Quantum Biochemistry. Jan H. Jensen Department of Chemistry University of Copenhagen. Slides can be found at: DOI: /m9.figshare.

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1 Quantum Biochemistry Jan H. Jensen Department of Chemistry University of Copenhagen Slides can be found at: DOI: /m9.figshare Dias 1

are thus completely known, and the difficulty is only that the exact application of these

2 Computational Chemistry Schrödinger Equation (1926) i t Ψ = ĤΨ The underlying physical laws necessary for the mathematical theory of a large part of physics and the whole of chemistry are thus completely known, and the difficulty is only that the exact application of these laws leads to equations much too complicated to be soluble. Paul Dirac, 1929 Not anymore! Dias 2

3 Numerically exact solutions: CCSD(T)/CBS Dias 3 Bartlett: /RevModPhys

4 CCSD(T)/CBS: benchmarking faster methods CCSD(T)/CBS currently too slow for routine chemical applications, but CCSD(T)/CBS now sufficiently fast to generate large amounts of data for benchmarking faster methods Dias 4

5 The rise of semi-empirical methods Semi-empirical methods: quantum mechanical (QM) methods with fitted parameters Fitting and validation can now done using CCSD(T)/CBS instead of experimental data: a huge conceptual and practical advance. Better QM: fewer parameters and wider applicability Examples: DFT-D, PM6-DH+, HF-3c HF-3c: HF/minimal basis set corrected for dispersion & BSSE using 9 parameters. No experimental input. Dias 5 Grimme: /jcc.23317

6 Validation against CCSD(T)/CBS: ΔE A+B è A B Dias 6 Grimme: /jcc.23317

7 Validation against experiment: ΔG Fast methods è frequencies è free energies Dias 7 MAD: 2.1 kcal/mol Grimme: /chem

8 Semi-empirical methods: new horizons QM structures and free energies for large systems Accurate protein structures Accurate activation free energies for enzymatic reactions Accurate binding free energies for protein-ligand complexes Automation and Computational High-Throughput Screening NMR chemical shift prediction for proteins Screening enzyme mutants Dias 8 Grimme: /chem

9 QM structures and free energies for proteins Large systems require different algorithms The Effective Fragment Molecular Orbital Method Jan H. Jensen, Anders Christensen and Casper Steinmann (SDU) University of Copenhagen Dmitri Fedorov AIST, Japan JPC A 2010, 114, 8705 PLoS ONE 2012, 7:e41117 PLoS ONE 2012, 7:e44480 PLoS ONE 2013, 8: e60602 PLoS ONE 2014 (arxiv: ) Dias 9

10 Large systems handled by fragmentation Fragmentation è QM calculations è reassembly Dias 10

11 All-QM enzymatic reaction barrier Dias /journal.pone

12 Automation and High-Throughput Screening Systematic Screening of Enzymatic Reaction Barriers Martin Hediger and Luca De Vico Allan Svendsen (Novozymes) PLoS ONE :e49849 PeerJ :e111 PeerJ :e145 Dias 12

13 Automation and High-Throughput Screening All possible single mutations è PM6 barrier è combination mutants ca mutants can be screened Dias 13

14 Automation and High-Throughput Screening Proteins Structure Determination from Chemical Shifts Anders Christensen (Novo Nordisk STAR PhD) & Lars Bratholm Thomas Hamelryck, Kresten Lindorff-Larsen, Kaare Teilum (BIO) JCTC 2011, PLoS ONE 2013, 8:e84123 Dias /ar900068s

15 A fast chemical shift predictor for proteins Representative fragments è QM calculations è empirical model QM calculations benchmarked against CCSD(T) Between 500,000 and 1,000,000 QM calculations needed Dias 15 PLoS ONE 2013, 8:e84123

16 Summary CCSD(T)/CBS: Experimental accuracy for small, but now chemically relevant, molecules. CCSD(T)/CBS replaces experiment for parameterization and validation of faster semi-empirical QM methods: more thorough and rigorous parameterization leads to more generally applicable methods. New semi-empirical QM methods are now finally sufficiently accurate to be of practical use. New semi-empirical methods are sufficiently fast for highthroughput screening (1000-1,000,000 QM calculations): new molecular design ideas for experimental chemists. Quantum chemists need to adapt: automation/cheminformatic considerations should be integral part of new modeling projects. Dias 16

17 Thank you! Questions? Slides are available at DOI: /m9.figshare Dias 17

18 Dias 18 Department of Chemistry

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