guanine formation mechanism from observed interstellar … · imagem: . international symposium and...
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Campinas, 04/07/2016
Imagem: www.nasa.org
INTERNATIONAL SYMPOSIUM AND WORKSHOP ON ASTROCHEMISTRY
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Guanine formation mechanism from observed interstellar
chemical species
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Summary
Facts about (bio)molecules in the ISM
Methodological background
Learnings from Adenine mechanism of Synthesis
Results on the Guanine Synthesis
Conclusions
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~ 150 molecules were observed in the ISM
Wand, T.; Bowie, J.H. Org. & Biomol. Chem. 10, 652(2012).
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1 D-Aspartic Acid 2 L-Aspartic Acid 3 L-Glutamic Acid 4 D-Glutamic Acid 5 D,L-Serine 6 Glycine 7 β-Alanine 8 γ-Amino-n-butyric Acid (g-ABA) 9 D,L-b-Aminoisobutyric Acid (b-AIB) 10 D-Alanine 11 L-Alanine 12 D,L-β-Amino-n-butyric Acid (b-ABA) 13 α-Aminoisobutyric Acid (AIB) 14 D,L-α-Amino-n-butyric Acid (a-ABA) 15 D,L-Isovaline 16 L-Valine 17 D-Valine X: unknown
Chromatogram Samples extracted from Meteors
Ehrenfreund, P. Rep. Prog. Phys., 65, 1427(2002).
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5 M. P. Callahan et al. PNAS, 108, 13995–13998(2011).
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6 M. P. Callahan et al. PNAS, 108, 13995–13998(2011).
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7 M. P. Callahan et al. PNAS, 108, 13995–13998(2011).
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Scanning Tunneling Microscope (STM)
PM3 Semi-empirical Calculations
Low-dimensional of super hydrogen-bond complexes of adenine on Cu(111) surfaces
Furukawa, M.; Tanaka, H.; Kawai, T. Surface Science 445 1 (2000).
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Mechanisms for the Synthesis of Adenine
D. Roy, K. Najafian, P. von R. Schleyer PNAS 104, 17272 (2007).
J.B.P. da Silva, E. C. de Aguiar, K. M. Merz J. Chem. Phys. A 118, 3637 (2014).
Adenine
5 X
Adenine
Carbodiimida
C3NH
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B3LYP/6-311+G(d,p) MP2/6-311++G(d,p)
Rate determinant step 71 kcal mol-1 Rate determinant step 23 kcal mol-1
First it forms the 5-member ring, then he 6-member ring
First it forms the 6-member ring, then he 5-member ring
Involves 14 steps Involves 6 steps
∆GR = -53.7 kcal mol-1 ∆GR = -142.2 kcal mol-1
D. Roy, K. Najafian, P. von R. Schleyer PNAS 104, 17272 (2007).
J.B.P. da Silva, E. C. de Aguiar, K. M. Merz J. Chem. Phys. A 118, 3637 (2014).
Mechanisms for the Synthesis of Adenine
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Mechanism for the Synthesis of Guanine
Carbodiimida
OC3NH
Guanine
retrosynthetic analysis
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Potencial Energy Surface (PES)
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Reactant
Product
TS
Harmonic approximation
For real reactants and products k > 0 f(x) is a real number
For saddle point k <0 f(x) is a imaginary number
Potencial Energy Surface (PES)
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Target: Solve the time independent Schrödinger equation
H EΨ Ψ=
Hm M
Zer
er
Z Z eRi
ii
n
AA
A
N
iAA
N
i
n
ij
A B
ABB A
N
A
N
j
n
i
n
= − ∇
+ − ∇
+ −
+ +
= = == >=>=∑ ∑ ∑∑ ∑∑∑∑ 2
2
1
22
1
2
11
2 2
1112 2
Kelectrons Knuclei Vel.-nucl. Vel.-el.. Vnucl.-nucl.
Ψ – wave funtion; E – total energy of the system
H = E + KT G = H - TS
Computation G09, MP2/6-311++G(d,p), gas phase, default internal criteria of convergence,
energy in kcal mol-1.
Methodological background
T = 10 K P = 1 bar
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R
P R R
P
P
TS
TS TS
Methodological background
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G = -150.885159
ν1 = 318.06 cm-1 µ = 1.29 D
1 2 G = -93.179530
ν1 = 440.23 cm-1 µ = 3.28 D
+ -123.78
G = -244.261938
ν1 = 32.72 cm-1 µ = 2.83 D
3
16
G = -392.629317
ν1 = 39.75 cm-1 µ = 4.75 D
5
1.571 Å
G = -244.261938
ν1 = 32.72 cm-1 µ = 2.83 D
3 G = -148.425378
ν1 = 535.15 cm-1 µ = 2.03 D
4
+ 36.39
MP2/6-311++G(2d,2p)
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G = -392.629317
ν1 = 39.75 cm-1 µ = 4.75 D
1.571 Å
G = -392.615104
ν1 = -276.05 cm-1 µ = 2.69 D
G = -392.657509
ν1 = 26.09 cm-1 µ = 2.43 D
8.92 -26.61
G = -541.096366
ν1 = 27.16 cm-1 µ = 2.93 D
7
2.147 Å
2.040 Å
17 G = -541.082887
+
-8.45
5 6 TS5,6
6
4 8
G = -541.126260
ν1 = 38.73 cm-1 µ = 2.99 D
2.052 Å 2.126 Å
G = -541.091327
ν1 = -1069.36 cm-1 µ = 2.78 D
TS7,8
1.751 Å 1.276 Å
1.275 Å 1.054 Å 3.16 -21.92
MP2/6-311++G(2d,2p)
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MP2/6-311++G(2d,2p)
8 G = -541.126260
ν1 = 38.73 cm-1 µ = 2.99 D
2.052 Å 2.126 Å
18
10.78
+ 8`
G = -541.109074
8` +
G = -541.102331
3.046 Å
2.556 Å
9 G = -541.108340
ν1 = 16.96 cm-1 µ = 6.39 D
-3.77 6.80 -77.42
10
G = -541.225662
ν1 = 143.27 cm-1 µ = 5.55 D
G = -541.102291
ν1 = -182.06 cm-1 µ = 3.14 D
TS9,10
2.395 Å
2.329 Å
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10
G = -689.651040
19
+
2.654 Å
2.013 Å
G = -689.664337
ν1 = 27.35 cm-1 µ = 7.82 D
11
-8.34
G = -689.720623
ν1 = 22.50 cm-1 µ = 7.36 D
2.062 Å
2.611 Å
12
TS11,12
1.251 Å
1.414 Å
2.184 Å
G = -689.661326
ν1 = -1112.70 cm-1 µ = 10.65 D
-37.21
1.89
11.32 +
G = -541.270455
ν1 = 137.12 cm-1 µ = 6.28 D
G = -148.432121
ν1 = 397.84 cm-1 µ = 4.41 D
13 (Guanine) 14
MP2/6-311++G(2d,2p)
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CCO (g) + HCN (g) + 4 HNCNH (g) C5N5H5O (g) + 2 H2NCN (g) (Guanine)
MP2/6-311++G(2d,2p)
H2NCN (g) HNCNH (g)
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Conclusion
1 – A new mechanism for the formation of guanine in gas phase was proposed
considering the species observed in the ISM: CCO, HCN and HNCNH.
2 – The new mechanism has 6 steps and involves only bimolecular reactions.
4 – We propose first the formation of the 6-membered heterocyclic ring
and then the formation of the 5-membered ring.
5 – The rate determinant step involves a energy barrier c.a. 36 kcal mol-1.
6 – This new mechanism is very exergonic, ∆GR = -228.24 kcal mol-1 .
3 – HNCNH plays a key rule for H-bond assisted proton transfer process.
7 – Formation of guanine may be more spontaneous than adenine at the ISM .
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Acknowledgments
Grupo de Química Teóricae Computacional - UFPE
Grupo de Química Teóricae Computacional - UFPE
da Silva Fundation