The assessment of density functionals for DNA–protein stacked and T-shaped complexes

Catalytic Mechanism of DNA Backbone Cleavage by the Restriction Enzyme EcoRV: A Quantum Mechanical/Molecular Mechanical Analysis

(2009) Petra Imhof et al.   BIOCHEMISTRY

A computational ONIOM model for the description of the H-bond interactions between NU2058 analogues and CDK2 active site

(2009) Jans H. Alzate-Morales et al.   CHEMICAL PHYSICS LETTERS

The Catalytic Mechanism of Fluoroacetate Dehalogenase: A Computational Exploration of Biological Dehalogenation

(2009) Takashi Kamachi et al.   CHEMISTRY-A EUROPEAN JOURNAL

Insights into the Structural Basis of N2 and O6 Substituted Guanine Derivatives as Cyclin-Dependent Kinase 2 (CDK2) Inhibitors: Prediction of the Binding Modes and Potency of the inhibitors by Docking and ONIOM Calculations

(2009) Jans H. Alzate-Morales et al.   Journal of Chemical Information and Modeling

Evidence for Stabilization of DNA/RNA−Protein Complexes Arising from Nucleobase−Amino Acid Stacking and T-Shaped Interactions

(2009) Lesley R. Rutledge et al.   Journal of Chemical Theory and Computation

Balance of Attraction and Repulsion in Nucleic-Acid Base Stacking: CCSD(T)/Complete-Basis-Set-Limit Calculations on Uracil Dimer and a Comparison with the Force-Field Description

(2009) Claudio A. Morgado et al.   Journal of Chemical Theory and Computation

Phenylalanyl-Glycyl-Phenylalanine Tripeptide: A Model System for Aromatic−Aromatic Side Chain Interactions in Proteins

(2009) H. Valdes et al.   Journal of Chemical Theory and Computation

Benchmark Data for Noncovalent Interactions in HCOOH···Benzene Complexes and Their Use for Validation of Density Functionals

(2009) Yan Zhao et al.   Journal of Chemical Theory and Computation

Evaluation of B3LYP, X3LYP, and M06-Class Density Functionals for Predicting the Binding Energies of Neutral, Protonated, and Deprotonated Water Clusters

(2009) Vyacheslav S. Bryantsev et al.   Journal of Chemical Theory and Computation

Artificial reaction coordinate “tunneling” in free-energy calculations: The catalytic reaction of RNase H

(2009) Edina Rosta et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

CH/π Interaction in Benzene and Substituted Derivatives with Halomethane: A Combined Density Functional and Dispersion-Corrected Density Functional Study

(2009) Ram Chandra Dey et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Evaluation of the ONIOM Method for Interpretation of Infrared Spectra of Gas-Phase Molecules of Biological Interest

(2009) Jean-Christophe Poully et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Application of Dispersion-Corrected Density Functional Theory

(2009) Sten O. Nilsson Lill   JOURNAL OF PHYSICAL CHEMISTRY A

The Hydrolysis Activity of Adenosine Triphosphate in Myosin: A Theoretical Analysis of Anomeric Effects and the Nature of the Transition State†

(2009) Yang Yang et al.   JOURNAL OF PHYSICAL CHEMISTRY A

An Assessment of Theoretical Methods for Nonbonded Interactions: Comparison to Complete Basis Set Limit Coupled-Cluster Potential Energy Curves for the Benzene Dimer, the Methane Dimer, Benzene−Methane, and Benzene−H2S†

(2009) C. David Sherrill et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Noncovalent Interactions Involving Histidine: The Effect of Charge on π−π Stacking and T-Shaped Interactions with the DNA Nucleobases

(2009) Cassandra D. M. Churchill et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Dispersion interactions in density-functional theory

(2009) Erin R. Johnson et al.   JOURNAL OF PHYSICAL ORGANIC CHEMISTRY

DFT and ONIOM(DFT:MM) Studies on Co−C Bond Cleavage and Hydrogen Transfer in B12-Dependent Methylmalonyl-CoA Mutase. Stepwise or Concerted Mechanism?

(2009) Xin Li et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Carbohydrate–aromatic π interactions: a test of density functionals and the DFT-D method

(2009) Rajesh K. Raju et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Empirically corrected DFT and semi-empirical methods for non-bonding interactions

(2009) Michael E. Foster et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Adenine versus guanine quartets in aqueous solution: dispersion-corrected DFT study on the differences in π-stacking and hydrogen-bonding behavior

(2009) Célia Fonseca Guerra et al.   THEORETICAL CHEMISTRY ACCOUNTS

Computational Enzymatic Catalysis

(2008) Maria J. Ramos et al.   ACCOUNTS OF CHEMICAL RESEARCH

Theoretical Thermodynamics for Large Molecules: Walking the Thin Line between Accuracy and Computational Cost

(2008) Tobias Schwabe et al.   ACCOUNTS OF CHEMICAL RESEARCH

Density Functionals with Broad Applicability in Chemistry

(2008) Yan Zhao et al.   ACCOUNTS OF CHEMICAL RESEARCH

To stack or not to stack: Performance of a new density functional for the uracil and thymine dimers

(2008) Jiande Gu et al.   CHEMICAL PHYSICS LETTERS

A Study of the Binding Energies of Efavirenz to Wild-Type and K103N/Y181C HIV-1 Reverse Transcriptase Based on the ONIOM Method

(2008) Pensri Srivab et al.   ChemMedChem

Highly Accurate CCSD(T) and DFT-SAPT Stabilization Energies of H-Bonded and Stacked Structures of the Uracil Dimer

(2008) Michal Pitoňák et al.   CHEMPHYSCHEM

ONIOM investigation of nucleotide selectivity in phosphodiesterases 3 and 4

(2008) E. A. Salter et al.   INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY

Remarkably Strong T-Shaped Interactions between Aromatic Amino Acids and Adenine: Their Increase upon Nucleobase Methylation and a Comparison to Stacking

(2008) Lesley R. Rutledge et al.   Journal of Chemical Theory and Computation

Assessment of the Performance of the M05−2X and M06−2X Exchange-Correlation Functionals for Noncovalent Interactions in Biomolecules

(2008) Edward G. Hohenstein et al.   Journal of Chemical Theory and Computation

Exploring the Limit of Accuracy of the Global Hybrid Meta Density Functional for Main-Group Thermochemistry, Kinetics, and Noncovalent Interactions

(2008) Yan Zhao et al.   Journal of Chemical Theory and Computation

Benzene Dimer: High-Level Wave Function and Density Functional Theory Calculations

(2008) M. Pitoňák et al.   Journal of Chemical Theory and Computation

Transition States in a Protein Environment − ONIOM QM:MM Modeling of Isopenicillin N Synthesis

(2008) Marcus Lundberg et al.   Journal of Chemical Theory and Computation

Accurate DFT Descriptions for Weak Interactions of Molecules Containing Sulfur

(2008) Philippe C. Aeberhard et al.   Journal of Chemical Theory and Computation

Extensive Conformational Transitions Are Required to Turn On ATP Hydrolysis in Myosin

(2008) Yang Yang et al.   JOURNAL OF MOLECULAR BIOLOGY

Development and application of ab initio QM/MM methods for mechanistic simulation of reactions in solution and in enzymes

(2008) Hao Hu et al.   JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM

Interactions in Large, Polyaromatic Hydrocarbon Dimers: Application of Density Functional Theory with Dispersion Corrections

(2008) Iain D. Mackie et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Probing Phenylalanine/Adenine π-Stacking Interactions in Protein Complexes with Explicitly Correlated and CCSD(T) Computations

(2008) Kari L. Copeland et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Spectral Tuning in Visual Pigments: An ONIOM(QM:MM) Study on Bovine Rhodopsin and its Mutants

(2008) Ahmet Altun et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Ab Initio and QM/MM Study of Electron Addition on the Disulfide Bond in Thioredoxin

(2008) Gail A. Rickard et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Interpretation of Protein/Ligand Crystal Structure using QM/MM Calculations: Case of HIV-1 Protease/Metallacarborane Complex

(2008) Jindřich Fanfrlík et al.   JOURNAL OF PHYSICAL CHEMISTRY B

General Base Catalysis for Cleavage by the Active-Site Cytosine of the Hepatitis Delta Virus Ribozyme: QM/MM Calculations Establish Chemical Feasibility

(2008) Pavel Banáš et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Progress inAb InitioQM/MM Free-Energy Simulations of Electrostatic Energies in Proteins: Accelerated QM/MM Studies of pKa, Redox Reactions and Solvation Free Energies†

(2008) Shina C. L. Kamerlin et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Quantum Chemical Approach to the Mechanism for the Biological Conversion of Tyrosine to Dopaquinone

(2008) Toshinori Inoue et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

The interaction of carbohydrates and amino acids with aromatic systems studied by density functional and semi-empirical molecular orbital calculations with dispersion corrections

(2008) Raman Sharma et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Describing weak interactions of biomolecules with dispersion-corrected density functional theory

(2008) I-Chun Lin et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

A QM/MM study of fluoroaromatic interactions at the binding site of carbonic anhydrase II, using a DFT method corrected for dispersive interactions

(2008) Claudio A. Morgado et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Nature and magnitude of aromatic stacking of nucleic acid bases

(2008) Jiří Šponer et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Double-Hybrid Functionals for Thermochemical Kinetics

(2007) Alex Tarnopolsky et al.   JOURNAL OF PHYSICAL CHEMISTRY A