Automated iterative assembly of chemical building blocks broadens access to innovation at the molecular scale1. Methods for reversibly attenuating the reactivity of the functional group handles used to link such blocks are critical for these platforms. For unsaturated (Csp2-rich) organic small molecules, such lego-like assembly in automated and/or manual fashion has been achieved by many different research groups worldwide using N-methyliminodiacetic acid (MIDA) boronates2,14,15,16, which are compatible with anhydrous basic Csp2 cross-coupling conditions (Fig. 1a). An important advantage of MIDA relative to other ligands that attenuate boronic acid reactivity (for example, 1,8-diaminonaphthalene, anthranilamide, ethanolamine, fluoride)17 is that MIDA boronates display a tuneable affinity for silica gel, which permits generalized automated purification2. This unique feature enabled assembly of 14 distinct classes of small organic molecules using one automated process2.

Fig. 1: Lego-like chemical synthesis.
figure 1

a, Iterative chemical synthesis. Automated synthesis is achieved using bifunctional MIDA boronate building blocks. Controlled removal of MIDA enables iterative synthesis. b, Leading Csp3–C bond-formation methods. Csp3–Csp2 cross-coupling of organoboranes is typically achieved under aqueous basic conditions. 1,2-Metallate rearrangements of boronic esters achieve Csp3–Csp3 bond formation by using Grignard and organolithium reagents. c, Sensitivity of MIDA boronates to Csp3–C bond-forming conditions. Conditions permissive of Csp3–C bond formation cleave MIDA boronates and are therefore incompatible with automated lego-like synthesis. p-tol, para-toluene; TIBO, 2,4,6-triisopropylbenzoate.

Important areas of chemical space remain inaccessible with this first-generation platform, particularly for molecules rich in non-planar and potentially stereogenic sp3-hybridized carbon atoms (Csp3). This represents a substantial limitation, because Csp3-rich molecules constitute some of the most notable natural products, medicines18, biological probes and functional materials19. An important goal is thus to expand automated modular synthesis to include Csp3-rich small molecules.

Many recent breakthroughs in stereospecific formation of Csp3–C bonds through Suzuki–Miyaura couplings6,7 and 1,2-metallate rearrangements8,9,10 stand to enable advances in this direction (Fig. 1b). However, most of these reactions require either aqueous basic conditions that hydrolyse MIDA boronates, or nucleophilic reagents that react with MIDA boronates (Fig. 1c). In both cases loss of the MIDA protecting group will lead to uncontrolled couplings and form complex mixtures and/or oligomeric products. We thus sought hyperstable boronates to enable lego-like small-molecule synthesis via iterative Csp3–C bond formation.

Identifying a hyperstable boronate

Mechanistic studies on MIDA boronate hydrolysis provided a foundation for developing hyperstabilized variants20. There are two mechanisms for MIDA boronate hydrolysis. The first involves frustrated Lewis pair-like activation of water by the dative N–B bond. The second mechanism involves ester hydrolysis-like cleavage of a MIDA carbonyl (C=O) group by hydroxide. Steric shielding would probably protect the carbonyl carbons from hydroxide and nucleophiles, yet steric effects are known to activate frustrated Lewis pair behaviour of N–B bonds21,22,23. Although hydrolysis studies of MIDA boronates20 indicated electronic tuning of the N–B bond could be achieved via modifying the organic group attached to boron, we required a building block-independent solution. So, at the outset it was unclear whether steric or electronic effects could be leveraged to create a more stable ligand.

Using [18O]water to probe the hydrolysis of MIDA boronate 1a20, we first established the N–B bond as the primary hydrolysis mechanism under aqueous basic Csp3–Csp2 Suzuki–Miyaura coupling conditions (THF/H2O, K2CO3, 60 °C) (Fig. 2a). We thus required a MIDA derivative that could suppress the frustrated Lewis pair like reactivity of the N–B bond. To better understand this behaviour, we used 1H NMR to study the stability of a range of substituted MIDA derivatives (1b, 39) in deuterated solvent (THF-d8/D2O, K2CO3, 60 °C) (Fig. 2b).

Fig. 2: TIDA boronates are exceptionally stable towards hydrolytic and nucleophilic cleavage.
figure 2

a, MIDA boronate 1a is hydrolysed via N–B bond-mediated water activation under standard stereospecific Csp3 coupling conditions. b, Modifications of the MIDA ligand yield varying degrees of stability for the corresponding iminodiacetic acid boronates under common aqueous basic stereospecific Csp3–Csp2 coupling conditions. TIDA boronate 9 is exceptionally stable. eq., equivalents . c, TIDA boronates resist hydrolysis during Csp3–Csp2 Suzuki–Miyaura coupling with 10, whereas MIDA boronates are completely hydrolysed. d, TIDA boronates were stable to the Grignard reagent iPrMgCl·LiCl enabling Csp3–Csp3 bond-forming 1,2-metallate rearrangements, whereas MIDA boronates were cleaved under these conditions. e, The remarkable stability of TIDA boronates extends to tBuLi. Diastereospecificity (d.s.) = (final diastereoisomeric ratio/initial diastereoisomeric ratio) × 100.  dan, 1,8-diaminonaphthalene; pin, pinacolato.

Consistent with earlier precedent22,23, bulky groups on nitrogen (Fig. 2b35 and Supplementary Fig. 2a) increased the rate of hydrolysis relative to MIDA (1b), probably increasing N–B frustrated Lewis pair-like behaviour. Remarkably, appending two n-butyl groups (6) to the iminodiacetic acid backbone caused almost no change in hydrolysis rate relative to MIDA (1b). Reducing the size of these substituents to ethyl groups (7) and methyl groups (8) provided impressive stabilization. Finally, we prepared a boronate derived from a highly sterically hindered tetramethylated variant of N-methyliminodiacetic acid 9 (TIDA) and, surprisingly, found it was highly stable under aqueous basic Csp3-Csp2 cross-coupling conditions, with more than 99% remaining after 6 h (Fig. 2b).

Additional hydrolysis studies of TIDA boronate 21 under these conditions in protic solvent (Supplementary Figs. 3, 4), [18O] labelling (Supplementary Fig. 5) and neutral hydrolysis (Supplementary Fig. 6) indicated that TIDA boronates were cleaved via N–B bond water activation. The hyperstable TIDA boronate was retained during Csp3-Csp2 Suzuki–Miyaura reaction between Csp3 boronate 10 and bifunctional halo-TIDA boronate 11b to provide 12, whereas MIDA boronate 11a (Fig. 2c) and related N-2-benzyloxycyclopentyliminodiacetic acid (BIDA) boronate SI-14 (Supplementary Fig. 2b) gave no desired product.

Encouraged by these results, we tested the stability of TIDA boronates to iPrMgCl·LiCl, which promotes stereospecific Csp3–Csp3 bond-forming 1,2-metallate rearrangements10 (Fig. 2d). TIDA boronate 14b resists cleavage by iPrMgCl·LiCl to form the target product 15 in high yield, whereas MIDA boronate 14a is cleaved under these conditions. Remarkably, TIDA boronates even tolerated highly reactive tBuLi, enabling the formation of 18 and 19 with excellent diastereocontrol (Fig. 2e). Providing an additional practical advantage, our bifunctional sulfoxide10 TIDA boronate building blocks (that is, 14, 16 and 17) are easily handled, bench-stable solids (Supplementary Fig. 1).

X-ray crystallographic studies

The stability of 9 towards aqueous base is surprising considering the strong precedent for increased reactivity of frustrated Lewis pairs derived from tetramethylpiperidine21. Hints at the origin of this stability were found on X-ray crystallographic analysis of single crystals of MIDA boronate 1c (Fig. 3a, inset) and TIDA boronate 20 (Fig. 3b, inset), which revealed a torsional shift of greater than 10° along the N–B axis in TIDA 20 relative to MIDA 1c.

Fig. 3: Steric and electronic effects collaborate to stabilize TIDA boronates.
figure 3

a, Examination of non-spherical (that is, bonding) electron density (ρ) in the plane of the iminodiacetic acid ring of MIDA boronate 1c. Contour level 0.0675 e Å−3. Shown inset is the perspective looking down from N to B. b, Non-spherical electron density in the plane of the iminodiacetic acid ring of TIDA boronate 12 shows substantial electronic redistribution compared to MIDA boronate 1c, particularly for the N–B bond. An associated 12° torsional shift increases hyperconjugative interactions along the N–B axis compared to MIDA 1c. c, Comprehensive steric shielding of all four π-faces of TIDA boronates suppresses nucleophilic attack on the carbonyl carbons. d, Despite their high stability towards Csp3 bond-forming reactions, TIDA boronates are easily removed under aqueous or protic conditions at elevated temperatures. Contour plots were generated using VESTA 3 (ref. 42).

Torsional effects can substantially influence24 the magnitude of hyperconjugative stabilization (that is, staggered versus eclipsed ethane25). Torsional shifts in 20 bring three donor N–C bonds nearly antiperiplanar to three acceptor bonds (two B–O bonds and one B–C bond), potentially elevating hyperconjugation across the N–B bond. Backbone methylation would probably increase N–C donor ability, and internal angle compression in 20 (approximately 5°) suggests thermodynamic Thorpe–Ingold effects make the framework more rigid (Extended Data Fig. 1a). Both effects probably reinforce putative hyperconjugation across the N–B bond in 20. We thus questioned whether stabilizing hyperconjugative interactions across the N–B bond in TIDA boronates drives a reduction in the rate of N–B hydrolysis.

Electron distribution analysis

To probe electronic effects experimentally, we performed quantum theory of atoms in molecules (QTAIM)-based charge density analysis11,12,13 on X-ray crystal structures of MIDA boronate 1c and TIDA boronate 20. Multiple lines of evidence revealed that the dramatic reduction in hydrolysis for TIDA boronates is attributable to hyperconjugation-mediated redistribution of electron density that increases the covalency of the N–B bond.

Topology maps of crystallographically determined bonding electron density, ρ, demonstrated electron redistribution across planar slices spanning the iminodiacetic acid rings of MIDA 1c and TIDA 20 (Fig. 3a, b). Notable features of TIDA 20 included increased electron density spanning the N–B interatomic space (Fig. 3b and Extended Data Fig. 2j), and formation of a contiguous ring of electron density around the iminodiacetic acid cage (Fig. 3b). The stabilizing nature of electronic redistribution with the N–B bond of TIDA 20 was supported by a negative Laplacian of electron density 2ρ(r) at boron and nitrogen valence shell charge concentrations (Extended Data Fig. 3j). TIDA 20 therefore possesses an N–B bond of substantially increased covalent character.

Elongation of nitrogen-attached donor bonds and boron-attached acceptor bonds (Extended Data Fig. 1b), consistent with previous studies of anomeric26 and gauche effects27, supports threefold hyperconjugation along the N–B linkage. Anticipated increased π-character manifested localized increased ellipticity (ε)11 (Extended Data Fig. 4c, f, g, j, l, m), and redistributed electron density was supported by changes in 2ρ(r) (Extended Data Fig. 3e, f, k)28. Electrostatic potential maps, reduced polarization of the N–B bond29 and 11B/13C NMR shifts were also consistent with electron redistribution (Extended Data Fig. 5). Additional stabilizing electronic redistributions were found on examination of ρ, 2ρ(r) and ε surrounding boron-attached oxygens O1 and O4, which revealed more equal distribution of electron density directed towards boron and the carbonyl carbons for TIDA 20 compared to MIDA 1c (Extended Data Figs. 2b, c, h, i, 3b, c, h, i, 4c, d, i, j and 6).

Increased electron sharing30 is consistent with reduced propensity for frustrated Lewis pair activity31,32,33, and rationalizes the increased robustness of TIDA boronates towards N–B bond hydrolysis. Remarkably, these stark differences in N–B bond character are contrasted with similar bond lengths (MIDA 1c: 1.6613(7) Å; TIDA 20: 1.6632(5) Å).

Steric shielding of TIDA boronates

Crystallographic data for TIDA 20 also indicated that the stability of TIDA boronates towards carbon nucleophiles (iPrMgCl·LiCl and tBuLi) arises from shielding of all four π-faces of the carbonyls by the attached methyl groups (Fig. 3c and Extended Data Fig. 7a34). Comparison with organolithium-stable Beak-type benzoates35 revealed that 20 mirrors Beak-like shielding interactions via a transannular methyl group spanning the back face of the iminodiacetic acid cage (Extended Data Fig. 7b).

Synthetic utility of TIDA boronates

Reversible ligation is a requirement for deploying TIDA boronates in iterative cross-coupling-based building block assembly. An orthogonal pathway for hydrolysis involving C=O attack (Supplementary Fig. 7 and Extended Data Fig. 8a) enabled TIDA boronates (21) to be deprotected to boronic acids (22), trifluoroboronate salts (23), and boronic esters36 (24, 25) by simply using aqueous basic or protic conditions at elevated temperature (Fig. 3d).

TIDA boronates retain all other key features of their MIDA boronate counterparts that enabled automated building block-based synthesis2: TIDA ligand is accessible on the kg scale (Extended Data Fig. 8b), TIDA boronates are prepared from boronic acids under Dean–Stark conditions or by using a dehydrated form of TIDA (Extended Data Fig. 8c), TIDA boronates are stable to a wide range of common cross-coupling reactions (that is, Stille, Suzuki, Sonogashira, Heck, photochemical; see Extended Data Fig. 9) and chemical transformations (that is, oxidation, reduction, borylation, olefination; see Extended Data Fig. 10). Representative TIDA boronates retain a tuneable affinity for silica gel, being minimally mobilized in Et2O and rapidly eluted in THF (Extended Data Fig. 8d). This feature enables the TIDA boronate group to act as a tag for generalized and automated catch-and-release purification2. The heightened stability of TIDA boronates further enabled us to create a self-contained next-generation synthesis machine (Supplementary Figs. 811 and 13) to enable automated iterative assembly of Csp3 boronate building blocks (Fig. 4a, d).

Fig. 4: TIDA boronates enable automated assembly of Csp3 boronate building blocks.
figure 4

a, TIDA boronates enable iterative Suzuki–Miyaura cross-coupling. b, Assembly of Csp3 building blocks via Csp3–Csp2 Suzuki–Miyaura cross-coupling enabled by TIDA boronates. MIDA boronates universally provided no product. c, Automated stereospecific Csp3 cross-coupling with TIDA boronate 32 enables lego-like synthesis of ieodomycin C. d, TIDA boronates enable iterative 1,2-metallate rearrangements. e, Assembly of Csp3 building blocks via Csp3–Csp3 bond-forming 1,2-metallate rearrangements enabled by TIDA boronates. f, Sequential automated stereospecific Csp3–Csp3 bond formation using TIDA boronates enables lego-like synthesis of sch725674. For detailed experimental procedures see Supplementary Information. Yields for automated synthesis shown in parentheses. d.r., diastereoisomeric ratio.

Having established an iterative synthesis platform (Fig. 4a), we investigated a series of stereospecific Csp3–Csp2 cross-coupling reactions with bifunctional halo-TIDA boronates (Fig. 4b). Across a range of carbonate-promoted aqueous/protic stereospecific Csp3 cross-coupling reactions6,7, MIDA boronates were fully hydrolysed, whereas the corresponding TIDA boronates universally provided the desired products in good yields both in manual and automated formats (12, 26, 27 and 28). The increased stability of TIDA boronates also permitted use of stronger bases KOH (31)5 and Ag2O (30)4.

Leveraging automated Csp3–Csp2 couplings with TIDA boronates, we targeted a lego-like total synthesis of ieodomycin C37 (Fig. 4c). Building block 31 (97:3 enantiomeric ration (e.r.)) underwent automated stereospecific Csp3 cross-coupling with bifunctional TIDA boronate 32 to provide 33 in >95:5 e.r. and 50% isolated yield after automated purification. TIDA boronate enabled functional group interconversion followed by deprotection (34), and Suzuki–Miyaura cross-coupling with vinyl halide 35 furnished diene 36 and ieodomycin C after deprotection.

The tolerability of TIDA boronates to iPrMgCl·LiCl enabled 1,2-metallate rearrangements to be executed with bifunctional sulfoxide-TIDA boronate building blocks in manual and automated formats (Fig. 4d) to prepare a variety of Csp3–Csp3 bonds in excellent yields (Fig. 4e, 15 and 37-42). A triply boron-selective reaction was also achieved in the diastereospecific preparation of 43 and 44. Csp2 boronic esters were also effective (45, 46).

Reactivity differences between unhindered/hindered boronic esters38,39 suggested potential for iteration-enabling kinetic selectivity within Csp3–Csp3 bond formation. Accordingly, we investigated the lego-like automated synthesis of macrocyclic antifungal natural product sch725674 (ref. 40) (Fig. 4f). Demonstrating the advantage ofour approach over previous strategies41 to access sch725674, our bifunctional sulfoxide-TIDA boronate 14b enabled recursive application of the same assembly chemistries to form Csp3–Csp3 bonds. Additionally, the inclusion of a TIDA boronate enabled this entire process of multiple building block assembly via iterative Csp3–Csp3 bond formation to be executed in a fully automated and uninterrupted fashion (Supplementary Figs. 14 and 15). n-Pentyl pinacol boronic ester 47 was subject to 1,2-metallate rearrangement with sulfoxide-boronate 14b to afford the target TIDA boronate 48 in high stereocontrol (>95:5 e.r.). Automated deprotection to the corresponding pinacol boronic ester 49 was followed by automated boronic ester-selective reaction with sulfoxide 50 to provide the core carbon scaffold of sch725674 (52) after oxidation of bisboronate 51. Deprotection (TBAF, 53), oxidative modification, macro-lactonization and final deprotection furnished sch725674 in only seven steps from bench-stable building blocks.