endohedral hydrocarbon cage complexes: X@C4H4, X@C8H8, X@C8H14, X@C10H16, X@C12H12, and X@C16H16; J. Am. Chem. Soc.; 2003; 125 (37); 11442-11451.
7. Papas BN, Wang SY, DeYonker NJ, H. Lee Woodcock, Schaefer HF; Naphthalenyl, anthracenyl, tetracenyl, and pentacenyl radicals and their anions; J. Phys. Chem. A; 2003; 107 (32); 6311-6316.
8. Speakman LD, Papas BN, H. Lee Woodcock, Schaefer HF; A reinterpretation of microwave and infrared spectroscopic studies of benzaldehyde; J. Chem. Phys.; 2004; 120 (9); 4247-4250.
9. Y. Shao, L. Fusti-Molnar, Y. Jung, J. Kussmann, C. Ochsenfeld, S. T. Brown, A. T. B. Gilbert, L. V. lipchenko, S. V. Levchenko, D. P. ONeill, R. A. Distasio, R. C. Lochan, T. Wang, G. J. O. Beran, N. A. Besley, J. M. Herbert, C. Y. Lin, T. Van Voorhis, S. H. Chien, A. Sodt, R. P. Steele, V. A. Rassolov, P. E. Maslen, P. P. Korambath, R. D. Adamson, B. Austin, J. Baker, E. F. C. Byrd, H. Daschel, R. J. Doerksen, A. Dreuw, B. D. Dunietz, A. D. Dutoi, T. R. Furlani, S. R. Gwaltney, A. Heyden, S. Hirata, C. P. Hsu, G. Kedziora, R. Z. Khalliulin, P. Klunzinger, A. M. Lee, M. S. Lee, W. Liang, I. Lotan, N. Nair, B. Peters, E. I. Proynov, P. A. Pieniazek, Y. M. Rhee, J. Ritchie, E. Rosta, D. C. Sherrill, A. C. Simmonett, J. E. Subotnik, H. Lee Woodcock, W. Zhang, A. T. Bell, A. K. Chakraborty, D. M. Chipman, F. J. Keil, A. Warshel, W. J. Hehre, H. F. Schaefer, J. Kong, A. I. Krylov, P. M. W. Gill, M. Head-Gordon; Advances in methods and algorithms in a modern quantum chemistry program package. (Phys. Chem. Chem. Phys.); 2006; 8; 3172-3191.
10. H. Lee Woodcock, Milan Hodosceck, Andrew T.B. Gilbert, Peter M.W. Gill, H.F. Schaefer, Bernard R. Brooks; Interfacing CHARMM and Q-Chem to perform QM/MM and QM/MM reaction pathway calculations. J. Comp. Chem.; 2007; 28(9); 1485-1502.
11. H. Lee Woodcock, Damian Moran, Paul v.R. Schleyer, H.F. Schaefer; Carbene Stabilization by Aryl Substitudents. Is Bigger Better? J. Am. Chem. Soc.; 2007; 129(12); 3763-3770.
12. H. Lee Woodcock, R. W. Pastor, A. D. MacKerell, B. R. Brooks; Ab initio modeling of glycosyl torsions and anomeric effects in a model carbohydrate : 2-Ethoxy Tetrahydropyran. Biophys. J.; 2007; 93(1); 1-10.
13. H. Lee Woodcock, Milan Hodosceck, B. R. Brooks; Exploring SCC-DFTB Paths for Mapping QM/MM Reaction Mechanisms; J. Phys. Chem. A; 2007; 111(26); 5720-5728.
14. N. H. Martin, R. M. Floyd, H. Lee Woodcock and S. Huffman; Computation of Through- Space NMR Shielding Effects in Aromatic Ring π-Stacked Complexes. J. Mol. Graphics Mod.; 2008; 26(7); 1125-1130.
15. H. Lee Woodcock, B. R. Brooks, R. W. Pastor; Pathways and populations: Stereo-electronic insights into the exocyclic torsion of 5-hydroxy-methyl-tetrahydropyran. J. Am. Chem. Soc.; 2008; 130(20); 6345-6347.
16. B. T. Miller, R. P. Singh, J. B. Klauda, M. Hodoscek, B. R. Brooks, and H. Lee Woodcock* CHARMMing: A New, Flexible, Web-based front-end to CHARMM. J. Chem. Inf. Mod.; 2008; 48(9); 1920-1929.
17. H. Lee Woodcock, W. Zheng, A. Ghysels, Y. Shao, J. Kong, B. R. Brooks; Vibrational Subsystem Analysis: A Method for Probing Free Energies and Correlations in the Harmonic Limit. J. Chem. Phys.; 2008; 129; 214109.
18. B. R. Brooks, C. L. Brooks III, A. D. MacKerell, Jr., L. Nilsson, B. Roux, Y. Won, G. Archontis, C. Bartels, S. Boresch, L. Caves, Q. Cui, A. Dinner, S. Fischer, J. Gao, M. Hodoscek, K. Kuczera, T. Lazaridis, J. Ma, E. Paci, R. W. Pastor, C. B. Post, M. Schaefer, B. Tidor, R. M. Venable, H. L. Woodcock, X. Wu and M. Karplus; CHARMM The Biomolecular Simulation Program. J. Comp. Chem.; 2009; 30 (10); 1545-1614.
19. E. Rosta, H. L. Woodcock B. R. Brooks, G. Hummer; Artificial reaction coordinate "tunneling" in free energy calculations: the catalytic reaction of RNase H. J. Comp. Chem.; 2009; 30 (11); 1634-1641.
20. A. Ghysels,* H. L. Woodcock,* J. D. Larkin, B. T. Miller, Y. Shao, J. Kong, D. Van Neck, V. Van Speybroek, M. Waroquier, and B. R. Brooks; Efficient calculation of QM/MM frequencies with the Mobile Block Hessian. J. Chem. Theory. Comput., 2011; 7(2); 496-514.
21. J. C. Hargis, E. Voehringer-Martinez, H. L. Woodcock, A. Toro-Labbe, H. F. Schaefer; Characterizing the Mechanism of the Double Proton Transfer in the Formamide Dimer. J. Phys. Chem. A, 2011; 115(12); 2650-2657.
22. H. L. Woodcock,* B. T. Miller, M. Hodoscek, A. Okur, J. D. Larkin, B. R. Brooks*; MSCALE: A General Utility for Multiscale Modeling. J. Chem. Theory Comput., 2011; 7(4); 1208-1219. (Top 10 Most Read 2011)
23. S. E. Larson, G. L. Li, G. B. Rowland, D. Junge, R. C. Huang, H. L. Woodcock, J. C. Antilla; Catalytic Asymmetric Aza-Darzens Reaction with a Vaulted Biphenanthrol Magnesium Phosphate Salt. Org. Lett., 2011; 13(9); 2188-2191.
24. J. L. Belof, C. R. Cioce, X. Xu, X. P. Zhang, B. Space, H. L. Woodcock*; Characterization of Tunable Radical Metal-Carbenes: Key Intermediates in Catalytic Cyclopropanation. Organometallics, 2011; 30(10); 2739-2746.
25. M. R. Mankbadi, M. A. Barakat, M. H. Ramadan, H. L. Woodcock, J. N. Kuhn*; Iron chelation by polyamidoamine dendrimers: a second-order kinetic model for metal-amine complexation. J. Chem. Phys. B., 2011; 115(46); 13534-13540.
26. C. L. Whittington, W. A. Maza, H. L. Woodcock,* R. W. Larsen*; Understanding Ion Sensing in Zn(II) Porphyrins: Spectroscopic and Computational Studies of Nitrite/Nitrate Binding. Inorg. Chem., 2012; 51(8); 4756-4762.
27. S. L. Vankayala, J. C. Hargis, H. L. Woodcock*; Unlocking the binding and reaction mechanism of hydroxyurea substrates as biological nitric oxide donors. J. Chem. Inf. Mod., 2012; 52(5); 1288-1297.
28. D. N. Santiago, Y. Pevzner, A. A. Durand, M. P. Tran, R. R. Scheerer, K. Daniel, S. S. Sung, H. L. Woodcock, W. C. Guida, W. H. Brooks; Validation of Virtual Target Screening. J. Chem. Inf. Mod., 2012; 52(8); 2192-2203.
29. M. A. Barakat, M.H. Ramadan, M.A. Al-Ghamdi, S. S. Al-Garny, H. L. Woodcock, J.N. Kuhn; Remediation of Cu(II), Ni(II), and Cr(III) ions from simulated wastewater by dendrimer/titania composites. J Environ Manage, 2013; 117; 50-57.
30. V. A. Castillo, V.A. M. A. Barakat, M. H. Ramadan, H. L. Woodcock, J. N. Kuhn; Metal Ion Remediation by Polyamidoamine Dendrimers: A Comparison of Metal Ion, Oxidation State, and Titania Immobilization. Int. J. Environ. Sci. Tech., 2013; DOI: 10.1007/s13762-013-0346-5.
31. M. H. Ramadan, M. A. Barakat, J. N. Kuhn, H. L. Woodcock; Equilibrium and Kinetics of Pb2+ removal from aqueous solution by dendrimer/titania composites. Desalination and Water Treatment, 2013; 1(1), 1-7 (DOI: 10.1080/19443994.2013.815584).
32. R. Kumar, M. A. Barakat, Y. A. Daza, H. L. Woodcock, J. N. Kuhn; EDTA functionalized silica for removal of Cu(II), Zn(II) and Ni(II) from aqueous solution. J. Colloid Interface Sci., 2013; 408; 200-205.
33. S. L. Vankayala, J. C. Hargis, H. L. Woodcock;* How Does Catalase Release Nitric Oxide? A Computational Structure Activity Relationship Study. J. Chem. Inf. Mod., 2013; 53(11), 2591-2961.
34. J. C. Hargis, S. L. Vankayala, J. K. White, H. L. Woodcock*; Identification and characterization of non-covalent interactions that drive binding and specificity in DD-peptidases and β-lactamases. J. Chem. Theory Comput., 2014; 20(2), 855-864.
35. G. Konig, P. S. Hudson, S. Boresch,* H. L. Woodcock*; Multiscale free energy simulations: An efficient method for connecting classical MD simulations to QM or QM/MM free energies using Non-Boltzmann Bennett reweighting schemes. J. Chem. Theory Comput., 2014; 10(4), 1406–1419.
36. J. C. Hargis, J. K. White, Y. Chen, H. L. Woodcock*; Can Molecular Dynamics and QM/MM solve the Penicillin Binding Protein Protonation Puzzle?. J. Chem. Inf. Mod., 2014; 54(5), 1412–1424.
37. Y. Pevzner, D. N. Santiago, J. S. Fries, R. S. Metcalf, K. G. Daniel, L. Calcul, H. L. Woodcock, B. J. Baker, W. C. Guida, W. H. Brooks; Virtual target screening to rapidly identify potential protein targets of natural products in drug discovery. AIMS Molec. Sci., 2014; 1(2), 81-98.
38. B. T. Miller, R. P. Singh, V. Schalk, Y. Pevzner, J. Sun, C. S. Miller, S. Boresch, T. Ichiye, B. R. Brooks, H. L. Woodcock*, Web based computational chemistry education with CHARMMing I: Lessons and Tutorial. PLOS Comput. Biol., 2014; 10: e1003719.
39. F. C. Pickard, B. T. Miller, V. Schalk, M. G. Lerner, H. L. Woodcock, B. R. Brooks; Web based computational chemistry education with CHARMMing II: Coarse Grained Protein Folding. PLOS Comput. Biol., 2014; 10: e1003738.
40. B. S. Perrin, B. T. Miller, V. Schalk, H. L. Woodcock, B. R. Brooks, T. Ichiye; Web-based computational chemistry lessons in CHARMMing III: Reduction potentials of electron transfer proteins. PLOS Comput. Biol., 2014; 10: e1003739.
41. Y. Pevzner, E. Frugier, V. Schalk, A. Caflisch, H. L. Woodcock*; Fragment-based docking: Development of the CHARMMing Web user interface as a platform for Computer-Aided Drug Design. J. Chem. Inf. Mod., 2014; 54 (9), 2612–2620.
42. P. S. Hudson, J. K. White, F. L. Kearns, M. Hodoscek, S. Boresch, H. L. Woodcock*; Efficiently computing pathway free energies: New approaches based on chain-of-replica and Non-Boltzmann Bennett reweighting schemes. Biochim. Biophys. Acta, 2015; 1850(5), 944-953. (PMID: 25239198, DOI: 10.1016/j.bbagen.2014.09.016).
43. I. Weidlich, Y. Pevzner, B. T. Miller, I. Filippov, H. L. Woodcock, B. R. Brooks; Development and implementation of (Q)SAR modeling within the CHARMMing Web-user interface. J. Comput. Chem., 2015; 36(1), 62–67 (PMID: 25362883, DOI: 10.1002/jcc.23765).
44. R. W. Larsen*, A. Karolak, T. A. Word, M. T. Kemp, C. L. Whittington, H. L. Woodcock, A. van der Vaart; Photoacoustic calorimtery study of ligand photorelease from Ru(II)bis(2,2’-bipyridine)(6,6’-dimethyl-2,2’-bipyridine) complexes in aqueous solution. Chem. Phys. Lett., 2015; 619, 214-218. (DOI: 10.1016/j.cplett.2014.11.012).
45. Y. Shao, Z. Gan, E. Epifanovsky, A. T. B. Gilbert, M. Wormit, J. Kussmann, A. W. Lange, A. Behn, J. Deng, X. Feng, D. Ghosh, M. Goldey, P. R. Horn, L. D. Jacobson, I. Kaliman, R. Z. Khaliullin, T. Kus, A. Landau, J. Liu, E. I. Proynov, Y. M. Rhee, R. M. Richard, M. A. Rohrdanz, R. P. Steele, E. J. Sundstrom, H. L. Woodcock III, P. M. Zimmerman, D. Zuev, B. Albrecht, E. Alguire, B. Austin, G. J. O. Beran, Y. A. Bernard, E. Berquist, K. Brandhorst, K. B. Bravaya, S. T. Brown, D. Casanova, C.-M. Chang, Y. Chen, S. H. Chien, K. D. Closser, D. L. Crittenden, M. Diedenhofen, R. A. DiStasio Jr., H. Dop, A. D. Dutoi, R. G. Edgar, S. Fatehi, L. Fusti-Molnar, A. Ghysels, A. Golubeva-Zadorozhnaya, J. Gomes, M. W. D. Hanson-Heine, P. H. P. Harbach, A. W. Hauser, E. G. Hohenstein, Z. C. Holden, T.-C. Jagau, H. Ji, B. Kaduk, K. Khistyaev, J. Kim, J. Kim, R. A. King, P. Klunzinger, D. Kosenkov, T. Kowalczyk, C. M. Krauter, K. U. Lao, A. Laurent, K. V. Lawler, S. V. Levchenko, C. Y. Lin, F. Liu, E. Livshits, R. C. Lochan, A. Luenser, P. Manohar, S. F. Manzer, S.-P. Mao, N. Mardirossian, A. V. Marenich, S. A. Maurer, N. J. Mayhall, C. M. Oana, R. Olivares-Amaya, D. P. O'Neill, J. A. Parkhill, T. M. Perrine, R. Peverati, P. A. Pieniazek, A. Prociuk, D. R. Rehn, E. Rosta, N. J. Russ, N. Sergueev, S. M. Sharada, S. Sharmaa, D. W. Small, A. Sodt, T. Stein, D. Stuck, Y.-C. Su, A. J. W. Thom, T. Tsuchimochi, L. Vogt, O. Vydrov, T. Wang, M. A. Watson, J. Wenzel, A. White, C. F. Williams, V. Vanovschi, S. Yeganeh, S. R. Yost, Z.-Q. You, I. Y. Zhang, X. Zhang, Y. Zhou, B. R. Brooks, G. K. L. Chan, D. M. Chipman, C. J. Cramer, W. A. Goddard III, M. S. Gordon, W. J. Hehre, A. Klamt, H. F. Schaefer III, M. W. Schmidt, C. D. Sherrill, D. G. Truhlar, A. Warshel, X. Xua, A. Aspuru-Guzik R. Baer, A. T. Bell, N. A. Besley, J.-D. Chai, A. Dreuw, B. D. Dunietz, T. R. Furlani, S. R. Gwaltney, C.-P. Hsu, Y. Jung, J. Kong, D. S. Lambrecht, W. Liang, C. Ochsenfeld, V. A. Rassolov, L. V. Slipchenko, J. E. Subotnik, T. Van Voorhis, J. M. Herbert, A. I. Krylov, P. M. W. Gill, M. Head-Gordon. Advances in molecular quantum chemistry contained in the Q-Chem 4 program package. Mol. Phys., 2015; 113(2), 184-215. (DOI: 10.1080/00268976.2014.952696).
46. D. Nichols, J. C. Hargis, R. Sanishvili, P. Jaishankar, K. DeFrees, E. Smith, K. Wang, F. Prati, A. Renslo, H. L. Woodcock, Y. Chen;* Ligand-induced proton transfer and low-barrier hydrogen bond revealed by X-ray crystallography. J. Am. Chem. Soc., 2015; 137(25), 8086–8095. (DOI: 10.1021/jacs.5b00749).
47. J. Konc BT Miller, T Stular, S. Lesnik, H. L. Woodcock, BR Brooks, D. Janezic;* ProBiS-CHARMMing: Web Interface for Prediction and Optimization of Ligands in Protein Binding Sites. J. Chem. Inf. Model., 2015; 55(11), 2308−2314. (DOI: 10.1021/acs.jcim.5b00534).
48. P. S. Hudson, H. L. Woodcock,* S. Boresch;* Use of Non-equilibrium Work Methods to Compute Free Energy Differences between MM and QM Representations of Molecular Systems. J. Phys. Chem. Lett., 2015; 6(23), 4850–4856. (DOI: 10.1021/acs.jpclett.5b02164).
49. G. Konig, Y. Mei, F. Pickard, A. Simmonett, B. T. Miller, J. Herbert, H. L. Woodcock, B. R. Brooks, Y. Shao;* Computation of Hydration Free Energies Using the Multiple Environment Single System Quantum Mechanical/Molecular Mechanical (MESS-QM/MM) Method J. Chem. Theory Comput., 2015; ASAP (DOI: 10.1021/acs.jctc.5b00874).