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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

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

Jiří Šponer, Pavel Hobza

Journal:

International Journal of Quantum Chemistry

Year:

1996

Language:

english

File:

PDF, 874 KB

english, 1996

4

Electronic properties, hydrogen bonding, stacking, and cation binding of DNA and RNA bases

Jiří Šponer, Jerzy Leszczynski, Pavel Hobza

Journal:

Year:

2001

Language:

english

File:

PDF, 628 KB

english, 2001

5

Prebiotic Routes to Nucleosides: A Quantum Chemical Insight into the Energetics of the Multistep Reaction Pathways

Dr. Judit E. Šponer, Prof. Jiří Šponer, Dr. Miguel Fuentes-Cabrera

Journal:

Chemistry - A European Journal

Year:

2011

Language:

english

File:

PDF, 396 KB

english, 2011

6

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

Pavel Hobza, Jiří Šponer

Journal:

Chemical Physics Letters

Year:

1996

Language:

english

File:

PDF, 481 KB

english, 1996

7

Intrathecal rubella antibodies in an adolescent with Guillain-Barré syndrome after mumps-measles-rubella vaccination

M. Mühlebach-Sponer, R. Zbinden, V. A. da Silva, H. E. Gnehm

Journal:

European Journal of Pediatrics

Year:

1995

Language:

english

File:

PDF, 124 KB

english, 1995

8

Is formamide natureʼs choice to create life?: Comment on the paper “Formamide and the origin of life” by Raffaele Saladino et al.

Judit E. Šponer, Jiří Šponer

Journal:

Physics of Life Reviews

Year:

2012

Language:

english

File:

PDF, 71 KB

english, 2012

9

Structure, Energetics, and Dynamics of the Nucleic Acid Base Pairs: Nonempirical Ab Initio Calculations

Hobza, Pavel, Šponer, Jiří

Journal:

Chemical Reviews

Year:

1999

Language:

english

File:

PDF, 344 KB

english, 1999

10

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

11

Morphologic Parameters Relevant for Visual Outcome During Anti-Angiogenic Therapy of Neovascular Age-Related Macular Degeneration

Simader, Christian, Ritter, Markus, Bolz, Matthias, Deák, Gabor G., Mayr-Sponer, Ulrike, Golbaz, Isabelle, Kundi, Michael, Schmidt-Erfurth, Ursula M.

Journal:

Year:

2014

Language:

english

File:

PDF, 1.40 MB

english, 2014

12

Comparison of ab Initio, DFT, and Semiempirical QM/MM Approaches for Description of Catalytic Mechanism of Hairpin Ribozyme

Mlýnský, Vojtěch, Banáš, Pavel, Šponer, Jiří, van der Kamp, Marc W., Mulholland, Adrian J., Otyepka, Michal

Journal:

Journal of Chemical Theory and Computation

Year:

2014

Language:

english

File:

PDF, 6.03 MB

english, 2014

13

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

Gkionis, Konstantinos, Kruse, Holger, Platts, James A., Mládek, Arnošt, Koča, Jaroslav, Šponer, Jiří

Journal:

Journal of Chemical Theory and Computation

Year:

2014

Language:

english

File:

PDF, 2.79 MB

english, 2014

14

The Near Ultraviolet Absorption of Pyridine Vapor

Journal:

Review of Modern Physics

Year:

1944

Language:

english

File:

PDF, 216 KB

english, 1944

15

The Lattice Energy of Solid CO2

Sponer, H., Bruch-Willstätter, M.

Journal:

The Journal of Chemical Physics

Year:

1937

Language:

english

File:

PDF, 658 KB

english, 1937

16

Conformational dynamics of the human propeller telomeric DNA quadruplex on a microsecond time scale

Islam, B., Sgobba, M., Laughton, C., Orozco, M., Sponer, J., Neidle, S., Haider, S.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 11.26 MB

english, 2013

17

In Vivo Behaviour of the Synthetic Porous Hydroxyapatite Prepared by Low Temperature Microwave Processing and Comparison with Deproteinized Bovine Bone

Strnadová, Marie, Strnad, Zdeněk, Šponer, Pavel, Jirošova, Jana, Strnad, Jakub

Journal:

Key Engineering Materials

Year:

2011

Language:

english

File:

PDF, 10.02 MB

english, 2011

18

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

19

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

20

Derivation of reliable geometries in QM calculations of DNA structures: explicit solvent QM/MM and restrained implicit solvent QM optimizations of G-quadruplexes.

Gkionis, Konstantinos, Kruse, Holger, Sponer, Jiri

Journal:

Journal of Chemical Theory and Computation

Year:

2016

Language:

english

File:

PDF, 6.77 MB

english, 2016

21

Cover Picture: Synthesis of Chiral Tertiary Alcohols by CuI-Catalyzed Enantioselective Addition of Organomagnesium Reagents to Ketones / Emergence of the First Catalytic Oligonucleotides in a Formamide-Based Origin Scenario / Intermolecular Peptide Cross-

Rong, Jiawei, Pellegrini, Tilde, Harutyunyan, Syuzanna R., Šponer, Judit E., Šponer, Jiří, Nováková, Olga, Brabec, Viktor, Šedo, Ondrej, Zdráhal, Zbyněk, Costanzo, Giovanna, Pino, Samanta, Saladino, R

Journal:

Chemistry - A European Journal

Year:

2016

File:

PDF, 447 KB

2016

22

Conservation of the Juan Fernandez firecrown and its island habitat

Roy, Michael S., Torres-Mura, Juan Carlos, Hertel, Fritz, Lemus, Marina, Sponer, Renate

Journal:

Year:

1999

Language:

english

File:

PDF, 1.73 MB

english, 1999

23

Molecular Mechanism of Diaminomaleonitrile to Diaminofumaronitrile Photoisomerization: An Intermediate Step in the Prebiotic Formation of Purine Nucleobases

Szabla, Rafał, Góra, Robert W., Šponer, Jiří, Šponer, Judit E.

Journal:

Chemistry - A European Journal

Year:

2014

Language:

english

File:

PDF, 691 KB

english, 2014

24

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

Szabla, Rafał, Havrila, Marek, Kruse, Holger, Šponer, Jiří

Journal:

Journal of Physical Chemistry B

Year:

2016

Language:

english

File:

PDF, 1.85 MB

english, 2016

25

Channeling through Two Stacked Guanine Quartets of One and Two Alkali Cations in the Li + , Na + , K + , and Rb + Series. Assessment of the Accuracy of the SIBFA Anisotropic Polarizable Molecular Mechanics Potential

Gresh, Nohad, Naseem-Khan, Sehr, Lagardère, Louis, Piquemal, Jean-Philip, Sponer, Judit E., Sponer, Jiri

Journal:

Journal of Physical Chemistry B

Year:

2017

Language:

english

File:

PDF, 4.40 MB

english, 2017

26

Selectivity of major isoquinoline alkaloids from Chelidomium majus towards telomeric G-quadruplex: A study using a modified transition-FRET (t-FRET) assay

Noureini, Sakineh Kazemi, Esmaeili, Hosein, Abachi, Farzane, Khiali, Soraia, Islam, Barira, Kuta, Martyna, Saboury, Ali A., Hoffmann, Marcin, Sponer, Jiri, Parkinson, Gary, Haider, Shozeb

Journal:

Biochimica et Biophysica Acta (BBA) - General Subjects

Year:

2017

Language:

english

File:

PDF, 1.33 MB

english, 2017

27

Novel electrochemical route to cleaner fuel dimethyl ether

Cassone, Giuseppe, Pietrucci, Fabio, Saija, Franz, Guyot, François, Sponer, Jiri, Sponer, Judit E., Saitta, A. Marco

Journal:

Scientific Reports

Year:

2017

Language:

english

File:

PDF, 1.30 MB

english, 2017

28

MD and QM/MM Study of the Quaternary HutP Homohexamer Complex with mRNA, L-histidine Ligand and Mg 2+ .

Pokorná, Pavlína, Krepl, Miroslav, Kruse, Holger, Sponer, Jiri

Journal:

Journal of Chemical Theory and Computation

Year:

2017

Language:

english

File:

PDF, 1.35 MB

english, 2017

29

Elution kinetics of vancomycin and gentamicin from carriers and their effects on mesenchymal stem cell proliferation: an in vitro study

Kucera, Tomas, Ryskova, Lenka, Soukup, Tomas, Malakova, Jana, Cermakova, Eva, Mericka, Pavel, Suchanek, Jakub, Sponer, Pavel

Journal:

BMC Musculoskeletal Disorders

Year:

2017

Language:

english

File:

PDF, 943 KB

english, 2017

30

Structural dynamics of propeller loop: towards folding of RNA G-quadruplex

Havrila, Marek, Stadlbauer, Petr, Kührová, Petra, Banáš, Pavel, Mergny, Jean-Louis, Otyepka, Michal, Šponer, Jiří

Journal:

Nucleic Acids Research

Year:

2018

Language:

english

File:

PDF, 3.93 MB

english, 2018

31

Local-to-global signal transduction at the core of a Mn2+ sensing riboswitch

Suddala, Krishna C., Price, Ian R., Dandpat, Shiba S., Janeček, Michal, Kührová, Petra, Šponer, Jiří, Banáš, Pavel, Ke, Ailong, Walter, Nils G.

Journal:

Nature Communications

Year:

2019

Language:

english

File:

PDF, 3.21 MB

english, 2019

32

Der photochemische Primärprozeß

Priv.-Doz. Dr. H. Sponer

Journal:

Angewandte Chemie

Year:

1930

Language:

german

File:

PDF, 1.06 MB

german, 1930

33

(Zu beziehen, soweit im Buchhandel erschienen, durch Verlag Chemie, G. m. b. H., Berlin W 35, Corneliusstr. 3.) Grundlagen der Photochemie, Bd. 1 der Sammlung „Die chemische Reaktion”, von Prof. Dr. K. F. Bonhoeffer und Priv.-Doz. Dr. P. Harteck. 295 Seiten mit 75 Abbildungen und 90 Tabellen. Verlag Theodor Steinkopff, 1933. Preis geh. RM. 24,---, geb. RM. 25,—

Journal:

Angewandte Chemie

Year:

1933

Language:

german

File:

PDF, 160 KB

german, 1933

34

Mechanismus der metallvermittelten Desaminierung von Cytosin – Experiment und DFT-Rechnungen

Judit E. Šponer, Pablo J. Sanz Miguel, Luis Rodríguez-Santiago, Andrea Erxleben, Michael Krumm, Mariona Sodupe, Jiří Šponer, Bernhard Lippert

Journal:

Angewandte Chemie

Year:

2004

Language:

german

File:

PDF, 169 KB

german, 2004

35

Metal-Mediated Deamination of Cytosine: Experiment and DFT Calculations

Judit E. Šponer, Pablo J. Sanz Miguel, Luis Rodríguez-Santiago, Andrea Erxleben, Michael Krumm, Mariona Sodupe, Jirí Šponer, Bernhard Lippert

Journal:

Angewandte Chemie International Edition

Year:

2004

Language:

english

File:

PDF, 168 KB

english, 2004

36

Molecular dynamics simulations of RNA: An in silico single molecule approach

S. Elizabeth McDowell, Nad'a Špačková, Jiří Šponer, Nils G. Walter

Journal:

Year:

2007

Language:

english

File:

PDF, 901 KB

english, 2007

37

Impact of an extruded nucleotide on cleavage activity and dynamic catalytic core conformation of the hepatitis delta virus ribozyme

Jana Sefcikova, Maryna V. Krasovska, Nad'a Špačková, Jiří Šponer, Nils G. Walter

Journal:

Year:

2007

Language:

english

File:

PDF, 770 KB

english, 2007

38

Conformational transitions of flanking purines in HIV-1 RNA dimerization initiation site kissing complexes studied by CHARMM explicit solvent molecular dynamics

Joanna Sarzyńska, Kamila Réblová, Jiří Šponer, Tadeusz Kuliński

Journal:

Year:

2008

Language:

english

File:

PDF, 1.68 MB

english, 2008

39

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

40

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

41

Theoretical Study on the Factors Controlling the Stability of the Borate Complexes of Ribose, Arabinose, Lyxose, and Xylose

Judit E. Šponer, Bobby G. Sumpter, Jerzy Leszczynski, Jiří Šponer, Miguel Fuentes-Cabrera

Journal:

Chemistry - A European Journal

Year:

2008

Language:

english

File:

PDF, 454 KB

english, 2008

42

Theoretical Studies on the Intermolecular Interactions of Potentially Primordial Base-Pair Analogues

Judit E. Šponer, Álvaro Vázquez-Mayagoitia, Bobby G. Sumpter, Jerzy Leszczynski, Jiří Šponer, Michal Otyepka, Pavel Banáš, Miguel Fuentes-Cabrera

Journal:

Chemistry - A European Journal

Year:

2010

Language:

english

File:

PDF, 413 KB

english, 2010

43

ChemInform Abstract: Structure, Energetics, and Dynamics of the Nucleic Acid Base Pairs: Nonempirical ab initio Calculations

Pavel Hobza, Jiri Sponer

Journal:

Year:

2000

File:

PDF, 26 KB

2000

44

Interactions of the “piano-stool” [ruthenium(II) (η6-arene)(en)CL]+ complexes with water and nucleobases; ab initio and DFT study

Zdeněk Futera, Julia Klenko, Judit E. Šponer, Jiří Šponer, Jaroslav V. Burda

Journal:

Journal of Computational Chemistry

Year:

2009

Language:

english

File:

PDF, 505 KB

english, 2009

45

Density functional theory and molecular clusters

Pavel Hobza, Jiří šponer, Tomáš Reschel

Journal:

Journal of Computational Chemistry

Year:

1995

Language:

english

File:

PDF, 774 KB

english, 1995

46

Molecular Systematics and Evolutionary History of Akalats (Genus Sheppardia): A Pre-Pleistocene Radiation in a Group of African Forest Birds

Michael S. Roy, Renate Sponer, Jon Fjeldså

Journal:

Molecular Phylogenetics and Evolution

Year:

2001

Language:

english

File:

PDF, 165 KB

english, 2001

47

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

P. Hobza, F. Hubálek, M. Kabeláč, P. Mejzlík, J. Šponer, J. Vondrášek

Journal:

Chemical Physics Letters

Year:

1996

Language:

english

File:

PDF, 287 KB

english, 1996

48

Theoretical estimation of the cavitation threshold for very short pulses of ultrasound

Journal:

Year:

1991

Language:

english

File:

PDF, 642 KB

english, 1991

49

Nonempirical ab initio calculations on DNA base pairs

Jiří Šponer, Pavel Hobza

Journal:

Chemical Physics

Year:

1996

Language:

english

File:

PDF, 827 KB

english, 1996

50

Triplet-singlet emission spectra of benzene in a crystalline matrix of cyclohexane at 4·2°K and 77°K

H. Sponer, Yoshiya Kanda, Lawrence A. Blackwell

Journal:

Spectrochimica Acta

Year:

1960

Language:

english

File:

PDF, 1.40 MB

english, 1960

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