Kristof Plankensteiner

Amino acids on the rampant primordial Earth: Electric discharges and the hot salty ocean

For more than 50 years scientists who study prebiotic chemistry have been dealing with chemical evolution as it could have possibly taken place on the primordial Earth. Since we will never know what processes have really taken place around 3.8 to 4 billion years ago we can only come up with plausible reaction pathways that work well in an early Earth scenario as indicated by geochemists. In our work we have investigated the plausibility of one particularly important branch of prebiotic chemistry, the formation of amino acids, by electric discharge in a neutral atmosphere composed of carbon dioxide, nitrogen, and water vapour above liquid water. We have found yields of various amino acids under different temperature conditions, with and without sodium chloride in a simulated primordial lake or ocean within extremely short reaction times compared to the timespan available for prebiotic evolution.

Glycine and Diglycine as Possible Catalytic Factors in the Prebiotic Evolution of Peptides

Mutual catalytic effects within the Salt-Induced Peptide Formation (SIPF) Reaction might be one little puzzle piece in the complicated process of the formation of complex peptidic systems and their chemical evolution on the prebiotic earth. The catalytic effects of glycine and diglycine on the formation of dipeptides from mixed amino acid systems in the SIPF Reaction was investigated for systems with leucine, proline, valine and aspartic acid and showed to result in a significant increase of the yield of the majority of the produced dipeptides. The results of the experiments strongly confirm previous theories on the catalytic mechanism and show the ability of the SIPF Reaction to produce a very diverse set of peptide products with relevance to the formation of a biosphere.

Stereoselective differentiation in the Salt-induced Peptide Formation reaction and its relevance for the origin of life

All living organisms on earth are almost totally made up of biomolecules of only one chiral form. For example, proteins are built almost exclusively of L-amino acids, and sugars are composed of D-saccharides, a fact that is usually referred to as biohomochirality. Its origin is the center of numerous investigations and theories but is not really elucidated yet. The results of experimental investigations of peptide formation in a prebiotically relevant scenario, as described in this paper, give indications on a possible pathway for the synthesis of homochiral L-peptides in the course of the Salt-induced Peptide Formation (SIPF) reaction.

Dynamics in the hydration shell of Hg2+ ion: classical and ab initio QM/MM molecular dynamics simulations

Abstract Classical and ab initio QM/MM molecular dynamics simulations have been performed for Hg 2+ in aqueous solution. The dynamical properties were evaluated in terms of librational and vibrational motions of water molecules in the first and second hydration shell. The frequencies of rotation of water molecules in the first shell are blue-shifted compared to those of pure liquid water. Water exchange between first and second hydration shell occurs with a mean ligand residence time of 87 ps, in good agreement with the experimentally estimated value.

Catalytically Increased Prebiotic Peptide Formation: Ditryptophan, Dilysine, and Diserine

Abstract“Mutual” amino acid catalysis of glycine on the formation of ditryptophan, dilysine, and diserine in the prebiotically relevant Salt-Induced Peptide Formation (SIPF) Reaction was investigated varying the starting concentration and chirality of the educt amino acid, and analyzing the increase of yield resulting from this catalytic effect. Our results show the possibility of an amplified diverse pool of peptides being available for chemical evolution of larger peptides and proteins using also these more complicated amino acids for the evolution of more complex functions in future biochemical cycles and thus for the emergence of life. Catalytic effects are especially high in the case of serine, the most basic amino acid of the three, but are also significant for the other two examples investigated in the present work. Besides that, especially for serine, but also in the case of tryptophan, differences in catalytic yield increase according to the chiral form of the amino acid used could be observed.

Structure and dynamics of the Cr(III) ion in aqueous solution: Ab initio QM/MM molecular dynamics simulation

Structural and dynamical properties of the Cr(III) ion in aqueous solution have been investigated using a combined ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulation. The hydration structure of Cr(III) was determined in terms of radial distribution functions, coordination numbers, and angular distributions. The QM/MM simulation gives coordination numbers of 6 and 15.4 for the first and second hydration shell, respectively. The first hydration shell is kinetically very inert but by no means rigid and variations of the first hydration shell geometry lead to distinct splitting in the vibrational spectra of Cr(H2O)  63+ . A mean residence time of 22 ps was obtained for water ligands residing in the second hydration shell, which is remarkably shorter than the experimentally estimated value. The hydration energy of −1108 ± 7 kcal/mol, obtained from the QM/MM simulation, corresponds well to the experimental hydration enthalpy value.

Catalytic effects of glycine on prebiotic divaline and diproline formation.

The catalytic effects of the simple amino acid glycine on the formation of diproline and divaline in the prebiotically relevant salt-induced peptide formation (SIPF) reaction was investigated in systems of different amino acid starting concentrations and using the two enantiomeric forms of the respective amino acid. Results show an improved applicability of the SIPF reaction to prebiotic conditions, especially at low amino acid concentrations, as presumably present in a primordial scenario, and indicate excellent conditions and resources for chemical evolution of peptides and proteins on the early earth. For valine, furthermore differences in catalytic yield increase are found indicating a chiral selectivity of the active copper complex of the reaction and showing a connection to previously found enantiomeric differences in complex formation constants with amino acids.

Structural and dynamical properties of Co(III) in aqueous solution: Ab initio quantum mechanical/molecular mechanical molecular dynamics simulation

A combined ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulation has been performed to evaluate the structural and dynamical properties of Co(III) in water. The average Co(III)–O distance resulting from the simulation is 1.97 A for the first hydration shell, and the coordination numbers are 6/15 for first/second hydration shell. Ligand exchanges between the second hydration shell and the bulk occur with a mean ligand residence time of ∼55 ps, estimated from three events observed during the simulation. The hydration enthalpy of −1144±8 kcal/mol, determined by the QM/MM molecular dynamics simulation, is in good agreement with experimental estimations.

CHAPTER 207 – Prebiotic Peptides

Based on modern geochemistrys view of the atmospheric and geological conditions on the primordial Earth ∼3.8–4 billion years ago, the most realistic scenario for the formation of amino acids and peptides in chemical evolution is discussed, including possible reasons for sequence preferences in early proteins and for biohomochirality. Arguments for a peptide/protein world as primary origin of life, preceding RNA/DNA-based evolution, are presented.