Double-helical Complex Research Articles

Cooperativity in Photofoldamer Chloride Double Helices Turned On with Sequences and Solvents, Around with Guests, and Off with Light.

Photofoldamers are sequence-defined receptors capable of switching guest binding on and off. When two foldamer strands wrap around the guest into 2:1 double helical complexes, cooperativity emerges, and with it comes the possibility to switch cooperativity with light and other stimuli. We use lessons from nonswitchable sequence isomers of aryl-triazole foldamers to guide how to vary the sequence location of azobenzenes from the end (FEND) to the interior (FIN) and report their impact on the cooperative formation of 2:1 complexes with Cl-. This sequence change produces a 125-fold increase from anti-cooperative (α = 0.008) for FEND to non-cooperative with FIN (α = 1.0). Density functional theory (DFT) studies show greater H-bonding and a more relaxed double helix for FIN. The solvent and guest complement the synthetic designs. Use of acetonitrile to enhance solvophobicity further enhances cooperativity in FIN (α = 126) but lowers the difference in cooperativity between sequences. Surprisingly, the impact of the sequence on cooperativity is inverted when the guest size is increased from Cl- (3.4 Å) to BF4- (4.1 Å). While photoconversion of interior azobenzenes was poor, the cis-cis isomer forms 1:1 complexes around chloride consistent with switching cooperativity. The effect of the guest, solvent, and light on the double-helix cooperativity depends on the sequence.

In situ-formed tetrahedrally coordinated double-helical metal complexes for improved coordination-activated n-doping

In situ coordination-activated n-doping by air-stable metals in electron-transport organic ligands has proven to be a viable method to achieve Ohmic electron injection for organic optoelectronics. However, the mutual exclusion of ligands with high nucleophilic quality and strong electron affinity limits the injection efficiency. Here, we propose meta-linkage diphenanthroline-type ligands, which not only possess high electron affinity and good electron transport ability but also favour the formation of tetrahedrally coordinated double-helical metal complexes to decrease the ionization energy of air-stable metals. An electron injection layer (EIL) compatible with various cathodes and electron transport materials is developed with silver as an n-dopant, and the injection efficiency outperforms conventional EILs such as lithium compounds. A deep-blue organic light-emitting diode with an optimized EIL achieves a high current efficiency calibrated by the y colour coordinate (0.045) of 237 cd A−1 and a superb LT95 of 104.1 h at 5000 cd m−2.

Synthesis and X-ray crystal structure of novel cobalt(II) complexes having oligopyridine ligands

The quinquepyridine analogue L1, diquinolylterpyridine analogue L3 and a new oligopyridine, quinolylquaterpyridine L2, have been prepared by an iridium-catalyzed synthetic method. The quinquepyridine L1 has five pyridine rings which are connected to each other at the 2- and 6-positions of each pyridine ring. One of the two terminal pyridine rings of L1 was replaced by a quinoline ring to give L2, while both terminal pyridine rings were replaced by two quinoline rings to give L3. All of these oligopyridines produce the corresponding new cobalt(II) complexes. The reaction of cobalt(II) chloride with L1 gave the dinuclear cobalt(II) complex [CoClL1]2(CoCl4) (4a), having an interesting double-stranded helical structure, differing from the double helical dinuclear cobalt complexes previously reported by other groups. The structure of 4a was determined by single-crystal X-ray crystallography. In 4a, the two cobalt centers are equivalent, while the other dinuclear cobalt complexes had non-equivalent cobalt centers. Each cobalt center in 4a displays a distorted octahedral coordination environment, and L1 coordinates to each cobalt with “terpyridyl” and “bipyridyl” fragments. The reaction of L2 with cobalt(II) nitrate gave the dinuclear cobalt(II) complex [Co2L2(NO3)4] (5). Complex 5 has one ligand molecule, while the complex 4a has two ligand molecules. In 5, the terpyridyl fragment of L2 is coordinated to one cobalt center and the quinolylpyridyl fragment is coordinated to the other cobalt center. The two cobalt centers are bridged by one oxygen atom of a nitrate group. The reaction of L3 with cobalt(II) nitrate gave a similar dinuclear cobalt complex, [Co2L3(NO3)4] (6). In 6, the quinolylbipyridyl and quinolylpyridyl fragments each coordinate to a different cobalt center. The bridging nitrate group in 6 is coordinated to the two cobalt centers through two oxygen atoms.

Tetranuclear Zn(II) cluster and dinuclear Cu(II) double helicate with multidentate mixed pyridine–pyrazole ligand

A new ligand, 2,6-bis{3-(2-pyridyl)-1H-pyrazol-1-yl}pyridine (L1), was designed and synthesized. The reactions of the ligand with Zn(OAc)2·(H2O)2, and Cu(ClO4)2·(H2O)6 were carried out and a tetra-nuclear cluster [ZnII4L12(CH3COO)4(OH)2](ClO4)2 (1) and a dinuclear double helical complex [CuII2L12(H2O)2](ClO4)4 (2), were obtained and characterized by single crystal X-ray diffraction analyses. The solution behaviors of the complexes are also investigated.

Chiral double helical silver complexes: subcomponent self-assembly and self-sorting

Four homochiral dinuclear complexes, namely, [Ag2(LC4)2](OTf)2 (1), [Ag2(LC4)2](ClO4)2 (2), [Ag2(LC5)2](OTf)2 (3), [Ag2(LC5)2](PF6)2 (4) have been successfully synthesized from subcomponent self-assembly of imidazole-2-carboxaldehyde derivatives, R-phenylethylamine and silver salt. LC4 and LC5 were flexible ligands, containing the same imidazole Schiff-bases coordination motif and varying in alkyl chain lengths with four and five carbon atom, respectively. Single crystal structures revealed that the silver(I) center in 1–4 coordinated with 4N donor atoms from two symmetrical chiral ligands assuming Δ configuration with a tetrahedral coordination environment. [Ag2(LCn)2]2+ components all presented double helical structures exhibiting only P-handedness with Ag–Ag, π–π, and C–H⋯π intramolecular interactions. Highly selective narcissistic self-sorting behavior can be observed during the self-assembly of 1 and 3.

Anion-directed assembly of helical copper(ii) complexes based on a bispyridylpyrrole ligand: synthesis, structural and magnetic properties

Helical copper(ii) complexes based on a bispyridylpyrrole ligand, namely the helical polymer {[Cu2(PDPH)2(N3)2]}n, a discrete double-helical complex [Cu2(PDPH)2(NO3)2] and triple-helical complex [Cu2(PDPH)3](OTf), were synthesized by displacement of Cl− in [Cu(PDPH)Cl].

Introduction

1. Deborah Josko, Ph.D. MLT(ASCP)M, SM[⇑][1] 1. Associate Professor and Program Director, Department of Clinical Laboratory Sciences, Medical Laboratory Science Program, Rutgers, The State University of New Jersey – School of Health Related Professions, Scotch Plains, NJ <!-- --> 1. Address for correspondence: Deborah Josko, Ph.D. MLT(ASCP)M, SM, Associate Professor, Department of Clinical Laboratory Sciences, Medical Laboratory Science Program, Rutgers, The State University of New Jersey – School of Health Related Professions 1776 Raritan Road, Scotch Plains, NJ 07076. (908) 889-2422. daj100{at}shrp.rutgers.edu. 1. Discuss the history of DNA sequencing. 2. Describe the components of DNA and DNA synthesis. 3. Compare and contrast dNTPs and ddNTPs. 4. List several next generation sequencing platforms. In 1953, James Watson and Francis Crick were credited with discovering the structure of the DNA molecule: a three dimensional, double helical complex which dictates the genetic code for all forms of life.1 Although much controversy exists over this discovery notably that the model Watson and Crick proposed was the compilation of the work of several pioneers before them,2 they were awarded the Noble Prize in Physiology or Medicine in 1962 along with Maurice Hugh Frederick Wilkins “for their discoveries concerning the molecular structure of nucleic acids and its significance for information transfer in living material.”3 The DNA molecule consists of a sugar (deoxyribose) and phosphate backbone along with four chemical base pairs: adenine (A), thymine (T), cytosine (C), and guanine (G). Each base pair is covalently linked to the sugar phosphate backbone. The double helical structure forms once each base pair links to the complementary base on the corresponding strand of deoxyribonucleic acid (DNA) through hydrogen bonding. Due to the chemical make-up of each base, adenine always binds with thymine while cytosine always binds with guanine. The base, sugar and phosphate together constitute a nucleotide.4 A key property of the DNA molecule is that it can replicate itself and synthesize a new copy of DNA from the preexisting strand during cell division. DNA synthesis requires several components: DNA template; primer; deoxyribonucleotide triphosphates (dNTPs): deoxyadenosine triphosphate (dATP), deoxycytidine triphosphate (dCTP), deoxyguanosine triphosphate (dGTP) and deoxythymidine triphosphate (dTTP); various enzymes; and an energy source to fuel the reaction adenosine triphosphate (ATP).5 ABBREVIATIONS : A - adenine; ATP - adenosine triphosphate; C - cytosine; dATP - deoxyadenosine triphosphate; dCTP - deoxycytidine triphosphate; ddNTP - dideoxynucleotide triphosphate; dGTP - deoxyguanosine triphosphate; DNA - deoxyribonucleic acid; dNTP - deoxynucleotide triphosphate; dTTP - deoxythymidine triphosphate; G - guanine; mRNA - messenger ribonucleic acid; NGS – next generation sequencing; OH - hydroxyl; SMRT - single molecule real time; T - thymine. 1. Discuss the history of DNA sequencing. 2. Describe the components of DNA and DNA synthesis. 3. Compare and contrast dNTPs and ddNTPs. 4. List several next generation sequencing platforms. [1]: #corresp-1

Helical π-Systems of Bidipyrrin–Metal Complexes

Abstract Various metal-bridged single and double helical complexes of π-conjugated ligand molecules, bidipyrrins, were prepared. The introduction of terminal end units enabled the formation of chiral single and double helices; their spectroscopic properties and temperature-dependent behaviors were examined.

Dinuclear double helicates assembled from a bis-bidentate ligand and Cu(I), Cu(II), Ag(I) and Cd(II) salts

A new bis-bidentate ligand, 1-[(5-methyl-2,2′-bipyridin-5′-yl)-methyl-1H-pyrazol-3-yl]-pyridine (L1), was designed and synthesized. The reactions of the ligand with [Cu(CH3CN)4]ClO4, Cu(ClO4)2·6H2O, AgNO3 and Cd(NO3)2·4H2O were carried out and dinuclear double helical complexes [CuI2L12][ClO4]2·CH3CN·0.5H2O (1), [CuII2L12(H2O)(CH3CN)][ClO4]4 (2), [AgI2L12](NO3)2·CH3CN (3) and [CdII2L12(NO3)4]·2H2O (4) were obtained and characterized by single crystal X-ray diffraction analyses, mass spectra, 1H NMR, and UV–Vis spectra. A dinuclear complex [NiII2L12(DMF)4](ClO4)4·H2O (5) was obtained by the reaction of the ligand with Ni(ClO4)2·6H2O. The results indicate that the formation of helicates is influenced by the structure of the bidentate ligand and the coordination geometry of the metal ions.

Hydrophobic Collapse of Foldamer Capsules Drives Picomolar-Level Chloride Binding in Aqueous Acetonitrile Solutions

Aqueous media are competitive environments in which to perform host-guest chemistry, particularly when the guest is highly charged. While hydrophobic binding is a recognized approach to this challenge in which apolar pockets can be designed to recognize apolar guests in water, complementary strategies are required for hydrophilic anions like chloride. Here, we present evidence of such an alternative mechanism, used everyday by proteins yet rare for artificial receptors, wherein hydrophobic interactions are shown to be responsible for organizing and stabilizing an aryl-triazole foldamer to help extract hydrophilic chloride ions from increasingly aqueous solutions. Therein, a double-helical complex gains stability upon burial of ∼80% of the π surfaces that simultaneously creates a potent, solvent-excluding microenvironment for hydrogen bonding. The chloride's overall affinity to the duplex is substantial in 25% water v/v in acetonitrile (logβ2 = 12.6), and it remains strong (logβ2 = 13.0) as the water content is increased to 50%. With the rise in predictable designs of abiological foldamers, this water-assisted strategy can, in principle, be utilized for binding other hydrophilic guests.

Helical Assembly Based on Quinoline-Based Molecular Clips

Molecule clips, di(2-quinoline-carboxaldehyde)-2,2′-bibenzoyl-hydrazone(H2L), with potential atropisomeric chirality was used as helicand for construction of dinuclear helicates. Reaction of the ligand with Co(NO3)2 and Cu(BF4)2 afforded dinuclear double helical complexes with the metal centers exhibiting the same absolute configurations. Thus the atropisomeric chiral bridging mode is main factor for the ligand to translate chirality of metal centers from one center to another.

Synthesis and Self-Association of Double-Helical AADD Arrays

The design and syntheses of four self-complementary oligomers that contain an underlying AADD hydrogen bond sequence are presented, and their self-association was examined in the solution and solid state. The molecular recognition between the two strands is highly sensitive to substitutions of their component heterocycles. Substitution with electron-donating and -withdrawing groups and the influence of preorganization has a large effect on the overall stabilities of the complexes studied. In particular, a wide range (>10(5) M(-1)) of stabilities with respect to substitutions at various positions in the AADD oligomers was demonstrated. In the most extreme case, the dimerization constant measured (K(dimer) ≥4.5×10(7) M(-1)) is comparable to the most stable homodimers of neutral AADD arrays reported to date.

Substituent Effects in Double‐Helical Hydrogen‐Bonded AAA‐DDD Complexes

Two series of DDD and AAA hydrogen-bond arrays were synthesized that form triply-hydrogen-bonded double-helical complexes when combined in CDCl(3) solution. Derivatization of the DDD arrays with electron-withdrawing groups increases the complex association constants by up to a factor of 30 in those arrays examined. Derivatization of the AAA arrays with electron donating substituents reveals a similar magnitude effect on the complex stabilities. The effect of substitution on both types of arrays are modeled quite satisfactorily (R(2) > 0.96 in all cases) as free energy relationships with respect to the sums of their Hammett substituent constants. In all, the complex stabilities can be manipulated over more than three orders of magnitude (>20 kJ mol(-1)) using this type of modification.

Bis[μ-N,N′-bis(quinolin-8-yl)pyridine-2,6-dicarboxamido]dizinc(II) dichloromethane disolvate

The title compound, [Zn(2)(C(25)H(15)N(5)O(2))(2)]·2CH(2)Cl(2), is a dinuclear double-helical complex which lies on a crystallographic twofold axis. In the complex, both ligands are partitioned into two tridentate domains which allow each ligand to bridge both metal centres. Each Zn(II) atom is six-coordinated in a distorted octahedral environment formed by two amide N atoms, two quinoline N atoms and two pyridine N atoms from two different ligand molecules, with the central pyridine ring, unusually, bridging two Zn(II) atoms. The deprotonated ligand is not planar, the amide side chains being considerably twisted out from the plane of the central pyridine ring.

Molecular pathways in DNA-DNA hybridization of surface-bound oligonucleotides

A molecular model of DNA, that has been shown to reproduce hybridization, is used here to study the transition from two single-stranded molecules to a double-helical complex in situations where one strand is attached to a surface. Transition Path Sampling simulations reveal that hybridization is initiated by forming specific contacts between distinct bases of the molecule. Molecules with repetitive sequences form double helices by sliding along each other after having formed initial contacts. For random sequences, it is shown that the pathway that molecules follow to hybridization depends on the linker length as well as the temperature, and is significantly different from that observed in the bulk.

Syntheses, Crystal Structure, and Magnetic Properties of a Self‐Assembling Dinickel(II) Helicate with Novel Bipyridine Ligand

AbstractA novel polydentate ligand, L = 2,2′‐bipyridyl‐6,6′‐bis(2‐acetylpyrazinohydrazone), was synthesized by condensation of 6,6′‐dihydrazine‐2,2′‐bipyridine and 2‐acetylpyrazine. Reaction of L ligand strands with nickel (II) perchlorate in CH3CN generates a double helical dinuclear complex. Its complexation behavior was studied by UV‐Vis spectrophotometric titration experiments that revealed the formation of dinuclear complexes [Ni2L2](ClO4)4. Moreover, the double‐helical structure of [Ni2L2](ClO4)4 was confirmed by X‐ray diffractometer. Each nickel(II) center occupies a distorted octahedral environment. Variable‐temperature magnetic measurements revealed weak antiferromagnetic interactions between Ni(II) ion centers with J = −0.34 cm−1.

Minimal complementary hydrogen-bonded double helices

Molecular strands incorporating three hydrogen bond donor (D) or acceptor (A) heterocycles form highly stable double helical complexes through a complementary AAA-DDD array structure.

Remarkable Tuning of the Coordination and Photophysical Properties of Lanthanide Ions in a Series of Tetrazole‐Based Complexes

A series of seven new tetrazole-based ligands (L1, L3-L8) containing terpyridine or bipyridine chromophores suited to the formation of luminescent complexes of lanthanides have been synthesized. All ligands were prepared from the respective carbonitriles by thermal cycloaddition of sodium azide. The crystal structures of the homoleptic terpyridine-tetrazolate complexes [Ln(Li)(2)]NHEt(3) (Ln = Nd, Eu, Tb for i = 1, 2; Ln = Eu for i = 3, 4) and of the monoaquo bypyridine-tetrazolate complex [Eu(H(2)O)(L7)(2)]NHEt(3) were determined. The tetradentate bipyridine-tetrazolate ligand forms nonhelical complexes that can contain a water molecule coordinated to the metal. Conversely, the pentadentate terpyridine-tetrazolate ligands wrap around the metal, thereby preventing solvent coordination and forming chiral double-helical complexes similarly to the analogue terpyridine-carboxylate. Proton NMR spectroscopy studies show that the solid-state structures of these complexes are retained in solution and indicate the kinetic stability of the hydrophobic complexes of terpyridine-tetrazolates. UV spectroscopy results suggest that terpyridine-tetrazolate complexes have a similar stability to their carboxylate analogues, which is sufficient for their isolation in aerobic conditions. The replacement of the carboxylate group with tetrazolate extends the absorption window of the corresponding terpyridine- (approximately 20 nm) and bipyridine-based (25 nm) complexes towards the visible region (up to 440 nm). Moreover, the substitution of the terpyridine-tetrazolate system with different groups in the ligand series L3-L6 has a very important effect on both absorption spectra and luminescence efficiency of their lanthanide complexes. The tetrazole-based ligands L1 and L3-L8 sensitize efficiently the luminescent emission of lanthanide ions in the visible and near-IR regions with quantum yields ranging from 5 to 53% for Eu(III) complexes, 6 to 35% for Tb(III) complexes, and 0.1 to 0.3% for Nd(III) complexes, which is among the highest reported for a neodymium complex. The luminescence efficiency could be related to the energy of the ligand triplet states, which are strongly correlated to the ligand structures.

Stereochemically non-rigid helical mercury(II) complexes

Reactions of the 1:2 condensate (L) of benzil dihydrazone and 2-acetylpyridine with Hg(ClO 4) 2 · xH 2O and HgI 2 yield yellow [HgL 2](ClO 4) 2 ( 1) and HgLI 2 ( 2), respectively. Homoleptic 1 is a 8-coordinate double helical complex with a Hg(II)N 8 core crystallising in the space group Pbca with cell dimensions: a = 16.2250(3), b = 20.9563(7), c = 31.9886(11) Å. Complex 2 is a 4-coordinate single helical complex having a Hg(II)N 2I 2 core crystallising in the space group P2 1/ n with cell dimensions a = 9.8011(3), b = 17.6736(6), c = 16.7123(6) Å and β = 95.760(3) o. In complex 1, the N-donor ligand L uses all of its binding sites to act as tetradentate. On the other hand, it acts as a bidentate N-donor ligand in 2 giving rise to a dangling part. From variable temperature 1H NMR studies both the complexes are found to be stereochemically non-rigid in solution. In the case of 2, the solution process involves wrapping up of the dangling part of L around the metal.

A Self-Associating ADADA Hydrogen-Bonded Double Helix

We report the design, synthesis, and characterization of an oligomer which incorporates a non-coplanar ADADA (hydrogen bond donor/acceptor) array within its structure. The molecule associates through self-complementary hydrogen bonding to form a dimeric double-helical complex.