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Molecular Evolution Earth as a molecular printer?

Molecular Evolution Earth as a molecular printer?. Béla Viskolcz University of Szeged Department of Chemical Informatics. Prebiotic molecular evolution. COMPLEXITY. VARIABILTY. Molecular evolution basic level. COMPLEXITY. Overview. Atom  Molecule Glycine Pyridine

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Molecular Evolution Earth as a molecular printer?

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  1. MolecularEvolutionEarthas a molecular printer? Béla Viskolcz University of Szeged Department of Chemical Informatics

  2. Prebioticmolecularevolution COMPLEXITY VARIABILTY

  3. Molecularevolutionbasiclevel COMPLEXITY

  4. Overview • Atom  Molecule • Glycine • Pyridine • Glycerin aldehyde • Molecular Network • Topic of Summerschool

  5. Ancient atmosphere

  6. Change in atmosphere Oxidation conditions: Carbon: -4 to +4 Nitrogen: -3 to 0

  7. University of Szeged, Department of ChemicalInformatics Atom  Molecules

  8. Number of molecules • KnownMolecules Organic: ~ 15 x 106 Inorganic: ~ 1 x 106 • VirtualMolecules? Organic: > 1012or 1060 COMPLEXITY VARIABILTY

  9. Motivation I. • MolecularInformatics • More Money forApplied Science

  10. Moleculesbygraph O O C H N H H C H H

  11. Workflow of the Com2Chem Initial input (.pdb,…) Terminated output (.log) Runable input (.com) Input preparation Regeneration of input x2 Output with no error termination Normal term. Conv. Crit. Freq Normal termination? Output with Error output Modified input Manipulation of the input (By hand) Calculation and collection of molecular properties Computational Know How Database Com2Chem: Computational Combinatorial Chemistry Methodology Know How Chemical Know How

  12. Higheststability

  13. Complexes

  14. Reactions N1

  15. Reactions

  16. More properties…

  17. University of Szeged, Department of ChemicalInformatics Pyrimidine - Formula C4H4N2- Guinness Molecule - Wide occurrence in natureas substituted and ring fused compounds.- Derivatives of pyrimidine are present in nucleotides, this are ADN structure.

  18. ReverseEntropyFunnel HCNxC2H2xHCN

  19. HCNxC2H2xHCN

  20. The most stable structures

  21. University of Szeged, Department of ChemicalInformatics Glyceraldehyde - Formula C3H6O3 - Organic molecule present in several biological process.- Important during the prebiotic stage of the Earth.

  22. Details of computations • Isomers and spatial conformations -Glyceraldehyde: 277 com files on gas phase and 277 in aqueous phase. -Pyrimidine: 7983 com files on gas phase and 7983 in aqueous phase. - Spatial conformations makes reference to the generation of some species that are exactly the same but the orientation in space (relative Cartesian coordinates of the entire specie) is different, which leads to different electronic/atomic interactions.

  23. Details of computations • Gaussian 09 • Calculation on G09 were made under G3MP2B3 method:Optimization, frequency, QCISD(T) and MP2 calculation.Each calculation used 8 processors from the cluster. • For the Gas Phase Glyceraldehyde isomers calculation took: 49 days, 9 hours, 59 minutes and 50 seconds CPU time 6 days, 4 hours, 14 minutes and 59 seconds clock time • For the Gas Phase Pyrimidine isomers calculation took:1131 days, 16 hours, 23 minutes and 47.1 seconds CPU time141 days, 11 hours, 3 minutes and 23.4 seconds, clock time

  24. CalculationMatrix 11 constitutionalisomers! C6H12O6 C1-6H0-14O0-6 http://www.lapszemle.ro/2011/08/07/a-cukor-nem-olvad-hanem-szetbomlik/

  25. C1Y H0(2Y+2) X0Y O0YS0YN0Y X=F,Cl,Br,I C+N+O+S+F+Cl+Br+I=Y S valence (connectivity) 2, 4, 6 N valence (connectivity) 3, 5 28746819 Σ= 663166 http://kbond4.wordpress.com/

  26. University of Szeged, Department of ChemicalInformatics Molecular Network

  27. The email-Network

  28. Network

  29. MoelcularNetwork

  30. University of Szeged, Department of ChemicalInformatics Elements of Molecular Network

  31. From atom tomolecules C2H4O3 C C2H6O3 H O N S C3H6O3

  32. Network elements I. C3H8O2 ±CH4 C3H8O3 C2H4O2 C H C3H6O2 O ±CH2O C3H6O3 C2H6O3 N S C3H4O2 ± CO C3H4O3 C3H2O2

  33. Network elements I. C3H8O2 ±CH2O C3H8O3 C2H4O2 C H C3H6O2 O ± CO C3H6O3 C2H6O3 N S ±(C/ ̶ H2O) C3H4O2 ±(C/-H2) C3H4O3 ±(CO/-2H2O) C3H2O2

  34. Network elements II. C3H8O2 C3H8O3 ±H2 C ±H2O ±H2 H C3H6O2 O C2H4O2 C3H6O3 N ±H2 C2H6O3 ±H2O ±H2 S C3H4O2 C3H4O3 ±H2 ±H2O C3H2O2

  35. Individual projects

  36. Köszönöm megtisztelő figyelmüket! THANK YOU FOR YOUR ATTENTION Financial support • TÁMOP 4.2.2-A: New functional materials … • TÁMOP 4.2.2-C: Supercomputer a national virtual laboratory

  37. References • SzoriMilan, JojartBalazs, Izsak Robert, SzoriKornel, Csizmadia Imre G, Viskolcz Bela: Chemicalevolution of biomolecule building blocks. Canthermodynamicsexplaintheaccumulation of glycineintheprebioticocean? PHYSICAL CHEMISTRY CHEMICAL PHYSICS 13:(16) pp. 7449-7458. (2011) • Franco Cimino, MilánSzőri,ClaudioA. Morgadoand Béla Viskolcz, Relative Stability of C4H4N2 isomers and complexes – Pyrimidineas a Guinessmolecule.inpreparation

  38. Thermodynamics • Givennumber of electrons Relative energy, enthalpyetc.

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