Prebiotic Chemistry of Formamidelrb.jinr.ru/astrobiology2011/program/18_Saladino.pdf · Prebiotic Chemistry of Formamide University of Tuscia, Viterbo, Italy ... nucleosides, nucleotides,

Prebiotic Chemistry of

Formamide

University of Tuscia, Viterbo, Italy

Raffaele Saladino

Dipartimento di Scienze Biologiche ed Ecologiche, Università della Tuscia,

Via S. Camillo de Lellis s.n.c., 01100 Viterbo, Italy.

[email protected]

Dubna,Russia, December 2011

http://www.unitus.it/

The RNA World Hypothesis

Joyce, G.F. (2002) Nature 418, 214-221.


GENETIC METABOLISM


Formamide as Prebiotic Probe

“Simulations based on Density Functional Theory show that

formamide is the most stable species with molecular formula “CHON”

Pauzat, F. et al. 6th EANA 2006

“This one-carbon molecule was detected in the gas phase of

interstellar medium” Crovisier, J. Astrobiology: Future Perspectives,

Kluwer Eds, 2004 Chapter 8, p. 179-203.

“in the long period comet Hale-Bopp“ Bockelee-Morvan,

D. et al. Astr. Astrophys. 2000

“and tentatively in the solid phase on grains

around the young stellar object W33A “

W.A. Schutte et al. Astr. Astrophys. 1999


And in Jupiter's satellite Europa


Colloids and surfacesA: Physicochem Eng. Aspects 2003

219: 281-290.

A comparison of micelle formation of ionic

surfactants in formamide, in N-methylformamide

and in N, N-dimethylformamide.

M.Salim Akhter, Sadeq M. Alawi

Langmuir. 2004 Jan 20;20(2):329-35.

Solvation dynamics of formamide and

N, N-dimethylformamide in aerosol OT reverse micelles.

Shirota H, Segawa H.

Formamide . Physical and chemical properties


“Formamide has a high boiling point, without azeotropic effects, and a wide range of

uses as a solvent. It has an efficient solubilizing effect on nucleobases, nucleosides,

nucleotides, amino acids, proteins, sugars, metalsand salts”

Becker, B. J. Chem. Eng. 1970


Elemental Formamide Chemistry



Formamide prebiotic chemistry:

Pioneering studies.

Koyama, T. et al Chem.Pharm. Bull. 1977, 1923.

Yamada, H. et al.Tetrahedron Lett. 1978, 4039

H

O

NH2

170°C-190°C N

N28 hrs NH

N

H

O

NH2

170°C-190°C N

N28 hrs N

H

NN

N NH

N

NH2

+

HCN

Purine

Purine Adenine

A)

B)



The role of minerals on prebiotic processes.

A general overview

•Minerals can accumulate the prebiotic precursors

(concentration effect)

•Minerals can act can act as catalytic environments,

•reducing the activation energy for the formation of

products

• Minerals can tune the selectivity of prebiotic syntheses

• Minerals may act as a template

•Minerals are benignin environments to preserve newly

formed biomolecules from degradation



First results

Bioorganic Med. Chem. 9 (2001) 1249-1253

A Possible Prebiotic Synthesis of Purine, Adenine, Cytosine, and 4(3H)-Pyrimidinone

From Formamide: Implications for the Origin of Life

Raffaele Saladino,a,* Claudia Crestini, b Giovanna Costanzo,c Rodolfo Negrid and Ernesto Di Mauro c, d



Analyzing the reaction mechanism. 13C-/15N-NMR

Experiments“route of the pyrimidine ring”

* NH2COHHeat

HCN + H2O

HCO2NH4* NH2COH + H2O




Analyzing the reaction mechanism. 13C-/15N-NMR

Experiments“route of the pyrimidine ring”


Si

Al

Si

O

NC

H

H H

O

H H H

Al

oo o

o o o

o o o

Mn+

xH2O

oSi

4+, occasionally Al

3+

Al3+

, Mg2+

ChemBioChem 5 (2004) 1-9

Synthesis and Degradation of of Nucleobases and Nucleic Acids by

Formamide in the Presence of Montmorillonites Raffaele Saladino,a,* Claudia Crestini, b Umberto Ciambecchini,a Fabiana Ciciriello,c Giovanna Costanzo,c and Ernesto Di

Mauro c, d

Bu, Y.; Lin, M.C. Langmuir 1994



AICA: Amino Imidazole CarboxyAmide

fAICA: formyl Amino Imidazole

CarboxyAmide

fpurine: N(9)-formyl purine



Analyzing the reaction pathway. The“route of the

pyrimidine ring”



H NH2

O HN

N NH

N

O

NH

N

H2N

O

H2N

NH

N

HOCHN

O

H2N - H2O

HCN

Clays

In exant cell !

The first example of Chemiomimetic pathway


“certain biosynthetic pathways can be considered as

chemiomimetic of early prebiotic chemistry”

Eschenmoser, A.; Loewenthal, E. Chem. Soc. Rev. 1992, 1.


The origin of sugars and nucleosides

ChemBioChem 4 (2003) 514-521

One-pot TiO2-Catalyzed Synthesis of Nucleic Bases and Acyclonucleosides

From Formamide: Implications for the Origin of Life Raffaele Saladino,a,* Claudia Crestini,b Umberto Ciambecchini,a Rodolfo Negri,c Giovanna Costanzo,c Ernesto Di Mauro c,



HN

NH

O

O

CH2OH

H OH

O

HN

NH

O

O

H2C

O

H O

HN

NH

O

O

CH2

H

- CO2

H3O+ HN

NH

O

O

CH3

H

+HN

N

O

O

CH3

H

H

H+

HN

NH

O

O

CH3

HN

NH

O

O

H

H H

O

Thymine synthetic pathway

HCO2NH4* NH2COH + H2O

* NH2COH

TiO2

HCOH R. H. Barker, 1975



Sugars synthetic pathway. The formose reaction.

Butlerow, 1861.

Single headed arrows represent aldol

Condensations. Double-headed arrows

represent enolizations. Aldotreose can

undergo a reverse aldol condensation

H H

O

Sugars

HO-



A novel formose reaction


Complex nucleoside derivatives



Philosophical Magazine 90 (2010) 2329-2337

Role of clays in the prebiotic synthesis of sugar from Formamide Raffaele Saladino,a,* Neri Veronica, Claudia Crestini,b



oo o

o o o

o o o

Mn+

xH2O

oSi

4+, occasionally Al

3+

Al3+

, Mg2+

KSF

N.W. Gabel,

C. Ponnamperuna

Nature 1967



= Site for nucleobase

construction


Formamide prebiotic chemistry

with extraterrestrial materials

ChemBioChem 6 (2005) 1368-1374

Synthesis and Degradation of Nucleic Acid Components by

Formamide and Cosmic Dust Analogues Raffaele Saladino,a,* Claudia Crestini, b Veronica Neri,a John R. Brucato,d Luigi Colangeli,d Fabiana Ciciriello,c Giovanna

Costanzo,c and Ernesto Di Mauro c, d



Cosmic dust analogue olivines (Mg,Fe)2SiO4 are

synthesized by laser ablation technique (Nd-YAG 108

Wcm-2). Oxide pellets of MgO, FeO2, SiO2 are used as

laser target vaporized in 10 mbar atmosphere of O2.

Brucato, J. R. et al in The Astronomy and Astrophysics Review, Volume 11,

Issue 2-3, pp. 97-152 (2003)

Fe2SiO4* (Fayalite)

Mg0.5Fe1.5SiO4 *

MgFeSiO4 *

(Olivine)

Mg1.5Fe0.5 SiO4

*

Mg2SiO4 * (Fosferite)

SiO2, MgO,

FeO2 Laser

Ablation

Preparation of cosmic dust analogues

1)

2)

3)

4)

5)



NH

NH

O

O

H NH2

O

160°C, 48h N

N NH

N

N

NH

NH2

O

CDAs or olivines

NH

N

O

NH

NH

O

OH2N NH2

O

pyrimidinone cytosine uracil

DHUpurine urea

Fe Si Mg

olivine

fayalite

forsterite

CDAs qualitative composition

DHU:5,6-DiHydroUracil



Moving towards the metabolism


ATP

GTP

AM

INO

AC

IDS

NU

CL

EIC

AC

ID B

AS

ES

SU

GA

RS

AN

D L

IPID

S

CITRIC ACID CYCLE

O2



ATP

GTP

AM

INO

AC

IDS

NU

CL

EIC

AC

ID B

AS

ES

SU

GA

RS

AN

D L

IPID

S

REDUCTIVE CITRIC ACID CYCLE In eubacteria and archea

CO2


Metabolism part 1. Thermal conditions

Borate and Prebiotic Chemistry: A possible relationship with formamide


Origin Life Evolution Biosphere 41 (2011) 317-330

The effect of borate minerals on the synthesis of nucleic acid bases, amino acids and

biogenic carboxylic acids from formamide Raffaele Saladino,a,* Maurizio Barontini, Cristina Cossetti, Ernesto Di Mauro, Claudia Crestini


The urea/carbodiimide condensig cycle




Baddeleyte ZrO2

Zircon ZrSiO4

Lithium zirconate Li2ZrO3

Lead zirconate PbZrO3

Barium zirconate BaZrO3

Zirconium oxinitrate ZrO(NO3)2

J. Molecular Evolution 71 (2010) 100-110

The role of the formamide/zirconia system in the synthesis of nucleobases and

Biogenic carboxylic acids Raffaele Saladino,a,* Neri Veronica, Claudia Crestini, Costanzo Giovanna, Michele Graciotti, Ernesto Di Mauro



Origin Life Evolution Biosphere 41 (2011) 437-451

Catalytic effects of Murchison material: prebiotic synthesis and degradation

of RNA precursors Raffaele Saladino,a,* Claudia Crestini, Cristina Cossetti, Ernesto Di Mauro, David Deamer



ATP

GTP

AM

INO

AC

IDS

NU

CL

EIC

AC

ID B

AS

ES

SU

GA

RS

AN

D L

IPID

S

FIST-REDUCTIVE CITRIC ACID CYCLE

CO2


Metabolism part 2. Photochemical conditions



Anatase commercial

Anatase ground

Monochromatic Irradiation 3.2 eV

Astrobiology 11 (2011) 815-824

Photochemical synthesis of citric acid cycle intermediates based on titanium dioxide Raffaele Saladino,a,* John Robert Brucato, Antonio de Sio,b

Giorgia Botta, Emanuele Pace, Lisa Gambicorti


150 200 250 300 350 400 450 500 550 600

108

109

1010

1011

1012

Flu

x (

Ph

/ s

)

Wavelength (nm)

400 600 800 1000 1200 1400 16001.50x10

11

3.00x1011

4.50x1011

6.00x1011

7.50x1011

9.00x1011

1.05x1012

Flu

x (

photo

ns /

s c

m2)

e- (mA)

Flux

Linear Fit of Flux

Equation y = a + b*x

Adj. R-Square 0.998

Value Standard Error

Flux Intercept -3.36692E9 4.32197E8

Flux Slope 5.66953E8 457797.44953

Tab 2.1: Integral of the photons and energy dose of the different irradiation runs at 387.5 nm.

Mineral Powder Photon Dose Energy dose

(mW*s=J)

Exp. : Anatase BG 5.32 15 Photons 2.7

Exp. : Anatase FG 5.32 15 Photons 2.7

Exp. : Rutile 3.56 15 Photons 1.8

Exp. : Mix Rutile + Anatase 2.90 15 Photons 1.5

Exp. : Formamide 2.94 15 Photons 1.5

BG= Big grains >500 nm

FG= Fine grains<100 nm

Monochromatic Irradiation 3.2 eV , 387.5 ± 2.14 nm





R. Saladino, J.R. Brucato, A. de Sio, E. Pace






ATP

GTP

AM

INO

AC

IDS

NU

CL

EIC

AC

ID B

AS

ES

SU

GA

RS

AN

D L

IPID

S

FIST-REDUCTIVE CITRIC ACID CYCLE

CO2


events

high

low

formamide

bases

nucleosides

phosphorylation

(polymerization)

thermodynamic

niches

stabilization

helpers

micelles

Minerals catalysed prebiotic synthesis of nucleic

acid components from formamide. Degree of

confidence



Claudia Crestini (U.Tor Vergata) Fabiana Ciciriello (U. La Sapienza)

Raffaele Saladino (U. Tuscia) Giovanna Costanzo (IBPM)

Ernesto Di Mauro (U. La Sapienza)

Documents

Prebiotic Chemistry of Formamidelrb.jinr.ru/astrobiology2011/program/18_Saladino.pdf · Prebiotic Chemistry of Formamide University of Tuscia, Viterbo, Italy ... nucleosides, nucleotides,