Thermal Behavior of Amino Acids in Inorganic Matrices

147 Pages·2014·1.95 MB·English

Thermal Behavior of Amino Acids
in Inorganic Matrices:
Relevance for Chemical Evolution

Dissertation zur Erlangung des Doktorgrades
der Naturwissenschaften (Dr. rer. nat.)

Fakultät Naturwissenschaften
Universität Hohenheim

Institut für Chemie

vorgelegt von
Punam Dalai
aus Allahabad
(India)

2013
Dekan: Prof. Dr. Heinz Breer
1. berichtende Person: Prof. Dr. Henry Strasdeit
2. berichtende Person: Prof. Dr. Hans Brückner

Eingereicht am: 30.08.2013
Mündliche Prüfung am: 17.12.2013
To
My Parents
Acknowledgements
With my profound sense of gratitude, I would like to express thanks to my supervisor
Prof. Dr. Henry Strasdeit for providing me the opportunity to pursue my PhD at the Institute
of Chemistry, University of Hohenheim. He helped me by excellent supervision, support, and
encouragement along the way to understand and explore certain interdisciplinary dimensions.
He has been a constant source of ideas and suggestions from the initial planning stage until
completion of research.
I wish to express my special thanks to Dr. Stefan Fox for his advice during the
experiments and writing of the thesis. I am grateful to Prof. Dr. Hans Brückner and Prof.
Dr. Uwe Beifuss for agreeing to be reviewer/examiner for my PhD thesis.
I gratefully thank Sonja Ringer, Melanie Wagner, Claudia Görgen, and the late Petra
Guni for their help during my research. I would like to express my thanks to Dr. J.-P. deVera
from the DLR Institute of Planetary Research, Berlin for providing Martian soil silmulants. I
would like to thank all my colleagues at the Department of Bioinorganic Chemistry for their
advice and support. I would like to extend my special thanks to Mrs. Malmström and
Ms. Franziska Wolz for their help in administrative works.
My appreciation also goes to all my friends in Germany and other parts of the world
for their warm company and numerous favors during my studies.
Finally, my special thanks and appreciation go to my parents, Vikas and my sister for
their love, patience, support, and understanding throughout my studies.
Preliminary Remarks
The work presented in this thesis was carried out under the supervision of Prof. Dr. Henry
Strasdeit at the Institute of Chemistry, University of Hohenheim, from April 2008 to
December 2012. Part of the results have been presented at international conferences:
Dalai, P. and Strasdeit, H. (2009) Dramatic alteration of the thermal behavior of glycine by
Ca-montmorillonite. Orig Life Evol Biosph 39: 230.
(presented at the 15th International Conference on the Origin of Life, Florence, Italy, 2008).
Dalai, P. and Strasdeit, H. (2009) The influence of a clay mineral on the behavior of glycine
at 200 degrees celsius. Orig Life Evol Biosph 39: 47.
(presented at the 8th European Workshop on Astrobiology, Neuchatel, Switzerland, 2008).
Dalai, P. and Strasdeit, H. (2010) The influence of various clay matrices on the thermal
behavior of glycine. Orig Life Evol Biosph 40: 520.
(presented at the 9th European Workshop on Astrobiology, Brussels, Belgium, 2009).
Dalai, P. and Strasdeit, H. (2010) Peptide formation and glycine protection by clays.
(presented at International Workshop on Chemical Evolution and Origin of Life, Indian
Institute of Technology, Roorkee, India, 2010).
Dalai, P. and Strasdeit, H. (2011) Thermal behavior of non-racemic alanine intercalated in
calcium-montmorillonite.
(presented at the 11th European Workshop on Astrobiology, Köln, Germany, 2011).
Strasdeit, H., Dalai, P., and Fox, S. (2011) A complex thermal polymer derived from the
simplest amino acid.
(presented at the 11th European Workshop on Astrobiology, Köln, Germany, 2011).
Contents Page No.
1 Introduction........................................................................................................... 1
1.1 Prebiotic chemical evolution............................................................................ 1
1.1.1 Peptides and proteins............................................................................... 1
1.1.2 RNA world hypothesis……………………...…………………....……. 2
1.1.3 Protometabolism and catalytic networks……….…………………...…. 3
1.2 Early climate and geological history of Earth and Mars.................................. 4
1.2.1 Water and atmosphere on the early Earth…………………………...…. 5
1.2.2 Geological history of Mars…………………………………………….. 6
1.2.3 Volcanism on Earth and Mars………………………..……………....... 7
1.3 Minerals of possible relevance to prebiotic chemistry..................................... 8
1.3.1 Clay minerals........................................................................................... 8
1.3.2 Chlorides.................................................................................................. 11
1.3.3 Carbonates............................................................................................... 11
1.3.4 Sulfates..................................................................................................... 12
1.3.5 Other minerals.......................................................................................... 13
1.4 Prebiotic amino acids........................................................................................ 14
1.4.1 Amino acid sources.................................................................................. 14
1.4.2 Possible origins of biomolecular homochirality of amino acids….......... 16
1.4.3 Thermal properties of amino acids…………………..…..……….…..... 20
1.5 Aims and objectives.......................................................................................... 21
2 Results and Discussion.......................................................................................... 23
2.1 Thermal treatment of neat glycine and glycine homopeptides …...…………. 23
2.1.1 Thermal treatment of neat glycine……………….................….…...…. 23
2.1.2 Thermal treatment of DKP and linear homopeptides of glycine…….... 28
2.2 Analysis and properties of the glycine thermo-melanoid…….………...…..... 32
2.2.1 Thermogravimetric analysis of glycine and homopeptides of
glycine……….......................................………..…………..…………. 32
2.2.2 Solubility and hydrolysis of the thermo-melanoid................................. 34
2.2.3 Biodegradability of the thermo-melanoid in soil………...……...…...... 35
2.3 Protection of glycine by different matrices…………….…………………...... 36
2.3.1 The influence of salts and salt mixtures…………..…...………..…........ 36
2.3.2 Thermal treatment of glycine embedded in clay minerals….......…..….. 47
2.3.3 Terrestrial volcanic rock and Martian soil simulants.......…..….............. 58
2.4 Racemization of amino acids intercalated in Ca-montmorillonite................... 61
2.4.1 Thermal treatment at 200 °C of Ca-montmorillonite loaded with
alanine having different starting L-ee…...............................……….….. 62
2.4.2 Thermal treatment at various temperatures of Ca-montmorillonite
loaded with L-alanine………………....................................................... 66
2.4.3 Thermal treatment of Ca-montmorillonite loaded with other amino
acids……………………….………………….…........…...…..…….…. 66
2.4.4 Racemization kinetics of alanine in Ca-montmorillonite…...............…. 70
2.5 Sublimation of neat alanine and valine……………….……………...…….… 75
3 Summary / Zusammenfassung............................................................................ 78
4 Materials and Methods......................................................................................... 87
4.1 Analytical methods…………………………………..…..….…………….…. 87
4.1.1 High performance liquid chromatography (HPLC)................................. 87
4.1.2 Infrared spectroscopy............................................................................... 87
4.1.3 Gas chromatography with mass spectrometric and flame ionization
detection (GC-MS and GC-FID)............................................................. 87
4.1.4 Matrix-assisted laser desorption ionization–time of flight/time of flight
mass spectrometry (MALDI–TOF/TOF mass spectrometry)…………. 89
4.1.5 Thermogravimetric analysis (TGA)......................................................... 90
4.1.6 Powder X-ray diffractometry (Powder XRD)......................................... 90
4.1.7 Elemental analysis................................................................................... 90
4.2 List of Chemicals.....……………………………………………………….… 90
4.3 Heating apparatus………………………………………………….....……… 93
4.4 Analysis of the thermo-melanoid.........................……….……………..…….. 94
4.4.1 Hydrolysis of the thermo-melanoid......................................................... 94
4.4.2 Biodegradability of the thermo-melanoid in soil..................................... 94
4.5 Preparative methods.......................................................................................... 95
4.5.1 Salts and salt mixtures with embedded glycine: Syntheses and thermal
treatment ……………………..……….….........................…................. 95
4.5.2 Clay minerals with embedded amino acids: Loading procedure and
thermal treatment............………............................................................. 96
4.5.3 Preparation and thermal treatment of glycine-loaded terrestrial
volcanic rock and Martian soil simulants……………............................ 100
4.5.4 Extraction of amino acids and peptides from clay minerals...…………. 101
5 Literature............................................................................................................... 103
6 Appendix................................................................................................................ 126
7 Curriculum Vitae.................................................................................................. 137
1 Introduction
1.1 Prebiotic chemical evolution
Prebiotic chemical evolution describes the series of events that led from simple molecules to
complex compounds before the presence of life. Charles Darwin suggested 150 years ago that
life may have begun in a “warm little pond” in the presence of inorganic salts and energy
sources (Peretó et al., 2009). Later, Oparin and Haldane independently developed the
“primordial soup” hypothesis. According to this hypothesis, simple organic molecules
(e.g. amino acids) were formed from the Earth’s primitive atmosphere and could have
accumulated to form the primordial soup. Based on this hypothesis, Stanley Miller conducted
experiments where it was found that amino acids could be synthesized from a simulated early
Earth’s atmosphere (CH , H , H O,NH ) in the presence of an energy source (Miller, 1953).
4 2 2 3
It is generally accepted that amino acids were present on the young Earth through
endogenous and exogenous sources (see 1.4.1). Thus, at the first instance, it seems obvious
that these amino acids could have been the building blocks of the first peptides.
It has been hypothesized that the primitive life may have used simple molecules such
as peptide nucleic acids (PNA) as their genetic material (Nielsen, 1993; Nelson et al., 2000).
The backbone of a PNA molecule consists of repeating units of diamino monocarboxylic acid
linked through a peptide bond (Strasdeit, 2010). The backbone is also attached to purine and
pyrimidine bases (Fig. 1). PNA is devoid of sugar and phosphate groups which makes it
different from RNA and DNA. A PNA molecule is generally achiral (Neilsen and Egholm,
1999; Pooga et al., 2001). Therefore, the problem of homochirality associated with nucleic
acids (RNA and DNA) could also be discarded in PNA. However, RNA and DNA should be
exclusively homochiral to be functional in modern organisms.
1.1.1 Peptides and proteins
Peptides are an important class of biomolecules. However, their formation by condensation of
amino acids is thermodynamically unfavorable under aqueous conditions (Lambert, 2008).
Peptides are susceptible to hydrolysis in aqueous medium. Therefore, the formation of
peptides with at least 20 amino acids (for catalytic activity) could have been difficult under
the early Earth’s “chaotic” conditions (Bada, 2004). The formation of di- and tripeptides has
been shown in Salt-Induced Peptide Formation (SIPF) experiments. These experiments were
performed in the presence of high concentrations of NaCl and CuCl . NaCl acts as a
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dehydrating agent, and Cu(II) forms the complex with the amino acid (see 1.3.2)
(Schwendinger and Rode, 1989, 1991; Rode and Schwendinger, 1990). However, longer
peptides were not observed in the SIPF reaction within the experimental time. Rode (1999)
assumed that macromolecules could be formed by increasing the reaction time of SIPF
reactions. Questions have been raised concerning the availability of soluble Cu(II) on the
young Earth. It has been assumed that dissolved Cu(II) was formed in the “green zones” of
precambrian rocks in the presence of trace amounts of oxygen (Ochiai, 1978; Rode, 1999).
The formation of homochiral peptides from a racemic mixture of amino acids is another
unsolved problem. Homochirality is a prerequisite condition for the activity of an enzyme.
Nowadays, proteins are required for the formation of nucleic acids and, in turn, nucleic acids
are needed for protein synthesis. The apparent paradox of which came first, the protein or the
nucleic acid, is referred to as the “chicken and egg problem”.
Base
N
O
NH
O
Base
Repeating unit N
O
NH
O
Base
N
O
NH
O
Fig. 1: Structure of a peptide nucleic acid (PNA). Base refers to purines (adenine, guanine) or
pyrimidines (thymine, cytosine)
1.1.2 RNA world hypothesis
The “RNA world” hypothesis considers RNA as the first genetic material that could replicate
before the evolution of DNA. In this approach, the existence of prebiotic RNA molecules is
proposed that had both the properties of catalysis and information storage, similar to
present-day ribozymes. According to this hypothesis, proteins were not required for the
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