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Astrochemical and Prebiotics Systems: Structures and Processes


Total hours: 50
Hours of lectures: 50

Examination procedure

  • oral exam


This course is directed to students with a good knowledge of basic organic chemistry with special reference to physical organic chemistry, including:

Qualitative molecular orbital theory and perturbation MO theory;

Basic structural properties of organic compounds and transient intermediates and the concept of aromaticity

Conformational analysis.

Kinetics and thermodynamics of organic reactions

Main reaction mechanisms and their discussion by perturbation MO theory


The course is based mainly on discussion of a range of astrochemical compounds and prebiotic processes selected from advanced textbooks or selected literature papers. It is thus conceived more as a collection of special topics rather than a systematic treatise.

In view of its character it is perfectly suited to a “flipped classroom” approach. It is recommended that students read all slides before the lesson, so that they can be prepared to discuss critical arguments of special interest or to ask for more supporting material in advance, based on their individual background.

A1) Astrochemistry of organic compounds (25 h)

1) Astrophysical objects and environments (general definitions) Cosmic ray astrochemistry and the various phases of the ISM Astrochemistry of dust, ice and gas. Gas-grain chemistry. Cosmic carbon chemistry.

2) Basics in physical organic chemistry Structure and chemical bond. Molecular orbital theory. Perturbation molecular orbital theory Walsh diagrams. Methane, Methyl, Ethane.

3) Methylene, Ethylene, Cyclopropane, Walsh orbitals. Huckel MO theory Polyenes, Alkynes, Polyynes Allenes and cumulenes Helical frontier orbitals of conjugated linear molecules

4) Aromaticity criteria The HOMA index. Calculated heats of formation/ heats of reaction: isodesmic-homodesmotic reactions. Heteroaromatic compounds

5) Structural classification of PAHs. Clar’s rule. Alternant and non-alternant hydrocarbons. Huckel and Mobius systems

6) Carbonyl compounds of astrochemical relevance. Formaldehyde. Propynal and cyclopropenone. Glyoxal. Glycolaldehyde. Glyoxylic acid.

7) Chemistry and astrochemistry of sulfur compounds. Sulfur compounds on Mars. Thiophene. Thiols and methanethiol. Thioformaldehyde

8) Conformational properties of organic molecules. Preferred conformations from conjugation in the sigma framework.

9) Astrochemistry of hydrocarbon compounds Planetary environments. Titan’s haze components and tholins. Non covalent interactions.

10) Fundamental chemical mechanisms Kinetics and thermodynamics of organic reactions BEP principle Hammond postulate Marcus theory of electron transfer. Linear free energy relationships.

11) Pericyclic reactions

12) Basic photophysical and photochemical processes. Photochemistry of interstellar ices and dust.  

13) Ketene structure and chemistry: addition, cycloaddition.

14) Carbenium ions/carbonium ions. Ethynyl cation. “Non-classical” protonated acetylene. Cyclopropenyl cation and propargyl cation. Formyl cation.

15) Carbenes: single and triplet states Methylidenecarbene. Cyclopropenylidene. Propadienylidene. Cheletropic reactions of carbenes.

16) Free radicals from organic compounds in astrochemical pathways. The ethynyl (C2H) radical. The propynylidyne radical . The propargyl radical.

17) Chemistry of energetically activated cumulenes. Cyanamide. Cyanamide-glyoxal oligomers in aqueous medium. Formamide. Keteneimine.

18) Dicyanoacetylene in Titan’s stratosphere. Photochemistry of dicyanoacetylene in the solid state. Isonitriles. Methylisocyanate.

19) Polycyclic aromatic hydrocarbons (PAHs) and The Unidentified Infrared Bands. the PAH hypothesis. Beyond the PAH hypothesis. Structural modifications of PAHs. Mixed aromatic-aliphatic organic nanoparticles (MAONs). Photochemistry of PAHs in ices.

20) Solid state photochemistry of hydroxylated naphthalene derivatives on minerals. Photochemistry of purine in ice analogs. UV Irradiation of Biomarkers Adsorbed on Minerals under Martian-like Conditions.

21-25) Special topics, seminars by students, classroom discussions, mid-term self-assessment tests


B2) Prebiotic systems and processes- Systems chemistry (25 h)

26) Astrobiology. Definitions of life. Theories of the origin of life.  

27) The origin of carbon on the early Earth. Organic compounds on comets. The RNA world hypothesis. The Last Universal Common Ancestor.

28) A Strategy for Origins of Life Research. Life’s Biological Chemistry: A Destiny or Destination Starting from Prebiotic Chemistry?

29) Prebiotic systems chemistry: complexity overcoming clutter. The three pillars of prebiotic chemistry. The Miller-Urey experiment and the spark discharge aminonitrile synthesis

30) Cyanosulfidic protometabolism: synthesis of RNA, lipids and protein precursor

31) The formose reaction. The hydrothermal formose reaction.

32)Prebiotic chemistry in eutectic solutions at the water–ice matrix. Photochemical steps in the prebiotic synthesis of purine precursors from HCN

33) The search for the chemistry of life’s origin. The chemistry of the glyoxylate scenario.

34) Production of Tartrates by Cyanide-Mediated Dimerization of Glyoxylate.

35) Exploratory experiments on the chemistry of the glyoxylate scenario. Prebiotic synthesis of simple sugars by photoredox systems chemistry.

36) Complexity in chemistry. Chemical systems, chemical contiguity and the emergence of life. Chemical systems, chemical contiguity and the emergence of life.

37) Systems chemistry

38) Current challenges in systems chemistry

39) Small-Molecule Systems Chemistry

40) Systems chemical analytics.

41) Prebiotic Systems Chemistry: New Perspectives for the Origins of Life. 

42) Systems of Creation: The Emergence of Life from Nonliving Matter

43) Complex Insoluble Organic Polymers from Meteorites

44) Complex Insoluble Organic Polymers in living organisms

45) Homochirality. On the Origin of Single Chirality of Amino Acids and Sugars in Biogenesis. The Soai reaction: autocatalysis and self-replication.

46-50) Special topics, seminars by students, classroom discussions, final self-assessment tests


 Educational goals:

 Knowledge and understanding: include a systematic understanding of the field of organic chemistry in contexts of astrochemical and astrobiological relevance and mastery of the methods of research associated with that field.

Applying knowledge and understanding: is demonstrated by the ability to conceive, design, implement and adapt a substantial process of astrochemical research on organic compounds and reactions, in the context of a contribution that extends the frontier of knowledge by developing a substantial body of work some of which merits international refereed publication.

Making judgements: requires being capable of critical analysis, evaluation and synthesis of new and complex ideas.

Communication: an ability to explain to peers, the larger scholarly community and with society in general the basic contents, impact and implications of astrochemical processes of organic compounds.

Learning skills: expected to be able to promote, within academic and professional contexts, research and/or cultural advancements in the field of astrobiology and the origin of life.