Project 1 Report File: Chem4PB3_project_1_2017-solutions last changed: 02-Feb-2017
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1 Project 1 Report File: Chem4PB3_project_1_2017-solutions last changed: 02-Feb Formaldehyde comparison of results from different methods Yellow shaded boxes are closest to experimental Method #e- DFT Experimental Property AM1 MM - UFF HF STO- 3G HF STO-3G forced C 2v RHF 6311G forced C 2v B3LYP forced C 2v E (ev), r (pm) wavenumbers method AM1 UFF RHF RHF RHF DFT - B3LYP - Basis set minimal none STO-3G STO-3G 6-311G 6-311G - # basis functions # iterations CPU time (s) Energy (hartree) (*) Dipole Moment (debye) Reported symmetry Cs Cs Cs C2v C2v C2v C2v R(C=O) (pm) R(C-H) (pm) φ(h-c=o) ( o ) φ(h-c-h) ( o ) Torsion (planarity) ( o ) O 1s a C 1s a O 2s a C 2s a σ(c-h) b σ(c-h) a π(c=o) b O LP/CH b π*(c=o) - b σ*(c-h) σ*(c-h) σ*(c=o) CH2 s-str a (IR, R) CO str a (IR) CH2 scis a (IR, R) CH2 a-str b (IR) CH2 rock b (IR) CH2 wag b (IR
2 Formaldehyde ground state DETAILS of the calculations AM1 ZDO basis set (*) computes valence electrons only Geometry : Cs E hartree (1 hartree = ev) Imaginary freq: 0 Dipole moment: Molecular Mechanics used UFF force field Amber did not produce results No electronic structure information, only geometry & Thermochemistry HF- small basis set: restricted, STO-3G basis Found I only ran it with frequency, not optimization Re-ran using CLEAN, and POINT GROUP = C2v. Did not run formaldehyde - HFR STO-3G Redundant internal coordinates taken from checkpoint file: formaldehyde-hfr-sto-3g.chk Charge = 0 Multiplicity = 1 C,0, , ,0. O,0, , ,0. H,0, , , H,0, , , WANTED AN INTEGER AS INPUT. FOUND A STRING AS INPUT. formaldehyde - HFR STO-3G STRANGE - the com file looked sensible - could not see a non-numerical value Problem was the additional keywords I had included, genchk in particular (that allows restart but only works AFTER you have one valid calculation to generate the first *.chk) 2
3 HF large basis set (6-311G) There are now way more (8 occ, 24 unocc) basis functions than the minimal basis description used to generate the simple LCAO-MO picture. The (extra) unoccupied orbitals are usually viewed as meaningless by the ab initio QM community. For spectroscopists however, they can be useful to describe the Rydberg excited states. In general they are fluffier orbitals than those that come out of the STO-3G minimal basis description. You need to look at the MO pictures to map specific ones of the 24 unocc. MOs in the 6311G picture to the 4 unocc. MOs of the minimal basis description. Orbital symmetries: Occupied (A1) (A1) (A1) (A1) (B2) (A1) (B1) (B2) Virtual (B1) (A1) (B2) (A1) (A1) (B1) (B2) (B2) (A1) (A1) (A1) (B1) (B2) (A1) (A1) (B2) (B1) (A1) (B2) (B1) (B2) (A1) (A1) (A1) The electronic state is 1-A1. Alpha occ. eigenvalues Alpha occ. eigenvalues Alpha virt. eigenvalues Alpha virt. eigenvalues Alpha virt. eigenvalues Alpha virt. eigenvalues Alpha virt. eigenvalues Some general comments 1. AM1 is by FAR the best at computing orbital energies that agree with PES IPs, within Koopman s Theorem. Perhaps that is no surprise as AM1 is most likely parametrized based on matching to valence IPs as well as other data. See for details on how the parameters in various semi-empirical codes were established. 3
4 AM AM1 Predicted vs. actual Vib. Freq. Calculated (ev) STO-3G HF 6311G DFT Calculated STO-3G HF-6311G DFT 1500 Calculated vs. experimental IPs Experimental (ev) Experimental Experimental data source of GEOMETRY, dipole moment: Sources of photoelectron spectra & IPs (a) XPS K. Kuramoto, M. Ehara, H. Nakatsujia, M. Kitajima, H. Tanaka, A. De Fanis, Y. Tamenori, K. Ueda J. El. Spec 142 (2005) (b) PES He(II) M.P. Kean, S. Lunell, A. Naves de Brito, M. Carlsson-Gothea, S. Svensson, B. Wannberg and L. Karlsson, J. El. Spec 56 (1991) (c) PES He(I) - A. D. Baker, C. Barer, C.R. Brundle and D. W. Turner,, Int. J. Mass Spec 1 (1968) 285 Adiabatic 10.88(4) ev, 14.09(5) ev, 15.85(4) ev, and 16.25(4) ev, ~20.5 Vertical 10.88(4) ev, 14.38(8)eV, 16.00(9)eV, and ev 4
5 Orbital plots (HF STO-3G) O 1s a1 C 1s a1 O 2s a1 C 2s a1 Pi & C-H sig (C-H) (σ*(c=o) π(c=o) σ(c-h) (& O lone pair using the default e- threshold π*(c=o) σ*(c-h) σ*(c-h) σ*(c=o) 5
6 1b. Electronic (UV-vis) Spectroscopy (Ann. Rev. Phys. Chem : 31-58) For the HF (STO-3G), HF (6-311G) and DFT calculations, using the TDSCF energy method gives Excited state AM-1 HF-STO-3G HF-6-311G DFT BL3LYP EXPERIMENT 1 symmetry A2 A2 A2 A2 Energy (ev) Intensity (osc str) Dominant config 6 7 (0.705) NB add 2 to match orb# 5 -> 9 (.12) 8 -> 9 (.70) 8 -> 9 (0.70) 8 -> 9 (0.70) 2 symmetry B1 B1 B1 B1 Energy (ev) Intensity (osc str) Dominant config 6 -> 8 (.61) 6 -> 9 (.71) 6 -> 9 (.70) 6 -> 9 (.70) 3 symmetry A1 A1 B2 B2 Energy (ev) Intensity (osc str) Dominant config 6 -> 9 (0.62) 6 -> 12 (.18) 8 -> 10 (0.69) 8 -> 10 (0.71) 7 -> 9 (.68) AM-1 HF STO-3G E in ev HF 6-311G DFT BL3LyP 6-311G STO-3G output Excited State 1: Singlet-A ev nm f= <S**2>= > > Homo (O LP) Lumo (π* C=O ) A 1 A 2 forbidden in C 2v Excited State 2: Singlet-B ev nm f= <S**2>= > σ(c-h) a1 Lumo (π*) Excited State 3: Singlet-A ev nm f= <S**2>= > > π C=O a1 Lumo (π*) Formaldehyde is a common preservative in cosmetics, but this compound is also known as an irritant agent that can cause contact allergy [1]. Formaldehyde is frequently used in water-based formulations such as shampoo, conditioner, shower/bath gel, liquid hand wash. [2]. Even products designed for children such as bubble bath or baby shampoo include formaldehyde in their composition. (Analytica Chimica Acta 674 (2010) 59 63) 6
7 7
8 2. Diels-Alder reaction PM3 semiempirical calculation Ground state Energies 1 atomic unit (or Hartree) equals kj/mol pm3 HF 3-21G Molecule Total energy (Hartree) Total energy (kj/mol) Total E (10 5 kj/mol) 1,3-Butadiene - cis ,3-Butadiene - trans Ethene REACTANTS Cyclohexene Transition state
9 Cis-Butadiene followed the instructions in the Harvey website NB the starting geometry was not carefully done. Perhaps should do an MM optimization first? (Spartan had a clean-up procedure in its input process; Gaussian has the same Edit~Clean ) For butadiene there are multiple SCF done cycles have to get to the LAST ONE to get final optimized energy line 248/4645 SCF Done: E(RPM3) = A.U. after 20 cycles line 479/4645 SCF Done: E(RPM3) = A.U. after 16 cycles line 652/4645 SCF Done: E(RPM3) = A.U. after 16 cycles line 826/4645 SCF Done: E(RPM3) = A.U. after 14 cycles line 998/4645 SCF Done: E(RPM3) = A.U. after 13 cycles line 1172/4645 SCF Done: E(RPM3) = A.U. after 12 cycles geometry restored to original line 1343/4645 SCF Done: E(RPM3) = E-01 A.U. after 12 cycles.... line 4371/4645 SCF Done: E(RPM3) = E-01 A.U. after 13 cycles ============ used clean, and then the default input file, not the Harvey modified one line 248/1774 SCF Done: E(RPM3) = E-01 A.U. after 12 cycles... line 1503/1774 SCF Done: E(RPM3) = E-01 A.U. after 13 cycles ============ using the Harvey format, get same answer line 1503/1774 SCF Done: E(RPM3) = E-01 A.U. after 13 cycles ======================== Cis-Butadiene Trans butadiene ======================== 9
![77 kj/mol] Thus pm3 method over-estimates the Thermochemistry by ~*4 ======================== Ethene SCF Done: E(RPM3) = 0.](/docs-images/71/65846055/images/10-1.jpg "264660251344E-01 A.U. after 7 cycles ======================== Cyclohexene SCF Done: E(RPM3) = -0.")
10 Trans butadiene line 993/1278 SCF Done: E(RPM3) = E-01 A.U. after 13 cycles Energy difference (cis trans) = 3.05 kj/mol [literature says trans is more stable than cis by 3.21 kcal/mol, or 0.77 kj/mol] Thus pm3 method over-estimates the Thermochemistry by ~*4 ======================== Ethene SCF Done: E(RPM3) = E-01 A.U. after 7 cycles ======================== Cyclohexene SCF Done: E(RPM3) = E-02 ======================== Diels Alder Thermochemistry 10
11 ============= using the supplied hint geometry, but had to rebond in a sensible manner 1st try, I used just OPT & TS (Berny) structure reverted to two non-bonded molecules with delocalized bonding in the butadiene 2 nd try, I added partial bonds to make the D-A adduct, and then used OPT&FREQ line 3212/4218 SCF Done: E(RPM3) = A.U. after 2 cycles is LAST of the SCF Done imaginary frequency (the ethane moving against the cis butadiene) = cm -1 Movie made of the motion along the reaction co-ordinate (the imaginary frequency) 11
12 3. nmr calculation for pyrazinamide used RHF/6-31G calculations (forgot the d ) from my RHF/6-31G calc nucleus Chem. Shift ppm wrt ref. Calc (*) isotropic anisotropy C C C C C H H H H H (*) Chis et al. Chem. Phys 316 (2005) 153 ; B3LYP/6-31G(d) for C-1 monomer (see below) My geometry 1 C C C C H H H N N N C O H H
13 C nmr H nmr The poor agreement of the predicted 1 H chemical shifts for H13 and H14 with experiment are because this molecule likes to dimerize by forming H-bonds between H14-O9 (see V. Chis et al. Chemical Phys. 316 (2005) 153). Note that the Chis et al calculations also show BOTH H-13 and H-14 too low, even though only H-14 is implicated in the H-bonding. 13
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