VBTutorial4
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To the Tutors
Sason remarks and prospective 2 hours talk +
Philippe's remark on the initially proposed tutorial. are included in bold.
Qualitative
- ?...
Computational
Proposal from Yirong
- benzene and formamide - focus is on the structural and energetic impact from conjugation, and how to correlate the results with experimental evidences;
- butadiene - focus is on the conjugation in the planar structure and the hyperconjugation in the staggered structure, and their impact on the rotational barrier;
- acid-base and H-bonding systems: BLW energy decomposition analyses.
- visualize the results. I have been using GaussView and ChemDraw, but other graphical software should be fine with me as well.
- Questions from any participant can be discussed and tested on site.
BLW within GAMESS (Version: MAR-25-2010 R2)
INPUT (for new file roblw.src)
$BLW group
BLW refers to the Block-Localized Wave function (BLW) method, which is a variant of the ab initio Valence Bond (VB) theory. This code can perform RBLW calculations for close-shell systems and ROBLW calculations for open-shell systems. It can also be combined with the grid-DFT calculations. The algorithm to derive self-consistent BLW is based on:
1) E. Gianinetti; M. Raimondi; E. Tornaghi, Int. J. Quant. Chem. 60, 157-166(1996). 2) A. Famulari, E. Gianinetti, M. Raimondi, M. Sironi, I. Vandoni, Theor. Chem. Acc. 99, 358-365(1998). 3) Y. Mo, S. D. Peyerimhoff, J. Chem. Phys. 109, 1687-1697 (1998). 4) Y. Mo, J. Gao, S. D. Peyerimhoff, J. Chem. Phys. 112, 5530-5538 (2000). 5) L. Song, Y. Lin, Y. Mo, J. Phys. Chem. A, 111, 8291-8301 (2007).
NBLOCK = number of blocks, the definition of each block shall be listed in $BLWDAT group. If nblock=1, it’s just a regular RHF/ROHF calculation.
ITER = maximum number of BLW cycles (default=50)
SCFCOV = NONE, do not take any actions during the SCF iterations DAMP, use damping of the Fock matrix if energy rises DIIS , selects Pulay's DIIS interpolation (based on FOCK matrix) DDIIS, selects Pulay's DIIS interpolation (based on density matrix) (default=DIIS)
COSGRD = a flag to disable/enable using coarse grid DFT calculation before the initial convergence. The GAMESS always starts grid DFT with coarse grid to accelerate the calculation. But if one needs to obtain the polarized energy, the energy of the first iteration shall be exact. Then the DFT calculation shall be switched to full grid from the first iteration. (default=.TRUE.)
IFZB(1) = an array that lists the blocks to be frozen (orbitals kept unchanged) during the optimization. This is useful to examine individual polarization effects, for example.
$BLWDAT group (required by $BLW) For each block: NE NBF IFLAG List of basis functions
NE is the number of electrons of that block. NBF is the number of basis functions of that block. IFLAG is an input control. IFLAG = 0, all the basis functions shall be specified;
1, the basis functions are sequential, and only the first one and the last one need be specified;
-1, this block has all the rest basis functions, thus no further specification.
The initial guess can be setup after the definitions of all blocks. It can be useful if the program fails to obtain convergence or one needs to derive the polarized energy term for the BLW-ED (energy decomposition) analysis. Note that the coefficients of MOs correspond to the list of basis functions in the definition lines of blocks.
For example: -------------------------------- $BLW NBLOCK=2 $END $BLWDAT 4 4 0 ← block 1 has 4 electrons and 4 basis functions 1 2 3 4 ← bfs of block 1 4 6 1 ← block 2 has 4 electrons and 6 basis functions 5 10 ← bfs of block 2 is from 5 to 10 1.0 0.0 0.0 0.0 0.0 1.0 0.0 0.0 ← initial guess for the 2 occupied orbitals(4/2) of block 2 1.0 0.0 0.0 0.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 0.0 ← initial guess for the 2 occupied orbitals(4/2) of block 2 $END ---------------------------------
Note: Eigenvalues and compositions of BLW-MOs are stored in $SCR/*.blw.
Exercices
Exercice 1 (Lewis structures of benzene, resonance) B3LYP/6-311+G* level
Subject
The benzene molecule is commonly represented as the resonance between the two Kékulé structures. The aim of the exercise is to understand the relative importance of the different Lewis structures in the benzene molecule using BLW and HuLis.
According to IUPAC’s Goldbook, resonance energy is defined as “The difference in potential energy between the actual molecular entity and the contributing structure of lowest potential energy”. However this definition does not precise what is the geometry of the contributing structure of lowest potential energy. Consequently, we can define two type of resonance energy: the vertical resonance energy (VRE) and the adiabatic resonance energy (ARE). This exercice tutorial will guide us toward Lewis structures and resonance of benzene.
To do
1/ Vertical Resonance Energy
- With the BLW program, and using the optimized geometry of benzene molecule, define one 1,3,5-cyclohexadiene Lewis structure, and optimize it's orbitals.
- Calculate the vertical resonance energy (VRE) - at the geometry of benzene.
- Compare the C-C bond distances. Comment.
- Optimize the structures to get the ARE. Comment.
- Compare the resonance energy computed by the BLW method and the conventional experimental resonance energy based on the hydrogenation heats of benzene and cyclohexene.
And good starting geometry is :
$DATA B3LYP/6-311+G* optimized geometry C1 C 6.0 0.0000006339 0.0000000000 1.3947932255 C 6.0 1.2082299733 0.0000000000 0.6973544513 C 6.0 1.2082233942 0.0000000000 -0.6973491014 C 6.0 0.0000000658 0.0000000000 -1.3948010538 C 6.0 -1.2082223644 0.0000000000 -0.6973489478 C 6.0 -1.2082278726 0.0000000000 0.6973527321 H 1.0 -0.0000049345 0.0000000000 2.4799156106 H 1.0 2.1470883835 0.0000000000 1.2408733122 H 1.0 2.1470838307 0.0000000000 -1.2408743510 H 1.0 -0.0000002627 0.0000000000 -2.4799186833 H 1.0 -2.1470846317 0.0000000000 -1.2408715385 H 1.0 -2.1470862154 0.0000000000 1.2408743441 $END
2 – With the hulis program: - Draw the benzene and create then the two kékulés structures - Add to the wave function the 3 covalent Dewar structures
Stéphane could you complete this part to add questions about the completude de base.
Access to files :
Exercice 2 (title)
Exercice 3 (title)
Exercice 4 (BH3... NH3) electronics at the B3LYP 6-31G(d) level
BLW energy decomposition analysis can be used to shed light into the nature of intermolecular interactions. Example of NH3∙∙∙BH3. Visualize the polarization and electron transfer effects using the electron density difference (EDD) maps.
1/ Make orbitals of BH3 alone (then NH3) in the geometry of the complex
$DATA BLW-ED Analysis C1 N 7.0 0.000000 0.000000 0.728869 H 1.0 0.000000 0.951707 1.095972 H 1.0 0.824202 -0.475853 1.095972 H 1.0 -0.824202 -0.475853 1.095972 B 5.0 0.000000 0.000000 -0.934793 H 1.0 0.000000 -1.170908 -1.238679 H 1.0 -1.014036 0.585454 -1.238679 H 1.0 1.014036 0.585454 -1.238679 $END
2/ Let fragment orbitals to polarize in the full complex.
3/ Let delocalize. This is just a standard DFT calculation. (TO CHECK with Yirong)
Preliminary Remarks : B3LYP calculation in Gamess is specified in $CONTRL :
$CONTRL SCFTYP=RHF DFTTYP=B3LYP runtyp=energy maxit=200 icharg=0 $END
And 6-31G(d) basis set is requested with
$BASIS GBASIS=N31 NGAUSS=6 NDFUNC=1 $END
Step by step help :
1/ Perform a NH3 BLW calculation of the fragment alone in the geometry of the complexe with $BLW NBLOCK=1 and keep the .blw file for next step (same for BH3).
We obtain
nh3.log: FINAL R-B3LYP ENERGY IS -56.5111505350
bh3.log: FINAL R-B3LYP ENERGY IS -26.5644674370
= > summ = -83.07561797
2/ Do the complex in a NBLOCK=2 BLW calculation and see the polarization of each fragment. The initial orbitals are obtained from .blw files of individual fragments ---ORBITALS (LOCAL BFS)--- part, and copied after the $BLWDAT fragments definition. A blank line separate each fragments’guess.
At this stage, we can want to do the calculation at full accuracy from the very first step. The following line avoid initial SCF cycles (SWOFF=0.0), and initial coarse grid DFT steps :
$DFT SWOFF=0.0 NRAD0=96 NLEB0=302 NTHE0=12 NPHI0=24 $END
We obtain
ITER 1 E(RBLW) = -83.05921870
FINAL R-B3LYP ENERGY IS -83.0932178520
3/ We let just the doublet to delocalize. TO CHECK with Yirong
We obtain
FINAL R-B3LYP ENERGY IS -83.1480131227 AFTER 12 ITERATIONS