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1

The DNA and RNA sugar–phosphate backbone emerges as the key player. An overview of quantum-chemical, structural biology and simulation studies

Šponer, Jiří, Mládek, Arnošt, Šponer, Judit E., Svozil, Daniel, Zgarbová, Marie, Banáš, Pavel, Jurečka, Petr, Otyepka, Michal

Journal:

Physical Chemistry Chemical Physics

Year:

2012

Language:

english

File:

PDF, 2.78 MB

english, 2012

2

RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview

Šponer, Jiří, Bussi, Giovanni, Krepl, Miroslav, Banáš, Pavel, Bottaro, Sandro, Cunha, Richard A., Gil-Ley, Alejandro, Pinamonti, Giovanni, Poblete, Simón, Jurečka, Petr, Walter, Nils G., Otyepka, Mich

Journal:

Chemical Reviews

Year:

2018

Language:

english

File:

PDF, 77.37 MB

english, 2018

3

How to understand quantum chemical computations on DNA and RNA systems? A practical guide for non-specialists

Šponer, Jiří, Šponer, Judit E., Mládek, Arnošt, Banáš, Pavel, Jurečka, Petr, Otyepka, Michal

Journal:

Year:

2013

Language:

english

File:

PDF, 1.19 MB

english, 2013

4

Quantum Monte Carlo Methods Describe Noncovalent Interactions with Subchemical Accuracy

Dubecký, Matúš, Jurečka, Petr, Derian, René, Hobza, Pavel, Otyepka, Michal, Mitas, Lubos

Journal:

Journal of Chemical Theory and Computation

Year:

2013

Language:

english

File:

PDF, 684 KB

english, 2013

5

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

Dubecký, Matúš, Derian, René, Jurečka, Petr, Mitas, Lubos, Hobza, Pavel, Otyepka, Michal

Journal:

Physical Chemistry Chemical Physics

Year:

2014

Language:

english

File:

PDF, 1.56 MB

english, 2014

6

Refinement of the Sugar–Phosphate Backbone Torsion Beta for AMBER Force Fields Improves the Description of Z- and B-DNA

Zgarbová, Marie, Šponer, Jiří, Otyepka, Michal, Cheatham, Thomas E., Galindo-Murillo, Rodrigo, Jurečka, Petr

Journal:

Journal of Chemical Theory and Computation

Year:

2015

Language:

english

File:

PDF, 2.60 MB

english, 2015

7

Microsecond-Scale MD Simulations of HIV-1 DIS Kissing-Loop Complexes Predict Bulged-In Conformation of the Bulged Bases and Reveal Interesting Differences between Available Variants of the AMBER RNA Force Fields

Havrila, Marek, Zgarbová, Marie, Jurečka, Petr, Banáš, Pavel, Krepl, Miroslav, Otyepka, Michal, Šponer, Jiří

Journal:

Journal of Physical Chemistry B

Year:

2015

Language:

english

File:

PDF, 3.81 MB

english, 2015

8

Noncovalent Interactions by Quantum Monte Carlo

Dubecký, Matúš, Mitas, Lubos, Jurečka, Petr

Journal:

Chemical Reviews

Year:

2016

Language:

english

File:

PDF, 6.19 MB

english, 2016

9

Are the Hydrogen Bonds of RNA (A⋅U) Stronger Than those of DNA (A⋅T)? A Quantum Mechanics Study

Alberto Pérez, Jiri Sponer, Petr Jurecka, Pavel Hobza, F. Javier Luque, Modesto Orozco

Journal:

Chemistry - A European Journal

Year:

2005

Language:

english

File:

PDF, 89 KB

english, 2005

10

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

Jiří Šponer, Petr Jurečka, Ivan Marchan, F. Javier Luque, Modesto Orozco, Pavel Hobza

Journal:

Chemistry - A European Journal

Year:

2006

Language:

english

File:

PDF, 232 KB

english, 2006

11

ChemInform Abstract: Bis(methylphosphonic acid) Derivatives of 1,4,8,11-Tetraazacyclotetradecane (Cyclam). Synthesis, Crystal and Molecular Structures, and Solution Properties.

Jan Kotek, Pavel Vojtisek, Ivana Cisarova, Petr Hermann, Petr Jurecka, Jan Rohovec, Ivan Lukes

Journal:

Year:

2001

File:

PDF, 31 KB

2001

12

On Differences between Hydrogen Bonding and Improper Blue-Shifting Hydrogen Bonding

Wiktor Zierkiewicz, Petr Jurečka, Pavel Hobza

Journal:

Year:

2005

Language:

english

File:

PDF, 159 KB

english, 2005

13

On the Reliability of the AMBER Force Field and its Empirical Dispersion Contribution for the Description of Noncovalent Complexes

Michal Kolář, Karel Berka, Petr Jurečka, Pavel Hobza

Journal:

Year:

2010

Language:

english

File:

PDF, 719 KB

english, 2010

14

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

Petr Jurečka, Jiří Černý, Pavel Hobza, Dennis R. Salahub

Journal:

Journal of Computational Chemistry

Year:

2007

Language:

english

File:

PDF, 202 KB

english, 2007

15

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

Petr Jurečka, Pavel Hobza

Journal:

Chemical Physics Letters

Year:

2002

Language:

english

File:

PDF, 125 KB

english, 2002

16

Complex formation between 1-chloro-4-(trifluoromethyl)benzene (guest) and 4-tert-butylcalix[4]arenes (host) distally substituted with phosphonic acid or phosphonic ester groups at the lower rim

Sándor Kunsági-Máté, Géza Nagy, Petr Jurecka, László Kollár

Journal:

Year:

2002

Language:

english

File:

PDF, 160 KB

english, 2002

17

Theoretical studies of RNA catalysis: Hybrid QM/MM methods and their comparison with MD and QM

Pavel Banáš, Petr Jurečka, Nils G. Walter, Jiří Šponer, Michal Otyepka

Journal:

Year:

2009

Language:

english

File:

PDF, 530 KB

english, 2009

18

Reference Simulations of Noncanonical Nucleic Acids with Different χ Variants of the AMBER Force Field: Quadruplex DNA, Quadruplex RNA, and Z-DNA

Krepl, Miroslav, Zgarbová, Marie, Stadlbauer, Petr, Otyepka, Michal, Banáš, Pavel, Koča, Jaroslav, Cheatham, Thomas E., Jurečka, Petr, Šponer, Jiří

Journal:

Journal of Chemical Theory and Computation

Year:

2012

Language:

english

File:

PDF, 2.29 MB

english, 2012

19

Noncanonical Hydrogen Bonding in Nucleic Acids. Benchmark Evaluation of Key Base–Phosphate Interactions in Folded RNA Molecules Using Quantum-Chemical Calculations and Molecular Dynamics Simulations

Zgarbová, Marie, Jurečka, Petr, Banáš, Pavel, Otyepka, Michal, Šponer, Judit E., Leontis, Neocles B., Zirbel, Craig L., Šponer, Jiří

Journal:

Journal of Physical Chemistry A

Year:

2011

Language:

english

File:

PDF, 4.89 MB

english, 2011

20

Synthesis, characterisation and extraction behaviour of calix[4]arene-based phosphonic acidsElectronic supplementary information (ESI) available: Tables S1–S3 and Figs. S1 and S2. See http://www.rsc.org/suppdata/p2/b1/b105489a/

Jurečka, Petr, Vojtíšek, Pavel, Novotný, Karel, Rohovec, Jan, Lukeš, Ivan

Journal:

Journal of the Chemical Society Perkin Transactions 2

Year:

2002

Language:

english

File:

PDF, 246 KB

english, 2002

21

Adsorption of Small Organic Molecules on Graphene

Lazar, Petr, Karlický, František, Jurečka, Petr, Kocman, Mikuláš, Otyepková, Eva, Šafářová, Klára, Otyepka, Michal

Journal:

Journal of the American Chemical Society

Year:

2013

Language:

english

File:

PDF, 374 KB

english, 2013

22

Benchmark quantum-chemical calculations on a complete set of rotameric families of the DNA sugar–phosphate backbone and their comparison with modern density functional theory

Mládek, Arnošt, Krepl, Miroslav, Svozil, Daniel, Čech, Petr, Otyepka, Michal, Banáš, Pavel, Zgarbová, Marie, Jurečka, Petr, Šponer, Jiří

Journal:

Physical Chemistry Chemical Physics

Year:

2013

Language:

english

File:

PDF, 2.14 MB

english, 2013

23

Lipid Enhanced Exfoliation for Production of Graphene Nanosheets

Pykal, Martin, Šafářová, Klára, Machalová Šišková, Karolína, Jurečka, Petr, Bourlinos, Athanasios B., Zbořil, Radek, Otyepka, Michal

Journal:

The Journal of Physical Chemistry C

Year:

2013

Language:

english

File:

PDF, 2.97 MB

english, 2013

24

Nature and magnitude of aromatic base stacking in DNA and RNA: Quantum chemistry, molecular mechanics and experiment

Šponer, Jiří, Šponer, Judit E., Mládek, Arnošt, Jurečka, Petr, Banáš, Pavel, Otyepka, Michal

Journal:

Year:

2013

Language:

english

File:

PDF, 1.07 MB

english, 2013

25

Toward Improved Description of DNA Backbone: Revisiting Epsilon and Zeta Torsion Force Field Parameters

Zgarbová, Marie, Luque, F. Javier, Šponer, Jiří, Cheatham, Thomas E., Otyepka, Michal, Jurečka, Petr

Journal:

Journal of Chemical Theory and Computation

Year:

2013

Language:

english

File:

PDF, 3.98 MB

english, 2013

26

Molecular Dynamics Simulations of Nucleic Acids. From Tetranucleotides to the Ribosome

Šponer, Jiří, Banáš, Pavel, Jurečka, Petr, Zgarbová, Marie, Kührová, Petra, Havrila, Marek, Krepl, Miroslav, Stadlbauer, Petr, Otyepka, Michal

Journal:

The Journal of Physical Chemistry Letters

Year:

2014

Language:

english

File:

PDF, 2.71 MB

english, 2014

27

Electric quadrupole moment of graphene and its effect on intermolecular interactions

Kocman, Mikuláš, Pykal, Martin, Jurečka, Petr

Journal:

Physical Chemistry Chemical Physics

Year:

2014

Language:

english

File:

PDF, 2.65 MB

english, 2014

28

Energies and 2′-Hydroxyl Group Orientations of RNA Backbone Conformations. Benchmark CCSD(T)/CBS Database, Electronic Analysis, and Assessment of DFT Methods and MD Simulations

Mládek, Arnošt, Banáš, Pavel, Jurečka, Petr, Otyepka, Michal, Zgarbová, Marie, Šponer, Jiří

Journal:

Journal of Chemical Theory and Computation

Year:

2014

Language:

english

File:

PDF, 3.32 MB

english, 2014

29

Spectroscopic and Theoretical Insights into Sequence Effects of Aminofluorene-Induced Conformational Heterogeneity and Nucleotide Excision Repair †,∇

Meneni, Srinivasa Rao, Shell, Steven M., Gao, Lan, Jurecka, Petr, Lee, Wang, Sponer, Jiri, Zou, Yue, Chiarelli, M. Paul, Cho, Bongsup P.

Journal:

Year:

2007

Language:

english

File:

PDF, 601 KB

english, 2007

30

A Novel Approach for Deriving Force Field Torsion Angle Parameters Accounting for Conformation-Dependent Solvation Effects

Zgarbová, Marie, Luque, F. Javier, Šponer, Jiří, Otyepka, Michal, Jurečka, Petr

Journal:

Journal of Chemical Theory and Computation

Year:

2012

Language:

english

File:

PDF, 1.92 MB

english, 2012

31

Can We Accurately Describe the Structure of Adenine Tracts in B-DNA? Reference Quantum-Chemical Computations Reveal Overstabilization of Stacking by Molecular Mechanics

Banáš, Pavel, Mládek, Arnošt, Otyepka, Michal, Zgarbová, Marie, Jurečka, Petr, Svozil, Daniel, Lankaš, Filip, Šponer, Jiří

Journal:

Journal of Chemical Theory and Computation

Year:

2012

Language:

english

File:

PDF, 4.17 MB

english, 2012

32

Base Pair Fraying in Molecular Dynamics Simulations of DNA and RNA

Zgarbová, Marie, Otyepka, Michal, Šponer, Jiří, Lankaš, Filip, Jurečka, Petr

Journal:

Journal of Chemical Theory and Computation

Year:

2014

Language:

english

File:

PDF, 4.08 MB

english, 2014

33

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

Zgarbová, Marie, Otyepka, Michal, Šponer, Jiří, Hobza, Pavel, Jurečka, Petr

Journal:

Physical Chemistry Chemical Physics

Year:

2010

Language:

english

File:

PDF, 1.68 MB

english, 2010

34

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

Morgado, Claudio A., Jurečka, Petr, Svozil, Daniel, Hobza, Pavel, Šponer, Jiří

Journal:

Physical Chemistry Chemical Physics

Year:

2010

Language:

english

File:

PDF, 1.87 MB

english, 2010

35

106 Deriving force field dihedral angle parameters that account for conformation-dependent solvation effects

Jurečka, Petr, Zgarbová, Marie, Luque, F. Javier, Šponer, Jiří, Otyepka, Michal

Journal:

Journal of Biomolecular Structure and Dynamics

Year:

2013

Language:

english

File:

PDF, 76 KB

english, 2013

36

Mechanical Model of DNA Allostery

Dršata, Tomáš, Zgarbová, Marie, Špačková, Naďa, Jurečka, Petr, Šponer, Jiří, Lankaš, Filip

Journal:

The Journal of Physical Chemistry Letters

Year:

2014

Language:

english

File:

PDF, 698 KB

english, 2014

37

Choosing a density functional for modeling adsorptive hydrogen storage: reference quantum mechanical calculations and a comparison of dispersion-corrected density functionals

Kocman, Mikuláš, Jurečka, Petr, Dubecký, Matúš, Otyepka, Michal, Cho, Yeonchoo, Kim, Kwang S.

Journal:

Physical Chemistry Chemical Physics

Year:

2015

Language:

english

File:

PDF, 1.33 MB

english, 2015

38

Coarse-Grain Simulations of Skin Ceramide NS with Newly Derived Parameters Clarify Structure of Melted Phase

Sovová, Žofie, Berka, Karel, Otyepka, Michal, Jurečka, Petr

Journal:

Journal of Physical Chemistry B

Year:

2015

Language:

english

File:

PDF, 3.86 MB

english, 2015

39

Reactive Conformation of the Active Site in the Hairpin Ribozyme Achieved by Molecular Dynamics Simulations with ε/ζ Force Field Reparametrizations

Mlýnský, Vojtěch, Kührová, Petra, Zgarbová, Marie, Jurečka, Petr, Walter, Nils G., Otyepka, Michal, Šponer, Jiří, Banáš, Pavel

Journal:

Journal of Physical Chemistry B

Year:

2015

Language:

english

File:

PDF, 2.42 MB

english, 2015

40

110 Refinement of force field torsion parameters for nucleic acids based on inclusion of conformation-dependent solvation effects

Zgarbová, Marie, Otyepka, Michal, Banáš, Pavel, Luque, F. Javier, Cheatham, Thomas E., Šponer, Jiří, Jurečka, Petr

Journal:

Journal of Biomolecular Structure and Dynamics

Year:

2013

Language:

english

File:

PDF, 62 KB

english, 2013

41

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

Řezáč, Jan, Dubecký, Matúš, Jurečka, Petr, Hobza, Pavel

Journal:

Physical Chemistry Chemical Physics

Year:

2015

Language:

english

File:

PDF, 1.82 MB

english, 2015

42

Modelling of Graphene Functionalization

Pykal, Martin, Jurecka, Petr, Karlicky, Frantisek, Otyepka, Michal

Journal:

Physical Chemistry Chemical Physics

Year:

2015

Language:

english

File:

PDF, 28.83 MB

english, 2015

43

SPIE Proceedings [SPIE 17th Slovak-Czech-Polish Optical Conference on Wave and Quantum Aspects of Contemporary Optics - Liptovsky Jan, Slovakia (Monday 6 September 2010)] 17th Slovak-Czech-Polish Optical Conference on Wave and Quantum Aspects of Contemporary Optics - Computer simulation of the speckle field propagation

Hamarová, Ivana, Horváth, Pavel, Šmíd, Petr, Hrabovský, Miroslav, Müllerová, Jarmila, Senderáková, Dagmar, Jurečka, Stanislav

Year:

2010

Language:

english

File:

PDF, 1.28 MB

english, 2010

44

Bis(methylphosphonic Acid) Derivatives of 1,4,8,11-Tetraazacyclotetradecane (Cyclam). Synthesis, Crystal and Molecular Structures, and Solution Properties

Kotek, Jan, Vojtíšek, Pavel, Císařová, Ivana, Hermann, Petr, Jurečka, Petr, Rohovec, Jan, Lukeš, Ivan

Journal:

Collection of Czechoslovak Chemical Communications

Year:

2000

Language:

english

File:

PDF, 331 KB

english, 2000

45

On the Use of Molecular Dynamics Simulations for Probing Allostery through DNA

Dršata, Tomáš, Zgarbová, Marie, Jurečka, Petr, Šponer, Jiří, Lankaš, Filip

Journal:

Biophysical Journal

Year:

2016

Language:

english

File:

PDF, 166 KB

english, 2016

46

Assessing the current state of AMBER force field modifications for DNA

Galindo-Murillo, Rodrigo, Robertson, James C., Zgarbova, Marie, Sponer, Jiri, Otyepka, Michal, Jurecka, Petr, Cheatham, Thomas E.

Journal:

Journal of Chemical Theory and Computation

Year:

2016

Language:

english

File:

PDF, 3.08 MB

english, 2016

47

SPIE Proceedings [SPIE Photonics Prague 2011 - Prague, Czech Republic (Wednesday 24 August 2011)] Photonics, Devices, and Systems V - The cavity resonator design: stochastic optimization of the transmission line method

Jurečka, Stanislav, Müllerová, Jarmila, Dado, Milan, Tománek, Pavel, Senderáková, Dagmar, Páta, Petr

Year:

2011

Language:

english

File:

PDF, 788 KB

english, 2011

48

Transferability and additivity of dihedral parameters in polarizable and nonpolarizable empirical force fields

Zgarbová, Marie, Rosnik, Andreana M., Luque, F. Javier, Curutchet, Carles, Jurečka, Petr

Journal:

Journal of Computational Chemistry

Year:

2015

Language:

english

File:

PDF, 1.03 MB

english, 2015

49

Influence of BII Backbone Substates on DNA Twist: A Unified View and Comparison of Simulation and Experiment for All 136 Distinct Tetranucleotide Sequences

Zgarbová, Marie, Jurečka, Petr, Lankaš, Filip, Cheatham, Thomas E., Šponer, Jiří, Otyepka, Michal

Journal:

Journal of Chemical Information and Modeling

Year:

2017

Language:

english

File:

PDF, 3.11 MB

english, 2017

50

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

Karlický, František, Otyepková, Eva, Lo, Rabindranath, Pitoňák, Michal, Jurečka, Petr, Pykal, Martin, Hobza, Pavel, Otyepka, Michal

Journal:

Journal of Chemical Theory and Computation

Year:

2017

Language:

english

File:

PDF, 1.72 MB

english, 2017

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