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., 2009, 466, 455-475.

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.