Analysis of NMR parameters with Localized Molecular Orbitals

Introduction

Localized molecular orbitals, such as Natural Bonding Orbitals (NBO) or Natural Localized Molecular Orbitals (NLMO) can be helpful in analyzing and interpreting properties computed in electronic structure calculations.

This tutorial analyses the effects of NH2 and NO2 substituents in ortho-, meta-, and para-positions on NMR chemical shifts of aromatic carbon atoms in a benzene ring. These shifts in aromatic systems are commonly believed to originate from a depletion or accumulation of electrons in the π-orbitals at these atoms. We examine this claim by means of NMR calculations with ADF and NBO/NLMO analysis tools.

This tutorial loosely follows the following publication: R. V. Viesser, L. C. Ducati, C. F. Tormena and J. Autschbach The unexpected roles of σ and π orbitals in electron donor and acceptor group effects on the 13C NMR chemical shifts in substituted benzenes, Chem. Sci. Phys. 8, 6570-6576 (2017).

Step 1: Preparations

The molecular structures needed for this tutorial can be downloaded by clicking on the following links:

Download Benzene.xyz
Download Aniline.xyz
Download Nitrobenzene.xyz

These structures have already been optimized and properly aligned. In general, you should optimize the structures first.

Note

The analysis of NMR and EFG results in terms of localized molecular orbitals requires some care about the alignment of the molecules when comparing results between different systems as in our case. This is, for example, because the analysis in terms of NLMOs is origin dependent. To obtain comparable orbital contributions one has furthermore to ensure that the different molecules are oriented in the same way. In ADFInput you can use the options Edit → Align and Edit → Set Origin to achieve this when performing localized orbital analysis with your custom models.

The main idea is now to compute the NMR shielding parameters for three different carbon atoms in the ring, C(1), C(4), and C(5), which are in ortho-, meta-, and para-position to the substituent at atom C(3):

../_images/EFGNMRNBO_Atoms.png

Step 2: Calculation Settings

We need to perform three ADF calculations, one for each molecule (i.e. Benzene, Aniline, and Nitrobenzene).

Let us start with Benzene:

Start ADFInput
Click on File → Import Coordinates... and select the file Benzene.xyz you just downloaded

Next, select the following settings in the main ADFInput panel

In the Main ADF panel:
Task → Single Point
XC functional → Hybrid → PBE0
Relativity → Scalar
Basis set → TZ2P
Frozen core → None
Numerical quality → Good

Note

An all-electron basis set is needed because a hybrid functional is used. Using an all-electron basis set also improves the quality of the NMR results.

Note

A scalar relativistic treatment (Relativity → Scalar) is required to perform the NBO analysis of the NMR shifts.

In order to compare the computed NMR results with their experimental counterparts (which were measured in Chloroform solution), we enable the COSMO solvation model:

Click on Model → Solvation
Solvation method → COSMO
COSMO solvent → Chloroform

We now select the atoms for which we want to compute the NMR properties:

View → Atom Info → Name → Show
Click on Properties → NMR
Select atoms C(1), C(4), and C(5) in the molecular editor
NMR shielding for atoms: click on the + button
Print: tick Isotropic shielding constants and Full shielding tensors
../_images/EFGNMRNBO_NMR_panel.png

and enable the NBO analysis of the NMR properties:

Click on Properties → Localized Orbitals, NBO
Perform NBO analysis: Tick yes
Analyse property → NMR
../_images/EFGNMRNBO_NLMO_NBO_panel.png

Finally, we need to disable the automatic symmetry treatment of ADF:

Click on Details → Symmetry
Symbol → NOSYM

Now that all options are set, save the job:

File → Save As...
Save e.g. as Benzene.adf
Click OK in the popup window to confirm using the FULL FOCK matrix

For the other two systems (i.e. Aniline, and Nitrobenzene), we can avoid having to set again most computational options:

Select and delete all atoms
File → Import Coordinates...
Select Aniline.xyz and click Open
View → Atom Info → Name → Show
Click on Properties → NMR
Select atoms C(1), C(4), and C(5) in the molecular editor
NMR shielding for atoms: click on the + button
File → Save As...
Save e.g. as Aniline.adf
Repeat for Nitrobenzene.xyz

Step 3: Running the Calculations

We are now ready to run all three calculations

Switch to ADFjobs using the SCM menu
Select the three jobs Benzene, Aniline, and Nitrobenzene
Job → Run

NMR Results

After all three calculations are completed we can retrieve the isotropic shielding constants

In ADFJobs click on the job Benzene
Switch to ADFoutput using the SCM menu
In ADFoutput, click on Other Properties → NMR shielding (NMR program)
../_images/EFGNMRNBO_BenzeneOutput.png

In the case of Benzene the atoms C(1), C(4), and C(5) are all equivalent, thus yielding shielding constants σi of the same value. This is different in the case of the other two systems, whose shielding constants are retrieved analogously from the corresponding output files.

The chemical shifts δi are then computed relative to the unsubstituted Benzene molecule as follows

δi = σBenzene - σi - δBenzene

whereas δBenzene = 128.55 ppm is the experimental chemical shift for 13C in Benzene, while σBenzene is the computed σi for Benzene (54 ppm in our case). This yields the following results:

Compound Substitution exp 13C-shift calc 13C-shift
Benzene   128.55 128.55 (see text)
Aniline o-NH2 115.29 113.46
m-NH2 129.65 129.65
p-NH2 118.73 116.36
Nitrobenzene o-NO2 123.65 125.22
m-NO2 129.48 128.92
p-NO2 134.76 136.78

The experimental NMR shifts are reproduced with an error margin of about 2 ppm, and the trend between the different substitutions is reproduced: the NH2 group leads to a significant decrease in the chemical shifts in ortho- and para- position. The meta-position remains almost unaffected by the NH2 group. This is also observed for the meta-position near a NO2 substitution, while the chemical shifts are lowered at the ortho-atom and increased at the para-position.

To rationalize this finding, we proceed to examine the contributions of individual orbitals to these substituent effects.

NLMO/NBO Analysis

We first look at the individual NLMO contributions to the isotropic shielding tensors. Each output file contains the NLMO and NBO decomposition of the isotropic shielding tensors (and other quantities) for the atoms C(1), C(4), and C(5).

The NMR shielding tensors consist of diamagnetic and paramagnetic (+SO) contributions. Diamagnetic terms are larger but mostly dominated by contributions from core orbitals and they essentially not affected by the local environment of an atom. As we are interested substitution effects, i.e. changing environments around an atom, we focus on the diamagnetic terms here as these are most influential on the magnitude and direction of the chemical shifts.

Switch to ADFoutput for the job Aniline
Type NLMO contributions to in the search bar
Use the arrows in the search bar to get the entries for the Isotropic Shielding Tensor
../_images/EFGNMRNBO_NLMOContributions.png

We find that the paramagnetic part of the isotropic shielding tensor at atom C(1) is mostly determined by contributions originating from three bonding NLMOs formed between C(1) and its three neighbors C(3), C(4), and H(7). Analogous results are obtained for C(4) and C(5) as well as for the corresponding atoms in the Nitrobenzene molecule.

One finds similar results when examining the NBO contributions to the isotropic shielding tensors. These contributions can be obtained by searching for NBO contributions to in the search bar of ADFoutput.

Inspecting NLMOs

We now examine in more detail the NLMOs with the largest contributions.

In ADFJobs, select the job Aniline
Open ADFview using the SCM menu
In ADFview, click on Add → Isosurface: With Phase
In the field bar at the bottom: Select Field ... → NLMOs..

The selection window allows you to pick individual orbitals for plotting in ADFview

../_images/EFGNMRNBO_NLMO_Selection.png

A visual inspection of the three NLMOs with the largest contribution to the isotropic shielding tensor reveals that they all have a pronounced σ-orbital character:

../_images/EFGNMRNBO_SigmaNLMO.png

Opposed to that, the π-orbitals of the aromatic system can be clearly identified as well, e.g. for NLMO #11 in the above listing of contributions

../_images/EFGNMRNBO_PiNLMO.png

As the results discussed above show, such π-orbitals are not contributing much to the isotropic shielding tensors.

The corresponding analysis in terms of NBOs can be done in exactly the same way

In the field bar at the bottom: Select Field ... → NBOs..
Select NBO from list

and suggests exactly the same finding

In conclusion, the chemical shifts due to substitutions on an aromatic ring are mainly influenced by contributions from σ-bonding orbitals rather than π-orbitals.

Further Reading

R. V. Viesser, L. C. Ducati, C. F. Tormena and J. Autschbach The unexpected roles of σ and π orbitals in electron donor and acceptor group effects on the 13C NMR chemical shifts in substituted benzenes, Chem. Sci. Phys. 8, 6570-6576 (2017).

J. A. Bohmann, F. Weinhold and T. C. Farrar Natural chemical shielding analysis of nuclear magnetic resonance shielding tensors from gauge-including atomic orbital calculations, J. Chem. Phys. 107, 1173-1184 (1997).

J. Autschbach Analyzing NMR shielding tensors calculated with two-component relativistic methods using spin-free localized molecular orbitals, J. Chem. Phys. 128, 164112 (2008).

R. V. Viesser, L. C. Ducati, C. F. Tormena and J. Autschbach The halogen effect on the 13C NMR chemical shift in substituted benzenes, Phys. Chem. Chem. Phys. 20, 11247 (2018).