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.

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, 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.