Jeffrey S. Mugridge

External and Internal Guest Binding of a Highly Charged Supramolecular Host in Water: Deconvoluting the Very Different Thermodynamics

NMR, UV-vis, and isothermal titration calorimetry (ITC) measurements probe different aspects of competing host-guest equilibria as simple alkylammonium guest molecules interact with both the exterior (ion-association) and interior (encapsulation) of the [Ga(4)L(6)](12-) supramolecular assembly in water. Data obtained by each independent technique measure different components of the host-guest equilibria and only when analyzed together does a complete picture of the solution thermodynamics emerge. Striking differences between the internal and external guest binding are found. External binding is enthalpy driven and mainly due to attractive interactions between the guests and the exterior surface of the assembly while encapsulation is entropy driven as a result of desolvation and release of solvent molecules from the host cavity.

Encapsulation and characterization of proton-bound amine homodimers in a water-soluble, self-assembled supramolecular host

Cyclic amines can be encapsulated in a water-soluble self-assembled supramolecular host upon protonation. The hydrogen-bonding ability of the cyclic amines, as well as the reduced degrees of rotational freedom, allows for the formation of proton-bound homodimers inside of the assembly that are otherwise not observable in aqueous solution. The generality of homodimer formation was explored with small N-alkyl aziridines, azetidines, pyrrolidines, and piperidines. Proton-bound homodimer formation is observed for N-alkylaziridines (R = methyl, isopropyl, tert-butyl), N-alkylazetidines (R = isopropyl, tert-butyl), and N-methylpyrrolidine. At high concentration, formation of a proton-bound homotrimer is observed in the case of N-methylaziridine. The homodimers stay intact inside the assembly over a large concentration range, thereby suggesting cooperative encapsulation. Both G3(MP2)B3 and G3B3 calculations of the proton-bound homodimers were used to investigate the enthalpy of the hydrogen bond in the proton-bound homodimers and suggest that the enthalpic gain upon formation of the proton-bound homodimers may drive guest encapsulation.

Encapsulated guest-host dynamics: guest rotational barriers and tumbling as a probe of host interior cavity space.

The supramolecular host assembly [Ga(4)L(6)](12-) (1; L = 1,5-bis[2,3-dihydroxybenzamido]naphthalene) encapsulates cationic guest molecules within its hydrophobic cavity and catalyzes a variety of chemical transformations within its confined interior space. Despite the well-defined structure, the host ligand framework and interior cavity are very flexible and 1 can accommodate a wide range of guest shapes and sizes. These observations raise questions about the steric effects of confinement within 1 and how encapsulation fundamentally changes the motions of guest molecules. Here we examine the motional dynamics (guest bond rotation and tumbling) of encapsulated guest molecules to probe the steric consequences of encapsulation within host 1. Encapsulation is found to increase the Ph-CH(2) bond rotational barrier for ortho-substituted benzyl phosphonium guest molecules by 3 to 6 kcal/mol, and the barrier is found to depend on both guest size and shape. The tumbling dynamics of guests encapsulated in 1 were also investigated, and here it was found that longer, more prolate-shaped guest molecules tumble more slowly in the host cavity than larger but more spherical guest molecules. The prolate guests reduce the host symmetry from T to C(1) in solution at low temperatures, and the distortion of the host framework that is in part responsible for this symmetry reduction is observed directly in the solid state. Analysis of guest motional dynamics is a powerful method for interrogating host structure and fundamental host-guest interactions.

High Precision Measurement of Isotope Effects on Noncovalent Host-Guest Interactions

The self-assembled supramolecular host [Ga(4)L(6)](12-) can bind cationic guest molecules to both the interior and exterior of the host assembly through noncovalent interactions. Very small equilibrium isotope effects (EIEs) have been precisely measured for the association of benzyltrimethylphosphonium isotopologues to the host exterior surface by adapting an NMR titration method originally developed by the Perrin group for measuring isotope effects on acidity constants. Deuteration of the phosphonium methyl groups was found to have a larger EIE than deuteration at the ring and benzyl positions, suggesting subtle differences in the noncovalent interactions between the host exterior and different guest C-H/D bonds. The application of this method to the measurement of EIEs on noncovalent host-guest interactions demonstrates the generality of this NMR technique in precisely measuring relative equilibrium constants.

Solvent and Pressure Effects on the Motions of Encapsulated Guests: Tuning the Flexibility of a Supramolecular Host

The supramolecular host assembly [Ga4L6](12-) [1; L = 1,5-bis(2,3-dihydroxybenzamido)naphthalene] contains a flexible, hydrophobic interior cavity that can encapsulate cationic guest molecules and catalyze a variety of chemical transformations. The Ar-CH2 bond rotational barrier for encapsulated ortho-substituted benzyl phosphonium guest molecules is sensitive to the size and shape of the host interior space. Here we examine how changes in bulk solvent (water, methanol, or DMF) or applied pressure (up to 150 MPa) affect the rotational dynamics of encapsulated benzyl phosphonium guests, as a way to probe changes in host cavity size or flexibility. When host 1 is dissolved in organic solvents with large solvent internal pressures (∂U/∂V)T, we find that the free energy barrier to Ar-CH2 bond rotation increases by 1-2 kcal/mol, compared with that in aqueous solution. Likewise, when external pressure is applied to the host-guest complex in solution, the bond rotational rates for the encapsulated guests decrease. The magnitude of these rate changes and the volumes of activation obtained using either solvent internal pressure or applied external pressure are very similar. NOE distance measurements reveal shorter average host-guest distances (~0.3 Å) in organic versus aqueous solution. These experiments demonstrate that increasing solvent internal pressure or applied external pressure reduces the host cavity size or flexibility, resulting in more restricted motions for encapsulated guest molecules. Changing bulk solvent or external pressure might therefore be used to tune the physical properties or reactivity of guest molecules encapsulated in a flexible supramolecular host.

Equilibrium isotope effects on noncovalent interactions in a supramolecular host-guest system.

The self-assembled supramolecular complex [Ga(4)L(6)](12-) (1; L = 1,5-bis[2,3-dihydroxybenzamido]naphthalene) can act as a molecular host in aqueous solution and bind cationic guest molecules to its highly charged exterior surface or within its hydrophobic interior cavity. The distinct internal cavity of host 1 modifies the physical properties and reactivity of bound guest molecules and can be used to catalyze a variety of chemical transformations. Noncovalent host-guest interactions in large part control guest binding, molecular recognition and the chemical reactivity of bound guests. Herein we examine equilibrium isotope effects (EIEs) on both exterior and interior guest binding to host 1 and use these effects to probe the details of noncovalent host-guest interactions. For both interior and exterior binding of a benzylphosphonium guest in aqueous solution, protiated guests are found to bind more strongly to host 1 (K(H)/K(D) > 1) and the preferred association of protiated guests is driven by enthalpy and opposed by entropy. Deuteration of guest methyl and benzyl C-H bonds results in a larger EIE than deuteration of guest aromatic C-H bonds. The observed EIEs can be well explained by considering changes in guest vibrational force constants and zero-point energies. DFT calculations further confirm the origins of these EIEs and suggest that changes in low-frequency guest C-H/D vibrational motions (bends, wags, etc.) are primarily responsible for the observed EIEs.

1H NMR Chemical Shift Calculations as a Probe of Supramolecular Host–Guest Geometry

The self-assembled supramolecular host [Ga(4)L(6)](12-) (1; L = 1,5-bis[2,3-dihydroxybenzamido]naphthalene) can encapsulate cationic guest molecules within its hydrophobic cavity and catalyze the chemical transformations of bound guests. The cavity of host 1 is lined with aromatic naphthalene groups, which create a magnetically shielded interior environment, resulting in upfield shifted (1-3 ppm) NMR resonances for encapsulated guest molecules. Using gauge independent atomic orbital (GIAO) DFT computations, we show that (1)H NMR chemical shifts for guests encapsulated in 1 can be efficiently and accurately calculated and that valuable structural information is obtained by comparing calculated and experimental chemical shifts. The (1)H NMR chemical shift calculations are used to map the magnetic environment of the interior of 1, discriminate between different host-guest geometries, and explain the unexpected downfield chemical shift observed for a particular guest molecule interacting with host 1.

Structural basis of mRNA-cap recognition by Dcp1-Dcp2

Removal of the 5′ cap on mRNA by the decapping enzyme Dcp2 is a critical step in 5′-to-3′ mRNA decay. Understanding the structural basis of Dcp2 activity has been a challenge because Dcp2 is dynamic and has weak affinity for the cap substrate. Here we present a 2.6-Å-resolution crystal structure of a heterotrimer of fission yeast Dcp2, its essential activator Dcp1, and the human NMD cofactor PNRC2, in complex with a tight-binding cap analog. Cap binding is accompanied by a conformational change in Dcp2, thereby forming a composite nucleotide-binding site comprising conserved residues in the catalytic and regulatory domains. Kinetic analysis of PNRC2 revealed that a conserved short linear motif enhances both substrate affinity and the catalytic step of decapping. These findings explain why Dcp2 requires a conformational change for efficient catalysis and reveals that coactivators promote RNA binding and the catalytic step of decapping, possibly through different conformational states.

A ferrocene-based catecholamide ligand: the consequences of ligand swivel for directed supramolecular self-assembly

A ferrocene-based biscatecholamide ligand was prepared and investigated for the formation of metal–ligand supramolecular assemblies with different metals. Reaction with Ge(IV) resulted in the formation of a variety of Ge n L m coordination complexes, including [Ge2L3]4− and [Ge2L2(μ-OMe)2]2−. The ligands ability to swivel about the ferrocenyl linker and adopt different conformations accounts for formation of many different Ge n L m species. This study demonstrates why conformational ligand rigidity is essential in the rational design and directed self-assembly of supramolecular complexes.

Structure of the activated Edc1-Dcp1-Dcp2-Edc3 mRNA decapping complex with substrate analog poised for catalysis

The conserved decapping enzyme Dcp2 recognizes and removes the 5′ eukaryotic cap from mRNA transcripts in a critical step of many cellular RNA decay pathways. Dcp2 is a dynamic enzyme that functions in concert with the essential activator Dcp1 and a diverse set of coactivators to selectively and efficiently decap target mRNAs in the cell. Here we present a 2.84 Å crystal structure of K. lactis Dcp1–Dcp2 in complex with coactivators Edc1 and Edc3, and with substrate analog bound to the Dcp2 active site. Our structure shows how Dcp2 recognizes cap substrate in the catalytically active conformation of the enzyme, and how coactivator Edc1 forms a three-way interface that bridges the domains of Dcp2 to consolidate the active conformation. Kinetic data reveal Dcp2 has selectivity for the first transcribed nucleotide during the catalytic step. The heterotetrameric Edc1–Dcp1–Dcp2–Edc3 structure shows how coactivators Edc1 and Edc3 can act simultaneously to activate decapping catalysis.The decapping enzyme Dcp2 removes the 5′ eukaryotic cap from mRNA transcripts and acts in concert with its essential activator Dcp1 and various coactivators. Here the authors present the structure of the fully-activated mRNA decapping complex, which reveals how Dcp2 recognizes the cap substrate and coactivators Edc1 and Edc3 activate catalysis.