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. 2022 Mar 23;12(15):9130–9138. doi: 10.1039/d2ra00258b

Theoretical study of a derivative of chlorophosphine with aliphatic and aromatic Grignard reagents: SN2@P or the novel SN2@Cl followed by SN2@C?†

Nandini Savoo 1, Lydia Rhyman 1,2,✉, Ponnadurai Ramasami 1,2,✉
PMCID: PMC8985194  PMID: 35424871

Abstract

The proposed SN2 reactions of a hindered organophosphorus reactant with aliphatic and aromatic nucleophiles [Ye et al., Org. Lett., 2017, 19, 5384–5387] were studied theoretically in order to explain the observed stereochemistry of the products. Our computations (using B3LYP as the functional) indicate that the reaction with the aliphatic nucleophile occurs through a backside SN2@P pathway while the reaction with the aromatic nucleophile proceeds through a novel SN2@Cl mechanism, followed by a frontside SN2@C mechanism.

The proposed SN2 reactions of a hindered organophosphorus reactant with aliphatic and aromatic nucleophiles [Ye et al., Org. Lett., 2017, 19, 5384–5387] were studied theoretically in order to explain the observed stereochemistry of the products.graphic file with name d2ra00258b-ga.jpg

Introduction

Organophosphorus derivatives possess significant value in disciplines such as asymmetric metal catalysis,1 pest control,2 medicine3 and bioorganic chemistry.4 An insight into their synthetic routes is thus essential.1,5–8 One of the reactions often encountered in the synthesis of organophosphorus derivatives is the bimolecular nucleophilic substitution (SN2) reaction at the trivalent tricoordinate phosphorus atom.5,8–10 The SN2 reaction at a trivalent phosphorus atom (SN2@P) refers to the replacement of a substituent (leaving group, L) around the phosphorus atom by an electron-rich molecule (nucleophile, Nu−). An SN2@P reaction occurs via the inversion and retention pathways in which molecular configuration around the phosphorus atom is inverted (P-inverted) and retained (P-retained), respectively [Fig. 1(a)].10 The inversion pathway takes place by the attack of the Nu− opposite to L which is synonymous to a backside SN2 pathway (SN2@P-b). Nucleophilic attack can also occur opposite to the lone pair of electrons on the phosphorus atom and on the same side as L in the retention pathway; this is analogous to a frontside SN2 attack (SN2@P-f).10

Fig. 1. (a) Inversion (SN2@P-b, black) and retention (SN2@P-f, red) pathways; (b) double-well; (c) single-well and; (d) triple-well PESs.

Fig. 1

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In the inversion and retention pathways of an archetypal SN2@P reaction, the initial interaction of the organophosphorus and the Nu− reactants (R) generates a reactant complex (RC) which forms a pentacoordinate transition state (TS). The TS dissociates to form the product complex (PC) and finally the separate products (P). The R, RC, TS, PC and P make up the typical double-well potential energy surface (PES) [Fig. 1(b)].11 An example is the retention pathway of the PH2Cl + Cl− reaction which occurs through a double-well PES with a Berry pseudorotation about the phosphorus atom.12 Studies also reported atypical PESs for SN2@P reactions when the bulkiness of the substituents around the phosphorus atom is changed.11,13–15 An example is the nucleophilic attack at unhindered trivalent phosphorus atom centres which may result in a single-well PES [Fig. 1(c)] with a relatively stable pentacoordinate intermediate, which is known as the transition complex (TC).12–15 The TC is in accordance with experimental reports.16–19 Such a reaction is spontaneous; the reactants form a stable TC followed by the products without the formation of the RC or PC. An increase in the bulkiness of substituents around the trivalent phosphorus atom separates the TC from the R and P by the pre-TS and the post-TS, respectively. This results in a triple-well PES [Fig. 1(d)] which constitutes a stepwise Walden inversion with favourable energy barriers in an addition-elimination fashion.6,10,11,14,20,21

The bulkiness of substituents around the phosphorus atom is one of several factors governing the stereochemical consequences of SN2@P synthesis of organophosphorus derivatives. Other factors include the effect of neighbouring groups,6,8 solvent6,22 and the choice of nucleophile.9,23–25 Ye et al. carried out an experimental study and they highlight the choice of nucleophile as a factor influencing the stereoselectivity of SN2@P reactions of organophosphorus compounds.25 The study deals with the synthesis of tertiary phosphines from diastereomeric mixtures of secondary phosphine oxides in tetrahydrofuran (THF) in the presence of boron trihydride (BH3) [Fig. 2(a)].25 One of the steps in the synthesis [highlighted in blue in Fig. 2(a)] involves the replacement of a Cl atom bonded to the trivalent tertiary phosphorus atom by an R group from a Grignard reagent. The authors reported diastereomeric ratios (dr) of 98 : 2 and 1 : 99 for the P-inverted and P-retained organophosphorus products in the reactions involving an aliphatic and aromatic Grignard reagent, respectively.25 Based on these observations, Ye et al. proposed that the aliphatic Grignard reagent attacks opposite to the leaving group Cl (SN2@P-b) and the aromatic Grignard reagent attacks opposite to the lone pair of electrons on the phosphorus atom (SN2@P-f).25

Fig. 2. (a) Ye and co-workers' work.25 The substitution step highlighted in blue shows the stereoselectivity of the reaction. (b) Gas-phase SN2 reactions studied in this work. (c) Solvation model employed.

Fig. 2

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In continuation to our research programme to understand substitution reactions and our reports on the influence of ion-pair nucleophiles on SN2 reactions,26–28 we attempted a computational study of the reaction mechanisms which were proposed by Ye and co-workers.25 The presence of BH3 was considered when investigating the reactions in THF so as to mimic the solvation conditions in the experiment,25 as it is reported that solvent systems constitute a crucial factor in influencing the stereoselectivity of reactions.29 The occurrence of activation barriers was explained using the distortion/interaction–activation strain model (D/I–ASM) of chemical reactivity.30,31 The mechanisms that we determined do not only explain the experimental outcome25 but also constitute a novel synthetic route, via SN2@Cl mechanism, for organophosphorus derivatives which experimentalists may explore in cases where a control over stereoselectivity is required. Such an SN2@Cl mechanism was reported by Zhang et al.32 In addition, we investigated the steric effect on SN2 reactions with Grignard reagents (a and b) as ion-pair nucleophiles in the gas phase and in THF. The results are shown in the ESI document in Fig. S1 and S2.†

Results and discussion

Mechanistic explanation of diastereoselectivity

In this section, we report on the mechanism by which the R1I + a and R1I + b reactions occur in order to explain their diastereoselectivity.25 Depending on the orientation of the nucleophiles, we located several SN2@P-b and SN2@P-f pathways in the gas phase and in THF (see ESI†). Only those with the lowest Gibbs free activation barriers are reported in the manuscript (Fig. 3 and 4).

Fig. 3. Geometries of the TSs and PESs of the R1I + a and R1I + b SN2@P reactions in the gas phase. The bond lengths/distances are in Å. The ΔG and ΔΔG≠ are in kcal mol−1.

Fig. 3

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Fig. 4. Geometries of the TSs and PESs of the R1I + a and R1I + b SN2@P reactions in THF. The bond lengths/distances are in Å. The ΔG and ΔΔG≠ are in kcal mol−1.

Fig. 4

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Both the gas-phase SN2@P-b and SN2@P-f pathways occur through a TS in which the Mg2+ cation interacts with both the Cl and C atoms and this causes the Cl–P–C bond angle to bend (Fig. 3). The bent Cl–P–C bond angle of the SN2@P-b pathways is contrary to the typical near-linear TSs which are reported for anionic SN2-b reactions.14,33 This reflects the effect of the presence of the countercation Mg2+. The small relative Gibbs free energy barriers (ΔΔG≠) between the TSs of SN2@P-b and SN2@P-f pathways do not explain the drs (98 : 2 and 1 : 99 for the P-inverted and P-retained organophosphorus products, respectively) obtained in the experiment.25 This mismatch between experiment and computations prompted us to consider the solvent effect.

We studied the solvent effect by incorporating a BH3 molecule in the R1I reactant and performing bulk solvation with THF as the solvent. Under such conditions, the SN2@P-b pathways feature TSs with near-linear Cl–P–C bond angles. The PESs adopt a unimodal or a hill-and-well shape, which differs from anionic reactions.14,15,29 The ΔΔG≠ of 2.6 kcal mol−1 of the R1I + a reaction (Fig. 4) indicates that the SN2@P-b pathway is preferred. Indeed, the P-inverted organophosphorus stereoisomer was obtained in a higher dr (98 : 2).25 Hence, the aliphatic nucleophile a prefers to react via the inversion pathway, as proposed by Ye et al.25

The ΔΔG≠ (5.2 kcal mol−1) of the R1I + b reaction in THF shows that, similar to the R1I + a reaction, the P-inverted stereoisomer should be obtained. However, the dr, higher for the P-retained stereoisomer (1 : 99),25 shows that the SN2@P-b mechanism is not at play. Hence, to explain the observations of Ye et al.,25 we went back to the basics of charge distribution in a molecule. We therefore employed ESP maps to determine the possible modes of attack, or approach, of the nucleophile b. Owing to the coulombic nature of molecular interactions, ESP maps serve as good indicators of molecular regions which favour particular interactions; for instance, Bhasi et al. expanded the use of ESP maps to the successful location of TSs for atmospheric reactions which were previously thought to be barrierless.34

The ESP map of the organophosphorus reactant R1I [Fig. 5(a)] shows a σ-hole at the extremity of and a belt of negative potential on the Cl atom. Previous reports related the σ-hole to the anisotropic charge distribution of the Cl atom in the molecule and to the occurrence of halogen-bonded complexes.35–37 In this study, the σ-hole gives rise to a halogen-bonded RC [RC in Fig. 5(c)] with an electronic interaction energy of −1.9 kcal mol−1; this qualifies as a halogen bonding interaction (that is, interaction between a halogen and a base) based on the study by Metrangolo et al.38 Hence, we investigated the possibility of a reaction mechanism which is initiated by a halogen-bonded RC.

Fig. 5. (a) ESP map of the R1I reactant. (b) PES of the R1I + b SN2@Cl reaction in THF. (c) Geometries of the RC, TSs, INTs, PC and P of the R1I + b SN2@Cl reaction in THF.

Fig. 5

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The C atom and the Mg2+ cation of nucleophile b interacts with the σ-hole and the belt of negative potential on the Cl atom, respectively, which forms RC. This halogen-bonded RC gives rise to a new type of SN2 reaction, namely, an SN2@Cl reaction. The RC [Fig. 5(c)] proceeds through a TS (TS1) where the C atom of the nucleophile b forms a bond with the Cl atom of R1I and simultaneously breaks the P–Cl bond of R1I. As such, in the SN2@Cl pathway, the Cl atom is the reactive centre and the organophosphorus moiety becomes the leaving group. The TS1 leads to an intermediate (INT1) in which the Mg2+ cation is attracted to the negatively-charged P atom of the organophosphorus moiety. The INT1 reorganises to form INT2 where the Mg2+ cation shifts to interact with the electron density of the BH3 moiety. This change in geometry brings the negatively-charged P atom in INT2 in a position where an attack on the C atom of the o-MeOPhCl moiety is possible. This attack occurs through a frontside SN2@C (SN2@C-f) pathway. The INT2 overcomes TS2 [Fig. 5(c)] leading to the PC and finally to the separate products. This mechanism causes no umbrella flip around the P atom of the organophosphorus reactant and thus, the organophosphorus product retains its geometry around the P atom.

The ΔG of TS1 [+43.9 kcal mol−1, Fig. 5(b)] is lower than the Gibbs free activation energy of the inversion pathway of the SN2@P reaction (+53.9 kcal mol−1) by 10 kcal mol−1. Hence, this explains the 1 : 99 dr obtained by Ye et al. for the P-retained product.25 We thus confirmed that the reaction with nucleophile b occurs via an SN2@Cl mechanism followed by an SN2@C-f mechanism.

In order to investigate the solvation, strain and interaction factors behind the trend in reactivity of the R1I + a and R1I + b reactions, we employed the D/I–ASM. An analysis of the ASDs in Fig. 6 shows that the SN2@P-b pathways are more stabilised by bulk solvation by THF than the SN2@P-f pathways. This happens because of the change in geometries along the PESs; the reactants along the SN2@P-b pathways deform to generate TSs with near-linear Cl–P–C bond angles (169.4° in TSIa-i and 175.3° in TSIb-i), whereas along the SN2@P-f pathway, the reactants deform and lead to a TS with bent Cl–P–C bond angles (61.7° in TSIa-r and 72.0° in TSIb-r). There is more charge separation along the pathways which form the TSs with linear Cl–P–C bond angles than along pathways which lead to cyclic geometries.26–28 The ΔEsolvation curve for the SN2@Cl reaction indicates that the PES is most stabilised by THF at the start of the reaction (C–Cl–P bond angle is 174.7°). As the INT1 is formed, the drop in charge separation causes less stabilisation by THF.

Fig. 6. ASDs of the (a) R1I + a and (b) R1I + b SN2 reactions in THF.

Fig. 6

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The R1I + a reaction experiences more strain in the SN2@P-b pathway which we ascribe to the umbrella flip about the phosphorus atom and to more geometrical deformation to reach the linear TSIa-i in THF. However, the SN2@P-b pathway has a lower Gibbs free energy barrier than the SN2@P-f pathway due to more favourable interaction between the deformed reactants and due to more stabilisation by THF. The initial stages of both the SN2@P pathways of the R1I + b reaction have similar strain curves while the SN2@Cl reaction experiences higher strain. However, as TS1 forms, the ΔEstrain lowers slightly [shown in magnified section in Fig. 5(b)] and the ΔEinteraction between the deformed reactants becomes comparable to the SN2@P pathways. As the reaction progresses, the ΔEstrain stays lower than the SN2@P-f pathway and comparable to the SN2@P-b pathway, and eventually becomes the highest due to the extent of deformation of the reactant fragments involved in reaching the INT1I. The interplay between the stabilisation by THF and reduction in strain while the TS forms that causes the SN2@Cl mechanism to be the most preferred. Hence, we confirmed that (i) the R1I + a reaction yields the P-inverted product in higher dr through an SN2@P-b pathway and (ii) the R1I + b reaction prefers the halogen bond-assisted SN2@Cl pathway over the SN2@P-b pathway by a factor of 10 kcal mol−1. The reactions were also investigated using the M06-2X-D3/6-31++G(d,p) method. The ΔG values are listed in Tables 1 and 2 in kcal mol−1.

ΔG values, in kcal mol−1, of the RCs, TSs, PCs and Ps of the SN2@P-b and SN2@P-f pathways of the R1I + a and R1I + b reactions in THF, computed using the M06-2X-D3/6-31++G(d,p) method. The values for the SN2@P-f pathways are in parentheses.

R1I + a R1I + b
RC +1.9 (+1.9) −2.7 (−1.7)
TS +29.3 (+41.6) +31.5 (+47.6)
PC −48.7 (−59.0) −2.9 (−7.6)
P −50.3 (−50.3) −34.3 (−37.2)
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ΔG values, in kcal mol−1, of the RC, TSs, INTs, PC and P of the SN2@Cl and SN2@C-f pathways of the R1I + b reaction in THF.

SN2@Cl pathway
RC +2.1
TS1 +42.2
INT1 +13.6
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SN2@C-f pathway
INT2 +8.5
TS2 +34.4
PC −21.2
P −38.4
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A comparison of the energy values shows that the R1I + a reaction has a lower activation barrier of +29.3 kcal mol−1 in the SN2@P-b pathway and thus, the reaction occurs through the SN2@P-b pathway. This explains the formation of the products of inverse geometry in the experiment.25 The R1I + b reaction has activation barriers of +31.5, +47.6 and +42.2 kcal mol−1 in the SN2@P-b, SN2@P-f and SN2@Cl pathways, respectively. Hence, the R1I + b reaction also prefers the SN2@P-b pathway. This differs from the results obtained using the B3LYP functional and does not explain the formation of the products of retained geometry in the experiment.25

The TSs were optimised using the MP2 method to obtain more accurate energy values. Due to the large size of the organophosphorus reactant and due to the computationally-demanding nature of the MP2 method, the ΔG values were computed only for the TSs instead of along the whole PESs. We employed the 6-31G(d) basis set because using any higher basis set causes the TS to converge to the RC. Table 3 shows the ΔG of the TSs of the SN2@P-b, SN2@P-f, SN2@Cl and SN2@C-f pathways. It was observed that the TS of the SN2@P-b pathway has the lowest activation energy. Hence, the SN2@P-b pathway is preferred, similar to the M06-2X-D3 results. This is in contrast to the B3LYP results. It was thus deduced that the product of retained geometry may be obtained through a different reaction mechanism instead of those investigated in this manuscript.

ΔG, in kcal mol−1, of the TSs of the SN2@P-b, SN2@P-f, SN2@Cl and SN2@C-f pathways.

SN2@P-b SN2@P-f SN2@Cl SN2@C-f
TS +32.4 +48.1 +37.2 +42.6
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Conclusions

Ye et al. substituted the chlorine atom in a derivative of chlorophosphine and obtained the P-inverted and P-retained organophosphorus products on using aliphatic and aromatic Grignard reagents, respectively.25 In this manuscript, we determined the reaction mechanisms of these two reactions (R1I + a and R1I + b) using the B3LYP/6-31++G(d,p) method. We also highlighted the use of a model of the THF-solvated reaction system with a dative bond between the P and B atoms to account for the presence of the BH3 molecule. The lower Gibbs free activation barrier of the SN2@P-b pathway of the R1I + a reaction explains the formation of the P-inverted product in THF. Our D/I–ASM analyses attribute the preference of the SN2@P-b pathway to more favourable interaction between the deformed reactants and more stabilisation by THF. In the case of the R1I + b reaction, the SN2@P mechanism fails to explain the formation of the P-retained product. In fact, our computations point to a halogen bond-assisted SN2@Cl mechanism. The SN2@Cl mechanism occurs with a lower free Gibbs activation barrier than the SN2@P pathways and is followed by an SN2@C-f mechanism. The preference of the SN2@Cl mechanism resulted from greater stabilisation by THF and reduction in strain while the TS1I forms.

We also investigated the effect of decreasing steric crowding of the phosphorus atom of the R1n organophosphorus reactants. The results are reported in the ESI.† As the bulkiness of the substituents decreases, the R1n + a reactions occur through the SN2@P-b pathways; the decrease in bulkiness lowers the Gibbs free energy barriers of the SN2@P-b pathways on account of more stabilisation by THF and lower deformational strain in the initial stages of the reactions. As the bulkiness of the substituents decreases in the R1n + b reactions, the relative Gibbs free energy barrier of the SN2@P-b pathways becomes lower than that of the SN2@Cl pathway due to the interplay between the strain and interaction components. Hence, a consideration of competing interactions, such as halogen bonding, becomes significant when determining the course of an SN2 reaction, especially in the presence of bulky substituents which hinder the reactive centre.

When the reactions were repeated using the M06-2X-D3/6-31++G(d,p) and MP2/6-31G(d) methods, the preference of the reaction changed to the SN2@P-b pathway. This does not explain the formation of the retention products in the experiment and shows that the computational findings depend on the level of theory used for computations. It is known that different methods give different results due to the different level of approximations.39–42 This may lead to benchmark studies with respect to such organophosphorus reactions.

Methodology

Full optimisation with no symmetry constraints was performed using the B3LYP43–45 hybrid functional and the 6-31++G(d,p) basis set in the gas phase. We selected this method based on previous reports involving SN2@P.20,33,46–48 The stationary points were characterised by frequency computations to verify that the TSs have only one imaginary frequency49 and these were checked by intrinsic reaction coordinate (IRC) computations.

The same computational method was employed based on the polarisable continuum model (PCM)50 to perform bulk solvation with THF by incorporating BH3 in the reaction system to mimic the experiment conditions.25 This procedure is reported in the literature.6 All the computations were carried out at 298.15 K and 1 atm. The reactions are reported in terms of the ΔG with respect to the separate reactants, unless otherwise specified.

We performed a non-covalent interaction (NCI) analysis of selected TSs using the Multiwfn program.51–53 The NCI plots, which are shown in the ESI in Fig. S3,† allow for a visualisation of non-covalent interactions between molecular fragments as real-space surfaces. Within the NCI framework, the sign of λ2 enables identification of the interaction type. Attractive interactions are negative, van der Waals interactions occur close to zero and steric repulsions are positive. The Visual Molecular Dynamics program was used to visualise the molecules in 3D.54 The Gnuplot 4.2 program55 and Ghostscript interpreter56 were employed to generate the 2D plots.

Moreover, the D/I–ASM of chemical reactivity was employed to explain the trends in reactivity along the reaction.30,31,57,58 In the D/I–ASM, the energy along the reaction coordinate is decomposed into its strain and interaction energies. Eqn (1) shows how the D/I–ASM relates the relative electronic energy of a reaction (ΔE) to the relative strain (ΔEstrain) and relative interaction (ΔEint) energies of the deformed reactant fragments along the reaction coordinate (ζ).

ΔE(ζ) = ΔEstrain(ζ) + ΔEint(ζ) 1

The ΔEstrain(ζ) corresponds to the relative electronic energy necessary to distort the reactant fragments throughout the reaction while the ΔEint(ζ) corresponds to the interactions between the deforming reactant fragments.

The D/I–ASM was also applied in THF to investigate the effect of solvation (ΔEsolvation). The solvent-phase PES is described in terms of its components, solute energy and solvation energy, as in eqn (2). The solvation energy englobes the solute–solvent interaction, as well as the formation of the solvent cavity.

ΔEsolution(ζ) = ΔEsolute(ζ) + ΔEsolvation(ζ) 2

We obtained the ΔEsolute(ζ) from the SP energy values of the reactant fragments in gas phase, computed using their geometry from solvent-phase computations. Eqn (3) shows a further breakdown of the ΔEsolute into ΔEstrain and ΔEint.

ΔEsolute(ζ) = ΔEstrain(ζ) + ΔEint(ζ) 3

The reaction coordinate was considered as the IRC projected onto P⋯Cl bond stretch, which constitutes the activation strain diagram (ASD).

In another attempt to explain the outcome of the experiment computationally under the experiment conditions employed by Ye et al.,25 the effect of a temperature of 193.15 K was considered on the ΔG; the results are reported in the ESI.† ΔE at both at 298.15 K and 193.15 K are reported in the ESI.† The ExcelAutomat tool59–61 facilitated file manipulation and file extraction. GaussView 6,62 Chemcraft63 and CylView64 were employed to visualise structures. All computations were carried out in Gaussian 09 65 and Gaussian 16 66 suites using the SEAGrid computing facilities.67–71 Explicit details about the computational methods are found in the ESI.†

According to several reports, the use of dispersion correction is necessary for the investigation of non-covalent interactions between the nucleophile and the σ-hole of the chlorine atom.29,72–74 Hence, these reactions were studied using the M06-2X functional and dispersion correction was considered; full optimisation computations were performed using the dispersion-corrected M06-2X-D3.72,75–78 Moreover, the second-order Møller–Plesset (MP2)79–83 method was also employed in order to obtain more reliable energy values. The energy values were compared with the results obtained using the B3LYP/6-31++G(d,p) method.

Author contributions

PR was responsible for project administration, conceptualisation, supervision and writing – review & editing.

LR was responsible for conceptualisation, supervision and writing – review & editing.

NS was responsible for conceptualisation, investigation, data curation and writing – original draft.

Conflicts of interest

There are no conflicts to declare.

Supplementary Material

RA-012-D2RA00258B-s001

Acknowledgments

The authors are grateful to the Higher Education Commission (HEC) of Mauritius. The authors are also grateful to SEAGrid and South African CHPC for providing computing facilities.

†

Electronic supplementary information (ESI) available. See DOI: 10.1039/d2ra00258b

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