SYNTHESIS OF A MECHANICALLY INTERLOCKED ROTAXANE FEATURING A PEROXIDE (O–O) BOND

ABSTRACT

This work presents a theoretical study on the design of a rotaxane capable of mechanically releasing a molecular payload via bond cleavage induced by the motion of a macrocycle under non-equilibrium conditions. The study begins with an overview of the chemistry of substances with topological bonds, relevant for controlled mechanical reactivity, historical developments, and recent achievements in the field. A conceptual synthetic strategy for the rotaxane is proposed, employing organolithium reagents and templating with crown ether. Various candidate bonds, including peroxide, disulfide, and ether linkages, are analyzed for their suitability to undergo mechanical cleavage; we assessed their relative bond strengths and structural parameters and compared them to the mechanical stresses expected from the macrocycle’s motion. The analysis identifies optimal bond choices for controlled, mechanically induced bond cleavage and release of the payload, emphasizing the balance between bond strength, macrocycle dynamics, and molecular architecture. These results provide theoretical insights for the rational design of stimuli-responsive molecular systems and offer guidance for future studies on mechanically active rotaxanes and related supramolecular assemblies.

АННОТАЦИЯ

В данной работе представлен теоретический анализ проектирования ротаксана, способного механически высвобождать молекулярный груз за счёт разрыва химической связи, индуцированного движением макроцикла в условиях неравновесия. Работа начинается с обзора химии веществ с топологическими связями, актуальных для контролируемой механической реактивности, исторических этапов развития и современных достижений в области. Предложена концептуальная синтетическая стратегия ротаксана с использованием органолитиевых реагентов и темплирования краун-эфиром. Проанализированы различные кандидаты на химические связи — пероксидные, дисульфидные и эфирные — с точки зрения их пригодности к механическому разрыву; оценены их относительные энергии связей и структурные параметры, сопоставленные с механическими нагрузками, возникающими при движении макроцикла. Анализ позволил определить оптимальные химические связи для контролируемого механического разрыва и высвобождения груза, подчеркнув баланс между прочностью связей, динамикой макроцикла и молекулярной архитектурой. Полученные результаты дают теоретическое понимание для рационального проектирования стимул-чувствительных молекулярных систем и могут служить ориентиром для будущих исследований механически активных ротаксанов и связанных с ними супрамолекулярных комплексов.

Keywords: rotaxane, mechanically interlocked molecules, topological bond, molecular delivery, stimuli-responsive systems, crown ether.

Ключевые слова: ротаксан, механически связанные молекулы, топологическая связь, доставка молекул, стимул-чувствительные системы, краун-эфир.

Introduction

In chemistry, there exists a unique type of bonding known as topological (mechanical) bonding, where molecules are connected through their topology rather than conventional covalent bonds. This is analogous to interlocking links in a chain or beads on a string, where the components cannot be separated without breaking the structure. The study of such topologically bonded compounds began in the 1960s, with early examples including catenanes and rotaxanes. Catenanes, consisting of two or more interlocked rings, were first synthesized by S. Wasserman and F. Schill [1]. Rotaxanes, in which a cyclic molecule is threaded onto a linear axle and blocked by bulky groups, were first reported by R. Harrison and J. Harrison [2].

The field of mechanically interlocked molecules (MIMs) advanced significantly in the 1980s and 1990s. J.-P. Sauvage [3] pioneered the synthesis of catenanes using metal–ligand coordination, while J. F. Stoddart [4] developed the concept of rotaxanes and demonstrated their potential in molecular machines. These achievements culminated in the award of the 2016 Nobel Prize in Chemistry to Sauvage, Stoddart, and B. L. Feringa [5] for the design and synthesis of molecular machines. Feringa contributed extensively to the field by developing molecular motors and switches, including unidirectional rotary motors and complex multifunctional molecular systems, demonstrating control over motion at the molecular level.

Mechanically interlocked molecules have found applications in a wide range of fields, including molecular switches, sensors, drug delivery systems, and nanomachines, due to their unique structural and dynamic properties.

In this work, we propose a novel approach to rotaxane synthesis, focusing on the design of a ring that becomes actively mobile in response to pH changes and mechanically cleaves a bond to release a cargo molecule .

Review of Existing solutions

The development of rotaxanes as stimuli-responsive carriers has attracted significant attention due to their potential in controlled release of guest molecules. Several strategies have been reported to exploit the unique mechanical bond of rotaxanes for drug delivery and related applications.

One representative example is the work by Takata and co-workers, who designed polyrotaxanes in which cyclic components act as movable stoppers. Upon enzymatic cleavage of end-groups, the rings were released from the polymer chain, enabling the liberation of encapsulated compounds [6].

Another important strategy was developed by Harada and colleagues, who demonstrated cyclodextrin-based polyrotaxanes as drug carriers. In their systems, the release of drugs was triggered by changes in pH or enzymatic activity, leading to dethreading of the rings from the axle [7].

Stoddart and co-workers also pioneered the use of bistable rotaxanes in which the macrocycle can shuttle between two recognition sites upon chemical or redox stimulation. These systems have been applied to construct molecular switches, but they were further adapted for controlled release, where the macrocycle’s movement exposed or hid a cleavable site [8].

More recently, rotaxane-based prodrugs have been reported. Leigh and co-workers described a rotaxane where the macrocycle mechanically shielded a drug until enzymatic cleavage freed the active agent, thus ensuring release only under biological conditions [9].

Our proposed solution differs from these earlier approaches in that we suggest the targeted synthesis of a rotaxane where release of the cargo is achieved through partial self-destruction: the mutual mechanical stress of the topological bonds leads to bond rupture. This function of our “molecular machine” is regulated by changes in the acidity of the medium.

Objective:

Design and theoretical investigation of a rotaxane capable of mechanically releasing a molecular payload through bond cleavage induced by macrocycle motion.

Tasks:

1. Review the chemistry of topological (mechanical) bonds and achievements in mechanically interlocked molecules.
2. Study existing approaches for stimuli-responsive rotaxanes and controlled molecular release systems.
3. Develop a conceptual synthetic pathway using organolithium reagents and crown ether templating.
4. Assess the bond strength of various chemical linkages (peroxide, disulfide, ether) for mechanical cleavage.
5. Analyze the rotaxane geometry, macrocycle motion, and interaction with stopper groups to ensure mechanical release of the payload.

Materials and methods

Rotaxanes consist of two key components: a ring (macrocycle) and an axle on which the ring is threaded. In our work, the macrocycle was chosen to be an azo-12-crown-4 ether.

Step 1 Reaction of crown ether with methylacetyl chloride (Scheme 1).

Figure 1. Reaction of azo-12-crown-4 ether with methylacetyl chloride

Amines react with acyl chlorides to give amides, with the loss of a leaving group [10].

Tetrahydrofuran was used as the solvent, while triethylamine was added to stabilize the chloride ion generated during the reaction, since aprotic solvents do not effectively solvate anions. Triethylamine also prevents acidification of the solution [11].

Step 2 The carbonyl group was protected using 2-mercaptoethanol in the presence of catalytic amounts of p-TsOH, affording a cyclic acetal [12]. This protection is necessary because a lithium–organic reagent will later be employed, which could otherwise attack the carbonyl group. This approach ensures stability of the carbonyl moiety [13].

Figure 2. Azo-12-crown-4 ether with a protected carbonyl group

Step 3 Next, we need to synthesize the following compound:

Figure 3. Structure of (tert-butyldimethylsilyl)oxyhex-3-en-1-yllithium

The TBDMS (tert-butyldimethylsilyl) group was chosen to protect the hydroxyl group from interaction with the lithium moiety of the molecule [14]. The synthesis proceeds in three stages.

Step 3.1 Preparation of 5-hydroxypent-3-en-1-bromide via a cross-metathesis reaction between 3-hydroxyprop-2-ene and 4-bromobut-1-ene [15]:

Figure 4. Protection of the carbonyl group with 2-mercaptoethanol (formation of a cyclic acetal)

Step 3.2 Protection of the hydroxyl group with TBDMS–Cl[16]:

Figure 5. Preparation of 5-hydroxypent-3-en-1-bromide via cross-metathesis

Step 3.3 Halogen–lithium exchange reaction to afford the desired organolithium intermediate [17]:

Figure 6. Protection of the hydroxyl group with TBDMS–Cl

Step 4 The crown ether and the organolithium compound were combined in tetrahydrofuran. The lithium atom, bearing a localized positive charge, becomes incorporated into the crown ether and stabilized by dipolar interactions with the oxygen and nitrogen atoms, which carry partial negative charges (Figure 3)[18].

Figure 7. Stabilization of the lithium ion within the crown ether cavity by dipolar interactions

The R substituent corresponds to –CH₂–CH₂–CH=CH–CH₂–O–TBDMS, derived from the organolithium reagent.

Steric effects are significant: since R is bulky, it is more favorable for the lithium to be accommodated   in the ether ring from the opposite side relative to the acetal moiety.

Step 5 Addition of p-TsOH induces hydrolysis of the acetal, regenerating the carbonyl group [19]. The organolithium reagent then reacts immediately with the carbonyl, forming a relatively stable tetrahedral intermediate (Figure 4).

Figure 8. Transition state                           Figure 9. Tetrahedral intermediate

Figure 10. Final rotaxane with a protected hydroxyl group on the axle

This intermediate is stabilized because all substituents attached to the electrophilic carbon are poor leaving groups. Upon protonation by p-TsOH, the amine (the best leaving group present) departs, resulting in the formationof the rotaxane which is shown in Figure 5.

It remains to attach onto the axle of the rotaxane the substance that we intend to transport.

Step 6 In order to anchor the cargo onto the axle, the molecule to bedelivered must contain a hydroxyl group (ROH). Reaction with hydrogen peroxide affords the corresponding hydroperoxide (ROOH) [21].

Step 7 The protecting group was removed using tetrabutylammonium fluoride (TBAF) at low temperature (–78 °C) [22]. The low temperature is required to minimize thermal motion, since after deprotection the terminal OH group of the axle is relatively small, which increases the risk of dethreading of the ring.The final structure of the obtained rotaxane is shown in Figure 6.

Step 8 Finally, the hydroperoxide prepared earlier was coupled to the deprotected hydroxyl group, yielding the peroxide linkage. This provides the final functionalized rotaxane capable of carrying and releasing a molecular payload:

Figure 11. Rotaxane bearing a free hydroxyl group after TBDMS deprotection

 Figure 12. Final rotaxane with a peroxide linkage anchoring the cargo molecule

Results and discussion

Mechanism of Delivery

The synthesized rotaxane is designed to release the desired cargo upon receiving a stimulus in the form of a change in medium acidity. Two possible regimes can be considered:

Regime 1. In an acidic environment, the nitrogen atom in the crown ether becomes protonated due to its lone pair of electrons. Under these conditions, the macrocycle is expected to localize above the double bond, which is nucleophilic and thus stabilizes the positive charge. This equilibrium state prevents cargo release. The crucial factor is to maintain sufficient acidity to avoid premature protonation and cleavage of the peroxide bond.

Regime 2. In a basic environment, the nitrogen atom is deprotonated, acquiring an excess negative charge. The axle of the rotaxane contains three nucleophilic regions: the peroxide bond, the double bond, and the carbonyl group. This creates an unstable equilibrium in which the crown ether continuously moves back and forth along the axle, being repelled by each nucleophilic site.

When the macrocycle approaches the peroxide bond, its heteroatom (e.g., negatively charged nitrogen) is repelled by the first oxygen atom of the O–O bond. This interaction twists the opposite part of the macrocycle toward the peroxide bond. Repeated repulsion events stretch the peroxide bond until it eventually breaks, since it is intrinsically weak. Among stable bonds between nonmetal atoms, the O–O bond has the lowest bond dissociation energy, which supports the hypothesis of mechanical rupture [23]:

Table 1.

Dissotiation energies 

Figure 13. Rotational motion of the macrocycle near the peroxide bond under basic conditions

This mechanical bond rupture results in release of the payload.

Geometry of the Rotaxane

Movement of the ring along the axle

The diameter of a 12-crown-4 ether ranges between 1.2 and 1.5 Å [24]. Introduction of a nitrogen atom into the macrocycle is not expected to significantly alter these dimensions. In comparison, the C–H bond length is approximately 1.08–1.09 Å [25] (for both sp³- and sp²-hybridized carbons). Considering the angular orientation of bonds, the vertical projection is even shorter, which allows the macrocycle to travel along the axle without steric hindrance.

Stopper groups

Carbonyl stopper. The double bond of a carbonyl group has a bond length of about 1.20–1.23 Å [26]. The bond length between the carbonyl carbon and an adjacent methyl carbon is approximately 1.49–1.51 Å [27]. These dimensions indicate that the macrocycle’s inner diameter is insufficient to overcome this stopper, thereby effectively blocking dethreading.

Peroxide stopper. When the macrocycle approaches the peroxide bond—this occurs only under basic conditions (in acidic media the ring remains localized near the double bond)—the oxygen atoms must be accommodated inside the macrocycle. The O–O bond length is approximately 1.45–1.48 Å [28], which is comparable to the larger diameter of the crown ether cavity. As a result, part of the macrocycle directly overlaps with this bond. This specific geometric relationship enables mechanical stress to be applied directly onto the peroxide linkage, facilitating its cleavage.

Conclusion

In this work, we briefly reviewed the chemistry of organic compounds with topological (mechanical) bonds and highlighted the most significant achievements in this field since its inception.

We proposed the synthesis of a rotaxane capable of releasing a target molecule in response to changes in medium acidity. Existing approaches to controlled release in rotaxane systems were discussed, and a multi-step synthetic pathway was presented for the preparation of the designed structure.

The mechanism of action was analyzed, demonstrating how the rotaxane can release its cargo by mechanically cleaving a peroxide bond. Geometric considerations were provided to show that steric factors do not hinder this process.

Two important limitations of this method should be noted:

1. The substance to be delivered must contain a hydroxyl group.

2. The peroxide bond is highly sensitive to changes in acidity and to nucleophiles, which may cause premature cleavage.

Nevertheless, the proposed molecule and the synthetic methods outlined for constructing this type of rotaxane may find potential applications in medicine, biomedicine, organic synthesis, nanotechnology, and as sensors for changes in medium acidity.

References:

1. Wasserman E., Schill G. The First Isolation of a Pure Catenane // J. Am. Chem. Soc. — 1964. — 86. — P. 2818–2819.
2. Harrison R., Harrison J. The Synthesis of a [2]Rotaxane // J. Am. Chem. Soc. — 1965. — 87. — P. 2044–2045.
3. Sauvage J.-P. et al. Template Routes to Interlocked Molecular Structures // J. Am. Chem. Soc. — 1994. — 116. — P. 10083–10084.
4. Stoddart J. F. et al. Transition Metal-Containing Rotaxanes and Catenanes in Motion // Chem. Soc. Rev. — 2017. — 46. — P. 2590–2601.
5. Feringa B. L. The Art of Building Small. NobelPrize.org, 2016.
6. Takata T. Polyrotaxane and Slide-Ring Materials // Polym. J. — 2006. — 38(1). — P. 1–16.
7. Harada A. et al. The Molecular Necklace: A Rotaxane Containing Many Threaded α-Cyclodextrins // Nature. — 1992. — 356. — P. 325–327.
8. Bissell R. A. et al. A Chemically and Electrochemically Switchable Molecular Shuttle // Nature. — 1994. — 369. — P. 133–137.
9. Cheng C. et al. An Artificial Molecular Pump // Nat. Nanotechnol. — 2015. — 10. — P. 547–553.
10. Clayden J. et al. Organic Chemistry. Oxford: Oxford University Press, 2012. — P. 107–125.
11. Gopalakrishnan J., Asha Devi S. Determination of Dimethylamine and Triethylamine in Hydrochloride Salts // Indian J. Pharm. Sci. — 2016. — 78(3). — P. 409–414.
12. Sartori G. et al. Protection (and Deprotection) of Functional Groups // Chem. Rev. — 2004. — 104(3). — P. 899–917.
13. Sartori G. et al. Protection (and Deprotection) of Functional Groups // Chem. Rev. — 2004. — 104(3). — P. 899–917.
14. Suresh C. H. Silylation of Alcohols using TBDMSCl, TBDPSCl and TIPSCl // J. Chem. Res. — 2013. — 37. — P. 456–462.
15. Connon S. J., Blechert S. Recent Developments in Olefin Cross-Metathesis // Angew. Chem. Int. Ed. — 2003. — 42(15). — P. 1900–1923.
16. Suresh C. H. Silylation of Alcohols using TBDMSCl, TBDPSCl and TIPSCl // J. Chem. Res. — 2013. — 37. — P. 456–462.
17. Clayden J. Regioselective Synthesis of Organolithiums // Organolithiums: Selectivity for Synthesis. — Oxford: Pergamon Press, 2002. — P. 111–147.
18. Lipshutz B. H., James B. New 1H and 13C NMR Spectral Data on "Higher Order" Cyanocuprates // J. Org. Chem. — 1996. — 61(7). — P. 2554–2556.
19. Suresh C. H. Thiourea: A Novel Cleaving Agent for 1,3-Dioxolanes // J. Org. Chem. — 1998. — 63(23). — P. 8485–8486.
20. Clayden J. Organolithiums: Selectivity for Synthesis. — Oxford: Pergamon Press, 2002. — P. 111–147.
21. Reinsdorf O. et al. Comprehensive Studies on Small Aliphatic Alcohols in H2O2 Synthesis // Catalysts. — 2023. — 13. — P. 753.
22. Bothwell J. M. et al. A Mild and Chemoselective Method for Deprotection of TBDMS Ethers // Tetrahedron Lett. — 2010. — 51(7). — P. 1056–1058.
23. Luo Y.-R. Bond Dissociation Energies. — CRC Press, 2003.
24. Liu Y., Li Y. A new configuration of 12-crown-4 // J. Phys. Chem. — 1991. — 95(6). — P. 2284–2286.
25. Ishigaki Y. et al. Bond lengths in organic compounds // CRC Handbook of Chemistry and Physics. — 2007. — 88. — P. 11.
26. Hocking R. K., Hambley T. W. Database analysis of transition metal carbonyl bond lengths // Organometallics. — 2007. — 26(11). — P. 2820–2829.
27. National Institute of Standards and Technology. Experimental data for CH₃COCH₃ (Acetone). — [Electronic resource]. — Accessed 2025-09-01.
28. Bach R. D. et al. A reassessment of the bond dissociation energies of peroxides // J. Am. Chem. Soc. — 1996. — 118(1). — P. 16–22.