Qm mm modelling lecture 3 some application examples workshop example cases for this afternoon
This presentation is the property of its rightful owner.
Sponsored Links
1 / 29

QM/MM Modelling Lecture 3 Some Application Examples Workshop Example cases for this afternoon PowerPoint PPT Presentation

  • Uploaded on
  • Presentation posted in: General

QM/MM Modelling Lecture 3 Some Application Examples Workshop Example cases for this afternoon. Quantum Simulation in Industry. Overview Objectives Extend QM/MM Codes and port to HPC architectures Incorporate QM/MM molecular dynamics for chemical reactions

Download Presentation

QM/MM Modelling Lecture 3 Some Application Examples Workshop Example cases for this afternoon

An Image/Link below is provided (as is) to download presentation

Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author.While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server.

- - - - - - - - - - - - - - - - - - - - - - - - - - E N D - - - - - - - - - - - - - - - - - - - - - - - - - -

Presentation Transcript

Qm mm modelling lecture 3 some application examples workshop example cases for this afternoon

QM/MM ModellingLecture 3Some Application ExamplesWorkshopExample cases for this afternoon

Quantum simulation in industry

Quantum Simulation in Industry


  • Objectives

    • Extend QM/MM Codes and port to HPC architectures

    • Incorporate QM/MM molecular dynamics for chemical reactions

    • Demonstrate the value of HPC simulations in industrial chemistry

  • Consortium

    • Daresbury (Coordinator)

    • Academic (Zurich/Muelheim, Royal Institution)

    • Industrial (Norsk Hydro, BASF, ICI)

  • Resources

    • Funded by the European Union (EU contribution of 1.2 MECU)

    • 1998-2001


Quasi partners

QUASI - Partners

  • Drs Paul Sherwood, Martyn Guest (Daresbury Laboratory)

    • Coordinator

    • Ab-initio and HPC implementations

    • ChemShell software

  • Prof Walter Thiel (MPI Muelheim)

    • Semi-emprical (MNDO94), QM/MM coupling

  • Prof Richard Catlow (Royal Insitution)

    • Classical simulation, shell model, force field derivation

  • Dr Steve Rogers (ICI)

    • Methanol synthesis by metal oxide catalysts (with Royal Institution)

  • Dr Ansgar Schaeffer (BASF)

    • Enzyme inhibitor simulation (with Zurich)

  • Dr Klaus Schoeffel (Norsk Hydro)

    • Zeolite catalysis for N2O abatement (with Daresbury)

Quasi workplan

QUASI - Workplan

  • Design

    • QM and MM validation

    • QM/MM coupling approaches (Daresbury,Zurich)

  • Enhancements to QM/MM Methodology

    • Geometry Optimisation for QM/MM Systems (Zurich/Daresbury)

    • Classical Shell Model QM/MM (Royal Institution/Daresbury)

    • Molecular Dynamics (DL/Royal Institution)

    • GUI Development (BASF/Daresbury)

    • Forcefield Development (Royal Institition)

  • Joint Academic/Industrial Applications

    • Demonstration and Commercial Calculations

    • Workshop 25-27 September 2000, Muelheim, Germany

Solvation studies using qm mm

Solvation studies using QM/MM

Hybrid modelling for zeolites

Hybrid modelling for zeolites

  • CVFF (Hill/Sauer forcefield)

  • Construct finite cluster (termination using charge corrections fitted to Ewald sum)

  • QM Model comprises T5 cluster + Cu, NO etc

  • Electrostatic embedding

The d h exchange reaction

The D/H Exchange Reaction

  • Collaboration with Shell KSLA

  • A symmetrical model for protonation reaction by zeolite Bronsted acid site

  • Extensively studied with bare cluster models

  • Study effects of zeolite environment by considering a range of possible acid sites

    • Embedding geometry

    • Electrostatics

    • Correlation with adsorbtion energies and acidities

  • Geometrical effects on the transition state are found to be dominant

CH4 + D+ CH3D + H+

Quasi applications focus

QUASI - Applications Focus

  • Norsk Hydro / Daresbury

    • Zeolites systems with adsorbed Cu species, decomposition of N2O and NOx

    • Based on CFF forcefield, GAMESS-UK+DL_POLY

  • BASF / Muelheim

    • Enzyme inhibitor binding (thrombin and anticoagulant drug candidates)

    • Enzyme reactivity modelling (Triose Phosphate Isomerase)

    • Using MNDO/TURBOMOLE with CHARMM forcefield (DL_POLY)

  • ICI/ Royal Institution

    • Modelling surface catalysis, methanol synthesis reaction

    • Using GULP shell model potentials and GAMESS-UK DFT

Embedded cluster and qm mm applications

Embedded cluster and QM/MM Applications

  • Proton transfer (ZOH+ + NH3 -> ZO- + NH4+)

    • S.P. Greatbanks, I.H.Hillier and P. Sherwood, J. Comp. Chem.,18, 562, 1997.

  • Methyl shift reaction of propenium ion

    • P. Sherwood, A.H. de Vries, S.J. Collins, S.P.Greatbanks, N.A. Burton, M.A. Vincent and I.H. Hillier, Faraday Discuss., 106, 1997

  • Alkene chemisorption

    • P.E. Sinclair, A.H. de Vries, P. Sherwood, C.R.A. Catlow and R.A. Van Santen, J. Chem. Soc., Faraday Trans.,94, 3401, 1998

  • D/H exchange reaction for methane

    • A.H. de Vries, P. Sherwood, S.J.Collins, A.M. Rigby, M. Rigutto and G.J. Kramer, J. Phys. Chem. B, 103, 6133 (1999)

Methane d h exchange reaction












Methane D/H Exchange Reaction

  • A. H. de Vries, in collaboration with Shell IOP, Amsterdam

  • A degenerate model reaction for acid-catalysed cracking processes

  • Rates experimentally accessible for a range of systems

  • Studied by QM/MM for a range of zeolite sites

D h exchange methodology

D/H Exchange - Methodology

  • QM/MM Scheme

    • T5 QM region, electrostatic embedding, 3-21G geometries and 6-31G* energies

    • 1500 atom finite MM cluster, Madelung correction

    • Si-H termination

    • Delete bond dipole contributions, apply charge shift and dipole correction

    • CFF valence forcefield (Hill and Sauer)

    • Electrostatics from charges fitted to Periodic HF potentials

  • Geometry Optimisation

    • relaxation of 5 bonds from QM region

    • P-RFO in mixed Z-matrix/cartesian coordinates






q=qSi +0.5*qO

D h exchange reaction results

D/H Exchange Reaction - Results

  • Relaxation and TS searching for embedded models now practical

  • Can differentiate of protonation energies for the 4 distinct oxygen sites (FAU)

    • correctly predict protonation at O3 (at 6-31G*), with O1 site slightly (1kJ/mol) higher

  • Results emphasise importance of mechanical constraints

    • Highest activation energies can be identified with sites with non-planar Si-O-Al-O-Si fragments

    • For remaining structures, a strong correlation seen between activation energy of D/H exchange with the chemisorption energy of ammonium (analogous bidentate structures)

  • Absolute values of D/H exchange activation energies too high (single point MP2 correction based on HF structures)

    • 160 (computed) vs 109 +/- 15 kJ/mol (MFI)

    • 175 (computed) vs 129 +/- 20 kJ/mol (FAU)

Methyl shift of the propenium ion

























Methyl shift of the propenium ion

  • QM/MM model similar to previous case

  • Optimise end-points (propoxides) and transition state

    • mechanical embedding

      • no charges on QM region, only includes geometric/steric effects

    • electrostatic embedding

      • introduce QM charge interaction with MM lattice

Analysis of energy barriers

Analysis of Energy Barriers

  • Mechanical embedding case is easy to decompose into QM and MM terms

    • Z-(C,H) nb is the zeolite…hydrocarbon non-bonded energy

  • QM-MM Electrostatic interaction is estimated by calculating interaction of a classical representation of the QM region (Dipole Preserving Charges, DPC) with the MM point charges

  • Role of MM polarisation is estimated using single-point calculation of interaction of DPC representation of QM region with polarisabilities at Si and O sites.

Quasi zeolite catalysis applications

Demonstration phase

NO, NO2 (Automotive exhaust gas)

Energetics and structure of Cu species coordinated to the zeolite framework.

Absorbed Cu-NO species, structure and vibrational spectra

Decomposition chemistry of NO to N2O, N2 and O2

Target Applications

N2O (off-gas from HNO3 production)

Binding of N2O with the active site

Binding energies and vibrational frequencies

Thermodynamics of N2O decomposition pathways

Influence of other components of the off-gas (O2, NOx ,H2O), inhibitor action, binding energies etc.

QUASI Zeolite catalysis applications

NOx decomposition on zeolite supported copper catalysts

Lead Partner: Norsk Hydro

Enzyme catalysis applications

Demonstration phase

Variation of inhibitor binding enthalpies and free energies with QM region and electrostatic interactions

Determination of activation energies, variation with QM scheme and QM/MM coupling.

Comparison of substrate structure with X-ray results

Target Applications

Influence of active site features on inhibitor binding energies and activation energies.

Systematic study of free energies of binding for novel inhibitors, inhibitor design

Understanding the mechanism of TIM action.

Enzyme catalysis applications

  • Enzyme/inhibitor binding energetics for thrombin

  • Mechanistic studies of enzyme catalysis - triosephosphate isomerase (TIM)

Lead Partner: BASF

Hybrid models for enzymes

Hybrid models for enzymes

  • Electrostatic embedding (L1 for semi-empirical, L2 and charge shift schemes)


  • MM: DL_POLY (CHARMM forcefield)

  • QM/MM cutoffs based on neutral groups

Qm mm application

QM/MM Application

  • Triosephosphate isomerase (TIM)

  • Central reaction in glycolysis, catalytic interconversion ofDHAP to GAP

  • Demonstration case within QUASI (Partners UZH, and BASF)

  • QM region (>33 atoms)

    • include residues with possible proton donor/acceptor roles


  • MM region (4,200 atoms + solvent)

    • CHARMM force-field, implemented in CHARMM, DL_POLY

Enzyme qm mm applications tim

Enzyme QM/MM Applications - TIM

Solid state embedding scheme

Classical cluster termination

Base model on finite MM cluster

QM region sees fitted correction charges at outer boundary

QM region termination

Ionic pseudopotentials (e.g. Zn2+, O2-) associated with atoms in the boundary region


Shell model polarisation

Classical estimate of long-range dielectric effects (Mott/Littleton)

Energy Expression



suitable for ionic materials


require specialised pseudopotentials


metal oxide surfaces

Solid-state Embedding Scheme



Implementation of solid state embedding

Implementation of solid-state embedding

  • Under development by Royal Institution and Daresbury

  • Based on shell model code GULP, from Julian Gale (Imperial College)

  • Both shell and core positions appear as point charges in QM code (GAMESS-UK)

  • Self-consistent coupling of shell relaxation

    • Import electrostatic forces on shells from GAMESS-UK

    • relax shell positions

GAMESS-UK SCF & shell forces

GULPshell relaxation

GAMESS-UK atomic forces

GULP forces

Quasi surface catalysis applications

Demonstration phase

Geometry and electronic structure of bulk and surface QM clusters as a function of cluster size.

Adsorption of Cu(I) on the ZnO surface

Absorption energies, IR spectra and PES for CO on Cu and Zn sites

Target Applications

Stability of Cu clusters of different sizes and ox. states

Structure and energetics of absorption for formate, methoxy and carbonate on the surface, 13C chemical shifts

Transition states for proton and hydride transfer steps

Understanding promoter action

QUASI - Surface catalysis applications

Methanol synthesis from synthesis gas (CO, CO2 and H2) using the ternary catalyst system Cu/ZnO/Al2O3

e.g. CO + 2H2 -> CH3(OH)

Lead Partner: ICI

Solid state embedding for oxide surfaces

Solid-state embedding for oxide surfaces

  • Finite cluster model, outer sleeve of fitted charges charges from 2D Ewald summation


  • MM: GULP

  • Solid-state embedding scheme

    • Based on ZnO shell model potential

    • Boundary atoms carrying both shell model forcefield and pseudopotentials

Qm mm modelling lecture 3 some application examples workshop example cases for this afternoon

Some sample clusters on the ZnO surface

Methanol synthesis reaction

Methanol Synthesis Reaction

  • Initial adsorption of CO2 and H2.

  • Upon adding an electron the CO2 bends and the extra electron populates an antibonding level. The interaction with the surface stabilises the radical CO2- species.

  • The adsorbed CO2- is hydrogenated by surface hydrogen to formate.

  • Further hydrogenation can proceed either through the formation of H2CO2- or HCOOH- (formic acid)

  • Further hydrogenation and interactions of the resulting species with the surface and possible surface defects lead to a large variety of possible intermediates.

  • Methanol is removed from the surface and the active site is recycled by desorption of carbon dioxide and water

Adsorption of copper clusters

Adsorption of copper clusters



  • QUASI software developments

    • Geometry optimisation, CHARMM interfacing, G98 interface

      • Walter Thiel, Frank Terstegen, Salomon Billeter, Alex Turner

    • TURBOMOLE interface

      • Ansgar Schäfer, Christian Lennartz

    • Solid-state embedding

      • Alexei Sokol, Sam French, Richard Catlow

  • Other Collaborators


      • Bernie Brooks, Eric Billings

    • ChemShell developments, models for zeolites

      • Alex de Vries, Simon Collins, Ian Hillier, Steve Greatbanks

      • CEC, Shell SIOP Amsterdam

Workshop examples

Workshop examples

  • Simple QM and MM calculations using ChemShell

Sn2 ts ch 3 cl cl with explicit solvent

SN2 TS (CH3Cl + Cl-) with explicit solvent

  • task -> optimise, qm/mm

  • load from mini_ts.pdb

  • QM code to mndo

  • QM Charge to -1

  • DLPOLY FF - choose “use charmm”

  • optimiser -> hdlcopt

  • check find ts

  • residue_treatment to “PDB Residues/Select”

  • Login