List of works - Jan Řezáč

A Nexus between Theory and Experiment: Non-Empirical Quantum Mechanical Computational Methodology Applied to Cucurbit[n]uril⋅Guest Binding Interactions

scientific article published on 10 October 2016

A Reliable Docking/Scoring Scheme Based on the Semiempirical Quantum Mechanical PM6-DH2 Method Accurately Covering Dispersion and H-Bonding: HIV-1 Protease with 22 Ligands

article

A Transferable H-Bonding Correction for Semiempirical Quantum-Chemical Methods

article by Martin Korth et al published 12 January 2010 in Journal of Chemical Theory and Computation

A halogen-bonding correction for the semiempirical PM6 method

Ab Initio Quantum Mechanical Description of Noncovalent Interactions at Its Limits: Approaching the Experimental Dissociation Energy of the HF Dimer

Accurate DFT-D3 Calculations in a Small Basis Set.

scientific article

Accurate Noncovalent Interactions via Dispersion-Corrected Second-Order Møller–Plesset Perturbation Theory

scientific article published on 22 August 2018

Adsorption of aromatic hydrocarbons and ozone at environmental aqueous surfaces

scientific article published on 8 May 2008

Advanced Corrections of Hydrogen Bonding and Dispersion for Semiempirical Quantum Mechanical Methods

scientific article published on 22 December 2011

Assessment of the performance of MP2 and MP2 variants for the treatment of noncovalent interactions.

scientific article published on 18 April 2012

B-Hπ: a nonclassical hydrogen bond or dispersion contact?

scientific article published in July 2017

Basis Set Dependence of Interaction Energies Computed Using Composite Post-MP2 Methods

scientific article published on 27 November 2012

Benchmark Calculations of Interaction Energies in Noncovalent Complexes and Their Applications

scientific article published on 4 March 2016

Benchmark Calculations of Noncovalent Interactions of Halogenated Molecules

Benchmark Calculations of Three-Body Intermolecular Interactions and the Performance of Low-Cost Electronic Structure Methods

scientific article published in July 2015

Benchmark Data Sets of Boron Cluster Dihydrogen Bonding for the Validation of Approximate Computational Methods

scientific article published on 12 November 2020

Benchmark database on isolated small peptides containing an aromatic side chain: comparison between wave function and density functional theory methods and empirical force field

scientific article published on 13 March 2008

Benchmarking of Semiempirical Quantum-Mechanical Methods on Systems Relevant to Computer-Aided Drug Design

scientific article published on 15 February 2020

Benzene Dimer: Dynamic Structure and Thermodynamics Derived from On-the-Fly ab initio DFT-D Molecular Dynamic Simulations

article by Jan Řezáč & Pavel Hobza published 11 November 2008 in Journal of Chemical Theory and Computation

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

scientific article published on November 2008

Binding energies of the π-stacked anisole dimer: new molecular beam-laser spectroscopy experiments and CCSD(T) calculations

scientific article published on 5 March 2015

CCSD[T] Describes Noncovalent Interactions Better than the CCSD(T), CCSD(TQ), and CCSDT Methods

scientific article published on 16 November 2012

Comparative Study of Selected Wave Function and Density Functional Methods for Noncovalent Interaction Energy Calculations Using the Extended S22 Data Set.

scientific article

Competition between Halogen, Hydrogen and Dihydrogen Bonding in Brominated Carboranes.

scientific article published on 5 September 2016

Competition between halogen, dihalogen and hydrogen bonds in bromo- and iodomethanol dimers

article

Convergence of the Interaction Energies in Noncovalent Complexes in the Coupled-Cluster Methods Up to Full Configuration Interaction

scientific article published on 18 July 2013

Correction to "Testing Semiempirical QM Methods on a Data Set of Interaction Energies Mapping Repulsive Contacts in Organic Molecules"

scientific article published on 03 December 2018

Correlation Between the Thermodynamic Stability of DNA Duplexes and the Interaction and Solvation Energies of DNA Building Blocks

Cuby: An integrative framework for computational chemistry

scientific article published on 3 February 2016

DFTB+, a software package for efficient approximate density functional theory based atomistic simulations

scientific article published on 01 March 2020

Density-functional, density-functional tight-binding, and wave function calculations on biomolecular systems.

scientific article published on 06 April 2007

Describing Noncovalent Interactions beyond the Common Approximations: How Accurate Is the "Gold Standard," CCSD(T) at the Complete Basis Set Limit?

scientific article published on 4 April 2013

Description of halogen bonding in semiempirical quantum-mechanical and self-consistent charge density-functional tight-binding methods

scientific article published on 03 April 2019

Description of non-covalent interactions in SCC-DFTB methods

scientific article published on 17 January 2017

Design of HIV protease inhibitors based on inorganic polyhedral metallacarboranes

scientific article

Efficient Covalent Bond Formation in Gas-Phase Peptide-Peptide Ion Complexes with the Photoleucine Stapler

scientific article published on 27 January 2016

Empirical D3 Dispersion as a Replacement for ab Initio Dispersion Terms in Density Functional Theory-Based Symmetry-Adapted Perturbation Theory.

scientific article

Empirical Self-Consistent Correction for the Description of Hydrogen Bonds in DFTB3.

scientific article published on 26 September 2017

Erratum to "S66: A Well-balanced Database of Benchmark Interaction Energies Relevant to Biomolecular Structures".

scientific article published on March 2014

Erratum: “DFTB+, a software package for efficient approximate density functional theory based atomistic simulations” [J. Chem. Phys. 152, 124101 (2020)]

correction of a scholarly article

Evaluation of composite schemes for CCSDT(Q) calculations of interaction energies of noncovalent complexes

scientific article published in September 2014

Evaluation of the performance of post-Hartree-Fock methods in terms of intermolecular distance in noncovalent complexes

article

Extensions and applications of the A24 data set of accurate interaction energies

scientific article

Extensions of the S66 Data Set: More Accurate Interaction Energies and Angular-Displaced Nonequilibrium Geometries

article by Jan Řezáč et al published 8 November 2011 in Journal of Chemical Theory and Computation

Extrapolation and Scaling of the DFT-SAPT Interaction Energies toward the Basis Set Limit

article

Free-Energy Simulations of Hydrogen Bonding versus Stacking of Nucleobases on a Graphene Surface

Gating the electron transfer at a monocopper centre through the supramolecular coordination of water molecules within a protein chamber mimic

scientific article published on 30 August 2018

Halogen bond tunability I: the effects of aromatic fluorine substitution on the strengths of halogen-bonding interactions involving chlorine, bromine, and iodine

scientific article published on 04 March 2011

Halogen bond tunability II: the varying roles of electrostatic and dispersion contributions to attraction in halogen bonds.

scientific article

Impressive Enrichment of Semiempirical Quantum Mechanics-Based Scoring Function: HSP90 Protein with 4541 Inhibitors and Decoys

scientific article published on 23 October 2019

Impressive Enrichment of Semiempirical Quantum Mechanics-Based Scoring Function: HSP90 Protein with 4541 Inhibitors and Decoys

scientific article published on 11 September 2019

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

article

Introduction: Noncovalent Interactions

article published in 2016

Investigation of the hydroxylation mechanism of noncoupled copper oxygenases by ab initio molecular dynamics simulations.

scientific article published on 20 November 2013

MP2.5 and MP2.X: approaching CCSD(T) quality description of noncovalent interaction at the cost of a single CCSD iteration

scientific article published on 11 January 2013

MP2.X: a generalized MP2.5 method that produces improved binding energies with smaller basis sets

article published in 2011

Macrocycle Conformational Sampling by DFT-D3/COSMO-RS Methodology.

scientific article published on 28 November 2017

Malonate-based inhibitors of mammalian serine racemase: kinetic characterization and structure-based computational study.

scientific article published on 16 October 2014

Modulation of aldose reductase inhibition by halogen bond tuning

scientific article

Multilevel Fragment-Based Approach (MFBA): A Novel Hybrid Computational Method for the Study of Large Molecules

New Insight into the Nature of Bonding in the Dimers of Lappert’s Stannylene and Its Ge Analogs: A Quantum Mechanical Study

scientific article published on 17 March 2016

New insights into the mechanism of electron transfer within flavohemoglobins: tunnelling pathways, packing density, thermodynamic and kinetic analyses

article published in 2012

Non-Covalent Interactions Atlas Benchmark Data Sets 2: Hydrogen Bonding in an Extended Chemical Space

scientific article published on 17 September 2020

Non-Covalent Interactions Atlas Benchmark Data Sets 3: Repulsive Contacts

scientific article published on 23 February 2021

Non-Covalent Interactions Atlas Benchmark Data Sets: Hydrogen Bonding

scientific article published on 09 March 2020

Non-Covalent Interactions Atlas benchmark data sets 5: London dispersion in an extended chemical space

scientific article published in 2022

Non-covalent interactions atlas benchmark data sets 4: σ-hole interactions

scientific article published in 2022

Non-covalent interactions in anisole-(CO2)n (n = 1, 2) complexes

scientific article

On the nature of DNA-duplex stability

scientific article published in January 2007

On the performance of the semiempirical quantum mechanical PM6 and PM7 methods for noncovalent interactions

On the reliability of the corrected semiempirical quantum chemical method (PM6-DH2) for assigning the protonation states in HIV-1 protease/inhibitor complexes

article

On the role of charge transfer in halogen bonding

scientific article published on 8 December 2016

Parallel low-memory quasi-Newton optimization algorithm for molecular structure

Parameterization of the DFTB3 Method for Br, Ca, Cl, F, I, K, and Na in Organic and Biological Systems

article

Pnictogen bonding in pyrazine•PnX5 (Pn = P, As, Sb and X = F, Cl, Br) complexes.

scientific article published on 30 October 2017

Potential-energy and free-energy surfaces of glycyl-phenylalanyl-alanine (GFA) tripeptide: experiment and theory

scientific article published in January 2008

QM/MM calculations reveal the different nature of the interaction of two carborane-based sulfamide inhibitors of human carbonic anhydrase II.

scientific article

QM/MM calculations with deMon2k.

scientific article published on 16 March 2015

Quantum Chemical Benchmark Energy and Geometry Database for Molecular Clusters and Complex Molecular Systems (www.begdb.com): A Users Manual and Examples

scholarly article by Jan Řezáč et al published 2008 in Collection of Czechoslovak Chemical Communications

Quantum Mechanics-Based Scoring Rationalizes the Irreversible Inactivation of Parasitic Schistosoma mansoni Cysteine Peptidase by Vinyl Sulfone Inhibitors

scientific article published on 21 November 2013

Quantum effects in biological electron transfer

Ranking Power of the SQM/COSMO Scoring Function on Carbonic Anhydrase II-Inhibitor Complexes

scientific article published on 8 January 2018

Reparametrization of the COSMO Solvent Model for Semiempirical Methods PM6 and PM7

scientific article published on 04 January 2019

Representative Amino Acid Side-Chain Interactions in Protein-DNA Complexes: A Comparison of Highly Accurate Correlated Ab Initio Quantum Mechanical Calculations and Efficient Approaches for Applications to Large Systems

scientific article published on 6 August 2015

Robust and Efficient Constrained DFT Molecular Dynamics Approach for Biochemical Modeling

scientific article published on 10 January 2012

Robust, Basis-Set Independent Method for the Evaluation of Charge-Transfer Energy in Noncovalent Complexes

article published in 2015

S66: A Well-balanced Database of Benchmark Interaction Energies Relevant to Biomolecular Structures.

scientific article published on July 2011

SQM/COSMO Scoring Function at the DFTB3-D3H4 Level: Unique Identification of Native Protein-Ligand Poses.

scientific article

SQM/COSMO Scoring Function: Reliable Quantum-Mechanical Tool for Sampling and Ranking in Structure-Based Drug Design

scientific article published on 02 June 2020

SQM/COSMO Scoring Function: Reliable Quantum-Mechanical Tool for Sampling and Ranking in Structure-Based Drug Design

scientific article published on 28 September 2020

Semiempirical Quantum Chemical PM6 Method Augmented by Dispersion and H-Bonding Correction Terms Reliably Describes Various Types of Noncovalent Complexes

scientific article published on 26 May 2009

Semiempirical Quantum Mechanical Method PM6-DH2X Describes the Geometry and Energetics of CK2-Inhibitor Complexes Involving Halogen Bonds Well, While the Empirical Potential Fails

scientific article published on 16 June 2011

Spin-component scaled coupled-clusters singles and doubles optimized towards calculation of noncovalent interactions

Stretched DNA investigated using molecular-dynamics and quantum-mechanical calculations.

scientific article

Structure and energetics of the anisole-Ar(n) (n = 1, 2, 3) complexes: high-resolution resonant two-photon and threshold ionization experiments, and quantum chemical calculations

scientific article published on May 2015

Superior Performance of the SQM/COSMO Scoring Functions in Native Pose Recognition of Diverse Protein–Ligand Complexes in Cognate Docking.

scientific article published on 27 July 2017

Surface residues dynamically organize water bridges to enhance electron transfer between proteins.

scientific article

Testing Semiempirical Quantum Mechanical Methods on a Data Set of Interaction Energies Mapping Repulsive Contacts in Organic Molecules

scientific article published on 02 March 2018

The Effect of Halogen-to-Hydrogen Bond Substitution on Human Aldose Reductase Inhibition

scientific article

The SQM/COSMO filter: reliable native pose identification based on the quantum-mechanical description of protein-ligand interactions and implicit COSMO solvation

scientific article published on 29 January 2016

The Semiempirical Quantum Mechanical Scoring Function for In Silico Drug Design

scientific article published on 13 August 2013

The Stabilization Energy of the GLU-LYS Salt Bridge in the Protein/Water Environment: Correlated Quantum Chemical ab initio, DFT and Empirical Potential Studies

The accuracy of quantum chemical methods for large noncovalent complexes.

scientific article published on August 2013

The performance of MP2.5 and MP2.X methods for nonequilibrium geometries of molecular complexes

Towards Accurate Conformational Energies of Smaller Peptides and Medium-Sized Macrocycles: MPCONF196 Benchmark Energy Data Set.

scientific article published on 20 February 2018

Transferable scoring function based on semiempirical quantum mechanical PM6-DH2 method: CDK2 with 15 structurally diverse inhibitors.

scientific article published in February 2011

Transmission Coefficients for Chemical Reactions with Multiple States: Role of Quantum Decoherence

article

List of works by Jan Řezáč

A Nexus between Theory and Experiment: Non-Empirical Quantum Mechanical Computational Methodology Applied to Cucurbit[n]uril⋅Guest Binding Interactions

A Reliable Docking/Scoring Scheme Based on the Semiempirical Quantum Mechanical PM6-DH2 Method Accurately Covering Dispersion and H-Bonding: HIV-1 Protease with 22 Ligands

A Transferable H-Bonding Correction for Semiempirical Quantum-Chemical Methods

A halogen-bonding correction for the semiempirical PM6 method

Ab Initio Quantum Mechanical Description of Noncovalent Interactions at Its Limits: Approaching the Experimental Dissociation Energy of the HF Dimer

Accurate DFT-D3 Calculations in a Small Basis Set.

Accurate Noncovalent Interactions via Dispersion-Corrected Second-Order Møller–Plesset Perturbation Theory

Adsorption of aromatic hydrocarbons and ozone at environmental aqueous surfaces

Advanced Corrections of Hydrogen Bonding and Dispersion for Semiempirical Quantum Mechanical Methods

Assessment of the performance of MP2 and MP2 variants for the treatment of noncovalent interactions.

B-Hπ: a nonclassical hydrogen bond or dispersion contact?

Basis Set Dependence of Interaction Energies Computed Using Composite Post-MP2 Methods

Benchmark Calculations of Interaction Energies in Noncovalent Complexes and Their Applications

Benchmark Calculations of Noncovalent Interactions of Halogenated Molecules

Benchmark Calculations of Three-Body Intermolecular Interactions and the Performance of Low-Cost Electronic Structure Methods

Benchmark Data Sets of Boron Cluster Dihydrogen Bonding for the Validation of Approximate Computational Methods

Benchmark database on isolated small peptides containing an aromatic side chain: comparison between wave function and density functional theory methods and empirical force field

Benchmarking of Semiempirical Quantum-Mechanical Methods on Systems Relevant to Computer-Aided Drug Design

Benzene Dimer: Dynamic Structure and Thermodynamics Derived from On-the-Fly ab initio DFT-D Molecular Dynamic Simulations

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

Binding energies of the π-stacked anisole dimer: new molecular beam-laser spectroscopy experiments and CCSD(T) calculations

CCSD[T] Describes Noncovalent Interactions Better than the CCSD(T), CCSD(TQ), and CCSDT Methods

Comparative Study of Selected Wave Function and Density Functional Methods for Noncovalent Interaction Energy Calculations Using the Extended S22 Data Set.

Competition between Halogen, Hydrogen and Dihydrogen Bonding in Brominated Carboranes.

Competition between halogen, dihalogen and hydrogen bonds in bromo- and iodomethanol dimers

Convergence of the Interaction Energies in Noncovalent Complexes in the Coupled-Cluster Methods Up to Full Configuration Interaction

Correction to "Testing Semiempirical QM Methods on a Data Set of Interaction Energies Mapping Repulsive Contacts in Organic Molecules"

Correlation Between the Thermodynamic Stability of DNA Duplexes and the Interaction and Solvation Energies of DNA Building Blocks

Cuby: An integrative framework for computational chemistry

DFTB+, a software package for efficient approximate density functional theory based atomistic simulations

Density-functional, density-functional tight-binding, and wave function calculations on biomolecular systems.

Describing Noncovalent Interactions beyond the Common Approximations: How Accurate Is the "Gold Standard," CCSD(T) at the Complete Basis Set Limit?

Description of halogen bonding in semiempirical quantum-mechanical and self-consistent charge density-functional tight-binding methods

Description of non-covalent interactions in SCC-DFTB methods

Design of HIV protease inhibitors based on inorganic polyhedral metallacarboranes

Efficient Covalent Bond Formation in Gas-Phase Peptide-Peptide Ion Complexes with the Photoleucine Stapler

Empirical D3 Dispersion as a Replacement for ab Initio Dispersion Terms in Density Functional Theory-Based Symmetry-Adapted Perturbation Theory.

Empirical Self-Consistent Correction for the Description of Hydrogen Bonds in DFTB3.

Erratum to "S66: A Well-balanced Database of Benchmark Interaction Energies Relevant to Biomolecular Structures".

Erratum: “DFTB+, a software package for efficient approximate density functional theory based atomistic simulations” [J. Chem. Phys. 152, 124101 (2020)]

Evaluation of composite schemes for CCSDT(Q) calculations of interaction energies of noncovalent complexes

Evaluation of the performance of post-Hartree-Fock methods in terms of intermolecular distance in noncovalent complexes

Extensions and applications of the A24 data set of accurate interaction energies

Extensions of the S66 Data Set: More Accurate Interaction Energies and Angular-Displaced Nonequilibrium Geometries

Extrapolation and Scaling of the DFT-SAPT Interaction Energies toward the Basis Set Limit

Free-Energy Simulations of Hydrogen Bonding versus Stacking of Nucleobases on a Graphene Surface

Gating the electron transfer at a monocopper centre through the supramolecular coordination of water molecules within a protein chamber mimic

Halogen bond tunability I: the effects of aromatic fluorine substitution on the strengths of halogen-bonding interactions involving chlorine, bromine, and iodine

Halogen bond tunability II: the varying roles of electrostatic and dispersion contributions to attraction in halogen bonds.

Impressive Enrichment of Semiempirical Quantum Mechanics-Based Scoring Function: HSP90 Protein with 4541 Inhibitors and Decoys

Impressive Enrichment of Semiempirical Quantum Mechanics-Based Scoring Function: HSP90 Protein with 4541 Inhibitors and Decoys

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

Introduction: Noncovalent Interactions

Investigation of the hydroxylation mechanism of noncoupled copper oxygenases by ab initio molecular dynamics simulations.

MP2.5 and MP2.X: approaching CCSD(T) quality description of noncovalent interaction at the cost of a single CCSD iteration

MP2.X: a generalized MP2.5 method that produces improved binding energies with smaller basis sets

Macrocycle Conformational Sampling by DFT-D3/COSMO-RS Methodology.

Malonate-based inhibitors of mammalian serine racemase: kinetic characterization and structure-based computational study.

Modulation of aldose reductase inhibition by halogen bond tuning

Multilevel Fragment-Based Approach (MFBA): A Novel Hybrid Computational Method for the Study of Large Molecules

New Insight into the Nature of Bonding in the Dimers of Lappert’s Stannylene and Its Ge Analogs: A Quantum Mechanical Study

New insights into the mechanism of electron transfer within flavohemoglobins: tunnelling pathways, packing density, thermodynamic and kinetic analyses

Non-Covalent Interactions Atlas Benchmark Data Sets 2: Hydrogen Bonding in an Extended Chemical Space

Non-Covalent Interactions Atlas Benchmark Data Sets 3: Repulsive Contacts

Non-Covalent Interactions Atlas Benchmark Data Sets: Hydrogen Bonding

Non-Covalent Interactions Atlas benchmark data sets 5: London dispersion in an extended chemical space

Non-covalent interactions atlas benchmark data sets 4: σ-hole interactions

Non-covalent interactions in anisole-(CO2)n (n = 1, 2) complexes

On the nature of DNA-duplex stability

On the performance of the semiempirical quantum mechanical PM6 and PM7 methods for noncovalent interactions

On the reliability of the corrected semiempirical quantum chemical method (PM6-DH2) for assigning the protonation states in HIV-1 protease/inhibitor complexes

On the role of charge transfer in halogen bonding

Parallel low-memory quasi-Newton optimization algorithm for molecular structure

Parameterization of the DFTB3 Method for Br, Ca, Cl, F, I, K, and Na in Organic and Biological Systems

Pnictogen bonding in pyrazine•PnX5 (Pn = P, As, Sb and X = F, Cl, Br) complexes.

Potential-energy and free-energy surfaces of glycyl-phenylalanyl-alanine (GFA) tripeptide: experiment and theory

QM/MM calculations reveal the different nature of the interaction of two carborane-based sulfamide inhibitors of human carbonic anhydrase II.

QM/MM calculations with deMon2k.

Quantum Chemical Benchmark Energy and Geometry Database for Molecular Clusters and Complex Molecular Systems (www.begdb.com): A Users Manual and Examples