Chiral recognition in cyclic alpha-hydroxy carbonyl compounds: a theoretical study

A theoretical study (DFT and MP2) of the self-association of homochiral (RR or SS) and heterochiral (RS or SR) dimers of three series of cyclic alpha-hydroxy-carbonyl derivatives has been carried out. The solvation effect on the parent derivative dimers has been explored, showing nonsignificant changes in the configurations preferred but altering in some cases the homo/heterochiral preference of the dimers. The results in the gas phase of the systems with different substituents show a preference for the heterochiral dimers. The energetic results have been analyzed with the NBO and AIM methodologies. Optical rotatory power calculations of the monomers and homochiral dimers show large variations of this parameter depending on the substituents and the complexation.     

Cyclization and catenation directed by molecular self-assembly

We report here that molecular self-assembly can effectively direct and enhance specific reaction pathways. Using perylene pi-pi stacking weak attractive forces, we succeeded in synthesizing perylene bisimide macrocyclic dimer and a concatenated dimer-dimer ring from dynamic self-assembly of monomeric bis-N,N'-(2-(2-(2-(2-thioacetylethoxy)ethoxy)ethoxy)ethyl)perylenetetracarboxylic diimide. The monocyclic ring closure and the dimer-dimer ring concatenation were accomplished through formation of disulfide bonds, which was readily triggered by air oxidization under basic deacetylation conditions. The perylene cyclic dimer and its concatenated tetramer were characterized using both structural methods (NMR, mass spectroscopy) and photophysical measurements (UV-vis spectroscopy). Kinetic analyses offer informative insights about reaction pathways and possible mechanisms, which lead to the formation of complex concatenated rings. Molecular dynamic behaviors of both the monocyclic dimer and the concatenated dimer-dimer ring were modeled with the NWChem molecular dynamics software module, which shows distinct stacking activities for the monocyclic dimer and the concatenated tetramer.     

Molecular self-assembly inhibition leads to basket-shaped cyclophane formation with chiral dynamics

Planar perylene derivatives form macrocyclic dimers and concatenated dimer-dimer rings under the action of molecular self-assembly. If this underpinning principle is true, highly twisted perylene derivatives should be more frustrated toward formation of multimeric cyclic compounds such as macrocyclic dimers and concatenated dimer-dimers because of perturbation resulting from intermolecular pi-pi stacking. Indeed, 1,6,7,12- tetraphenoxy-substituted perylene is highly twisted and undergoes unimolecular cyclization rather than bimolecular or multimolecular cyclization. The resulting monocyclic monomer exhibits interesting conformation switching from one chiral structure (left-handedness) to another chiral structure (right-handedness) at room temperature. NMR studies of conformational dynamics reveal that such configuration change between the two enantiomers can be frozen at low temperature (-45 degrees C). An activation enthalpy barrier of 13.4 +/- 0.5 kcal.mol-1 for twisting the perylene plane in order to convert from one enantiomer to the other has been found.     

Effect of chirality on the structural behaviour of hydrogen-bonded n-alkylammonium pyroglutamates in the crystalline and smectic state

A set of optically active and racemic n-alkylammonium pyroglutamates from dodecyl to octadecyl were synthesized and characterised. Their thermotropic polymorphism was investigated by polarizing optical microscopy, differential scanning calorimetry and dilatometry. Their structure in the crystalline and smectic state was analysed by X-ray diffraction. The hydrogen bonding of the molecules in the crystalline and smectic layers was examined by infrared spectroscopy. The chirality control over the supramolecular self-assembly of the molecules along with the homochiral and heterochiral architecture of the self-assembled dimers are briefly discussed.     

Enantioselective molecular recognition between beta-sheets

This communication asks whether homochiral or heterochiral interaction is preferred between enantiomeric beta-sheets and finds that homochiral pairing is strongly preferred. Interactions between beta-sheets occur widely among proteins through pairing of the hydrogen-bonding edges. Although the hydrogen-bonding edges of both l- and d-beta-sheets put forth the same pattern of hydrogen-bond donor and acceptor groups, the side chains point in opposite directions. Homochiral pairing of beta-sheets generates structures in which the pleats and side chains of adjacent beta-strands are parallel to each other, while heterochiral pairing of beta-sheets generates structures in which the pleats and side chains are antiparallel. To test which pairing is preferred, we have prepared and studied the interactions of beta-sheets 1a-d, which comprise all l-amino acids, and beta-sheets 2a-c, which comprise all d-amino acids. Previous studies in our laboratory have established that these compounds form well-defined dimers in organic solvents. In the current study, 1H NMR experiments establish that when the l-beta-sheets (1) are mixed with the enantiomeric d-beta-sheets (2), homochiral beta-sheet dimers predominate, and only small quantities of heterochiral beta-sheet dimers form. Ratios of homochiral and heterochiral dimers ranging from 95.8:4.2 to 98.5:1.5 are measured in CDCl3 at 253 K, which correspond to statistically corrected free-energy differences of 3.1-4.2 kcal/mol (0.6-0.8 kcal/mol per interacting residue). Possible explanations for the high enantioselectivity of molecular recognition between beta-sheets include favorable nonbonded contacts between the adjacent beta-strands of the homochiral beta-sheets and poor fit of the heterochiral beta-strands, which should twist in opposite directions.     

Folding versus self-assembling

Model foldable polymers with sequences of rigid hydrophobic chromophores and flexible hydrophilic tetra(ethylene glycol) were synthesized and used as a paradigm for studying molecular-folding and self-assembly phenomena. Our results demonstrate that intramolecular association or folding prevails over intermolecular interaction or self-assembling in the concentration region from 1 microM to 0.1 M. Importantly, folded polymeric nanostructures have absorption and fluorescence properties that are distinct from those of unfolded polymers or free monomers. We hypothesize that the origins of folding and self-assembly come from interactions between molecular units, and that the key parameter that regulates the on-and-off of such interactions is the distance R separating the two molecular units. Each molecular unit produces a characteristic force field, and when another molecular unit enters this field, the probability that the two units will interact increases significantly. A preliminary estimate of the radius of such a force field for the perylene tetracarboxylic diimide chromophore is about 90-120 A. As a result, phenomena associated with folding or self-assembly of molecular species are observed when these conditions are met in solution.     

Stability Enhancement of a Dimeric HER2-Specific Affibody Molecule through Sortase A-Catalyzed Head-to-Tail Cyclization

Natural backbone-cyclized proteins have an increased thermostability and resistance towards proteases, characteristics that have sparked interest in head-to-tail cyclization as a method to stability-enhance proteins used in diagnostics and therapeutic applications, for example. In this proof-of principle study, we have produced and investigated a head-to-tail cyclized and HER2-specific Z_HER2:342 Affibody dimer. The sortase A-mediated cyclization reaction is highly efficient (>95%) under optimized conditions, and renders a cyclic Z_HER3:342-dimer with an apparent melting temperature, T_m, of 68 °C, which is 3 °C higher than that of its linear counterpart. Circular dichroism spectra of the linear and cyclic dimers looked very similar in the far-UV range, both before and after thermal unfolding to 90 °C, which suggests that cyclization does not negatively impact the helicity or folding of the cyclic protein. The cyclic dimer had an apparent sub-nanomolar affinity (K_d ~750 pM) to the HER2-receptor, which is a ~150-fold reduction in affinity relative to the linear dimer (K_d ~5 pM), but the anti-HER2 Affibody dimer remained a high-affinity binder even after cyclization. No apparent difference in proteolytic stability was detected in an endopeptidase degradation assay for the cyclic and linear dimers. In contrast, in an exopeptidase degradation assay, the linear dimer was shown to be completely degraded after 5 min, while the cyclic dimer showed no detectable degradation even after 60 min. We further demonstrate that a site-specifically DyLight 594-labeled cyclic dimer shows specific binding to HER2-overexpressing cells. Taken together, the results presented here demonstrate that head-to-tail cyclization can be an effective strategy to increase the stability of an Affibody dimer.     

Symmetry Breaking Charge Transfer in DNA-Templated Perylene Dimer Aggregates

Molecular aggregates are of interest to a broad range of fields including light harvesting, organic optoelectronics, and nanoscale computing. In molecular aggregates, nonradiative decay pathways may emerge that were not present in the constituent molecules. Such nonradiative decay pathways may include singlet fission, excimer relaxation, and symmetry-breaking charge transfer. Singlet fission, sometimes referred to as excitation multiplication, is of great interest to the fields of energy conversion and quantum information. For example, endothermic singlet fission, which avoids energy loss, has been observed in covalently bound, linear perylene trimers and tetramers. In this work, the electronic structure and excited-state dynamics of dimers of a perylene derivative templated using DNA were investigated. Specifically, DNA Holliday junctions were used to template the aggregation of two perylene molecules covalently linked to a modified uracil nucleobase through an ethynyl group. The perylenes were templated in the form of monomer, transverse dimer, and adjacent dimer configurations. The electronic structure of the perylene monomers and dimers were characterized via steady-state absorption and fluorescence spectroscopy. Initial insights into their excited-state dynamics were gleaned from relative fluorescence intensity measurements, which indicated that a new nonradiative decay pathway emerges in the dimers. Femtosecond visible transient absorption spectroscopy was subsequently used to elucidate the excited-state dynamics. A new excited-state absorption feature grows in on the tens of picosecond timescale in the dimers, which is attributed to the formation of perylene anions and cations resulting from symmetry-breaking charge transfer. Given the close proximity required for symmetry-breaking charge transfer, the results shed promising light on the prospect of singlet fission in DNA-templated molecular aggregates.     

Chiral recognition in self-complexes of tetrahydroimidazo[4,5-d]imidazole derivatives: from dimers to heptamers

The chiral discrimination in the self-association of chiral 1,3a,4,6a-tetrahydroimidazo[4,5-d]imidazoles has been studied using density functional theory methods. Clusters from dimers to heptamers have been considered. The heterochiral dimers (RR:SS or SS:RR) are more stable than the homochiral ones (RR:RR or SS:SS) with energy differences up to 17.5 kJ/mol. Besides, in larger clusters the presence of two adjacent homochiral molecules impose an energetic penalty when compared to alternated chiral systems (RR:SS:RR:SS...). The differences in interaction energy within the dimers of the different derivatives have been analyzed based on the atomic energy partition carried out within the atoms in molecules framework. The mechanism of proton transfer in the homo- and heterochiral dimers shows large transition-state barriers except in those cases in which a third additional molecule is involved in the transfer. The optical rotatory power of several clusters of the parent compound have been calculated and rationalized based on the number of homochiral interactions and the number of monomers of each enantiomer within the complexes.     

Mechanism of the Asymmetric Autocatalytic Soai Reaction Studied by Density Functional Theory

The mechanism of the Soai reaction has been thoroughly investigated at the M05‐2X/6‐31G(d) level of theory, by considering ten energetically distinct paths. The study indicates the fully enantioselective catalytic cycle of the homochiral dimers to be the dominant mechanism. Two other catalytic cycles are shown to both be important for correct understanding of the Soai reaction. These are the catalytic cycle of the heterochiral dimer and the non‐enantioselective catalytic cycle of the homochiral dimers. The former has been proved to be not really competitive with the principal cycle, as required for the Soai reaction to manifest chiral amplification, whereas the latter, which is only slightly competitive with the principal one, nicely explains the experimental enantioselectivity observed in the reaction of 2‐methylpyrimidine‐5‐carbaldehyde. The study has also evidenced the inadequacy of the B3LYP functional for mechanistic investigations of the Soai reaction.     

Mechanistic study of the Soai autocatalytic reaction informed by kinetic analysis

Detailed kinetic studies of the Soai reaction affirm the basic mechanistic picture previously developed in kinetic, spectroscopic and molecular modelling studies, and also suggest that refinements to the proposed elementary reaction steps must be considered. The alkanol reaction product is driven strongly and without bias towards the formation of homochiral and heterochiral dimers. The reaction is catalyzed by only the homochiral dimers. Consideration of the kinetic profiles from reactions carried out with different initial dialkylzinc concentrations support a proposal for a tetrameric transition state, but further experimental work is required to delineate the nature of this species. The power of reaction calorimetry as a kinetic tool for discerning subtle effects of the shape of the kinetic profile is highlighted. The importance of combining kinetic evidence with spectroscopic and other characterization tools is emphasized.     

Self-organization of lactates in the gas phase

Chiral recognition and subsequent selective self-organisation into hydrogen-bonded n-mers is observed in supersonic methyl lactate expansions. The nu(OH) and nu(C=O)-vibrations are investigated by ragout-jet FTIR-spectroscopy and lead to the assignment of homo- and heterochiral clusters of at least three different cluster sizes. Whereas homo- and heterochiral dimers are formed in similar amounts in the racemic mixture, prominent absorptions due to different homochiral and heterochiral lactate trimers and tetramers indicate highly specific chiral self-recognition beyond molecular pairs. Chemical modification of the ester-group (methyl-, ethyl- and isopropyl-lactate) and argon admixture to the helium expansion contribute importantly to an understanding of the cluster spectra and topology.     

Metal-directed self-assembly of cavitand frameworks

The self-assembly between bidentate cavitand ligands and mono/dinuclear metal precursors to give cavitand frameworks has been explored. For this purpose, two new cavitands bearing AB and AC phenylpyridyl moieties at the upper rim have been synthesized. A series of self-assembled molecular dimers featuring fac-Re(CO)(3)Br as metal corners have been prepared and characterized. Two possible dimeric structures (C-shaped and S-shaped) are possible when AB cavitand 2 is used in the self-assembly reaction; only one is obtained in the case of AC cavitand 3. In addition, the self-assembly of AB-dibridged cavitand 2 with dinuclear Pd/Pt metal precursors 5a and 5b has been studied. At this level of complexity, the self-assembly can lead to more than one structure. Several different final structures have been envisioned and their formation analyzed in silico and in solution. Out of the three possible cyclic structures (dimer, trimer, and tetramer), only the entropically favored dimer 6a (6b) is formed, as predicted from molecular modeling and demonstrated by PGSE NMR experiments.     

Theoretical study of peptide model dimers. Homo versus heterochiral complexes

The study of possible chiral recognition of a series of peptide models (For-Gly-NH₂, For-Ala-NH₂ and four of their fluoro substituted derivatives) has been carried out by means of DFT calculations. Homo (L,L) and heterochiral (L,D) dimers formed by hydrogen bond (HB) complexation have been considered. Initially, the conformational preferences of the monomers have been calculated and used to generate all the possible homo and heterochiral dimers. The energetic results show that in most cases, the β monomers are the most stable while in the dimers, the γ–γ complexes show the strongest interaction energies. In three of the four chiral cases studied, a heterochiral dimer is the most stable one. In addition, the electron density and nuclear shielding of the complexes have been studied.     

Chiral J-aggregates of atropo-enantiomeric perylene bisimides and their self-sorting behavior

Herein we report on structural, morphological, and optical properties of homochiral and heterochiral J-aggregates that were created by nucleation-elongation assembly of atropo-enantiomerically pure and racemic perylene bisimides (PBIs), respectively. Our detailed studies with conformationally stable biphenoxy-bridged chiral PBIs by UV/Vis absorption, circular dichroism (CD) spectroscopy, and atomic force microscopy (AFM) revealed structurally as well as spectroscopically quite different kinds of J-aggregates for enantiomerically pure and racemic PBIs. AFM investigations showed that enantiopure PBIs form helical nanowires of unique diameter and large length-to-width ratio by self-recognition, while racemic PBIs provide irregular-sized particles by self-discrimination of the enantiomers at the stage of nucleation. Steady-state fluorescence spectroscopy studies revealed that the photoluminescence efficiency of homochiral J-aggregated nanowires (47±3%) is significantly higher than that of heterochiral J-aggregated particle-like aggregates (12±3%), which is explained in terms of highly ordered molecular stacking in one-dimensional nanowires of homochiral J-aggregates. Our present results demonstrate the high impact of homochirality on the construction of well-defined nanostructures with unique optical properties.     

Homo- and heterochiral alkylzinc fencholates: linear or nonlinear effects in dialkylzinc additions to benzaldehyde

Scalemic mixtures of chiral anisyl fenchols with different ortho-substituents (X) in the anisyl moieties [X = H (1), Me (2), SiMe3 (3) and tBu (4)] are employed as pre-catalysts in enantioselective additions of diethylzinc to benzaldehyde. While a remarkable asymmetric depletion is apparent for X = H and Me, a linear relationship between the enantiomeric purity of the chiral source and the product 1-phenylpropanol is observed for X = SiMe3 and tBu. X-ray single crystal analyses show that racemic methylzinc fencholates obtained from 1 (X = H) and 2 (X = Me) yield homochiral dimeric complexes, while for 3 (X = SiMe3) and 4 (X = tBu) the heterochiral dimeric alkylzinc structures are formed. The enantiopure fenchols 1-4 all yield homochiral dimeric methylzinc complexes. Computed relative energies of homo- and heterochiral fencholate dimers with X = H and Me reveal an intrinsic preference for the formation of the homochiral dimers, consistent with the observed negative NLE. In contrast, similar stabilities are computed for homo- and heterochiral complexes of ligands 3 (X = SiMe3) and 4 (X = tBu), in agreement with the absence of a nonlinear effect for bulky ortho-subsituents.     

Enantioselective cyclization of racemic supramolecular polymers

Homochiral hydrogen-bonded cyclic assemblies are formed in dilute solutions of racemic supramolecular polymers based on the quadruple hydrogen bonding 2-ureido-4[1H]-pyrimidinone unit, as observed by 1H NMR and SEC experiments. Preorganization of the monomers and the combined binding strength of the eight hydrogen bonds result in a very high stability of the cyclic aggregates with pronounced selectivity between homochiral and heterochiral cyclic species, usually only observed in crystalline or liquid crystalline phases.     

Effects of the alternating backbone configuration on the secondary structure and self-assembly of beta-peptides

Heterochiral homo-oligomers with alternating backbone configurations were constructed by using the different enantiomers of the cis- and trans-2-aminocyclopentanecarboxylic acid (ACPC) monomers. Molecular modeling and the spectroscopic techniques (NMR, ECD, and VCD) unequivocally proved that the alternating heterochiral cis-ACPC sequences form an H10/12 helix, where extra stabilization can be achieved via the cyclic side chains. The ECD and TEM measurements, together with molecular modeling, revealed that the alternating heterochiral trans-ACPC oligomers tend to attain a polar-strand secondary structure in solution, which can self-assemble into nanostructured fibrils. The observations indicate that coverage of all the possible secondary structures (various helix types and strand-mimicking conformations) can be attained with the help of cyclic beta-amino acid diastereomers. A relationship has been established between the backbone chirality pattern and the prevailing secondary structure, which underlines the role of stereochemical control in the beta-peptide secondary structure design and may contribute to future biological applications.     

Vibrational Spectroscopy of Homo- and Heterochiral Amino Acid Dimers: Conformational Landscapes

The homo- and heterochiral protonated dimers of asparagine with serine and with valine were investigated using infrared multiple-photon dissociation (IRMPD) spectroscopy. Extensive quantum-chemical calculations were used in a three-tiered strategy to screen the conformational spaces of all four dimer species. The resulting binary structures were further grouped into five different types based on their intermolecular binding topologies and subunit configurations. For each dimer species, there are eight to fourteen final conformational geometries within a 10 kJ mol⁻¹ window of the global minimum structure for each species. The comparison between the experimental IRMPD spectra and the simulated harmonic IR features allowed us to clearly identify the types of structures responsible for the observation. The monomeric subunits of the observed homo- and heterochiral dimers are compared to the corresponding protonated/neutral amino acid monomers observed experimentally in previous IRMDP/rotational spectroscopic studies. Possible chirality and kinetic influences on the experimental IRMPD spectra are discussed.     

A reverse turn structure induced by a D,L-alpha-aminoxy acid dimer

Our previous work revealed that two adjacent D-alpha-aminoxy acids could form two homochiral N-O turns, with the backbone folding into an extended helical structure (1.8(8)-helix). Here, we report the conformational studies of linear peptides 3-6, which contain a D,L-alpha-aminoxy acid dimer segment. The NMR and X-ray analysis of 3 showed that it folded into a loop conformation with two heterochiral N-O turns. This loop segment can be used to constrain tetrapeptides 4 and 6 to form a reverse turn structure. (1)H NMR dilution studies, DMSO-d6 addition studies, and 2D-NOESY data indicated that tetrapeptides 4 and 6 folded into reverse turn conformations featured by a head-to-tail 16-membered-ring intramolecular hydrogen bond. In contrast, tetrapeptide 5 with L-Ala instead of Gly or D-Ala as the N-terminal amino acid could not form the desired reverse turn structure for steric reasons. Quantum mechanics calculations showed that model pentamide 7, with the same substitution pattern of 4, adopted a novel reverse turn conformation featuring two heterochiral N-O turns (each of an 8-membered ring hydrogen bond), a cross-strand 16-membered ring hydrogen bond, and a 7-membered ring gamma-turn.