GitHub - gkxiao/xtb-scan: torsion scan at DFT//xTB-GNF2 theory level with xTB, ORCA and Gaussian

Dihedral scan with xTB

Figure 1. Example molecule. Highlighted dihedral: C3-C2-C1-O8

1. Convert SDF into tmol:

obabel -isdf 7jrn_ligand_fragment.sdf -otmol -O fragment.coord

2. Prepare input file: scan.inp

$constrain
 force constant=50.0
 dihedral: 3,2,1,8,0.0
$scan
 1: 0.0,180.0,37
$end

3. Perform torsion scan

/public/apps/xtb-6.5.1/bin/xtb fragment.coord --opt verytight --input scan.inp --chrg 0 --uhf 0

4. Convet xyz into sdf

obabel -ixyz xtbscan.log -osdf -O xtbscan.sdf

5. Extract dihedral scan result:

extract_result_from_xtbscan.py xtbscan.sdf 3 2 1 8

CONF_ID,Angle,Relative_energy
CONF_1,-0.0024379306925366028,2.5660529817770072
CONF_2,5.008868625895336,2.421691246670976
CONF_3,10.006264798942436,2.093297027544123
CONF_4,15.00388321707389,1.6735896340333944
CONF_5,20.00715882152012,1.2647560229912802
CONF_6,25.000484601098798,0.8956625742899149
CONF_7,30.007529505425715,0.58213106163155
CONF_8,35.004095113856685,0.33556458569846015
CONF_9,40.00801862447416,0.15920944683461613
CONF_10,45.00804589818885,0.05284170597375848
CONF_11,49.99270415026529,0.0
CONF_12,55.00734179011268,0.028588644606113434
CONF_13,60.000498933417326,0.12004189644131635
CONF_14,64.99456640846694,0.2535721908962252
CONF_15,69.99701297899928,0.4036983160734575
CONF_16,74.99655532565676,0.5444593369536221
CONF_17,80.00179918843254,0.673358565949691
CONF_18,85.00122039028727,0.77231599804092
CONF_19,89.9975075815823,0.8223022320087292
CONF_20,95.00738375966014,0.8516286609974788
CONF_21,100.00259993427802,0.8521607966847
CONF_22,104.99847953686145,0.8453869191246799
CONF_23,110.0011877780128,0.806081963800489
CONF_24,115.00441978156354,0.7774579526672376
CONF_25,119.9984682367587,0.77084727154201
CONF_26,125.00170760464812,0.7636051145771461
CONF_27,129.9950398843348,0.8105056405111188
CONF_28,134.99836088974644,0.9126517408357859
CONF_29,139.99480548215223,1.075909500156742
CONF_30,144.99631665389828,1.304110102778182
CONF_31,149.99225955738748,1.6134768207537142
CONF_32,154.99316032897417,1.9901157699614114
CONF_33,159.9907292258415,2.4379784477945154
CONF_34,164.99021865644528,2.9415040766211753
CONF_35,169.98836838604416,3.4729742068748326
CONF_36,174.98865151282774,3.9824196092070707
CONF_37,179.99766277109416,4.283353778243777

6. Plot result

Optimize conformer at DFT level with ORCA

7. Split conformer ensemble into single SDF/XYZ file

Split the conformer ensemble into xyz file:

obabel -ixyz xtbscan.log -oxyz -O CONF_.xyz -m

Split the conformer ensemble into sdf file:

obabel -ixyz xtbscan.xyz -osdf -O CONF_.sdf -m

8. Generate ORCA input file to optimize conformer with dihedral angle constrained

Create ORCA input file from SDF:

sdf2orca.py CONF_1.sdf 3 2 1 8 CONF_1_opt.inp

Alterantively, create ORCA input file from XYZ:

xyz2orca.py CONF_1.xyz 0 3 2 1 8 CONF_1_opt.inp

cat CONF_1.xyz

22
energy: -31.864953576915 xtb: 6.5.1 (579679a)
C         10.56195      -10.60435       32.85972
C         10.19983       -9.15743       32.99504
C         11.21189       -8.17992       33.00934
C          8.87240       -8.73805       33.10874
C         12.66448       -8.50784       32.89355
C          8.53742       -7.40450       33.23466
C          9.53471       -6.44568       33.25005
O         11.71025      -10.99973       32.75833
C         10.85208       -6.84167       33.13765
N          9.53246      -11.49006       32.85262
C          9.75040      -12.90960       32.73279
H         12.97318       -9.16647       33.70268
H         12.86352       -9.04205       31.96701
H         13.26278       -7.59950       32.92114
H          8.05858       -9.44826       33.10138
H          9.28610       -5.39937       33.34851
H         11.63184       -6.09337       33.14895
H          8.57975      -11.18552       32.94396
H         10.82360      -13.06841       32.63810
H          9.38379      -13.43432       33.61796
H          9.24587      -13.30419       31.84828
H          7.50011       -7.11642       33.32045

cat CONF_1_opt.inp

%PAL NPROCS 24 END
! BP86 DEF2-TZVP D3 OPT RIJCOSX Def2/J
%geom Constraints
{D 2 1 0 7 C}
end
end
* xyzfile 0 1 CONF_1.xyz

9. Perform optimization with ORCA at BP86-D3/DEF2-TZVP level

orca CONF_1_opt.inp > CONF_1_opt.out

Chemistry model r2scan-3c/def2-mtzvpp and r2scan-3c/def2-tzvp is recommnnded.

Optimize conformer at DFT level with Gaussian 16

Create Gaussian input file from XYZ:

xyz2g16.py CONF_1.xyz 0 3 2 1 8 CONF_1.com

Perform optimization with Gaussian 16 at B3LYP-D3BJ/6-311+G(d,p) level:

g16 -p=24 -m=24GB CONF_1.com

cat CONF_1.com

%chk=CONF_1_D_3-2-1-8_constrained_opt.chk
# B3LYP/6-311+G(d,p) OPT=(modredundant) symmetry=(none) EmpiricalDispersion=(gd3bj)

CONF_1 Dihedral angle 3-2-1-8 constrained optimization

0 1
C         10.56195      -10.60435       32.85972
C         10.19983       -9.15743       32.99504
C         11.21189       -8.17992       33.00934
C          8.87240       -8.73805       33.10874
C         12.66448       -8.50784       32.89355
C          8.53742       -7.40450       33.23466
C          9.53471       -6.44568       33.25005
O         11.71025      -10.99973       32.75833
C         10.85208       -6.84167       33.13765
N          9.53246      -11.49006       32.85262
C          9.75040      -12.90960       32.73279
H         12.97318       -9.16647       33.70268
H         12.86352       -9.04205       31.96701
H         13.26278       -7.59950       32.92114
H          8.05858       -9.44826       33.10138
H          9.28610       -5.39937       33.34851
H         11.63184       -6.09337       33.14895
H          8.57975      -11.18552       32.94396
H         10.82360      -13.06841       32.63810
H          9.38379      -13.43432       33.61796
H          9.24587      -13.30419       31.84828
H          7.50011       -7.11642       33.32045

3 2 1 8 F

!a blank line

Optimize conformer at DFT level with PSI4

Create PSI4 input file from XYZ:

xyz2psi4_dihedral_angle_constrained.py CONF_1.xyz 0 3 2 1 8 > CONF_1.dat

Perform optimization with PSI4 at R2SCAN-3c/DEF2-mTZVPP level:

psi4 -i CONF_1.dat -o CONF_1.out -n 24 --memory 24GB

cat CONF_1.dat

molecule mol{
0 1
C         10.56195      -10.60435       32.85972
C         10.19983       -9.15743       32.99504
C         11.21189       -8.17992       33.00934
C          8.87240       -8.73805       33.10874
C         12.66448       -8.50784       32.89355
C          8.53742       -7.40450       33.23466
C          9.53471       -6.44568       33.25005
O         11.71025      -10.99973       32.75833
C         10.85208       -6.84167       33.13765
N          9.53246      -11.49006       32.85262
C          9.75040      -12.90960       32.73279
H         12.97318       -9.16647       33.70268
H         12.86352       -9.04205       31.96701
H         13.26278       -7.59950       32.92114
H          8.05858       -9.44826       33.10138
H          9.28610       -5.39937       33.34851
H         11.63184       -6.09337       33.14895
H          8.57975      -11.18552       32.94396
H         10.82360      -13.06841       32.63810
H          9.38379      -13.43432       33.61796
H          9.24587      -13.30419       31.84828
H          7.50011       -7.11642       33.32045
}
set optking {
frozen_dihedral = ("
3 2 1 8
")
}
optimize('R2SCAN-3C/DEF2-mTZVPP')

Reference

User Guide to Semiempirical Tight Binding.https://xtb-docs.readthedocs.io/en/latest
ORCA tutorials. ORCA tutorials - Compatible with ORCA 5.0!
ORCA input library. https://sites.google.com/site/orcainputlibrary
M. Bursch, J.-M. Mewes, A. Hansen, S. Grimme. Best-Practice DFT Protocols for Basic Molecular Computational Chemistry. Angew. Chem. Int. Ed. 2022, 61, e202205735. https://doi.org/10.1002/anie.202205735
Grimme S, Hansen A, Ehlert S, Mewes J-M. r2SCAN-3c: An Efficient “Swiss Army Knife” Composite Electronic-Structure Method. ChemRxiv. 2020; doi:10.26434/chemrxiv.13333520.v2 This content is a preprint and has not been peer-reviewed.
Thomas Gasevic, Julius B. Stückrath, Stefan Grimme, and Markus Bursch.Optimization of the r2SCAN-3c Composite Electronic-Structure Method for Use with Slater-Type Orbital Basis Sets. The Journal of Physical Chemistry A 2022 126 (23), 3826-3838. DOI: 10.1021/acs.jpca.2c02951

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Dihedral scan with xTB

1. Convert SDF into tmol:

2. Prepare input file: scan.inp

3. Perform torsion scan

4. Convet xyz into sdf

5. Extract dihedral scan result:

6. Plot result

Optimize conformer at DFT level with ORCA

7. Split conformer ensemble into single SDF/XYZ file

8. Generate ORCA input file to optimize conformer with dihedral angle constrained

9. Perform optimization with ORCA at BP86-D3/DEF2-TZVP level

Optimize conformer at DFT level with Gaussian 16

Optimize conformer at DFT level with PSI4

Reference

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Name		Name	Last commit message	Last commit date
Latest commit History 42 Commits
7jrn_ligand_fragment.sdf		7jrn_ligand_fragment.sdf
README.md		README.md
example.png		example.png
extract_result_from_xtbscan.py		extract_result_from_xtbscan.py
fragment.png		fragment.png
scan.inp		scan.inp
sdf2orca.py		sdf2orca.py
xyz2g16.py		xyz2g16.py
xyz2orca.py		xyz2orca.py

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Dihedral scan with xTB

1. Convert SDF into tmol:

2. Prepare input file: scan.inp

3. Perform torsion scan

4. Convet xyz into sdf

5. Extract dihedral scan result:

6. Plot result

Optimize conformer at DFT level with ORCA

7. Split conformer ensemble into single SDF/XYZ file

8. Generate ORCA input file to optimize conformer with dihedral angle constrained

9. Perform optimization with ORCA at BP86-D3/DEF2-TZVP level

Optimize conformer at DFT level with Gaussian 16

Optimize conformer at DFT level with PSI4

Reference

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