Complementary Hydrogen Bonds Research Articles

Design, synthesis, and complementary recognition of β-hairpin peptides stabilized by artificial DNA base-pairing amino acids

A novel DNA base-pairing beta-hairpin peptide involving intramolecular hydrogen bonds for induction of beta-hairpin secondary structure and intermolecular complementary hydrogen bonds between thymine and diaminopyridine for molecular recognition has been synthesized.

Hydrogen-bond induced side-chain liquid crystalline polymers based on nicotinic acid derivatives

Supramolecular side-chain liquid crystalline poly(acrylate)s have been prepared by self-assembly of H-bond donor and acceptor complexes through intermolecular complementary hydrogen bond formation. Poly[4-(m-acryloyloxyalkyloxy)benzoic acid]s [ m = 6 ( P1) and 8 ( P2)] were employed as polymer components. Liquid crystalline nicotinic acid derivatives ( C1, C2, C3, and C4) were used as complementary H-bond donor/acceptor counterparts. The liquid crystalline properties of the nicotinic acid derivatives, the polymers and their complexes were investigated by DSC and POM. Methylene spacers present at the terminal position of the nicotinic acid derivatives played a key role in mesophase arrangements. The columnar phase exhibited by the nicotinic acid derivatives completely disappeared in the H-bonded complexes to afford a nematic phase, thereby substantiating the complex formation.

Hydrogen‐Bonded Molecular Networks of Melamine and Cyanuric Acid on Thin Films of NaCl on Au(111)

Self-assembly of organized molecular structures on insulators is technologically very relevant, but in general rather challenging to achieve due to the comparatively weak molecule-substrate interactions. Here the self-assembly of a bimolecular hydrogen-bonded network formed by melamine (M) and cyanuric acid (CA) on ultrathin NaCl films grown on a Au(111) surface is reported. Using scanning tunneling microscopy under ultrahigh-vacuum conditions it is demonstrated that it is possible to exploit strong intermolecular forces in the M-CA system, resulting from complementary triple hydrogen bonds, to grow 2D bimolecular networks on an ultrathin NaCl film that are stable at a relatively high temperature of approximately 160 K and at a coverage below saturation of the first molecular monolayer. These hydrogen-bonded structures on NaCl are identical to the self-assembled structures observed for the M-CA system on Au(111), which indicates that the molecular self-assembly is not significantly affected by the isolating NaCl substrate.

Crystal structure and properties of charge-transfer complex of N-butylguanine and FTCNQ

Charge-transfer complex formation between N-butyl guanine and FTCNQ yielded an ionic product composed of neutral and protonated N-butyl guanines and fully ionized FTCNQ molecules in a 1:1:1 ratio. Neutral and protonated N-butyl guanines were alternately connected by complementary hydrogen-bonds to form a one-dimensional ribbon, which stacked to establish a two-dimensional cation layer. FTCNQ formed a face-to-face dimer, which was separated from adjacent dimers because of the butyl group of N-butyl guanine. This salt was an insulator, and exhibited a strong antiferromagnetic interaction within the FTCNQ dimer.

Synthesis and structure of an arylpyran normal, pseudodiacid showing recognition

Oxidation of 1,4-bis(4′-oxo-2′,2′-dimethylpent-2-yl)benzene with hypochlorite produces 1,4-bis(3′-carboxy-2′-methylbut-2-yl)benzene and 3-(4′-carboxyphenyl)-3,3-dimethylpropanoic acid. Cyclization of this mixture forms 3,3,7,7-tetramethyl-1,2,3,5,6,7-hexahydro-s-indacen-1,5-dione, 3,3,7,7-tetramethyl-1,2,3,5,6,7-hexahydro-as-indacen-1,5-dione (5) and 6-carboxy-3,3-dimethyl-1-indanone (6). Ketoacid (6) is converted to the arylpyran pseudoacid 7-carboxy-3-hydroxy-4,4-dimethylisobenzopyran-1-one (7). In the crystal structure of (7), carboxylic acid and the pseudoacid groups each form complementary dimer hydrogen bonds linking the molecules in chains. Contact O···O distances reflect their differing energetics, with pseudoacyl O···O at 2.78(1)A and carboxylic O···O at 2.62(1)A. A normal, pseudodiacid shows complementary hydrogen bonds between the two similar functions forming chains.

Silylated Melamine and Cyanuric Acid as Precursors for Imprinted and Hybrid Silica Materials with Molecular Recognition Properties

Two monotrialkoxysilylated compounds that consist of complementary fragments of melamine (M) and cyanuric acid (CA) have been synthesised. The molecular recognition properties of the M and CA fragments through complementary hydrogen bonds (DAD and ADA; D=donor, A=acceptor) are the key factor used to direct the formation of hybrid silica materials by using a sol-gel process. These materials were synthesised following two methods: First, an organo-bridged silsesquioxane was obtained by the hydrolysis of the two complementary monotrialkoxysilylated melamine and cyanuric acid derivatives, with fluoride ions as a catalyst. The hydrogen-bonding interactions between the two organic fragments are responsible for the formation of the bridging unit. The transcription of the assembly into the hybrid material was characterised and evidenced by solid-state NMR (29Si, 13C) and FTIR spectroscopic experiments. Second, the molecular recognition was exploited to synthesise an imprinted hybrid silica. This material was prepared by co-condensation of tetraethyl orthosilicate (TEOS) with the monosilylated cyanuric acid derivative (CA) templated by nonsilylated melamine. The melamine template was completely removed by treating the solid material with hydrochloric acid. The reintroduction of the template was performed by treating the resulting material with an aqueous suspension of melamine. These steps were monitored and analysed by several techniques, such as solid-state NMR (29Si, 13C) and FTIR spectroscopic analysis and nitrogen adsorption-desorption isotherms.

Evidence for transcriptase quantum processing implies entanglement and decoherence of superposition proton states

Evidence requiring transcriptase quantum processing is identified and elementary quantum methods are used to qualitatively describe origins and consequences of time-dependent coherent proton states populating informational DNA base pair sites in T4 phage, designated by G–C → G′–C′, G–C → *G–*C and AT → *A–*T. Coherent states at these ‘point’ DNA lesions are introduced as consequences of hydrogen bond arrangement, keto– amino → enol– imine, where product protons are shared between two sets of indistinguishable electron lone-pairs, and thus, participate in coupled quantum oscillations at frequencies of ∼10 13 s −1. This quantum mixing of proton energy states introduces stability enhancements of ∼0.25–7 kcal/mole. Transcriptase genetic specificity is determined by hydrogen bond components contributing to the formation of complementary interstrand hydrogen bonds which, in these cases, is variable due to coupled quantum oscillations of coherent enol–imine protons. The transcriptase deciphers and executes genetic specificity instructions by implementing measurements on superposition proton states at G′–C′, *G–*C and *A–*T sites in an interval Δ t ≪ 10 −13 s. After initiation of transcriptase measurement, model calculations indicate proton decoherence time, τ D, satisfies the relation Δ t < τ D < 10 −13 s. Decohered states participate in Topal–Fresco replication to introduce substitutions G′ → T, G′ → C, *C → T and *G → A. Measurements of 37 °C lifetimes of the keto–amino DNA hydrogen bond indicate a range of ∼3200–68,000 yrs. Arguments are presented that quantum uncertainty limits on amino protons may drive the keto– amino → enol– imine arrangement. Data imply that natural selection at the quantum level has generated effective schemes (a) for introducing superposition proton states – at rates appropriate for DNA evolution – in decoherence-free subspaces and (b) for creating entanglement states that augment (i) transcriptase quantum processing and (ii) efficient decoherence for accurate Topal–Fresco replication.

Syntheses, structures and properties of seven H2BTA coordinating 3-D metallic complexes containing 0-, 1-, 2-, and 3-D frameworks (H2BTA = bis(tetrazolyl)amine)

Seven 3-D metallic complexes coordinated and controlled by the deprotonated anions of H2BTA ligand (H2BTA = bis(tetrazolyl)amine): a 0-D compound of Co(HBTA)3·4.5H2O (1), two 1-D compounds of Cu(BTA)(H2O)2 (2) and Mn4(BTA)4(H2O)12·2H2O (3), a 2-D compounds [Mn7(BTA)6(OH)2(H2O)12] (4) and three 3-D compounds containing two isomorphous complexes of [Mn(BTA)2Na2(H2O)2] (5) and [Co(BTA)2Na2(H2O)2] (6) as well as Mn(BTA)(H2O) (7) have been synthesized under different synthetic conditions and characterized by single crystal X-ray diffraction analysis. In 1–7, the deprotonated anions of the H2BTA ligand control the different crystal structures using not only the different coordinations to transition metal ions as several different multidentate ligands but simultaneously the formation of complementary intermolecular hydrogen bonds.

Controlled Super-Structures of Hydrogen Bonding Ni&lt;SUP&gt;II&lt;/SUP&gt; Complexes Organizing One-Dimensional Double Cationic Arrays

Anionic tris-biimidazolato Ni(II) complexes ([Ni(Hbim)3]-), which represent a hydrogen-bonding molecular building blocks, are self-organized to form honeycomb-sheet super-structures connected with complementary intermolecular hydrogen bonds by cations in the crystal. The crystal formed by the stacking of the sheets has nano-channel structures having width of ca. 2 nm-scale width, which confines one-dimensional double columnar arrays of cationic molecules. Thus, relative large cations such as potassium crown-ether complexes and PPh4+ can generally cause [Ni(Hbim)3]- to assemble to a honeycomb-sheet formation forming these channel structures. However, smaller cations such as 4-phenylethyl pyridinuim and trimethyl ethynyl ammonium also lead to the same honeycomb-sheet network by forming the cationic ion-pairs containing an anion in the channels; this is a new finding that we present in this paper.

A sextuple hydrogen bonding molecular duplex bearing 1,8-naphthalimide moieties and polymer light-emitting diode based on it

In this paper, the molecular structure of a 1,8-naphthalimide fluorophore modified sextuple H-bond self-assembly homodimer, comprising two linear oligoamide molecular strands bearing arrays on one edge with complementary hydrogen bond sequences of DDADAA and AADADD, is characterized via1H NMR, ESI-MS, 13C NMR, and elementary analysis. The target duplex emits strong yellowish green light with emission peaks at 518 nm and 535 nm under UV photoexcitation in solution and solid film, respectively, and its photoluminescence quantum efficiency (solid state) has been enhanced greatly compared to its small molecular 1,8-naphthalimide counterpart (0.637 versus 0.324). Employing the duplex and the counterpart as emitting dopants, two yellowish green polymer light-emitting diodes (PLED) with the device configuration of ITO/PEDOT:PSS (50 nm)/PFO + dopant (5wt%) (80 nm)/CsF (3 nm)/Al (150 nm) have been fabricated. The results indicate that the PLED with the duplex as emitter has dramatically improved performance, for example, a much higher external electroluminescence quantum efficiency (QEext) of 1.87% (ph/el), and a much lower turn-on voltage of 6.4 V, compared to the one with the counterpart as emitter (QEext: 0.12%; turn-on voltage: 15 V), suggesting that the incorporation of H-bond self-assembly motif with the light-emitting fluorophore is an effective way for the design of electroluminescent materials.

The Amino Group in Adenine: MP2 and CCSD(T) Complete Basis Set Limit Calculations of the Planarization Barrier and DFT/B3LYP Study of the Anharmonic Frequencies of Adenine

The amino group in adenine plays a key role in formation of hydrogen bonds in nucleic acids and in other molecular systems. Thus, the structure of this group is of fundamental importance in the molecular recognition phenomena. Ab initio MP2 and density functional B3LYP methods with various basis sets have been used to calculate the optimized structure and the infrared spectrum of adenine (the N9-H tautomer). Calculations at the MP2 level with larger basis sets tend to decrease the degree of pyramidalization of the C-NH2 group, whereas the B3LYP method consistently yields the planar or nearly planar structure of adenine. MP2 complete basis set (CBS) limit method with the aug-cc-pVTZ --> aug-cc-pVQZ (aTZ --> aQZ) extrapolation scheme has predicted very small planarization barrier of adenine, 0.015 kcal/mol, which is in very good agreement with the MP2-predicted planarization barrier of 0.020 kcal/mol, reported by S. Wang and H. F. Schaefer III, J. Chem. Phys. 2006, 124, 044303. Similar results were obtained in calculations by the coupled cluster CCSD(T) CBS method. Thus, it can be concluded that the amino group in adenine, in the gas phase, is very flexible with a small degree of nonplanarity. Extremely low planarization barrier implies that adenine requires very little energy to conform the structure of the amino group to formation of the complementary hydrogen bonds with other molecules. This fact is very important for base pairing in nucleic acids or other polymers containing adenine residues. The anharmonic frequencies of adenine have been calculated at the B3LYP/6-311++G(df,pd) level of theory. The theoretical results show excellent agreement with the available experimental data. The revised assignment of the infrared spectrum of adenine in Ar matrix has been made. The predicted anharmonic frequency of the NH2 inversion, 181 cm(-1), is supported by the experimental data. It is demonstrated that the vibrational frequencies and potential energy distribution (PED) obtained from the B3LYP calculations are more reliable than those obtained at the MP2 level.

Trimodular Engineering of Linear Supramolecular Miniatures on Ag(111) Surfaces Controlled by Complementary Triple Hydrogen Bonds

Thespecificity, directionality, dynamics, and complementarity ofsuchinteractionscanallowforthedesignofalargelibraryoforganic modules bearing H-bond donor (D) and/or acceptor(A) moieties with specific programmed functions and struc-tures that could ultimately lead to the construction of manydesired functional assemblies. So far, this method has beensuccessfullyemployedonsolidsurfacesforthepreparationofextendedone-

Trimodular Engineering of Linear Supramolecular Miniatures on Ag(111) Surfaces Controlled by Complementary Triple Hydrogen Bonds

Trimodular Engineering of Linear Supramolecular Miniatures on Ag(111) Surfaces Controlled by Complementary Triple Hydrogen Bonds

Taking Advantage of Tailored Electrostatics and Complementary Hydrogen Bonding in the Design of Nanostructures for Biomedical Applications

AbstractFour‐armed, star‐shaped poly(D,L‐lactide) (PDLLA) was synthesized and terminally‐functionalized with either adenine or thymine complementary hydrogen bonding groups (PDLLA‐A and PDLLA‐T, respectively). The strong hydrogen bonding led to increased viscosity below the dissociation temperature of the hydrogen bonds. Rheology confirmed that these bonds were thermally reversible, with a sharp reduction in viscosity near 100 °C. PDLLA, PDLLA‐A, and PDLLA‐T were melt electrospun with no significant change in fiber diameter (all between 3.6 and 4.0 µm). However, a blend of PDLLA‐A and PDLLA‐T formed fibers with an average diameter of 9.8 ± 2.0 µm, resulting from the hydrogen bond associations. Also, the phospholipid 1‐palmitoyl‐2‐oleoyl‐sn‐glycero‐3‐phosphoethanolamine (POPE) was melt electrospun at 200 °C and formed uniform fibers with average fiber diameter of 6.5 ± 2.0 µm.

Synthesis and crystallographic characterization of a seven‐coordinate Mn(II) complex

AbstractA seven‐coordinate Mn(II) complex of N,N,N ′,N ′‐tetrakis[(2‐benzimidazolyl)methyl]‐1,2‐cyclohexanediamine (CDTB), namely, [Mn(CDTB)(DMF)](Pic)2·C2H5OH was synthesized and characterized by elemental analyses, IR spectra and X‐ray single‐crystal diffraction. The complex crystallizes in a typical hybrid organic‐inorganic pattern. The crystal belongs to the monoclinic system, space group P 2 (1) / n with cell constants a = 13.3343(6) Å, b = 33.7015(16) Å, c = 13.7286(6) Å, β = 108.9990(10)°, Z = 4. The structure was solved by direct methods and refined to R = 0.0561 (wR2 = 0.1172). The structure analysis reveals that the Mn(II) has a capped octahedron geometry with seven‐coordination mode, furthermore, the [Mn(CDTB)(DMF)]2+ building blocks were extended into well‐ordered supramolecular networks by complementary hydrogen bonds, and the linkers of the ethanol molecules and the picrate anions play an important role in the self‐assembly process. (© 2008 WILEY‐VCH Verlag GmbH &amp; Co. KGaA, Weinheim)

Formation of Supramolecular Polymers and Discrete Dimers of Perylene Bisimide Dyes Based on Melamine−Cyanurates Hydrogen-Bonding Interactions

Melamine-linked perylene bisimide dyes (MPBIs) bearing an ethylene or trimethylene group as linker moieties were synthesized, and their self-aggregation and coaggregation with cyanurates through complementary triple hydrogen bonds have been investigated. UV/vis studies revealed that both the MPBIs self-assemble in nonpolar organic solvent through pi-pi stacking interaction between perylene cores, giving self-aggregates with nearly identical thermal stabilities. Upon addition of 1 equiv of cyanurate components, however, the stabilities of the resulting aggregates were dramatically changed between the two systems, suggesting the formation of different types of hydrogen-bonded supramolecular species. Dynamic light scattering and atomic force microscopic studies revealed that the system featuring ethylene linker moieties generates a discrete dimer of MPBI supported by two cyanurate molecules, whereas the system featuring trimethylene linker moieties affords extended supramolecular polymers hierarchically organizing into nanoscopic fibers. These results demonstrate that it is possible to obtain distinct supramolecular species by just changing the number of carbon atoms at the linker moieties of MPBI components. The present strategy for the fabrication of discrete or polymeric supramolecular assemblies should be applicable to other functional pi-conjugated molecules.

Complex Formation between a Nucleobase and Tetracyanoquinodimethane Derivatives: Crystal Structures and Transport Properties of Charge-Transfer Solids of Cytosine

Abstract Reaction between cytosine, a nucleobase, in methanol and several 7,7,8,8-tetracyanoquinodimethane derivatives (R-TCNQ) in acetonitrile yielded three kinds of ionic solids; (I) insulators composed of methoxy-substituted R-TCNQ anions, (II) semiconducting fully ionic R-TCNQ radical anion salts, and (III) conductive partially ionic or mixed-valent R-TCNQ radical anion salts. Electronic and chemical structures of these products were characterized by optical and magnetic measurements, and structural and elemental analyses. Cation units in all products were found to be protonated cytosine species. Crystal structures were determined for methoxy-substituted anion salts (R = F4 and H) in Group I and R-TCNQ radical anion salts (R = H and Et2) in Group II with hemiprotonated cytosine pairs formed by triple self-complementary hydrogen bonds. They established one-dimensional hemiprotonated cytosine ribbons by double complementary hydrogen bonds. Hydrogen bonds between cytosine and R-TCNQ anions exhibited high potential to regulate molecular arrangements producing a segregated layered structure and uniform arrangement of R-TCNQ radical anion columns stable down to low temperature. The partially ionic salt of MeTCNQ in Group III exhibited metallic behavior and the highest conductivity of 10+1 S cm−1 so far observed for charge-transfer complexes based on biological molecules.

Exploration of charge-transfer complexes of a nucleobase: Crystal structure and properties of cytosine–Et 2TCNQ salt

A charge-transfer solid composed of a hemiprotonated cytosine pair and fully ionized Et 2TCNQ radical anion was investigated in terms of crystal structure analysis, optical spectra, and electrical and magnetic measurements. Complementary hydrogen bonds and π-stack of the hemiprotonated cytosine pair established a two-dimensional cation layer, and the hydrogen bond with Et 2TCNQ moiety aligned them to construct a segregated bilayer structure of this salt. The robust hydrogen bond network strengthened the crystal packing against structural distortion and preserved the uniform arrangement down to low temperature.

Structure and Activity of Y-class DNA Polymerase DPO4 from Sulfolobus solfataricus with Templates Containing the Hydrophobic Thymine Analog 2,4-Difluorotoluene

The 2,4-difluorotoluene (DFT) analog of thymine has been used extensively to probe the relative importance of shape and hydrogen bonding for correct nucleotide insertion by DNA polymerases. As far as high fidelity (A-class) polymerases are concerned, shape is considered by some as key to incorporation of A(T) opposite T(A) and G(C) opposite C(G). We have carried out a detailed kinetic analysis of in vitro primer extension opposite DFT-containing templates by the trans-lesion (Y-class) DNA polymerase Dpo4 from Sulfolobus solfataricus. Although full-length product formation was observed, steady-state kinetic data show that dATP insertion opposite DFT is greatly inhibited relative to insertion opposite T (approximately 5,000-fold). No products were observed in the pre-steady-state. Furthermore, it is noteworthy that Dpo4 strongly prefers dATP opposite DFT over dGTP (approximately 200-fold) and that the polymerase is able to extend an A:DFT but not a G:DFT pair. We present crystal structures of Dpo4 in complex with DNA duplexes containing the DFT analog, the first for any DNA polymerase. In the structures, template-DFT is either positioned opposite primer-A or -G at the -1 site or is unopposed by a primer base and followed by a dGTP:A mismatch pair at the active site, representative of a -1 frameshift. The three structures provide insight into the discrimination by Dpo4 between dATP and dGTP opposite DFT and its inability to extend beyond a G:DFT pair. Although hydrogen bonding is clearly important for error-free replication by this Y-class DNA polymerase, our work demonstrates that Dpo4 also relies on shape and electrostatics to distinguish between correct and incorrect incoming nucleotide.

Synthetic Model of the Phosphate Binding Protein: Solid-State Structure and Solution-Phase Anion Binding Properties of a Large Oligopyrrolic Macrocycle

The macrocyclic receptors 4-6 were synthesized via the anion-templated condensation of appropriately chosen dialdehyde and diamine building blocks. Whereas all three products could be obtained directly via the appropriate choice of reaction conditions, the larger [3+3] product, 6, which incorporates three of each precursor subunit, could also be obtained conveniently via an indirect procedure involving ring expansion of the smaller [2+2] macrocycle 4. As detailed earlier (Sessler, J. L.; Katayev, E. A.; Pantos, G. D.; Reshetova, M. D.; Khrustalev, V. N.; Lynch, V. M.; Ustynyuk, Y. A. Angew. Chem. 2005, 117, 7552-7556; Angew. Chem., Int. Ed. 2005, 44, 7386-7390), this ring expansion occurs under thermodynamic control in the presence of HSO4- and H2PO4- anions in acetonitrile solution and serves to effect the conversion of 4 to 6. An analysis of the X-ray crystal structure of complex 6H22+.HPO42- revealed a strong resemblance to the active site of the phosphate binding protein (PBP) with similar structural analogies being drawn between the active site of the sulfate binding protein (SBP) and the corresponding hydrogensulfate anion complex. In both cases, the anions are bound in a 1:1 fashion in the solid state through a complementary hydrogen bond network involving both the receptor 6 and the anions. UV-vis spectroscopic titrations provide support for the conclusion that macrocycle 6 binds the hydrogensulfate and dihydrogenphosphate anion (studied as the corresponding tetrabutylammonium salts) with high selectivity and affinity in acetonitrile (log Ka for the first binding interaction approaching 7), albeit with different receptor-to-anion binding stoichiometries (1:1 vs 1:3 for HSO4- and H2PO4-, respectively).