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.