Šponer Judit, Ph.D.

Extension: +420 541-517- 246

- MSc. (in chemistry) 1993 Eötvös University, Budapest.
- PhD. (in chemistry) 1996 Hungarian Academy of Sciences and Technical University, Budapest.
- 2002- Senior research scientist at the Institute of Biophysics, Academy of Sciences of the Czech Republic.
My research focuses on the combination of experiments and theoretical calculations in the search for life's origins both in terrestrial and extraterrestrial contexts. Our previous studies focussed on the formamide-based scenario of the origin of life. In this topic we closely collaborated with the Di Mauro (Rome, Italy) and Saladino (Tuscia, Italy) groups. We have formulated a simple, non-equilibrium formamide-based origin model, in which the stepwise decrease of the temperature of the prebiotic environment drives those complex chemical transformations that could lead to more and more complex molecules on the early Earth. Our more recent studies in cooperation with the Di Mauro and Braun (LMU, Munich) groups deal with the non-enzymatic synthesis of the first RNA molecules. Based on the unique ability of 3',5' cyclic GMP to self-assemble and polymerize under a wide variety of geochemical conditions we suggested that this nucleotide could serve as the seed of terrestrial life.

Selected papers related to the formamide and polymerization topic:
- J. E. Šponer, J. Šponer, O. Nováková, V. Brabec, O. Šedo, Z. Zdráhal, G. Costanzo, S. Pino, R. Saladino and E. Di Mauro, Emergence of the First Catalytic Oligonucleotides in a Formamide-Based Origin Scenario, Chem. – Eur. J. 2016, 22, 3572-3586.
- J. E. Šponer, J. Šponer, A. Giorgi, E. Di Mauro, S. Pino and G. Costanzo, Untemplated Nonenzymatic Polymerization of 3′,5′cGMP: A Plausible Route to 3′,5′-Linked Oligonucleotides in Primordia, J. Phys. Chem. B, 2015, 119, 2979-2989.
- S. Wunnava, C. F. Dirscherl, J. Výravský, A. Kovařík, R. Matyásek, J. Šponer, D. Braun and J. E. Šponer, Acid-Catalyzed RNA-Oligomerization from 3’,5’-cGMP, Chem. – Eur. J., 2021, 27, 17581-17585.
- J. E. Šponer, J. Šponer, J. Výravský, R. Matyásek, A. Kovařík, W. Dudziak and K. Ślepokura, Crystallization as a selection force at the polymerization of nucleotides in a prebiotic context, iScience, 2023, 26, 107600.

Selected press releases:

Chemistry World: https://www.chemistryworld.com/news/early-rna-reactions-characterised/8249.article

Deutschlandfunk (in German): www.deutschlandfunk.de/asteroideneinschlaege-notwendige-hitze-fuer-die-ursuppe-des.676.de.html?dram:article_id=305699

Respekt (in Czech): https://www.respekt.cz/zkumavka/vesmir-vstricny-k-zivotu

Lidove noviny (in Czech): http://www.ibp.cz/filesystem.app/get/Departments/DSDNA/media/lnb.pdf

Complete list of publications (on old papers under maiden name, Judit Molnar):

1. Hargittai, M.; Molnar, J.; Klapotke, T. M.; Tornieporthoetting, I. C.; Kolonits, M.; Hargittai, I. Iodine azide - molecular-structure from gas-phase electron-diffraction. Journal of Physical Chemistry 1994, 98 (40), 10095-10097. http://dx.doi.org/10.1021/j100091a025

2. Molnar, J.; Hargittai, M. Prediction of the molecular shape of lanthanide trihalides. Journal of Physical Chemistry 1995, 99 (27), 10780-10784. http://dx.doi.org/10.1021/j100027a017

3. Molnar, J.; Marsden, C. J.; Hargittai, M. Molecular-structures and force-fields of monomeric and dimeric magnesium dichloride from electron-diffraction and quantum-chemical calculations. Journal of Physical Chemistry 1995, 99 (22), 9062-9071. http://dx.doi.org/10.1021/j100022a018

4. Molnar, J.; Kolonits, M.; Hargittai, M.; Konings, R. J. M.; Booij, A. S. Molecular structure of SbI3 and BiI3 from combined electron diffraction and vibrational spectroscopic studies. Inorganic Chemistry 1996, 35 (26), 7639-7642. http://dx.doi.org/10.1021/ic960601k

5. Molnar, J.; Konings, R. J. M.; Kolonits, M.; Hargittai, M. Molecular structure of CeI3 from gas-phase electron diffraction and vibrational spectroscopy. Journal of Molecular Structure 1996, 375 (3), 223-229. http://dx.doi.org/10.1016/0022-2860(95)09093-2

6. Molnar, J.; Kolonits, M.; Hargittai, M. Molecular structure of SbF3 and BiF3: an electron diffraction study. Journal of Molecular Structure 1997, 413, 441-446. http://dx.doi.org/10.1016/s0022-2860(97)00057-4

7. Cejka, J.; Zilkova, N.; Sponer, J. E.; Wichterlova, B. Kinetic and theoretical study of the effect of molecular sieve structure on the selectivity to propylbenzenes in alkylation of benzene with isopropyl alcohol. Collection of Czechoslovak Chemical Communications 1998, 63 (11), 1769-1780. http://dx.doi.org/10.1135/cccc19981769

8. Sponer, J.; Cejka, J.; Wichterlova, B. 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. Journal of Physical Chemistry B 1998, 102 (37), 7169-7175. http://dx.doi.org/10.1021/jp980637t

9. Sponer, J.; Sponer, J. E.; Gorb, L.; Leszczynski, J.; Lippert, B. Metal-stabilized rare tautomers and mispairs of DNA bases: N6-metalated adenine and N4-metalated cytosine, theoretical and experimental views. Journal of Physical Chemistry A 1999, 103 (51), 11406-11413. http://dx.doi.org/10.1021/jp992337x

10. Sponer, J.; Cejka, J.; Dedecek, J.; Wichterlova, B. Coordination and properties of cobalt in the molecular sieves CoAPO-5 and-11. Microporous and Mesoporous Materials 2000, 37 (1-2), 117-127. http://dx.doi.org/10.1016/s1387-1811(99)00258-9

11. Sponer, J.; Florian, J.; Ng, H. L.; Sponer, J. E.; Spackova, N. Local conformational variations observed in B-DNA crystals do not improve base stacking: computational analysis of base stacking in a d(CATGGGCCCATG)(2) B <-> A intermediate crystal structure. Nucleic Acids Research 2000, 28 (24), 4893-4902.

12. Sponer, J.; Sponer, J. E.; Leszczynski, J. Cation-pi and amino-acceptor interactions between hydrated metal cations and DNA bases. A quantum-chemical view. Journal of Biomolecular Structure & Dynamics 2000, 17 (6), 1087-1096.

13. Sponer, J. E.; Glahe, F.; Leszczynski, J.; Lippert, B.; Sponer, J. How nucleobases rotate when bonded to a metal ion: Detailed view from an ab initio quantum chemical study of a cytosine complex of trans-a(2)Pt(II). Journal of Physical Chemistry B 2001, 105 (48), 12171-12179. http://dx.doi.org/10.1021/jp012795h

14. Sponer, J. E.; Leszczynski, J.; Glahe, F.; Lippert, B.; Sponer, J. Protonation of platinated adenine nucleobases. Gas phase vs condensed phase picture. Inorganic Chemistry 2001, 40 (14), 3269-3278. http://dx.doi.org/10.1021/ic001276a

15. Sponer, J. E.; Sobalik, Z.; Leszczynski, J.; Wichterlova, B. Effect of metal coordination on the charge distribution over the cation binding sites of zeolites. A combined experimental and theoretical study. Journal of Physical Chemistry B 2001, 105 (35), 8285-8290. http://dx.doi.org/10.1021/jp010098j

16. Sponer, J. E.; Sponer, J.; Cejka, J. Ab initio quantum chemical study on the zeolite catalyzed transformations of para-xylene. Journal of Molecular Structure-Theochem 2001, 540, 145-152. http://dx.doi.org/10.1016/s0166-1280(00)00732-6

17. Reha, D.; Kabelac, M.; Ryjacek, F.; Sponer, J.; Sponer, J. E.; Elstner, M.; Suhai, S.; Hobza, P. 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. Journal of the American Chemical Society 2002, 124 (13), 3366-3376. http://dx.doi.org/10.1021/ja011490d

18. Schmidt, K. S.; Reedijk, J.; Weisz, K.; Janke, E. M. B.; Sponer, J. E.; Sponer, J.; Lippert, B. Loss of Hoogsteen pairing ability upon N1 adenine platinum binding. Inorganic Chemistry 2002, 41 (11), 2855-2863. http://dx.doi.org/10.1021/ic0109602

19. Sobalik, Z.; Kubanek, P.; Bortnovsky, O.; Vondrova, A.; Tvaruzkova, Z.; Sponer, J. E.; Wichterlova, B. On the necessity of a basic revision of the redox properties of H-zeolites. In Impact of Zeolites and Other Porous Materials on the New Technologies at the Beginning of the New Millennium, Pts a and B, Aiello, R.; Giordano, G.; Testa, F., Eds. 2002; Vol. 142, pp 533-540.

20. Warmlander, S.; Sponer, J. E.; Sponer, J.; Leijon, M. The influence of the thymine C5 methyl group on spontaneous base pair breathing in DNA. Journal of Biological Chemistry 2002, 277 (32), 28491-28497. http://dx.doi.org/10.1074/jbc.M202989200

21. Gresh, N.; Sponer, J. E.; Spackova, N.; Leszczynski, J.; Sponer, J. Theoretical study of binding of hydrated Zn(II) and Mg(II) cations to 5 '-guanosine monophosphate. Toward polarizable molecular mechanics for DNA and RNA. Journal of Physical Chemistry B 2003, 107 (33), 8669-8681. http://dx.doi.org/10.1021/jp022659s

22. Reblova, K.; Spackova, N.; Sponer, J. E.; Koca, J.; Sponer, J. Molecular dynamics simulations of RNA kissing-loop motifs reveal structural dynamics and formation of cation-binding pockets. Nucleic Acids Research 2003, 31 (23), 6942-6952. http://dx.doi.org/10.1093/nar/gkg880

23. Sponer, J.; Mokdad, A.; Sponer, J. E.; Spackova, N.; Leszczynski, J.; Leontis, N. B. Unique tertiary and neighbor interactions determine conservation patterns of Cis Watson-Crick A/G base-pairs. Journal of Molecular Biology 2003, 330 (5), 967-978. http://dx.doi.org/10.1016/s0022-2836(03)00667-3

24. Sponer, J. E.; Miguel, P. J. S.; Rodriguez-Santiago, L.; Erxleben, A.; Krumm, M.; Sodupe, M.; Sponer, J.; Lippert, B. Metal-mediated deamination of cytosine: Experiment and DFT calculations. Angewandte Chemie-International Edition 2004, 43 (40), 5396-5399. http://dx.doi.org/10.1002/anie.200460107

25. Sponer, J. E.; Sychrovsky, V.; Hobza, P.; Sponer, J. 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. Physical Chemistry Chemical Physics 2004, 6 (10), 2772-2780. http://dx.doi.org/10.1039/b404306p

26. Sponer, J. E.; Leszczynski, J.; Sychrovsky, V.; Sponer, J. Sugar edge/sugar edge base pairs in RNA: Stabilities and structures from quantum chemical calculations. Journal of Physical Chemistry B 2005, 109 (39), 18680-18689. http://dx.doi.org/10.1021/jp053379q

27. Sponer, J. E.; Spackova, N.; Kulhanek, P.; Leszczynski, J.; Sponer, J. Non-Watson-Crick base pairing in RNA. Quantum chemical analysis of the cis Watson-Crick/sugar edge base pair family. Journal of Physical Chemistry A 2005, 109 (10), 2292-2301. http://dx.doi.org/10.1021/jp050132k

28. Sponer, J. E.; Spackova, N.; Leszczynski, J.; Sponer, J. Principles of RNA base pairing: Structures and energies of the trans Watson-Crick/sugar edge base pairs. Journal of Physical Chemistry B 2005, 109 (22), 11399-11410. http://dx.doi.org/10.1021/jp051126r

29. Sponer, J. E.; Leszczynski, J.; Sponer, J. Mechanism of action of anticancer titanocene derivatives: An insight from quantum chemical calculations. Journal of Physical Chemistry B 2006, 110 (39), 19632-19636. http://dx.doi.org/10.1021/jp063477r

30. Fuentes-Cabrera, M.; Sumpter, B. G.; Sponer, J. E.; Sponer, J.; Petit, L.; Wells, J. C. Theoretical study on the structure, stability, and electronic properties of the guanine-Zn-cytosine base pair in M-DNA. Journal of Physical Chemistry B 2007, 111 (4), 870-879. http://dx.doi.org/10.1021/jp066465e

31. Sponer, J. E.; Reblova, K.; Mokdad, A.; Sychrovsky, V.; Leszczynski, J.; Sponer, J. Leading RNA tertiary interactions: Structures, energies, and water insertion of a-minor and p-interactions. A quantum chemical view. Journal of Physical Chemistry B 2007, 111 (30), 9153-9164. http://dx.doi.org/10.1021/jp0704261

32. Vokacova, Z.; Sponer, J.; Sponer, J. E.; Sychrovsky, V. Theoretical study of the scalar coupling constants across the noncovalent contacts in RNA base pairs: The cis- and trans-Watson-Crick/sugar edge base pair family. Journal of Physical Chemistry B 2007, 111 (36), 10813-10824. http://dx.doi.org/10.1021/jp072822p

33. Sponer, J. E.; Sumpter, B. G.; Leszczynski, J.; Sponer, J.; Fuentes-Cabrera, M. Theoretical Study on the Factors Controlling the Stability of the Borate Complexes of Ribose, Arabinose, Lyxose, and Xylose. Chemistry-a European Journal 2008, 14 (32), 9990-9998. http://dx.doi.org/10.1002/chem.200800961

34. Svozil, D.; Sponer, J. E.; Marchan, I.; Perez, A.; Cheatham, T. E.; Forti, F.; Luque, F. J.; Orozco, M.; Sponer, J. Geometrical and electronic structure variability of the sugar-phosphate backbone in nucleic acids. Journal of Physical Chemistry B 2008, 112 (27), 8188-8197. http://dx.doi.org/10.1021/jp801245h

35. Futera, Z.; Klenko, J.; Sponer, J. E.; Sponer, J.; Burda, J. V. Interactions of the "Piano-stool" Ruthenium(II)(eta(6)-arene)(en)Cl (+) Complexes With Water and Nucleobases; A initio and DFT Study. Journal of Computational Chemistry 2009, 30 (12), 1758-1770. http://dx.doi.org/10.1002/jcc.21179

36. Mladek, A.; Sharma, P.; Mitra, A.; Bhattacharyya, D.; Sponer, J.; Sponer, J. E. Trans Hoogsteen/Sugar Edge Base Pairing in RNA. Structures, Energies, and Stabilities from Quantum Chemical Calculations. Journal of Physical Chemistry B 2009, 113 (6), 1743-1755. http://dx.doi.org/10.1021/jp808357m

37. Sponer, J.; Zgarbova, M.; Jurecka, P.; Riley, K. E.; Sponer, J. E.; Hobza, P. Reference Quantum Chemical Calculations on RNA Base Pairs Directly Involving the 2 '-OH Group of Ribose. Journal of Chemical Theory and Computation 2009, 5 (4), 1166-1179. http://dx.doi.org/10.1021/ct800547k

38. Zirbel, C. L.; Sponer, J. E.; Sponer, J.; Stombaugh, J.; Leontis, N. B. Classification and energetics of the base-phosphate interactions in RNA. Nucleic Acids Research 2009, 37 (15), 4898-4918. http://dx.doi.org/10.1093/nar/gkp468

39. Zirbel, C. L.; Sponer, J. E.; Sponer, J.; Stombaugh, J.; Leontis, N. B. Classification and Energetics of the Base-Phosphate Interactions in RNA. Journal of Biomolecular Structure & Dynamics 2009, 26 (6), 819-819.

40. Mladek, A.; Sponer, J. E.; Jurecka, P.; Banas, P.; Otyepka, M.; Svozil, D.; Sponer, J. Conformational Energies of DNA Sugar-Phosphate Backbone: Reference QM Calculations and a Comparison with Density Functional Theory and Molecular Mechanics. Journal of Chemical Theory and Computation 2010, 6 (12), 3817-3835. http://dx.doi.org/10.1021/ct1004593

41. Sharma, P.; Sponer, J. E.; Sponer, J.; Sharma, S.; Bhattacharyya, D.; Mitra, A. On the Role of the cis Hoogsteen:Sugar-Edge Family of Base Pairs in Platforms and Triplets-Quantum Chemical Insights into RNA Structural Biology. Journal of Physical Chemistry B 2010, 114 (9), 3307-3320. http://dx.doi.org/10.1021/jp910226e

42. Sponer, J.; Sponer, J. E.; Petrov, A. I.; Leontis, N. B. Quantum Chemical Studies of Nucleic Acids Can We Construct a Bridge to the RNA Structural Biology and Bioinformatics Communities? Journal of Physical Chemistry B 2010, 114 (48), 15723-15741. http://dx.doi.org/10.1021/jp104361m

43. Sponer, J. E.; Vazquez-Mayagoitia, A.; Sumpter, B. G.; Leszczynski, J.; Sponer, J.; Otyepka, M.; Banas, P.; Fuentes-Cabrera, M. Theoretical Studies on the Intermolecular Interactions of Potentially Primordial Base-Pair Analogues. Chemistry-a European Journal 2010, 16 (10), 3057-3065. http://dx.doi.org/10.1002/chem.200902068

44. Mladek, A.; Sponer, J.; Sumpter, B. G.; Fuentes-Cabrera, M.; Sponer, J. E. On the Geometry and Electronic Structure of the As-DNA Backbone. Journal of Physical Chemistry Letters 2011, 2 (5), 389-392. http://dx.doi.org/10.1021/jz200015n

45. Mladek, A.; Sponer, J.; Sumpter, B. G.; Fuentes-Cabrera, M.; Sponer, J. E. Theoretical modeling on the kinetics of the arsenate-ester hydrolysis: implications to the stability of As-DNA. Physical Chemistry Chemical Physics 2011, 13 (23), 10869-10871. http://dx.doi.org/10.1039/c1cp20423h

46. Reblova, K.; Sponer, J. E.; Spackova, N.; Besseova, I.; Sponer, J. A-Minor Tertiary Interactions in RNA Kink-Turns. Molecular Dynamics and Quantum Chemical Analysis. Journal of Physical Chemistry B 2011, 115 (47), 13897-13910. http://dx.doi.org/10.1021/jp2065584

47. Sponer, J. E.; Sponer, J.; Fuentes-Cabrera, M. Prebiotic Routes to Nucleosides: A Quantum Chemical Insight into the Energetics of the Multistep Reaction Pathways. Chemistry-a European Journal 2011, 17 (3), 847-854. http://dx.doi.org/10.1002/chem.201002057

48. Vazquez-Mayagoitia, A.; Horton, S. R.; Sumpter, B. G.; Sponer, J.; Sponer, J. E.; Fuentes-Cabrera, M. On the Stabilization of Ribose by Silicate Minerals. Astrobiology 2011, 11 (2), 115-121. http://dx.doi.org/10.1089/ast.2010.0508

49. Zgarbova, M.; Jurecka, P.; Banas, P.; Otyepka, M.; Sponer, J. E.; Leontis, N. B.; Zirbel, C. L.; Sponer, J. 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. Journal of Physical Chemistry A 2011, 115 (41), 11277-11292. http://dx.doi.org/10.1021/jp204820b

50. Ferus, M.; Civis, S.; Mladek, A.; Sponer, J.; Juha, L.; Sponer, J. E. 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. Journal of the American Chemical Society 2012, 134 (51), 20788-20796. http://dx.doi.org/10.1021/ja310421z

51. Fonville, J. M.; Swart, M.; Vokacova, Z.; Sychrovsky, V.; Sponer, J. E.; Sponer, J.; Hilbers, C. W.; Bickelhaupt, F. M.; Wijmenga, S. S. Chemical Shifts in Nucleic Acids Studied by Density Functional Theory Calculations and Comparison with Experiment. Chemistry-a European Journal 2012, 18 (39), 12372-12387. http://dx.doi.org/10.1002/chem.201103593

52. Mladek, A.; Sponer, J. E.; Kulhanek, P.; Lu, X. J.; Olson, W. K.; Sponer, J. Understanding the Sequence Preference of Recurrent RNA Building Blocks Using Quantum Chemistry: The Intrastrand RNA Dinucleotide Platform. Journal of Chemical Theory and Computation 2012, 8 (1), 335-347. http://dx.doi.org/10.1021/ct200712b

53. Ovaere, M.; Sponer, J.; Sponer, J. E.; Herdewijn, P.; Van Meervelt, L. How does hydroxyl introduction influence the double helical structure: the stabilization of an altritol nucleic acid: ribonucleic acid duplex. Nucleic Acids Research 2012, 40 (15), 7573-7583. http://dx.doi.org/10.1093/nar/gks470

54. Sponer, J.; Mladek, A.; Sponer, J. E.; Svozil, D.; Zgarbova, M.; Banas, P.; Jurecka, P.; Otyepka, M. The DNA and RNA sugar-phosphate backbone emerges as the key player. An overview of quantum-chemical, structural biology and simulation studies. Physical Chemistry Chemical Physics 2012, 14 (44), 15257-15277. http://dx.doi.org/10.1039/c2cp41987d

55. Sponer, J. E.; Mladek, A.; Sponer, J.; Fuentes-Cabrera, M. Formamide-Based Prebiotic Synthesis of Nucleobases: A Kinetically Accessible Reaction Route. Journal of Physical Chemistry A 2012, 116 (1), 720-726. http://dx.doi.org/10.1021/jp209886b

56. Sponer, J. E.; Sponer, J. Is formamide nature's choice to create life? Comment on the paper "Formamide and the origin of life" by Raffaele Saladino et al. Physics of Life Reviews 2012, 9 (1), 109-110. http://dx.doi.org/10.1016/j.plrev.2011.12.015

57. Pino, S.; Costanzo, G.; Giorgi, A.; Sponer, J.; Sponer, J. E.; Di Mauro, E. Ribozyme Activity of RNA Nonenzymatically Polymerized from 3 ',5 '-Cyclic GMP. Entropy 2013, 15 (12), 5362-5383. http://dx.doi.org/10.3390/e15125362

58. Sponer, J.; Sponer, J. E.; Mladek, A.; Banas, P.; Jurecka, P.; Otyepka, M. How to understand quantum chemical computations on DNA and RNA systems? A practical guide for non-specialists. Methods 2013, 64 (1), 3-11. http://dx.doi.org/10.1016/j.ymeth.2013.05.025

59. Sponer, J.; Sponer, J. E.; Mladek, A.; Jurecka, P.; Banas, P.; Otyepka, M. Nature and Magnitude of Aromatic Base Stacking in DNA and RNA: Quantum Chemistry, Molecular Mechanics, and Experiment. Biopolymers 2013, 99 (12), 978-988. http://dx.doi.org/10.1002/bip.22322

60. Sponer, J. E.; Mladek, A.; Ferus, M.; Civis, S.; Sponer, J. Quantum chemical studies on the formamide-based origin of life. Journal of Biomolecular Structure & Dynamics 2013, 31, 11-12. http://dx.doi.org/10.1080/07391102.2013.786327

61. Sponer, J. E.; Mladek, A.; Sponer, J. Structural and energetic factors controlling the enantioselectivity of dinucleotide formation under prebiotic conditions. Physical Chemistry Chemical Physics 2013, 15 (17), 6235-6242. http://dx.doi.org/10.1039/c3cp44156c

62. Szabla, R.; Sponer, J. E.; Sponer, J.; Gora, R. W. Theoretical studies of the mechanism of 2-aminooxazole formation under prebiotically plausible conditions. Physical Chemistry Chemical Physics 2013, 15 (20), 7812-7818. http://dx.doi.org/10.1039/c3cp50320h

63. Civis, S.; Ferus, M.; Sponer, J. E.; Sponer, J.; Kavan, L.; Zukalova, M. Room temperature spontaneous conversion of OCS to CO2 on the anatase TiO2 surface. Chemical Communications 2014, 50 (57), 7712-7715. http://dx.doi.org/10.1039/c4cc01992j

64. Ferus, M.; Michalcikova, R.; Shestivska, V.; Sponer, J.; Sponer, J. E.; Civis, S. High-Energy Chemistry of Formamide: A Simpler Way for Nucleobase Formation. Journal of Physical Chemistry A 2014, 118 (4), 719-736. http://dx.doi.org/10.1021/jp411415p

65. Szabla, R.; Gora, R. W.; Sponer, J.; Sponer, J. E. Molecular Mechanism of Diaminomaleonitrile to Diaminofumaronitrile Photoisomerization: An Intermediate Step in the Prebiotic Formation of Purine Nucleobases. Chemistry-a European Journal 2014, 20 (9), 2515-2521. http://dx.doi.org/10.1002/chem.201304224

66. Szabla, R.; Sponer, J. E.; Sponer, J.; Sobolewski, A. L.; Gora, R. W. Solvent effects on the photochemistry of 4-aminoimidazole-5-carbonitrile, a prebiotically plausible precursor of purines. Physical Chemistry Chemical Physics 2014, 16 (33), 17617-17626. http://dx.doi.org/10.1039/c4cp02074j

67. Ferus, M.; Nesvorny, D.; Sponer, J.; Kubelik, P.; Michalcikova, R.; Shestivska, V.; Sponer, J. E.; Civis, S. High-energy chemistry of formamide: A unified mechanism of nucleobase formation. Proceedings of the National Academy of Sciences of the United States of America 2015, 112 (3), 657-662. http://dx.doi.org/10.1073/pnas.1412072111

68. Gresh, N.; Sponer, J. E.; Devereux, M.; Gkionis, K.; de Courcy, B.; Piquemal, J. P.; Sponer, J. Stacked and H-Bonded Cytosine Dimers. Analysis of the Intermolecular Interaction Energies by Parallel Quantum Chemistry and Polarizable Molecular Mechanics. Journal of Physical Chemistry B 2015, 119 (30), 9477-9495. http://dx.doi.org/10.1021/acs.jpcb.5b01695

69. Sponer, J. E.; Sponer, J.; Giorgi, A.; Di Mauro, E.; Pino, S.; Costanzo, G. Untemplated Nonenzymatic Polymerization of 3 ',5 ' cGMP: A Plausible Route to 3 ',5 '-Linked Oligonucleotides in Primordia. Journal of Physical Chemistry B 2015, 119 (7), 2979-2989. http://dx.doi.org/10.1021/acs.jpcb.5b00601

70. Stadlbauer, P.; Sponer, J.; Costanzo, G.; Di Mauro, E.; Pino, S.; Sponer, J. E. Tetraloop-like Geometries Could Form the Basis of the Catalytic Activity of the Most Ancient Ribooligonucleotides. Chemistry-a European Journal 2015, 21 (9), 3596-3604. http://dx.doi.org/10.1002/chem.201406140

71. Szabla, R.; Campos, J.; Sponer, J. E.; Sponer, J.; Gora, R. W.; Sutherland, J. D. Excited-state hydrogen atom abstraction initiates the photochemistry of beta-2 '-deoxycytidine. Chemical Science 2015, 6 (3), 2035-2043. http://dx.doi.org/10.1039/c4sc03761h

72. Civis, S.; Szabla, R.; Szyja, B. M.; Smykowski, D.; Ivanek, O.; Knizek, A.; Kubelik, P.; Sponer, J.; Ferus, M.; Sponer, J. E. TiO2-catalyzed synthesis of sugars from formaldehyde in extraterrestrial impacts on the early Earth. Scientific Reports 2016, 6. http://dx.doi.org/10.1038/srep23199

73. Costanzo, G.; Pino, S.; Timperio, A. M.; Sponer, J. E.; Sponer, J.; Novakova, O.; Sedo, O.; Zdrahal, Z.; Di Mauro, E. Non-Enzymatic Oligomerization of 3 ', 5 ' Cyclic AMP. Plos One 2016, 11 (11). http://dx.doi.org/10.1371/journal.pone.0165723

74. Šponer, J. E.; Šponer, J.; Di Mauro, E. New evolutionary insights into the non-enzymatic origin of RNA oligomers. Wiley Interdisciplinary Reviews: RNA 2016. http://dx.doi.org/10.1002/wrna.1400

75. Sponer, J. E.; Sponer, J.; Di Mauro, E. Four Ways to Oligonucleotides Without Phosphoimidazolides. Journal of Molecular Evolution 2016, 82 (1), 5-10. http://dx.doi.org/10.1007/s00239-015-9709-5

76. Sponer, J. E.; Sponer, J.; Novakova, O.; Brabec, V.; Sedo, O.; Zdrahal, Z.; Costanzo, G.; Pino, S.; Saladino, R.; Di Mauro, E. Emergence of the First Catalytic Oligonucleotides in a Formamide-Based Origin Scenario. Chemistry-a European Journal 2016, 22 (11), 3572-3586. http://dx.doi.org/10.1002/chem.201503906

77. Sponer, J. E.; Szabla, R.; Gora, R. W.; Saitta, A. M.; Pietrucci, F.; Saija, F.; Di Mauro, E.; Saladino, R.; Ferus, M.; Civis, S.; Sponer, J. Prebiotic synthesis of nucleic acids and their building blocks at the atomic level - merging models and mechanisms from advanced computations and experiments. Physical Chemistry Chemical Physics 2016, 18 (30), 20047-20066. http://dx.doi.org/10.1039/c6cp00670a

78. Xu, J.; Tsanakopoulou, M.; Magnani, C. J.; Szabla, R.; Šponer, J. E.; Šponer, J.; Góra, R. W.; Sutherland, J. D. A prebiotically plausible synthesis of pyrimidine β-ribonucleosides and their phosphate derivatives involving photoanomerization. Nat Chem 2016, advance online publication. http://dx.doi.org/10.1038/nchem.2664

79. Cassone, G.; Sponer, J.; Saija, F.; Di Mauro, E.; Marco Saitta, A.; Sponer, J. E. Stability of 2',3' and 3',5' cyclic nucleotides in formamide and in water: a theoretical insight into the factors controlling the accumulation of nucleic acid building blocks in a prebiotic pool. Physical Chemistry Chemical Physics 2017. http://dx.doi.org/10.1039/c6cp07993h

80. Cassone, G.; Pietrucci, F.; Saija, F.; Guyot, F.; Sponer, J.; Sponer, J. E.; Saitta, A. M. Novel electrochemical route to cleaner fuel dimethyl ether. Scientific Reports 2017, 7. DOI: 10.1038/s41598-017-07187-8.

81. Costanzo, G.; Giorgi, A.; Scipioni, A.; Timperio, A. M.; Mancone, C.; Tripodi, M.; Kapralov, M.; Krasavin, E.; Kruse, H.; Sponer, J. S.; et al. Nonenzymatic Oligomerization of 3′,5′-Cyclic CMP Induced by Proton and UV Irradiation Hints at a Nonfastidious Origin of RNA. Chembiochem 2017, 18 (15), 1535-1543. DOI: 10.1002/cbic.201700122.

82. Gresh, N.; Naseem-Khan, S.; Lagardère, L.; Piquemal, J. P.; Sponer, J. E.; Sponer, J. 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. Journal of Physical Chemistry B 2017, 121 (16), 3997-4014. DOI: 10.1021/acs.jpcb.7b01836.

83. Saladino, R.; Bizzarri, B. M.; Botta, L.; Sponer, J.; Sponer, J. E.; Georgelin, T.; Jaber, M.; Rigaud, B.; Kapralov, M.; Timoshenko, G. N.; et al. Proton irradiation: a key to the challenge of N-glycosidic bond formation in a prebiotic context. Scientific Reports 2017, 7. DOI: 10.1038/s41598-017-15392-8.

84. Sponer, J. E.; Sponer, J.; Di Mauro, E. New evolutionary insights into the non-enzymatic origin of RNA oligomers. Wiley Interdisciplinary Reviews-Rna 2017, 8 (3). DOI: 10.1002/wrna.1400.

85. Xu, J. F.; Tsanakopoulou, M.; Magnani, C. J.; Szabla, R.; Sponer, J. E.; Sponer, J.; Góra, R. W.; Sutherland, J. D. A prebiotically plausible synthesis of pyrimidine β-ribonucleosides and their phosphate derivatives involving photoanomerization. Nature Chemistry 2017, 9 (4), 303-309. DOI: 10.1038/nchem.2664.

86. Cassone, G.; Saija, F.; Sponer, J.; Sponer, J. E.; Ferus, M.; Krus, M.; Ciaravella, A.; Jiménez-Escobar, A.; Cecchi-Pestellini, C. Dust Motions in Magnetized Turbulence: Source of Chemical Complexity. Astrophysical Journal Letters 2018, 866 (2).
http://dx.doi.org/10.3847/2041-8213/aae529

87. Cassone, G.; Sponer, J.; Sponer, J. E.; Pietrucci, F.; Saitta, A. M.; Saija, F. Synthesis of (D)-erythrose from glycolaldehyde aqueous solutions under electric field. Chemical Communications 2018, 54 (26), 3211-3214. DOI: 10.1039/c8cc00045j.

88. Ferus, M.; Laitl, V.; Knizek, A.; Kubelík, P.; Sponer, J.; Kára, J.; Sponer, J. E.; Lefloch, B.; Cassone, G.; Civis, S. HNCO-based synthesis of formamide in planetary atmospheres. Astronomy & Astrophysics 2018, 616. DOI: 10.1051/0004-6361/201833003.

89. Saladino, R.; Sponer, J. E.; Sponer, J.; Costanzo, G.; Pino, S.; Di Mauro, E. Chemomimesis and Molecular Darwinism in Action: From Abiotic Generation of Nucleobases to Nucleosides and RNA. Life-Basel 2018, 8 (2). DOI: 10.3390/life8020024.

90. Saladino, R.; Sponer, J. E.; Sponer, J.; Di Mauro, E. Rewarming the Primordial Soup: Revisitations and Rediscoveries in Prebiotic Chemistry. Chembiochem 2018, 19 (1), 22-25. DOI: 10.1002/cbic.201700534.

91. Ferus, M.; Pietrucci, F.; Saitta, A. M.; Ivanek, O.; Knizek, A.; Kubelík, P.; Krus, M.; Juha, L.; Dudzak, R.; Dostál, J.; et al. Prebiotic synthesis initiated in formaldehyde by laser plasma simulating high-velocity impacts. Astronomy & Astrophysics 2019, 626. DOI: 10.1051/0004-6361/201935435.

92. Pastorek, A.; Hrncírová, J.; Jankovic, L.; Nejdl, L.; Civis, S.; Ivanek, O.; Shestivska, V.; Knízek, A.; Kubelík, P.; Sponer, J.; et al. Prebiotic synthesis at impact craters: the role of Fe-clays and iron meteorites. Chemical Communications 2019, 55 (71), 10563-10566. DOI: 10.1039/c9cc04627e.

93. Pino, S.; Di Mauro, E.; Costanzo, G.; Saladino, R.; Sedo, O.; Zdráhal, Z.; Sponer, J.; Sponer, J. E. Stabilization of Short Oligonucleotides in the Prebiotic Mix: The Potential Role of Amino Alcohols. Chemsystemschem 2019, 1 (4). DOI: 10.1002/syst.201900006.

94. Saladino, R.; Bizzarri, B. M.; Botta, L.; Sponer, J.; Sponer, J. E.; Georgelin, T.; Jaber, M.; Rigaud, B.; Kapralov, M.; Timoshenko, G. N.; et al. Proton irradiation: a key to the challenge of N-glycosidic bond formation in a prebiotic context (vol 7, 14709, 2017). Scientific Reports 2019, 9. DOI: 10.1038/s41598-019-40290-6.

95. Sponer, J. E.; Sponer, J.; Di Mauro, E. Structural and Energetic Compatibility: The Driving Principles of Molecular Evolution. Astrobiology 2019, 19 (9), 1117-1122. DOI: 10.1089/ast.2018.1978.

96. Bizzarri, B. M.; Manini, P.; Lino, V.; D'Ischia, M.; Kapralov, M.; Krasavin, E.; Mrazikova, K.; Sponer, J.; Sponer, J. E.; Di Mauro, E.; et al. High-Energy Proton-Beam-Induced Polymerization/Oxygenation of Hydroxynaphthalenes on Meteorites and Nitrogen Transfer from Urea: Modeling Insoluble Organic Matter? Chemistry-a European Journal 2020, 26 (65), 14919-14928. DOI: 10.1002/chem.202002318.

97. Bizzarri, B. M.; Sponer, J. E.; Sponer, J.; Cassone, G.; Kapralov, M.; Timoshenko, G. N.; Krasavin, E.; Fanelli, G.; Timperio, A. M.; Di Mauro, E.; et al. Meteorite-Assisted Phosphorylation of Adenosine Under Proton Irradiation Conditions. Chemsystemschem 2020, 2 (3). DOI: 10.1002/syst.201900039.

98. Ferus, M.; Rimmer, P.; Cassone, G.; Knízek, A.; Civis, S.; Sponer, J. E.; Ivanek, O.; Sponer, J.; Saeidfirozeh, H.; Kubelík, P.; et al. One-Pot Hydrogen Cyanide-Based Prebiotic Synthesis of Canonical Nucleobases and Glycine Initiated by High-Velocity Impacts on Early Earth. Astrobiology 2020, 20 (12), 1476-1488. DOI: 10.1089/ast.2020.2231.

99. Mohammadi, E.; Petera, L.; Saeidfirozeh, H.; Knízek, A.; Kubelík, P.; Dudzák, R.; Krus, M.; Juha, L.; Civis, S.; Coulon, R.; et al. Formic Acid, a Ubiquitous but Overlooked Component of the Early Earth Atmosphere. Chemistry-a European Journal 2020, 26 (52), 12075-12080. DOI: 10.1002/chem.202000323.

100. Sponer, J. E.; Sponer, J. Formic acid, the precursor of formamide, from serpentinization Comment on the paper:"Mineral self-organization on a lifeless planet" by Juan Manuel Garcia-Ruiz, Mark A. van Zuilen and Wolfgang Bach. Physics of Life Reviews 2020, 34-35, 94-95. DOI: 10.1016/j.plrev.2020.06.002.

101. Vojácková, P.; Michalska, L.; Necas, M.; Shcherbakov, D.; Bottger, E. C.; Sponer, J.; Sponer, J. E.; Svenda, J. Stereocontrolled Synthesis of (-)-Bactobolin A. Journal of the American Chemical Society 2020, 142 (16), 7306-7311. DOI: 10.1021/jacs.0c01554.

102. Cassone, G.; Saija, F.; Sponer, J.; Sponer, J. E.; Jiménez-Escobar, A.; Ciaravella, A.; Cecchi-Pestellini, C. Atomistic simulations of the free-energy landscapes of interstellar chemical reactions: the case of methyl isocyanate. Monthly Notices of the Royal Astronomical Society 2021, 504 (2), 1565-1570. DOI: 10.1093/mnras/stab958.

103. Costanzo, G.; Sponer, J. E.; Sponer, J.; Cirigliano, A.; Benedetti, P.; Giliberti, V.; Polito, R.; Di Mauro, E. Sustainability and Chaos in the Abiotic Polymerization of 3′,5′ Cyclic Guanosine Monophosphate: The Role of Aggregation. Chemsystemschem 2021, 3 (1). DOI: 10.1002/syst.202000011.

104. Ferus, M.; Cassone, G.; Táborsky, V.; Heays, A.; Petera, L.; Knízek, A.; Kalvoda, T.; Bousa, M.; Sponer, J.; Sponer, J. E.; et al. Thermal Decomposition of Cocaine and Methamphetamine Investigated by Infrared Spectroscopy and Quantum Chemical Simulations. Acs Omega 2021, 6 (22), 14447-14457. DOI: 10.1021/acsomega.1c01325.

105. Sponer, J. E.; Di Mauro, E.; Sponer, J. Reconciling the Genetics-first and Metabolism-first Scenarios of the Origin of Life: Cyclic GMP as the Seed of Life; 2021.

106. Sponer, J. E.; Sponer, J. Insoluble organic matter-an "organic" cradle of life Comment on the paper "Insoluble organic matter in chondrites: Archetypal melanin-like PAH-based multifunctionality at the origin of life?" by Marco d'Ischia et al. Physics of Life Reviews 2021, 38, 135-136. DOI: 10.1016/j.plrev.2021.05.003.

107. Sponer, J. E.; Sponer, J.; Vyravsky, J.; Sedo, O.; Zdráhal, Z.; Costanzo, G.; Di Mauro, E.; Wunnava, S.; Braun, D.; Matyásek, R.; et al. Non-Enzymatic, Template-Free Polymerization of 3',5' Cyclic Guanosine Monophosphate on Mineral Surfaces. Chemsystemschem 2021, 3 (6). DOI: 10.1002/syst.202100017.

108. Wunnava, S.; Dirscherl, C. F.; Vyravsky, J.; Kovarík, A.; Matyásek, R.; Sponer, J.; Braun, D.; Sponer, J. E. Acid-Catalyzed RNA-Oligomerization from 3',5'-cGMP. Chemistry-a European Journal 2021, 27 (70), 17581-17585. DOI: 10.1002/chem.202103672.

109. Amante, G.; Sponer, J. E.; Sponer, J.; Saija, F.; Cassone, G. A Computational Quantum-Based Perspective on the Molecular Origins of Life's Building Blocks. Entropy 2022, 24 (8). DOI: 10.3390/e24081012.

110. Cassone, G.; Sponer, J.; Sponer, J. E.; Saija, F. Electrofreezing of Liquid Ammonia. Journal of Physical Chemistry Letters 2022, 13 (42), 9889-9894. DOI: 10.1021/acs.jpclett.2c02576.

111. Ferus, M.; Knizek, A.; Petera, L.; Pastorek, A.; Hrncirova, J.; Jankovic, L.; Ivanek, O.; Sponer, J.; Krivkova, A.; Saeidfirozeh, H.; et al. Formamide-Based Post-impact Thermal Prebiotic Synthesis in Simulated Craters: Intermediates, Products and Mechanism. Frontiers in Astronomy and Space Sciences 2022, 9. DOI: 10.3389/fspas.2022.882145.

112. Coulon, R.; Papouskova, B.; Mohammadi, E.; Otyepka, M.; Wunnava, S.; Sponer, J.; Sponer, J. E. Prebiotic Synthesis of 3',5'-Cyclic Adenosine and Guanosine Monophosphates through Carbodiimide-Assisted Cyclization. Chembiochem 2023, 24 (24). DOI: 10.1002/cbic.202300510.

113. Dass, A. V.; Wunnava, S.; Langlais, J.; von der Esch, B.; Krusche, M.; Ufer, L.; Chrisam, N.; Dubini, R. C. A.; Gartner, F.; Angerpointner, S.; et al. RNA Oligomerisation without Added Catalyst from 2',3'-Cyclic Nucleotides by Drying at Air-Water Interfaces. Chemsystemschem 2023, 5 (1). DOI: 10.1002/syst.202200026.

114. Sponer, J. E.; Klouzek, J.; Vyravsky, J.; Wunnava, S.; Scheu, B.; Braun, D.; Mojzsis, S. J.; Palacky, J.; Vorlícková, M.; Sponer, J.; et al. Influence of Silicate Rock Glass Compositions on the Efficacy of Prebiotic RNA Polymerization Reactions: The Case of 3',5' Cyclic Guanosine Monophosphate. Chemsystemschem 2023, 5 (5). DOI: 10.1002/syst.202300016.

115. Sponer, J. E.; Sponer, J.; Vyravsky, J.; Matyasek, R.; Kovarik, A.; Dudziak, W.; Slepokura, K. Crystallization as a selection force at the polymerization of nucleotides in a prebiotic context. Iscience 2023, 26 (9). DOI: 10.1016/j.isci.2023.107600.