Molecular discrimination of N-protected amino acid esters by a self-assembled cylindrical capsule: spectroscopic and computational studies

Expanding Coefficient: A Parameter To Assess the Stability of Induced-Fit Complexes

Here we propose a new parameter, the Expanding Coefficient (EC), that can be correlated with the thermodynamic stability of supramolecular complexes governed by weak secondary interactions and obeying the induced-fit model. The EC values show a good linear relationship with the log Kapp of the respective pseudorotaxane complexes investigated. According to Cram's Principle of Preorganization, the EC can be considered an approximate mechanical measure of the host's reorganization energy cost upon adopting the final bound geometry.

Adaptive binding and selection of compressed 1,ω-diammonium-alkanes via molecular encapsulation in water

Guest molecules confined inside hollow molecular assemblies and thus protected from their environment can show unexpected structural behavior or special reactivity compared to their behavior in a bulk, unprotected environment. A special case is the coiling behavior of variable-length alkane chains in rigid hydrogen-bonded molecular cages. It has been found before that coiling may occur in such circumstances, but no experimental evidence concerning the exact conformation of the chains has yet been presented. We reveal in this study the self-assembly of a molecular cage in water and the crystalline state from three distinct components in which linear 1,ω-diammonium-alkanes chains are confined with different degrees of compression. The exact coiling behavior is determined from atomic resolution X-ray diffraction showing crenel-like conformations in the compressed state. Chemical selection can be obtained from mixtures of alkane chains via the encapsulation of kinetically stable conformations observed during the encapsulation of pure components. Moreover, it was found that uncompressed and compressed chains can be competitively trapped inside the capsule. These findings may provide insight in areas to a better understanding of biological processes, such as the fatty acid metabolism.

Kinetic resolution of constitutional isomers controlled by selective protection inside a supramolecular nanocapsule

The concept of self-assembling container molecules as yocto-litre reaction flasks is gaining prominence. However, the idea of using such containers as a means of protection is not well developed. Here, we illustrate this idea in the context of kinetic resolutions. Specifically, we report on the use of a water-soluble, deep-cavity cavitand to bring about kinetic resolutions within pairs of esters that otherwise cannot be resolved because they react at very similar rates. Resolution occurs because the presence of the cavitand leads to a competitive binding equilibrium in which the stronger binder primarily resides inside the host and the weaker binding ester primarily resides in the bulk hydrolytic medium. For the two families of ester examined, the observed kinetic resolutions were highest within the optimally fitting smaller esters.

Enantioselective fluorescent sensors for chiral carboxylates based on BINOL — Synthesis and chiral recognition

The four novel derivatives of 1,1′-bi-2-naphthol (BINOL) have been prepared, and the structures of these compounds have been characterized by IR, MS, 1H and 13C NMR spectroscopy, and elemental analysis. The enantioselective recognition of these receptors has been studied by fluorescence titration and 1H NMR spectroscopy. The receptors exhibited different chiral-recognition abilities towards some enantiomers of chiral materials and formed 1:1 complexes between host and guest. The receptors exhibit excellent enantioselective fluorescent-recognition ability towards the amino acid derivatives.

Contortions of encapsulated alkyl groups

Rotors are recalled as early molecular devices that transmit information through changes in conformation. Specific cases involve bipyridyls and biphenyls in which the biaryl bond acts as a fulcrum to relay applied stresses from one site to another. New types of molecular stress encountered by encapsulated molecules are identified--including bending, straightening, squeezing, grinding and compression. For flexible molecules in reversibly formed capsules a fluid model of recognition is proposed that is neither lock-and-key nor induced fit. Instead, the guest assumes the shape that best fills the available space, even if contortions to higher energy conformations are required. For encapsulated alkanes, a delicate balance of attraction and repulsion exists when the size of a guest molecule approaches the space available to it. The complexes are analyzed by both NMR and computational methods and detailed maps of the host-guest interfaces in solution are provided. The reversible transition of an encapsulated alkane between a compressed, coiled conformation and a relaxed, extended one is described. The system is a spring-loaded molecular device under the control of acids and bases that offers an alternative to the rotors of current molecular machinery.

Dynamics of Benzene Guest Inside a Self-Assembled Cylindrical Capsule: A Combined Solid-State 2H NMR and Molecular Dynamics Simulation Study

The reorientational dynamics of benzene-d(6) molecules hosted into the cavity of a cavitand-based, self-assembled capsule was investigated by Molecular Dynamics (MD) simulations and temperature-dependent solid-state (2)H NMR spectroscopy. MD simulations were preliminarily performed to assess the motional models of the guest molecules inside the capsules. An in-plane fast reorientation of the benzene guest around the C(6) symmetry axis (B1 motion), characterized by correlation times of the order of picoseconds, was predicted with an activation barrier ( approximately 8 kJ/mol) very similar to that found for neat benzene in the liquid state. An out-of-plane reorientation corresponding to a nutation of the C(6) symmetry axis in a cone angle of 39 degrees (B2 motion, 373 K) with an activation barrier ( approximately 39 kJ/mol) definitely larger than that of liquid benzene was also anticipated. In the temperature range 293-373 K correlation times of the order of a nanosecond have been calculated and a transition from fast to slow regime in the (2)H NMR scale has been predicted between 293 and 173 K. (2)H NMR spectroscopic analysis, carried out in the temperature range 173-373 K on the solid capsules containing the perdeuterated guest (two benzene molecules/capsule), confirmed the occurrence of the B1 and B2 motions found in slow exchange in the (2)H NMR time scale. Line shape simulation of the (2)H NMR spectral lines permitted defining a cone angle value of 39 degrees at 373 K and 35 degrees at 173 K for the nutation axis. The T(1) values measured for the (2)H nuclei of the encapsulated aromatic guest gave correlation times and energetic barrier for the in-plane motion B1 in fine agreement with theoretical calculation. The experimental correlation time for B2 as well as the corresponding energetic barrier are in the same range found for B1. A molecular mechanism for the encapsulated guest accounting for the B1 and B2 motions was also provided.

Moving Targets: Recognition of Alkyl Groups

Alkyl chains can adopt seemingly unusual conformations, such as helices, when bound to natural and synthetic hydrophobic receptors. This plasticity allows the alkanes to assume shapes that are congruent to the receptor's space and fill that space properly. We describe here the use of cavitands and capsules as tools that expose the forces involved in the molecular recognition of hydrocarbons. Studies using NMR spectroscopy reveal how attractive interactions and solvophobic forces are maximized in solution through unprecedented contortions of alkanes and hint at a new generation of nanoscale mechanical devices.

Self-fulfilling cavitands: packing alkyl chains into small spaces

The present research was undertaken to determine the conformations of alkyl groups that are forced into small spaces. Unbranched alkyl groups assume fully extended conformations in the free space of solutions, because any bends in the structure create steric clashes between hydrogens along the chain. We synthesized a series of alkyl esters of a carboxylic acid attached to the inner surface of a vase-shaped container structure. The shorter esters (ethyl and propyl) can be accommodated in extended conformations, and even small solvent molecules can share the container's space. Longer (butyl-octyl) esters adopt increasingly coiled conformations that writhe rapidly in the limited space of the cavity. Even longer esters (nonyl and decyl) can be synthesized, but their containers become distorted, and their spectra indicate slowed internal motions of the alkyl groups within the space. In general, alkyl groups are readily contorted when their internal strains are compensated by attraction with the inner surfaces and the proper filling of space.

Oxazolidin-2-one-Containing Pseudopeptides That Fold into β-Bend Ribbon Spirals

Three sets of oligomers containing the 4-carboxy-5-methyloxazolidin-2-one (Oxd) moiety have been synthesized with the aim of checking whether these molecules are able to fold in ordered structures: A set [Boc-(L-Ala-L-Oxd)(n)-OR], B set [Boc-(L-Ala-D-Oxd)(n)-OR], and C set [Boc-(Aib-L-Oxd)(n)-OR] preferential conformations have been analyzed with IR absorption, NMR, and CD. We have noticed that in these oligomers three stabilizing effects are active: (i) the rigid Oxd -CO-N(CH<)-CO- moiety, which always tend to assume a trans conformation; (ii) the formation of Oxd C=O...H-(alpha)C intramolecolar H-bonds; (iii) the alternate formation of 1 <-- 4 intramolecular C=O...H-N H-bonds. Through the analysis of the experimental data, we could demonstrate that only the oligomers of the B set are able to meet all three requirements listed above. By a deeper insight into the CD spectra, we gathered that the secondary structure adopted by the B set oligomers is a beta-bend ribbon spiral, which is a subtype of the 3(10)-helix.

High Yielding Methyl Esterification Catalyzed by Indium(III) Chloride

The carboxylic acids are efficiently converted into the methyl esters in methanol using indium(III) chloride as the catalyst. This method is applicable for aromatic and aliphatic carboxyl moieties as well as amino acids in high yields.

Enzymatic Removal of Carboxyl Protecting Groups. 1. Cleavage of thetert-Butyl Moiety

[reaction: see text] A recent discovery that a certain amino acid motif (GGG(A)X-motif) in lipases and esterases determines their activity toward tertiary alcohols prompted us to investigate the use of these biocatalysts in the mild and selective removal of tert-butyl protecting groups in amino acid derivatives and related compounds. An esterase from Bacillus subtilis (BsubpNBE) and lipase A from Candida antarctica (CAL-A) were identified as the most active enzymes, which hydrolyzed a range of tert-butyl esters of protected amino acids (e.g., Boc-Tyr-O(t)Bu, Z-GABA-O(t)Bu, Fmoc-GABA-O(t)Bu) in good to high yields and left Boc, Z, and Fmoc-protecting groups intact.

Encapsulation of oligoethylene glycols and perfluoro-n-alkanes in a cylindrical host molecule

Oligoethylene glycols and perfluoro-n-alkanes are suitable guests for the synthetic cylindrical host molecule 1(2); an investigation of these host-guest systems is reported.

A New Class of Non-Racemic Chiral Macrocycles: A Conformational and Synthetic Study

Amino alcohols have been used to introduce non-racemic chirality into macrocycles using a modular approach that relies on a Heck macrocyclisation reaction. A wide variety of macrocycles have been synthesised, and their structures studied using X-ray crystallography and molecular modelling. A fragmentation reaction encountered during the use of (S)-1,1-dimethylvalinol revealed that carboxylic acids generate acylals under reaction conditions often used for Heck reactions.

Hydrogen-Bonded Encapsulation Complexes in Protic Solvents

We describe here the behavior of the hydrogen-bonded capsule 1.1 and its complexes in protic solvents. The kinetics and thermodynamics of the encapsulation process were determined through conventional (1)H NMR methods. The enthalpies and entropies of encapsulation are both positive, indicating a process that liberates solvent molecules. The rates of dissociation-association of the capsule were comparable to the rates for the in-out exchange of large guests, which suggests that guest exchange occurs by complete dissociation of the capsule in protic solvents. The stability of the hydrogen-bonded capsule 1.1 toward protic solvents depends strongly on the guests, with the best guest being dimethylstilbene 8. The results establish guidelines for the properties of capsules that could be accessed in water.

Helical Folding of Alkanes in a Self-Assembled, Cylindrical Capsule

The reversible encapsulation of a series of normal alkane guests in a cylindrical host was studied by NMR methods. For small hydrocarbons such as n-pentane or n-hexane, two guests enter the host, and they move freely within. With n-heptane no encapsulation takes place. For longer alkanes such as n-decane, a single guest enters and the aromatic walls of the host are seen to twist to avoid empty spaces and increase favorable interactions with the hydrocarbon. The best guest (n-undecane) adopts a conformation with minimal gauche interactions. The longest alkane accommodated, n-tetradecane, adopts a helical conformation to fit in the cavity, a shape that maximizes CH/pi interactions with the aromatic walls of the receptor. These reciprocal conformational changes are discussed in terms of optimal host/guest interactions.

Single Molecule Solvation and Its Effects on Tautomeric Equilibria in a Self-Assembled Capsule

A self-assembled cylindrical capsule provides a nanoscale environment that affects keto-enol equilibria. The equilibrium constants for encapsulated beta-ketoesters show values that differ by an order of magnitude from that of the free tautomers in solution. For complexes with a single, large encapsulated guest, the inner surfaces of the capsule and the seam of the hydrogen bonds influence the equilibrium between the encapsulated keto and enol forms. For complexes of smaller beta-ketoesters, the coencapsulated solvent influences the equilibria. The solvent reduces the space available and affects the positioning of the ester in the capsule.

Mimicking enzymatic transaminations: attempts to understand and develop a catalytic asymmetric approach to chiral alpha-amino acids

Attempts are made to build a bridge between asymmetric catalysis and enzymatic reactions by mechanistic investigations and the development of a catalytic and enantioselective approach to amination of alpha-keto esters by primary amines catalyzed by chiral Lewis acids as a model for transamination enzymes. Different Lewis acids can catalyze the half-transamination of alpha-keto esters using primary amine nitrogen sources such as pyridoxamine and 4-picolylamine. The mechanistic studies of the Lewis-acid catalyzed half-transamination using deuterium-labelled compounds show the incorporation of deuterium atoms in several positions of the alpha-amino acid derivative, indicating that the enol of the alpha-keto ester plays an important role along the reaction path. The catalytic enantioselective reactions are dependent on the pKa-value of the solvent since enantioselectivities were only obtained in solvents with high pKa-values relative to methanol. However, stronger acidic conditions generally gave better yields, but poor enantioselectivities. A series of chiral Lewis acids were screened as catalysts for the enantioselective half-transamination reactions and moderate yields and enantioselectivities of up to 46% ee were obtained.

Some Got Away, but Others Didn't

A history of research projects undertaken in the group-ranging from mechanistic investigations to biomimetic chemistry to molecular devices and synthesis-is presented.

Recognition of α-amino acid derivatives by N,N′-dibenzylated S,S-(+)-tetrandrine

Complexation of free and N-acetylated alpha-amino acid anions (Gly, Ala, Phe) and some structurally related guests by a dicationic cyclophane-type N,N'-dibenzylated chiral derivative of a bisisoquinoline macrocyclic alkaloid S,S-(+)-tetrandrine (DBT) has been studied by (1)H-NMR titrations in D(2)O. In contrast to other macrocyclic hosts like cyclodextrins and calixarenes, DBT shows highest affinity and large enantioselectivity (K(S)/K(R) >/=10) toward smaller N-acetylalanine and binds larger phenylalanine derivatives more weakly and non-selectively. With 1,2,3,4-tetrahydroisoquinoline-3-carboxylate, a rigid analog of phenylalanine, binding again becomes enantioselective with K(S)/K(R)= 3.8. The binding specificity of DBT is rationalized on the basis of molecular mechanics calculations.

Asymmetric environments in encapsulation complexes

Symmetrical, self-assembled capsules capable of surrounding two guests offer a new approach to enantioselection through coencapsulation: when one guest is chiral, the space remaining is also chiral. This notion is explored within a cylindrical capsule. The dimensions of the capsule select appropriately sized combinations of guests, the shape of the capsule prevents tumbling of rigid molecules, and the chemical surface of the capsule orients polar functions within. Chiral carboxylic acids such as mandelic acid and alpha-Br-butyric acid are identified as promising compounds for this purpose, but diastereoselection is modest (<25% de).