Bert H. Bakker

Operation mechanism of a molecular machine revealed using time-resolved vibrational spectroscopy

Not So Random Walk In rotaxanes, a molecular ring can shuttle back and forth between docking sites along an axle. Panman et al. (p. 1255) traced the intricacies of this shuttling motion using vibrational spectroscopy. The kinetics were dominated by the slow scission of hydrogen bonds tying the ring to its starting site. Varying the length of the axle allowed the extraction of relative rates for forward and backward motion once the ring was free: Somewhat surprisingly, forward motion toward the destination site was slightly hindered relative to regression toward the starting place. Measuring the travel of a molecular ring along an axle explains its shuttling motion. Rotaxanes comprise macrocycles that can shuttle between docking stations along an axle. We explored the nanosecond shuttling mechanism by reversing the relative binding affinities of two stations through ultraviolet-induced transient reduction. We monitored the ensuing changes in the CO-stretching bands of the two stations and the shuttling macrocycle by means of an infrared probing pulse. Because hydrogen-bond scission and formation at the initial and final stations led to well-resolved changes in the respective CO-stretch frequencies, the departure and arrival of the macrocycle could be observed separately. We found that the shuttling involves two steps: thermally driven escape from the initial station, followed by rapid motion along the track ending either at the initial or final station. By varying the track’s length, we found that the rapid motion approximates a biased one-dimensional random walk. However, surprisingly, the direction of the overall motion is opposite that of the bias.

Two-dimensional vibrational spectroscopy of rotaxane-based molecular machines

It has recently become possible to synthesize mechanical devices the size of a single molecule. Although it is tempting to regard such molecular machines as nanoscale versions of their macroscopic analogs, many notions from macroscopic mechanics no longer apply at a molecular level. For instance, the concept of viscous friction is meaningless for a molecular machine because the size of the solvent molecules that cause the friction is comparable to that of the machine itself. Furthermore, in many cases, the interactions between a molecular machine and its surroundings are comparable to the force driving the machine. As a result, a certain amount of intrinsic randomness exists in the motion of molecular machines, and the details of their mechanics are largely unknown. For a detailed understanding of the mechanical behavior of molecular machines, experiments that probe their motion on an ultrafast time scale, such as two-dimensional (2D) vibrational spectroscopy, are essential. This method uses coupling between vibrational modes in a molecule to investigate the molecular conformation. The coupling shows up as off-diagonal peaks in a 2D graph of the vibrational response of the molecule, analogous to the spin coupling observed in multidimensional NMR spectroscopy. Both spin coupling and vibrational coupling are sensitive probes of the molecular conformation, but 2D vibrational spectroscopy shows orders of magnitude better time resolution than NMR. In this Account, we use 2D vibrational spectroscopy to study molecular machines based on rotaxanes. These devices consist of a linear thread and a macrocycle that is noncovalently locked onto the thread. In the rotaxanes we study, the macrocycle and the thread both contain CO and NH groups. By determining the coupling between the stretching modes of these goups from the cross peaks in the 2D spectrum, we directly and quantitatively probe the relative position and orientation of the macrocycle and the thread for both a small model rotaxane and a rotaxane-based molecular shuttle. Our results demonstrate the feasibility of using time-resolved 2D-IR experiments to measure externally triggered structural changes of molecular devices with subpicosecond time resolution. We can observe each of the elementary events that underlie the mechanical motion separately. With this ability to investigate the nature of the mechanical motions at the molecular level and with unprecedented time resolution, we expect that 2D-IR spectroscopy on molecular machines will lead to new insights into their function.

Sulfonation of alkenes with sulfur trioxide. Stereospecific β-sultone formation

Abstract Sulfonation of 1-octene, ( E )-1-deuterio-1-octene, and ( Z )- and ( E )-4-octene with one mol-equiv of sulfur trioxide yields the β-sultones 2a - d respectively. The reaction proceeds stereospecifically via a concerted cis -cycloaddition.

Sulfonation of alkenes with an excess of sulfur trioxide; stereospecific formation of carbyl sulfates

Abstract Sulfonation of the α- and internal alkenes 1a - d with an excess of sulfur trioxide initially yield stereospecifically the β-sultones 2a - d and subsequently the carbyl sulfates 3a - d via stereospecific SO3 insertion.

Sulfonation of alkenes with sulfur trioxide; reversible stereospecific β-sultone formation

Abstract The small differences in the rate coefficients of β-sultone formation between the internal and the terminal double bond in the octenes 2a-c and (Z)-1,10-nonadecadiene are evidence for a concerted cycloaddition of sulfur trioxide. The formation of β-sultone 1d is accompanied by 15% of 2-octene-1-sulfonic acid, formed in a primary side-reaction. The sulfonation of the octenes 2a-d to their β-sultones 1a-d is reversible. Desulfonation of the β-sultones 1a-d by water to the olefins 2a-d proceeds in a stereospecific syn fashion.

Sulfonation of Alkenes by Chlorosulfuric Acid, Acetyl Sulfate, and Trifluoroacetyl Sulfate

An exploratory study has been made on the reaction of a number of non-branched alkenes in [D]chloroform as an aprotic solvent, using chlorosulfuric acid as reagent both in the presence and the absence of [D8]1,4-dioxane as complexing agent. Reaction of cyclopentene (1a) with 1.1 mol-equiv. of chlorosulfuric acid in [D]chloroform in the presence of 2.2 mol-equiv. of [D8]1,4-dioxane at 0 °C yielded quantitatively 1,2-cyclopentanesultone (2a). Under similar reaction conditions, the linear alkenes 1b–g afforded the corresponding β-sultones 2b–g. The ClSO3H–dioxane complex acted as a sulfonating reagent with the alkenes to yield the corresponding β-sultones in a syn cycloaddition of SO3 to the Carbon-Carbon double bond. In the absence of [D8]1,4-dioxane the reaction of the linear alkenes 1a–1k in [D]chloroform with chlorosulfuric acid at –40 °C led to the formation of the sec-alkyl chlorosulfates 5a–i, which were formed after initial protonation of the alkene by the strongly acidic ClSO3H. Cyclopentyl chlorosulfate (5a) in [D]chloroform at 0 °C was quantitatively converted into 1,2-cyclopentanesultone (2a). The sec-alkyl chlorosulfates 5b–i at 0 °C gave rise to a mixture of the internal trans- and cis-β-sultones 2b–m. Reaction of 1-octene (1g) with both acetyl sulfate (6a) and trifluoroacetyl sulfate (6b) as reagent in [D]chloroform at –20 °C directly afforded the products 1,2-octanesultone (2g), and the (E) and (Z) isomer of 2-octene-1-sulfonic acid (4g).

Synthesis and Spectroscopic Characterization of 1,8-Naphthalimide Derived “Super” Photoacids

The ground- and excited-state acid-base properties of three novel naphthalimide-based “super” photoacids were studied using steady-state and time-resolved spectroscopy. The compounds exhibit pKa = 8.8-8.0 and pKa* = -1.2 to -1.9. The decrease in both ground- and excited-state pKa is achieved by attachment of an electron withdrawing group (sulfonate) on the aromatic system. All compounds are deprotonated upon excitation in alcohols and DMSO. Good correlation is established between the pKa* and the ratio of the neutral and anion emission intensities in a certain solvent. The excited-state intermolecular proton transfer to solvent (H2O and DMSO) is explained by a two-step model. In the first step, short-range proton transfer takes place, resulting in the formation of a contact ion pair. Free ion pairs are formed in the diffusion controlled second step.

REACTIONS OF ALKENES AND ω-PHENYLALKENES WITH SULFUR TRIOXIDE; SULFONATION AND FRIEDEL-CRAFTS TYPE OF CYCLIZATION

Abstract Reaction of alkenes with SO3 leads to the formation of β-sultones, carbyl sulfates, alkenesulfonic acids and γ-sultones, depending on the alkene structure and on the reaction conditions. The high selectivity for the cyclisation to 1,2,3,4-tetrahydronaphthalene sulfonic acid derivatives on reaction of well chosen ω-phenylalkenes with SO3 infers the occurrence of a relatively fast equilibrium between ω-phenyl-m,n- and the ω-phenyl-n,m-alkanesultone intermediate.

Complexes of a naphthalimide photoacid with organic bases, and their excited-state dynamics in polar aprotic organic solvents.

Complex formation and intermolecular excited-state proton transfer (ESPT) between a dihydroxy-1,8-naphthalimide photoacid and organic bases are investigated in polar aprotic solvents. First, quantum chemical calculations are used to explore the acid-base and spectroscopic properties and to identify energetically favorable complexes. The two hydroxyl groups of the photoacid enable stepwise formation of 1 : 1 and 1 : 2 complexes. Weak bases exhibit only hydrogen-bonding interactions whereas strong bases are able to deprotonate one of the hydroxyl groups resulting in strong negative cooperativity (K1≫ 4K2) in the formation of the 1 : 2 complex. Time-resolved fluorescence studies of the complexes provide strong indications of a three-step dissociation process. The species involved in the model are: a hydrogen-bonded complex, a hydrogen-bonded ion pair, a solvent separated ion pair, and a free ion pair.

An optically transparent thin-layer electrochemical cell for the study of vibrational circular dichroism of chiral redox-active molecules

An optically transparent thin-layer electrochemical (OTTLE) cell with a locally extended optical path has been developed in order to perform vibrational circular dichroism (VCD) spectroscopy on chiral molecules prepared in specific oxidation states by means of electrochemical reduction or oxidation. The new design of the electrochemical cell successfully addresses the technical challenges involved in achieving sufficient infrared absorption. The VCD-OTTLE cell proves to be a valuable tool for the investigation of chiral redox-active molecules.