Computational Modelling of Chemical and Biochemical Reactivity Chemistry Ian Williams.

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Presentation transcript:

Computational Modelling of Chemical and Biochemical Reactivity Chemistry Ian Williams

Bath English Lake District Buttermere Borrowdale Honister Pass Youth Hostel + car park

B C D T E W G R W ‡ ‡ ‡ ‡ ‡ ‡ ‡ ‡ A Chemical Landscape: mountain pass ‡  transition state  E peak  E pass geometry the transition state ‡ of a molecular system controls the direction and rate of chemical change between reactants R and products P Map coordinates: longitude & latitude Contour lines: vertical height  potential energy (gravitational)

glycoprotein O cell sialic acid 

Relenza and Tamiflu stop the virus from budding out of the cell

neuraminidase 37 atoms 85 atoms quantum mechanics: Schrödinger equation

37 atoms 85 atoms quantum mechanics: Schrödinger equation Neuraminidase 5668 atoms

classical mechanics: Hooke & Coulomb 37 atoms 85 atoms quantum mechanics: Schrödinger equation 5668 atoms Neuraminidase 5668 atoms Neuraminidase in water: atoms

MMQM QM/MM “QM/MM” E total = E QM + E MM + E QM/MM quantumclassicalinteraction QM only too many electrons MM only cannot treat electronic reorganisation Quantum mechanicsMolecular mechanics

‡ ‡ ‡ ‡ ‡ ‡ ‡ TYR ASP GLU ‡ ‡ ‡ ‡ ‡‡ ‡ ‡ ‡ ‡ ‡ ‡ ~36 CPU hrs per point on 2D projection of ~10 5 D QM/MM PE surface

Elaboration of series of MD simulations along an appropriate coordinate using a biasing potential Molecular dynamics: Newton’s Laws T = 300K QM/MM potential for 50,000 atoms within periodic boundary conditions A typical MD trajectory within an “umbrella sampling” window takes ~10 CPU days to perform 20 ps equilibration + 20 ps production run to average over the sampled configurations  Potential of Mean Force  Free energy changes corresponding to chemical kinetics and equilibria

timescale Pople: systematic improvement of QM methods electron correlation basis set systematic improvement of QM/MM MD simulations requires simultaneous advances in multiple dimensions, each one being computationally demanding MM atoms degrees of freedom exchange /correlation functional

Chemistry machine room: ~ 30 x Pentium PCs running Linux 3 x dual 2.2 GHz AMD Opteron, 2 x 4 Gb + 1 x 8 Gb memory, 2 x 80 Gb + 1 x 300 Gb disk IHW group’s computing resources at Bath BUCS machine room: Share of Skein (HEFCE JREI, May 2002) Upgrade 2007 with EPSRC funding (awarded) Further BBSRC pending decision Pauling (BBSRC, June 2005) Linux (SUSE 9) cluster with: 1 x Front-end dual 2.2 GHz AMD Opteron, 2 Gb memory, 1 Tb RAID 5 32 x (dual 2.4 GHz CPU, 4 Gb memory, 120 Gb disk) 4 x (dual-core dual 2.2 GHz CPU, 8 Gb memory, 120 Gb disk) Gigabit interconnect Thank you for listening!