Solid-state molecular folding and supramolecular structures of triptycene-derived secondary dicarboxamides

The synthesis and X-ray crystal structures of triptycene-derived secondary dicarboxamides 1 and 4-7 and reference compounds 2, 3, and 8 are reported. For comparison, molecular conformations of 1-8 in the gas phase and those of 1 and 3-6 in CD2Cl2 investigated by AM1 modeling and 1H NMR spectroscopy, respectively, are also included. The solid-state conformations of 1 and 5-8 are folded and compact, resulting from the cooperative effects of intramolecular amide-amide hydrogen bonding and edge-to-face arene-arene interactions between the triptycene and the N-acetylsulfanilyl groups. The sulfonyl ester groups are also essential in the folding of 1 and 5-8 and function as structural turn units. In contrast, the conformations of 2-4 are unfolded due to the lack of one of these three essentials. The extended triptycene ring systems in 6 and 7 provide an arene-arene contact mode that is different from that for 1 and 5. While AM1 calculations suggest that the two possible arene-arene contact modes in 6 and 7 have similar conformational energies, the one observed in the solid state is also favored in solutions. To achieve a more regular shape for compact crystal packing, the bulky triptycene groups tend to pack in pairs. As a result, the intermolecular amide-amide hydrogen bonding is perturbed and modified with the participation of either the sulfonyl groups or the methanol solvent molecules, leading to various hydrogen-bonding motifs for these triptycene diamides.     

Drug-dendrimer supramolecular complexation studied from molecular dynamics simulations and NMR spectroscopy

Fully atomistic molecular dynamics (MD) simulations and NMR spectroscopy were employed to get insights about the molecular details of drug-dendrimer supramolecular association phenomena, using piroxicam (PRX) and the third generation poly(amido amine) (PAMAM-G3) dendrimer as model systems. Theoretical results concerning the complex stoichiometry suggest that PRX forms drug-dendrimer complexes of the type 24:1 at pH 7.0. This result was validated with the experimental quantities obtained from aqueous solubility profiles, which led to an empiric stoichiometry of 23:1 for the PRX:PAMAM-G3 system. The predicted binding mode between PRX and PAMAM-G3 accounts for the preferred encapsulation of the drug inside dendrimer cavities, which is mainly driven by van der Waals and hydrogen bonding interactions, and to a lesser extent, for the external association of the guest through electrostatic contacts with the positively charged amino groups of PAMAM periphery. The binding mode obtained from MD simulations was confirmed with 2D-NOESY experiments, which evidence the preferred internal complexation of PRX with PAMAM-G3. The predominance of internal encapsulation over external contacts in the PRX:PAMAM-G3 system differs from the general behaviour expected for acidic anionic guests, for which external electrostatic interactions with the positively charged PAMAM surface have been postulated as the most relevant factor for drug association.     

Crystal and molecular structures of ionophore-siderophore host-guest supramolecular assemblies relevant to molecular recognition

Ionophore-siderophore host-guest assemblies composed of 18-crown-6 and ferrioxamine B, benzo-18-crown-6 and ferrioxamine B, and cis-syn-cis-dicyclohexano-18-crown-6 and ferrioxamine B were successfully crystallized, and their structures were determined by single-crystal X-ray diffraction. All three crystal lattices also include solvated Mg(II) and perchlorate ions. The ionophore-siderophore host-guest assembly is noncovalently held together by a hydrogen bonding interaction between the pendant protonated amine in the second coordination sphere of ferrioxamine B and the hydrogen bond acceptor oxygen atoms in the crown ether. The crystals of 18-crown-6:ferrioxamine B host-guest assembly are monoclinic, with space group P2(1)/c, and four molecules per unit cell with dimensions a = 19.8327(11) A, b = 20.4111(11) A, c = 15.1698(8) A, and beta = 96.435(1) degrees. The crystals of benzo-18-crown-6:ferrioxamine B host-guest assembly are triclinic, with space group P(-)1, and two molecules per unit cell with dimensions a = 11.1747(10) A, b = 16.0580(15) A, c = 18.4175(17) A, alpha = 80.469(3) degrees, beta = 81.481(3) degrees and gamma = 70.212(2) degrees. The crystals of cis-syn-cis-dicyclohexano-18-crown-6:ferrioxamine B host-guest assembly are monoclinic, with space group P2(1)/c, and four molecules per unit cell with dimensions a = 20.1473(13) A, b = 21.5778(15) A, c = 14.8013(10) A, and beta = 94.586(2) degrees. The crystal structures of all three host-guest assemblies contain a racemic mixture of Lambda-N-cis, cis and Delta-N-cis, cis coordination isomers of ferrioxamine B. The crystal structures indicate that the steric rigidity of the benzo-18-crown-6 and cis-syn-cis-dicyclohexano-18-crown-6 cavity has a pronounced effect on the conformation of the crown ring and ultimately on the hydrogen bonding interactions between the crown ethers and ferrioxamine B. The structural parameters and the conformational features of the ferrioxamine B guests compare very well with each other and with those of the ferrioxamine B structure obtained in the absence of a host. Structural features relevant to siderophore molecular recognition are discussed.     

Quantitative chirality/enantioselectivity relations in large random supramolecular structures

We study the relationship between shape and enantioselectivity, employing quantitative geometric chirality measurements. The model we use comprises of the boundary surfaces of two-dimensional (2D) chiral, large, random selectors (diffusion limited aggregates), interacting with homologous series of small 2D-chiral S-shaped probes (the selectands). We show how the enantioselectivity of the selectors depends on the chirality of the selectands and report the following findings: I) The enantioselectivity of a chiral selector can switch preference from the "right" to the "left" enantiomer within a homologous series of selectands. II) At this switch point the chiral selector is functionally achiral. III) Within a homologous series of chiral selectands, there is a "resonance of recognition", namely, the classical key-lock concept is replaced by a picture of various degrees of recognition. IV) The degree of enantioselectivity and the switch in handedness preference are the outcome of a complex interplay between the details of the specific geometry of the selector and the selectand, and the global shape parameter of chirality measure. V) It is shown that isochiral selectands, namely selectands of the same chirality value, may be recognized differently by a chiral selector. VI) It is proposed that a more realistic way to treat the issue of minimal points needed for chiral interaction is resolution based. VII) It is shown how to attach handedness to purely random objects.     

Labile supramolecular structures and their dynamics in associated liquids based on NMR data

The results of experimental research into structuration of associated pure liquids and electrolyte solutions in these liquids by NMR spectroscopy are summarized. The influence of self-organization on the rate and relay mechanism of proton mobility, chemical kinetics, and thermodynamics is analyzed. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 4, pp. 577–601, April, 2006.     

Six polycyclic pyrimidoazepine derivatives: syntheses,molecular structures and supramolecular assembly

A versatile synthetic method has been developed for the formation of variously substituted polycyclic pyrimidoazepine derivatives, formed by nucleophilic substitution reactions on the corresponding chloro‐substituted compounds; the reactions can be promoted either by conventional heating in basic solutions or by microwave heating in solvent‐free systems. Thus, (6RS)‐6,11‐dimethyl‐3,5,6,11‐tetrahydro‐4H‐benzo[b]pyrimido[5,4‐f]azepin‐4‐one, C₁₄H₁₅N₃O, (I), was isolated from a solution containing (6RS)‐4‐chloro‐8‐hydroxy‐6,11‐dimethyl‐6,11‐dihydro‐5H‐benzo[b]pyrimido[5,4‐f]azepine and benzene‐1,2‐diamine; (6RS)‐4‐butoxy‐6,11‐dimethyl‐6,11‐dihydro‐5H‐benzo[b]pyrimido[5,4‐f]azepin‐8‐ol, C₁₈H₂₃N₃O₂, (II), was formed by reaction of the corresponding 6‐chloro compound with butanol, and (RS)‐4‐dimethylamino‐6,11‐dimethyl‐6,11‐dihydro‐5H‐benzo[b]pyrimido[5,4‐f]azepin‐8‐ol, C₁₆H₂₀N₄O, (III), was formed by reaction of the chloro analogue with alkaline dimethylformamide. (6RS)‐N‐Benzyl‐8‐methoxy‐6,11‐dimethyl‐6,11‐dihydro‐5H‐benzo[b]pyrimido[5,4‐f]azepin‐4‐amine, C₂₂H₂₄N₄O, (IV), (6RS)‐N‐benzyl‐6‐methyl‐1,2,6,7‐tetrahydropyrimido[5′,4′:6,7]azepino[3,2,1‐hi]indol‐8‐amine, C₂₂H₂₂N₄, (V), and (7RS)‐N‐benzyl‐7‐methyl‐2,3,7,8‐tetrahydro‐1H‐pyrimido[5′,4′:6,7]azepino[3,2,1‐ij]quinolin‐9‐amine, C₂₃H₂₄N₄, (VI), were all formed by reaction of the corresponding chloro compounds with benzylamine under microwave irradiation. In each of compounds (I)–(IV) and (VI), the azepine ring adopts a conformation close to the boat form, with the C‐methyl group in a quasi‐equatorial site, whereas the corresponding ring in (V) adopts a conformation intermediate between the twist‐boat and twist‐chair forms, with the C‐methyl group in a quasi‐axial site. No two of the structures of (I)–(VI) exhibit the same range of intermolecular hydrogen bonds: different types of sheet are formed in each of (I), (II), (V) and (VI), and different types of chain in each of (III) and (IV).     

Coordination supramolecular structures

Supramolecular coordination ensembles with d-metal ions directly incorporated into their structures are the subject of the present review. Diversity of such structures considerably exceeds that of purely organic supramolecules due to inclusion of additional polyvalent metal atoms (totally sixty) with diverse coordination geometry. Such metal-containing constructions are generated by self-assembling and (or) by templating, as 2D and 3D geometric figures (polygons and polyhedra) and “furniture” constructions (ladders, racks, grids) together with helicates, interwoven species and metallodendrimers as combinations of 1D coordination compounds. Besides, is presented a numerous of coordination polymers and supramolecular crystal lattices as infinite structures.     

Refinement of NMR structures using implicit solvent and advanced sampling techniques

NMR biomolecular structure calculations exploit simulated annealing methods for conformational sampling and require a relatively high level of redundancy in the experimental restraints to determine quality three-dimensional structures. Recent advances in generalized Born (GB) implicit solvent models should make it possible to combine information from both experimental measurements and accurate empirical force fields to improve the quality of NMR-derived structures. In this paper, we study the influence of implicit solvent on the refinement of protein NMR structures and identify an optimal protocol of utilizing these improved force fields. To do so, we carry out structure refinement experiments for model proteins with published NMR structures using full NMR restraints and subsets of them. We also investigate the application of advanced sampling techniques to NMR structure refinement. Similar to the observations of Xia et al. (J.Biomol. NMR 2002, 22, 317-331), we find that the impact of implicit solvent is rather small when there is a sufficient number of experimental restraints (such as in the final stage of NMR structure determination), whether implicit solvent is used throughout the calculation or only in the final refinement step. The application of advanced sampling techniques also seems to have minimal impact in this case. However, when the experimental data are limited, we demonstrate that refinement with implicit solvent can substantially improve the quality of the structures. In particular, when combined with an advanced sampling technique, the replica exchange (REX) method, near-native structures can be rapidly moved toward the native basin. The REX method provides both enhanced sampling and automatic selection of the most native-like (lowest energy) structures. An optimal protocol based on our studies first generates an ensemble of initial structures that maximally satisfy the available experimental data with conventional NMR software using a simplified force field and then refines these structures with implicit solvent using the REX method. We systematically examine the reliability and efficacy of this protocol using four proteins of various sizes ranging from the 56-residue B1 domain of Streptococcal protein G to the 370-residue Maltose-binding protein. Significant improvement in the structures was observed in all cases when refinement was based on low-redundancy restraint data. The proposed protocol is anticipated to be particularly useful in early stages of NMR structure determination where a reliable estimate of the native fold from limited data can significantly expedite the overall process. This refinement procedure is also expected to be useful when redundant experimental data are not readily available, such as for large multidomain biomolecules and in solid-state NMR structure determination.     

Dihydrooxazolones and dihydroimidazolones derived from acylglycines: syntheses,molecular structures and supramolecular assembly

Syntheses and structures are described for some alkylidene‐substituted dihydrooxazolones and dihydroimidazoles derived from simple acylglycines. A second, triclinic, polymorph of 4‐benzylidene‐2‐(4‐methylphenyl)‐1,3‐oxazol‐5(4H)‐one, C₁₇H₁₃NO₂, (I), has been identified and the structure of 2‐methyl‐4‐[(thiophen‐2‐yl)methylidene]‐1,3‐oxazol‐5(4H)‐one, C₉H₇NO₂S, (II), has been rerefined taking into account the orientational disorder of the thienyl group in each of the two independent molecules. The reactions of phenylhydrazine with 2‐phenyl‐4‐[(thiophen‐2‐yl)methylidene]‐1,3‐oxazol‐5(4H)‐one or 2‐(4‐methylphenyl)‐4‐[(thiophen‐2‐yl)methylidene]‐1,3‐oxazol‐5(4H)‐one yield, respectively, 3‐anilino‐2‐phenyl‐5‐[(thiophen‐2‐yl)methylidene]‐3,5‐dihydro‐4H‐imidazol‐4‐one, C₁₀H₁₅N₃OS, (III), and 3‐anilino‐2‐(4‐methylphenyl)‐5‐[(thiophen‐2‐yl)methylidene]‐3,5‐dihydro‐4H‐imidazol‐4‐one, C₂₁H₁₇N₃OS, (IV), which both exhibit orientational disorder in their thienyl groups. The reactions of 2‐phenyl‐4‐[(thiophen‐2‐yl)methylidene]‐1,3‐oxazol‐5(4H)‐one with hydrazine hydrate or with water yield, respectively, N‐[3‐hydrazinyl‐3‐oxo‐1‐(thiophen‐2‐yl)prop‐1‐en‐2‐yl]benzamide and 2‐(benzoylamino)‐3‐(thiophen‐2‐yl)prop‐2‐enoic acid, which in turn react, respectively, with thiophene‐2‐carbaldehyde to form 2‐phenyl‐5‐[(thiophen‐2‐yl)methylidene]‐3‐{[(E)‐(thiophen‐2‐yl)methylidene]amino}‐3,5‐dihydro‐4H‐imidazol‐4‐one, C₁₉H₁₃N₃OS₂, (V), which exhibits orientational disorder in only one of its thienyl groups, and with methanol to give methyl (2Z)‐2‐(benzoylamino)‐3‐(thiophen‐2‐yl)prop‐2‐enoate, C₁₅H₁₃NO₃S, (VI). There are no direction‐specific intermolecular interactions in the crystal structure of the triclinic polymorph of (I), but the molecules of (II) are linked by two independent C—H...O hydrogen bonds to form C₂²(14) chains. Compounds (III) and (IV) both form centrosymmetric R₂²(10) dimers built from N—H...O hydrogen bonds, while compound (V) forms a centrosymmetric R₂²(10) dimer built from C—H...O hydrogen bonds. In the structure of compound (VI), a combination of N—H...O and C—H...π(arene) hydrogen bonds links the molecules into sheets. Comparisons are made with some similar compounds.     

Solution structure of papain as studied by molecular mechanics and molecular dynamics techniques

In this paper, we report the molecular mechanics and molecular dynamics studies of the hydration of papain using the AMBER and CHARMm programs. We studied papain in an environment with minimal hydration involving only the X-ray waters and also in the hydrated environment by adding an extra 9 Å layer of water around the residues. The effect of nonbond cutoff was studied by performing minimizations with 8 Å and 15 Å nonbond cutoffs using the program AMBER. Two different solvent models—a constant dielectric and a distance-dependent dielectric—were considered. The AMBER-minimized structure and the average structure obtained from the CHARMm simulations for papain solvated with X-ray waters are presented and compared with the X-ray crystal structure results. Results of a similar comparison of the hydrated structures were also presented. The calculated root mean square deviation between the minimized structure and the X-ray structure is smaller for the hydrated system than for the system hydrated with only the X-ray waters. Results of the molecular mechanics and molecular dynamics simulations were presented for the various regions of papain. The hydration of the active site of papain and the effect of hydration on the torsional motion of the active site residues are presented. © 1996 by John Wiley & Sons, Inc.     

Protein supramolecular systems for molecular information processing

Several protein supramolecular systems have been assembled for processing molecular information through intramolecular transfer of conformational change on the model of the biomolecular information network in biological systems. Intermolecular conformation transfer systems consist of calmodulin and phosphodiesterase. Calmodulin selectively binds calcium ions with a resulting change in its conformation that causes phosphodiesterase to change its conformation on being activated. Intermolecular transfer of conformational change has been successfully performed in response to the calcium ion by three different supramolecular systems: (1) calmodulin covalently conjugated with phosphodiesterase and immobilized on solid matrix; (2) lipid-conjugated calmodulin of monolayer on the water surface and coupled with phosphodiesterase in solution and (3) genetically engineered calmodulin self-assembled on a solid matrix and coupled with phosphodiesterase in solution. These supramolecular systems were found to be responsive to such environmental conditions as calcium ion concentration in the reversible alteration of enzyme activity.     

Solution structures of cyclosporin a and its complex with dysprosium(III) in SDS micelles: NMR and molecular dynamics studies

Cyclosporin A (CsA) is a cyclic naturally occurring peptide used to prevent graft rejection in organ transplantations. Its immunosuppressive activity is due to the formation of a complex with cyclophilin A (Cyp), in which the cis 9MeLeu-10MeLeu amide bond of CsA assumes a trans conformation. The mechanism of the conformational inversion has not been delineated, but it has been postulated that metal ions binding induces a conformational change that enables CsA to bind Cyp. In this work, we solved the structures of CsA in sodium dodecyl sulfate (SDS) micelles (which enhance its solubility and mimic the hydrophobic environment clinically used for drug delivery) and its complex with Dy(III) ion, whose coordination chemistry is frequently used to reproduce the effect of Ca(II). The paramagnetic properties of Dy(III) allowed us to build up a structure using proton relaxation enhancements, which remains stable in a MD simulation in the micelle environment.     

Spin-labelled cyclodextrins as hosts for large supramolecular assemblies

EPR spectroscopy was used to study formation of inclusion complexes of monofunctionalised spin-labelled beta-cyclodextrins; this method is very sensitive to the interactions of cyclodextrins with large guest molecules.     

Dioxotetraamines derived molecular and supramolecular devices

Various molecular and supramolecular molecular devices (i.e., pH-based fluorescent sensors for transition metal ions and multi-compartmental systems for the intra-compartments translocation of metal ions with external pH stimulus) designed suitably by using linear and cyclic dioxotetraamines as chelating unit have been reviewed. The various aspects such as effect due to change of pH and of metal ions are narrated.     

Synthesis,molecular and supramolecular structures,electrochemistry and magnetic properties of two macrocyclic dicopper(II) complexes: Microporous supramolecular assembly

Synthesis, molecular and supramolecular structures, electrochemistry and magnetic properties of two diphenoxo-bridged dicopper(II) compounds [Cu^II₂L(H₂O)(ClO₄)]·ClO₄·2H₂O (1) and [Cu^II₂L(N₃)₂]·2H₂O (2) derived from a tetraimino diphenolate macrocyclic ligand H₂L, obtained on [2+2] condensation of 4-methyl-2,6-diformylphenol and 2,2′-dimethyl-1,3-diaminopropane, are presented. Supramolecular structure of both 1 and 2 are three-dimensional resulting from hydrogen bonding interactions. Interestingly, the 3-D self-assembly of 2 contains micropores having the dimension of 0.35 nm. Electrochemical analyses reveal that both of these compounds exhibit two-step couples in the reduction window. Variable-temperature (2–300 K) magnetic susceptibilities measurements of the two compounds reveal that the metal centers in both of the complexes are coupled by strong antiferromagnetic interactions with J values (H = ?JS₁·S₂) ?776 and ?836 cm^?1 for 1 and 2, respectively.     

Macromolecules with specific constitution and supramolecular structures

Segmented triblock and multiblock copolymers consisting of highly flexible polydisperse segments and molecularly uniform segments of well defined architecture capable of either the formation of a mesophase, chainfolded crystallites or double-helical metal complexes have been synthesized; the bulk superstructure as well as the physical and material properties correlated with the primary structure: block copolymers with liquid crystalline segments formed microphase separated systems, and the phase behaviour depended on the constitutional composition. Multiblock copolymers with symmetrically chain-folded polyurethane hard segments and associative groups in the chain fold led to specially shaped lamellar superstructures. Block copolymers with bipyridine containing segments gave tetracoordinated and double-helical copper(I) complexes which segregated resulting in supramolecular polymer systems.     

Solution structures by NMR of a novel antifungal drug: Petriellin A

Petriellin A is a novel cyclic depsipeptide antifungal compound consisting of nine l-configured residues, one d-phenyllactic acid (PhLac) and three unknown chiral centres: two N-methyl-threonines (MeThr1 & MeThr2) and one N-methyl-isoleucine (MeIle). NMR experiments including 2D ROESY, NOESY along with structural and energy calculations predicted that the unknown chiral centres were all l-configured, which was later verified chemically. Simulated annealing, dynamics calculations and minimisation processes showed Petriellin A to have a folded "C-shaped" structure.