39. Z. Ke, Y. Zhou, P. Hu, S. Wang, D. Xie and Y. Zhang, J. Phys. Chem. B, ASAP. ( Cover Article)
31. C. Xiao and Y. Zhang,
J.
Chem. Phys., 127,
124102 (2007).
Design-Atom Approach
for
the Quantum Mechanical/Molecular Mechanical Covalent Boundary: A
Design-Carbon Atom with Five Valence Electrons.
30. C. Xiao and Y. Zhang,
J. Phys. Chem. B , 111, 6229-6235 (2007).
Catalytic Mechanism and
Metal Specificity of Bacterial Peptide Deformylase: a
Density Functional Theory QM/MM Study.
29. L. Wang, X. Yu, P. Hu, S. Broyde and Y. Zhang, J. Am. Chem. Soc. , 129, 4731-4737 (2007).
A
Water-mediated and
Substrate-assisted Catalytic Mechanism for Sulfolobus
solfataricus DNA Polymerase IV
28. S. Wang, P. Hu and Y. Zhang,
J. Phys. Chem. B , 111, 3758-3764 (2007).
Ab
initio Quantum Mechanical/Molecular Mechanical Molecular
Dynamics Simulation of Enzyme Catalysis:
The Case of Histone Lysine
Methyltransferase SET7/9
27. C. Corminboeuf, P. Hu, M. E. Tuckerman and Y. Zhang, J. Am. Chem. Soc. (Communication) , 128, 4530-4531 (2006).
Unexpected
Deacetylation Mechanism
Suggested by a Density Functional Theory QM/MM Study of
Histone-Deacetylase-Like Protein
26. P. Hu and Y. Zhang,
J. Am. Chem. Soc. , 128, 1272-1278 (2006).
Catalytic
Mechanism and
Product Specificity of the Histone Lysine Methyltransferase
SET7/9. An
ab initio
QM/MM-FE
Study with Multiple Initial Structures.
25. Y. Cheng, Y. Zhang
and J. A. McCammon, Protein
Sci. , 15, 672-683
(2006).
How
does Activation Loop
Phosphorylation Modulate Catalytic Activity in the cAMP-dependent
Protein Kinase:
A Theoretical Study.
24. V. V. Karambelkar, C. Xiao, Y. Zhang, A. Sarjeant and D. P.
Goldberg, Inorg. Chem. ,
45, 1409--1411 (2006).
Geometric
Preferences in Iron(II) and Zinc(II)
Model Complexes of Peptide Deformylase.
23. Y. Zhang, Theor. Chem. Acc. , Special Issue of ``New Perspectives in
Theoretical Chemistry'' , 116,
43-50 (2006).
Pseudobond
ab initio QM/MM
approach and its Applications to
Enzyme Reactions.
22. C. F. Wong, J. Kua, Y.
Zhang, T. P. Straatsma and J. A. McCammon, Proteins, 61, 850-858 (2005).
Molecular
Docking of Balanol to
Dynamics Snapshots of Protein Kinase A.
21. X. H. Chen, Y.
Zhang, J. Z.H. Zhang, J.
Chem. Phys., 122,
184105 (2005).
An
efficient approach for ab
initio energy calculation of biopolymers.
20. Y. Zhang,
J. Chem. Phys., 122, 024114 (2005).
Improved Pseudobonds for Combined
ab initio Quantum Mechanical/Molecular Mechanical (QM/MM) Methods.
19. Y. Cheng, Y. Zhang,
and J. A. McCammon, J. Am. Chem. Soc.,
.
How Does the cAMP-Dependent
Protein Kinase Catalyze the Phosphorylation Reaction: an ab
initio QM/MM Study
18. A. M. Gao, D.W. Zhang, J. Z.H. Zhang and
Y. Zhang ,
Chem. Phys. Lett., 394, 293-297 (2004).
An
efficient linear scaling method for ab initio calculation of electron
density of proteins.
17. J. Kua, Y. Zhang, A. C.
Eslami, J. R. Butler, and J. A. McCammon, Protein Sci., 12, 2675-2684 (2003)
Studying
the Roles of W86, E202, Y337 in Binding of Acetylcholine to
Acetylcholinesterase using a Combined Molecular Dynamics and Multiple
Docking Approach
16. G. A. Cisneros, H. Liu, Y.
Zhang, and W. Yang, J. Am. Chem. Soc., 125,
10384-10393 (2003).
Ab
Initio QM/MM Study Shows There Is No General Acid in the Reaction
Catalyzed by 4-Oxalocrotonate Tautomerase
15. Y. Zhang, J. Kua and J.
A. McCammon, J. Phys. Chem. B, 107, 4459-4463 (2003).
Influence
of Structural Fluctuation on Enzyme Reaction Energy Barriers in
Combined Quantum Mechanical/Molecular Mechanical Studies.
14. Y. Zhang and J. A.
McCammon, J. Chem. Phys., 118, 1821-1827 (2003).
Studying
the Affinity and Kinetics of Molecular Association with Molecular
Dynamics Simulation.
13. Y. Zhang, J. Kua and J.
A. McCammon, J. Am. Chem. Soc., 124, 10572-10577
(2002).
Role
of the Catalytic Triad and Oxyanion Hole in
Acetylcholinesterase Catalysis: An ab initio QM/MM Study.
12. J. Kua, Y. Zhang and J.
A. McCammon, J. Am. Chem. Soc., 124, 8260-8267 (2002).
Studying
Enzyme Binding Specificity in Acetylcholinesterase using a Combined
Molecular Dynamics and Multiple Docking Approach.
11. Y. Zhang, H. Liu, and
W. Yang, ``Ab initio qm/mm and free energy
calculationsof enzyme reactions,''
in Computational Methods for Macromolecules -Challenges and
Applications (T.~Schlick and H.~H. Gan, eds.), 332-354,
Springer-Verlag, 2002.
10. Y. Zhang, H. Liu and W. Yang , J. Chem. Phys, 112, 3483-3492 (2000). Free energy calculations on enzyme reactions with an efficient iterative procedure to determine minimum energy paths on a combined ab initio QM/MM potential
9. H. Liu, Y. Zhang and W.
Yang , J. Am. Chem. Soc. , 122, 6560-6570 (2000).
How
is the active site of enolase organized to catalyze two different
reaction steps?
8. W. Yang, Y. Zhang and P.
W. Ayers, Phys. Rev. Lett., 84, 5172-5175 (2000).
Degenerate
Ground States and a Fractional Number of Electrons in Density and
Reduced Density Matrix Functional Theory,
7. Y. Zhang and W. Yang, Theore.
Chem. Acc., 103, 346-348 (2000).
Perspective
on ``Density-Functional Theory for Fractional Particle
Number:Derivative Discontinuities of the Energy'' by J.P. Perdew, R.G.
Parr,M. Levy and J.L. Balduz,Jr.
6. C. Enkvist, Y. Zhang and
W. Yang, Int. J. Quan. Chem., 79, 325-329 (2000).
Density
Functional Study of a Weakly Hydrogen Bonded Benzene-Ammonia Complex:
the Importance of the Exchange Functional .
5. Y. Zhang, T. S. Lee and
W. Yang, J. Chem. Phys., 110, 46-54 (1999).
A
Pseudobond Approach to Combining Quantum Mechanical and Molecular
Mechanical Methods.
4. Y. Zhang and W. Yang, J.
Chem. Phys.,109, 2604-2608 (1998).
A
Challenge for Density Functionals: Self-interaction Error Increases
for Systems with a Noninteger Number of Electrons.
3. Y. Zhang and W. Yang, Phys.
Rev. Lett., 80, 890 (1998).
Comment on
"Generalized Gradient Approximation Made Simple" .
2. Y. Zhang, W. Pan and W.
Yang, J. Chem. Phys., 107, 7921-7925 (1997).
Describing
van der Waals Interactions in Diatomic Molecules with Generalized
Gradient Approximations: the role of the Exchange Functional .
1. Y. Zhang, G. Wang and Y.
Jiang, J. of Nanjing Univ. (Natural Science Edition), 29,
400-406 (1993).
Application of the Faraday Effect in Chemistry.