Using Web-Based Computations in Organic Chemistry

Transcription

1 10/30/ Using Web-Based Computations in Organic Chemistry John Keller UAF Department of Chemistry & Biochemistry The UAF WebMO site Practical aspects of computational chemistry theory and nomenclature MOPAC2016: fast and approximate NWChem: slow and accurate Example tasks: Energy, Optimization, vibrational spectra; UV spectra.

2 10/30/ Click here to log in (guest/webmo or yourusername/password)

3 10/30/ How does a WebMO job work? webserver world wide web User Draw molecule & choose options WebMO creates input file for MOPAC or NWChem When the job is done, the output file is parsed and shown on Results page. The updated, intermediate results can be visualized in the Job Manager. compute servers obsidian antec12 (& others). Running Gaussian, MOPAC, and NWChem

4 10/30/ User Accounts MOPAC NWChem Gaussian CPU job time limit (h) guest 4 uaaguest 12 Non-UAF unlimited UAF unlimited Machines Server Cores Procs Mem (GB) CPU Gaussian 09 NWChem 6.6 Chemlinux Xeon (2) Chemlinux Xeon (2) Chemlinux Xeon (2) Antec Core i7 5820K Corsair Core i7 6950X Obsidian Core i7 930 MOPAC 2016

5 10/30/ Levels of theory Correlated ab initio MO (MP2 & others) Molecular mechanics (MM+, OPLS, etc) Ball-andspring model no orbitals no electronics Semi-empirical MO (PM3, PM6, PM7) Uses 27 orbital parameters for each element Parameters derived from stable molecules Electron correlation implicit, since the parameters are fr real molecules, where actual electron correlation occurs. Ab initio MO (Hartree-Fock HF) MOs = linear combination of basis orbitals. Parameters derived from isolated atoms Some electron correlation Density Functional Theory (DFT) (B3LYP ) MOs = linear combination of basis orbitals Parameters derived from atoms and molecular databases More electron correlation MOs = linear combination of basis orbitals. Parameters derived from isolated atoms Includes excited state configurations Most electron correlation

6 10/30/ Basic WebMO and MOPAC 1) Build hexatriene; load and modify morphine. 2) Optimize Use MOPAC PM7

7 10/30/ Log in

8 10/30/ Begin with New Job, Create New Job

9 10/30/2017 9

10 10/30/ Select with mouse. Then use the Adjust menu to change torsion angles, bond distances

11 10/30/ Optimize your molecule 1) Right Arrow 2) Engine: MOPAC 3) Select Server: First Available

12 10/30/ Enter an informative Job Name Type of calculation Geometry Optimization Theory: PM7 (a recent version of PM3 semi-empirical) Charge: (0 for molecule) Multiplicity: generally singlet (unless odd # of valence e - )

13 10/30/ Generate on the Preview tab shows the input file automatically created by WebMO. It can be modified manually. Submit job by clicking the right arrow

14 10/30/

15 10/30/ NWChem software Review MOs Basis sets Performance comparison: system size and basis set choice Typical NWChem jobs: Energy, Opt, Vibrations, UV

16 10/30/ On-line NWChem User s Reference

17 H 2 MOs: formed by linear combination of 1s atomic orbitals. 17 Electron density (0.008 e/å 3 ) node node anti-bonding MO H atom H atom bonding MO 1s AO 1s AO d = 0.76 Å d = 2.8 Å d =

18 18 In semi-empirical MO theory (PM6 and others), molecular orbitals are formed by linear combinations of s, (and on heavy atoms) p x, p y, and p z AOs. s p x p y p z The orbital functions on the constituent atoms are the basis set.

19 10/30/ NWChem and other QM programs use larger basis sets. The most common are split-valence basis sets. Basis orbital for core electrons of 2 nd row atom contains 6 Gaussian terms. 6-31G(d) 2 nd row atoms have an additional set of six d-type orbitals. Inner valence shell orbital contains 3 Gaussian terms. Outer valence shell orbital contains 1 Gaussian. H 2 O has 19 orbitals in the 6-31G(d) basis. O: 1s + 2s,2p x,2p y,2p z + (2s,2p x,2p y,2p z ) + 2(d xx,d yy,d zz,d xy,d yz,d xz ) H: - 1s + (1s) H: - 1s + (1s)

20 10/30/ Tetracycline (32) Vitamin B-6 (16) a-cyclodextrin (66) SO 2 -formic acid (6 heavy atoms)

21 10/30/ # Heavy atoms Basis set/# of basis orbitals 3-21G 6-31G(d,p) G(2d,2p) G(3df,3pd) SO 2 -formic acid Vitamin B Tetracycline a-cyclodextrin

22 10/30/ ~ 20 optimization steps 6.5 da 20 h Basis set Basis set small large Small molecule OK OK Large molecule OK (no) Hartree-Fock; Corsair3; 10 processors

23 10/30/ NWChem input file format Energy Geometry Optimization Vibrational Frequency UV spectrum

24 10/30/ NWChem input file format Energy (single point) Job name charge molecular description Basis set theory multiplicity Calculation type

25 10/30/ NWChem input file format WebMO default - Optimization

26 10/30/ You may wish to add sections to modify some parts of the input file. scf noprint "final vectors analysis" singlet end driver maxiter 100 end NWChem stops after 20 optimization steps by default so, increase the limit this way. task scf optimize

27 10/30/ Geometry Optimization View Results

28 10/30/ NWChem input file format - Vibrational frequencies title "H2O-631Gs-HF-Freq" echo charge 0 geometry O H H end basis noprint * library 6-31G* end scf noprint "final vectors analysis" singlet end task scf freq Sally 3249 pulegone vib

29 10/30/ Vibrational Frequencies View Results

30 10/30/ From Japan Spectral database Pulegone Exp tl B3LYP/6-31G(d) HF/6-31G(d) (This is why one should use HF or DFT methods for IR.)? PM7

31 10/30/ UV-Vis spectra More conjugated double bonds lead to lower energy gap, lower frequency and longer wavelength. DE = hn = hc/l

32 10/30/ NWChem CIS (configuration interaction singles) mixes 10 single excited states Etc

33 10/30/ UV-Vis spectra

34 10/30/

35 10/30/ C=C yellow Plot line colors are arbitrary. 9 yellow-orange 11 orange-red

36 10/30/ Your questions