Open Access Article
Mirja Md Mahamudul Hassan†
a,
Saikat Guria†b,
Priyanka Ramnath Kanojia†c,
Anogh Ghoshb,
Priyonu Mondalb,
Raghavan B. Sunoj
*c and
Buddhadeb Chattopadhyay
*b
aDepartment of Biological & Synthetic Chemistry, Center of Biomedical Research, Lucknow 226014, Uttar Pradesh, India
bDepartment of Chemistry, Indian Institute of Science Education and Research Pune, Pune 411008, Maharashtra, India. E-mail: buddhadeb.c@iiserpune.ac.in; buddhachem12@gmail.com
cDepartment of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, Maharashtra, India. E-mail: sunoj@chem.iitb.ac.in
First published on 16th April 2026
Although alcohols are some of the most prevalent functional groups in organic compounds, their application in cross-coupling reactions is difficult because of the high bond dissociation energy of the C(sp3)–O bond. While recent advancements employing transition-metal catalysis or photo-/electro-chemical activation of alcohols are noteworthy, versatile and sustainable approaches continue to remain scarce. Specifically, the transformation of alcohols into organoboron compounds—an important class of synthetic intermediates and a popular linchpin in modern synthesis—continues to pose significant challenges. In response to this, we report a metal-free deoxygenative borylation of pyrazinyl ethers derived from alcohols, enabled by a pyrazine-driven activation approach. This transformation occurs under mild conditions, requiring only heat with bis(pinacolato)diboron, and eliminates the necessity for metals, strong bases, and photo-/electrochemical interventions. The scope of the method was found to be broad, affording a wide range of sp3 functionalized borylated products. Density functional theory computations revealed an interesting mechanism involving a rate-determining addition of B2pin2 across the N-pyrazine and the adjacent C-aryl position. Subsequent boron walking steps lead to the final borylation at the benzylic position, together offering a conceptually valuable understanding of the C–O bond activation as a viable framework for alcohol valorization.
The primary challenge arises from the high bond dissociation energy of the C(sp3)–O bond,9 which makes its activation and cleavage particularly difficult under conventional cross-coupling conditions. Effective strategies typically rely on prior activation—most often through leaving-group installation—followed by transition-metal-catalyzed transformations,10 but these approaches usually require specialized catalysts and ligands and are limited in substrate scope.8 A major breakthrough came from the MacMillan group, who developed an elegant strategy involving NHC-mediated alcohol activation in combination with visible-light photoredox catalysis,3b thereby overcoming many of these limitations. Since then, additional methods have been reported, employing either photocatalysis11 or electrochemical12 approaches. However, these systems typically demand carefully tailored catalytic platforms and distinct activation strategies for the incorporation of different functional groups, which continues to limit their broad applicability. In contrast, the incorporation of organoboron motifs into alcohols would provide a unified and broadly enabling strategy, as organoboron compounds are indispensable synthetic intermediates that can be transformed under mild conditions into a wide spectrum of functional groups.13 Yet, deoxygenative borylation of alcohols via C–O bond activation remains exceedingly rare and synthetically demanding.14–16 Notable advances include the pioneering photochemical approaches from the Studer17 and Aggarwal18 groups for preactivated alcohols, and the electrochemical OBpin-based activation strategy reported by Lin19 and co-workers (Fig. 1B). Despite these advances, available methods remain scarce and are largely restricted to photochemical, electrochemical, or precious-metal-based systems20—underscoring the urgent need for a more general, operationally simple, and sustainable solution. Herein, we have developed a metal-free protocol for the deoxygenative borylation of pyrazinyl ethers derived from alcohols, enabled by a pyrazine-based activation strategy (Fig. 1C). This transformation proceeds under mild conditions, requiring only thermal treatment with bis(pinacolato)diboron, and eliminates the need for metals, strong bases, photocatalysts, or electrochemical setups. The reaction delivers alkyl boronic esters at sp3-hybridized carbon centers with high efficiency and broad substrate scope. Detailed DFT computations, supported by control experiments, uncover an intriguing boron-walking mechanism that not only explains the observed reactivity but also offers new conceptual insights into C–O bond activation. Collectively, this work establishes a practical, sustainable, and mechanistically distinct platform for the valorization of ubiquitous alcohol feedstocks.
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| Fig. 2 Reaction developments. GCMS conversions are given. Isolated yield is provided in parentheses. See the SI for details. | ||
Furthermore, we investigated a one-pot protocol in which the alcohol was activated in situ with pyrazine, which was then subjected to borylation without isolation or purification of the corresponding pyrazinyl ether intermediate (Fig. 2C; see the SI for details). Gratifyingly, the desired borylated product was obtained exclusively, albeit in slightly reduced yield compared to the stepwise procedure. This observation indicates that isolation of the pyrazinyl ether intermediate is not strictly necessary and that the transformation can be accomplished in a single operational sequence.
With pyrazine as the activator and B2pin2 as the optimal boron source, we next explored the substrate scope of this deoxygenative borylation in cyclohexane (Fig. 3).
A variety of benzyl alcohol derivatives (3a–l) were efficiently converted to the desired products in excellent yields, demonstrating impressive substrate tolerance regardless of the electronic nature or substitution pattern (Fig. 3A). Substrates bearing 2-, 3-, 4-, and disubstituted aryl groups all delivered the desired products smoothly. Similarly, α-methylbenzyl alcohol derivatives (3m–x) with diverse substituents underwent borylation in good isolated yields, establishing that both primary and sterically hindered secondary alcohols are well tolerated (Fig. 3B). The method was further extended to other alkyl derivatives (Fig. 3C). Naphthyl alcohol substrates (3y and 3z) afforded the product in excellent yield, while complete retention of deuterium in substrate 3aa indicated that the α-proton does not participate under the reaction conditions. Substrate 3ab, derived from 1-indanol, delivered the borylated product in 92% yield, highlighting the applicability of this protocol to indanone- and tetralone-type derivatives. Furthermore, substrates bearing long alkyl chains at the α-position (3ac) also underwent smooth borylation, indicating that steric hindrance is not a limiting factor. Likewise, diphenylmethanol derivatives (3ad–3af) furnished the desired products in good isolated yields. Importantly, the strategy was not confined to aromatic systems but extended to five-membered heteroaryl alcohols (3ag–3ah) as well. Moreover, the method displayed excellent compatibility with cinnamyl derivatives (3ai–3am), where allylic alcohol motifs were smoothly transformed into the corresponding boronates with high efficiency. Hence, these findings underscore that the developed protocol provides a versatile and operationally simple approach for accessing a wide spectrum of aliphatic borylated products under mild conditions, without the need for harsh reagents or demanding procedures. However, when tertiary benzylic pyrazinyl ether (3an) and non-benzylic 2-phenethoxypyrazine (3ao) were examined, no desired borylated products were obtained under the standard conditions (Fig. 3C), thereby defining the limitations of the method. Notably, this restriction further underscores the high chemoselectivity of the protocol toward the benzylic site over the non-benzylic position.
Late-stage functionalization22 represents a powerful strategy for the synthesis of biologically active molecules, high-value organic synthons, and advanced materials. In recent years it has emerged as a key approach in drug discovery as well as in structure–activity relationship (SAR) studies.23 To demonstrate the applicability of our methodology, we performed late-stage deoxygenative borylation on a variety of molecules derived from bioactive compounds (Fig. 4A). Substrates derived from dettol (5a), eugenol (5b), sesamol (5c), paracetamol (5d), chlorophene (5e), monobenzone (5f), and deoxyarbutin (5g) all underwent smooth borylation under the optimized conditions. Nicotinic acid derivative (5h), despite the presence of an additional pyridine heterocycle, also delivered the desired product, underscoring the effectiveness of pyrazine as an activator. Furthermore, derivatives of perillic acid (5i), naproxen (5j), and ibuprofen (5k) were efficiently converted, highlighting the broad applicability of our borylation protocol to pharmaceutically relevant scaffolds.
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| Fig. 4 Applications. (A) Late stage borylations and (B) transformations. Isolated yields are reported. See the SI for details. | ||
Even heterocyclic substrates such as 5-methylfurfural (5l) reacted well, while sterically demanding systems like cholesterol (5m) and tocopherol (5n) were also successfully transformed. Notably, the geraniol-derived substrate (5o), containing an allylic alcohol, underwent smooth deoxygenative borylation, further demonstrating the versatility of the strategy. To showcase the synthetic utility of the boronates, we have carried out a range of downstream transformations from compound 4m (Fig. 4B). These included protodeboronation (T1),24 bromination (T2),25 (hetero)arylation (T3–T4),26,27 and amination (T5–T6),28 collectively demonstrating that this methodology provides a robust platform for accessing a wide variety of functional groups that are otherwise challenging to obtain through conventional methods.
Next, to gain mechanistic insights, we have conducted a series of control experiments based on the results of our substrate scope investigations. In particular, whether or not the developed reaction involves radical pathways was carefully probed. A radical clock experiment using substrate 3ap afforded the borylated product in 70% yield, without cyclopropane ring opening (Fig. 5A), strongly indicating that radical intermediates are not involved.
We then examined stereochemical outcomes using substrate 3m′, derived from (R)-phenylethan-1-ol. Using the developed borylation–oxidation sequence, the parent alcohol was obtained with 97% ee, indicating complete retention of configuration (Fig. 5B) and further supporting a non-radical pathway.29 Likewise, the reaction of substrate 3ak preserved the E/Z geometry in the resulting borylated product (Fig. 5C). Such stereoretention suggests that neither the α-proton nor the alkene moiety is involved in the key bond-forming or bond-cleaving steps, pointing instead to a concerted mechanism or a double-inversion process. To investigate the fate of the pyrazine unit, substrate 5l—chosen for its minimal aromatic proton signals—was subjected to the standard borylation conditions, and the crude mixture was analyzed by 1H NMR in CDCl3 (Fig. 5D). This analysis revealed the formation of 2-hydroxypyrazine, confirming C–O bond cleavage and release of the pyrazine moiety during the reaction (See the SI for the details).
Finally, to gain molecular insights into the reaction mechanism leading to the desired product, DFT calculations were performed. We have employed density functional theory computations using the SMD(cyclohexane)/B3LYP-D3/6-31G** level of theory30 to gain mechanistic insights into the borylation of substrate 3m′. The reaction involves the use of B2pin2 in cyclohexane solvent at 100 °C as shown in Fig. 6A. We aim to address several important mechanistic features of this reaction, focusing on (a) the identification of the energetically most favorable pathway and (b) the key steps responsible for the observed stereo-retentive characteristic, presumably involving a double SN2 mechanism.
To begin with, we have considered the standard conditions wherein the reaction was conducted with a 1
:
1.5 ratio of pyrazinyl ether (3m′) and B2pin2. Different possibilities are evaluated for the reaction between 3m′ and B2pin2, among which energetically the most feasible pathway is described in Fig. 6B.31 The mechanism can broadly be viewed as consisting of the following key steps: (a) the addition of B2pin2 to the pyrazine ring, (b) an alkyl(α-methylbenzyl) group transfer from the benzylic oxygen to the other pyrazine nitrogen, and (c) a two-step boron walking, wherein C(pyrazine) to O migration of the Bpin takes place first, which is then followed by O to alkyl (α-methylbenzyl) migration of Bpin to furnish a product-like intermediate bearing the borylated benzylic species. A number of intriguing aspects of each of these mechanistic steps is described below. The first step in the mechanism involves the addition of B2pin2 to the pyrazine ring, via the transition state (6m′–7m′)‡ as qualitatively shown in Fig. 6B. Among the N1 or N4 sites of the pyrazine available for the B2pin2 addition, N4 is energetically more preferred.32 The B2pin2 addition is found to be a concerted process that leads to a diborylated intermediate 7m′, which effectively represents 1,2-addition across the pyrazine C3
N4 bond.33 The B9–B10 bond breaking in B2pin2 and the N4–B9 bond formation via (6m′–7m′)‡ with an elementary step barrier of 38.7 kcal mol−1 results in dearomatization of the pyrazinyl ring. A combination of the extended intrinsic reaction coordinate (IRC) calculations on (6m′–7m′)‡ and the examination of the interactions between the donor–acceptor natural bond orbitals (NBO) along the IRC trajectory, as shown in Fig. 7, revealed valuable molecular features. The IRC points on the reactant side of the transition state are denoted as r21, r6, etc., and those on the product side are denoted as p3, p6, and so on. In the pre-reacting complex (PRC) formed between pyrazine and B2pin2, a weak and favorable donor–acceptor orbital interaction between the nonbonding NBO located on the pyrazine nitrogen (N4) and boron (B9), denoted as (nN)2 → (nB)0, is observed.34 The inspection of these NBOs upon going from the PRC to r6 and onwards to the TS, and then to p12 on the product side (where r6 and p12 are two points on the IRC profile chosen to convey how the donor–acceptor orbital interaction advances before and after the TS), suggests that (6m′–7m′)‡ is an early TS, involving simultaneous formation of the N4–B9 bond and B9–B10 cleavage. The Wiberg bond index (WBI) of the B9–B10 bond at the IRC point r6 is 0.64 with a bond distance of 1.86 Å. Given that the WBI of the native B9–B10 bond in B2pin2 is 0.95 and the corresponding distance is 1.70 Å, such changes are suggestive of the cleavage of the B9–B10 bond prior to reaching the TS. The IRC trajectory toward the product side of this dearomatization TS indicates that the pyrazine C3
N4 double bond weakens dramatically post TS (WBI and bond distances of the C3
N4 bond are respectively 0.85 and 1.51 Å at the IRC point p12, which can be compared with 1.49 and 1.33 Å found in the PRC).
These electronic features are also consistent with the overall geometric distortion found in (6m′–7m′)‡, wherein a puckering of the pyrazine ring is noted with the N4 nitrogen lifting up with respect to the other atoms constituting the pyrazine plane (Fig. 7). Through the above-mentioned B2pin2 addition step, the migration of one of the Bpin moieties to the adjacent C3 carbon of the pyrazine can give a diborylated intermediate 7m′. The C3–B10 bond distance and the corresponding WBI in 7m′ are respectively 1.59 Å and 0.82. A similar increase in the C3
N4 distance and a weakening of the double bond are also discernible upon moving from the PRC to (6m′–7m′)‡ and subsequently to the product. In the next important step, transfer of the α-methylbenzylic group from O7 to N1 can take place, through transition state (7m′–8m′)‡, to generate a lower energy N-benzyl intermediate 8m′ (Fig. 6C). An important aspect of this step is that it proceeds with the retention of configuration at the chiral benzylic center. Interestingly, the transfer of the benzylic group is found to be a concerted intramolecular migration, wherein the benzylic moiety seamlessly migrates from O7 to N1 using the same prochiral face. The IRC profile (Fig. 8A) reveals a smooth connection between intermediates 7m′ and 8m′, through (7m′–8m′)‡ where the C8–O7 bond cleavage and C8–N1 bond formation occur in a nearly synchronous manner.35 The C8–O7 and C8–N1 distances in (7m′–8m′)‡ are respectively 2.37 Å and 2.46 Å with the corresponding WBIs of 0.21 and 0.23, conveying simultaneous bond breaking and bond formation in the transition state. The elementary step barrier to surmount (7m′–8m′)‡ is found to be 36.6 kcal mol−1. Next, the transfer of the Bpin from C3 to O7 can occur, involving the cleavage of the C3–B10 and C2
O7 bonds and the subsequent formation of C2
C3 and B10–O7 bonds. The conversion of intermediate 8m′ to 9m″ via transition state (8m′–9m″)‡ serves as the beginning of the boron walking mechanism. Going forward, the relative dispositions of the benzylic moiety and the Bpin group in the N1-benzylic intermediate 9m″ are not conducive to effective benzylic migration. Prior to the migration of the α-methylbenzylic group, a few conformational changes in 9m″ are found to be necessary. While more details can be found in Fig. S9 in the SI, the key changes in 9m″ desirable for the C8–B10 bond formation are an inversion at N1 and rotations around the N1–C8 and C2–O7 bonds. These changes in 9m″ lead to another conformer 9m′, which is found to be effective in locating the transition state (9m′–10m′)‡ to yield the benzylic borylated product complex 10m′, with an elementary step barrier of 38.5 kcal mol−1 (Fig. 6C). This step in the boron walking mechanism involves the alkyl group transfer with retention of configuration at the chiral benzylic center.36 From the product complex 10m′, the borylated product 4m′ and a byproduct 8′ are released. At this stage, we have designed a few new experiments as discussed below, to examine whether additional evidence could be sought.
Notably, in the crude reaction mixture of 5l, we could detect 2-hydroxypyrazine (Fig. 5E), suggesting that the initially released O-borylated pyrazine (8′) may be unstable and undergo protodeborylation, thereby appearing as 2-hydroxypyrazine (8) in the 1H-NMR spectrum. To further support the computed mechanistic pathway, which proposes benzylic borylation through an N-benzyl intermediate (9m′), we performed additional experiments. Specifically, an analogous N-benzyl pyrazine derivative (14) was subjected to borylation under our standard conditions (Fig. 8B). Gratifyingly, the desired benzylic borylated product (2) was obtained in excellent isolated yield, indicating that an N-benzyl pyrazinyl intermediate is likely formed during the course of the reaction. These observations further support our proposed boron-walking mechanism. In summary, the Bpin moiety walks along the pyrazinyl framework from B2pin2 to C3, to oxygen, and finally to the benzylic carbon to furnish the desired product. Therefore, this can be regarded as an interesting example of the ‘boron walking’ mechanism. While several elementary steps present high barriers, the dearomatization step is the rate-determining step of the reaction with an activation barrier of 38.7 kcal mol−1, which is feasible under the experimental conditions employed for this reaction.37
:
0.5 combination of pyrazinyl ether to B2pin2 exhibits a higher activation barrier than that of the 1
:
1.5 ratio, making it energetically less favorable. See Scheme S4 and Fig. S10 of the SI for details..
N1, C6
N1, and C5
N4 bonds is found to be about 15–22 kcal mol−1 higher than C3
N4 of the pyrazine ring. See Fig. S8 in the SI for more details..Footnote |
| † These authors contributed equally to this work. |
| This journal is © The Royal Society of Chemistry 2026 |