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Cover
Prebiotic Chemistry and Life's Origin
Preface
Acknowledgments
Contents
Chapter 1 - Origin of the Universe and Planetary Systems
1.1 Short History of the Universe Before Primordial Nucleosynthesis
1.2 Primordial Nucleosynthesis
1.3 Recombination
1.4 Dark Ages and First Molecules
1.5 First Objects, Reionization and Reheating of Matter
1.6 Star Formation and Astrochemistry
1.7 From Molecular Clouds to Star Forming Cores
1.8 Young Stellar Objects and Their Molecular Inventories
1.9 Chemical Links Between Natal Clouds and Star-forming Planets
1.10 Early Stages of Planet Formation: Planetesimals
1.11 The Formation of Terrestrial Planets
1.12 The Formation of Giant Planets
1.13 Planet Migration
1.14 Conclusion
List of Abbreviations
References
Chapter 2 - Geoastronomy: Rocky Planets as the Lavoisier-Lomonosov Bridge from the Non-living to the Living World†
2.1 Introduction
2.1.1 Follow the (Cosmo)Chemistry
2.1.2 Guideposts for Life
2.1.2.1 Miller-Urey vs. Geochemistry
2.1.2.2 Darwin Ponds
2.1.2.3 Late Accretion
2.1.2.4 Early Earth vs. the RNA World
2.2 The Lavoisier-Lomonosov Bridge on Small Rocky Planets Around Other Stars
2.2.1 Modelling Terrestrial-type Exoplanet Compositions
2.2.1.1 Planetary Diversity
2.2.1.2 Planetary Internal Heat Production
2.2.2 Composition of the Star
2.2.2.1 Cosmochemical Inheritance
2.2.3 Chemical Evolution of the Galaxy Expressed in Planets
2.2.3.1 Elemental Feedstocks to Molecular Clouds that Form Star-Planet Systems
2.2.3.2 Synthesis and Concentration Evolution of the Rock-forming Elements
2.2.3.3 56-Iron Evolution in the Galaxy
2.2.3.4 The Special Case of 40K
2.2.4 Lingering Problems
2.2.4.1 GCE Helps Us Understand the Compositions of Planets, Not Define Them.
2.2.4.2 Making Sense of Likely vs. Unlikely Characteristics of Rocky Exoplanets
2.3 Geodynamical Inferences
2.3.1 Iron Availability
2.3.2 Different (Exo)Planet Compositions Lead to Different Geophysical States
2.3.2.1 Problems with Direct Scaling of Solar to Planetary Abundances
2.3.3 Bulk Exoplanet Compositions
2.3.3.1 Quantitative Abundances from Devolatilization
2.3.4 Bulk Chemistry and Dynamics
2.3.4.1 (Exo)mantle Viscosity
2.3.4.2 (Exo)mantle Oxygen Fugacity
2.3.5 Remaining Limitations
2.4 Conclusions and the New Field of Geoastronomy
Acknowledgements
References
Chapter 3 - First Steps of Prebiotic Chemistry Catalyzed by Minerals and Metals
3.1 Introduction
3.2 Emergence of Simple Molecules
3.2.1 The Atmospheric Conundrum
3.2.2 Prebiotic Reaction Conditions
3.2.3 The Formation of Hydrogen
3.2.4 The Formation of Ammonia
3.2.5 The Formation of Methane
3.2.6 Fischer-Tropsch-type Reactions
3.3 Emergence of Complex Molecules
3.3.1 Reactions Starting From Hydrogen Cyanide and Aminonitriles
3.3.2 Formose Reaction
3.3.2.1 Aldoses and Ketoses
3.3.2.2 The Activation of Formaldehyde
3.3.2.3 The Basic Aldol Reaction
3.3.2.4 The Cannizzaro Reaction
3.3.2.5 The Formose Reaction Network
3.3.3 Mineral Catalyzed Monosaccharide Formation
3.3.3.1 The Formose Reaction Under Prebiotically Plausible Conditions
3.3.4 Amino Acids
3.3.4.1 The Strecker Synthesis
3.3.4.2 Amino Acids as Organocatalysts
3.3.5 Towards RNA and DNA
3.4 Iron in Prebiotic Synthesis
3.4.1 Hydrothermal Systems
3.4.2 Wächtershäuser Iron Sulfur Clusters
3.5 Emergence of Catalytic Systems
3.5.1 Photocatalytic Systems
3.5.2 Chemical Evolution of Organocatalytic Systems
Acknowledgements
References
Chapter 4 - Prebiotic Condensing Agents
4.1 Introduction.
4.2 C-N Based Condensing Agents: Cyanamide, Dicyandiamide and Urea
4.2.1 Cyanamide
4.2.2 Cyanamide as Condensing Agent
4.2.3 Cyanamide as Source of Carbons for the Prebiotic Synthesis of Nucleotide Precursors and Other Plausible Prebiotic Molecules...
4.2.4 Dicyandiamide
4.2.5 Urea
4.3 Other Carbon/Nitrogen Based Condensing Agents
4.3.1 Dicyanamide and Sodium Dicyanamide
4.3.2 Cyanate, Cyanogen and (cis) Hydrogen-Cyanide Tetramer
4.4 Phosphorus Based Condensing Agents
4.4.1 Condensed Phosphates
4.4.2 Diamidophosphate
4.5 Other Condensing Agents for Nucleotides
4.6 Conclusion
Acknowledgements
References
Chapter 5 - Soft Matter Science in Prebiotic Chemistry and the Origins of Life
5.1 Introduction
5.2 Problems of Selection in Prebiotic Chemistry
5.2.1 The Vast Chemical Landscape
5.2.2 Non-biological Compounds With Potential Value to Prebiotic Chemistry
5.2.2.1 Peptide Nucleic Acid (PNA)
5.2.2.2 Depsipeptides
5.2.2.3 Polyesters
5.3 Water and the Origins of Life
5.4 Gels and Their Possible Links to the Origins of Life
5.5 Summary
List of Abbreviations
References
Chapter 6 - The Miller-Urey Experiment's Impact on Modern Approaches to Prebiotic Chemistry
6.1 Introduction
6.2 The Nature of the Primitive Environment
6.3 Interpretation of the Results of the Experiment
6.4 Was There Ever a Reducing Atmosphere
6.5 Connection to Extraterrestrial Materials
6.6 Conclusions
Acknowledgements
References
Chapter 7 - From Amino Acids to Peptides before the Coming of Ribosomes
7.1 Introduction
7.2 Direct Amino Acid Condensation Reactions
7.3 Nitrogen and Phosphorus Condensing Agents
7.4 Peptides From Esters, Thioesters and Thioacids
7.5 Peptides From Nitriles
7.6 Amino Acid N-Carboxyanhydrides (NCAs)
7.7 Symmetry Breaking.
7.8 Ancestral Peptides
7.9 A Tentative Conclusion
References
Chapter 8 - Prebiotic Chemistry of Nucleobases and Nucleotides
8.1 Introduction to the Prebiotic Chemistry of Nucleic Acids
8.2 Contextualizing the Knowledge upon the Origin of Biological Nucleic Acids
8.2.1 Ribocentric and Pre-RNA Hypotheses for the Prebiotic Origin of Nucleic Acids
8.2.2 The Phosphorylation and Polymerization Problems
8.2.3 DNA: Prebiotic or Biological Product
8.3 Simple Prebiotic Precursors and the Historical and Central Role of Urea
8.4 Prebiotic Syntheses of Pyrimidines and the Role of S-Triazines in Chemical Evolution
8.5 The Prebiotic Synthesis of Purines
8.6 Urea and Nucleobases in Space and Astrobiology Exploration
8.7 Prebiotic Chemistry of Hydantoins: Integration with Pyrimidines
8.8 Prebiotic Phosphorylation and Phosphate Mobilization
8.8.1 A Urea-based Scenario for the Phosphorylation Problem
8.8.2 Proposed Mechanisms for Urea-driven Phosphorylation
8.8.3 Eutectics and Urea-rich Solvents in Prebiotic Phosphorylation and Mineralogy
8.9 Conclusion
Acknowledgements
References
Chapter 9 - Prebiotic Amphiphiles: The Systems Chemistry Perspective
9.1 Introduction: The Prebiotic Systems Chemistry Perspective
9.2 Synthesis of Phospholipids Under Abiotic Conditions
9.2.1 Hydrothermal Vents, Hydrothermal Fields and Fluctuating Hydrothermal Pools
9.2.2 Phospholipid Chain Precursors
9.2.3 Prebiotic Origin of Glycerol and Glycerol Precursors
9.2.4 Prebiotic Synthesis of Glycerophosphates
9.3 Prebiotic Synthesis of Complete and Incomplete Phospholipids Esters
9.3.1 Incomplete Lipids (ILs)
9.3.2 Complete Lipids (CLs)
9.3.3 Alternative Prebiotic Synthesis of Phospholipid Esters
9.4 Prebiotic Synthesis of Phospholipid Ethers.
9.5 The Unsolved Problem of Symmetry Breaking of Phospholipids: State of the Art
9.6 Conclusion
References
Chapter 10 - The Handy Formamide Model System for Prebiotic Chemistry
10.1 The Need for a Multiple-products Model
10.2 A Model Based on the Properties of Formamide
10.2.1 Properties of Formamide
10.2.2 Formation of Formamide, in Space and on Earth
10.3 In Order to Have Evolution a Complex Environment is Needed
10.3.1 The Level of Complexity Reached by Organic Compounds in Space
10.3.2 The Need for Complexity
10.3.3 The Complexity Reached in Laboratory Syntheses of Organic Compounds in Planet Earth Conditions
10.3.4 Terrestrial Catalysts
10.3.5 Catalytic Activity of Meteorites
10.3.6 Reactions in the Presence of Water
10.3.7 Geochemical Scenarios Based on Serpentinization-related Chemistry
10.4 Which Level of Complexity can be Reached by the Formamide System
10.4.1 The Carboxylic Acids in Ordered Series
10.4.2 The Tenuous but Continuous Path to RNA
10.5 Conclusion
References
Chapter 11 - How did the Proteome Emerge From Pre-biotic Chemistry
11.1 Introduction
11.2 Translation Substantially Amplifies Gene Functionality
11.3 A Bidirectional Aminoacyl-tRNA Synthetase Gene Provided the Initial Differentiation into Two Amino Acid/Adaptor RNA Cognate...
11.3.1 Abiotic Polymer Assembly: Stereochemical Complementarity and the Probable Cooperation of Polypeptides and Polynucleotides
11.3.2 The Bidirectional Rodin-Ohno Gene Encoding Ancestral Class I and II Aminoacyl-tRNA Synthetases on Opposite Strands Underl...
11.3.3 Amino Acid Physical Chemistry Determined aaRS Substrate Recognition and the Operational RNA Code
11.3.4 The Earliest Assignment Catalysts had to Obey Protein Folding Rules
11.4 The First Coded Polypeptides were Quasispecies.
11.4.1 Secondary Structure, "Closed Loops," and Modules.
Prebiotic Chemistry and Life's Origin
Preface
Acknowledgments
Contents
Chapter 1 - Origin of the Universe and Planetary Systems
1.1 Short History of the Universe Before Primordial Nucleosynthesis
1.2 Primordial Nucleosynthesis
1.3 Recombination
1.4 Dark Ages and First Molecules
1.5 First Objects, Reionization and Reheating of Matter
1.6 Star Formation and Astrochemistry
1.7 From Molecular Clouds to Star Forming Cores
1.8 Young Stellar Objects and Their Molecular Inventories
1.9 Chemical Links Between Natal Clouds and Star-forming Planets
1.10 Early Stages of Planet Formation: Planetesimals
1.11 The Formation of Terrestrial Planets
1.12 The Formation of Giant Planets
1.13 Planet Migration
1.14 Conclusion
List of Abbreviations
References
Chapter 2 - Geoastronomy: Rocky Planets as the Lavoisier-Lomonosov Bridge from the Non-living to the Living World†
2.1 Introduction
2.1.1 Follow the (Cosmo)Chemistry
2.1.2 Guideposts for Life
2.1.2.1 Miller-Urey vs. Geochemistry
2.1.2.2 Darwin Ponds
2.1.2.3 Late Accretion
2.1.2.4 Early Earth vs. the RNA World
2.2 The Lavoisier-Lomonosov Bridge on Small Rocky Planets Around Other Stars
2.2.1 Modelling Terrestrial-type Exoplanet Compositions
2.2.1.1 Planetary Diversity
2.2.1.2 Planetary Internal Heat Production
2.2.2 Composition of the Star
2.2.2.1 Cosmochemical Inheritance
2.2.3 Chemical Evolution of the Galaxy Expressed in Planets
2.2.3.1 Elemental Feedstocks to Molecular Clouds that Form Star-Planet Systems
2.2.3.2 Synthesis and Concentration Evolution of the Rock-forming Elements
2.2.3.3 56-Iron Evolution in the Galaxy
2.2.3.4 The Special Case of 40K
2.2.4 Lingering Problems
2.2.4.1 GCE Helps Us Understand the Compositions of Planets, Not Define Them.
2.2.4.2 Making Sense of Likely vs. Unlikely Characteristics of Rocky Exoplanets
2.3 Geodynamical Inferences
2.3.1 Iron Availability
2.3.2 Different (Exo)Planet Compositions Lead to Different Geophysical States
2.3.2.1 Problems with Direct Scaling of Solar to Planetary Abundances
2.3.3 Bulk Exoplanet Compositions
2.3.3.1 Quantitative Abundances from Devolatilization
2.3.4 Bulk Chemistry and Dynamics
2.3.4.1 (Exo)mantle Viscosity
2.3.4.2 (Exo)mantle Oxygen Fugacity
2.3.5 Remaining Limitations
2.4 Conclusions and the New Field of Geoastronomy
Acknowledgements
References
Chapter 3 - First Steps of Prebiotic Chemistry Catalyzed by Minerals and Metals
3.1 Introduction
3.2 Emergence of Simple Molecules
3.2.1 The Atmospheric Conundrum
3.2.2 Prebiotic Reaction Conditions
3.2.3 The Formation of Hydrogen
3.2.4 The Formation of Ammonia
3.2.5 The Formation of Methane
3.2.6 Fischer-Tropsch-type Reactions
3.3 Emergence of Complex Molecules
3.3.1 Reactions Starting From Hydrogen Cyanide and Aminonitriles
3.3.2 Formose Reaction
3.3.2.1 Aldoses and Ketoses
3.3.2.2 The Activation of Formaldehyde
3.3.2.3 The Basic Aldol Reaction
3.3.2.4 The Cannizzaro Reaction
3.3.2.5 The Formose Reaction Network
3.3.3 Mineral Catalyzed Monosaccharide Formation
3.3.3.1 The Formose Reaction Under Prebiotically Plausible Conditions
3.3.4 Amino Acids
3.3.4.1 The Strecker Synthesis
3.3.4.2 Amino Acids as Organocatalysts
3.3.5 Towards RNA and DNA
3.4 Iron in Prebiotic Synthesis
3.4.1 Hydrothermal Systems
3.4.2 Wächtershäuser Iron Sulfur Clusters
3.5 Emergence of Catalytic Systems
3.5.1 Photocatalytic Systems
3.5.2 Chemical Evolution of Organocatalytic Systems
Acknowledgements
References
Chapter 4 - Prebiotic Condensing Agents
4.1 Introduction.
4.2 C-N Based Condensing Agents: Cyanamide, Dicyandiamide and Urea
4.2.1 Cyanamide
4.2.2 Cyanamide as Condensing Agent
4.2.3 Cyanamide as Source of Carbons for the Prebiotic Synthesis of Nucleotide Precursors and Other Plausible Prebiotic Molecules...
4.2.4 Dicyandiamide
4.2.5 Urea
4.3 Other Carbon/Nitrogen Based Condensing Agents
4.3.1 Dicyanamide and Sodium Dicyanamide
4.3.2 Cyanate, Cyanogen and (cis) Hydrogen-Cyanide Tetramer
4.4 Phosphorus Based Condensing Agents
4.4.1 Condensed Phosphates
4.4.2 Diamidophosphate
4.5 Other Condensing Agents for Nucleotides
4.6 Conclusion
Acknowledgements
References
Chapter 5 - Soft Matter Science in Prebiotic Chemistry and the Origins of Life
5.1 Introduction
5.2 Problems of Selection in Prebiotic Chemistry
5.2.1 The Vast Chemical Landscape
5.2.2 Non-biological Compounds With Potential Value to Prebiotic Chemistry
5.2.2.1 Peptide Nucleic Acid (PNA)
5.2.2.2 Depsipeptides
5.2.2.3 Polyesters
5.3 Water and the Origins of Life
5.4 Gels and Their Possible Links to the Origins of Life
5.5 Summary
List of Abbreviations
References
Chapter 6 - The Miller-Urey Experiment's Impact on Modern Approaches to Prebiotic Chemistry
6.1 Introduction
6.2 The Nature of the Primitive Environment
6.3 Interpretation of the Results of the Experiment
6.4 Was There Ever a Reducing Atmosphere
6.5 Connection to Extraterrestrial Materials
6.6 Conclusions
Acknowledgements
References
Chapter 7 - From Amino Acids to Peptides before the Coming of Ribosomes
7.1 Introduction
7.2 Direct Amino Acid Condensation Reactions
7.3 Nitrogen and Phosphorus Condensing Agents
7.4 Peptides From Esters, Thioesters and Thioacids
7.5 Peptides From Nitriles
7.6 Amino Acid N-Carboxyanhydrides (NCAs)
7.7 Symmetry Breaking.
7.8 Ancestral Peptides
7.9 A Tentative Conclusion
References
Chapter 8 - Prebiotic Chemistry of Nucleobases and Nucleotides
8.1 Introduction to the Prebiotic Chemistry of Nucleic Acids
8.2 Contextualizing the Knowledge upon the Origin of Biological Nucleic Acids
8.2.1 Ribocentric and Pre-RNA Hypotheses for the Prebiotic Origin of Nucleic Acids
8.2.2 The Phosphorylation and Polymerization Problems
8.2.3 DNA: Prebiotic or Biological Product
8.3 Simple Prebiotic Precursors and the Historical and Central Role of Urea
8.4 Prebiotic Syntheses of Pyrimidines and the Role of S-Triazines in Chemical Evolution
8.5 The Prebiotic Synthesis of Purines
8.6 Urea and Nucleobases in Space and Astrobiology Exploration
8.7 Prebiotic Chemistry of Hydantoins: Integration with Pyrimidines
8.8 Prebiotic Phosphorylation and Phosphate Mobilization
8.8.1 A Urea-based Scenario for the Phosphorylation Problem
8.8.2 Proposed Mechanisms for Urea-driven Phosphorylation
8.8.3 Eutectics and Urea-rich Solvents in Prebiotic Phosphorylation and Mineralogy
8.9 Conclusion
Acknowledgements
References
Chapter 9 - Prebiotic Amphiphiles: The Systems Chemistry Perspective
9.1 Introduction: The Prebiotic Systems Chemistry Perspective
9.2 Synthesis of Phospholipids Under Abiotic Conditions
9.2.1 Hydrothermal Vents, Hydrothermal Fields and Fluctuating Hydrothermal Pools
9.2.2 Phospholipid Chain Precursors
9.2.3 Prebiotic Origin of Glycerol and Glycerol Precursors
9.2.4 Prebiotic Synthesis of Glycerophosphates
9.3 Prebiotic Synthesis of Complete and Incomplete Phospholipids Esters
9.3.1 Incomplete Lipids (ILs)
9.3.2 Complete Lipids (CLs)
9.3.3 Alternative Prebiotic Synthesis of Phospholipid Esters
9.4 Prebiotic Synthesis of Phospholipid Ethers.
9.5 The Unsolved Problem of Symmetry Breaking of Phospholipids: State of the Art
9.6 Conclusion
References
Chapter 10 - The Handy Formamide Model System for Prebiotic Chemistry
10.1 The Need for a Multiple-products Model
10.2 A Model Based on the Properties of Formamide
10.2.1 Properties of Formamide
10.2.2 Formation of Formamide, in Space and on Earth
10.3 In Order to Have Evolution a Complex Environment is Needed
10.3.1 The Level of Complexity Reached by Organic Compounds in Space
10.3.2 The Need for Complexity
10.3.3 The Complexity Reached in Laboratory Syntheses of Organic Compounds in Planet Earth Conditions
10.3.4 Terrestrial Catalysts
10.3.5 Catalytic Activity of Meteorites
10.3.6 Reactions in the Presence of Water
10.3.7 Geochemical Scenarios Based on Serpentinization-related Chemistry
10.4 Which Level of Complexity can be Reached by the Formamide System
10.4.1 The Carboxylic Acids in Ordered Series
10.4.2 The Tenuous but Continuous Path to RNA
10.5 Conclusion
References
Chapter 11 - How did the Proteome Emerge From Pre-biotic Chemistry
11.1 Introduction
11.2 Translation Substantially Amplifies Gene Functionality
11.3 A Bidirectional Aminoacyl-tRNA Synthetase Gene Provided the Initial Differentiation into Two Amino Acid/Adaptor RNA Cognate...
11.3.1 Abiotic Polymer Assembly: Stereochemical Complementarity and the Probable Cooperation of Polypeptides and Polynucleotides
11.3.2 The Bidirectional Rodin-Ohno Gene Encoding Ancestral Class I and II Aminoacyl-tRNA Synthetases on Opposite Strands Underl...
11.3.3 Amino Acid Physical Chemistry Determined aaRS Substrate Recognition and the Operational RNA Code
11.3.4 The Earliest Assignment Catalysts had to Obey Protein Folding Rules
11.4 The First Coded Polypeptides were Quasispecies.
11.4.1 Secondary Structure, "Closed Loops," and Modules.