Sequence-specific association in aqueous media by integrating hydrogen bonding and dynamic covalent interactions

Oligoamide strands that associate in a sequence-specific fashion into hydrogen-bonded duplexes in nonpolar solvents were converted into disulfide cross-linked duplexes in aqueous media. Thus, by incorporating trityl-protected thiol groups, which allows the reversible formation of disulfide bonds, into the oligoamide strands, only duplexes consisting of complementary hydrogen-bonding sequences were formed in aqueous solution as well as in methanol. The sequence-specific cross-linking of oligoamide strands was confirmed by MALDI-TOF, reverse-phase HPLC, and by isolating a cross-linked duplex. This study demonstrates that the sequence-specificity characteristic of multiply hydrogen-bonded systems can be extended into competitive media through the interplay of H-bonding and reversible covalent interactions, based on which a new class of molecular associating and ligating units that are compatible with both polar and nonpolar environments can be conveniently obtained.     

Reactivity of guanine at m5CpG steps in DNA: evidence for electronic effects transmitted through the base pairs.

BACKGROUND: Mitomycin C (MC), a DNA cross-linking and alkylating agent, targets guanines in the m5CpG sequence with 2-3-fold preference over guanines in unmethylated CpG. Benzo[a]pyrenediolepoxide (BPDE) and several other aromatic carcinogens form guanine adducts with an identical selectivity for m5CpG, and in certain cancers G to T transversion mutation 'hotspots' in the p53 tumor suppressor gene are more frequent at this sequence than at guanines in other sequences. MC appears suitable to probe the general mechanism of this selectivity. RESULTS: A 162-bp DNA fragment containing C, m5C or f5C (5-fluoro cytosine) at all cytosine positions was cross-linked by MC at guanines in CpG steps. The extent of cross-linking increased in the order f5C < C < m5C. Monoalkylation or cross-linking of duplex 12-mer oligonucleotides containing a single CpG, f5CpG or m5CpG step gave yields of adducts that increased in the same order. The rates showed a correlation with the Hammett sigma constant of the methyl and fluoro substituents of the cytosine. Only the base-pair cytosine substituent influenced reactivity of guanine. CONCLUSIONS: The 2-amino group of guanine in the m5CpG sequence of DNA has a greater nucleophilic reactivity with mitomycin than CpG. Evidence is presented for a novel mechanism: transmission of the electron-donating effect of the 5-methyl substituent of the cytosine to guanine through H-bonding of the m5C.G base pair. The results explain the enhanced reaction of BPDE at m5CpG in DNA and the origin of G-T mutational hotspots in the p53 gene in cancer.     

A series of long-chain lamellar hydrated copper(II) alkylsulfonates with different chain molecular assemblies

Reaction of copper(II) salts with n-alkylsulfonate anions yields light blue lamellar Cu(C(n)H(2n + 1)SO3)2 x zH2O displaying distinct (mono/bi-layer) chain packing with increasing alkyl chain lengths. This may be attributed to the amphiphilic nature of the surfactants, i.e., the hydrophilic sulfonate head groups, mediating the coordination, and H-bonding interactions, and the hydrophobic alkyl chains.     

Calculation of trans-hydrogen-bond 13C-15N three-bond and other scalar J-couplings in cooperative peptide models. A density functional theory study

We report B3LYP DFT calculations on peptide models that consider the effects of cooperative interactions with proximate H-bonds and local geometry at the H-bonding site upon trans-H-bond (13)C-(15)N three-bond scalar J-couplings. The calculations predict that cooperative interactions with other H-bonds within a H-bonding chain can significantly increase the magnitude of these couplings. Such increases are due to a combination of the presence of the neighboring H-bonds and the slight increase in C=O distances expected for peptide H-bonds near the centers of H-bonding chains. The energies of H-bonds inferred from H-bonding distances, alone, could be significantly in error if the effects of neighboring H-bonds are ignored.     

CH···O hydrogen bonds in "clicked" diketopiperazine-based amide rotaxanes

Two amide [2]rotaxanes were synthesized in high yields using a novel N,N'-dipropargyl diketopiperazine axle centerpiece as the template to which the stoppers are attached through "click chemistry". (1)H and 2D NMR spectra provide evidence for two different H-bonding motifs, in one of which the triazole CH groups form C-H···O═C bonds with the wheel carbonyl O atoms. This motif can be controlled and switched reversibly by competitive anion binding.     

The influence of substituents on preparation and tautomerism of open-chain β-thioketoesters Structure determination by NMR and IR spectroscopy

With special regard to the synthesis of β-thioketoesters, the acid catalysed reactions of 36 differently substituted β-keto esters with H₂S have been studied under various conditions in order to determine the influence of the substituents on reaction course. gem-Dithiols may also be obtained in good yields by this reaction. Treatment of T1(I)-salts of β-thioketo esters with alkyl halides results exclusively in S-alkylation. A slow cis-trans isomerization of S-alkylated ,β-unsaturated β-mercapto esters through rotation about the C=C double bond is demonstrated. Ethyl thioacetothionoacetate has been prepared by self-condensation of ethyl thionoacetate.

The tautomerism of the β-thioketo esters has been studied by NMR and IR spectroscopy. In the -H esters, the intramolecularly H-bonded cis-enethiol tautomer is predominant. This tautomer is also important in the -substituted esters but due to steric crowding, H-bonding occurs to the alkoxy O-atom as well as to the carbonyl O-atom; further, the trans-enethiol form appears in percentages comparable with those of the cis-enethiol form. Ethyl -isopropyl thioacetoacetate exists almost exclusively in the thione form.

¹H NMR chemical shifts and couplings of informative value for structure determination are reported and discussed. The application of the chemical shift of potentially chelated enethiolic protons as an indicator of intramolecular H-bonding is confirmed, although a general application of it (and also of corresponding proton chemical shifts in related systems) as a measure on H-bonding strength is questioned. An intramolecular H-bonding involving chlorine as acceptor atom is presented. New long-range “through bondings” couplings as well as a “through space” coupling involving enethiolic protons are also presented.     

Quadruple H-Bonding and Polyrotaxanes Dual Cross-linking Supramolecular Elastomer for High Toughness and Self-healing Conductors

Tough and self-healable substrates can enable stretchable electronics long service life. However, for substrates, it still remains a challenge to achieve both high toughness and autonomous self-healing ability at room temperature. Herein, a strategy by using the combined effects between quadruple H-bonding and slidable cross-links is proposed to solve the above issues in the elastomer. The elastomer exhibits high toughness (77.3 MJ m⁻³), fracture energy (≈127.2 kJ m⁻²), and good healing efficiency (91 %) at room temperature. The superior performance is ascribed to the inter and intra crosslinking structures of quadruple H-bonding and polyrotaxanes in the dual crosslinking system. Strain-induced crystallization of PEG in polyrotaxanes also contributes to the high fracture energy of the elastomers. Furthermore, based on the dual cross-linked supramolecular elastomer, a highly stretchable and self-healable electrode containing liquid metal is also fabricated, retaining resistance stability (0.16–0.26 Ω) even at the strain of 1600 %.     

Chemoenzymatic dynamic kinetic resolution of primary amines catalyzed by CAL-B at 38-40 °C

The (R)-selective chemoenzymatic dynamic kinetic resolution of primary amines was performed at 38-40 °C in MTBE, in good to high yields and with high enantiomeric excesses. These reactions associating CAL-B to octanethiol as radical racemizing agent were carried out in the presence of methyl β-methoxy propanoate as acyl donor, under photochemical irradiation at 350 nm in glassware.     

Crucial role of three-center hydrogen bonding in a challenging chiral molecular recognition

The enantio-discrimination of beta-chiral primary ammonium ions is achieved by a rational approach that utilizes three-center (bifurcated) hydrogen bonding. The extraction experiments on various selected guests reveal that the bifurcated H-bonding plays a crucial role for the chiral discrimination. The X-ray data obtained for an inclusion complex substantiate such interactions. Using the bifurcated H-bonding, the chiral molecular recognition with our C(3)-symmetric tripodal oxazoline receptors is extended generally toward ammonium ions of alpha-, beta-, and alpha,beta-chiral amines. Simple molecular models, evoking the bifurcated H-bonding, explain the chiral discrimination modes.     

In situ FTIR spectroscopic study of the effect of CO2 sorption on H-bonding in PEG-PVP mixtures

A study of the H-bonding between poly(ethylene glycol) (PEG) and polyvinylpyrrolidone (PVP) in the presence of supercritical carbon dioxide at various temperatures, pressures, different M(w) of PEG and PVP and different PEG/PVP ratios is presented. In situ attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopy was used to investigate H-bonding by examining changes in the relative intensities and positions of peak maxima of the 2nd derivative ν(C=O) bands associated with 'free' and H-bonded C=O groups. In general, relative intensities of bands associated with H-bonded CO groups decreased upon CO(2) sorption and was accompanied by an increase in intensity of bands associated with 'free' C=O groups. At the same time, these bands were shifted to higher wavenumbers. These shifts were attributed to the shielding effect of CO(2) molecules on H-bonding interactions between PEG and PVP. The magnitude of the effects of CO(2) shielding generally increased with decreasing polymer M(w) and increasing CO(2) content. However, upon CO(2) venting the extent of the H-bonding between PEG and PVP reappeared. The extent of H-bonding recovery was greatest for blends with low M(w) PEG (M(w): 4×10(2)) and PVP (M(w): 9×10(3)) and PEG content ≥0.54 wt% under mild conditions of pressure (80 bar) and temperature (35°C). For the same low M(w) blends, increasing pressure to 150 bar, or temperature to 50°C, showed poor H-bond recovery upon CO(2) venting. Overall, it was shown that supercritical CO(2)-induced shielding of H-bonding interactions in polymer blends is reversible upon CO(2) venting, and the magnitude of both was influenced by processing conditions and blend composition.     

Sequence-specific, dynamic covalent crosslinking in aqueous media

This article describes an associating system that integrates the specificity of multiple hydrogen bonding and the strength of dynamic covalent interactions. Linear oligoamides that sequence-specifically pair into H-bonded duplexes in nonpolar solvents were modified with S-trityl groups, allowing the reversible formation of disulfide bonds. The disulfide-crosslinking reactions of oligoamides capable of pairing via two, four, and six intermolecular H-bonds, along with several control strands, were examined using ESI, MALDI-TOF, reverse phase HPLC, and two-dimensional NMR. Results from these studies demonstrate that this system possesses both the high fidelity of multiply H-bonded assemblies and the high stability of covalent interaction, leading to the sequence-specific crosslinking of complementary oligoamides in not only nonpolar (methylene chloride) solutions but also highly competitive (aqueous) media. Experiments were designed to systematically probe the mechanism behind the specific formation of the sequence-matched products, which revealed a thermodymically controlled process. Multiple pairs in the same solution were crosslinked in a sequence-specific fashion. In addition, a length-dependent selectivity was also observed. Thus, oligoamides with different lengths or sequences did not crosslink into mismatched products. As few as two H-bonds is sufficient to bias the specific formation of the crosslinked product in aqueous media, suggesting that associating units with tunable sizes, high stability, and high specificity can be conveniently designed. The combination of H-bonding and dynamic covalent interactions represents a new, generalizable strategy for developing highly specific molecular associating units that are stable in a wide variety of media. These associating units will greatly facilitate the construction of various structures with many applications.     

Study of a nanocomposite based on a conducting polymer: polyaniline

A simple way to obtain a conducting nanocomposite is described, and the conducting particles are characterized. Core-shell particles [polystyrene-polyaniline (PANI)] have been obtained by the dispersion process from three types of polystyrene latexes: a no-cross-linked core stabilized by a nonylphenolethoxylate (NP40) and two cross-linked cores stabilized by NP40 and a mixture NP40/Surfamid (a surfactant bearing an amide group). The surface of these particles has been extensively characterized by X-ray photoelectron spectroscopy (XPS), atomic force microscopy, and scanning electron microscopy. A maximum coverage of 94% was obtained for the high PANI content as revealed by XPS analysis. A better coverage was obtained for the cross-linked polystyrene latex stabilized by the Surfamid. The amide group of this surfactant allows the H-bonding formation with the PANI backbone and, thus, improves the conductivity. It was shown that a uniform coverage of the core particles was not required to ensure a good conductivity.     

A density functional theory study of vibrational coupling in the amide I band of beta-sheet models

We report the first molecular orbital/density functional theory (DFT) calculations on the vibrational frequencies involved in the amide I band of completely geometrically optimized models for beta-sheet peptides based upon (up to 16) glycine residues. These calculations use the B3LYP/D95** level of DFT. The primary means of vibrational coupling occurs through H bond, rather than through space, interactions, which is consistent with a previous report on alpha-helical polyalanines and H-bonding chains of both formamides and 4-pyridones. We decoupled the C=O stretching vibrations using selected 14C substitutions to probe the coupling mechanism and to determine "natural" frequencies for individual 14C=Os. The intermolecular H-bonding interactions affect the geometries of the amide groups. Those near the center of H-bonding chains have long C=O bonds. The C=O bond lengths correlate with these "natural" frequencies, The frequencies obtained from the DFT calculations are generally more coupled, and the most intense are more red shifted than those calculated by transition dipole coupling (TDC). TDC inverts the order of the shifted frequencies compared to DFT in several cases.     

An indole-linked C8-deoxyguanosine nucleoside acts as a fluorescent reporter of Watson-Crick versus Hoogsteen base pairing

Pyrrole- and indole-linked C(8)-deoxyguanosine nucleosides act as fluorescent reporters of H-bonding specificity. Their fluorescence is quenched upon Watson-Crick H-bonding to dC, while Hoogsteen H-bonding to G enhances emission intensity. The indole-linked probe is ～ 10-fold brighter and shows promise as a fluorescent reporter of Hoogsteen base pairing.     

Solvent effects on the absorption and fluorescence characteristics of tin(IV) mesoporphyrin.

The absorption and fluorescence characteristics of tin(IV) mesoporphyrin (SnMP) and its analog tin(IV) protoporphyrin (SnPP) were studied in a series of organic solvents. Fluorescence quantum yields were calculated using the Strickler-Berg equation. Good correlation was found between calculated values and measured relative values. Fluorescence lifetime, radiative lifetime and non-radiative lifetime were also calculated. The parameters showed variation depending on ligation as well as H-bonding. Unusual long lifetime and high quantum yields were found in alcohol solvents. This finding might contribute to elucidation of the nature of tin porphyrins to inhibit heme oxygenase.     

Vinylic nucleophilic substitution in functionalized 2-vinylpyrroles: a route to a new family of stable enols

2-(2-Cyano-1-ethylthioethenyl)pyrroles easy exchange their ethylthio group for hydroxyl (NaOH, H₂O-methanol, 40-45 °C, 1 h) to give 2-(2-cyano-1-hydroxyethenyl)pyrroles, a new family of stable enols, in 50-94% yields. The vinylic nucleophilic substitution proceeds at the double bond of both the starting pyrroles and their cyclic isomers, 3-iminopyrrolizines. X-ray structure analysis and NMR spectra show the enols to be stabilized by exceptionally strong intramolecular H-bonding.     

Density functional studies on the effects of hydrogen bonding on the formation of a charge-transfer complex between p-benzoquinone and 2,6-dimethoxyphenol

The ability to form a ground-state charge-transfer (CT) complex between an electron acceptor, p-benzoquinone (BQ) and an electron donor, 2,6-dimethoxyphenol (DMOPh) was found to be enhanced by H-bonding of BQ to a hydrogen-bond donor, trifluoroacetic acid (TFA) and H-bonding DMOPh to a hydrogen-bond acceptor, 4-(N,N-dimethylamino)pyridine (DMAPy) [Chem. Phys. Lett. 2005, 401, 200]. Here is reported density functional theory (DFT) calculations to study the effect of H-bonding to electron donor and electron acceptor moieties on the ground-state CT complex formation ability between the aforementioned electron donor/acceptor pair. DFT calculations using B3LYP with the 6-311G(d,p) basis set show that the HOMO and LUMO energies of BQ drop on H-bonding to TFA through its C=O groups and the HOMO and LUMO energies of DMOPh increase on H-bonding to DMAPy via its O-H group. BQ molecules hydrogen-bonded as 1:1 and 1:2 complexes to TFA act as stronger acceptors than the bare molecule, while 1:1 complexes of DMOPh and DMAPy act as better donors. Vertical excitation energies for electronic transitions from the ground state to the first few excited states of BQ, DMOPh, DMAPy, and their different complexes have been investigated in the framework of time-dependent density functional theory (TD-DFT) to simulate and interpret experimental ultraviolet absorption spectra. Good agreement between experimental and calculated spectra is established. The enhancement of the CT complex formation ability between the BQ and DMOPh pair is favored by the strong H-bonding interaction of BQ with TFA as well as by the H-bonding interaction of DMOPh with DMAPy.     

H-bonding patterns in the platinated guanine-cytosine base pair and guanine-cytosine-guanine-cytosine base tetrad: an electron density deformation analysis and AIM study

The atoms in molecule theory (AIM) and electronic structure analysis are applied together to investigate H-bonding patterns in metalated nucleobase complexes. The influence of Pt on the intra GC base pair H-bonding has been found to reduce intra base pair H-bonding of N4(C)...O6(G) in the platinated GC pair and GCGC tetrad. The relaxation of geometry constrains in metalated nucleobases is found to be decisively important in the formation of novel molecular architectures from nucleobases and metal entities. The incorporation of the platinum in the GCGC tetrad benefits the formation of the unique CH...N (H5(C)...N1(G)) hydrogen bond pattern in the tetrad by offering improved geometric constraints rather than through changing the electronic properties around the H5(C) and N1(G) sites. Platination at the N7 of guanine reduces the deprotonation energy considerably.     

Chemical synthesis of cross-link lesions found in nitrous acid treated DNA: a general method for the preparation of N2-substituted 2'-deoxyguanosines

Treatment of DNA with nitrous acid results in the formation of DNA-DNA cross-links. Two cross-link lesions have previously been isolated and their structures assigned based on spectroscopic data. The major lesion has been proposed to consist of two deoxyguanosine (dG) nucleosides sharing a common N2 atom (1), while the structure of the minor lesion has been proposed to consist of a common nitrogen atom linking C2 of a dG nucleoside to C6 of deoxyadenosine (2). The chemical synthesis of 1 and 2, utilizing a palladium-catalyzed coupling, is described herein. It is demonstrated that the spectroscopic properties of synthetic 1 are identical to that of lesion 1 obtained from nitrous acid cross-linked DNA, thus providing a proof of its structure. Comparison of the limited spectroscopic data available for lesion 2 originating from nitrous acid cross-linked DNA to synthetic 2 supports its structural assignment. The synthetic approach used for synthesis of 1 and 2 is shown to be a general method for the preparation of a variety of N2-substituted dG nucleosides in good yields.     

Direct probing of sorbent-solvent interactions for amylose tris(3,5-dimethylphenylcarbamate) using infrared spectroscopy, X-ray diffraction, solid-state NMR, and DFT modeling

The sorbent-solvent interactions for amylose tris(3, 5-dimethylphenylcarbamate) (ADMPC) with five commonly used solvents, hexane, methanol, ethanol, 2-propanol (IPA), and acetonitrile (ACN), are studied using attenuated total reflection infrared spectroscopy (ATR-IR) of thin sorbent films, X-ray diffraction (XRD) of thin films, (13)C cross polarization/magic angle spinning (CP/MAS) and MAS solid state NMR of polymer-coated silica beads (commercially termed "Chiralpak AD"), and DFT modeling. The ADMPC-polymer-coated silica beads are used commercially for analytical and preparative scale separations of chiral enantiomers. The polymer forms helical rods with intra- and inter-rod hydrogen bonds (H-bonds). There are various nm-sized cavities formed between the polymer side-chains and rods. The changes in the H-bonding states of the C=O and NH groups of the polymer upon absorption of each of the five solvents at 25 degrees C are determined with ATR-IR. The IR wavenumbers, the H-bonding interaction energies, and the H-bonding distances of the polymer side-chains with each of the solvent molecules are predicted using the DFT/B3LYP/6-311+g(d,p) level of theory. The changes in the polymer crystallinity upon absorption of each solvent are characterized with XRD. The changes in the polymer crystallinity and the H-bonding states of C=O groups are also probed with (13)C CP/MAS solid-state NMR. The changes in the polymer side-chain mobility are detected using (13)C MAS solid-state NMR. The H-bonding states of the polymer change upon absorption of each polar solvent and usually result in an increase in the polymer crystallinity and the side-chain mobility. The polymer rods are reorganized upon solvent absorption, and the distance between the rods increases with the increase in the solvent molecular size. These results have implications for understanding the role of the solvent in modifying the structure and behavior of the polymer sorbents.