Alternative strategy for adjusting the association specificity of hydrogen-bonded duplexes

A strategy for creating new association specificity of hydrogen-bonded duplexes by varying the spacings between neighboring hydrogen bonds is described. Incorporation of naphthalene-based residues has provided oligoamide strands that pair into duplexes sharing the same H-bonding sequences (e.g., DDAA) but differing in the spacings between their intermolecular hydrogen bonds, leading to homo- or heteroduplexes. The ability to manipulate association-specificity as demonstrated by this work may be extended to other multiple hydrogen bonded systems, thereby further enhancing the diversity of multiple hydrogen-bonded association units for constructing supramolecular structures.     

Self-assembly of dipeptidyl ureas: a new class of hydrogen-bonded molecular duplexes

The dipeptidyl urea 1 composed of two dipeptide chains bearing the C-terminal pyridyl moiety (-L-Ala-L-Pro-NHPy) was prepared. Two molecules of 1 are revealed to be held together by six intermolecular hydrogen bonds to form a hydrogen-bonded duplex by the single-crystal X-ray structure determination. Proton magnetic resonance nuclear Overhauser effect (NOE) study indicates the hydrogen-bonded duplex even in solution. Furthermore, a shuttle-like molecular dynamics based on recombination of the hydrogen bonds was observed. The dipeptidyl urea composed of two dipeptide chains bearing the C-terminal pyrenyl moiety (-L-Ala-L-Pro-NHCH(2)Pyr) exhibited both monomer and eximer emissions in the fluorescence spectra, supporting the formation of a duplex. A combination of the C-terminal amide NH function in each side and the designed sequence of hydrogen-bonding sites are considered to be a crucial factor for the duplex formation.     

Stability of a new class of unnatural hydrogen-bonded molecular duplexes: A computational study

The stability of a series of hydrogen-bonded duplexes was studied using molecular mechanics method with a modified AMBER GAFF force field, in which the original atomic charges were replaced by ones that are more appropriate for non-polar solvents. The free energy change of dimerization was calculated in vacuo and good agreement with experimental data was found. It is also shown that the stability of these duplexes increases linearly with the number of hydrogen bonds, in agreement with experimental data.     

Self-complementary quadruply hydrogen-bonded duplexes based on imide and urea units

The quadruply hydrogen-bonded duplexes based on an imide-urea structure preorganized by three-center hydrogen bonds were found to associate via bifurcated hydrogen bonds. (1)H NMR dilution experiments revealed the high stability of the homodimer in apolar solvent (K(dim) > 10(5) M(-1) in CDCl(3)) and enhancement of association ability due to electron-withdrawing substituent effects. The ready synthetic availability and adjustable association affinity via electronic effects may render these association units potentially applicable in constructing supramolecular architectures.     

Electrochemically switchable hydrogen-bonded molecular shuttles

A series of [2]rotaxanes containing succinamide and naphthalimide hydrogen-bonding stations for a benzylic amide macrocycle is described. Electrochemical reduction and oxidation of the naphthalimide group alters its ability to form hydrogen bonds to the macrocycle to such a degree that redox processes can be used to switch the relative macrocycle-binding affinities of the two stations in a rotaxane by over 8 orders of magnitude. The structure of the neutral [2]rotaxane in solution is established by (1)H NMR spectroscopy and shows that the macrocycle exhibits remarkable positional integrity for the succinamide station in a variety of solvents. Cyclic voltammetry experiments allow the simultaneous stimulation and observation of a redox-induced dynamic process in the rotaxane which is both reversible and cyclable. Model compounds in which various conformational and co-conformational changes are prohibited demonstrate unequivocally that the redox response is the result of shuttling of the macrocycle between the two stations. At room temperature in tetrahydrofuran the electrochemically induced movement of the macrocycle between the two stations takes approximately 50 micros.     

Electrostatic molecular potentials in hydrogen-bonded systems

A study is made of the modifications of the electrostatic molecular potential brought about by hydrogen bonding both in the hydrogen-bond region itself and in the external regions of the proton-acceptor and proton-donor molecules. Systems up to four successive units in a chain of donor-acceptors are considered. The possibility of obtaining a satisfactory picture of the global potential by a simple superposition of the potentials of the individual units is evaluated.     

Dynamic combinatorial libraries based on hydrogen-bonded molecular boxes

This article describes two different types of dynamic combinatorial libraries of host and guest molecules. The first part of this article describes the encapsulation of alizarin trimer 2a3 by dynamic mixtures of up to twenty different self-assembled molecular receptors together with the amplification and selection of the best binder. Receptors (1a-d)3.(DEB)6 are formed by the self-assembly of six diethyl barbiturate (DEB) and calix[4]arene dimelamine derivatives 1a-d by using hydrogen bonds. The largest amplification factor (2.8) for a host assembly (1a3.(DEB)6) was observed after the addition of 2a to four-component library 1a(n).1b(3-n).(DEB)6 (n=0-3). Addition of 2a to twenty-component library 1a(n).1b(m).1c(o).1d(3-(n+m+o)).(DEB)6 (n, m, o=0-3; (n+m+o)相似文献   

Computational studies of the photophysics of hydrogen-bonded molecular systems

The role of electron- and proton-transfer processes in the photophysics of hydrogen-bonded molecular systems has been investigated with ab initio electronic-structure calculations. Adopting indole, pyridine, and ammonia as molecular building blocks, we discuss generic mechanisms of the photophysics of isolated aromatic chromophores (indole), complexes of pi systems with solvent molecules (indole-ammonia, pyridine-ammonia), hydrogen-bonded aromatic pairs (indole-pyridine), and intramolecularly hydrogen-bonded pi systems (7-(2'-pyridyl)indole). The reaction mechanisms are discussed in terms of excited-state minimum-energy paths, conical intersections, and the properties of frontier orbitals. A common feature of the photochemistry of the various systems is the electron-driven proton-transfer (EDPT) mechanism: highly polar charge-transfer states of 1pipi*, 1npi*, or 1pisigma* character drive the proton transfer, which leads, in most cases, to a conical intersection of the S1 and S0 surfaces and thus ultrafast internal conversion. In intramolecularly hydrogen-bonded aromatic systems, out-of-plane torsion is additionally needed for barrierless access to the S1-S0 conical intersection. The EDPT process plays an essential role in diverse photophysical phenomena, such as fluorescence quenching in protic solvents, the function of organic photostabilizers, and the photostability of biological molecules.     

First zipper-featured molecular duplexes driven by cooperative donor-acceptor interaction

[structure: see text] The first class of zipper-shaped artificial duplexes, which are driven by multiple donor-acceptor interactions between electron-rich 1,5-dioxynaphthalene or 1,4-dioxybenzene and electron-deficient pyromellitic dimide units, have been studied in organic media by (1)H NMR, UV-vis, and vapor pressure osmometry. (1)H NMR binding investigations reveal substantial cooperativity of the donor-acceptor interaction in the duplexes.     

Long hydrogen-bonded rod of molecular oxide: a hexatantalate tetramer

A tetra-n-butylammonium (TBA) salt of [H(4.5)(Ta(6)O(19))](3.5-) was synthesized by reacting hydrous tantalum oxide with TBAOH. X-ray structural analysis of TBA(3.5)[H(4.5)(Ta(6)O(19))]·2THF·5.5H(2)O (THF = tetrahydrofuran) revealed that this compound consists of a hydrogen-bonded, rod-shaped tetramer of hexatantalate that is almost 30 ? long together with TBA cations and solvent molecules of crystallization [a = 20.6354(5) ?, b = 25.5951(7) ?, c = 37.2058(8) ?, α = 77.092(1)°, β = 86.177(1)°, γ = 88.683(1)°, V = 19110.9(8) ?(3), Z = 8, and space group P ?1]. (1)H NMR spectra showed that this tetrameric structure is maintained in solution.     

Supramolecular Chirality: Chiral hydrogen-bonded supermolecules from achiral molecular components

Chiral supermolecules may be obtained from suitable achiral molecular constituents associated through a dissymmetrizing interaction mode. This is the case for the supermolecules I–IV formed by hydrogen-bonding association between the achiral complementary components 1a , b and 2a , b , c . The crystal structures of the supermolecular pairs I–III and of the homochiral aggregate of two ternary supermolecules IV have been determined. The structural data are discussed.     

From molecular to macroscopic engineering: shaping hydrogen-bonded organic nanomaterials

The self‐assembly and self‐organization behavior of chromophoric acetylenic scaffolds bearing 2,6‐bis(acetylamino)pyridine ( 1 , 2 ) or uracyl‐type ( 3 – 9 ) terminal groups has been investigated by photophysical and microscopic methods. Systematic absorption and luminescence studies show that 1 and 2 , thanks to a combination of solvophilic/solvophobic forces and π–π stacking interactions, undergo self‐organization in apolar solvents (i.e., cyclohexane) and form spherical nanoparticles, as evidenced by wide‐field optical microscopy, TEM, and AFM analysis. For the longer molecular module, 2 , a more uniform size distribution is found (80–200 nm) compared to 1 (20–1000 nm). Temperature scans in the range 283–353 K show that the self‐organized nanoparticles are reversibly formed and destroyed, being stable at lower temperatures. Molecular modules 1 and 2 were then thoroughly mixed with the complementary triply hydrogen‐bonding units 3 – 9 . Depending on the specific geometrical structure of 3 – 9 , different nanostructures are evidenced by microscopic investigations. Combination of modules 1 or 2 with 3 , which bears only one terminal uracyl unit, leads to the formation of vesicular structures; instead, when 1 is combined with bis‐uracyl derivative 4 or 5 , a structural evolution from nanoparticles to nanowires is observed. The length of the wires obtained by mixing 1 and 4 or 1 and 5 can be controlled by addition of 3 , which prompts transformation of the wires into shorter rods. The replacement of linear system 5 with the related angular modules 6 and 7 enables formation of helical nanostructures, unambiguously evidenced by AFM. Finally, thermally induced self‐assembly was studied in parallel with modules 8 and 9 , in which the uracyl recognition sites are protected with tert‐butyloxycarbonyl (BOC) groups. This strategy allows further control of the self‐assembly/self‐organization process by temperature, since the BOC group is completely removed on heating. Microscopy studies show that the BOC‐protected ditopic modules 8 self‐assemble and self‐organize with 1 into ordered linear nanostructures, whereas BOC‐protected tritopic system 9 gives rise to extended domains of circular nano‐objects in combination with 1 .     

A combined quantum chemical/molecular mechanical study of hydrogen-bonded systems

A computational approach, which involves the combination of the OPLS force field and molecular orbital MNDO , AM 1, and PM 3 methods, has been developed to describe the effects of a large, molecular mechanically simulated environment on the Hamiltonian of a quantum chemical system. To test the validity of the combined quantum mechanical/molecular mechanical (QM /MM ) potential, a systematic study of the structures and energies of neutral and charged hydrogen-bonded complexes has been carried out, including comparisons with pure semiempirical calculations and available experimental and ab initio data. It is shown that, in many cases, the hybrid QM /MM potential behaves better than do related MNDO /M , AM 1, and PM 3 methods. As a case in point, the draw-back of AM 1 favoring bifurcated H-bonded structures over single ones is not presented in the combined AM 1/OPLS scheme. Possible ways of improvement of the combined QM /MM potential are discussed. © 1992 John Wiley & Sons, Inc.     

Vibrational density of states of the hydrogen sites in hydrogen-bonded molecular solids

Inelastic neutron scattering measurements of the incoherent dynamical structure factor of hydrogen-bonded molecular solids are reviewed. Particular attention is devoted to ice and ice-like polycrystalline samples. Their vibrational density of states is discussed in terms of the influence of proton disorder, anharmonicity and fluctuations of the force constants on the width and shape of the band.     

DSC studies on thermally induced structural transformation of hydrogen-bonded amphoteric molecular assemblage

Summary Thermally induced structural transformation of fibrous hydrogen-bonded molecular assemblage formed from an amphoteric pyridinecarboxylic acid of 6-[2-propyl- 4-(4-pyridylazo)phenoxy]hexanoic acid (C5PR) was studied using differential scanning calorimetry (DSC), differential thermal analysis (DTA), and thermogravimetry (TG). The organized fibrous morphology formed in an aqueous solution was stable at temperatures below 150°C. The ordered crystalline solid phase (K1) of the original fibrous material altered to a disordered crystalline solid phase (K2) at 150°C and subsequently to an isotropic phase (I) at 172°C. In the isotropic state, the C5PR molecule was slowly decomposed by decarboxylation. Once the molecular assemblage was subjected to the mesophase by heating, another ordered crystalline solid phase (K3) appeared reversibly at 17°C. The heat budget analyses by DSC indicated that a conformational entropy change such as the side-chain propyl group and the main-chain pentamethylene unit in the hydrogen-bonded molecular assemblage took place between the two ordered crystalline solid phases K1 and K3.     

Enforced face-to-face stacking of organic semiconductor building blocks within hydrogen-bonded molecular cocrystals

We report a method to enforce face-to-face stacking of the aromatic rings of organic semiconductor molecules in the solid state that employs bifunctional hydrogen-bond donors, in the form of semiconductor cocrystal formers, to align semiconductor building blocks.     

Engineering hydrogen-bonded molecular crystals built from derivatives of hexaphenylbenzene and related compounds

Hexakis[4-(2,4-diamino-1,3,5-triazin-6-yl)phenyl]benzene (4) incorporates a disc-shaped hexaphenylbenzene core and six peripheral diaminotriazine groups that can engage in hydrogen bonding according to established motifs. Under all conditions examined, compound 4 crystallizes as planned to give closely related noninterpenetrated three-dimensional networks built from sheets in which each molecule has six hydrogen-bonded neighbors. In the structure of compound 4, the number of hydrogen bonds per molecule and the percentage of volume accessible to guests approach the highest values so far observed in molecular networks. Analogue 5 (which has the same hexaphenylbenzene core but only four diaminotriazine groups at the 1,2,4,5-positions) and analogue 7 (in which the two unsubstituted phenyl groups of compound 5 are replaced by methyl groups) crystallize according to a closely similar pattern. Analogues with flatter pentaphenylbenzene or tetraphenylbenzene cores crystallize differently, underscoring the importance of maintaining a consistent molecular shape in attempts to engineer crystals with predetermined properties.     

Application of 2-pyridyl-substituted hemithioindigo as a molecular switch in hydrogen-bonded porphyrins

When the photochromism of 2-(3'-pyridylmethylene)-7-ethylbenzo[b]thiophen-3(2H)-ones (4) was investigated, high thermal stability of the E isomer of 4, 4(E) and good repeatability of the photoinduced E,Z-isomerization were found. Association constants of the 1:1 complexations of 4(Z) and 4(E) with the ureidoporphyrin 1 and with the pentafluorobenzamidoporphyrin 2 were evaluated. We found that 1 captures 4(E) preferentially to 4(Z) and, reversely, 2 prefers 4(Z) to 4(E). On the basis of these differences in the binding ability, we concluded that the repeatable movement of the hemithioindigo, so-called the hemithioindigo shuttle, between two kinds of porphyrins was controlled by the photoirradiation. These movements were applied to create a molecular switch for changes in the quinone distribution between two kinds of porphyrins.