NMR
CENSO is not only capable of ensemble refinement, but also allows the automated computation of NMR spectra for an entire ensemble. Since NMR is a structure-sensitive property, this is a prime example of the importance of ensemble quality.
Exercise
Note: Due to technical reasons, you are going to use censo v1 in the following exercise. However, censo 2 is generally advised due to additional features, and updated methods. Please note that the input file structure differs a little, while the principle functionality remains similar. For an overview over the different input file formats, please see the documentation.
As an example, use crest to first generate an ensemble of 2-Fluoropropan-1-ol with GFN2-xTB in water.
10
O 1.398839 1.025407 -0.886750
C 0.372477 0.456264 -0.628697
C -0.032777 -0.054166 0.729167
H -0.916315 0.504071 1.066256
H -0.386361 0.248155 -1.401738
C -0.304030 -1.554058 0.707502
H -0.567187 -1.886134 1.707543
H -1.123368 -1.765489 0.029484
H 0.585461 -2.087710 0.383005
F 0.964760 0.230530 1.658525
Important: For the next steps, the ORCA software is required.
Next, you will refine the ensemble using DFT calculations.
crest uses GFN2-xTB as the default method, which produces ensemble rankings that are not accurate enough for, e.g., NMR calculations. Therefore, it is necessary to refine the initial ensemble.
You can do this using CENSO, which automates the process of ensemble refinement.
Use the following input to refine the ensemble.
censo -inp crest_conformers.xyz -inprc censorc -T 8 > censo.out &
$CENSO global configuration file: .censorc
$VERSION:1.2.0
ORCA: /home/software/cluster/orca_5_0_4_linux_x86-64_openmpi411
ORCA version: 5.0.4
GFN-xTB: /home/abt-grimme/AK-bin/xtb
CREST: /home/abt-grimme/AK-bin/crest
mpshift: /path/including/binary/mpshift-binary
escf: /path/including/binary/escf-binary
#COSMO-RS
ctd = BP_TZVP_C30_1601.ctd cdir = "/software/cluster/COSMOthermX16/COSMOtherm/CTDATA-FILES" ldir = "/software/cluster/COSMOthermX16/COSMOtherm/CTDATA-FILES"
$ENDPROGRAMS
$CRE SORTING SETTINGS:
$GENERAL SETTINGS:
nconf: all # ['all', 'number e.g. 10 up to all conformers']
charge: 0 # ['number e.g. 0']
unpaired: 0 # ['number e.g. 0']
solvent: water # ['gas', 'acetone', 'acetonitrile', 'aniline', 'benzaldehyde', 'benzene', 'ccl4', '...']
prog_rrho: xtb # ['xtb']
temperature: 298.15 # ['temperature in K e.g. 298.15']
trange: [273.15, 378.15, 5] # ['temperature range [start, end, step]']
multitemp: on # ['on', 'off']
evaluate_rrho: on # ['on', 'off']
consider_sym: on # ['on', 'off']
bhess: on # ['on', 'off']
imagthr: automatic # ['automatic or e.g., -100 # in cm-1']
sthr: automatic # ['automatic or e.g., 50 # in cm-1']
scale: automatic # ['automatic or e.g., 1.0 ']
rmsdbias: off # ['on', 'off']
sm_rrho: alpb # ['alpb', 'gbsa']
progress: off # ['on', 'off']
check: on # ['on', 'off']
prog: orca # ['tm', 'orca']
func: r2scan-3c # ['b3-lyp', 'b3lyp', 'b3lyp-3c', 'b3lyp-d3', 'b3lyp-d3(0)', 'b3lyp-d4', 'b3lyp-nl', '...']
basis: automatic # ['automatic', 'def2-TZVP', 'def2-mSVP', 'def2-mSVP', 'def2-mSVP', 'def2-mSVP', '...']
maxthreads: 1 # ['number of threads e.g. 2']
omp: 1 # ['number cores per thread e.g. 4']
balance: off # ['on', 'off']
cosmorsparam: automatic # ['automatic', '12-fine', '12-normal', '13-fine', '13-normal', '14-fine', '...']
$PART0 - CHEAP-PRESCREENING - SETTINGS:
part0: on # ['on', 'off']
func0: b97-d3 # ['b3-lyp', 'b3lyp', 'b3lyp-3c', 'b3lyp-d3', 'b3lyp-d3(0)', 'b3lyp-d4', '...']
basis0: def2-SV(P) # ['automatic', 'def2-SV(P)', 'def2-TZVP', 'def2-mSVP', 'def2-mSVP', 'def2-mSVP', '...']
part0_gfnv: gfn2 # ['gfn1', 'gfn2', 'gfnff']
part0_threshold: 4.0 # ['number e.g. 4.0']
$PART1 - PRESCREENING - SETTINGS:
# func and basis is set under GENERAL SETTINGS
part1: on # ['on', 'off']
smgsolv1: smd # ['alpb_gsolv', 'cosmo', 'cosmors', 'cosmors-fine', 'cpcm', 'dcosmors', '...']
part1_gfnv: gfn2 # ['gfn1', 'gfn2', 'gfnff']
part1_threshold: 3.5 # ['number e.g. 5.0']
$PART2 - OPTIMIZATION - SETTINGS:
# func and basis is set under GENERAL SETTINGS
part2: on # ['on', 'off']
prog2opt: prog # ['tm', 'orca', 'prog', 'automatic']
part2_threshold: 2.5 # ['number e.g. 4.0']
sm2: smd # ['cosmo', 'cpcm', 'dcosmors', 'default', 'smd']
smgsolv2: smd # ['alpb_gsolv', 'cosmo', 'cosmors', 'cosmors-fine', 'cpcm', 'dcosmors', '...']
part2_gfnv: gfn2 # ['gfn1', 'gfn2', 'gfnff']
ancopt: on # ['on']
hlow: 0.01 # ['lowest force constant in ANC generation, e.g. 0.01']
opt_spearman: on # ['on', 'off']
part2_P_threshold: 99 # ['Boltzmann sum threshold in %. e.g. 95 (between 1 and 100)']
optlevel2: automatic # ['crude', 'sloppy', 'loose', 'lax', 'normal', 'tight', 'vtight', 'extreme', '...']
optcycles: 8 # ['number e.g. 5 or 10']
spearmanthr: -4.0 # ['value between -1 and 1, if outside set automatically']
radsize: 10 # ['number e.g. 8 or 10']
crestcheck: off # ['on', 'off']
$PART3 - REFINEMENT - SETTINGS:
part3: on # ['on', 'off']
prog3: prog # ['tm', 'orca', 'prog']
func3: pw6b95 # ['b3-lyp', 'b3lyp', 'b3lyp-3c', 'b3lyp-d3', 'b3lyp-d3(0)', 'b3lyp-d4', 'b3lyp-nl', '...']
basis3: def2-TZVPD # ['DZ', 'QZV', 'QZVP', 'QZVPP', 'SV(P)', 'SVP', 'TZVP', 'TZVPP', 'aug-cc-pV5Z', '...']
smgsolv3: smd # ['alpb_gsolv', 'cosmo', 'cosmors', 'cosmors-fine', 'cpcm', 'dcosmors', '...']
part3_gfnv: gfn2 # ['gfn1', 'gfn2', 'gfnff']
part3_threshold: 99 # ['Boltzmann sum threshold in %. e.g. 95 (between 1 and 100)']
$NMR PROPERTY SETTINGS:
$PART4 SETTINGS:
part4: off # ['on', 'off']
couplings: on # ['on', 'off']
progJ: prog # ['tm', 'orca', 'prog']
funcJ: pbe0 # ['b3-lyp', 'b3lyp', 'b3lyp-3c', 'b3lyp-d3', 'b3lyp-d3(0)', 'b3lyp-d4', 'b3lyp-nl', '...']
basisJ: def2-TZVP # ['DZ', 'QZV', 'QZVP', 'QZVPP', 'SV(P)', 'SVP', 'TZVP', 'TZVPP', 'aug-cc-pV5Z', '...']
sm4J: smd # ['cosmo', 'cpcm', 'dcosmors', 'smd']
shieldings: on # ['on', 'off']
progS: prog # ['tm', 'orca', 'prog']
funcS: pbe0 # ['b3-lyp', 'b3lyp', 'b3lyp-3c', 'b3lyp-d3', 'b3lyp-d3(0)', 'b3lyp-d4', 'b3lyp-nl', '...']
basisS: def2-TZVP # ['DZ', 'QZV', 'QZVP', 'QZVPP', 'SV(P)', 'SVP', 'TZVP', 'TZVPP', 'aug-cc-pV5Z', '...']
sm4S: smd # ['cosmo', 'cpcm', 'dcosmors', 'smd']
reference_1H: TMS # ['TMS']
reference_13C: TMS # ['TMS']
reference_19F: CFCl3 # ['CFCl3']
reference_29Si: TMS # ['TMS']
reference_31P: TMP # ['TMP', 'PH3']
1H_active: on # ['on', 'off']
13C_active: on # ['on', 'off']
19F_active: off # ['on', 'off']
29Si_active: off # ['on', 'off']
31P_active: off # ['on', 'off']
resonance_frequency: 300.0 # ['MHz number of your experimental spectrometer setup']
$OPTICAL ROTATION PROPERTY SETTINGS:
$PART5 SETTINGS:
optical_rotation: off # ['on', 'off']
funcOR: pbe # ['functional for opt_rot e.g. pbe']
funcOR_SCF: r2scan-3c # ['functional for SCF in opt_rot e.g. r2scan-3c']
basisOR: def2-SVPD # ['basis set for opt_rot e.g. def2-SVPD']
frequency_optical_rot: [589.0] # ['list of freq in nm to evaluate opt rot at e.g. [589, 700]']
$END CENSORC
The best structure found is written to coord.enso_best, the whole ensemble after part 2 to enso_ensemble_part2.xyz and the refined ensemble after part 3 to enso_ensemble_part3.xyz. Compare the ranking of the conformers with the GFN2-xTB ensemble resulting with crest.
Optional
With censo, also NMR computations can be done. Use the refined ensemble as input for an additional censo calculation where every part is turned of except part 4.
Note: The NMR calculation can also be done together with the refinment in one calculation by activating all the respective parts with the
censorc.