New developments in applying quantum mechanics to proteins.

[1]  Minoru Sakurai,et al.  Study of the Opsin Shift of Bacteriorhodopsin: Insight from QM/MM Calculations with Electronic Polarization Effects of the Protein Environment , 2001 .

[2]  J. M. Lluch,et al.  A QM/MM study of the racemization of vinylglycolate catalyzed by mandelate racemase enzyme. , 2001, Journal of the American Chemical Society.

[3]  Richard J. Hall,et al.  Aspects of hybrid QM/MM calculations: The treatment of the QM/MM interface region and geometry optimization with an application to chorismate mutase , 2000, J. Comput. Chem..

[4]  W F van Gunsteren,et al.  Molecular‐dynamics simulation of the β domain of metallothionein with a semi‐empirical treatment of the metal core , 2000, Proteins.

[5]  A. Warshel,et al.  Remarkable rate enhancement of orotidine 5'-monophosphate decarboxylase is due to transition-state stabilization rather than to ground-state destabilization. , 2000, Biochemistry.

[6]  J. Bertrán,et al.  A QM/MM Study of the Conformational Equilibria in the Chorismate Mutase Active Site. The Role of the Enzymatic Deformation Energy Contribution , 2000 .

[7]  Iwao Ohmine,et al.  Proton Transfer in Bacteriorhodopsin: Structure, Excitation, IR Spectra, and Potential Energy Surface Analyses by an ab Initio QM/MM Method , 2000 .

[8]  Manuel F. Ruiz-López,et al.  Calibration of the Quantum/Classical Hamiltonian in Semiempirical QM/MM AM1 and PM3 Methods , 2000 .

[9]  Kenneth M. Merz,et al.  Quantum mechanical/quantum mechanical methods. I. A divide and conquer strategy for solving the Schrödinger equation for large molecular systems using a composite density functional–semiempirical Hamiltonian , 2000 .

[10]  D. Fairlie,et al.  Is Oxidative Damage by β-Amyloid and Prion Peptides Mediated by Hydrogen Atom Transfer from Glycine α-Carbon to Methionine Sulfur within β-Sheets? , 2000 .

[11]  M. Rooman,et al.  Contribution of cation-pi interactions to the stability of protein-DNA complexes. , 2000, Journal of molecular biology.

[12]  Charles L. Brooks,et al.  Are Many-Body Effects Important in Protein Folding? , 2000 .

[13]  J. Hajdu,et al.  Quantum mechanical interpretation of nitrite reduction by cytochrome cd1 nitrite reductase from Paracoccus pantotrophus. , 2000, Biochemistry.

[14]  Martin J. Field,et al.  The dynamo library for molecular simulations using hybrid quantum mechanical and molecular mechanical potentials , 2000, J. Comput. Chem..

[15]  S. Shaik,et al.  A Model “Rebound” Mechanism of Hydroxylation by Cytochrome P450: Stepwise and Effectively Concerted Pathways, and Their Reactivity Patterns , 2000 .

[16]  Lars Ridder,et al.  A Quantum Mechanical/Molecular Mechanical Study of the Hydroxylation of Phenol and Halogenated Derivatives by Phenol Hydroxylase , 2000 .

[17]  I. Tvaroška,et al.  Ab Initio Molecular Orbital Study of the Catalytic Mechanism of Glycosyltransferases: Description of Reaction Pathways and Determination of Transition-State Structures for Inverting N-Acetylglucosaminyltransferases , 2000 .

[18]  P. Siegbahn,et al.  A Mechanistic Study of Isopenicillin N Formation Using Density Functional Theory , 2000 .

[19]  Martin J. Field,et al.  The generalized hybrid orbital method for combined quantum mechanical/molecular mechanical calculations: formulation and tests of the analytical derivatives , 2000 .

[20]  Martin J. Field,et al.  A Hybrid-Potential Free-Energy Study of the Isomerization Step of the Acetohydroxy Acid Isomeroreductase Reaction , 2000 .

[21]  W. Goddard,et al.  Stabilization of α-Helices by Dipole−Dipole Interactions within α-Helices , 2000 .

[22]  Alistair P. Rendell,et al.  Comparison of enzyme polarization of ligands and charge‐transfer effects for dihydrofolate reductase using point‐charge embedded ab initio quantum mechanical and linear‐scaling semiempirical quantum mechanical methods , 2000 .

[23]  A. Nemukhin,et al.  Quantum Chemical Studies of Reactions of the Cyclic Disulfides with the Zinc Finger Domains in the HIV-1 Nucleocapsid Protein (NCp7) , 2000 .

[24]  Weitao Yang,et al.  How Is the Active Site of Enolase Organized To Catalyze Two Different Reaction Steps , 2000 .

[25]  Jan H. Jensen,et al.  QM/MM Boundaries Across Covalent Bonds: A Frozen Localized Molecular Orbital-Based Approach for the Effective Fragment Potential Method , 2000 .

[26]  H. Scheraga,et al.  Ion Pair Interactions in Aqueous Solution: Self-Consistent Reaction Field (SCRF) Calculations with Some Explicit Water Molecules , 2000 .

[27]  Rubicelia Vargas,et al.  How Strong Is the Cα−H···OC Hydrogen Bond? , 2000 .

[28]  Scott R. Wilson,et al.  Experimental, Hartree-Fock, and Density Functional Theory Investigations of the Charge Density, Dipole Moment, Electrostatic Potential, and Electric Field Gradients in L-Asparagine Monohydrate , 2000 .

[29]  Sharon Hammes-Schiffer,et al.  Computational Studies of the Mechanism for Proton and Hydride Transfer in Liver Alcohol Dehydrogenase , 2000 .

[30]  R. Friesner,et al.  Frozen orbital QM/MM methods for density functional theory , 2000 .

[31]  Dimas Suárez,et al.  Zinc Metallo-β-Lactamase from Bacteroides fragilis: A Quantum Chemical Study on Model Systems of the Active Site , 2000 .

[32]  J. Gready,et al.  Combined Quantum and Molecular Mechanics (QM/MM) Study of the Ionization State of 8-Methylpterin Substrate Bound to Dihydrofolate Reductase , 2000 .

[33]  Sangyoub Lee,et al.  Ab Initio Studies on the Catalytic Mechanism of Aspartic Proteinases: Nucleophilic versus General Acid/General Base Mechanism , 2000 .

[34]  Alistair P. Rendell,et al.  Comparison of linear-scaling semiempirical methods and combined quantum mechanical/molecular mechanical methods applied to enzyme reactions , 2000 .

[35]  M. Karplus,et al.  Molecular Properties from Combined QM/MM Methods. 2. Chemical Shifts in Large Molecules , 2000 .

[36]  Yixiang Cao,et al.  Large Scale ab Initio Quantum Chemical Calculation of the Intermediates in the Soluble Methane Monooxygenase Catalytic Cycle , 2000 .

[37]  Peter A. Kollman,et al.  QM−FE and Molecular Dynamics Calculations on Catechol O-Methyltransferase: Free Energy of Activation in the Enzyme and in Aqueous Solution and Regioselectivity of the Enzyme-Catalyzed Reaction , 2000 .

[38]  E. Pai,et al.  Electrostatic stress in catalysis: structure and mechanism of the enzyme orotidine monophosphate decarboxylase. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[39]  Weitao Yang,et al.  Free energy calculation on enzyme reactions with an efficient iterative procedure to determine minimum energy paths on a combined ab initio QM/MM potential energy surface , 2000 .

[40]  Nathalie Reuter,et al.  Frontier Bonds in QM/MM Methods: A Comparison of Different Approaches , 2000 .

[41]  J. Gallivan,et al.  A Computational Study of Cation−π Interactions vs Salt Bridges in Aqueous Media: Implications for Protein Engineering , 2000 .

[42]  Adrian J. Mulholland,et al.  Ab initio QM/MM study of the citrate synthase mechanism. A low-barrier hydrogen bond is not involved , 2000 .

[43]  Martin Karplus,et al.  Molecular properties from combined QM/MM methods. I. Analytical second derivative and vibrational calculations , 2000 .

[44]  R. A. Torres,et al.  Theoretical investigation of the [1,2]-sigmatropic hydrogen migration in the mechanism of oxidation of 2-aminobenzoyl-CoA by 2-aminobenzoyl-CoA monooxygenase/reductase. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[45]  Vicent Moliner,et al.  Catalytic Mechanism of Dihydrofolate Reductase Enzyme. A Combined Quantum-Mechanical/Molecular-Mechanical Characterization of Transition State Structure for the Hydride Transfer Step , 1999 .

[46]  Richard A. Friesner,et al.  Mixed ab initio QM/MM modeling using frozen orbitals and tests with alanine dipeptide and tetrapeptide , 1999, J. Comput. Chem..

[47]  Iris Antes,et al.  Adjusted Connection Atoms for Combined Quantum Mechanical and Molecular Mechanical Methods , 1999 .

[48]  W. Richards,et al.  Modelling the catalytic reaction in human aldose reductase , 1999, Proteins.

[49]  M. Field,et al.  Is There a Covalent Intermediate in the Viral Neuraminidase Reaction? A Hybrid Potential Free-Energy Study , 1999 .

[50]  Kenneth M. Merz,et al.  The Role of Polarization and Charge Transfer in the Solvation of Biomolecules , 1999 .

[51]  Kenneth M. Merz,et al.  Combined Quantum Mechanical/Molecular Mechanical Methodologies Applied to Biomolecular Systems , 1999 .

[52]  S. Goedecker.  Linear scaling electronic structure methods , 1999 .

[53]  Kenneth M. Merz,et al.  Fully Quantum Mechanical Description of Proteins in Solution. Combining Linear Scaling Quantum Mechanical Methodologies with the Poisson−Boltzmann Equation , 1999 .

[54]  Gustavo E. Scuseria,et al.  Linear Scaling Density Functional Calculations with Gaussian Orbitals , 1999 .

[55]  Gustavo E. Scuseria,et al.  What is the Best Alternative to Diagonalization of the Hamiltonian in Large Scale Semiempirical Calculations , 1999 .

[56]  Darrin M. York,et al.  Quantum Mechanical Treatment of Biological Macromolecules in Solution Using Linear-Scaling Electronic Structure Methods , 1998 .

[57]  C. Carter,et al.  Active Species for the Ground-State Complex of Cytidine Deaminase: A Linear-Scaling Quantum Mechanical Investigation , 1998 .

[58]  D. York,et al.  Linear‐scaling semiempirical quantum calculations for macromolecules , 1996 .

[59]  Martin Head-Gordon,et al.  Quantum chemistry and molecular processes , 1996 .

[60]  Kohn,et al.  Density functional and density matrix method scaling linearly with the number of atoms. , 1996, Physical review letters.

[61]  Kenneth M. Merz,et al.  Mechanism of the human carbonic anhydrase II-catalyzed hydration of carbon dioxide , 1992 .

[62]  Scott F. Smith,et al.  SN2 reaction profiles in the gas phase and aqueous solution , 1984 .

[63]  Efthimios Kaxiras,et al.  A QM/MM Implementation of the Self-Consistent Charge Density Functional Tight Binding (SCC-DFTB) Method , 2001 .

[64]  Kalju Kahn,et al.  Transition-State and Ground-State Structures and Their Interaction with the Active-Site Residues in Catechol O-Methyltransferase , 2000 .

[65]  A. Warshel,et al.  Ab initio/LD studies of chemical reactions in solution: Reference free‐energy surfaces for acylation reactions occurring in serine and cysteine proteases , 2000 .

[66]  Tai-Sung Lee,et al.  A pseudobond approach to combining quantum mechanical and molecular mechanical methods , 1999 .

[67]  James J. P. Stewart,et al.  Application of localized molecular orbitals to the solution of semiempirical self‐consistent field equations , 1996 .