|
|
|
|
|
2005
Publications back to index
|
 |
"Transesterification thio effects of phosphate diesters: free
energy barriers, kinetic and equilibrium isotope effects from
density-functional theory" , Yun
Liu, Brent A. Gregersen, Alvan Hengge and Darrin M.
York
Biochemistry, submitted.
|
|
"CHARMM force field parameters for simulation of reactive
intermediates in native and thio-substituted ribozymes" ,
Evelyn Mayaan, Adam Moser, Alexander D. Mackerell, Jr. and Darrin M.
York
J. Comput. Chem., submitted.
|
|
"Density-functional study of the in-line
mechanism of
methanolysis of cyclic phosphate and thiophosphate esters in solution:
insight into thio effects in RNA transesterification" , Yun
Liu, Brent A. Gregersen, Xabier Lopez and Darrin M.
York , J. Phys. Chem. B, 109, 19987-20003 (2005). [Abstract][PDF] |
|
"Theoretical Studies of Dissociative
Phosphoryl Transfer in Interconversion of Phosphoenolpyruvate to
Phosphonopyruvate: Solvent Effects, Thio Effects, and Implications for
Enzymatic Reactions" , Dingguo Xu, Hua Guo, Yun Liu and Darrin
M. York, J. Phys. Chem. B, 109, 13827-13834 (2005). [Abstract][PDF] |
|
"Improvement of semiempirical response
properties with charge-dependent response density" , Timothy J.
Giese and Darrin M. York, J. Chem. Phys.,
in press.
|
|
"A charge-scaling implementation of the
variational
electrostatic projection method" , Brent A. Gregersen and
Darrin M. York, J. Comput. Chem.,
in press.
|
|
"Simuations of phosphoryl transfer
reactions using multi-scale quantum models", Brent A. Gregersen,
Timothy J. Giese, Yun Liu, Evelyn Mayaan, Kwangho Nam, Kevin Range, and
Darrin M. York, Royal Society of Chemistry
special issue (WATOC 2005), in press.
|
|
"Benchmark calculations of proton
affinities and gas phase basicities of molecules important in the study
of biological phosphoryl transfer", Kevin Range, Demian
Riccardi, Qiang Cui, Marcus Elstner and Darrin M. York, Phys. Chem. Chem. Phys., 7, 3070-3079 (2005). [Abstract][PDF] |
|
"A semiempirical quantum model for hydrogen
bonded nucleic acid base pairs", Timothy J. Giese and Edward C.
Sherer and Christopher J. Cramer and Darrin M. York, J. Chem. Theory Comput., in press.
|
|
"High-order discretization schemes for
biochemical applications of boundary element solvation and variational
electrostatic projection methods", Brent A. Gregersen and Darrin
M. York, J. Chem. Phys., 122,
194110 (2005).[Abstract][PDF] |
|
"An efficient
linear-scaling Ewald method for long-range electrostatic interactions
in combined QM/MM calculations", Kwangho Nam, Jiali Gao and
Darrin M. York, J. Chem. Theory Comput., 1,
2-13 (2005). [Abstract][PDF] |
|
"Kinetic isotope effects on
thio-substituted biological phosphoryl transfer reactions from
density-functional theory", Yun Liu, Xabier Lopez and Darrin M.
York, Chem. Commun. ,
31, 3909-3911 (2005). [Abstract][PDF] |
|
"Ellipticity:
A convenient tool to characterize electrocyclic reactions", Carlos Silva López, Olalla Nieto Faza, Fernando P.
Cossío, Darrin M. York and Angel R. de Lera, Chem. Eur. J., 11, 1734-1738 (2005). [Abstract][PDF]
|
|
"Pseudorotation barriers of
biological
oxyphosphoranes: a challenge for simulations of ribozyme catalysis",
Carlos Silva López, Olalla Nieto Faza, Angel R. de Lera, and
Darrin M. York, Chem. Eur. J., 11, 2081-2093 (2005). [Abstract][PDF]
|
|
"The contribution of
phosphate-phosphate repulsions to the free energy of DNA bending",
Kevin Range, Evelyn Mayaan, L. James Maher, III, and Darrin M. York, Nucleic Acids Res., 33,
1257-1268 (2005). [Abstract][PDF]
|
|
"Variational
electrostatic projection (VEP) methods for efficient modeling of the
macromolecular electrostatic and solvation environment in activated
dynamics simulations", Brent A. Gregersen and Darrin M. York, J. Phys. Chem. B, 109,
536-556 (2005). [Abstract][PDF] |
|
"Smooth solvation method
for d-orbital semiempirical
calculations of biological reactions I: Implementation", Jana
Khandogin, Brent A. Gregersen, Walter Thiel and Darrin M. York, J. Phys. Chem. B, 109, 9799-9809 (2005). [Abstract][PDF] |
|
"Smooth solvation
method for d-orbital semiempirical calculations of biological
reactions II: application to
transphosphorylation thio effects in solution.", Brent A.
Gregersen, Jana Khandogin, Walter Thiel
and Darrin M. York, J. Phys. Chem. B, 109, 9810-9817 (2005). [Abstract][PDF]
|
|
"Theoretical methods
that help understanding the structure and reactivity of gas phase ions",
J. M. Mercero, J. M. Matxain, X. Lopez, Darrin M. York , A. Largo, L.
A. Eriksson and J. M. Ugalde, Int. J. Mass.
Spectrom., 240,
37-99 (2005). [Abstract][PDF] |
|
|
|
2004 Publications back to index
|
|
"Structure
and binding of Mg(II) ions and di-metal bridge complexes with
biological phosphates and phosphoranes", Evelyn A. Mayaan, Kevin
M. Range and Darrin M. York, J. Biol. Inorg.
Chem., 9, 807-817
(2004). [Abstract][PDF] |
|
"Many-body
force field models based solely on pairwise Coulomb screening do not
simultaneously reproduce correct gas-phase and condensed-phase
polarizability limits", Timothy J. Giese and Darrin M. York, J. Chem. Phys., (Communication) 120, 9903-9906 (2004). [Abstract][PDF]
Also featured in: Virtual
Journal of Biological Physics Research, 7 (10), (2004). |
|
"Hybrid QM/MM study of
thio effects in transphosphorylation reactions: the role of solvation",
Brent A. Gregersen, Xabier Lopez and Darrin M. York, J. Am. Chem. Soc., 126,
7504-7513 (2004). [Abstract][PDF] |
|
"Theoretical
Study of the Vinyl Allene Oxide to Cyclopent-2- en-1-one Rearrangement:
Mechanism, Torquoselectivity and Solvent Effects", Carlos Silva
López, Olalla Nieto Faza, Darrin M. York and Angel R. de Lera, J. Org. Chem., 69, 3635-3644 (2004). [Abstract][PDF] |
|
"Pseudorotation
of natural and chemically modified biological phosphoranes:
implications for RNA catalysis", Carlos Silva López,
Olalla Nieto Faza, Brent A. Gregersen, Xabier Lopez, Angel R. de Lera,
and Darrin M. York, Chem.
Phys. Chem., (Communication) 5, 1045-1049 (2004).
[Abstract][PDF] |
|
"Complete basis set extrapolated potential
energy, dipole, and polarizability surfaces of alkali halide
ion-neutral weakly avoided crossings with and without applied electric
fields", Timothy J. Giese and Darrin M. York, J. Chem. Phys., 120, 7939-7948 (2004). [Abstract][PDF] |
|
"Quantum descriptors for biological
macromolecules from linear-scaling electronic structure methods",
Jana Khandogin and Darrin M. York, Proteins:
Structure, Function and Bioinformatics, 56, 724-737 (2004). [Abstract][PDF] |
|
"High-level
ab initio methods for calculation of potential energy surfaces
of van der Waals complexes", Timothy J. Giese and Darrin M.
York, Int. J. Quantum Chem., 98,
388-408 (2004). [Abstract][PDF] |
|
"Design and application of a
multi-coefficient correlation method for dispersion interactions",
Timothy J. Giese and Darrin M. York, J. Chem. Phys., 120, 590-602 (2004). [Abstract][PDF] |
|
"The structure and
stability of biological metaphosphate, phosphate and phosphorane
compounds in the gas phase and in solution", Kevin Range,
Matthew J. McGrath, Xabier Lopez and Darrin M. York, J. Am. Chem. Soc., 126, 1654-1665 (2004). [Abstract][PDF] |
|
|
|
2000-2003 Publications back to index
|
|
"Examination of the Correlation Energy and
Second Virial Coefficients from Accurate ab initio Calculations of Rare Gas Dimers",
Timothy J. Giese, Vanessa M. Audette and Darrin M. York, J. Chem. Phys., 119, 2618-2622 (2003). [Abstract][PDF]
|
|
"Insights into the regioselectivity and RNA
binding affinity of HIV-1 nucleocapsid protein from linear-scaling
quantum methods", Jana Khandogin, Karin Musier-Forsyth and
Darrin M. York, J. Mol. Biol. 330,
993-1004 (2003). [Abstract][PDF]
|
|
"Hybrid QM/MM study of thio effects in
transphosphorylation reactions", Brent A. Gregersen, Xabier
Lopez and Darrin M. York, J. Am. Chem. Soc. (Communication)
125, 7178-7179 (2003). [Abstract][PDF] |
|
"Parameterization of semiempirical methods
to treat nucleophilic attacks to biological phosphates: AM1/d
parameters for phosphorus", Xabier Lopez and Darrin M. York, Theor. Chem. Acc.
109, 149-159 (2003). [Abstract][PDF] |
|
"Fast Approximate Methods for Calculating
Nucleic Acid Base Pair Interaction Energies", Edward C. Sherer,
Darrin M. York and Christopher J. Cramer, J. Comput. Chem.24, 57-67 (2003). [Abstract][PDF] |
|
"Theoretical Studies on the Hydrolysis of
Phosphate Diesters in the Gas Phase, Solution, and RNase A",
Xabier Lopez, Darrin M. York, Annick Dejaegere and Martin Karplus, Int. J. Quantum Chem.
86, 10-26 (2002). [Abstract][PDF] |
|
"Spectroscopic Properties of Tyrosyl
Radicals in Dipeptides", Idelisa Ayala, Kevin Range,
Darrin M. York and Bridgette A. Barry, J. Am. Chem. Soc. 124, 5496-5505 (2002). [Abstract][PDF] |
|
"Quantum Mechanical Characterization of
Nucleic Acids in Solution: A Linear-Scaling Study of Charge
Fluctuations in DNA and RNA", Jana Khandogin and Darrin M. York,
J. Phys. Chem. B
106, 7693-7703 (2002). [Abstract][PDF] |
|
"Time-dependent density functional theory
calculations of molecular static and dynamic polarizabilities, cauchy
coefficients and their anisotropies with atomic numerical basis
functions", Anguang Hu, Darrin M. York and Tom K. Woo, J. Mol. Struct.
(Theochem)591,
255-266 (2002). [Abstract][PDF] |
|
"Electronic Structure
Properties of Solvated Biomolecules: A Quantum Approach for
Macromolecular Characterization", Jana Khandogin, Anguang Hu and
Darrin M. York, J. Comput. Chem.
21, 1562-1571 (2000). [Abstract][PDF] |
|
|
|
1990-1999 Publications back to index
|
|
"A
smooth solvation potential based on the Conductor-Like Screening model",
Darrin M. York and Martin Karplus, J. Phys. Chem. A 103, 11060-11079 (1999). [Abstract][PDF] |
|
"Quantum
Mechanical Treatment of Biological Macromolecules in Solution Using
Linear-Scaling Electronic Structure Methods", Darrin M. York,
Tai-Sung Lee and Weitao Yang, Phys. Rev. Lett.
80, 5011-5014 (1998). [Abstract][PDF] |
|
"Application
of linear-scaling electronic structure methods to the study of
polarization of proteins and DNA in solution", Darrin M. York,
in ACS Symposium Series 712:
Combined Quantum Mechanical and Molecular Mechanical Methods
(Jiali Gao and Mark Thompson, Eds.), Oxford University Press, New York,
1998, pp. 275-287.
|
|
"Linear-scaling
semiempirical quantum calculations for macromolecules", Tai-Sung
Lee, Darrin M. York and Weitao Yang, J. Chem. Phys.
105, 2744-2750 (1996). [Abstract][PDF] |
|
"A
chemical potential equalization method for molecular simulations",
Darrin M. York and Weitao Yang, J. Chem. Phys.
104, 159-172 (1996). [Abstract][PDF] |
|
"A
new definition of atomic charges based on a variational principle for
the electrostatic potential energy", Tai-Sung Lee, Darrin M.
York and Weitao Yang, J. Chem. Phys.
102, 7549-7556 (1996). [Abstract][PDF] |
|
"Quantum
mechanical study of aqueous polarization effects on biological
macromolecules", Darrin M. York, Tai-Sung Lee and Weitao Yang, J. Am. Chem. Soc.(Communication) 118, 10940-10941 (1996). [Abstract][PDF] |
|
"Density-functional
study of the geometries, stabilities, and bond energies of group III-V
(13-15) four-membered-ring compounds", Haihong Ni, Darrin M.
York, Lee J. Bartolotti, Richard L. Wells and Weitao Yang, J. Am. Chem. Soc. 118, 5732-5736 (1996). [Abstract][PDF] |
|
"Parameterization
and efficient implementation of a solvent model for linear-scaling
semiempirical quantum mechanical calculations of biological
macromolecules", Darrin M. York, Tai-Sung Lee and Weitao Yang, Chem. Phys. Lett. 263, 297-306 (1996). [Abstract][PDF] |
|
"Toward
the accurate modeling of DNA: the importance of long-range
electrostatics", Darrin M. York, Weitao Yang, Hsing Lee, Tom
Darden and Lee G. Pedersen J. Am. Chem. Soc. (Communication) 117, 5001-5002 (1995). [Abstract][PDF] |
|
"The
effect of hydrostatic pressure on protein crystals investigated by
molecular simulation", Darrin M. York, Tom Darden and Lee G.
Pedersen, in Proceedings of the 27th
Jerusalem Symposia on Quantum Chemistry and Biochemistry: Modelling of
Biomolecular Structures and Mechanisms (B. Pullman, A. Pullman
and J. Jortner, Eds.), Kluwer Academic Publishers, Dordrecht, 1995, pp.
203-215.
|
|
"The
fast Fourier Poisson method for calculating Ewald sums", Darrin
M. York and Weitao Yang, J. Chem. Phys. 101,
3298-3300 (1994). [Abstract][PDF] |
|
"Density-functional
calculations of the structure and stability of C240",
Darrin M. York, Jian Ping Lu and Weitao Yang, Phys. Rev. B (Rapid
Communication) 49,
8526-8528 (1994). [Abstract][PDF] |
|
"Atomic level accuracy
in simulations of protein crystals", Darrin M. York, Alexander
Wlodawer, Lee G.Pedersen and Tom Darden, Proc. Natl. Acad. Sci. 91, 8715-8718 (1994). [Abstract][PDF] |
|
"Simulations
of the solution structure of the HIV-1 protease in the presence and
absence of bound zinc", Darrin M. York, Libero J. Bartolotti,
Tom Darden and Lee G. Pedersen, J. Comput. Chem.
15, 61-71 (1994). [Abstract][PDF] |
|
"The effect of long-range electrostatic
interactions in simulations of macromolecular crystals: a comparison of
the Ewald and truncated list methods", Darrin M. York, Tom
Darden and Lee G. Pedersen, J. Chem. Phys.
(Communication)
99, 8345-8348
(1993). [Abstract][PDF] |
|
"Particle
mesh Ewald: An N log(N) method for Ewald sums in large systems",
Tom Darden and Darrin M.York and Lee G. Pedersen, J. Chem. Phys. (Communication) 98, 10089-10092 (1993). [Abstract][PDF] |
|
"Molecular Modeling
Studies Suggest That Zinc Ions Inhibit HIV-1 Protease by Binding at
Catalytic Aspartates", Darrin M. York, Tom A. Darden, Lee G.
Pedersen and Marshall W. Andersen, Environ. Health
Persp. 101, 246-250
(1993). [Abstract][PDF] |
|
"Molecular
Dynamics Simulation of HIV-1 Protease in a Crystalline Environment and
in Solution", Darrin M. York, Tom A. Darden, Lee G. Pedersen and
Marshall W. Anderson, Biochemistry 32, 1443-1453 (1993). [Abstract][PDF] |
|
"The interaction of
Na(I), Ca(II), and Mg(II) metal ions with duplex DNA: a theoretical
modeling study", Darrin M. York, Tom Darden and David W.
Deerfield, III and Lee G. Pedersen, Int. J. Quantum Chem. QBS19, 145-166 (1992). [Abstract][PDF] |
|
back to index |