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List of works by Pavel Hobza

(HX)2 species (X=F through At) in the groups of the periodic system:

article published in 1998

2 Theoretical studies of hydrogen bonding

A DFT-D investigation of the mechanisms for activation of the wild-type and S810L mutated mineralocorticoid receptor by steroid hormones

scientific article

A Molecular Dynamics Study of the Benzene.cntdot..cntdot..cntdot.Arn (n = 3-5) Complex Using the ab Initio Intermolecular Potential

article

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 comparison of ab initio quantum-mechanical and experimental D0 binding energies of eleven H-bonded and eleven dispersion-bound complexes

scientific article

A halogen-bonding correction for the semiempirical PM6 method

A molecular dynamics study of the benzene…Ar2 complex. Application of the nonempirical ab initio and empirical Lennard-Jones 6–12 potentials

article

A quantum chemical study of the effect of Na+ on the hydrogen bonds in the adenine-thymine base-pair

scientific article published on 01 May 1984

A π-stacked phenylacetylene dimer

article

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

Ab Initio Study of the Interaction of Guanine and Adenine with Various Mono- and Bivalent Metal Cations (Li+, Na+, K+, Rb+, Cs+; Cu+, Ag+, Au+; Mg2+, Ca2+, Sr2+, Ba2+; Zn2+, Cd2+, and Hg2+)

Ab initio Calculations of the Rotation-Vibration Spectrum of Na3+

article

Ab initio and DFT studies of the interaction between carbonyl and thiocarbonyl groups: the role of S···O chalcogen bonds

Ab initio calculations on Ar–NO+: Structure and vibrational frequencies

article

Ab initio calculations on the structure, stabilization, and dipole moment of benzene⋅⋅⋅Ar complex

Ab initio calculations on the structure, vibrational frequencies, and valence excitation energies of the benzene…Ar and benzene…Ar2 cluster

article

Ab initio calculations on theo-benzyne?Ar ando-benzyne?CO complexes

Ab initio second‐ and fourth‐order Mo/ller–Plesset study on structure, stabilization energy, and stretching vibration of benzene⋅⋅⋅X (X=He,Ne,Ar,Kr,Xe) van der Waals molecules

article

Ab initio study of the phenol‐water cation radical

Ab initio study on the methanol-water cation radical potential energy surface

Ability of empirical potentials (AMBER, CHARMM, CVFF, OPLS, Poltev) and semi-empirical quantum chemical methods (AM1, MNDO/M, PM3) to describe H-bonding in DNA base pairs; comparison with ab initio results

article by Pavel Hobza et al published July 1996 in Chemical Physics Letters

Accuracy of Several Wave Function and Density Functional Theory Methods for Description of Noncovalent Interaction of Saturated and Unsaturated Hydrocarbon Dimers

scientific article published on 4 June 2012

Accurate Interaction Energies of Hydrogen-Bonded Nucleic Acid Base Pairs

scientific article published on 01 August 2004

Accurate Theoretical Determination of the Structure of Aromatic Complexes Is Complicated: The Phenol Dimer and Phenol···Methanol Cases

scientific article published on 13 June 2007

Acetic Acid Dimer in the Gas Phase, Nonpolar Solvent, Microhydrated Environment, and Dilute and Concentrated Acetic Acid: Ab Initio Quantum Chemical and Molecular Dynamics Simulations

article

Adenine ribbon stabilized by Watson-Crick and Hoogsteen hydrogen bonds: WFT and DFT study

scientific article published on 29 January 2010

Adenine⋯2,4-difluorotoluene (modified base) pair: potential and free-energy surfaces

Adsorption of Organic Electron Acceptors on Graphene-like Molecules: Quantum Chemical and Molecular Mechanical Study

article

Adsorption of Organic Molecules to van der Waals Materials: Comparison of Fluorographene and Fluorographite with Graphene and Graphite.

scientific article

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

Already two water molecules change planar H-bonded structures of the adenine···thymine base pair to the stacked ones: a molecular dynamics simulations study

article

Amino groups in nucleic acid bases, aniline, aminopyridines, and aminotriazine are nonplanar: Results of correlatedabinitioquantum chemical calculations and anharmonic analysis of the aniline inversion motion

scientific article published on 22 December 1996

An Isolated Molecule of Iron(II) Phthalocyanin Exhibits Quintet Ground-State: A Nexus between Theory and Experiment

scientific article published on 29 August 2018

An empirical potential for interactions of large molecules: Application to binding of dipeptides to DNA

An essay on the theory and calculations of intermolecular interactions

Analysis of energy stabilization inside the hydrophobic core of rubredoxin.

scientific article

Anharmonic and harmonic intermolecular vibrational modes of the DNA base pairs

scientific article published on 22 January 1997

Another role of proline: stabilization interactions in proteins and protein complexes concerning proline and tryptophane.

scientific article

Anti-Hydrogen Bond in the Benzene Dimer and Other Carbon Proton Donor Complexes

Anti-hydrogen bond between chloroform and fluorobenzene

Applicability of the supermolecule MP2 approach to intermolecular interactions: He2 and Ne2

Application of Berlin's Theorem to Bond-Length Changes in Isolated Molecules and Red- and Blue-Shifting H-Bonded Clusters

Are the hydrogen bonds of RNA (AU) stronger than those of DNA (AT)? A quantum mechanics study.

scientific article published in August 2005

Assessing the Accuracy and Performance of Implicit Solvent Models for Drug Molecules: Conformational Ensemble Approaches

article

Assessment of the MP2 method, along with several basis sets, for the computation of interaction energies of biologically relevant hydrogen bonded and dispersion bound complexes

scientific article published on 25 July 2007

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

scientific article published on 18 April 2012

Assigning the NH stretches of the guanine tautomers using adiabatic separation: CCSD(T) benchmark calculations

scientific article published on 13 February 2008

Autobiography of Pavel Hobza ⬇️

scientific article published on October 20, 2011

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

scientific article published in July 2017

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

scientific article published on 29 April 2009

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 RI-MP2 database of nucleic acid base trimers: performance of different density functional models for prediction of structures and binding energies

scientific article published on 09 July 2007

Benchmark database of accurate (MP2 and CCSD(T) complete basis set limit) interaction energies of small model complexes, DNA base pairs, and amino acid pairs

article

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

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

Benzene trimer and benzene tetramer: Structures and properties determined by the nonempirical model (NEMO) potential calibrated from the CCSD(T) benzene dimer energies

article

Bifurcated hydrogen bonds in DNA crystal structures. An ab initio quantum chemical study

article by Jirí Sponer & Pavel Hobza published January 1994 in Journal of the American Chemical Society

Binary twinned-icosahedral [B21H18]- interacts with cyclodextrins as a precedent for its complexation with other organic motifs

scientific article

Binding Energies of the π-Stacked Anisole Dimer: New Molecular Beam-Laser Spectroscopy Experiments and CCSD(T) Calculations

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

Binding of cationic and neutral phenanthridine intercalators to a DNA oligomer is controlled by dispersion energy: quantum chemical calculations and molecular mechanics simulations

scientific article

Blue shifts vs red shifts in sigma-hole bonding

scientific article published on 26 April 2008

Blue-Shifting Hydrogen Bonds ⬇️

scientific article published on November 8, 2000

Bonding ability of surface sites on silica and their effect on hydrogen bonds. A quantum-chemical and statistical thermodynamic treatment

article published in 1981

Br···O Complexes as Probes of Factors Affecting Halogen Bonding: Interactions of Bromobenzenes and Bromopyrimidines with Acetone

scientific article published on 18 December 2008

C-H stretching vibrational shift of benzene dimer: consistency of experiment and calculation

scientific article

CCSDT and CCSD(T) calculations on model H-bonded and stacked complexes

article

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

scientific article published on 16 November 2012

Calculations on Noncovalent Interactions and Databases of Benchmark Interaction Energies ⬇️

scientific article published on 06 January 2012

Carborane-based carbonic anhydrase inhibitors: insight into CAII/CAIX specificity from a high-resolution crystal structure, modeling, and quantum chemical calculations.

scientific article published on 18 September 2014

Cation–π complexes between alkali metal cation andpara-halogenophenols. Structures, binding energies and thermodynamic properties: DFT study and CCSD(T) complete basis set limit calculations

Chalcogen Bonding due to the Exo-Substitution of Icosahedral Dicarbaborane

scientific article published on 23 July 2019

Chalcogen and Pnicogen Bonds in Complexes of Neutral Icosahedral and Bicapped Square-Antiprismatic Heteroboranes

scientific article published on 12 February 2015

Characteristics of a σ-Hole and the Nature of a Halogen Bond

scientific article published on 01 January 2015

Chelating Polymers for Hereditary Hemochromatosis Treatment

scientific article published on 21 September 2020

Clusters of hydrogen molecules: Ab initio SCF calculations corrected semiempirically for correlation energies

Comment on “Electron-Correlated Calculations of Electric Properties of Nucleic Acid Bases”

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

scientific article

Comparison of Intrinsic Stacking Energies of Ten Unique Dinucleotide Steps in A-RNA and B-DNA Duplexes. Can We Determine Correct Order of Stability by Quantum-Chemical Calculations?

Comparison of intrinsic stacking energies of ten unique dinucleotide steps in A-RNA and B-DNA duplexes. Can we determine correct order of stability by quantum-chemical calculations?

scientific article

Comparison of the DFT-SAPT and Canonical EDA Schemes for the Energy Decomposition of Various Types of Noncovalent Interactions

scientific article published on 21 June 2018

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

Competition between stacking and hydrogen bonding: theoretical study of the phenol⋯Ar cation and neutral complex and comparison to experiment

article

Complete Basis Set Extrapolation and Hybrid Schemes for Geometry Gradients of Noncovalent Complexes

article

Computational methods for the description of pharmacologically relevant platinum complexes – molecular structure and bond dissociation

scholarly article by Malte Kokoschka et al published 2016 in Physical Chemistry Chemical Physics

Computer Modeling of Halogen Bonds and Other σ-Hole Interactions

scientific article published on 3 February 2016

Convergence of the CCSD(T) Correction Term for the Stacked Complex Methyl Adenine−Methyl Thymine: Comparison with Lower-Cost Alternatives

scientific article published on 01 July 2009

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: The strength and directionality of a halogen bond are co-determined by the magnitude and size of the σ-hole

scientific article published on 17 August 2015

Correlated ab Initio Study of Nucleic Acid Bases and Their Tautomers in the Gas Phase, in a Microhydrated Environment, and in Aqueous Solution. Part 3. Adenine

Correlated ab initio study of nucleic acid bases and their tautomers in the gas phase, in a microhydrated environment and in aqueous solution : Part 1. Cytosine

Correlated ab initio study of nucleic acid bases and their tautomers in the gas phase, in a microhydrated environment and in aqueous solution. Part 4. Uracil and thymine

scientific article published in May 2005

Correlated ab initio study of nucleic acid bases and their tautomers in the gas phase, in a microhydrated environment and in aqueous solution. guanine: surprising stabilization of rare tautomers in aqueous solution

scientific article

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

Counterpoise-Corrected Potential Energy Surfaces of Simple Hydrogen-Bonded Systems

article by Pavel Hobza & Zdeněk Havlas published 1998 in Collection of Czechoslovak Chemical Communications

Counterpoise-corrected potential energy surfaces of simple H-bonded systems

article by Pavel Hobza & Zdenv &#157 k Havlas published 2 November 1998 in Theoretical Chemistry Accounts

Critical effect of the N2 amino group on structure, dynamics, and elasticity of DNA polypurine tracts

scientific article

Czech bibliometric system fosters mediocre research

scientific article published in Nature

C−H···O Contacts in the Adenine···Uracil Watson−Crick and Uracil···Uracil Nucleic Acid Base Pairs: Nonempirical ab Initio Study with Inclusion of Electron Correlation Effects

DNA Base Trimers: Empirical and Quantum Chemical Ab Initio Calculations versus Experiment in Vacuo

scientific article published on 01 January 2007

DNA adduct formation from quaternary benzo[c]phenanthridine alkaloids sanguinarine and chelerythrine as revealed by the 32P-postlabeling technique

scientific article published in August 2002

DNA base amino groups and their role in molecular interactions: Ab initio and preliminary density functional theory calculations

scientific article published on 5 March 1996

Defining the hydrogen bond: An account (IUPAC Technical Report)

article

Definition of the hydrogen bond (IUPAC Recommendations 2011)

scientific article published on 8 January 2011

Density functional theory and molecular clusters

article published in 1995

Density functional theory augmented with an empirical dispersion term. Interaction energies and geometries of 80 noncovalent complexes compared with ab initio quantum mechanics calculations

scientific article published on 30 January 2007

Density functional theory-symmetry adapted perturbation treatment energy decomposition of nucleic acid base pairs taken from DNA crystal geometry

article

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

Design of HIV protease inhibitors based on inorganic polyhedral metallacarboranes

scientific article

Differences in the sublimation energy of benzene and hexahalogenbenzenes are caused by dispersion energy

scientific article published on 10 May 2013

Discriminative interactions between chiral molecules: internal discrimination in 1,2-difluorohydrazine

Dispersion Interactions Govern the Strong Thermal Stability of a Protein

scientific article published on 01 January 2007

Does stacking restrain the photodynamics of individual nucleobases?

scientific article published in June 2010

Double Proton Transfer: From the Formamide Dimer to the Adenine.cntdot..cntdot..cntdot.Thymine Base Pair

Double-Helical → Ladder Structural Transition in the B-DNA is Induced by a Loss of Dispersion Energy

scientific article published on 01 November 2008

Effect of substituents on the excited-state dynamics of the modified DNA bases 2,4-diaminopyrimidine and 2,6-diaminopurine

scientific article

Electronic coupling in the excited electronic state of stacked DNA base homodimers

scientific article published on 26 February 2007

Electronic splitting in the excited states of DNA base homodimers and -trimers: an evaluation of short-range and Coulombic interactions

scientific article published on 30 July 2008

Electronic structure of established and potential oxidizing agents in biological systems

scientific article published on 01 June 1977

Electronic structures, vibrational spectra, and revised assignment of aniline and its radical cation: Theoretical study

article

Energy Matrix of Structurally Important Side-Chain/Side-Chain Interactions in Proteins

scientific article published on July 2010

Energy barriers between H-bonded and stacked structures of 9-methyladenine...1-methylthymine and 9-methylguanine...1-methylcytosine complexes.

scientific article published on 13 November 2009

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

scientific article published on March 2014

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

scientific article published in September 2014

Evaluation of the intramolecular basis set superposition error in the calculations of larger molecules: [n]helicenes and Phe-Gly-Phe tripeptide.

scientific article published in April 2008

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

article

Exceptional thermodynamic stability of DNA duplexes modified by nonpolar base analogues is due to increased stacking interactions and favorable solvation: Correlated ab initio calculations and molecular dynamics simulations.

scientific article published in April 2006

Experimental and Theoretical Investigation of the Aromatic−Aromatic Interaction in Isolated Capped Dipeptides†

scientific article published on 01 March 2010

Experimental and Theoretical Study for the Assessment of the Conformational Stability of Polymethylene-Bridged Heteroaromatic Dimers: A Case of Unprecedented Folding

article published in 2016

Explicit treatment of active-site waters enhances quantum mechanical/implicit solvent scoring: Inhibition of CDK2 by new pyrazolo[1,5-a]pyrimidines.

scientific article published on 11 December 2016

Exploring the Structure of a DNA Hairpin with the Help of NMR Spin−Spin Coupling Constants: An Experimental and Quantum Chemical Investigation

article by Vladimír Sychrovský et al published October 2002 in Journal of Physical Chemistry

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

Ferrocene-modified purines as potential electrochemical markers: synthesis, crystal structures, electrochemistry and cytostatic activity of (ferrocenylethynyl)- and (ferrocenylethyl)purines

scientific article published on April 2004

First local minimum of the formic acid dimer exhibits simultaneously red-shifted O–H⋯O and improper blue-shifted C–H⋯O hydrogen bonds

article by Jana Chocholoušová et al published 2004 in Physical Chemistry Chemical Physics

Floppy structure of the benzene dimer: Ab initio calculation on the structure and dipole moment

Formation of hydrogen-bonded van der waals molecules: applicability of 3–21G intermolecular interaction energies

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

From Dibismuthenes to Three- and Two-Coordinated Bismuthinidenes by Fine Ligand Tuning: Evidence for Aromatic BiC3N Rings through a Combined Experimental and Theoretical Study

article

Functionalization of Graphene: Covalent and Non-Covalent Approaches, Derivatives and Applications

scientific article published on 14 November 2012

Gas-Phase Solvation of Benzene by 2-8 Argon Atoms. A Molecular Dynamics Study with ab Initio Intermolecular Potential

article

Gas-phase spectroscopy of biomolecular building blocks

scientific article published on January 2007

Geometry of the Phosphate Group and Its Interactions with Metal Cations in Crystals andab InitioCalculations

scientific article published in 1996

Global Minimum of the Adenine···Thymine Base Pair Corresponds Neither to Watson−Crick Nor to Hoogsteen Structures. Molecular Dynamic/Quenching/AMBER and ab Initio beyond Hartree−Fock Studies

scientific article published in 2000

Glycine in an Electronically Excited State: Ab Initio Electronic Structure and Dynamical Calculations

scientific article published on 27 May 2007

Ground state of the Fe(ii)-porphyrin model system corresponds to quintet: a DFT and DMRG-based tailored CC study

scientific article published on 27 July 2020

Ground state potential surface for van der Waals complexes: Ab initio second‐order Mo/ller–Plesset study on benzene...N2 van der Waals molecule

Guanine-aspartic acid interactions probed with IR-UV resonance spectroscopy

scientific article published on 8 March 2010

H-Bonded and Stacked DNA Base Pairs: Cytosine Dimer. An Ab Initio Second-Order Moeller-Plesset Study

article by Pavel Hobza et al published January 1995 in Journal of the American Chemical Society

H-Bonding Cooperativity Effects in Amyloids: Quantum Mechanical and Molecular Mechanics Study

article

HF-ClF: minima on the 4-31G and 4-31G * energy hypersurfaces and thermodynamics of formation

HF-HCl: stationary points on the scf energy hypersurface and thermodynamics of formation

article by Pavel Hobza et al published September 1980 in Chemical Physics Letters

Halogen bonded complexes between volatile anaesthetics (chloroform, halothane, enflurane, isoflurane) and formaldehyde: a theoretical study

scientific article

Halogen bonds in crystal TTF derivatives: an ab initio quantum mechanical study

scientific article published on 01 February 2014

High Level ab initio Calculations on Acetylene Dimer - A Prototype for Estimation of the Accuracy of the Benzene Dimer Stabilization Energy

Highly accurate CCSD(T) and DFT-SAPT stabilization energies of H-bonded and stacked structures of the uracil dimer.

scientific article published in August 2008

Highly correlated calculations using optimized virtual orbital space with controlled accuracy. Application to counterpoise corrected interaction energy calculations

How the Shape of the NH2Group Depends on the Substituent Effect and H-Bond Formation in Derivatives of Aniline

scientific article published on 01 January 2007

How the Stabilization of INK4 Tumor Suppressor 3D Structure Evaluated by Quantum Chemical and Molecular Mechanics Calculations Corresponds Well with Experimental Results: Interplay of Association Enthalpy, Entropy, and Solvation Effects

Hydration Gibbs Energies of Nucleic Acid Bases Determined by Gibbs Energy Perturbation, Continuous and Hybrid Approaches

Hydration and stability of nucleic acid bases and base pairs

scientific article published on 08 December 2006

Hydration of Sulfo and Methyl Groups in Dimethyl Sulfoxide Is Accompanied by the Formation of Red-Shifted Hydrogen Bonds and Improper Blue-Shifted Hydrogen Bonds: An ab Initio Quantum Chemical Study

article

Hydrogen Bond versus Anti-Hydrogen Bond: A Comparative Analysis Based on the Electron Density Topology

article

Hydrogen bonding and stacking interactions of nucleic acid base pairs: A density-functional-theory based treatment

article

Hydrogen-bonded complexes of phenylacetylene with water, methanol, ammonia, and methylamine. The origin of methyl group-induced hydrogen bond switching.

scientific article

Hydrogen-bonded nucleic acid base pairs containing unusual base tautomers: complete basis set calculations at the MP2 and CCSD(T) levels.

scientific article

IDD388 Polyhalogenated Derivatives as Probes for an Improved Structure-Based Selectivity of AKR1B10 Inhibitors

scientific article

IR-UV double resonance spectroscopy of guanine-H2O clusters.

scientific article published on 20 July 2005

Identifying stabilizing key residues in proteins using interresidue interaction energy matrix.

scientific article

Imidazo[1,2-c]pyrimidin-5(6H)-one as a novel core of cyclin-dependent kinase 2 inhibitors: Synthesis, activity measurement, docking, and quantum mechanical scoring.

scientific article published on 23 April 2018

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

Improper, Blue-Shifting Hydrogen Bond between Fluorobenzene and Fluoroform

Improper, blue-shifting hydrogen bond

article published in 2002

Influence of hydrophobic residues on the binding of CB[7] toward diammonium ions of common ammonium⋯ammonium distance

article

Influence of local electric fields on the properties and reactivity of hydrogen bonds. Complexes between molecular hydrogen fluoride and molecular hydrogen chloride and M (M = Li+, Na+, Mg2+)

Infrared-optical double resonance spectroscopic measurements and high level ab initio calculations on a binary complex between phenylacetylene and borane-trimethylamine. Understanding the role of C-H...pi interactions

scientific article published on 26 August 2009

Inside Back Cover: A Nexus between Theory and Experiment: Non-Empirical Quantum Mechanical Computational Methodology Applied to Cucurbit[n ]uril⋅Guest Binding Interactions (Chem. Eur. J. 48/2016)

scientific article published on 25 October 2016

Insights into Stability and Folding of GNRA and UNCG Tetraloops Revealed by Microsecond Molecular Dynamics and Well-Tempered Metadynamics

scientific article published on August 2015

Interaction Energies of Hydrogen-Bonded Formamide Dimer, Formamidine Dimer, and Selected DNA Base Pairs Obtained with Large Basis Sets of Atomic Orbitals

article published in 2000

Interaction between the Guanine−Cytosine Watson−Crick DNA Base Pair and Hydrated Group IIa (Mg2+, Ca2+, Sr2+, Ba2+) and Group IIb (Zn2+, Cd2+, Hg2+) Metal Cations

Interaction energies for the purine inhibitor roscovitine with cyclin-dependent kinase 2: correlated ab initio quantum-chemical, DFT and empirical calculations

scientific article published on May 2006

Interaction of Carboranes with Biomolecules: Formation of Dihydrogen Bonds

scientific article published on 01 May 2006

Interaction of DNA Base Pairs with Various Metal Cations (Mg2+, Ca2+, Sr2+, Ba2+, Cu+, Ag+, Au+, Zn2+, Cd2+, and Hg2+): Nonempirical ab Initio Calculations on Structures, Energies, and Nonadditivity of the Interaction

Interaction of Graphene and Arenes with Noble Metals

article

Interaction of Lysine-Alanine-Alanine tripeptide with a fragment of DNA: An empirical potential study

Interaction of heteroboranes with biomolecules : Part 2. The effect of various metal vertices and exo-substitutions

scientific article published on 15 February 2007

Interaction of the Adenine−Thymine Watson−Crick and Adenine−Adenine Reverse-Hoogsteen DNA Base Pairs with Hydrated Group IIa (Mg2+, Ca2+, Sr2+, Ba2+) and IIb (Zn2+, Cd2+, Hg2+) Metal Cations: Absence of the Base Pair Stabilization by Metal-Indu

Interactions of Hydrated Mg2+Cation with Bases, Base Pairs, and Nucleotides. Electron Topology, Natural Bond Orbital, Electrostatic, and Vibrational Study

article

Interactions of boranes and carboranes with aromatic systems: CCSD(T) complete basis set calculations and DFT-SAPT analysis of energy components

scientific article published on October 2010

Interactions of hydrated divalent metal cations with nucleic acid bases. How to relate the gas phase data to solution situation and binding selectivity in nucleic acids

Interactions of model biomolecules. Benchmark CC calculations within MOLCAS

Intercalators. 1. Nature of Stacking Interactions between Intercalators (Ethidium, Daunomycin, Ellipticine, and 4‘,6‘-Diaminide-2-phenylindole) and DNA Base Pairs. Ab Initio Quantum Chemical, Density Functional Theory, and Empirical Potential Study

scientific article published in 2003

Intercalators. 1. Nature of stacking interactions between intercalators (ethidium, daunomycin, ellipticine, and 4',6-diaminide-2-phenylindole) and DNA base pairs. Ab initio quantum chemical, density functional theory, and empirical potential study

scientific article published in April 2002

Intermolecular interactions between medium-sized systems. Nonempirical and empirical calculations of interaction energies. Successes and failures

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

article

Intramolecular flexibility of DNA bases in adenine–thymine and guanine–cytosine Watson–Crick base pairs

Introduction: Noncovalent Interactions

article published in 2016

Investigations into the Nature of Halogen Bonding Including Symmetry Adapted Perturbation Theory Analyses

scientific article published in February 2008

Isolated Gramicidin Peptides Probed by IR Spectroscopy

scientific article published on 08 June 2011

Isomer selective IR experiments and correlated ab initio quantum chemical calculations support planar H-bonded structure of the 7-methyl adenine?adenine and stacked structure of the 9-methyl adenine?adenine base pairs

Isomorphous Substitution of Si for Al, Ga, Fe, In and B in Molecular Sieves of MFI Structure. A Quantum Chemical, Ammonia Desorption and Catalytic Activity Study of Framework Si-OH-M Acid Site Strength

Large-Scale Quantitative Assessment of Binding Preferences in Protein-Nucleic Acid Complexes.

scientific article published in April 2015

Large-scale compensation of errors in pairwise-additive empirical force fields: comparison of AMBER intermolecular terms with rigorous DFT-SAPT calculations

article published in 2010

Ligand Conformational and Solvation/Desolvation Free Energy in Protein−Ligand Complex Formation

scientific article published on 05 April 2011

Lipid hydration: headgroup CH moieties are involved in water binding.

scientific article

Loss of dispersion energy changes the stability and folding/unfolding equilibrium of the Trp-cage protein.

scientific article

MM2 study of 20-hydroxy-4,7,13,16-tetraoxa-1,10-diazabicyclo [8,8,3] heneicosane and its formation controlled by hydrogen bonding

MP2 and CCSD(T) calculations on H-bonded and stacked formamide…formamide and formamidine…formamidine dimers

MP2 and CCSD(T) study on hydrogen bonding, aromatic stacking and nonaromatic stacking

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

MP4 Interaction energies and basis set superposition errors for the (H2)2dimer

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

scientific article published on 16 October 2014

Metal ions in non-complementary DNA base pairs: an ab initio study of Cu(I), Ag(I), and Au(I) complexes with the cytosine-adenine base pair

scholarly article

Methylated uracil dimers: potential energy and free energy surfaces

Microhydration of guanine...cytosine base pairs, a theoretical Study on the role of water in stability, structure and tautomeric equilibrium.

scientific article published on 5 March 2009

Minimal basis set MINI-1 ? powerful tool for calculating of molecular interactions. I. Neutral complexes

Model of peptide bond-aromatic ring interaction: correlated ab initio quantum chemical study

scientific article published on 2 August 2007

Modulation of aldose reductase inhibition by halogen bond tuning

scientific article

Molecular Interactions of Nucleic Acid Bases. A Review of Quantum-Chemical Studies

article

Molecular dynamics simulations and thermodynamics analysis of DNA-drug complexes. Minor groove binding between 4',6-diamidino-2-phenylindole and DNA duplexes in solution

scientific article

Molecular-orbital study of hydroxylation of collagenous proline and lysine

Mutagenic properties of 5-halogenuracils: correlated quantum chemical ab initio study

scientific article

N-H· · ·F improper blue-shifting H-bond

Na+, Mg2+, and Zn2+Binding to All Tautomers of Adenine, Cytosine, and Thymine and the Eight Most Stable Keto/Enol Tautomers of Guanine: A Correlated ab Initio Quantum Chemical Study

scientific article published on 01 July 2006

Nature and magnitude of aromatic stacking of nucleic acid bases

scientific article published on 07 April 2008

Nature of Base Stacking: Reference Quantum-Chemical Stacking Energies in Ten Unique B-DNA Base-Pair Steps

scientific article published on 01 March 2006

Nature of Nucleic Acid−Base Stacking: Nonempirical ab Initio and Empirical Potential Characterization of 10 Stacked Base Dimers. Comparison of Stacked and H-Bonded Base Pairs

Nature of bonding in nine planar hydrogen-bonded adenine...thymine base pairs

scientific article published in March 2009

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 parameterization of the Cornell et al. empirical force field covering amino group nonplanarity in nucleic acid bases

scientific article published in November 2003

New structure for the most stable isomer of the benzene dimer: a quantum chemical study

article by Pavel Hobza et al published April 1993 in The journal of physical chemistry

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

scientific article

Non-covalent interactions in biomacromolecules.

scientific article published on 14 June 2007

Non-standard base pairing and stacked structures in methyl xanthine clusters

scientific article

Nonadiabatic Dynamics of Uracil: Population Split among Different Decay Mechanisms

article

Noncovalent Interactions in Specific Recognition Motifs of Protein-DNA Complexes

scientific article published on 19 December 2016

Noncovalent Interactions of Heteroboranes

article

Noncovalent Interactions: A Challenge for Experiment and Theory

scientific article published on 01 January 2000

Noncovalent interactions in biochemistry

Nonempirical ab initio calculations on DNA base pairs

Nonempirical calculations on all the 29 possible DNA base pairs

article

Nonplanar geometries of DNA bases. Ab initio second-order Moeller-Plesset study

article by Jiri Sponer & Pavel Hobza published March 1994 in The journal of physical chemistry

Nuclear Dynamics of Benzene···(Ar)nClusters

article

N−H···π Interactions in Indole···Benzene-h6,d6and Indole···Benzene-h6,d6Radical Cation Complexes. Mass Analyzed Threshold Ionization Experiments and Correlated ab Initio Quantum Chemical Calculations

Off-Center Gaussian Functions, an Alternative Atomic Orbital Basis Set for Accurate Noncovalent Interaction Calculations of Large Systems

scientific article published on 19 November 2013

On Extension of the Current Biomolecular Empirical Force Field for the Description of Halogen Bonds

scientific article published on 20 March 2012

On differences between hydrogen bonding and improper blue-shifting hydrogen bonding

scientific article published in April 2005

On geometries of stacked and H-bonded nucleic acid base pairs determined at various DFT, MP2, and CCSD(T) levels up to the CCSD(T)/complete basis set limit level

scientific article published in May 2005

On the Association of the Base Pairs on the Silica Surface Based on Free Energy Biased Molecular Dynamics Simulation and Quantum Mechanical Calculations

article

On the Nature of Bonding in Lone Pair···π-Electron Complexes: CCSD(T)/Complete Basis Set Limit Calculations

scientific article published on 23 March 2009

On the Nature of the Stabilization of Benzene⋅⋅⋅Dihalogen and Benzene⋅⋅⋅Dinitrogen Complexes: CCSD(T)/CBS and DFT-SAPT Calculations

article

On the Role of London Dispersion Forces in Biomolecular Structure Determination

scientific article published on 27 May 2011

On the Structure and Geometry of Biomolecular Binding Motifs (Hydrogen-Bonding, Stacking, X-H···π): WFT and DFT Calculations

scientific article published on 9 December 2009

On the Structure and Geometry of Biomolecular Binding Motifs (Hydrogen-Bonding, Stacking, X-H···π): WFT and DFT Calculations.

scientific article published on 27 January 2011

On the convergence of the (ΔECCSD(T)−ΔEMP2) term for complexes with multiple H-bonds

On the importance and origin of aromatic interactions in chemistry and biodisciplines

scientific article

On the importance of electron correlation effects for the intramolecular stacking geometry of a bis-thiophene derivative.

scientific article

On the nature of DNA-duplex stability

scientific article published in January 2007

On the nature of LiH2

On the nature of the stabilisation of the E⋯π pnicogen bond in the SbCl3⋯toluene complex

scientific article published on 03 February 2016

On the nature of the surprisingly small (red) shift in the halothane...acetone complex

scientific article published in June 2007

On the nature of unusual intensity changes in the infrared spectra of the enflurane⋯acetone complexes ⬇️

scientific article published on March 15, 2013

On the origin of red and blue shifts of X-H and C-H stretching vibrations in formic acid (formate ion) and proton donor complexes

scientific article published in January 2007

On the origin of the substantial stabilisation of the electron-donor 1,3-dithiole-2-thione-4-carboxyclic acid⋯I2 and DABCO⋯I2 complexes

article

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

On the reliability of the AMBER force field and its empirical dispersion contribution for the description of noncovalent complexes.

scientific article published on August 2010

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 van der Waals interactions in organic chemistry

article

Optimization of norbornyl-based carbocyclic nucleoside analogs as cyclin-dependent kinase 2 inhibitors

scientific article published on 25 March 2020

Origin of Difference between One-Electron Redox Potentials of Guanosine and Guanine: Electrochemical and Quantum Chemical Study

Origin of high efficiency and specificity of biochemical reactions

Origin of the X-Hal (Hal = Cl, Br) bond-length change in the halogen-bonded complexes

scientific article published on 18 March 2008

PCILO Calculations on ?true? van der Waals complexes

article by R. Lochmann & Pavel Hobza published January 1979 in International Journal of Quantum Chemistry

Parallelized implementation of the CCSD(T) method in MOLCAS using optimized virtual orbitals space and Cholesky decomposed two-electron integrals

Performance of the DFT-D method, paired with the PCM implicit solvation model, for the computation of interaction energies of solvated complexes of biological interest

scientific article published on 5 September 2007

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

article

Photochemical selectivity in guanine-cytosine base-pair structures

scientific article

Photodynamics of the adenine model 4-aminopyrimidine embedded within double strand of DNA

article

Plugging the explicit σ-holes in molecular docking

scientific article

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

scientific article published on 30 October 2017

Polar Flattening and the Strength of Halogen Bonding

article

Polar isomer of formic acid dimers formed in helium nanodroplets

scientific article published on 01 June 2004

Potential Energy Surface for the Benzene Dimer. Results ofab InitioCCSD(T) Calculations Show Two Nearly Isoenergetic Structures: T-Shaped and Parallel-Displaced

article by Pavel Hobza et al published January 1996 in The journal of physical chemistry

Potential Energy Surface of the Benzene Dimer: Ab Initio Theoretical Study

article by Pavel Hobza et al published April 1994 in Journal of the American Chemical Society

Potential Energy Surface of the Cytosine Dimer: MP2 Complete Basis Set Limit Interaction Energies, CCSD(T) Correction Term, and Comparison with the AMBER Force Field

Potential Energy Surfaces of an Adenine−Thymine Base Pair and Its Methylated Analogue in the Presence of One and Two Water Molecules: Molecular Mechanics and Correlated Ab Initio Study

scientific article published on 01 June 2005

Potential energy and free energy surfaces of the formic acid dimer: Correlated ab initio calculations and molecular dynamics simulationsElectronic supplementary information (ESI) available: Optimised geometries of the structures in Tables 1 and 2. Se

article

Potential energy surface of the (H2)2 dimer: an MP2 study

Potential energy surfaces of the microhydrated guanine...cytosine base pair and its methylated analogue

scientific article published in February 2006

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

scientific article published in January 2008

Properties and Reactivity in Groups of the Periodic System: Ion−Molecule Reactions HX + HX•+(X = F, Cl, Br, I, At)

Properties of fluorobenzene⋅⋅⋅Ar and p‐difluorobenzene⋅⋅⋅Ar complexes: Ab initio study

Proton Transfer in the Adenine-Thymine Base Pair

scientific article published in 1994

Purines Bearing Phenanthroline or Bipyridine Ligands and Their RuII Complexes in Position 8 as Model Compounds for Electrochemical DNA Labeling – Synthesis, Crystal Structure, Electrochemistry, Quantum Chemical Calculations, Cytostatic and Antivira

article

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

scientific article

Quantification of the Interaction Forces between Metals and Graphene by Quantum Chemical Calculations and Dynamic Force Measurements under Ambient Conditions

article

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 Monte Carlo Methods Describe Noncovalent Interactions with Subchemical Accuracy

scientific article published on 6 September 2013

Quantum Monte Carlo for noncovalent interactions: an efficient protocol attaining benchmark accuracy ⬇️

scientific article published on 29 August 2014

Quantum chemical and statistical thermodynamic investigations of anesthetic activity. 1. The interaction between chloroform, fluoroform, cyclopropane and an O-H.cntdot..cntdot..cntdot.O hydrogen bond

scientific article published in 1981

Quantum chemical and statistical thermodynamic investigations of anesthetic activity. 2. The interaction between chloroform, fluoroform, and an NH...O:C hydrogen bond

scientific article published in 1982

Quantum chemical and statistical thermodynamic investigations of anesthetic activity. 3. The interaction between CH4, CH3Cl, CH2Cl2, CHCl3, CCl4, and an O—H … O hydrogen bond

Quantum chemical investigation of interaction sites in zeolites and silica

Quantum chemical study of the mechanism of collagen proline hydroxylation

scientific article published on 01 April 1973

Quantum mechanical scoring: structural and energetic insights into cyclin-dependent kinase 2 inhibition by pyrazolo[1,5-a]pyrimidines.

scientific article published in March 2013

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

scientific article published on 8 January 2018

Reactions between H+3 and rare gas atoms

Reference MP2/CBS and CCSD(T) quantum-chemical calculations on stacked adenine dimers. Comparison with DFT-D, MP2.5, SCS(MI)-MP2, M06-2X, CBS(SCS-D) and force field descriptions

scientific article published on 12 February 2010

Reference Quantum Chemical Calculations on RNA Base Pairs Directly Involving the 2′-OH Group of Ribose

scientific article published on 01 April 2009

Relaxation mechanisms of UV-photoexcited DNA and RNA nucleobases

scientific article

Reliable theoretical treatment of molecular clusters: Counterpoise-corrected potential energy surface and anharmonic vibrational frequencies of the water dimer

article

Representative Amino Acid Side Chain Interactions in Proteins. A Comparison of Highly Accurate Correlated ab Initio Quantum Chemical and Empirical Potential Procedures

scientific article published on April 2009

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

Resolution of identity density functional theory augmented with an empirical dispersion term (RI-DFT-D): a promising tool for studying isolated small peptides.

scientific article

Role of entropy in formation of van der Waals complexes

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

Scaled MP3 non-covalent interaction energies agree closely with accurate CCSD(T) benchmark data

scientific article

Search for simplified procedure for the evaluation of the Gibbs free energy of hydrogen-bond formation

Selective binding of choline by a phosphate-coordination-based triple helicate featuring an aromatic box.

scientific article published on 16 October 2017

Selective induced polarization through electron transfer in acetone and pyrazole ester derivatives via C–H⋯OC interaction

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

Semiempirical estimates of the correlation energy in small clusters of hydrogen atoms

article

Sequence dependent intrinsic deformability of the DNA base amino groups. An ab initio quantum chemical analysis

scientific article published in January 1994

Sequence-dependent configurational entropy change of DNA upon intercalation

scientific article published on October 2010

Significant structural deformation of nucleic acid bases in stacked base pairs: an ab initio study beyond Hartree–Fock

Spin modification of iron(ii) complexes via covalent (dative) and dispersion guided non-covalent bonding with N-heterocyclic carbenes: DFT, DLPNO-CCSD(T) and MCSCF studies

scientific article published on 03 December 2019

Spin-Crossing in an Organometallic Pt-Benzene Complex

scientific article published on 28 February 2013

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

Stabilisation energy of C6H6⋯C6X6(X = F, Cl, Br, I, CN) complexes: complete basis set limit calculations at MP2 and CCSD(T) levels

scientific article published on 19 December 2006

Stability of Nucleic Acid Base Pairs in Organic Solvents: Molecular Dynamics, Molecular Dynamics/Quenching, and Correlated Ab Initio Study

article

Stabilization and structure calculations for noncovalent interactions in extended molecular systems based on wave function and density functional theories.

scientific article

Stabilization energies of the hydrogen-bonded and stacked structures of nucleic acid base pairs in the crystal geometries of CG, AT, and AC DNA steps and in the NMR geometry of the 5'-d(GCGAAGC)-3' hairpin: Complete basis set calculations at the MP2

scientific article published in February 2005

Stacked Structure of the Glycine Dimer Is More Stable than the Cyclic Planar Geometry with Two O−H···O Hydrogen Bonds: Concerted Action of Empirical, High-Level Nonempirical ab Initio, and Experimental Studies

Stacking interactions

scientific article published on 14 April 2008

State of the art theoretical study and comparison to experiment for the phenol...argon complex.

scientific article

State-of-the-art correlated ab initio potential energy curves for heavy rare gas dimers: Ar2, Kr2, and Xe2

article by Petr Slavı́ček et al published 22 July 2003 in Journal of Chemical Physics

Statistical analysis of σ-holes: a novel complementary view on halogen bonding

scientific article

Stimuli-Responsive Nanoparticles Based on Interaction of Metallacarborane with Poly(ethylene oxide)

Strength and Character of Halogen Bonds in Protein–Ligand Complexes

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

scientific article

Structural Basis of the Interaction of Cyclin-Dependent Kinase 2 with Roscovitine and Its Analogues Having Bioisosteric Central Heterocycles.

scientific article published on 27 January 2017

Structure and IR spectrum of phenylalanyl-glycyl-glycine tripetide in the gas-phase: IR/UV experiments, ab initio quantum chemical calculations, and molecular dynamic simulations.

scientific article published in November 2005

Structure and Properties of Benzene-Containing Molecular Clusters: Nonempirical ab Initio Calculations and Experiments

Structure and binding energy of the phenol dimer: correlated ab initio calculations compared with results from rotational coherence spectroscopy

Structure and dynamics of the phenol–water–argon cation radical

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

Structure of Isolated Tryptophyl-Glycine Dipeptide and Tryptophyl-Glycyl-Glycine Tripeptide: Ab Initio SCC-DFTB-D Molecular Dynamics Simulations and High-Level Correlated ab Initio Quantum Chemical Calculations

article

Structure, Energetics, and Dynamics of the Nucleic Acid Base Pairs: NonempiricalAb InitioCalculations

article

Structure, energetics, and harmonic vibrational spectra of the adenine-thymine and adenine*-thymine* base pairs: gradient nonempirical and semiempirical study

article

Structures and Energies of Hydrogen-Bonded DNA Base Pairs. A Nonempirical Study with Inclusion of Electron Correlation

Study of the nature of improper blue-shifting hydrogen bonding and standard hydrogen bonding in the X3CH...OH2 and XH...OH2 complexes (X = F, Cl, Br, I): A correlated Ab initio study

scientific article published in June 2002

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

The Dominant Role of Chalcogen Bonding in the Crystal Packing of 2D/3D Aromatics

scientific article published on 27 July 2014

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

scientific article

The Effect of Metal Binding to the N7 Site of Purine Nucleotides on Their Structure, Energy, and Involvement in Base Pairing

article published in 2000

The H-index unambiguously discriminates between hydrogen bonding and improper blue-shifting hydrogen bonding

The Nature of the Binding of Au, Ag, and Pd to Benzene, Coronene, and Graphene: From Benchmark CCSD(T) Calculations to Plane-Wave DFT Calculations

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 World of Non-Covalent Interactions: 2006

The X3LYP extended density functional accurately describes H-bonding but fails completely for stacking

scientific article published in April 2005

The ab initio assigning of the vibrational probing modes of tryptophan: linear shifting of approximate anharmonic frequencies vs. multiplicative scaling of harmonic frequencies.

scientific article published on 12 March 2009

The accuracy of quantum chemical methods for large noncovalent complexes.

scientific article published on August 2013

The amino group in adenine: MP2 and CCSD(T) complete basis set limit calculations of the planarization barrier and DFT/B3LYP study of the anharmonic frequencies of adenine

scientific article published in December 2008

The barrier to internal rotation and electronic effects in para-halogenophenols: theoretical study

The calculation of intermolecular interaction energies

The charge-transfer states in a stacked nucleobase dimer complex: A benchmark study

scientific article published on 29 November 2010

The dihydrogen bond in X3C–H⋯H–M complexes (X = F, Cl, Br; M = Li, Na, K). A correlated quantum chemical ab initio and density functional theory study

The effect of C5 substitution on the photochemistry of uracil

scientific article published on 27 March 2010

The effect of water on NMR spin–spin couplings in DNA: Improvement of calculated values by application of two solvent models

The fluoroform⋯ethylene oxide complex exhibits a C–H⋯O anti-hydrogen bond

article published in 1999

The lithium bond reexamined

The methylation effect in amine...HF hydrogen-bonded systems. Quantum chemical and statistical thermodynamic study

The mid-IR absorption spectrum of gas-phase clusters of the nucleobases guanine and cytosine

The mid-IR spectra of 9-ethyl guanine, guanosine, and 2-deoxyguanosine

scientific article published on 11 July 2007

The minimal basis set MINI-1?powerful tool for calculating intermolecular interactions. II. Ionic complexes

The nature of bonding and electronic properties of graphene and benzene with iridium adatoms

scientific article published on 28 August 2014

The nature of improper, blue-shifting hydrogen bonding verified experimentally.

scientific article published in December 2001

The non-planarity of the benzene molecule in the X-ray structure of the chelated bismuth(III) heteroboroxine complex is not supported by quantum mechanical calculations.

scientific article published in January 2016

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

The photodynamics of 2,4-diaminopyrimidine in comparison with 4-aminopyrimidine: The effect of amino-substitution

The properties of substituted 3D-aromatic neutral carboranes: the potential for σ-hole bonding.

scientific article published on 27 July 2015

The relative roles of electrostatics and dispersion in the stabilization of halogen bonds

scientific article published on 01 November 2013

The role of the σ-holes in stability of non-bonded chalcogenidebenzene interactions: the ground and excited states

scientific article published on 5 December 2017

The strength and directionality of a halogen bond are co-determined by the magnitude and size of the σ-hole

scientific article published on 30 January 2014

The structure and vibrational dynamics of the pyrrole dimer.

scientific article published on 14 March 2009

The structures of LiNC, NaNC, and KNC: Potential energy surface for the orbiting motion of the metal cation around the CN group

The unusual stability of H‐bonded complexes in solvent caused by greater solvation energy of complex compared to those of isolated fragments

scientific article published on 26 May 2022

Theoretical calculation of the NMR spin-spin coupling constants and the NMR shifts allow distinguishability between the specific direct and the water-mediated binding of a divalent metal cation to guanine

scientific article

Theoretical insight into the stabilization of triazole fungicides via their interactions with dications

Theoretical investigations into the blue-shifting hydrogen bond in benzene complexes

scientific article published in March 2006

Theoretical study of photoacidity of HCN: the effect of complexation with water.

scientific article published on 26 September 2006

Theoretical study of the ground and excited states of 7-methyl guanine and 9-methyl guanine: comparison with experiment

scientific article published on 09 May 2006

Theoretical study of the stability of the DNA duplexes modified by a series of hydrophobic base analogues.

scientific article published in August 2009

Theoretical study on the complexes of benzene with isoelectronic nitrogen-containing heterocycles

scientific article published on May 2008

Thermodynamic characteristics for the formation of H-bonded DNA base pairs

Thioguanine and Thiouracil: Hydrogen-Bonding and Stacking Properties

Three- and four-body nonadditivities in nucleic acid tetramers: a CCSD(T) study.

scientific article published on 18 December 2009

Toward true DNA base-stacking energies: MP2, CCSD(T), and complete basis set calculations

scientific article published in October 2002

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

scientific article published in February 2011

True stabilization energies for the optimal planar hydrogen-bonded and stacked structures of guanine...cytosine, adenine...thymine, and their 9- and 1-methyl derivatives: complete basis set calculations at the MP2 and CCSD(T) levels and comparison w

scientific article

Understanding of assembly phenomena by aromatic-aromatic interactions: benzene dimer and the substituted systems

scientific article

Understanding the non-covalent interaction mediated modulations on the electronic structure of quasi-zero-dimensional graphene nanoflakes

scientific article published on 01 July 2018

Unexpectedly Strong Energy Stabilization Inside the Hydrophobic Core of Small Protein Rubredoxin Mediated by Aromatic Residues: Correlated Ab Initio Quantum Chemical Calculations [J. Amer. Chem. Soc.2005,127, 2615−2617]

scientific article published in 2005

Unexpectedly strong energy stabilization inside the hydrophobic core of small protein rubredoxin mediated by aromatic residues: correlated ab initio quantum chemical calculations

scientific article

Unraveling the Structure-Affinity Relationship between Cucurbit[n]urils (n = 7, 8) and Cationic Diamondoids.

scientific article

Uracil Dimer: Potential Energy and Free Energy Surfaces. Ab Initio beyond Hartree−Fock and Empirical Potential Studies

article published in 1998

Van der Waals molecules: Quantum chemistry, physical properties, and reactivity

scholarly article by Pavel Hobza & R. Zahradník published January 1983 in International Journal of Quantum Chemistry

Vibrational Spectroscopy of the G· · ·C Base Pair: Experiment, Harmonic and Anharmonic Calculations, and the Nature of the Anharmonic Couplings

article

Vibrational dynamics of the benzene…argon complex

article

Weak intermolecular interaction

Weak intermolecular interaction

Weak intermolecular interactions: Statics and dynamics

article

Why Is the L-Shaped Structure of X2···X2 (X = F, Cl, Br, I) Complexes More Stable Than Other Structures?

article

Why is the N1–H stretch vibration frequency of guanine shifted upon dimerization to the red and the amino N–H stretch vibration frequency to the blue?

article

World of van der Waals Species

on the Nature of Stabilization in Weak, Medium, and Strong Charge-Transfer Complexes: CCSD(T)/CBS and SAPT Calculations

article

van der Waals Molecules III: Introduction

scientific article published on 01 November 2000

Slabé mezimolekulové interakce v chemii a biologii. Aplikace II

book edition published in 1980

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