相关参考文献
注意:仅列出部分参考文献,下载原文获取全部文献信息。Quantum mechanics/molecular mechanics minimum free-energy path for accurate reaction energetics in solution and enzymes: Sequential sampling and optimization on the potential of mean force surface
Hao Hu et al.
JOURNAL OF CHEMICAL PHYSICS (2008)
Ab initio quantum mechanical/molecular mechanical simulation of electron transfer process:: Fractional electron approach
Xiancheng Zeng et al.
JOURNAL OF CHEMICAL PHYSICS (2008)
First principles study of alkali-tyrosine complexes: Alkali solvation and redox properties
Francesca Costanzo et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2008)
A classical point charge model study of system size dependence of oxidation and reorganization free energies in aqueous solution
Regla Ayala et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2008)
Cuaq+/Cuaq2+ Redox Reaction Exhibits Strong Nonlinear Solvent Response Due to Change in Coordination Number
Jochen Blumberger
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2008)
Mechanism of OMP Decarboxylation in Orotidine 5′-Monophosphate Decarboxylase
Hao Hu et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2008)
Absolute standard hydrogen electrode potential measured by reduction of aqueous nanodrops in the gas phase
William A. Donald et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2008)
Free energies for biological electron transfer from QM/MM calculation: method, application and critical assessment
Jochen Blumberger
PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2008)
Localization and delocalization errors in density functional theory and implications for band-gap prediction
Paula Mori-Sanchez et al.
PHYSICAL REVIEW LETTERS (2008)
Insights into current limitations of density functional theory
Aron J. Cohen et al.
SCIENCE (2008)
Combined quantum mechanical and molecular mechanical simulations of one- and two-electron reduction potentials of flavin cofactor in water, medium-chain acyl-CoA dehydrogenase, and cholesterol oxidase
Sudeep Bhattacharyya et al.
JOURNAL OF PHYSICAL CHEMISTRY A (2007)
Fitting molecular electrostatic potentials from quantum mechanical calculations
Hao Hu et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2007)
Computational electrochemistry:: The aqueous Ru3+|Ru2+ reduction potential
Pablo Jaque et al.
JOURNAL OF PHYSICAL CHEMISTRY C (2007)
Calculation of redox properties: Understanding short- and long-range effects in rubredoxin
Marialore Sulpizi et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2007)
A water-mediated and substrate-assisted catalytic mechanism for Sulfolobus solfataricus DNA polymerase IV
Lihua Wang et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2007)
Ab initio quantum mechanical/molecular mechanical molecular dynamics simulation of enzyme catalysis: The case of histone lysine methyltransferase SET7/9
Shenglong Wang et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2007)
QM/MM minimum free-energy path: Methodology and application to triosephosphate isomerase
Hao Hu et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2007)
Role of protein frame and solvent for the redox properties of azurin from Pseudomonas aeruginosa
Michele Cascella et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2006)
Aqueous solvation free energies of ions and ion-water clusters based on an accurate value for the absolute aqueous solvation free energy of the proton
Casey P. Kelly et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2006)
Realistic quantitative descriptions of electron transfer reactions: Diabatic free-energy surfaces from first-principles molecular dynamics
P. H. -L. Sit et al.
PHYSICAL REVIEW LETTERS (2006)
Unexpected deacetylation mechanism suggested by a density functional theory QM/MM study of histone-deacetylase-like protein
C Corminboeuf et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2006)
Nuclear quantum effects on an enzyme-catalyzed reaction with reaction path potential: Proton transfer in triosephosphate isomerase
ML Wang et al.
JOURNAL OF CHEMICAL PHYSICS (2006)
QM/MM free-energy perturbation compared to thermodynamic integration and umbrella sampling:: Application to an enzymatic reaction
J Kästner et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2006)
Diabatic free energy curves and coordination fluctuations for the aqueous Ag+/Ag2+ redox couple:: A biased Born-Oppenheimer molecular dynamics investigation -: art. no. 064507
J Blumberger et al.
JOURNAL OF CHEMICAL PHYSICS (2006)
Catalytic mechanism and product specificity of the histone lysine methyltransferase SET7/9: An ab initio QM/MM-FE study with multiple initial structures
P Hu et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2006)
On possible pitfalls in ab initio quantum mechanics/molecular mechanics minimization approaches for studies of enzymatic reactions
M Klähn et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2005)
Density-functional molecular-dynamics study of the redox reactions of two anionic, aqueous transition-metal complexes
Y Tateyama et al.
JOURNAL OF CHEMICAL PHYSICS (2005)
Ab initio molecular dynamics simulation of the aqueous Ru2+/Ru3+ redox reaction:: The Marcus perspective
J Blumberger et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2005)
Simulating redox coupled proton transfer in cytochrome c oxidase:: Looking for the proton bottleneck
MHM Olsson et al.
FEBS LETTERS (2005)
A molecular dynamics study of the hydroxyl radical in solution applying self-interaction-corrected density functional methods
J VandeVondele et al.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2005)
Calculating potentials of mean force from steered molecular dynamics simulations
S Park et al.
JOURNAL OF CHEMICAL PHYSICS (2004)
Electronic structure and solvation of copper and silver ions: A theoretical picture of a model aqueous redox reaction
J Blumberger et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2004)
Transmission coefficient calculation for proton transfer in triosephosphate isomerase based on the reaction path potential method
ML Wang et al.
JOURNAL OF CHEMICAL PHYSICS (2004)
The protein backbone makes important contributions to 4-oxalocrotonate tautomerase enzyme catalysis: Understanding from theory and experiment
GA Cisneros et al.
BIOCHEMISTRY (2004)
Free energy of oxidation of metal aqua ions by an enforced change of coordination
J Blumberger et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2004)
Density-functional theory calculations of aqueous redox potentials of fourth-period transition metals
M Uudsemaa et al.
JOURNAL OF PHYSICAL CHEMISTRY A (2003)
Ab initio QM/MM study shows there is no general acid in the reaction catalyzed by 4-oxalocrotonate tautornerase
GA Cisneros et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2003)
Free energy perturbation calculations with combined QM/MM Potentials complications, simplifications, and applications to redox potential calculations
GH Li et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2003)
Frozen density functional free energy simulations of redox proteins: Computational studies of the reduction potential of plastocyanin and rusticyanin
MHM Olsson et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2003)
Comparison of a QM/MM force field and molecular mechanics force fields in simulations of alanine and glycine dipeptides (Ace-Ala-Nme and Ace-Gly-Nme) in water in relation to the problem of modeling the unfolded peptide backbone in solution
H Hu et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2003)
Ab initio molecular dynamics for molecules with variable numbers of electrons -: art. no. 213002
I Tavernelli et al.
PHYSICAL REVIEW LETTERS (2002)
Reversibility of free energy simulations: Slow growth may have a unique advantage. (With a note on use of Ewald summation)
H Hu et al.
MOLECULAR SIMULATION (2002)
Free energy reconstruction from nonequilibrium single-molecule pulling experiments
G Hummer et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2001)
Ab initio calculation of homogeneous outer sphere electron transfer rates:: Application to M(OH2)63+/2+ redox couples
KM Rosso et al.
JOURNAL OF PHYSICAL CHEMISTRY A (2000)
Computation of electronic chemical potentials using free energy density functionals
R Vuilleumier et al.
JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM (2000)
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
YK Zhang et al.
JOURNAL OF CHEMICAL PHYSICS (2000)