3D automatic kinetic model generation
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1 3D automatic kinetic model generation Ruben Van de Vijver, Nick M. Vandewiele, Kevin M. Van Geem, Marie-Françoise Reyniers, Guy B. Marin Laboratory for Chemical Technology, Ghent University International Conference on Chemical Kinetics, Ghent, 28/6-2/7/2015 1
2 2.5D automatic kinetic model generation Nick M. Vandewiele, Ruben Van de Vijver, Kevin M. Van Geem, Marie-Françoise Reyniers, Guy B. Marin Laboratory for Chemical Technology, Ghent University International Conference on Chemical Kinetics, Ghent, 28/6-2/7/2015 2
3 Outline Introduction Stereocenter detection and generation Stereoselective and stereospecific Applications: Pinanol rearrangement Conclusion 3
4 Reaction network generation k 1 k 2 Molecules Unique Representation Thermodynamics k 4 k 3 Reaction families Reaction Identification Kinetic Parameters k 5 k 7 k 8 k 9 k 6 Reaction rules Kinetic model enlargement Termination criterion k k k 12 k 13 k 14 k 15 Flexible 4
5 Graph representation of molecules Graph theory and algorithms can be applied: main methods for chemistry apps: Sub-graph matching ~ functional group query Equivalence test ~ structure database query 5 InChI=1S/C2H4O2/c1-2(3)4/h1H3,(H,3, C H 3 CH CH CH H CH3 Defining sub-molecular patterns: SMARTS (SMILES Arbitrary Target Specification)
6 Don t re-invent the wheel: chemo-informatics Andrew Dalke s EuroQSAR 2008 Poster ( Multiple ligands alignment within 3D field potential from Qmol LLC. 6
7 Genesys: Architecture Aim create a program that is general applicable Input Processing Postprocessing Initial species pool InChI/ SMILES Reaction Family Definition -Reactive moiety -Recipe -Constraints -Kinetics -Evans-Polanyi -Blowers-Masel -Group-additivity Reaction network generation Kinetic/thermodynamic parameter assignment Thermochemistry: NASA polynomials Chemkin readable format Species & reaction visualization 7
8 Why stereochemistry? New applications involving stereochemistry Terpene chemistry Pharmaceuticals Automatic generation of kinetic models Reactants Reaction families Improved code to incorporate stereochemistry LCT 8
9 Molecular representation Chemoinformatics starts from graph representation Use of binary stereodescriptors, e.g. cis/trans, +/-, R/S, E/Z, or +1/-1 (so-called attributes) Graph representation with stereochemical information is called 2.5D representation 2D 2.5D Trans +1 3D Cis -1 9
10 Unambiguous stereocenter identification Classical definition based on constitution of ligands Complete definition includes para-stereocenters 1 Defined by a set of rules. International Conference on Chemical Kinetics, Ghent, 28/6-2/7/2015 Para True True HO 5-methylcyclohexane-1,3-diol Carbon bearing methyl group: Two identical ligands doesn t comply with classical definition The identical ligands contain a true stereocenter para-stereocenter Use of open source chemo-informatics libraries Open Babel CDK 1. Razinger et al. (1993). Stereoisomer generation in computer-enhanced structure elucidation, J. Chem. Inf. Comput. Sci. 33,
11 Stereoisomer generation n stereocenters lead to 2 n possible stereoisomers Each stereoisomer can be described by configuration vector containing the stereodescriptors of each center topological symmetry some combinations of stereoparities represent the same stereoisomer β-terpineol: twofold rotational symmetry axis two stereocenters four configuration vectors only two stereoisomers: two configuration vectors are identical 11
12 Stereoisomer generation: algorithm Aim: identify configuration vectors that represent the same stereoisomer 1. Perception of topological symmetry 1 2. Impact of atom permutations on the stereoparities of the stereocenters 4-fluoro-3-difluoroethylpentan-2-ol 1. Vandewiele et al. (2015). Symmetry calculation for molecules and transition states, J. Comput. Chem. 36,
13 Steric relations Priority of ligands at C1 Priority of ligands at C2 13
14 How is this implemented in Genesys Three key concepts: modularity, standardization, general applicability Reactants Reaction Families STEREO MODULE Stereocenter detection Stereoisomer generation Steric relation detection ΔGAV Database Δ RES Δ GAV SIGMA MODULE BensonThermo Database Symmetry number calculation Reaction path degeneracy calculation n e σ GAV RSC HBI RES SpeciesThermo Database Δ f H (298K) S (298K) C p (T) Reaction Network Generation GENESYS MODULE Reaction network Rate Coefficient Calculation k Thermochemistry Calculation Δ f H (298K) S (298K) C p (T) THERMO MODULE Kinetic Model 14
15 Stereoselectivity and specificity Stereoselectivity is the preferential formation of stereoisomers from a molecule with a prostereogenic element Stereospecificity is the difference in reaction rates of two stereochemically different molecules, i.e. diastereomers or enantiomers k 1+ k 1+ k 2+ Product selectivity k 1- F k 2+ k 2- k 1- k 2- Reactant selectivity F F 15
16 Pinanol rearrangement 2-pinanol belongs to the terpenoids, which are used in fragrance, flavor and pharmaceutical industry 2-pinanol is converted to linalool, a precursor for vitamins A and E HO 2-pinanol HO Diastereomers 2 pairs of enantiomers linalool 16
17 Application: Linalool synthesis HO O HO HO -pinene -pinene pinane pinane hydroxide 2-pinanol linalool 17
18 Ghent Flow tube Set-up 18 ANALYSIS FEED REACTOR ONLINE Reactor: L = 1.5m ID = 6mm Conditions: P = 1.7 atm Tau ~ s T = K 7-10 mol % JP-10 in N2 ID reactor = 6mm, 8mm No noticeable differences Wall chemistry negligible
19 Stereochemistry is vital to take into account Cis-2- pinanol Trans-2- pinanol 19
20 Stereoselectivity is vital to take into account k A k B k C k D 20
21 Pinanol: network generation Input Species InChI without absolute configuration of stereocenters InChI=1S/C10H18O/c1-9(2) (3,11)8 (9)6-7/h7-8,11H,4-6H2,1-3H3 Homolytic C-C scission HO Reaction families Kinetic model 20 reactions between 20 species HO HO Biradical β-scission Sigmatropic [1,5]-H-shift H Enecyclization 21
22 Pinanol rearrangement: kinetics Reaction families HO = 10 Cis Homolytic C-C scission HO = 10 1 cis, 2 cis Trans = HO HO Biradical β-scission 1 cis, 2 trans = No stereoselectivity 1 trans, 2 cis Sigmatropic [1,5]-H-shift = trans, 2 trans = H Enecyclization 22
23 Pinanol rearrangement: results Cis Trans Leiner et al. (2013). Thermal behavior of pinan-2-ol and linalool, Molecules 18,
24 Conclusion Use of graphs with addition of stereo information: 2.5D molecular representation New automatic kinetic model generator includes detection of stereocenters, generation of stereoisomers and estimation of kinetics and thermodynamics for each stereoisomer Successful application of the new tool to the thermal rearrangement of pinanol 24
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