Insight into the Folding and Cooperative Multi-Recognition Mechanism in Supramolecular Anion-Binding Catalysis

H-bond donor catalysts able to modulate the reactivity of ionic substrates for asymmetric reactions have gained great attention in the past years, leading to the development of cooperative multidentate H-bonding supramolecular structures. However, there is still a lack of understanding of the forces driving the ion recognition and catalytic performance of these systems. Herein, insight into the cooperativity nature, anion binding strength, and folding mechanism of a model chiral triazole catalyst is presented. Our combined experimental and computational study revealed that multi-interaction catalysts exhibiting weak binding energies (≈3–4 kcal mol⁻¹) can effectively recognize ionic substrates and induce chirality, while strong dependencies on the temperature and solvent were quantified. These results are key for the future design of catalysts with optimal anion binding strength and catalytic activity in target reactions.     

Comparison of hydrogen bonding in 1-octanol and 2-octanol as probed by spectroscopic techniques

Liquid 1-octanol and 2-octanol have been investigated by infrared (IR), Raman, and Brillouin experiments in the 10-90 degrees C temperature range. Self-association properties of the neat liquids are described in terms of a three-state model in which OH oscillators differently implicated in the formation of H-bonds are considered. The results are in quantitative agreement with recent computational studies for 1-octanol. The H-bond probability is obtained by Raman data, and a stochastic model of H-bonded chains gives a consistent picture of the self-association characteristics. Average values of hydrogen bond enthalpy and entropy are evaluated. The H-bond formation enthalpy is ca. -22 kJ/mol and is slightly dependent on the structural isomerism. The different degree of self-association for the two octanols is attributed to entropic factors. The more shielded 2-isomer forms larger fractions of smaller, less cooperative, and more ordered clusters, likely corresponding to cyclic structures. Signatures of a different cluster organization are also evidenced by comparing the H-bond energy dispersion (HBED) of OH stretching IR bands. A limiting cooperative H-bond enthalpy value of 27 kJ/mol is found. It is also proposed that the different H-bonding capabilities may modulate the extent of interaggregate hydrocarbon interactions, which is important in explaining the differences in molar volume, compressibility, and vaporization enthalpy for the two isomers.     

Molecular basis of the recognition process: hydrogen-bonding patterns in the guanine primary recognition site of ribonuclease T1

Investigation of the intrinsic H-bonding pattern of the guanine complex with a sizable segment (from Asn43 to Glu46) of the primary recognition site (PRS) in RNase T1 at the B3LYP/6-311G(d,p) level of theory enables the electronic density characteristics of the H-bonding patterns of the guanine-PRS complexes to be identified. The perfect H-bonding pattern in the guanine recognition site is achieved through the guanine complex interactions with the large segment of the PRS. Two significant short H-bonds, O epsilon 1...HN1 and O epsilon 2...HN2, have been identified. The similar short H-bond distances found in the anionic GC- base pair and in this study suggest that the short hydrogen-bond distances may be characteristic of the multiple H-bonded anionic nucleobases. The H-bonding energy distribution, the geometric analysis of the H-bonding pattern, and the electron structure characteristics of the H-bonds in the guanine PRS of RNase T1 all suggest that the O epsilon 1...HN1 and O epsilon 2...HN2 side-chain H-bonds dominate the binding at the guanine recognition site of RNase T1. Also, the geometry evidence, the electron structure characteristics, and the properties of the bond critical points of the H-bonds reveal that the side-chain H-bonding and the main-chain H-bonding are mutually intensifying. Thus the positive cooperativity between Asn43 to Tyr45 and Glu46 is proposed.     

Self-assembled metallocycles with two interactive binding domains

Five metallocycles 1 a-e have been self-assembled from S-shaped bispyridyl ligands 2 a-e and a palladium complex, [Pd(dppp)(OTf)(2)] (dppp=1,3-bis(diphenylphosphanyl)propane), and have been characterized by elemental analysis and various spectroscopic methods including (1)H NMR spectroscopy and electrospray ionization (ESI) mass spectrometry. These metallocycles all are monocyclic compounds, but can fold to generate two binding domains bearing hydrogen-bonding sites based on pyridine-2,6-dicarboxamide units. The binding properties of the metallocycles with N,N,N',N'-tetramethylterephthalamide (G) have been probed by means of ESI mass spectrometry and (1)H NMR spectroscopy. The results both in the gas phase and in solution are consistent with the fact that the metallocycles accommodate two molecules of the guest G. Thus, the ESI mass spectra clearly show fragments corresponding to the 1:2 complexes in all cases. (1)H NMR studies on 1 a and G support the formation of a 1:2 complex in solution; the titration curves are nicely fitted to a 1:2 binding isotherm, but not to a 1:1 binding isotherm. In addition, a Job plot also suggests a 1:2 binding mode between 1 a and G, showing maximum complexation at approximately 0.33 mol fraction of the metallocycle 1 a in CDCl(3). The binding constants K(1) and K(2) are calculated to be 1600 and 1400 M(-1) (+/-10 %), respectively, at 25 degrees C in CDCl(3), indicative of positively cooperative binding. This positive cooperativity was confirmed by the Hill equation, affording a Hill coefficient of n = 1.6. Owing to insufficient solubility in CDCl(3), for comparison purposes the binding properties of the metallocycles 1 b-e were investigated in a more polar medium, 3 % CD(3)CN/CDCl(3). (1)H NMR titrations revealed that the metallocycles all bind two molecules of the guest G with Hill coefficients ranging from 1.4 to 1.8. This positive cooperativity may be attributed to a structural reorganization of the second binding cavity when the first guest binds to either one of the subcavities present in the metallocycles.     

Positive homotropic allosteric binding of benzenediols in a hydrindacene-based exoditopic receptor: cooperativity in amide hydrogen bonding

The preparation and complexation properties of a hydrindacene-based exoditopic receptor, that exhibits a positive homotropic allosteric binding process toward benzenediols, are described. The exoditopic receptors form 1:2 complexes with resorcinols, catechol, and 3-hydroxybenzyl alcohol with K2/K1 = 3-33. Both the entropy and the enthalpy terms are important in this allosteric system; the crystallographic studies provide the first clear evidence that the cooperativity in amide hydrogen bonding by polarization contributes to the positive homotropic allosteric binding property.     

Understanding noncovalent interactions: ligand binding energy and catalytic efficiency from ligand-induced reductions in motion within receptors and enzymes

Noncovalent interactions are sometimes treated as additive and this enables useful average binding energies for common interactions in aqueous solution to be derived. However, the additive approach is often not applicable, since noncovalent interactions are often either mutually reinforcing (positively cooperative) or mutually weakening (negatively cooperative). Ligand binding energy is derived (positively cooperative binding) when a ligand reduces motion within a receptor. Similarly, transition-state binding energy is derived in enzyme-catalyzed reactions when the substrate transition state reduces the motions within an enzyme. Ligands and substrates can in this way improve their affinities for these proteins. The further organization occurs with a benefit in bonding (enthalpy) and a limitation in dynamics (cost in entropy), but does not demand the making of new noncovalent interactions, simply the strengthening of existing ones. Negative cooperativity induces converse effects: less efficient packing, a cost in enthalpy, and a benefit in entropy.     

Buried solvent determines both anion-binding selectivity and binding stoichiometry with hydrogen-bonding receptors

[reaction: see text] The crystal structure of a tetraurea picket porphyrin-chloride anion complex has previously shown the anion to be situated between two adjacent ureas and hydrogen bonded via four NH protons (J. Am. Chem. Soc. 1998, 120, 11684-11692). The porphyrin receptor also binds a DMSO molecule and utilizes it as a participant in its anion recognition unit, in a manner similar to enzymes that bind water for use as part of their substrate recognition unit. The bound solvent molecule determines the anion-binding affinity, selectivity, and stoichiometry of binding. With a bound DMSO molecule, the tetraurea picket porphyrin is a highly selective receptor for chloride anion and binds all anions with a 1:1 binding stoichiometry. Absent the buried DMSO molecule, the receptor is selective for phosphate anion and binds chloride and phosphate anions with both 1:1 and 1:2 receptor-anion stoichiometries. Additionally, a remarkable reversal in the selectivity of anion complexation between various picket porphyrin receptors is observed, wherein the binding constant ratios change over 3 orders of magnitude as the receptor's number of urea pickets change from four to two. The latter receptor has no urea pickets available to bind to solvent after complexation with an anion. The results demonstrate that anion complexation with hydrogen-bonding receptors in a competitive solvent is enhanced when a ubiquitous solvent molecule is incorporated into the binding motif. In this way, competitive solvent adds to the overall complexation energy and thereby strengthens binding rather than weakens it, as commonly believed. The results are pertinent to drug design, for they suggest that pharmaceuticals need not be completely desolvated to selectively bind to their biological target when water can be included in the binding motif.     

Studies into the thermodynamic origin of negative cooperativity in ion-pairing molecular recognition

The association of synthetic receptors to target guests often proceeds through the cooperative action of multiple binding forces. An investigation into the thermodynamic origin of cooperativity in ion-pairing host-guest binding in water is described. The binding affinities of 1,2,3,4-butanetetracarboxylate, tricarballate, glutarate, and acetate to a C(3)(v) symmetric metallo-host (1) are characterized in terms of the binding constants (K(a)) and the thermodynamic parameters deltaG degrees, deltaH degrees, and deltaS degrees, as determined by isothermal titration calorimetry (ITC). These values are used to determine the individual contributions of the binding interaction to the overall binding. Several ways to view the combination of the individual binding events that make up the whole are analyzed, all of which lead to the conclusion of negative cooperativity. Combined, the data were used to evaluate the thermodynamic origin of negative cooperativity for this series of guests, revealing that entropy is the largest contributing factor. An interpretation of this result focuses upon differences in the number of water molecules displaced upon binding.     

Cooperative multipoint recognition of organic dyes by bis(beta-cyclodextrin)s with 2,2'-bipyridine-4,4'-dicarboxy tethers

A series of novel 6,6'-bis(beta-cyclodextrin)s linked by 2,2'-bipyridine-4,4'-dicarboxy tethers; that is, 2,2'-bipyridine-4,4'-dicarboxy-bridged bis(6-O-beta-cyclodextrin) (2) and N,N'-bis(2-aminoethyl )-2,2'-bipyridine-4,4'-dicarboxamide-bridged (3), N,N'-bis(5-amino-3-azapentyl)-2,2'-bipyridine-4,4'-dicarboxamide-bridged (4) and N,N'-bis(8-amino-3,6-diazaoctyl)-2,2'-bipyridine-4,4'-dicarboxamide-bridged bis(6-amino-6-deoxy-beta-cyclodextrin) (5), has been synthesized as cooperative multipoint-recognition receptor models. The inclusion complexation behavior of 2-5 with organic dyes; that is, ammonium 8-anilino-1-naphthalenesulfonate, Brilliant Green, Methyl Orange, Acridine Red, and Rhodamine B, has been investigated in aqueous phosphate buffer solutions (pH 7.20) at 25 degrees C by means of ultraviolet, fluorescence, and circular dichroism spectrometry as well as by fluorescence lifetime measurements. The spectral titrations gave the complex stability constants (Ks) and Gibbs' free energy changes (deltaG degrees) for the inclusion complexation of 2-5 with the organic dyes and other thermodynamic parameters (deltaH degrees and deltaS degrees) for the inclusion complexation of 2-4 with the fluorescent dyes Acridine Red and Rhodamine B. Bis(beta-cyclodextrin)s 2-5 displayed higher binding abilities toward most of the examined dye molecules than native beta-cyclodextrin 1; this is discussed from the viewpoints of the size/shape-fit concept, the induced-fit interaction, and cooperative, multipoint recognition by the bridging chain and the dual hydrophobic cavities. Thermodynamically, the inclusion complexation of 2-4 with Acridine Red is totally enthalpy driven with a negative or minor positive entropic contribution, but the inclusion complexation with Rhodamine B is mainly entropy-driven with a mostly positive, but occasionally negative, enthalpic contribution; in some cases this determines the complex stability.     

The Electron-Donor Function of the Phosphorylic Oxygen

Abstract

The values of the enthalpy and free energy factors (E_j and C_j) of the pnospiiorylic compounds were estimated on the basis of literature (1) and experimental material (2). The ability of carbonylic compounds to H-bond formation was found to be remarkably lower than of the phosphorylic compounds. The H-bonding complex formation of both one and two hydrogen atoms with the phosphorylic oxygen atom was established. The spectrophotometric and calorimetric study of the complex formation of model uncyclic and biologically active macrocyclic phosphorylic compounds with calcium as a biometal was carried out. The tendency to form complexes of both 1:1 and 1:2 (metal to ligand) compositions was revealed. An essential effect of entropy on the 1:2 complex stability and an effect of macrocycle size as well as the phosphorous atom's substituent on the complexation ability with calcium cation was established.     

Complexation and chiral recognition thermodynamics of 6-amino-6-deoxy-beta-cyclodextrin with anionic, cationic, and neutral chiral guests: counterbalance between van der Waals and coulombic interactions

The stability constant (K), standard free energy (Delta G degrees), enthalpy (Delta H degrees), and entropy changes (T Delta S degrees) for the complexation of 6-amino-6-deoxy-beta-cyclodextrin with more than 50 negatively or positively charged as well as neutral guests, including 22 enantiomer pairs, have been determined in aqueous phosphate buffer (pH 6.9) at 298.15 K by titration microcalorimetry. The thermodynamic parameters obtained in this study and the relevant data for native beta-cyclodextrin indicate that the complexation and chiral discrimination behavior of the cationic host with charged guests are governed by the critical counterbalance between the electrostatic interactions of the charged groups in host and guest and the conventional intracavity interactions of the hydrophobic moiety of guest, such as hydrophobic, van der Waals, solvation/desolvation, and hydrogen-bonding interactions.     

Dynamics of a protein and water molecules surrounding the protein: hydrogen-bonding between vibrating water molecules and a fluctuating protein

Internal and rigid-body motions of bovine pancreatic trypsin inhibitor (BPTI) and of water molecules surrounding the BPTI are studied in a vicinity of an energy minimum using a normal mode analysis proposed as the independent molecule model. Water's rigid-body motion is predominant in comparison to its internal motions. We have derived information about the relationship between the magnitude of a thermal ellipsoid of an H-bonding atom and the anisotropy of its ellipsoid, and the relationship between the magnitude of the ellipsoid and the H-bond strength. We see a relationship between vibrational frequencies (assuming rigid-body motion of the water molecules) and the H-bond strength of the water taking part in this H-bonding. Analyzing the H-bond strength, we found that a hydrogen in water is likely to H-bond to oxygen in the protein, whereas an oxygen in water has a less strong preference to H-bond to the protein. For water molecules acting as the hydrogen acceptor, strong H-bonding has longer lifetimes than weak H-bonding.     

Characterizing the cooperativity in H-bonded amino structures

Density functional theory calculations were used to examine the effect of H-bond cooperativity on the magnitude of the NMR chemical shifts and spin-spin coupling constants in a C4h-symmetric G-quartet and in structures consisting of six cyanamide monomers. These included two ring structures (a planar C6h-symmetric structure and a nonplanar S6-symmetric structure) and two linear chain structures (a fully optimized planar Cs-symmetric chain and a planar chain structure where all intra- and intermolecular parameters were constrained to be identical). The NMR parameters were computed for the G-quartet and cyanamide structures, as well as for shorter fragments derived from these assemblies without reoptimization. In the ring structures and the chain with identical monomers, the intra- and intermolecular geometries of the cyanamides were identical, thereby allowing the study of cooperative effects in the absence of geometry changes. The magnitude of the |1JNH| coupling, 1H and 15N chemical shifts of the H-bonding amino N-H group, and the |h2JNN| H-bond coupling increased, whereas the size of the |1JNH| coupling of the non-H-bonded amino N-H bonds of the first amino group in the chain, which are roughly perpendicular to the H-bonding network, decreased in magnitude when H-bonding monomers were progressively added to extending ring or chain structures. These effects are attributed to electron redistribution induced by the presence of the nearby H-bonding guanine or cyanamide molecules.     

Entropy-Driven Cooperativity in the Guest Binding of an Octaphosphonate Bis-cavitand

Uncommon entropy-driven cooperativity is reported in the guest binding of an octaphosphonate bis-cavitand. Isothermal titration calorimetry determined the thermodynamic parameters for the 1:2 host–guest binding of bis-cavitands with ammonium guests in methanol, ethanol, 2-propanol, and chloroform. Chloroform drove uncommon entropy-driven cooperative binding, whereas the alcohols resulted in enthalpy-driven noncooperative binding. ¹H NMR studies revealed that each cavity contained six water molecules in chloroform, which were liberated on guest binding. The enthalpy–entropy compensation relationship produced a large positive intrinsic entropy in chloroform, which implies that water desolvation causes a considerable entropic gain by paying an enthalpic penalty due to breaking the hydrogen-bonding networks of the water clusters.     

Molecular recognition of anions through hydrogen bonding stabilization of anion-ionophore adducts: a novel trifluoroacetophenone-based binding motif

[reaction: see text] A novel trifluoroacetophenone-based binding motif has been developed that recognizes anions such as carboxylates through reversible formation of anion-ionophore adducts that are stabilized by intramolecular H-bonding. The intramolecular H-bonding resulted in more than 10-fold enhancement in the binding affinity and an enthalpy gain (DeltaH degrees ) of 3.0 kcal/mol for the binding of an acetate ion when compared to the case without the intramolecular H-bonding.     

Silver-Free Au(I) Catalysis Enabled by Bifunctional Urea- and Squaramide-Phosphine Ligands via H-Bonding

A library of gold(I) chloride complexes with phosphine ligands incorporating pendant (thio)urea and squaramide H-bond donors was prepared with the aim of promoting chloride abstraction from Au(I) via H-bonding. In the absence of silver additives, complexes bearing squaramides and trifluoromethylated aromatic ureas displayed good catalytic activity in the cyclization of N-propargyl benzamides, as well as in a 1,6-enyne cycloisomerization, a tandem cyclization-indole addition reaction and the hydrohydrazination of phenylacetylene. Kinetic studies and DFT calculations indicate that the energetic span of the reaction is accounted by both the chloride abstraction step, facilitated by the bidentate H-bond donor via an associative mechanism, and the subsequent cyclization step.     

Conductance and Thermodynamic Study of Thallium and Silver Ion Complexes with Crown Ethers in Different Binary Acetonitrile–Water Solvent Mixtures

The complexation reactions between Ag⁺ andTl⁺ ions with 15-crown-5 (15C5) and phenyl-aza-15-crown-5(PhA15C5) have been studied conductometrically in 90%acetonitrile-water and 50% acetonitrile - water mixed solvents attemperatures of 293, 298, 303 and 308 K. The stability constants of theresulting 1 : 1 complexes were determined, indicating that theTl⁺ complexes are more stable than the Ag⁺complexes. The enthalpy and entropy of crown complexation reactions were determined from the temperature dependence of the complexation constants.The enthalpy and entropy changes depend on solvent composition and the T S⁰ _o–H⁰ plotshows a good linear correlation, indicating the existence of entropy –enthalpy compensation in the crown complexation reactions.     

A prototype calix[4]arene-based receptor for carbohydrate recognition containing peptide and phosphate binding groups

A novel class of macrobicyclic receptors for carbohydrate recognition based on upper rim, peptide-bridged calix[4]arenes has been designed and synthesized. Receptor 12, in which a charged phosphate group cooperates with peptide hydrogen-bonding donor and acceptor groups in the binding process, is the most efficient and selective in the complexation of simple carbohydrate derivatives. The selectivity observed is toward beta-glucoside 13a, which is better bound (DeltaG degrees = 19.6 kJ mol(-)(1)) compared to the corresponding alpha anomer 13b (DeltaG degrees = 17.0 kJ mol(-)(1)) and to the beta-galactoside 13c (DeltaG degrees = 17.7 kJ mol(-)(1)) in CDCl(3). A substantial drop in the stability constant is observed by esterification of the phosphate group in the host 12 or by alkylation of the OH groups in the 2 and 3 positions in the beta-glucoside and beta-galactoside derivatives. On the basis of a careful analysis of the (1)H NMR data available, a binding mode of the beta-octylglucoside 13a to receptor 12 is proposed.