béla viskolcz university of szeged department of chemical informatics
TRANSCRIPT
Molecular EvolutionEarth as a molecular printer?
Béla ViskolczUniversity of Szeged
Department of Chemical Informatics
University of Szeged, Department of Chemical Informatics
Prebiotic molecular evolution
COMPLEXITY
VARIABILTY
University of Szeged, Department of Chemical Informatics
Molecular evolution basic level
COMPLEXITY
University of Szeged, Department of Chemical Informatics
Overview Atom Molecule
o Glycineo Pyridine o Glycerin aldehyde
Molecular Network Topic of Summerschool
University of Szeged, Department of Chemical Informatics
Ancient atmosphere
University of Szeged, Department of Chemical Informatics
Change in atmosphere
Oxidation conditions: Carbon: -4 to +4 Nitrogen: -3 to 0
Atom Molecules
University of Szeged, Department of Chemical Informatics
University of Szeged, Department of Chemical Informatics
Number of molecules Known Molecules
Organic: ~ 15 x 106
Inorganic: ~ 1 x 106
Virtual Molecules?Organic: > 1012 or 1060
COMPLEXITY
VARIABILTY
University of Szeged, Department of Chemical Informatics
Motivation I.
Molecular Informatics More Money for Applied Science
University of Szeged, Department of Chemical Informatics
Molecules by graph
CO
O
N HH
C HH
H
University of Szeged, Department of Chemical Informatics
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 inputx2
Workflow of the Com2Chem
University of Szeged, Department of Chemical Informatics
Highest stability
University of Szeged, Department of Chemical Informatics
University of Szeged, Department of Chemical Informatics
Complexes
University of Szeged, Department of Chemical Informatics
Reactions
N1
University of Szeged, Department of Chemical Informatics
Reactions
University of Szeged, Department of Chemical Informatics
More properties…
University of Szeged, Department of Chemical Informatics
Pyrimidine- Formula C4H4N2
- Guinness Molecule - 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
University of Szeged, Department of Chemical Informatics
Reverse Entropy Funnel
HCNxC2H2xHCN
University of Szeged, Department of Chemical Informatics
HC
NxC
2 H2 x
HC
N
University of Szeged, Department of Chemical Informatics
The most stable structures
University of Szeged, Department of Chemical Informatics
Glyceraldehyde
- Formula C3H6O3
- Organic molecule present in several biological process.
- Important during the prebiotic stage of the Earth.
University of Szeged, Department of Chemical Informatics
University of Szeged, Department of Chemical Informatics
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.
University of Szeged, Department of Chemical Informatics
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 time 141 days, 11 hours, 3 minutes and 23.4 seconds, clock time
University of Szeged, Department of Chemical Informatics
http://www.lapszemle.ro/2011/08/07/a-cukor-nem-olvad-hanem-szetbomlik/
C1-6H0-14O0-6
Stochiometry Σ267 258
17 121 162
C6H12O611 constitutional isomers!
Calculation Matrix
University of Szeged, Department of Chemical Informatics
http://kbond4.wordpress.com/
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
Mr (g/mol) Σ(Y=5) Σ(Y=6)1-75 26 398 378
76-100 153 058 928 593
101-125 235 070 7 731 832
126-150 160 848 10 924 887
151-175 29 932 4 917 433
176-200 18 266 1 697 180
201-225 28 781 1 025 626
226-250 8 462 825 300
251-275 1 383 589 487
275-300 968 106 103
663 166Σ= 28 746 819
C1Y H0(2Y+2) X0Y O0YS0YN0Y
Molecular Network
University of Szeged, Department of Chemical Informatics
University of Szeged, Department of Chemical Informatics
The email-Network
University of Szeged, Department of Chemical Informatics
Network
University of Szeged, Department of Chemical Informatics
Moelcular Network
Elements of Molecular Network
University of Szeged, Department of Chemical Informatics
University of Szeged, Department of Chemical Informatics
N(isomer) Stochiometry
934 C1_H0_N0_O2_F0_S345 C2_H4_N0_O3_F0_S043 C2_H6_N0_O3_F0_S041 C3_H2_N0_O2_F0_S0129 C3_H2_N0_O3_F0_S077 C3_H4_N0_O2_F0_S0255 C3_H4_N0_O3_F0_S077 C3_H6_N0_O2_F0_S0277 C3_H6_N0_O3_F0_S054 C3_H8_N0_O2_F0_S0191 C3_H8_N0_O3_F0_S0
From atom to molecules
CH
ON
SC3H6O3
C2H4O3
C2H6O3
University of Szeged, Department of Chemical Informatics
Network elements I.
C3H6O3
C3H8O2
C3H8O3
C3H6O2
C3H4O3
C3H4O2
C3H2O2
C2H4O2
C2H6O3
± CO
±CH2O
CH
ON
S
±CH4
University of Szeged, Department of Chemical Informatics
Network elements I.
C3H6O3
C3H8O2
C3H8O3
C3H6O2
C3H4O3
C3H4O2
C3H2O2
C2H4O2
C2H6O3
± CO
±CH2O
CH
ON
S±(C/ ̶ H2O)
±(CO/-2H2O)
±(C/-H2)
University of Szeged, Department of Chemical Informatics
Network elements II.
C3H6O3
C3H8O2
C3H8O3
C3H6O2
C3H4O3
C3H4O2
C3H2O2
±H2
±H2
±H2
±H2
±H2
±H2O
±H2O
±H2O
C2H4O2
C2H6O3
CH
ON
S
University of Szeged, Department of Chemical Informatics
Individual projectsNo. Name University N(isomer) Stochiometry
12 Dhiraj Sinha University of South-Bohemia 934 C1_H0_N0_O2_F0_S36 Bedard Joe University of Ryerson 45 C2_H4_N0_O3_F0_S0
10 Park Hyemin University of Toronto 43 C2_H6_N0_O3_F0_S09 Ramkissoon Chaitnandanie University of Toronto 41 C3_H2_N0_O2_F0_S04 Ying Lu University of Toronto 129 C3_H2_N0_O3_F0_S05 Lee Kyungseop University of Toronto 77 C3_H4_N0_O2_F0_S03 Yu Peiqi University of Toronto 255 C3_H4_N0_O3_F0_S08 Xu Xuan Ting University of Toronto 77 C3_H6_N0_O2_F0_S01 Li Jian Bin University of Toronto 277 C3_H6_N0_O3_F0_S02 Wang Daniel Yunwen University of Toronto 54 C3_H8_N0_O2_F0_S07 Chen Keyue University of Toronto 191 C3_H8_N0_O3_F0_S0
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
University of Szeged, Department of Chemical Informatics
References Szori Milan, Jojart Balazs, Izsak Robert, Szori Kornel, Csizmadia
Imre G, Viskolcz Bela: Chemical evolution of biomolecule building blocks. Can thermodynamics explain the accumulation of glycine in the prebiotic ocean? PHYSICAL CHEMISTRY CHEMICAL PHYSICS 13:(16) pp. 7449-7458. (2011)
Franco Cimino, Milán Szőri,Claudio A. Morgado and Béla Viskolcz, Relative Stability of C4H4N2 isomers and complexes – Pyrimidine as a Guiness molecule. in preparation
University of Szeged, Department of Chemical Informatics
Thermodynamics Given number of electrons Relative energy,
enthalpy etc.