Influence of 2'-Modifications (O-Methylation, Fluorination, and Stereochemical Inversion) on the Base Pairing Energies of Protonated Cytidine Nucleoside Analogue Base Pairs: Implications for the Stabilities of i-Motif Structures

Naturally occurring and chemically engineered modifications are among the most powerful strategies explored for fine-tuning the conformational characteristics and intrinsic stability of nucleic acids topologies. Modifications at the 2'-position of the ribose or 2'-deoxyribose moieties differentiate nucleic acid structures and have a significant impact on their electronic properties and base-pairing interactions. 2'-O-Methylation, a common post-transcriptional modification of tRNA, is directly involved in modulating specific anticodon-codon base-pairing interactions. 2'-Fluorinated and arabino nucleosides possess novel and beneficial medicinal properties and find use as therapeutics for treating viral diseases and cancer. However, the potential to deploy 2'-modified cytidine chemistries for tuning i-motif stability is largely unknown. To address this knowledge gap, the effects of 2'-modifications including O-methylation, fluorination, and stereochemical inversion on the base-pairing interactions of protonated cytidine nucleoside analogue base pairs, the core stabilizing interactions of i-motif structures, are examined using complementary threshold collision-induced dissociation techniques and computational methods. The 2'-modified cytidine nucleoside analogues investigated here include 2'-O-methylcytidine, 2'-fluoro-2'-deoxycytidine, arabinofuranosylcytosine, 2'-fluoro-arabinofuranosylcytosine, and 2',2'-difluoro-2'-deoxycytidine. All five 2'-modifications examined here are found to enhance the base-pairing interactions relative to the canonical DNA and RNA cytidine nucleosides with the greatest enhancements arising from 2'-O-methylation and 2',2'-difluorination, suggesting that these modifications should well be tolerated in the narrow grooves of i-motif conformations.

Influence of 5-Halogenation on the Base-Pairing Energies of Protonated Cytidine Nucleoside Analogue Base Pairs: Implications for the Stabilities of Synthetic i-Motif Structures for DNA Nanotechnology Applications

DNA nanotechnology has been employed to develop devices based on i-motif structures. The protonated cytosine-cytosine base pairs that stabilize i-motif conformations are favored under slightly acidic conditions. This unique property has enabled development of the first DNA molecular motor driven by pH changes. The ability to alter the stability and pH transition range of such DNA molecular motors is desirable. Understanding how i-motif structures are influenced by modifications, and which modifications enhance stability and/or affect the pH characteristics, are therefore of great interest. Here, the influence of 5-halogenation of the cytosine nucleobases on the base pairing of protonated cytidine nucleoside analogue base pairs is examined using complementary threshold collision-induced dissociation techniques and computational methods. The nucleoside analogues examined here include the 5-halogenated forms of the canonical DNA and RNA cytidine nucleosides. Comparisons among these systems and to the analogous canonical base pairs previously examined enable the influence of 5-halogenation and the 2'-hydroxy substituent on the base pairing to be elucidated. 5-Halogenation of the cytosine nucleobases is found to enhance the strength of base pairing of DNA base pairs and generally weakens the base pairing for RNA base pairs. Trends in the strength of base pairing indicate that both inductive and polarizability effects influence the strength of base pairing. Overall, the present results suggest that 5-halogenation, and in particular, 5-fluorination and 5-iodination, provide effective means of stabilizing DNA i-motif conformations for applications in nanotechnology, whereas only 5-iodination is effective for stabilizing RNA i-motif conformations but the enhancement in stability is less significant.

1-Alkyl-3-methylimidazolium cation binding preferences in hexafluorophosphate ionic liquid clusters determined using competitive TCID measurements and theoretical calculations

Ionic liquids (ILs) exhibit unique properties that have led to their development and widespread use for a variety of applications. Development efforts have generally focused on achieving desired macroscopic properties via tuning of the IL through variation of the cations and anions. Both the macroscopic and microscopic properties of an IL influence its tunability and thus feasibility of use for selected applications. Works geared toward a microscopic understanding of the nature and strength of the intrinsic cation-anion interactions of ILs have been limited to date. Specifically, the intrinsic strength of the cation-anion interactions in ILs is largely unknown. In previous work, we employed threshold collision-induced dissociation (TCID) approaches supported and enhanced by electronic structure calculations to determine the bond dissociation energies (BDEs) and characterize the nature of the cation-anion interactions in a series of four 2 : 1 clusters of 1-alkyl-3-methylimidazolium cations with the hexafluorophosphate anion, [2C_nmim:PF₆]⁺. To examine the effects of the 1-alkyl chain on the structure and energetics of binding, the cation was varied over the series: 1-ethyl-3-methylimidazolium, [C₂mim]⁺, 1-butyl-3-methylimidazolium, [C₄mim]⁺, 1-hexyl-3-methylimidazolium, [C₆mim]⁺, and 1-octyl-3-methylimidazolium, [C₈mim]⁺. The variation in the strength of binding among these [2C_nmim:PF₆]⁺ clusters was found to be similar in magnitude to the average experimental uncertainty in the measurements. To definitively establish an absolute order of binding among these [2C_nmim:PF₆]⁺ clusters, we extend this work again using TCID and electronic structure theory approaches to include competitive binding studies of three mixed 2 : 1 clusters of 1-alkyl-3-methylimidazolium cations and the hexafluorophosphate anion, [C_n-2mim:PF₆:C_nmim]⁺ for n = 4, 6, and 8. The absolute BDEs of these mixed [C_n-2mim:PF₆:C_nmim]⁺ clusters as well as the absolute difference in the strength of the intrinsic binding interactions as a function of the cation are determined with significantly improved precision. By combining the thermochemical results of the previous independent and present competitive measurements, the BDEs of the [2C_nmim:PF₆]⁺ clusters are both more accurately and more precisely determined. Comparisons are made to results for the analogous [2C_nmim:BF₄]⁺ and [C_n-2mim:BF₄:C_nmim]⁺ clusters previously examined to elucidate the effects of the [PF₆]^- and [BF₄]^- anions on the binding.

Influence of 5-Methylation and the 2'- and 3'-Hydroxy Substituents on the Base Pairing Energies of Protonated Cytidine Nucleoside Analogue Base Pairs: Implications for the Stabilities of i-Motif Structures

Repetitive nucleic acid sequences, which occur in abundance throughout the mammalian genome, are of enormous research interest due to their potential to adopt fascinating and unusual molecular structures such as the i-motif. In remarkable contrast to the DNA double helix, i-motif conformations are stabilized by protonated cytosine base pairs, (Cyt)H⁺(Cyt), that are centrally located in the core of the i-motif and intercalated vertically in an antiparallel fashion. An in-depth understanding of how modifications influence the stability of i-motif conformations is a prerequisite to understanding their biological functions and the development of effective means of tuning their stability for specific medical and technological applications. Here, the influence of the 2'- and 3'-hydroxy substituents of the sugar moieties and 5-methylation of the cytosine nucleobases on the base-pairing interactions of protonated cytidine nucleoside analogue base pairs, (xCyd)H⁺(xCyd), are examined by complementary threshold collision-induced dissociation techniques and computational methods. The xCyd nucleosides examined include the canonical DNA and RNA cytidine nucleosides, 2'-deoxycytidine (dCyd) and cytidine (Cyd), as well as several modified cytidine nucleoside analogues, 2',3'-dideoxycytidine (ddCyd), 5-methyl-2'-deoxycytidine (m⁵dCyd), and 5-methylcytidine (m⁵Cyd). Comparisons among these model base pairs indicate that the 2'- and 3'-hydroxy substituents of the sugar moieties have very little influence on the strength of the base-pairing interactions, whereas 5-methylation of the cytosine nucleobases is found to enhance the strength of the base-pairing interactions. The increase in stability resulting from 5-methylation is only modest but is more than twice as large for the DNA than RNA protonated cytidine base pair. Overall, present results suggest that canonical DNA i-motif conformations should be more stable than analogous RNA i-motif conformations and that 5-methylation of cytosine residues, a significant epigenetic marker, provides greater stabilization to DNA than RNA i-motif conformations.

Nature and strength of intrinsic cation-anion interactions of 1-alkyl-3-methylimidazolium hexafluorophosphate clusters

Imidazolium-based cations and the hexafluorophosphate anion are among the most commonly used ionic liquids (ILs). Yet, the nature and strength of the intrinsic cation-anion interactions, and how they influence the macroscopic properties of these ILs are still not well understood. Threshold collision-induced dissociation is utilized to determine the bond dissociation energies (BDEs) of the 2 : 1 clusters of 1-alkyl-3-methylimidazolium cations and the hexafluorophosphate anion, [2Cnmim:PF6]+. The cation, [Cnmim]+, is varied across the series, 1-ethyl-3-methylimidazolium [C2mim]+, 1-butyl-3-methylimidazolium [C4mim]+, 1-hexyl-3-methylimidazolium [C6mim]+, 1-octyl-3-methylimidazolium [C8mim]+, to examine the structural and energetic effects of the size of the 1-alkyl substituent of the cation on the binding to [PF6]-. Complementary electronic structure methods are employed for the [Cnmim]+ cations, (Cnmim:PF6) ion pairs, and [2Cnmim:PF6]+ clusters to elucidate details of the cation-anion interactions and their impact on structure and energetics. Multiple levels of theory are benchmarked with the measured BDEs including B3LYP, B3LYP-GD3BJ, and M06-2X each with the 6-311+G(d,p) basis set for geometry optimizations and frequency analyses and the 6-311+G(2d,2p) basis set for energetic determinations. The modest structural variation among the [Cnmim]+ cations produces only minor structural changes and variation in the measured BDEs of the [2Cnmim:PF6]+ clusters. Present results are compared to those previously reported for the analogous 1-alkyl-3-methylimidazolium tetrafluoroborate IL clusters to compare the effects of these anions on the nature and strength of the intrinsic binding interactions.

Absolute Trends and Accurate and Precise Gas-Phase Binding Energies of 1-Alkyl-3-Methylimidazolium Tetrafluoroborate Ionic Liquid Clusters from Combined Independent and Competitive TCID Measurements

Ionic liquid (IL) development efforts have focused on achieving desired properties via tuning of the IL through variation of the cations and anions. However, works geared toward a microscopic understanding of the nature and strength of the intrinsic cation-anion interactions of ILs have been rather limited such that the intrinsic strength of the cation-anion interactions in ILs is largely unknown. In previous work, we employed threshold collision-induced dissociation approaches supported and enhanced by electronic structure calculations to characterize the nature of the cation-anion interactions in and determine the bond dissociation energies (BDEs) of a series of four 2:1 clusters of 1-alkyl-3-methylimidazolium cations and tetrafluoroborate anions, [2C_nmim:BF₄]⁺. The cation was varied over the series: 1-ethyl-3-methylimidazolium, [C₂mim]⁺, 1-butyl-3-methylimidazolium, [C₄mim]⁺, 1-hexyl-3-methylimidazolium, [C₆mim]⁺, and 1-octyl-3-methylimidazolium, [C₈mim]⁺, to determine the structural and energetic effects of the size of the 1-alkyl substituent on the binding. The variation in the strength of binding determined for these [2C_nmim:BF₄]⁺ clusters was found to be similar in magnitude to the average experimental uncertainty in these determinations. To definitively establish an absolute order of binding among these [2C_nmim:BF₄]⁺ clusters, we extend this work here to include competitive binding studies of three mixed 2:1 clusters of 1-alkyl-3-methylimidazolium cations and tetrafluoroborate anions, [C_n-2mim:BF₄:C_nmim]⁺ for n = 4, 6, and 8. Importantly, the results of the present work simultaneously provide the absolute BDEs of these mixed [C_n-2mim:BF₄:C_nmim]⁺ clusters and the absolute relative order of the intrinsic binding interactions as a function of the cation with significantly improved precision. Further, by combining the thermochemical results of the previous and present studies, the BDEs of the [2C_nmim:BF₄]⁺ clusters are more accurately and precisely determined.

Gas-Phase Binding Energies and Dissociation Dynamics of 1-Alkyl-3-Methylimidazolium Tetrafluoroborate Ionic Liquid Clusters

Ionic liquids (ILs) have become increasingly popular due to their useful and unique properties, yet there are still many unanswered questions regarding their fundamental interactions. In particular, details regarding the nature and strength of the intrinsic cation-anion interactions and how they influence the macroscopic properties of ILs are still largely unknown. Elucidating the molecular-level details of these interactions is essential to the development of better models for describing ILs and enabling the purposeful design of ILs with properties tailored for specific applications. Current uses of ILs are widespread and diverse and include applications for energy storage, electrochemistry, designer/green solvents, separations, and space propulsion. To advance the understanding of the energetics, conformations, and dynamics of gas-phase IL clustering relevant to space propulsion, threshold collision-induced dissociation approaches are used to measure the bond dissociation energies (BDEs) of the 2:1 clusters of 1-alkyl-3-methylimidazolium cations and tetrafluoroborate, [2C_nmim:BF₄]⁺. The cation, [C_nmim]⁺, is varied across the series, 1-ethyl-3-methylimidazolium [C₂mim]⁺, 1-butyl-3-methylimidazolium [C₄mim]⁺, 1-hexyl-3-methylimidazolium [C₆mim]⁺, and 1-octyl-3-methylimidazolium [C₈mim]⁺, to examine the structural and energetic effects of the size of the 1-alkyl substituent on binding. Complementary electronic structure calculations are performed to determine the structures and energetics of the [C_nmim]⁺ and [BF₄]^- ions and their binding preferences in the (C_nmim:BF₄) ion pairs and [2C_nmim:BF₄]⁺ clusters. Several levels of theory, B3LYP, B3LYP-GD3BJ, and M06-2X, using the 6-311+G(d,p) basis set for geometry optimizations and frequency analyses and the 6-311+G(2d,2p) basis set for energetics, are benchmarked to examine their abilities to properly describe the nature of the binding interactions and to reproduce the measured BDEs. The modest structural variation among these [C_nmim]⁺ cations produces only minor structural changes and variation in the measured BDEs of the [2C_nmim:BF₄]⁺ clusters. Present findings indicate that the dominant cation-anion interactions involve the 3-methylimidazolium moieties and that these clusters are sufficiently small that differences in packing effects associated with the variable length of the 1-alkyl substituents are not yet significant.

Cation-π Interactions in Graphene-Containing Systems for Water Treatment and Beyond

Cation-π interactions are common in nature, especially in organisms. Their profound influences in chemistry, physics, and biology have been continuously investigated since they were discovered in 1981. However, the importance of cation-π interactions in materials science, regarding carbonaceous nanomaterials, has just been realized. The interplay between cations and delocalized polarizable π electrons of graphene would bring about significant changes to the intrinsic characteristics of graphene and greatly affect the device performance based on graphene and its derivatives. Here, the cation-π interactions in graphene containing systems for water treatment applications (e.g., separation membranes, adsorbents) are highlighted. The cross-linking effects caused by cation-π interactions contribute to membrane stability and selectivity and enhanced adsorption. Their roles in dominating the performance of graphene-based structures for other specific applications are also discussed. Relevant theoretical modeling and calculations are summarized to offer an in-depth understanding of the underlying mechanisms which can help in designing more functional materials and structures. Perspectives on the potential directions that deserve effort are also presented.

Influence of Transition Metal Cationization versus Sodium Cationization and Protonation on the Gas-Phase Tautomeric Conformations and Stability of Uracil: Application to [Ura+Cu]+ and [Ura+Ag]<sup/>

The gas-phase conformations of transition metal cation-uracil complexes, [Ura+Cu]⁺ and [Ura+Ag]⁺, were examined via infrared multiple photon dissociation (IRMPD) action spectroscopy and theoretical calculations. IRMPD action spectra were measured over the IR fingerprint and hydrogen-stretching regions. Structures and linear IR spectra of the stable tautomeric conformations of these complexes were initially determined at the B3LYP/6-31G(d) level. The four most stable structures computed were also examined at the B3LYP/def2-TZVPPD level to improve the accuracy of the predicted IR spectra. Two very favorable modes of binding are found for [Ura+Cu]⁺ and [Ura+Ag]⁺ that involve O2N3 bidentate binding to the 2-keto-4-hydroxy minor tautomer and O4 monodentate binding to the canonical 2,4-diketo tautomer of Ura. Comparisons between the measured IRMPD and calculated IR spectra enable elucidation of the conformers present in the experiments. These comparisons indicate that both favorable binding modes are represented in the experimental tautomeric conformations of [Ura+Cu]⁺ and [Ura+Ag]⁺. B3LYP suggests that Cu⁺ exhibits a slight preference for O4 binding, whereas Ag⁺ exhibits a slight preference for O2N3 binding. In contrast, MP2 suggests that both Cu⁺ and Ag⁺ exhibit a more significant preference for O2N3 binding. The relative band intensities suggest that O4 binding conformers comprise a larger portion of the population for [Ura+Ag]⁺ than [Ura+Cu]⁺. The dissociation behavior and relative stabilities of the [Ura+M]⁺ complexes, M⁺ = Cu⁺, Ag⁺, H⁺, and Na⁺) are examined via energy-resolved collision-induced dissociation experiments. The IRMPD spectra, dissociation behaviors, and binding preferences of Cu⁺ and Ag⁺ are compared with previous and present results for those of H⁺ and Na⁺. Graphical Abstract ᅟ.

Cationic Noncovalent Interactions: Energetics and Periodic Trends

In this review, noncovalent interactions of ions with neutral molecules are discussed. After defining the scope of the article, which excludes anionic and most protonated systems, methods associated with measuring thermodynamic information for such systems are briefly recounted. An extensive set of tables detailing available thermodynamic information for the noncovalent interactions of metal cations with a host of ligands is provided. Ligands include small molecules (H2, NH3, CO, CS, H2O, CH3CN, and others), organic ligands (O- and N-donors, crown ethers and related molecules, MALDI matrix molecules), π-ligands (alkenes, alkynes, benzene, and substituted benzenes), miscellaneous inorganic ligands, and biological systems (amino acids, peptides, sugars, nucleobases, nucleosides, and nucleotides). Hydration of metalated biological systems is also included along with selected proton-based systems: 18-crown-6 polyether with protonated peptides and base-pairing energies of nucleobases. In all cases, the literature thermochemistry is evaluated and, in many cases, reanchored or adjusted to 0 K bond dissociation energies. Trends in these values are discussed and related to a variety of simple molecular concepts.

Silver cation affinities of monomeric building blocks of polyethers and polyphenols determined by guided ion beam tandem mass spectrometry

Energy-resolved collision-induced dissociation (CID) of seven silver cation-ligand complexes, Ag(+)(L), with Xe is studied using guided ion beam tandem mass spectrometry techniques. The ligands, L, investigated are monomeric building blocks of polyethers and polyphenols including phenol, 2-hydroxyphenol, 3-hydroxyphenol, 4-hydroxyphenol, 2-hydroxymethyl phenol, 3-hydroxymethyl phenol, and 4-hydroxymethyl phenol. In all cases, Ag(+) is observed as the primary CID product, corresponding to endothermic loss of the intact neutral ligand. The kinetic-energy-dependent cross sections for CID of these Ag(+)(L) complexes are analyzed using an empirical threshold law to extract absolute 0 and 298 K Ag(+)-L bond dissociation energies (BDEs). Density functional theory calculations at the B3LYP/6-31G* level of theory are used to determine the structures of the neutral ligands and their complexes to Ag(+) using either the Stuttgart RSC 1997 valence basis set and effective core potential (SRSC ECP) or DZVP-DFT to describe Ag(+). Theoretical BDEs are determined at the B3LYP/6-311+G(2d,2p) level of theory again using the SRSC ECP or DZVP-DFT for Ag(+). For all systems, the most stable binding conformations found involve cation-π interactions when the SRSC ECP is used to describe Ag(+). When DZVP-DFT is employed, the most stable binding geometries remain cation-π complexes except for the complex to 2HP, where the ground-state conformer involves bidentate binding of Ag(+) to the hydroxyl oxygen atoms of both substituents. The agreement between the measured and calculated BDEs is excellent with a MAD of 2.9 ± 1.7 kJ/mol when the SRSC ECP is used to describe Ag(+) and less satisfactory for DZVP-DFT, which underestimates the strength of binding in these systems by ~14% or 26.0 ± 6.7 kJ/mol.

Accurate prediction of cation-π interaction energy using substituent effects

Substituent effects on cation-π interactions have been quantified using a variety of Φ-X···M(+) complexes where Φ, X, and M(+) are the π-system, substituent, and cation, respectively. The cation-π interaction energy, E(M(+)), showed a strong linear correlation with the molecular electrostatic potential (MESP) based measure of the substituent effect, ΔV(min) (the difference between the MESP minimum (V(min)) on the π-region of a substituted system and the corresponding unsubstituted system). This linear relationship is E(M(+)) = C(M(+))(ΔV(min)) + E(M(+))' where C(M(+)) is the reaction constant and E(M(+))' is the cation-π interaction energy of the unsubstituted complex. This relationship is similar to the Hammett equation and its first term yields the substituent contribution of the cation-π interaction energy. Further, a linear correlation between C(M(+))() and E(M(+))()' has been established, which facilitates the prediction of C(M(+)) for unknown cations. Thus, a prediction of E(M(+)) for any Φ-X···M(+) complex is achieved by knowing the values of E(M(+))' and ΔV(min). The generality of the equation is tested for a variety of cations (Li(+), Na(+), K(+), Mg(+), BeCl(+), MgCl(+), CaCl(+), TiCl(3)(+), CrCl(2)(+), NiCl(+), Cu(+), ZnCl(+), NH(4)(+), CH(3)NH(3)(+), N(CH(3))(4)(+), C(NH(2))(3)(+)), substituents (N(CH(3))(2), NH(2), OCH(3), CH(3), OH, H, SCH(3), SH, CCH, F, Cl, COOH, CHO, CF(3), CN, NO(2)), and a large number of π-systems. The tested systems also include multiple substituted π-systems, viz. ethylene, acetylene, hexa-1,3,5-triene, benzene, naphthalene, indole, pyrrole, phenylalanine, tryptophan, tyrosine, azulene, pyrene, [6]-cyclacene, and corannulene and found that E(M)(+) follows the additivity of substituent effects. Further, the substituent effects on cationic sandwich complexes of the type C(6)H(6)···M(+)···C(6)H(5)X have been assessed and found that E(M(+)) can be predicted with 97.7% accuracy using the values of E(M(+))' and ΔV(min). All the Φ-X···M(+) systems showed good agreement between the calculated and predicted E(M(+))() values, suggesting that the ΔV(min) approach to substituent effect is accurate and useful for predicting the interactive behavior of substituted π-systems with cations.

Infrared spectrum of the Ag(+)-(pyridine)2 ionic complex: probing interactions in artificial metal-mediated base pairing

The isolated pyridine-Ag(+)-pyridine unit (Py-Ag(+)-Py) is employed as a model system to characterize the recently observed Ag(+)-mediated base pairing in DNA oligonucleotides at the molecular level. The structure and infrared (IR) spectrum of the Ag(+)-Py(2) cationic complex are investigated in the gas phase by IR multiple-photon dissociation (IRMPD) spectroscopy and quantum chemical calculations to determine the preferred metal-ion binding site and other salient properties of the potential-energy surface. The IRMPD spectrum has been obtained in the 840-1720 cm(-1) fingerprint region by coupling the IR free electron laser at the Centre Laser Infrarouge d'Orsay (CLIO) with a Fourier-transform ion cyclotron resonance (FT-ICR) mass spectrometer equipped with an electrospray ionization source. The spectroscopic results are interpreted with quantum chemical calculations conducted at the B3LYP/aug-cc-pVDZ level. The analysis of the IRMPD spectrum is consistent with a σ complex, in which the Ag(+) ion binds to the nitrogen lone pairs of the two Py ligands in a linear configuration. The binding motif of Py-Ag(+)-Py in the gas phase is the same as that observed in Ag(+)-mediated base pairing in solution. Ag(+) bonding to the π-electron system of the aromatic ring is predicted to be a substantially less-favorable binding motif.

Bilability is defined when one electron is used to switch between concerted and stepwise pathways in Cu(I)-based bistable [2/3]pseudorotaxanes

Supramolecular switches operate as simple machines by using a stimulus to turn stations off and on, generating thermodynamic differences that define bistability and enable motion. What has not been previously investigated, yet is required to gain further control over molecular movements for complex operations, is an understanding of how the same stimulus can also switch pathways off and on, thus, defining the kinetic property of bilability. To address this challenge, the mechanisms of the forward and return reactions of redox-switchable Cu(I)-based [2/3]pseudorotaxanes have been quantitatively characterized utilizing mechanistic cyclic voltammetry and employing a series of isosteric bis-bidentate ligands. First, the bistability of the switch is retained across the series of ligands: Reduction of the ligand drives the reaction forward where a [2]pseudorotaxane switches into a reduced [3]pseudorotaxane and reoxidation drives the switching cycle back to the beginning. Second, the switch is bilabile with the forward reaction following an association-activated interchange pathway (concerted), whereas the reverse reaction follows a different dissociation-based dethreading pathway (stepwise). The forward reaction is more sensitive to denticity (bidentate tetrazinyl ligand, k(2) = 12,000 M(-1) s(-1), versus the monodentate pyrazinyl ligand, k(2) = 1500 M(-1) s(-1)) than to electronics (k(2) = 12,000 M(-1) s(-1) for methyl and trifluoromethyl substituents). The rate of return with the pyrazinyl ligand is k(1) = 50 s(-1). Consequently, both the mechanism and the thermodynamics of switching are stimuli dependent; they change with the oxidation state of the ligand. These findings have implications for the future design of molecular motors, which can be built from systems displaying allosterically coupled bistability and bilability.