JNU demo/hands-on Support: [email protected] Licenses: [email protected] Hands-on session 12 January 2017 Outline Background & overview Hands-on / demo o o o o o o o Getting started: building & optimizing molecules Results: MOs & fragment analysis, charges, Fukui functions
TDDFT and fast approximations Transition states (proton transfer) MO level diagrams, fragment analysis DFTB: fast DFT approximation COSMO-RS/SAC: thermodynamic properties ADF hands-on & demo for JNU, 12 January 2017 SCM 2 ADF Modeling Suite Easy to use: 1 GUI, 1 binary ADF hands-on & demo for JNU, 12 January 2017 SCM 3 EU fellows Business Developers The SCM team
Olivier: GUI Alexei: ADF ReaxFF Erik: ADF COSMO-RS Pier: BAND Hans: Linux GPU Python Thomas: DFTB Scripting Laurens:
GUI Ole: GUI ReaxFF Stan: CEO Fedor: Marketing Marc: BAND Damien: Scripting MOFs Sergio: Collaborations Mirko: ADF
BAND Evert Jan: Adviser Frieda: Invoices Licenses Anna: ReaxFF MOFs Kitty: Finance Michal, Robert: QM/ MM, excited states MD + many academic collaborations ADF hands-on & demo for JNU, 12 January 2017 SCM
4 Making computational chemistry work for you Latest computational chemistry tools Set up, run & analyze Passionate scientists Cross-platform 1 package: all modules Decades of expertise Easy install Windows, Mac, Linux [email protected] m
ADF hands-on & demo for JNU, 12 January 2017 SCM 5 ADF: Molecular DFT Strong & unique points All-electron Slaters, H-Og Relativity: ZORA (SR, SOC) Spectroscopy o Environments o
EPR, NMR, IR (VCD), UVVIS, XAS Subsystem DFT (FDE), DIM/QM, QM/MM Bonding analysis: o ETS-NOCV, QTAIM, MO diagrams, NCI, .... ADF hands-on & demo for JNU, 12 January 2017 SCM 6 ADFjobs: job bookkeeping switch GUI functionalitydefine & switch queues reports & templates see files for this job queue search
change default e.g. cores / nodes job status all jobs / folder view ADF hands-on & demo for JNU, 12 January 2017 SCM 7 Basic calculations & settings switch modules job types & set up search job type / template charge/spin functional & relativistic appr basis & numerical accuracy builder tools
ADF hands-on & demo for JNU, 12 January 2017 SCM = more details 8 Building molecules www.scm.com/doc/Tutorials/GUI_overview/Building_Molecules.html Import: SMILES, xyz, cif, pdb, Included library + building / drawing tools tools Nanoparticles: start from periodic => cut a cluster Surfaces from bulk ... Excercise: Build p-dicholorobenzene symmetrize & optimize (SR-BP-D3/DZP) ADF hands-on & demo for JNU, 12 January 2017 SCM 9
Visualizing results (I) See also the introductory GUI tutorial Open ADFlevels to see how the MOs are built up from atomic AOs o To analyze chemical bonding in detail: define fragments and run an EDA / ETS-NOCV Visualize the HOMO by right-clicking on it in ADFlevels ADF hands-on & demo for JNU, 12 January 2017 SCM 10 Visualizing results (II) Single point, select Fukui function as a property (see also tutorial) Find the condensed Fukui charges and local softness in the output and f describe electrophile / nucleophile reactivity from density change upon adding / removing an f Visualize the Fukui function(s) and/or dual descriptor electron
+ f=(N) (N 1) f+=(N + 1) (N) f(r) = f+ f- Dual Descriptor: >0 (<0) for electrophilic (nucleophilic) sites Condensed Fukui function fk: partition per atom, based on atomic charges Hardness h = I A DE(HOMO-LUMO) Softness S = 1/h Local softness = S* fk = fk/h See Yang & Parr, VUB, and others ADF hands-on & demo for JNU, 12 January 2017 SCM 11 Energy decomposition analysis E = Eprep + Eint Rev. Comput. Chem. 2000, 15, 1
Velstat + EPauli + Eoi + Edisp Esteric = Velstat + Epauli Eoi = decomposed in irreps. See tutorial & teaching exercises Extensions: ETS-NOCV: orbital interactions + deformation density M. Mitoraj et al., J. Chem. Theor. Comput. 5, 962 (2009) Periodic EDA: M. Raupach & R. Tonner, J. Chem. Phys.ADF 142, 194105&(2015): molecule-surface hands-on demo for JNU, 12 January 2017 SCM interactions 12 Excited states: TDDFT
Calculate the UVVIS spectrum for p-dichlorobenzene (see also tutorial) o o Under properties select Allowed only and the lowest 10 excitations Visualize the spectrum, change to nm, and select the NTOs for the lowest E peak (~265nm) ADF hands-on & demo for JNU, 12 January 2017 SCM 13 Fast excited states: sTDDFT, TD-DFT+TB, TDDFTB Calculate again with sTDDFT, TD-DFT+TB and TDDFTB (SCC halorg-0-1) o o o Compare timings & spectra
Why is sTDDFT or TD-DFT+TB not faster than TDDFT in this case? Try larger non-symmetric molecules again for a proper comparison! ADF hands-on & demo for JNU, 12 January 2017 SCM 14 Spin-orbit coupling TDDFT Calculate again with perturbative and full spin-orbit coupling o Do you see any difference? o Try again for dibromo-benzene (reoptimize!) ADF hands-on & demo for JNU, 12 January 2017 SCM 15 Transition states
Get close to the transition state See package finding TSs on 2. Good guess for the transition mode the teaching materials How to get a good guess geometry? pages Intuition*) + constrained optimization Linear transit Nudged elastic band *) e.g. from literature, geometry from a previous TS 1. How to get a good guess for the transition mode? Transition State Reaction Coordinate (TSRC) Hessian: full, partial, or mobile-block, maybe smaller basis & lower accuracy? Remember: a TS has 1 and only 1 negative Hessian eigenvalue ADF hands-on & demo for JNU, 12 January 2017 SCM 16
Proton transfer TS: tautomerization Import acetaldehyde from the database Add formic acid as catalyst Optimize with C-HO & OH distances constrained at 1.35 (PBE/DZP) Stop after ~ a dozen cycles update a good geometry in input as TS guess ADF hands-on & demo for JNU, 12 January 2017 SCM 17 Proton transfer TS: tautomerization
Remove the constraints Change the preset to TS search (change the numerical quality to good) Select details & define TSRC as increasing / decreasing proton distances After the job has finished, calculate frequencies (scan -100 to 0) ADF hands-on & demo for JNU, 12 January 2017 SCM 18 Proton transfer TS multi-layer Subtractive QM/MM: change ADF to QUILD Add two phenyl groups to acetaldehyde, define QM and QM region
For the total energy choose DFTB (SCC-DFTB) For the QM region choose ADF & subtract SCC-DFTB Change task to TransitionState ADF hands-on & demo for JNU, 12 January 2017 SCM 19 Multiple jobs, conformers Within the GUI you can o o o average spectra generate conformers set up a batch of similar jobs (e.g. change functionals, basis set etc.) See tutorials
With scripting (python or shell using adfprep/adfreport you can do even more advanced things ADF hands-on & demo for JNU, 12 January 2017 SCM 20 Faster methods: MOPAC, DFTB Search for vancomycin SMILES and paste it into GUI (will take some time) Pre-optimize a few times with UFF (cogwheel) Add water as a solvent with a sphere of 13.5 , (~1000 atoms in total) Run DFTB3/3ob and MOPAC optimizations o
o Which is faster? Does Mozyme help? Run a MOPAC/COSMO-RS on bare vancomycin ADF hands-on & demo for JNU, 12 January 2017 SCM 21 COSMO-RS with MOPAC Remove the solvent layer Run a MOPAC/COSMO-RS on bare vancomycin Calculate the octanol-water partition coefficient (log kOW) with COSMO-RS ADF hands-on & demo for JNU, 12 January 2017 SCM
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