PEER-REVIEWED JOURNAL ARTICLES AND BOOK CHAPTERS

22. J. A. Wallace and J. K. Shen, “Predicting protein pKa’s with continuous constant pH molecular dynamics”, Methods Enzymol., in press, 2009.

21. J. K. Shen, “Uncovering specific electrostatic interactions in the denatured state of proteins”, under review, 2009.

20. X. Nan, A. L. O. Campbell, D. R. Powell, J. Khandogin, and G. B. Richter-Addo, "A stable hyponitrite-bridged iron porphyrin complex", J. Am. Chem. Soc., 2009, 130, 16498-16499.

19. J. W. Wickham, J. Halye, S. Kashtanov, J. Khandogin, and C. V. Rice, "Revisiting magnesium chelation by teichoic acid with phosphorus solid-state NMR and theoretical calculations", J. Phys. Chem. B, 113, 2177-2183.

18. J. Khandogin, "Modeling protonation equilibria in biological macromolecules", In Challenges and Advances in Computational Chemistry and Physics, Springer Verlag, chapt. 10, 261-284.

17. J. Qian, J. Khandogin, A. H. West, P. Cook, "Evidence for a catalytic dyad in the active site of homocitrate synthase from saccaromyces cerevisiae", Biochemistry, 2008, 47, 6851-6858.

16. J. Chen, C. L. Brooks III, and J. Khandogin, "Recent advances in implicit solvent based methods for biomolecular simulations", Curr. Opin. Struct. Biol., 2008, 18, 140-148.

15. J. Khandogin and C. L. Brooks III, "Linking folding with aggregation in Alzheimer's beta-amyloid peptides", Proc. Natl. Acad. Sci. USA, 2007, 104, 16880-16885.

14. J. Khandogin and C. L. Brooks III, "Molecular simulations of pH-mediated biological processes", In Annu. Report Comput. Chem., Elsevier, 2007, vol. 3, 3-11.

13. J. Khandogin, D. P. Raleigh, and C. L. Brooks III, "Folding intermediate in the villin headpiece domain arises from disruption of an N-terminal hydrogen-bonded network", J. Am. Chem. Soc., 2007, 129, 3056-3057.

12. J. Khandogin, J. Chen, and C. L. Brooks III, "Exploring atomistic details of pH-dependent peptide folding", Proc. Natl. Acad. Sci. USA, 2006, 103, 18546-18550.

11. J. Khandogin and C. L. Brooks III, "Toward the accurate first-principles prediction of ionization equilibria in proteins", Biochemistry, 2006, 45, 9363-9373.

10. J. Khandogin and C. L. Brooks III, "Constant pH molecular dynamics simulation with proton tautomerism", Biophys. J., 2005, 89, 141-157.

9. B. A. Gregersen, J. Khandogin, W. Thiel, and D. M. York, "Smooth solvation method for d-orbital semiempirical calculations of biological reactions II: application to transphosphorylation thio effects in solution", J. Phys. Chem. B, 2005, 109, 9799-9809.

8. J. Khandogin, B. A. Gregersen, W. Thiel, and D. M. York, "Smooth solvation method for d-orbital semiempirical calculations of biological reactions I: implementation", J. Phys. Chem. B, 2005, 109, 536-556.

7. J. Khandogin and D. M. York, "Quantum descriptors for biological macromolecules from linear-scaling electronic structure methods", Proteins, 2004, 56, 724-737.

6. J. Khandogin, K. Musier-Forsyth, and D. M. York, "Insights into the regioselectivity and RNA binding affinity of HIV-1 nucleocapsid protein from linear-scaling quantum methods", J. Mol. Biol., 2003, 303, 993-1004.

5. J. Khandogin and D. M. York, "Quantum mechanical characterization of nucleic acids in solution: a linear-scaling study of charge fluctuations in DNA and RNA", J. Phys. Chem. B., 2002, 106, 7693-7703.

4. J. Khandogin, A. Hu, and D. M. York, "Electronic structure properties of solvated biomolecules: a quantum approach for macromolecular characterization", J. Comput. Chem., 2000, 21, 1562-1571.

3. J. Khandogin and T. Ziegler, "A simple relativistic correction to the Nuclear Spin-Spin Coupling Constant", J. Phys. Chem. A, 2000, 104, 113-120.

2. J. Khandogin and T. Ziegler, "Density functional study of nuclear magnetic resonance spin-spin coupling constants", Spectrochim. Acta A, 1999, 55, 607-624 (Special Issue "Theoretical spectroscopy: State of the Science").

1. Y. Khandogin, A.B. Alexeyev, H.-P.Liebermann, G. Hirsh, and R.J. Buenker, "Ab initio relativistic CI calculations of the spectroscopic constants and transition probabilities for the low-lying states of the BiOH/HBiO isomers", J. Mol. Spectr., 1997, 186, 22-33.