Theoretical calculations of NMR/EPR parameters

Exercises Michal Straka 17.7.2003

Assisted by Christian Remenyi and Alexander Panchenko

Motivation

• Why do we need calculations?

– To complement, support, confirm experiment – To calculate immeasurable – To understand – To predict

What can be calculated?

• NMR/EPR parameters: –

g-tensors

– Chemical shifts,

including SO correction

– Spin-spin coupling – Hyperfine coupling,

including SO correction

–

Zero-field splitting

(coming soon) • Analysis in terms of orbitals, spin density etc.

• Generally single gas-phase molecule, but: – Solvation effects (HFC) possible – Molecular dynamics (shots from MD) possible

Software (selection)

• Common packages – Gaussian www.gaussian.com

– Turbomole www.turbomole.com

- ADF www.scm.com

, Aces II www.qtp.ufl.edu/Aces2 • Our wavefunction packages + property codes – deMon( www.deMon-software.com

) + Master – Respect + Mag • Our special interfaces – GS2RS, DEM2MAG,TM2MAG • Visualization packages – Molden ( www.cmbi.kun.nl/~schaft/molden ) – Molekel ( www.cscs.ch/molekel )

Possibilities

Software Gaussian 98 Turbomole Mag ADF ACES CS Y Y Y Y Y SOCS SSC HFC SOHFC GT ZFS N N N N Y N N N N N N N Y Y Y Y Y Y Y Y Y Y ?

Y ?

N N N N N CS - chemical shift SOCS – spin-orbit chemical shift SSC – spin-spin coupling HFC - hyperfine coupling SOHFC – spin-orbit hyperfine coupling GT – g-tensor ZFS – zero-field splitting

Calculations

• We should know which method, level of approximation, basis set ,and code to use to get

desired accuracy

in

reasonable

time.

• Depends of

size

and

type

of system – Carbohydrates easy, actinides difficult (rel.+ corr.) • Might be simple: CS or HFC with Gaussian 98 – One input , one run • Might be complicated: MD simulations of g-tensor of the semibenzoquinon radical anion in water (James Asher) – CPMD (dymanics)>TURBOMOLE(calculate WF of shots)>TM2MAG(interface)>MAG(g-tensor)

• • • • Praktikum

Login:

“ssh [email protected]

”, then “ssh mk62” – For password write mail to [email protected]

– Current password valid till end of July, then e-mail me Linux comands “ls” list, “cd” change dir, “cp” copy. For more, see linux_small.ps in ~/Documentation

Policy:

– Always make special directory with your name and do everything there • mkdir ~/remenyi;cd remenyi – Or use one of the student? directories • “cd;cd student4/seminar2003” – See /home/straka/dqs how to run specifically in queue • “qsub –q machine Job” • “qstat -f” shows jobs in queue – Longer jobs (>1h) always to the queue, see also /home/prog/OUR_HAREM

Documentation:

is in ~/Documentation – Linux book, using vi, DFT theory and this document • scp –r Documentation mylogin@myhost:mydir

Exercise 1 :Calculating HFC of nitrogen atom • • • – – – Use different programs to calculate HFC on N atom Gaussian 98 > GS2RS > MAG Respect + Mag Gaussian 98 does not calculate SO correction, but knows more functionals – Use Gaussian 98 to see the method dependence Possible methods HF, BP86, BLYP, BPW91, B3P86, B3LYP, B3PW91, MP2 – Use IGLO-II basis set Optional: Use Gaussian 98 to see basis set dependence

Doing exercise 1 (~/seminar2003/HYPERFINE_N_ATOM) • HFC with Gaussian 98 – Have a look at Gaussian input (less hf_n) – Look into Job file (JobHFCG98) – Run Gaussian Job (./JobHFCG98) – Have a look at output (less hf_n.out) – Try different functional (optional, look in TASK file) • SO correction to HFC – Run makefchk (makefchk hf_n) – Run GS2RS interface(GS2RS-FC hf_n) – Look at produced input (hf_n.out) and at SOHFC.M

– Run Job(./JobHFCMAG) – Have a look at output (less *OUT*) • HFC with Respect + Mag (./SO) – Look at input for Respect (less so-resp.inp) – Run Job (./JobHFCSO) – Have a look at input for Mag and both outputs(less SOHFC.M, less *.out, less *OUT*)

• • • Exercise 2: Chemical shifts, SO correction Optimize geometry of HCCI at B3LYP/SDDAll level using Gaussian 98 • • Use optimized geometry to calculate chemical shifts in HCCI, suppose 13 C Using Gaussian, GIAO, IGLO-II basis set Using deMon+Master and common gauge origin on iodine, IGLO-II basis set • Calculate spin-orbit chemical shifts of 1 H and 13 C atoms in HCCI Use deMon+Master, IGLO-II basis set, and common gauge origin on iodine

Doing exercise 2(~/seminar2003/CSHIFTS) • Geometry optimization with Gaussian – Prepare Z-matrix, look at optgeo input (Molden, less optgeo) – Run it first with JobOPTGEO (./JobOPTGEO) – Look at optgeo.out (less optgeo.out) • NMR with Gaussian – Copy optgeo.chk to cs.chk, run JobCS(cp optgeo.chk cs.chk;./JobCS) – Meanwhile look at input (less cs_giao) – Look at output cs_giao.out(less cs_giao.out) • 32.34-30.58=1.76, exp. +2.23

• NMR with deMon + Master (./demon) – Run ./JobCS – Get optimized xyz, put into hcci.inp, look at hcci.inp(less hcci.inp) – Look at output, for H atom 31.02-28.36=+2.66, exp. +2.23

• SO NMR with deMon + Master (./SO) – Look at so4.inp, run JobSO, look at COMM_I.M

– Look at so4.out, so4*OUT* • H atom, exp=+2.23; we get 31.02-28.36-(-0.53)=3.19

• or 32.24-30.58-(-0.53)=2.19

Exercise 3:Optional • • Look at each exercise we tried and find TASK files inside, there you find some additional exercises Find exercises from 2002 in /home/prog/Documentation/GK_theory.doc and try to work them out

Acknowledgement

• Martin Kaupp • Christian Remenyi • Alexander Panchenko • Herbert Dilger