4 steps for fluorescence calculation

Outline of this blog:

Ground state optimization (to get ideal geometry of the molecule)
1. build the molecules (input)
2. geometry optimization of the molecule (output)
Ground state single point calculation (to get the HOMO and LUMO orbital)
1. based on the geometry configuration gained from last step (input)
2. MO information (output)
TD-DFT calculation of the ground state configuration (to get fluorescence absorption)
1. based on the geometry configuration gained from last step (input)
2. Excited state information gained
TD-DFT calculation of the first excited state (S1) configuration (to get fluorescence emission)
1. based on the geometry of the ground state configuration
2. Excited state information gained

I. Ground state optimization
We can use WebMO to draw the molecule and generate input file and submit the gaussian job onto hpc using the script given here.

#!/bin/bash -l
#SBATCH --job-name="QChem"
#SBATCH --time=72:00:00
#SBATCH --nodes=1
#SBATCH -c 1 # replacing --ntasks=1 recommended by admin
#SBATCH --mem=1000mb
#SBATCH --output=MYJOBNAME-MYJOBID.%j.out
#SBATCH --error=MYJOBNAME-MYJOBID.%j.err
##SBATCH --mail-type=ALL
##SBATCH --mail-user=NetID@nyu.edu
##SBATCH --gres=gpu:1
#SBATCH --partition=serial
##SBATCH --share echo "SLURM_JOBID="$SLURM_JOBID
echo "SLURM_JOB_NODELIST"=$SLURM_JOB_NODELIST
echo "SLURM_NNODES"=$SLURM_NNODES
echo "SLURMTMPDIR="$SLURMTMPDIR
echo "SLURM_SUBMIT_DIR="$SLURM_SUBMIT_DIR
USERNAME=zl3289
EXEPATH=/xspace/zl3289/qchem_dye/3
echo "Submit job with sbatch script.slurm"
cd $EXEPATH
module purge
module use /xspace/sungroup/modules
module load gaussian16g16 < tddft_gs_b3lyp.inp > tddft_gs_b3lyp.logecho "Finished JOB MYJOBID"

The input file (when using this file, please delete the contents behind //) is given by

%chk=tddft_gs_b3lyp.chk //generating chk file (this is a checking point for Gaussian file)

#N B3LYP/6-311+G(d,p) Geom=Connectivity Density=Current Pop=Regular out=wfn //theory/basis set, geom is calculated with connectivity, density of state goes with theory and out=wfn keyword specifies the output files including w(ave)f(unctio)n information, which is readable for multiwfn

C13H10O2S2

0 1
C
S 1 B1
C 2 B2 1 A1
C 3 B3 2 A2 1 D1
C 4 B4 3 A3 2 D2
C 5 B5 4 A4 3 D3
C 6 B6 5 A5 4 D4
C 7 B7 6 A6 5 D5
C 8 B8 7 A7 6 D6
C 9 B9 8 A8 7 D7
C 6 B10 7 A9 8 D8
C 4 B11 5 A10 6 D9
O 12 B12 4 A11 5 D10
H 10 B13 11 A12 6 D11
H 9 B14 10 A13 11 D12
H 8 B15 7 A14 6 D13
H 7 B16 8 A15 9 D14
O 5 B17 6 A16 7 D15
S 3 B18 4 A17 5 D16
C 19 B19 3 A18 4 D17
C 1 B20 2 A19 3 D18
H 21 B21 1 A20 2 D19
H 21 B22 1 A21 2 D20
H 20 B23 21 A22 1 D21
H 20 B24 21 A23 1 D22
H 1 B25 2 A24 3 D23
H 1 B26 2 A25 3 D24

B1 1.788433001
B2 1.360158138
B3 1.370067000
B4 1.373571588
B5 1.350561486
B6 1.338195502
B7 1.345861135
B8 1.347603000
B9 1.345861656
B10 1.326892000
B11 1.373571588
B12 1.210289629
B13 1.103467608
B14 1.103892252
B15 1.103893123
B16 1.103468606
B17 1.210289848
B18 1.360158138
B19 1.788433046
B20 1.517426570
B21 1.117597704
B22 1.117597704
B23 1.115177881
B24 1.115177881
B25 1.115177330
B26 1.115177330
A1 119.1857831
A2 116.6128070
A3 125.5672472
A4 105.9305398
A5 128.2635548
A6 116.5228342
A7 121.3774280
A8 121.3774644
A9 122.0997377
A10 108.8655056
A11 131.7980910
A12 122.2462657
A13 119.2337264
A14 119.2337882
A15 121.2309521
A16 122.2714154
A17 116.6128070
A18 119.1858151
A19 118.7442107
A20 108.7736303
A21 108.7736303
A22 109.1971837
A23 109.1971837
A24 107.2547807
A25 107.2547807
D1 180.0000000
D2 0.000000000
D3 180.0000000
D4 180.0000000
D5 180.0000000
D6 0.000000000
D7 0.000000000
D8 0.000000000
D9 0.000000000
D10 180.0000000
D11 180.0000000
D12 180.0000000
D13 180.0000000
D14 180.0000000
D15 0.000000000
D16 180.0000000
D17 180.0000000
D18 0.000000000
D19 123.9649048
D20 -123.9649048
D21 123.3123463
D22 -123.3123463
D23 124.2681569
D24 -124.2681569

1 2 1 21 1 26 1 27 1
2 3 1 1 1
3 4 2 2 1 19 1
4 5 1 12 1 3 2
5 6 1 4 1 18 2
6 7 1 11 2 5 1
7 8 2 6 1 17 1
8 7 2 9 1 16 1
9 10 2 8 1 15 1
10 11 1 9 2 14 1
11 6 2 10 1 12 1
12 4 1 11 1 13 2
13 12 2
14 10 1
15 9 1
16 8 1
17 7 1
18 5 2
19 20 1 3 1
20 21 1 19 1 24 1 25 1
21 1 1 20 1 22 1 23 1
22 21 1
23 21 1
24 20 1
25 20 1
26 1 1
27 1 1

/xspace/zl3289/qchem_dye/3/tddft_gs_b3lyp.wfn //(specify the path and route)

Notice here the keyword opt appears, which means geometry of the molecules changed during the QC calculation.

II. Single point energy calculation

We need to grab the frontier orbital information in this step of quantum chemistry calculation of the single point energy with input file given by

%chk=tddft_gs_b3lyp.chk

#N B3LYP/6-311+G(d,p) Geom=Connectivity Density=Current Pop=Regular out=wfn

C13H10O2S2

/xspace/zl3289/qchem_dye/3/tddft_gs_b3lyp.wfn

III. TDDFT calculation with ground state

This step using the geometry given as the result of the first step is to calculate the excited state properties of the molecule with ground state. Since we use the same geometry of the last job so we just show the first three lines of the input file given by

%chk=tddft_s0_b3lyp.chk

#N td(NStates=10,singlets,root=1) b3lyp/6-311+G(d,p) Geom=Connectivity Pop=regular Density=current out=wfn

New Keyword (function):

TD (time-dependent DFT calculation)
- NStates (# of states is modified)
- root (specify state of interest, which state we are interested in)
- singlets (calculation singlet states only)

IV. TD-DFT on S1 geometry

In this step, we optimized the nuclear geometry of molecule with the first singlet excited state and calculate the excited state properties of the molecules with optimized molecules with the input file shown in section II and changing the first 3 lines into

%chk=tddft_s1_b3lyp.chk

#N opt td(NStates=10,singlets,root=1) b3lyp/6-311+G(d,p) Geom=Connectivity Pop=regular Density=current out=wfn

Notice here keyword opt moves the nuclear coordinates.

4 steps for fluorescence calculation

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