1. MOLECULAR DATABASE Béla Viskolcz University of Szeged Department of Chemical Informatics University of Szeged, Department of Chemical Informatics

2. Number of molecules  Known Molecules Organic: ~ 15 x 10 6 Inorganic: ~ 1 x 10 6  Virtual Molecules? Organic: > 10 12 University of Szeged, Department of Chemical Informatics

3. Motivation I. Molecular Informatics More Money for Applied Science University of Szeged, Department of Chemical Informatics

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

5. Calculation Matrix I. Σ x\yx\y012345678910111213141516 2 100011 6 20111111 22 3122534221 0 4 37 719 11 21 9 12 5 42 146 5627 2187 40116 4085 2635 10 83 3020 617109834351856852175931593137710025175 4398 750 532315 24259134379 1227 437610312732 5751111 222284 56 399 152963 8196281517651489452573032979463408874262430646781167320823809654801137 http://stuff-stock.deviantart.com/art/Flame-STOCK-153459617 CxHyCxHy University of Szeged, Department of Chemical Informatics

6. Calculation Matrix II. http://kbond4.wordpress.com/ C 1-Y H 0-2Y+2 X 0-Y O 0-Y S 0-Y N 0-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 M r (g/mol) Σ(Y=5)Σ(Y=6) 1-7526 398378 76-100153 058928 593 101-125235 0707 731 832 126-150160 848 10 924 887 151-17529 932 4 917 433 176-20018 2661 697 180 201-22528 7811 025 626 226-2508 462825 300 251-2751 383589 487 275-300968106 103 663 166Σ=Σ= 28 746 819 University of Szeged, Department of Chemical Informatics

7. Calculation Matrix III. http://www.lapszemle.ro/2011/08/07/a-cukor-nem-olvad-hanem-szetbomlik/ C 1-6 H 0-14 O 0-6 Stochiometry Σ 267 258 17 121 162 C 6 H 12 O 6 11 constitutional isomers! University of Szeged, Department of Chemical Informatics

8. Example I. Glyceraldehyde - Formula C 3 H 6 O 3 - Organic molecule present in several biological process. - Important during the prebiotic stage of the Earth. University of Szeged, Department of Chemical Informatics

9. Example II. Pyrimidine - Formula C 4 H 4 N 2 - Wide occurrence in nature as substituted and ring fused compounds. - Derivatives of pyrimidine are present in nucleotides, this are ADN structure. University of Szeged, Department of Chemical Informatics

10. 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 the space (relative Cartesian coordinates of the entire specie) is different, This leads to different electronic/atomic interactions. University of Szeged, Department of Chemical Informatics

11. Details of computations Gaussian 09 - Calculation on G09 were made under G3MP2B3 method: Optimization, frequency, QCISD(T) and MP2 calculation. Each calculation used 8 processor from the cluster. - For the Gas Phase Glyceraldehyde isomers calculation it 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 it took: 1131 days, 16 hours, 23 minutes and 47.1 seconds CPU time 141 days, 11 hours, 3 minutes and 23.4 seconds, clock time University of Szeged, Department of Chemical Informatics

12. Database STRUCTURAL HIERARCHY University of Szeged, Department of Chemical Informatics

13. Database MODULS 15 x 10 6 „known small molecule” 55000 „know protein structure” University of Szeged, Department of Chemical Informatics

14. Selections of models Molecule tautormer2 Definition of standard process The definitions should be flexible Database, as a useful product trans cis tautormer1 H+H+ H+H+ H+H+ H+H+ 0000 University of Szeged, Department of Chemical Informatics

15. Köszönöm megtisztel ő figyelmüket! THANK YOU FOR YOUR ATTENTION Financial support HURO/0901/037/2.2.2 Complex molecular database for environmental protection TÁMOP 4.2.2-A: Új funkcionális anyagok… TÁMOP 4.2.2-C: Szuperszámítógép a nemzeti virtuális laboratórium

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