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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

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

3

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

4

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

5

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

6

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

7

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

8

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

9

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

10

Theoretical Model of the n -Propylbenzene Formation in the Benzene Isopropylation over Zeolites. An Anti-Markovnikov-Type Proton Addition Promoted by the Steric Effect of MFI and MEL Zeolite Channels

Šponer, Judit, Šponer, Jiří, Čejka, Jiří, Wichterlová, Blanka

Journal:

Journal of Physical Chemistry B

Year:

1998

Language:

english

File:

PDF, 90 KB

english, 1998

11

From Formamide to RNA, the Path Is Tenuous but Continuous

Pino, Samanta, Sponer, Judit, Costanzo, Giovanna, Saladino, Raffaele, Mauro, Ernesto

Journal:

Year:

2015

Language:

english

File:

PDF, 641 KB

english, 2015

12

Untemplated Nonenzymatic Polymerization of 3′,5′cGMP: A Plausible Route to 3′,5′-Linked Oligonucleotides in Primordia

Šponer, Judit E., Šponer, Jiří, Giorgi, Alessandra, Di Mauro, Ernesto, Pino, Samanta, Costanzo, Giovanna

Journal:

Journal of Physical Chemistry B

Year:

2015

Language:

english

File:

PDF, 3.41 MB

english, 2015

13

Coordination and properties of cobalt in the molecular sieves CoAPO-5 and -11

Judit Šponer, Jiřı́ Čejka, Jiřı́ Dědeček, Blanka Wichterlová

Journal:

Microporous and Mesoporous Materials

Year:

2000

Language:

english

File:

PDF, 268 KB

english, 2000

14

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

Řeha, David, Kabeláč, Martin, Ryjáček, Filip, Šponer, Jiří, Šponer, Judit E., Elstner, Marcus, Suhai, Sándor, Hobza, Pavel

Journal:

Journal of the American Chemical Society

Year:

2002

Language:

english

File:

PDF, 427 KB

english, 2002

15

Sugar Edge/Sugar Edge Base Pairs in RNA: Stabilities and Structures from Quantum Chemical Calculations

Šponer, Judit E., Leszczynski, Jerzy, Sychrovský, Vladimír, Šponer, Jiří

Journal:

Journal of Physical Chemistry B

Year:

2005

Language:

english

File:

PDF, 379 KB

english, 2005

16

19 Quantum chemical studies on the formamide-based origin of life

Šponer, Judit E., Mládek, Arnošt, Ferus, Martin, Civiš, Svatopluk, Šponer, Jiří

Journal:

Journal of Biomolecular Structure and Dynamics

Year:

2013

Language:

english

File:

PDF, 101 KB

english, 2013

17

Loss of Hoogsteen Pairing Ability upon N1 Adenine Platinum Binding

Schmidt, Kathrin S., Reedijk, Jan, Weisz, Klaus, Basilio Janke, Eline M., Sponer, Judit E., Sponer, Jiri, Lippert, Bernhard

Journal:

Inorganic Chemistry

Year:

2002

Language:

english

File:

PDF, 171 KB

english, 2002

18

Corrigendum: TiO2-catalyzed synthesis of sugars from formaldehyde in extraterrestrial impacts on the early Earth

Civiš, Svatopluk, Szabla, Rafał, Szyja, Bartłomiej M., Smykowski, Daniel, Ivanek, Ondřej, Knížek, Antonín, Kubelík, Petr, Šponer, Jiří, Ferus, Martin, Šponer, Judit E.

Journal:

Scientific Reports

Year:

2016

Language:

english

File:

PDF, 124 KB

english, 2016

19

Theoretical studies of the mechanism of 2-aminooxazole formation under prebiotically plausible conditions

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

Journal:

Physical Chemistry Chemical Physics

Year:

2013

Language:

english

File:

PDF, 5.13 MB

english, 2013

20

Dust Motions in Magnetized Turbulence: Source of Chemical Complexity

Cassone, Giuseppe, Saija, Franz, Sponer, Jiri, Sponer, Judit E., Ferus, Martin, Krus, Miroslav, Ciaravella, Angela, Jiménez-Escobar, Antonio, Cecchi-Pestellini, Cesare

Journal:

The Astrophysical Journal

Year:

2018

Language:

english

File:

PDF, 914 KB

english, 2018

21

Principles of RNA Base Pairing: Structures and Energies of the Trans Watson−Crick/Sugar Edge Base Pairs

Šponer, Judit E., Špačková, Nad'a, Leszczynski, Jerzy, Šponer, Jiří

Journal:

Journal of Physical Chemistry B

Year:

2005

Language:

english

File:

PDF, 389 KB

english, 2005

22

Mechanism of Action of Anticancer Titanocene Derivatives: An Insight from Quantum Chemical Calculations

Šponer, Judit E., Leszczynski, Jerzy, Šponer, Jiří

Journal:

Journal of Physical Chemistry B

Year:

2006

Language:

english

File:

PDF, 58 KB

english, 2006

23

Emergence of the First Catalytic Oligonucleotides in a Formamide-Based Origin Scenario

Šponer, Judit E., Šponer, Jiří, Nováková, Olga, Brabec, Viktor, Šedo, Ondrej, Zdráhal, Zbyněk, Costanzo, Giovanna, Pino, Samanta, Saladino, Raffaele, Di Mauro, Ernesto

Journal:

Chemistry - A European Journal

Year:

2016

Language:

english

File:

PDF, 6.40 MB

english, 2016

24

Frontispiece: Tetraloop-like Geometries Could Form the Basis of the Catalytic Activity of the Most Ancient Ribooligonucleotides

Stadlbauer, Petr, Šponer, Jiří, Costanzo, Giovanna, Di Mauro, Ernesto, Pino, Samanta, Šponer, Judit E.

Journal:

Chemistry - A European Journal

Year:

2015

File:

PDF, 617 KB

2015

25

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

26

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

27

Non-Watson−Crick Base Pairing in RNA. Quantum Chemical Analysis of the cis Watson−Crick/Sugar Edge Base Pair Family

Šponer, Judit E., Špačková, Nad'a, Kulhánek, Petr, Leszczynski, Jerzy, Šponer, Jiří

Journal:

Journal of Physical Chemistry A

Year:

2005

Language:

english

File:

PDF, 188 KB

english, 2005

28

On the Road from Formamide Ices to Nucleobases: IR-Spectroscopic Observation of a Direct Reaction between Cyano Radicals and Formamide in a High-Energy Impact Event

Ferus, Martin, Civiš, Svatopluk, Mládek, Arnošt, Šponer, Jiří, Juha, Libor, Šponer, Judit E.

Journal:

Journal of the American Chemical Society

Year:

2012

Language:

english

File:

PDF, 1.47 MB

english, 2012

29

Prebiotic synthesis of nucleic acids and their building blocks at the atomic level – merging models and mechanisms from advanced computations and experiments

Sponer, Judit E., Szabla, Rafal, Góra, Robert Władysław, Saitta, A. Marco, Pietrucci, Fabio, Saija, Franz, Di Mauro, Ernesto, Saladino, Raffaele, Ferus, Martin, Civiš, Svatopluk, Sponer, Jiri

Journal:

Physical Chemistry Chemical Physics

Year:

2016

Language:

english

File:

PDF, 1.98 MB

english, 2016

30

Rewarming the Primordial Soup: Revisitations and Rediscoveries in Prebiotic Chemistry

Saladino, Raffaele, Šponer, Judit E., Šponer, Jiří, Di Mauro, Ernesto

Journal:

Year:

2018

Language:

english

File:

PDF, 486 KB

english, 2018

31

Structural and Energetic Compatibility: The Driving Principles of Molecular Evolution

Šponer, Judit E., Šponer, Jiří, Di Mauro, Ernesto

Journal:

Year:

2019

Language:

english

File:

PDF, 1.37 MB

english, 2019

32

Unique Tertiary and Neighbor Interactions Determine Conservation Patterns of Cis Watson–Crick A/G Base-pairs

Jiřı́ Šponer, Ali Mokdad, Judit E. Šponer, Nad'a Špačková, Jerzy Leszczynski, Neocles B. Leontis

Journal:

Journal of Molecular Biology

Year:

2003

Language:

english

File:

PDF, 817 KB

english, 2003

33

ChemInform Abstract: Emergence of the First Catalytic Oligonucleotides in a Formamide-Based Origin Scenario

Sponer, Judit E., Sponer, Jiri, Novakova, Olga, Brabec, Viktor, Sedo, Ondrej, Zdrahal, Zbynek, Costanzo, Giovanna, Pino, Samanta, Saladino, Raffaele, Di Mauro, Ernesto

Journal:

Year:

2016

File:

PDF, 16 KB

2016

34

Non-Enzymatic Oligomerization of 3',5' Cyclic CMP Induced by Proton- and UV-Irradiation Hints at a Non-Fastidious Origin of RNA

Costanzo, Giovanna, Giorgi, Alessandra, Scipioni, Anita, Timperio, Anna Maria, Mancone, Carmine, Tripodi, Marco, Kapralov, Michail, Krasavin, Eugene, Kruse, Holger, Sponer, Jiri, Sponer, Judit E., Ran

Journal:

Year:

2017

Language:

english

File:

PDF, 2.89 MB

english, 2017

35

Structural and energetic factors controlling the enantioselectivity of dinucleotide formation under prebiotic conditions

Šponer, Judit E., Mládek, Arnošt, Šponer, Jiří

Journal:

Physical Chemistry Chemical Physics

Year:

2013

Language:

english

File:

PDF, 1.71 MB

english, 2013

36

Excited-state hydrogen atom abstraction initiates the photochemistry of β-2′-deoxycytidine

Szabla, Rafał, Campos, Jesús, Šponer, Judit E., Šponer, Jiří, Góra, Robert W., Sutherland, John D.

Journal:

Chemical Science

Year:

2015

Language:

english

File:

PDF, 881 KB

english, 2015

37

Metal-Stabilized Rare Tautomers and Mispairs of DNA Bases: N6-Metalated Adenine and N4-Metalated Cytosine, Theoretical and Experimental Views

Šponer, Jiří, Šponer, Judit E., Gorb, Leonid, Leszczynski, Jerzy, Lippert, Bernhard

Journal:

Journal of Physical Chemistry A

Year:

1999

Language:

english

File:

PDF, 270 KB

english, 1999

38

Ribozyme Activity of RNA Nonenzymatically Polymerized from 3′,5′-Cyclic GMP

Pino, Samanta, Costanzo, Giovanna, Giorgi, Alessandra, Šponer, Jiří, Šponer, Judit, Mauro, Ernesto

Journal:

Year:

2013

Language:

english

File:

PDF, 1.98 MB

english, 2013

39

Synthesis of (D)-erythrose from glycolaldehyde aqueous solutions under electric field

Cassone, Giuseppe, Sponer, Jiri, Šponer, Judit, Pietrucci, Fabio, Saitta, A. Marco, Saija, Franz

Journal:

Chemical Communications

Year:

2018

Language:

english

File:

PDF, 3.96 MB

english, 2018

40

Understanding the Sequence Preference of Recurrent RNA Building Blocks Using Quantum Chemistry: The Intrastrand RNA Dinucleotide Platform

Mládek, Arnošt, Šponer, Judit E., Kulhánek, Petr, Lu, Xiang-Jun, Olson, Wilma K., Šponer, Jiří

Journal:

Journal of Chemical Theory and Computation

Year:

2012

Language:

english

File:

PDF, 612 KB

english, 2012

41

On the Stabilization of Ribose by Silicate Minerals

Vázquez-Mayagoitia, Álvaro, Horton, Scott R., Sumpter, Bobby G., Šponer, Jiří, Šponer, Judit E., Fuentes-Cabrera, Miguel

Journal:

Year:

2011

Language:

english

File:

PDF, 274 KB

english, 2011

42

Formamide-Based Prebiotic Synthesis of Nucleobases: A Kinetically Accessible Reaction Route

Šponer, Judit E., Mládek, Arnošt, Šponer, Jiří, Fuentes-Cabrera, Miguel

Journal:

Journal of Physical Chemistry A

Year:

2012

Language:

english

File:

PDF, 1.71 MB

english, 2012

43

Cation—π and Amino-Acceptor Interactions Between Hydrated Metal Cations and DNA Bases. A Quantum-Chemical View

Šponer, Jiří, Šponer, Judit E., Leszczynski, Jerzy

Journal:

Journal of Biomolecular Structure and Dynamics

Year:

2000

Language:

english

File:

PDF, 199 KB

english, 2000

44

High-Energy Chemistry of Formamide: A Simpler Way for Nucleobase Formation

Ferus, Martin, Michalčíková, Regina, Shestivská, Violetta, Šponer, Jiří, Šponer, Judit E., Civiš, Svatopluk

Journal:

Journal of Physical Chemistry A

Year:

2014

Language:

english

File:

PDF, 2.97 MB

english, 2014

45

A prebiotically plausible synthesis of pyrimidine β-ribonucleosides and their phosphate derivatives involving photoanomerization

Xu, Jianfeng, Tsanakopoulou, Maria, Magnani, Christopher J., Szabla, Rafał, Šponer, Judit E., Šponer, Jiří, Góra, Robert W., Sutherland, John D.

Journal:

Nature Chemistry

Year:

2016

Language:

english

File:

PDF, 708 KB

english, 2016

46

Chemomimesis and Molecular Darwinism in Action: From Abiotic Generation of Nucleobases to Nucleosides and RNA

Saladino, Raffaele, Šponer, Judit, Šponer, Jiří, Costanzo, Giovanna, Pino, Samanta, Di Mauro, Ernesto

Journal:

Year:

2018

Language:

english

File:

PDF, 694 KB

english, 2018

47

Effect of Metal Coordination on the Charge Distribution over the Cation Binding Sites of Zeolites. A Combined Experimental and Theoretical Study

Šponer, Judit E., Sobalík, Zdeněk, Leszczynski, Jerzy, Wichterlová, Blanka

Journal:

Journal of Physical Chemistry B

Year:

2001

Language:

english

File:

PDF, 97 KB

english, 2001

48

Theoretical modeling on the kinetics of the arsenate-ester hydrolysis: implications to the stability of As-DNA

Mládek, Arnošt, Šponer, Jiří, Sumpter, Bobby G., Fuentes-Cabrera, Miguel, Šponer, Judit E.

Journal:

Physical Chemistry Chemical Physics

Year:

2011

Language:

english

File:

PDF, 1.01 MB

english, 2011

49

New evolutionary insights into the non-enzymatic origin of RNA oligomers

Šponer, Judit E., Šponer, Jiří, Mauro, Ernesto Di

Journal:

Wiley Interdisciplinary Reviews: RNA

Year:

2016

Language:

english

File:

PDF, 910 KB

english, 2016

50

Formic acid, a ubiquitous but overlooked component of the early Earth atmosphere

Sponer, Judit E., Mohammadi, Elmira, Petera, LukÃ¡Å¡, Saeidfirozeh, Homa, KnÃÅ¾ek, AntonÃn, KubelÃk, Petr, KrÅ¯s, Miroslav, Juha, Libor, CiviÅ¡, Svatopluk, Coulon, RÃ©mi, Malina, OndÅej, Ugolotti,

Journal:

Chemistry - A European Journal

Year:

2020

File:

PDF, 1.17 MB

2020

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