Altering the folding patterns of naphthyl trimers

Proteins can adopt helical and sheet-type secondary structures that depend on their primary sequence of amino acids. Nonnatural foldamers have been developed to emulate these protein structures as well as investigate various types of noncovalent interactions. Here we report a strategy to access two distinct folding topologies in aqueous solutions using the inherent recognition properties of aromatic donor/acceptor interactions. These oligomers are constructed of electron-rich 1,5-dialkoxynaphthalene (Dan) and electron-deficient 1,4,5,8-naphthalenetetracarboxylic diimide (Ndi) units. A trimer of the sequence Dan-Ndi-Dan was shown to adopt a pleated fold in solution, while its constitutional isomer, Dan-Dan-Ndi, adopted an intercalative or turn-type fold. UV-vis and NOESY spectroscopy analyses were consistent with the two different conformations. This study illustrates the designability of folding naphthyl oligomers and encourages the use of directed aromatic interactions to construct larger and more complex assemblies in water.     

Aromatic oligomers that form hetero duplexes in aqueous solution

The electron-deficient 1,4,5,8-naphthalenetetracarboxylic diimide (Ndi) and electron-rich 1,5-dialkoxynaphthalene (Dan) have been shown to complex strongly with each other in water due to the hydrophobic effect as modulated through the electrostatic complementarity of the stacked dimer. Previously, oligomers of alternating Ndi and Dan units, termed aedamers, were the first foldamers to employ intramolecular aromatic stacking to effect the formation of secondary structure of nonnatural chains in aqueous solution. Described here is the use of this aromatic-aromatic (or pi-pi) interaction, this time in an intermolecular format, to demonstrate the self-assembly of stable hetero duplexes from a set of molecular strands (1a-4a) and (1b-4b) incorporating Ndi and Dan units, respectively. A 1-to-1 binding stoichiometry was determined from NMR and isothermal titration calorimetry (ITC) investigations, and these experiments indicated that association is enthalpically favored with the tetra-Ndi (4a) and tetra-Dan (4b) strands forming hetero duplexes (4a:4b) with a stability constant of 350 000 M-1 at T = 318 K. Polyacrylamide gel electrophoresis (PAGE) also illustrated the strong interaction between 4a and 4b and support a 1-to-1 binding mode even when one component is in slight excess. Overall, this system is the first to utilize complementary aromatic units to drive discrete self-assembly in aqueous solution. This new approach for designing assemblies is encouraging for future development of duplex systems with highly programmable modes of binding in solution or on surfaces.     

新型丁二炔-二酰胺大环化合物的合成及与TTF和DNP在溶液中的络合行为

由三甘醇和四甘醇出发,经炔丙基烷基化、Mitsunobu反应和Eglinton偶联反应3步合成了2个含均苯四甲酸二酰亚胺结构单元以及丁二炔结构单元的大环化合物,关环产率分别为81%和85%.大环化合物及中间体的化学结构经核磁共振氢谱、碳谱、低分辨质谱、高分辨质谱或元素分析等确认.通过氘代丙酮中1HNMR实验以及氯仿中紫外滴定实验研究了这类大环化合物与客体分子四硫富瓦烯(TTF)和1,5-二甲氧基萘(DNP)在溶液中的相互作用,结果发现,大环化合物的核磁化学位移及紫外光谱均发生变化.通过得到的主-客体间的络合常数可知,此类新型大环化合物与TTF和DNP之间有一定的络合作用.     

The aromatic sidechains of amino acids as neutral donor groups for alkali metal cations

An aromatic residue that can serve as a pi-donor occurs in all known protein sequences about one out of every 11 amino acids. Benzene, phenol, and indole, the sidechains of phenylalanine, tyrosine, and tryptophan, are particularly important in protein structure. Solid state structures confirm the interactions of these neutral arenes, along with double and triple bonds, with sodium and potassium cations.     

Intervalence near-IR spectra of delocalized dinitroaromatic radical anions

The Class III (delocalized) intervalence radical anions of 1,4-dinitrobenzene, 2,6-dinitronaphthalene, 2,6-dinitroanthracene, 9,9-dimethyl-2,7-dinitrofluorene, 4,4'-dinitrobiphenyl, and 1,5-dinitronaphthalene show charge-transfer bands in their near-IR spectra. The dinitroaromatic radical anions have comparable but slightly larger electronic interactions (H(ab) values) through the same aromatic bridges as do the corresponding dianisylamino-substituted radical cations. H(ab) values range from 5410 cm(-)(1) (1,4- dinitrobenzene) to 3400 cm(-)(1) (9,9-dimethyl-2,7-dinitrofluorene), decreasing as the number of bonds between the nitro groups increases, except for the 1,5-dinitronaphthalene radical-anion, which has a coupling similar to that of 9,9-dimethyl-2,7-dinitrofluorene. All charge-transfer bands show vibrational fine structure. The vertical excitation energies (lambda(v)) were estimated from the vibrational components, obtained by simulation of the entire band. The large 2H(ab)/lambda(v) values confirm these radicals to be Class III delocalized mixed-valence species. Analysis using Cave and Newton's generalized Mulliken-Hush theory relating the transition dipole moment to the distance on the diabatic surfaces suggests that the electron-transfer distance on the diabatic surfaces, d(ab), is only 26-40% of the nitrogen-to-nitrogen distance, which implies that something may be wrong with our analysis.     

Investigation of mandelic acid bonding on Pirkle type chromatographic stationary phases by Raman spectroscopy

The bonding of mandelic acid enantiomers has been studied on benzene-leucine, dinitrobenzene-leucine and dinitrobenzene-phenylalanine type chiral stationary phases connected to zeolite A supports. The pi-donor, pi-acceptor and H-bonding interactions responsible for diastereomer pair formations can be studied under quasi in situ chromatographic conditions by Fourier transform Raman and surface enhanced Raman spectroscopic techniques. Structural differences between diastereomer pairs result in observable spectral differences at a phase load of approx. 50%. It was shown that the decreasing pi-acceptor character of the phase is associated with its increasing capability of H-bond formation. Correlating spectral data to chromatographic results it can be concluded that, in addition to H-bonding as well as to pi-donor-pi-acceptor interactions, steric hindrances due to bulky moieties of either the stationary phase or the analyte molecules are of importance in successful separations.     

Versatile self-complexing compounds based on covalently linked donor-acceptor cyclophanes

A range of covalently linked donor-acceptor compounds which contain 1) a hydroquinone (HQ) unit, 2) a 1,5-dioxynaphthalene (DNP) ring system, or 3) a tetrathiafulvalene (TTF) unit as the pi-donor, and 4) cyclobis(paraquat-p-phenylene) (CBPQT(4+)) as the pi-accepting tetracationic cyclophane were prepared and shown to operate as simple molecular machines. The pi-donating arms can be included inside the cyclophane in an intramolecular fashion by virtue of stabilizing noncovalent bonding interactions. What amounts to self-complexing/decomplexing equilibria were shown to be highly temperature dependent when the pi-donating arm contains either an HQ or DNP moiety. The thermodynamic parameters associated with the equilibria have been unraveled by using variable-temperature (1)H NMR spectroscopy. The negative DeltaH degrees and DeltaS degrees values account for the fact that the "uncomplexed" conformation becomes the dominant species, since the entropy gain associated with the decomplexation process overcomes the enthalpy loss resulting from the breaking of the donor-acceptor interactions. The arm's in-and-out movements with respect to the linked cyclophanes can be arrested by installing a bulky substituent at the end of the arm. In the case of compounds carrying a DNP ring system in their side arm, two diastereoisomeric, self-complexing conformations are observed below 272 K in hexadeuterioacetone. By contrast, control over the TTF-containing arm's movement is more or less ineffective through the thermally sensitive equilibrium although it can be realized by chemical and electrochemical ways as a result of TTF's excellent redox properties. Such self-complexing compounds could find applications as thermo- and electroswitches. In addition, the thermochromism associated with the arm's movement could lead to some of the compounds finding uses as imaging and sensing materials.     

Allosteric Control of Naphthalene Diimide Encapsulation and Electron Transfer in Porphyrin Containers: Photophysical Studies and Molecular Dynamics Simulation

The complexation processes of N,N’-dibutyl-1,4,5,8-naphthalene diimide ( NDI ) into two types of π-electron-rich molecular containers consisting of two Zn(II)-porphyrins connected by four flexible linkers of two different lengths, were characterized by means of absorption and emission spectroscopies and molecular dynamics simulation. Notably, the addition of NDI leads to a strong quenching of the fluorescence of both cages only when they are in an open conformation suitable for guest encapsulation, a situation triggered by silver(I) ions binding to the lateral triazoles. Molecular dynamics simulations confirm the fast binding of NDI , likely assisted by NDI -silver(I) interactions. Upon NDI complexation, the two porphyrin macrocycles get closer, with an optimized face to face orientation, suggesting an induced-fit mechanism through π–π interactions with the NDI aromatic cycle. Ultrafast transient absorption experiments allowed to identify the process of quenching of the Zn-porphyrin fluorescence as an efficient photoinduced electron transfer reaction between the cage porphyrin and the included NDI guest. The process occurs on fast and ultrafast time scales in the two complexes (1.5 ps and ≤300 fs) leading to a short-lived charge separated state (charge recombination lifetimes in the order of 30–40 ps). The combined computational and experimental approach used here is able to furnish a reliable model of the NDI -cage complexation mechanism and of the corresponding electron transfer reaction, attesting the allosteric control of both processes by the silver(I) ions.     

Phosphorylated macrocycles: structures,complexing properties,and molecular recognition

Procedures were developed for functionalization of macrocycles by introducing a phosphonic group either directly linked to the aromatic rings (in the case of cyclophanes or calixarenes) or as a pendant arm. For these compounds to be used as artificial receptors for amino alcohols and amino acids, the host molecule must possess not only negative charges arising from the phosphonate moieties but also a hydrophobic binding site, such as electron-rich aromatic residues. We designed inter alia new dissymmetric macrocycles capable of being involved in three binding modes with guest molecules, viz., hydrogen bonding, electrostatic attraction, and π-cation interactions. The NMR characterization of the macrocycles, their stereochemistry in solution and in the solid state, and the use as chiral receptors for biologically relevant molecules are described. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 6, pp. 1313–1330, June, 2005.     

Comment on: “FTIR,FT-Raman,scaled quantum chemical studies of the structure and vibrational spectra of 1,5-dinitronaphthalene” by Arivazhaga et al. [Spectrochim. Acta A72 (2009) 941–946]

The title paper [1] reports ab initio calculations of the structure and molecular vibrations of 1,5-dinitronaphthalene. The calculations are unminimised, the molecular structure is wrong and the vibrational spectra are misinterpreted. These errors have been corrected and the vibrational spectra of 1,5-dinitronaphthalene have been reassigned in agreement with the optical and neutron spectroscopic data.     

Recognition of Free Tryptophan in Water by Synthetic Pseudopeptides: Fluorescence and Thermodynamic Studies

Pseudopeptidic receptors containing an acridine unit have been prepared and their fluorescence response to a series of amino acids was measured in water. Free amino acids, not protected either at the C or the N terminus, were used for this purpose. The prepared receptors display a selective response to tryptophan (Trp) versus the other assayed amino acids under acidic conditions. The macrocyclic nature of the receptor is important as the fluorescence quenching is higher for the macrocyclic compound than for the related open‐chain receptor. Notably, under the experimental acidic conditions used, both the receptor and guest are fully protonated and positively charged; thus, the experimental results suggest the formation of supramolecular species that contain two positively charged organic molecular components in proximity stabilized through aromatic–aromatic interactions and a complex set of cation‐anion‐cation interactions. The selectivity towards Trp seems to be based on the existence of a strong association between the indole ring of the monocharged amino acid and the acridinium fragment of the triprotonated form of the receptor, which is established to be assisted by the interaction of the cationic moieties with hydrogen sulfate anions.     

Reactivities of carboxyalkyl-substituted 1,4,5,8-naphthalene diimides in aqueous solution

A series of water-soluble 1,4,5,8-naphthalene diimide derivatives has been prepared and their redox and photophysical properties characterized. From laser flash photolysis studies, the triplet excited state of N,N'-bis[2-(N-pyridinium)ethyl]-1,4,5,8-naphthalene diimide (NDI-pyr) was found to undergo oxidative quenching with the electron donors DABCO, tyrosine, and tryptophan as expected from thermodynamics. Interestingly, the reactivities of naphthalene diimides (NDI) possessing alpha- and beta-carboxylic acid substituents (R = -CH2COO-, -C(CH3)2COO-, and -CH2CH2COO-) were strikingly different. In these compounds, the transient produced upon 355 nm excitation did not react with the electron donors. Instead, this transient reacted rapidly (k > 10(8)-10(9) M-1 s-1) with known electron acceptors, benzyl viologen and ferricyanide. The transient spectrum of the carboxyalkyl-substituted naphthalimides observed immediately after the laser pulse was nearly identical to the one-electron-reduced form of 1,4,5,8-naphthalene diimide (produced independently using the bis-pyridinium-substituted naphthaldiimide). From our studies, we conclude that the transient produced upon nanosecond laser flash photolysis of NDI-(CH2)nCOO- is the species produced upon intramolecular electron transfer from the carboxylate moiety to the singlet excited state of NDI. In separate experiments, we verified that the singlet excited state of NDI-pyr does, indeed, react intermolecularly with acetate, alanine, and glycine. The process is further substantiated using thermodynamic driving force calculations. The results offer new prospects of the efficient photochemical production of reactive carbon-centered radicals.     

Host-guest interactions with hydrophobic cyclophanes in aqueous media

Hydrophobic cyclophanes containing amide nitrogens in a rigid macrocyclic skeleton and flexible hydrocarbon chains, branched out at such nitrogen atoms, were prepared and their substrate-binding behavior was studied in aqueous media. the fluorescence spectroscopy was primarily adopted for the investigation of host-guest interactions by the aid of various hydrophobic probes. These host molecules provide cavities that are deep and hydrophobic enough to incorporate hydrophobic substrates of various bulkiness through an induced-fit mechanism originated from the flexible character of the alkyl branches. In addition to the hydrophobic interaction, the roles of electrostatic and charge-transfer interactions in molecular recognitions were clarified. Much hydrophobic, less polar, and highly viscous binding sites for hydrophobic guest molecules were provided by the octopus azaparacyclophane bearing eight hydrocarbon chains and the tetraazacyclotetradecane-capped azaparacyclophane having four flexible hydrocarbon chains connecting both macrocycles.     

Computational chemistry applied to the design of chiral stationary phases for enantiomeric separation

A general computational scheme for the rational design of chiral stationary phases for the chromatographic separation of enantiomers has been established. The developed scheme was based on applying different interaction models (force field methods versus semi empirical quantum chemical methods), different docking algorithms (systematic grid search methods versus interactive methods guided by rules based on binding modes) and different levels of approximations (rigid versus flexible docking) to a representative test problem containing the 3,5-dinitrobenzoyl group. The computational methods in use covered the most sophisticated methods which could presently be applied to problems of such a size (about 80 atoms). It has been shown that the current computational approaches using rigid body approximations for the docked molecules and simple molecular mechanics (not taking pi-“effects” into account) are invalid in view of the required predictive precision of about 1–2 Kcal/mole for the differential binding energy. Another surprising result was the failure of the commonly used systematic search methods in determining the most favorable binding modes. Based on our calculations on the representative test problem we propose a new arrangement for the most stable complexes without parallel stacking of the aromatic pi-donor and the 3,5-dinitrobenzoyl pi-acceptor systems.     

Thermally and electrochemically controllable self-complexing molecular switches

Self-complexing molecular systems are obtained when an arm component (a pi-donor) is covalently linked to a preformed macrocycle (a pi-acceptor). The resulting self-complexing compounds are not only attractive in relation to their topology, but also for their potential to undergo reversible movements, i.e., the arm can be driven out of or into the cavity of the linked macrocycle in response to temperature or applied voltage. These structurally sensitive changes render them potential thermosensors or electroswitches.     

Conformational Modularity of an Abiotic Secondary‐Structure Motif in Aqueous Solution

We have investigated an abiotic secondary structure based on the stacking of alternating electron‐rich (1,5‐dialkoxynaphthalene (Dan)) and electron‐deficient (1,4,5,8‐naphthalene‐tetracarboxylic diimide (Ndi)=benzo[lmn][3,8]phenanthroline‐1,3,6,8(2H,7H)‐tetrone) aromatic units. Previously, the specifics of conformational behavior were uncovered in the minimal folding unit, namely the dimer, consisting of one Dan and one Ndi unit linked through various amino acid residues. Here is reported the investigation of a series of larger oligomers (trimers and tetramers) composed of selected dimer units. We determined that some of the larger oligomers displayed conformational modularity, that is, the persistence of subunit‐conformational propensities when those subunits were used as components of larger structures. Conformational modularity can be viewed as a desirable property of folding molecules because it simplifies not only the design of larger, more complex oligomers, but also the structural analyses of such species.     

Comparison of various types of hydrogen bonds involving aromatic amino acids

Ab initio calculations are used to compare the abilities of the aromatic groups of the Phe, Tyr, Trp, and His amino acids (modeled respectively by benzene, phenol, indole, and imidazole) to form H-bonds of three different types. Strongest of all are the conventional H-bonds (e.g., OH..O and OH..N). His forms the strongest such H-bond, followed by Tyr, and then by Trp. Whereas OH..phi bonds formed by the approach of a proton donor to the pi electron cloud above the aromatic system are somewhat weaker, they nonetheless represent an important class of stabilizing interactions. The strengths of H-bonds in this category follow the trend Trp > His > Tyr approximately Phe. CH.O interactions are weaker still, and only those involving His and Trp are strong enough to make significant contributions to protein structure. A protonated residue such as HisH(+) makes for a very powerful proton donor, such that even its CH..O H-bonds are stronger than the conventional H-bonds formed by neutral groups.     

Sonogashira reaction on quinolizium cations

The four isomeric bromoquinolizium bromides reacted with aryl- and heteroarylacetylenes under Sonogashira conditions. The reactions proceed with moderate-to-high yields to afford aryl- and heteroarylethynyl quinolizium cations. This is the first reported example of the Sonogashira reaction on heteroaromatic cations, and it allowed easy access to potential pi-donor pi-acceptor systems bearing cationic units.     

EDA study of pi-conjugation in tunable Bis(gem-diethynylethene) fluorophores

The strength of pi-conjugation in a family of bis(gem-diethynylethene) fluorophores is estimated within the density functional theory framework using the energy decomposition analysis (EDA) method. The observed very good linear correlations between the calculated pi-conjugation and the experimental values for the UV absorption and fluorescence emission for this series of compounds suggest that the values given by the EDA are useful for the interpretation and prediction of photochemical properties of the molecules. The calculated data predict that adequate modifications in the core moiety of the molecule such as pi-donor substituents in the aromatic ring or in the periphery of the bis-enedyine unit like pi-acceptor groups placed in the para position of the aryl substituent increase the total pi-conjugation in the systems and thus provoke significant changes in both the absorption and emission spectra leading to large Stokes shifts. The effect of such substituents is quantitatively predicted by the EDA data.     

Photoinduced electron transfer between cytochrome c and a novel 1,4,5,8-naphthalenetetracarboxylic diimide with amphiphilic character

N-dodecyl-N'-(2-phosphonoethyl)-1,4,5,8-naphthalenetetracarboxylic diimide (DNDI) is a novel naphthalenic diimide with amphiphilic character. DNDI was synthesized through the sequential reaction of 1,4,5,8-naphthalenetetracarboxylic dianhydride, first with dodecylamine and then with 2-aminoethylphosphonic acid. Fluorescence measurements showed that DNDI forms excimers in water at sufficiently high concentrations. The fluorescence quantum yield of DNDI in diluted solutions is sensitive to the polarity of the microenvironment, decreasing as going from water to less polar solvents. This property allowed to monitor the incorporation of DNDI into cetyl trimethyl ammonium bromide (CTAB) micelles, with a binding constant of 1.2x10(4) M-1. UV irradiation (365 nm) of solutions containing DNDI and the redox protein cytochrome c (cyt c) resulted in the reduction of the heme iron from the Fe(III) to the Fe(II) state, a reaction that was inhibited by the incorporation of DNDI into CTAB micelles. DNDI formed host-guest complexes with alpha-cyclodextrin (alpha-CD) through the inclusion of the dodecyl group, resulting in an increased aqueous solubility of the compound.