References
- [1] Alder B. J. and Wainwright T. E., Studies in molecular dynamics. I. General method, The Journal of Chemical Physics, vol. 31, pp. 459–466, 1959.10.1063/1.1730376
- [2] Aylward N. and Bofinger N., The reactions of methanimine and cyanogen with carbon monoxide in prebiotic molecular evolution on earth., Origins of life and evolution of the biosphere : the journal of the International Society for the Study of the Origin of Life, vol. 31, pp. 481–500, 2001.10.1023/A:1012702913934
- [3] Aylward N. and Bofinger N., Possible origin for porphin derivatives in prebiotic chemistry-a computational study., Origins of life and evolution of the biosphere : the journal of the International Society for the Study of the Origin of Life, vol. 35, pp. 345–68, 2005.10.1007/s11084-005-2044-x16228648
- [4] Aylward N. and Bofinger N., A plausible prebiotic synthesis of pyridoxal phosphate: vitamin B6 - a computational study., Biophysical chemistry, vol. 123, pp. 113–21, 2006.10.1016/j.bpc.2006.04.01416730878
- [5] Barone V., Biczysko M. and Puzzarini C., Quantum Chemistry Meets Spectroscopy for Astrochemistry: Increasing Complexity toward Prebiotic Molecules., Accounts of chemical research, vol. 48, pp. 1413–22, 2015.10.1021/ar5003285
- [6] Barucci M. A. et al., MarcoPolo-R near earth asteroid sample return mission, Experimental Astronomy, vol. 33, pp. 645–684, 2012.10.1007/s10686-011-9231-8
- [7] Błazewicz J., Formanowicz P., Guinand F. and Kasprzak M., A heuristic managing errors for DNA sequencing., Bioinformatics (Oxford, England), vol. 18, pp. 652–60, 2002.10.1093/bioinformatics/18.5.65212050060
- [8] Born M. and Oppenheimer R., Zur Quantentheorie der Molekeln, Annalen der Physik, vol. 389, pp. 457–484, 1927.10.1002/andp.19273892002
- [9] Burns L. A., Vázquez-Mayagoitia Á., Sumpter B. G. and Sherrill C. D., Density-functional approaches to noncovalent interactions: A comparison of dispersion corrections (DFT-D), exchange-hole dipole moment (XDM) theory, and specialized functionals, Journal of Chemical Physics, vol. 134, 2011.10.1063/1.354597121361527
- [10] Bussi G. and Branduardi D., Free-Energy Calculations with Metadynamics: Theory and Practice, in pp. 1–49, John Wiley & Sons, Ltd, 2015. doi:10.1002/9781118889886.ch1.10.1002/9781118889886.ch1
- [11] Car R. and Parrinello M., Unified Approach for Molecular Dynamics and Density-Functional Theory, Physical Review Letters, vol. 55, pp. 2471–2474, 1985.10.1103/PhysRevLett.55.2471
- [12] Carota E., Botta G., Rotelli L., Di Mauro E. and Saladino R., Current Advances in Prebiotic Chemistry Under Space Conditions, Current Organic Chemistry, vol. 19, pp. 1963–1979, 2015.10.2174/1385272819666150622175143
- [13] Carrascoza Mayén J. F., Rydzewski J., Szostak N., Blazewicz J. and Nowak W., Prebiotic Soup Components Trapped in Montmorillonite Nanoclay Form New Molecules: Car-Parrinello Ab Initio Simulations., Life (Basel, Switzerland), vol. 9, 2019.10.3390/life9020046661712531167366
- [14] Casalini T. et al., Molecular Modeling for Nanomaterial-Biology Interactions: Opportunities, Challenges, and Perspectives., Frontiers in bioengineering and biotechnology, vol. 7, pp. 268, 2019.10.3389/fbioe.2019.00268681149431681746
- [15] Chyba C. and Sagan C., Endogenous production, exogenous delivery and impact-shock synthesis of organic molecules: An inventory for the origins of life, Nature, vol. vol. 355 pp. 125–132, 1992.10.1038/355125a011538392
- [16] Coveney P. V., Swadling J. B., Wattis J. A. D. and Greenwell H. C., Theory, modelling and simulation in origins of life studies, Chemical Society Reviews, vol. vol. 41 pp. 5430–5446, 2012.10.1039/c2cs35018a
- [17] Cygan R. T., Romanov V. N. and Myshakin E. M., Molecular Simulation of Carbon Dioxide Capture by Montmorillonite Using an Accurate and Flexible Force Field, The Journal of Physical Chemistry C, vol. 116, pp. 13079–13091, 2012.10.1021/jp3007574
- [18] Darve E. and Pohorille A., Calculating free energies using average force, Journal of Chemical Physics, vol. 115, pp. 9169–9183, 2001.10.1063/1.1410978
- [19] Davis W. L. and McKay C. P., Origins of life: A comparison of theories and application to mars, Origins of Life and Evolution of the Biosphere, vol. 26, pp. 61–73, 1996.10.1007/BF018081608920171
- [20] Espinosa-García J. and Corchado J. C., Reliability of the Single-Point Calculation Technique at Characteristic Points of the Potential Energy Surface, J. Phys. Chem, vol. vol. 99 https://pubs.acs.org/sharingguidelines (1995).10.1021/j100021a026
- [21] Ferris J. P., Catalysis and Prebiotic Synthesis, Reviews in Mineralogy and Geochemistry, vol. 59, pp. 187–210, 2005.10.2138/rmg.2005.59.8
- [22] Ferris J. P., Hill A. R., Liu R. and Orgel L. E., Synthesis of long prebiotic oligomers on mineral surfaces, Nature, vol. 381, pp. 59–61, 1996.10.1038/381059a08609988
- [23] Ferus M. et al., High-energy chemistry of formamide: A simpler way for nucleobase formation, Journal of Physical Chemistry A, vol. 118, pp. 719–736, 2014.10.1021/jp411415p24437678
- [24] Ferus M. et al., Formation of nucleobases in a Miller-Urey reducing atmosphere., Proceedings of the National Academy of Sciences of the United States of America, vol. 114, pp. 4306–4311, 2017.10.1073/pnas.1700010114
- [25] Fock V., Näherungsmethode zur Lösung des quantenmechanischen Mehrkörperproblems, Zeitschrift für Physik, vol. 61, pp. 126–148, 1930.10.1007/BF01340294
- [26] Gallet G. A., Pietrucci F. and Andreoni W., Bridging Static and Dynamical Descriptions of Chemical Reactions: An ab Initio Study of CO 2 Interacting with Water Molecules, Journal of Chemical Theory and Computation, vol. 8, pp. 4029–4039, 2012.10.1021/ct300581n
- [27] Ghoshal S., Pramanik A., Biswas S. and Sarkar P., CH 3 NO as a potential intermediate for early atmospheric HCN: a quantum chemical insight, Physical Chemistry Chemical Physics, vol. 21, pp. 25126–25138, 2019.10.1039/C9CP03874D
- [28] Goldman N., Reed E. J., Fried L. E., William Kuo I.-F. and Maiti A., Synthesis of glycine-containing complexes in impacts of comets on early Earth, Nature Chemistry, vol. 2, pp. 949–954, 2010.10.1038/nchem.82720966951
- [29] Grimme S., Bannwarth C. and Shushkov P., A Robust and Accurate Tight-Binding Quantum Chemical Method for Structures, Vibrational Frequencies, and Noncovalent Interactions of Large Molecular Systems Parametrized for All spd-Block Elements (Z = 1-86)., Journal of chemical theory and computation, vol. 13, pp. 1989–2009, 2017.10.1021/acs.jctc.7b00118
- [30] Hartree D. R., The Wave Mechanics of an Atom with a Non-Coulomb Central Field Part II Some Results and Discussion, Mathematical Proceedings of the Cambridge Philosophical Society, vol. 24, pp. 111–132, 1928.10.1017/S0305004100011920
- [31] Huber C. and Wächtershäuser G., Peptides by activation of amino acids with CO on (Ni,Fe)S surfaces: implications for the origin of life., Science (New York, N.Y.), vol. 281, pp. 670–2, 1998.10.1126/science.281.5377.670
- [32] Islam S. and Powner M. W., Prebiotic Systems Chemistry: Complexity Overcoming Clutter, Chem, vol. 2, pp. 470–501, 2017.10.1016/j.chempr.2017.03.001
- [33] Jamialahmadi M. et al., Molecular structure and vibrational assignments of bis(4-aminopent-3-en-2- onato)copper(II): A detailed density functional theoretical study, Journal of Molecular Structure, vol. 985, pp. 139–147, 2011.10.1016/j.molstruc.2010.10.034
- [34] Kawamura K., Konagaya N. and Maruoka Y., Enhancement and inhibitory activities of minerals for alanine oligopeptide elongation under hydrothermal conditions, Astrobiology, vol. 18, pp. 1403–1413, 2018.10.1089/ast.2017.1732
- [35] Kühne T. D., Krack M., Mohamed F. R. and Parrinello M., Efficient and accurate carparrinello-like approach to born-oppenheimer molecular dynamics, Physical Review Letters, vol. 98, pp. 066401, 2007.10.1103/PhysRevLett.98.066401
- [36] Laio A. and Parrinello M., Escaping free-energy minima, Proceedings of the National Academy of Sciences of the United States of America, vol. 99, pp. 12562–12566, 2002.10.1073/pnas.202427399
- [37] Laporte S. et al., Strong electric fields at a prototypical oxide/water interface probed by ab initio molecular dynamics: MgO(001), Physical Chemistry Chemical Physics, vol. 17, pp. 20382–20390, 2015.10.1039/C5CP02097B
- [38] Lelimousin M., Limongelli V. and Sansom M. S. P., Conformational Changes in the Epidermal Growth Factor Receptor: Role of the Transmembrane Domain Investigated by Coarse-Grained MetaDynamics Free Energy Calculations., Journal of the American Chemical Society, vol. 138, pp. 10611–22, 2016.10.1021/jacs.6b05602
- [39] Liu P., Kim B., Friesner R. A. and Berne B. J., Replica exchange with solute tempering: A method for sampling biological systems in explicit water, Proceedings of the National Academy of Sciences of the United States of America, vol. 102, pp. 13749–13754, 2005.10.1073/pnas.0506346102
- [40] Maragliano L. and Vanden-Eijnden E., A temperature accelerated method for sampling free energy and determining reaction pathways in rare events simulations, Chemical Physics Letters, vol. 426, pp. 168–175, 2006.10.1016/j.cplett.2006.05.062
- [41] Mariscal C. et al., Hidden Concepts in the History and Philosophy of Origins-of-Life Studies: a Workshop Report, Origins of Life and Evolution of Biospheres, vol. vol. 49 pp. 111–145, 2019.10.1007/s11084-019-09580-x
- [42] Marrink S. J., Risselada H. J., Yefimov S., Tieleman D. P. and De Vries A. H., The MARTINI force field: Coarse grained model for biomolecular simulations, Journal of Physical Chemistry B, vol. 111, pp. 7812–7824, 2007.10.1021/jp071097f
- [43] Marrink S. J. et al., Computational Modeling of Realistic Cell Membranes., Chemical reviews, vol. 119, pp. 6184–6226, 2019.10.1021/acs.chemrev.8b00460
- [44] Marsili S., Barducci A., Chelli R., Procacci P. and Schettino V., Self-healing umbrella sampling: A non-equilibrium approach for quantitative free energy calculations, Journal of Physical Chemistry B, vol. 110, pp. 14011–14013, 2006.10.1021/jp062755j
- [45] Martínez-Bachs B. and Rimola A., Prebiotic Peptide Bond Formation Through Amino Acid Phosphorylation. Insights from Quantum Chemical Simulations., Life (Basel, Switzerland), vol. 9, 2019.10.3390/life9030075
- [46] Martins Z., Price M. C., Goldman N., Sephton M. A. and Burchell M. J., Shock synthesis of amino acids from impacting cometary and icy planet surface analogues, Nature Geoscience, vol. 6, pp. 1045–1049, 2013.10.1038/ngeo1930
- [47] Miller S. L., A Production of Amino Acids Under Possible Primitive Earth Conditions, Science, vol. 117, pp. 528 LP – 529, 1953.10.1126/science.117.3046.528
- [48] Nagendrappa G., Organic synthesis using clay and clay-supported catalysts, Applied Clay Science, vol. vol. 53 pp. 106–138, 2011.10.1016/j.clay.2010.09.016
- [49] Oro J., Chemical evolution and the origin of life., Advances in space research : the official journal of the Committee on Space Research (COSPAR), vol. 3, pp. 77–94, 1983.10.1016/0273-1177(83)90044-3
- [50] Pérez-Villa A. et al., Synthesis of RNA Nucleotides in Plausible Prebiotic Conditions from ab Initio Computer Simulations., The journal of physical chemistry letters, vol. 9, pp. 4981–4987, 2018.10.1021/acs.jpclett.8b02077
- [51] Pérez-Villa A., Pietrucci F. and Saitta A. M., Prebiotic chemistry and origins of life research with atomistic computer simulations, Physics of Life Reviews, 2018 doi:10.1016/j.plrev.2018.09.004.10.1016/j.plrev.2018.09.00430243920
- [52] Ranjan S., Todd Z. R., Sutherland J. D. and Sasselov D. D., Sulfidic Anion Concentrations on Early Earth for Surficial Origins-of-Life Chemistry, 2018 doi:10.1089/ast.2017.1770.10.1089/ast.2017.1770
- [53] Rimola A. et al., Can Formamide Be Formed on Interstellar Ice? An Atomistic Perspective, ACS Earth and Space Chemistry, vol. 2, pp. 720–734, 2018.10.1021/acsearthspacechem.7b00156
- [54] Rimola A., Sodupe M. and Ugliengo P., Role of Mineral Surfaces in Prebiotic Chemical Evolution. In Silico Quantum Mechanical Studies., Life (Basel, Switzerland), vol. 9, 2019.10.3390/life9010010
- [55] Rosso L., Mináry P., Zhu Z. and Tuckerman M. E., On the use of the adiabatic molecular dynamics technique in the calculation of free energy profiles, Journal of Chemical Physics, vol. 116, pp. 4389–4402, 2002.10.1063/1.1448491
- [56] Saitta A. M. and Saija F., Miller experiments in atomistic computer simulations, Proceedings of the National Academy of Sciences, vol. 111, pp. 13768–13773, 2014.
- [57] Saitta A. M. and Saija F., Miller experiments in atomistic computer simulations, Proceedings of the National Academy of Sciences of the United States of America, vol. 111, pp. 13768–13773, 2014.10.1073/pnas.1402894111
- [58] Salomon-Ferrer R., Case D. A. and Walker R. C., An overview of the Amber biomolecular simulation package, Wiley Interdisciplinary Reviews: Computational Molecular Science, vol. 3, pp. 198–210, 2013.10.1002/wcms.1121
- [59] Schrödinger E., What is life? The physical aspect of the living cell and mind, Cambridge University Press Cambridge, 1944.
- [60] Schütt K. T., Gastegger M., Tkatchenko A., Müller K.-R. and Maurer R. J., Unifying machine learning and quantum chemistry with a deep neural network for molecular wavefunctions, Nature Communications, vol. 10, pp. 5024, 2019.10.1038/s41467-019-12875-2
- [61] Senanayake S. D. and Idriss H., Photocatalysis and the origin of life: Synthesis of nucleoside bases from formamide on TiO2(001) single surfaces, Proceedings of the National Academy of Sciences, vol. 103, pp. 1194–1198, 2006.10.1073/pnas.0505768103
- [62] Smith M. D., Rao J. S., Segelken E. and Cruz L., Force-Field Induced Bias in the Structure of Aβ 21–30 : A Comparison of OPLS, AMBER, CHARMM, and GROMOS Force Fields, Journal of Chemical Information and Modeling, vol. 55, pp. 2587–2595, 2015.10.1021/acs.jcim.5b00308
- [63] Sowerby S. J. and Heckl W. M., The role of self-assembled monolayers of the purine and pyrimidine bases in the emergence of life, Origins of Life and Evolution of the Biosphere, vol. 28, pp. 283–310, 1998.10.1023/A:1006570726326
- [64] Šponer J. E. et al., 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, vol. vol. 18 pp. 20047–20066, 2016.10.1039/C6CP00670A
- [65] Stanton J. F. and Bartlett R. J., The equation of motion coupled-cluster method. A systematic biorthogonal approach to molecular excitation energies, transition probabilities, and excited state properties, The Journal of Chemical Physics, vol. 98, pp. 7029–7039, 1993.10.1063/1.464746
- [66] Stirling A., Rozgonyi T., Krack M. and Bernasconi M., Prebiotic NH3 Formation: Insights from Simulations, Inorganic Chemistry, vol. 55, pp. 1934–1939, 2016.10.1021/acs.inorgchem.5b02911
- [67] Sugita Y. and Okamoto Y., Replica-exchange molecular dynamics method for protein folding, Chemical Physics Letters, vol. 314, pp. 141–151, 1999.10.1016/S0009-2614(99)01123-9
- [68] Szostak N., Wasik S. and Blazewicz J., Understanding Life: A Bioinformatics Perspective, in European Review, vol. vol. 25 pp. 231–245, Cambridge University Press, 2017.10.1017/S1062798716000570
- [69] Tabacchi G., Fabbiani M., Mino L., Martra G. and Fois E., The Case of Formic Acid on Anatase TiO2 (101): Where is the Acid Proton?, Angewandte Chemie (International ed. in English), vol. 58, pp. 12431–12434, 2019.10.1002/anie.201906709
- [70] Takahagi W. et al., Peptide Synthesis under the Alkaline Hydrothermal Conditions on Enceladus, ACS Earth and Space Chemistry, vol. 3, pp. 2559–2568, 2019.10.1021/acsearthspacechem.9b00108
- [71] Torrie G. M. and Valleau J. P., Nonphysical sampling distributions in Monte Carlo free-energy estimation: Umbrella sampling, Journal of Computational Physics, vol. 23, pp. 187–199, 1977.10.1016/0021-9991(77)90121-8
- [72] VandeVondele J. and Rothlisberger U., Canonical adiabatic free energy sampling (CAFES): A novel method for the exploration of free energy surfaces, Journal of Physical Chemistry B, vol. 106, pp. 203–208, 2002.10.1021/jp013346k
- [73] Viani A., Gualtieri A. F. and Artioli G., The nature of disorder in montmorillonite by simulation of X-ray powder patterns, American Mineralogist, vol. 87, pp. 966–975, 2002.10.2138/am-2002-0720
- [74] Walker M., Harvey A. J. A., Sen A. and Dessent C. E. H., Performance of M06, M06-2X, and M06-HF density functionals for conformationally flexible anionic clusters: M06 functionals perform better than B3LYP for a model system with dispersion and ionic hydrogen-bonding interactions., The journal of physical chemistry. A, vol. 117, pp. 12590–600, 2013.10.1021/jp408166m
- [75] Xu J. et al., A prebiotically plausible synthesis of pyrimidine β-ribonucleosides and their phosphate derivatives involving photoanomerization., Nature chemistry, vol. 9, pp. 303–309, 2017.10.1038/nchem.2664557653228338689
- [76] Yang G., Neretnieks I. and Holmboe M., Atomistic simulations of cation hydration in sodium and calcium montmorillonite nanopores, The Journal of Chemical Physics, vol. 147, pp. 084705, 2017.10.1063/1.4992001
- [77] Zaia D. A. M., Zaia C. T. B. V. and De Santana H., Which amino acids should be used in prebiotic chemistry studies?, Origins of Life and Evolution of Biospheres, vol. vol. 38 pp. 469–488, 2008.10.1007/s11084-008-9150-518925425
- [78] Zhao Y. and Truhlar D. G., Density functionals with broad applicability in chemistry., Accounts of chemical research, vol. 41, pp. 157–167, 2008.10.1021/ar700111a18186612