Department of Chemistry, University of Minnesota

Recent
 2006
 [2000-2005] [1990-1999]
Recent Publications     back to index
"Spherical tensor gradient operator method for integral rotation: A simple, efficient, and extendable alternative to Slater-Koster tables", Timothy J. Giese and Darrin M. York, J. Chem. Phys., 129, 016102, (2008). [DOI]
"Extension of adaptive tree code and fast multipole methods to high angular momentum particle charge densities", Timothy J. Giese and Darrin M. York, J. Comput. Chem., 29, 1895-1904, (2008). [DOI]
"Origin of Mutational Effects at the C3 and G8 Positions on Hammerhead Ribozyme Catalysis from Molecular Dynamics Simulations", Tai-Sung Lee and Darrin M. York, J. Am. Chem. Soc., accepted. [DOI]
"Solvent structure and hammerhead ribozyme catalysis", Monika Martick, Tai-Sung Lee, Darrin M. York, and William G. Scott, Chem. Biol., 15, 332-342, (2008). [DOI]
"Role of Mg2+ in hammerhead ribozyme catalysis from molecular simulation", Tai-Sung Lee, Carlos Silva-Lopez, George M. Giambasu, Monika Martick, William G. Scott, and Darrin M. York, J. Am. Chem. Soc., 130, 3053-3064, (2008). [DOI]
"Quantum mechanical/molecular mechanical simulation study of the mechanism of Hairpin ribozyme catalysis", Kwangho Nam, Jiali Gao, and Darrin M. York, J. Am. Chem. Soc., 130, 4680-4691, (2008). [DOI]
"Contracted auxiliary Gaussian basis integral and derivative evaluation", Timothy J. Giese and Darrin M. York, J. Chem. Phys., 128, 064104, (2008). [DOI]
"New QM/MM Models for Multi-scale Simulation of Phosphoryl Transfer Reactions in Solution", Kwangho Nam, Jiali Gao, and Darrin M. York, in Multiscale Simulation Methods for Nanomaterials, Richard B. Ross and Sanat Mohanty eds., Wiley, New York, 201-218, (2007). [DOI]
"Charge-dependent model for many-body polarization, exchange and dispersion interactions in hybrid QM/MM calculations", Timothy J. Giese and Darrin M. York, J. Chem. Phys., 127, 194101, (2007). [DOI]
"Extension of the Self-Consistent-Charge Tight-Binding-Density-Functional (SCC-DFTB) method: third order expansion of the DFT total energy and introduction of a modified effective Coulomb interaction", Yang Yang, Haibo Yu, Darrin M. York, Qiang Cui and Marcus Elstner, J. Phys. Chem. A, 111, 10861-10873, (2007). [DOI]
"Specific reaction parametrization of the AM1/d Hamiltonian for phosphoryl transfer reactions: H, O, and P atoms", Kwangho Nam, Qiang Cui, Jiali Gao, and Darrin M. York, J. Chem. Theory Comput., 3, 486-504, (2007). [DOI]
"Insight into the role of Mg2+ in hammerhead ribozyme catalysis from x-ray crystallography and molecular dynamics simulation", Tai-Sung Lee, Carlos Silva-Lopez, Monika Martick, William G. Scott, and Darrin M. York, J. Chem. Theory Comput., 3, 325-327, (2007). [DOI]
"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., 28, 495-507, (2007). [DOI]
2006 Publications     back to index
"Simulations 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, in Modelling Molecular Structure and Reactivity in Biological Systems, Kevin J. Naidoo, John Brady, Martin J. Field, Jiali Gao, and Michael Hann eds., Royal Society of Chemistry, Cambridge, 181-192, (2006).
"Enzyme dynamics and tunneling enhanced by compression in the hydrogen abstraction catalyzed by soybean lipoxygenase-1", Ismael Tejero, Mireia Garcia-Viloca, Àngels González-Lafont, José M. Lluch, and Darrin M. York, J. Phys. Chem. B, 110, 24708-24719, (2006). [DOI]
"Transesterification thio effects of phosphate diesters: free energy barriers and kinetic and equilibrium isotope effects from density-functional theory", Yun Liu, Brent A. Gregersen, Alvan Hengge, and Darrin M. York, Biochemistry, 45, 10043-10053, (2006). [DOI]
"Nucleophilic attack on phosphate diesters: a density functional study of in-line reactivity in dianionic, monoanionic, and neutral systems", Xabier Lopez, Annick Dejagere, Fabrice Leclerc, Darrin M. York, and Martin Karplus, J. Phys. Chem. B, 110, 11525-11539, (2006). [DOI]
"Normal modes of redox-active tyrosine: conformation dependence and comparison to experiment", Kevin Range, Idelisa Ayala, Darrin M. York, and Bridgette A. Barry, J. Phys. Chem. B, 110, 10970-10981, (2006). [DOI]
"QCRNA 1.0: A database of quantum calculations for RNA catalysis", Timothy J. Giese, Brent A. Gregersen, Yun Liu, Kwangho Nam, Evelyn Mayaan, Adam Moser, Kevin Range, Olalla Nieto Faza, Carlos Silva Lopez, Angel Rodriguez de Lera, Gijs Schaftenaar, Xabier Lopez, Tai-Sung Lee, George Karypis, and Darrin M. York, J. Mol. Graph. Model., 25, 423-433, (2006). [DOI]
"Multi-level and density functional electronic structure calculations of proton affinities and gas-phase basicities involved in biological phosphoryl transfer", Kevin Range, Carlos Silva Lopez, Adam Moser, and Darrin M. York, J. Phys. Chem. A, 110, 791-797, (2006). [DOI]
"A charge-scaling implementation of the variational electrostatic projection method", Brent A. Gregersen and Darrin M. York, J. Comput. Chem., 27, 103-115, (2006). [DOI]
2000-2005 Publications     back to index
"Improvement of semiempirical response properties with charge-dependent response density", Timothy J. Giese and Darrin M. York, J. Chem. Phys., 123, 164108, (2005). [DOI]
"A semiempirical quantum model for hydrogen bonded nucleic acid base pairs", Timothy J. Giese, Edward Sherer, Christopher Cramer, and Darrin M. York, J. Chem. Theory Comput., 1, 1275-1285, (2005). [DOI]
"Solvent polarization and kinetic isotope effects in nitroethane deprotonation and implications to the nitroalkane oxidase reaction", Dan T. Major, Darrin M. York, and Jiali Gao, J. Am. Chem. Soc., 127, 16374-16375, (2005). [DOI]
"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). [DOI]
"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). [DOI]
"Ellipticity: a convenient tool to characterize electrocyclic reactions", Carlos Silva Lopez, Olalla Nieto Faza, Fernando P. Cossio, Darrin M. York, and Angel R. de Lera, Chem. Eur. J., 11, 1734-1738, (2005). [DOI]
"Pseudorotation barriers of biological oxyphosphoranes: a challenge for simulations of ribozyme catalysis", Carlos Silva Lopez, Olalla Nieto Faza, Angel R. de Lera, and Darrin M. York, Chem. Eur. J., 11, 2081-2093, (2005). [DOI]
"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). [DOI]
"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). [DOI]
"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). [DOI]
"Smooth solvation method for d-orbital semiempirical calculations of biological reactions. 2. 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). [DOI]
"Smooth solvation method for d-orbital semiempirical calculations of biological reactions. 1. Implementation", Jana Khandogin, Brent A. Gregersen, Walter Thiel, and Darrin M. York, J. Phys. Chem. B, 109, 9799-9809, (2005). [DOI]
"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). [DOI]
"Theoretical methods that help understanding the structure and reactivity of gas phase ions", J. M. Mercero, J. M. Matxain, X. Lopez, D. M. York, A. Largo, L. A. Eriksson, and J. M. Ugalde, Int. J. Mass. Spectrom., 240, 37-99, (2005). [DOI]
"The contribution of phosphate-phosphate repulsions to the free energy of DNA bending", Kevin Range, Evelyn Mayaan, L. J. Maher III, and Darrin M. York, Nucleic Acids Res., 33, 1257-1268, (2005). [DOI]
"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). [DOI]
"Pseudorotation of natural and chemically modified biological phosphoranes: implications for RNA catalysis", Carlos Silva Lopez, Olalla Nieto Faza, Brent A. Gregersen, Xabier Lopez, Angel R. de Lera, and Darrin M. York, Chem. Phys. Chem., 5, 1045-1049, (2004). [DOI]
"High-level ab initio methods for calculation of accurate potential energy surfaces of van der Waals complexes", Timothy J. Giese and Darrin M. York, Int. J. Quantum Chem., 98, 388-408, (2004). [DOI]
"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). [DOI]
"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). [DOI]
"Structure and binding of Mg(II) ions and di-metal bridge complexes with biological phosphates and phosphoranes", Evelyn Mayaan, Kevin Range, and Darrin M. York, J. Biol. Inorg. Chem., 9, 807-817, (2004). [DOI]
"Design and application of a multicoefficient correlation method for dispersion interactions", Timothy J. Giese and Darrin M. York, J. Chem. Phys., 120, 590-602, (2004). [DOI]
"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). [DOI]
"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., 120, 9903-9906, (2004). [DOI]
"Theoretical study of the vinyl allene oxide to cyclopent-2-en-1-one rearrangement: mechanism, torquoselectivity and solvent effects ", Carlos Silva Lopez, Olalla Nieto Faza, Darrin M. York, and Angel R. de Lera, J. Org. Chem., 69, 3635-3644, (2004). [DOI]
"Quantum descriptors for biological macromolecules from linear-scaling electronic structure methods", Jana Khandogin and Darrin M. York, Proteins, 56, 724-737, (2004). [DOI]
"Hybrid QM/MM study of thio effects in transphosphorylation reactions", Brent A. Gregersen, Xabier Lopez, and Darrin M. York, J. Am. Chem. Soc., 125, 7178-7179, (2003). [DOI]
"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). [DOI]
"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). [DOI]
"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). [DOI]
"Preface to proceedings of the symposium on methods and applications of combined quantum mechanical and molecular mechanical potentials (2001)", J. Gao and D. York, Theor. Chem. Acc., 109, 99, (2003). [DOI]
"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). [DOI]
"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). [DOI]
"Spectroscopic properties of tyrosyl radicals in dipeptides", Idelisa Ayala, Kevin Range, Darrin York, and Bridgette A. Barry, J. Am. Chem. Soc., 124, 5496-5505, (2002). [DOI]
"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). [DOI]
"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). [DOI]
"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). [DOI]
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). [DOI]
"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). [DOI]
"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 A. Thompson eds., American Chemical Society, Whashington, DC, 275-287, (1998).
"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). [DOI]
"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 Bartolotti, Richard L. Wells, and Weitao Yang, J. Am. Chem. Soc., 118, 5732-5736, (1996). [DOI]
"Quantum mechanical study of aqueous polarization effects on biological macromolecules", Darrin M. York, Tai-Sung Lee, and Weitao Yang, J. Am. Chem. Soc., 118, 10940-10941, (1996). [DOI]
"Linear-scaling semiempirical quantum calculations for macromolecules", Tai-Sung Lee, Darrin M. York, and Weitao Yang, J. Chem. Phys., 105, 2744-2750, (1996). [DOI]
"A chemical potential equalization method for molecular simulations", Darrin M. York and Weitao Yang, J. Chem. Phys., 104, 159-172, (1996). [DOI]
"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, (1995). [DOI]
"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., 117, 5001-5002, (1995). [DOI]
"A generalized formulation of electronegativity equalization from density-functional theory", Darrin M. York, Int. J. Quantum Chem., 56, 385-394, (1995). [DOI]
"The effect of hydrostatic pressure on protein crystals investigated by molecular simulation", Darrin M. York, Tom Darden, and Lee G. Pedersen, Proceedings of the 27th Jerusalem Symposia on Quantum Chemistry and Biochemistry: Modelling of Biomolecular Structures and Mechanisms, 27, 203-215, (1995).
"The fast Fourier-Poisson method for calculating Ewald sums", Darrin M. York and Weitao Yang, J. Chem. Phys., 101, 3298-3300, (1994). [DOI]
"Simulations of the solution structure of the HIV-1 protease in the presence and absence of bound zinc", Darrin M. York, Libero Bartolotti, Tom Darden, and Lee G. Pedersen, J. Comput. Chem., 15, 61-71, (1994). [DOI]
"Density-functional calculations of the structure and stability of C240", Darrin M. York, Jian Ping Lu, and Weitao Yang, Phys. Rev. B, 49, 8526-8528, (1994). [DOI]
"Atomic level accuracy in simulations of protein crystals", Darrin M. York, Alexander Wlodawer, Lee G. Pedersen, and Tom Darden, Proc. Natl. Acad. Sci. USA, 91, 8715-8718, (1994). [DOI]
"Molecular dynamics simulation of HIV-1 protease in a crystalline environment and in solution", Darrin M. York, T. A. Darden, L. G. Pedersen, and M. W. Anderson, Biochemistry, 32, 1443-1453, (1993). [DOI]
"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). [DOI]
"Particle mesh Ewald: An N log(N) method for Ewald sums in large systems", Tom Darden, Darrin York, and Lee Pedersen, J. Chem. Phys., 98, 10089-10092, (1993). [DOI]
"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., 99, 8345-8348, (1993). [DOI]
"The interaction of Na(I), Ca(II), and Mg(II) metal ions with duplex DNA: a theoretical modeling study", Darrin M. York, Tom Darden, David W. Deerfield, III, and Lee G. Pedersen, Int. J. Quantum Chem., 44, 145-166, (1992). [DOI]