List of works - Holger Kruse

A geometrical correction for the inter- and intra-molecular basis set superposition error in Hartree-Fock and density functional theory calculations for large systems.

scientific article published in April 2012

An intricate balance of hydrogen bonding, ion atmosphere and dynamics facilitates a seamless uracil to cytosine substitution in the U-turn of the neomycin-sensing riboswitch

scientific article published on 01 July 2018

Benchmarking Density Functional Methods against the S66 and S66x8 Datasets for Non-Covalent Interactions

scientific article published on 23 November 2011

Comment on "Evaluating Unexpectedly Short Non-covalent Distances in X-ray Crystal Structures of Proteins with Electronic Structure Analysis"

scientific article published on 19 August 2019

Comparative Assessment of Different RNA Tetranucleotides from the DFT-D3 and Force Field Perspective.

scientific article

Derivation of Reliable Geometries in QM Calculations of DNA Structures: Explicit Solvent QM/MM and Restrained Implicit Solvent QM Optimizations of G-Quadruplexes

scientific article published on 8 March 2016

Enantioselective helical folding inside a self-assembled, cylindrical capsule

scientific article published on 05 February 2010

Exploring Nature and Predicting Strength of Hydrogen Bonds: A Correlation Analysis Between Atoms-in-Molecules Descriptors, Binding Energies, and Energy Components of Symmetry-Adapted Perturbation Theory

scientific article published on 13 September 2019

Identification of thiazolidinones spiro-fused to indolin-2-ones as potent and selective inhibitors of the Mycobacterium tuberculosis protein tyrosine phosphatase B.

scientific article published on August 2010

Including crystallographic symmetry in quantum-based refinement: Q|R#2

scientific article published on 01 January 2020

Interactions between cyclic nucleotides and common cations: an ab initio molecular dynamics study

scientific article published on 01 April 2019

Investigating inclusion complexes using quantum chemical methods.

scientific article published on 27 January 2012

Investigations of Stacked DNA Base-Pair Steps: Highly Accurate Stacking Interaction Energies, Energy Decomposition, and Many-Body Stacking Effects

scientific article published on 12 December 2018

Ion Binding to Quadruplex DNA Stems. Comparison of MM and QM Descriptions Reveals Sizable Polarization Effects Not Included in Contemporary Simulations

scientific article published on 01 March 2014

MD and QM/MM Study of the Quaternary HutP Homohexamer Complex with mRNA, l-Histidine Ligand, and Mg2.

scientific article published on 16 October 2017

Nonenzymatic Oligomerization of 3',5'-Cyclic CMP Induced by Proton and UV Irradiation Hints at a Nonfastidious Origin of RNA.

scientific article published on 4 May 2017

Psi4 1.4: Open-source software for high-throughput quantum chemistry

scientific article published on 01 May 2020

QM Computations on Complete Nucleic Acids Building Blocks: Analysis of the Sarcin-Ricin RNA Motif Using DFT-D3, HF-3c, PM6-D3H, and MM Approaches

scientific article published on 6 May 2014

QM/MM Calculations on Protein-RNA Complexes: Understanding Limitations of Classical MD Simulations and Search for Reliable Cost-Effective QM Methods

scientific article published on 24 September 2018

Quantum chemical benchmark study on 46 RNA backbone families using a dinucleotide unit.

scientific article published on 15 September 2015

Real-space quantum-based refinement for cryo-EM: Q|R#3

scientific article published on 19 November 2020

Revisiting the Potential Energy Surface of the Stacked Cytosine Dimer: FNO-CCSD(T) Interaction Energies, SAPT Decompositions, and Benchmarking

scientific article published on 09 October 2019

Ring-Expanded Bicyclic β-Lactams: A Structure−Chiroptical Properties Relationship Investigation by Experiment and Calculations

scientific article published on 25 March 2011

Sequential electron transfer governs the UV-induced self-repair of DNA photolesions.

scientific article

Surprisingly broad applicability of the cc-pVnZ-F12 basis set for ground and excited states

scientific article published on 01 June 2020

The Mechanism of Dihydrogen Activation by Frustrated Lewis Pairs Revisited

scientific article published on 01 February 2010

Towards biochemically relevant QM computations on nucleic acids: controlled electronic structure geometry optimization of nucleic acid structural motifs using penalty restraint functions.

scientific article published on 27 November 2014

UUCG RNA Tetraloop as a Formidable Force-Field Challenge for MD Simulations

scientific article published on 20 November 2020

Water-chromophore electron transfer determines the photochemistry of cytosine and cytidine.

scientific article

Why the Standard B3LYP/6-31G* Model Chemistry Should Not Be Used in DFT Calculations of Molecular Thermochemistry: Understanding and Correcting the Problem

article

List of works by Holger Kruse

A geometrical correction for the inter- and intra-molecular basis set superposition error in Hartree-Fock and density functional theory calculations for large systems.

An intricate balance of hydrogen bonding, ion atmosphere and dynamics facilitates a seamless uracil to cytosine substitution in the U-turn of the neomycin-sensing riboswitch

Benchmarking Density Functional Methods against the S66 and S66x8 Datasets for Non-Covalent Interactions

Comment on "Evaluating Unexpectedly Short Non-covalent Distances in X-ray Crystal Structures of Proteins with Electronic Structure Analysis"

Comparative Assessment of Different RNA Tetranucleotides from the DFT-D3 and Force Field Perspective.

Derivation of Reliable Geometries in QM Calculations of DNA Structures: Explicit Solvent QM/MM and Restrained Implicit Solvent QM Optimizations of G-Quadruplexes

Enantioselective helical folding inside a self-assembled, cylindrical capsule

Exploring Nature and Predicting Strength of Hydrogen Bonds: A Correlation Analysis Between Atoms-in-Molecules Descriptors, Binding Energies, and Energy Components of Symmetry-Adapted Perturbation Theory

Identification of thiazolidinones spiro-fused to indolin-2-ones as potent and selective inhibitors of the Mycobacterium tuberculosis protein tyrosine phosphatase B.

Including crystallographic symmetry in quantum-based refinement: Q|R#2

Interactions between cyclic nucleotides and common cations: an ab initio molecular dynamics study

Investigating inclusion complexes using quantum chemical methods.

Investigations of Stacked DNA Base-Pair Steps: Highly Accurate Stacking Interaction Energies, Energy Decomposition, and Many-Body Stacking Effects

Ion Binding to Quadruplex DNA Stems. Comparison of MM and QM Descriptions Reveals Sizable Polarization Effects Not Included in Contemporary Simulations

MD and QM/MM Study of the Quaternary HutP Homohexamer Complex with mRNA, l-Histidine Ligand, and Mg2.

Nonenzymatic Oligomerization of 3',5'-Cyclic CMP Induced by Proton and UV Irradiation Hints at a Nonfastidious Origin of RNA.

Psi4 1.4: Open-source software for high-throughput quantum chemistry

QM Computations on Complete Nucleic Acids Building Blocks: Analysis of the Sarcin-Ricin RNA Motif Using DFT-D3, HF-3c, PM6-D3H, and MM Approaches

QM/MM Calculations on Protein-RNA Complexes: Understanding Limitations of Classical MD Simulations and Search for Reliable Cost-Effective QM Methods

Quantum chemical benchmark study on 46 RNA backbone families using a dinucleotide unit.

Real-space quantum-based refinement for cryo-EM: Q|R#3

Revisiting the Potential Energy Surface of the Stacked Cytosine Dimer: FNO-CCSD(T) Interaction Energies, SAPT Decompositions, and Benchmarking

Ring-Expanded Bicyclic β-Lactams: A Structure−Chiroptical Properties Relationship Investigation by Experiment and Calculations

Sequential electron transfer governs the UV-induced self-repair of DNA photolesions.

Surprisingly broad applicability of the cc-pVnZ-F12 basis set for ground and excited states

The Mechanism of Dihydrogen Activation by Frustrated Lewis Pairs Revisited

Towards biochemically relevant QM computations on nucleic acids: controlled electronic structure geometry optimization of nucleic acid structural motifs using penalty restraint functions.

UUCG RNA Tetraloop as a Formidable Force-Field Challenge for MD Simulations

Water-chromophore electron transfer determines the photochemistry of cytosine and cytidine.

Why the Standard B3LYP/6-31G* Model Chemistry Should Not Be Used in DFT Calculations of Molecular Thermochemistry: Understanding and Correcting the Problem