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Vincent Lynch

Publications and source records attributed to Vincent Lynch.

At least 19 recordsLinked to original sources
PubMed2006

Diindolylquinoxalines: effective indole-based receptors for phosphate anion.

The synthesis of a new series of 2,3-diindol-3'yl quinoxalines (DIQ), as well as a comparison of their anion recognition properties to those of our previously reported pyrrole based sensors, 2,3-dipyrrol-2'yl quinoxalines, is reported. To the best of our knowledge, this new DIQ system represents the first example of a free-standing indole-based small molecule receptor for which evidence of anion binding is available both in solution and in the solid-state. It also provides one of the few structurally characterized neutral receptor-dihydrogen phosphate complexes. This work thus serves to demonstrate the utility of indoles as an anion recognition motif.

Anions↗
PubMed2006

Inverted sapphyrin: a new family of doubly N-confused expanded porphyrins.

The synthesis of an inverted, methoxylated sapphyrin derivative is described. This system, wherein inversion of pyrrolic nitrogen atoms is configurationally enforced via the use of a 3,3'-bipyrrolic precursor, displays what is best described as "weak aromaticity" as judged from its spectroscopic features and supporting theoretical calculations.

Crystallography, X-Ray↗
PubMed2006

Electron transfer vs coordination chemistry: isomer-specific binding of HgII by an ortho-Wurster's thiacrown ether.

Isomeric p- and o-phenylenediamine-containing macrocyclic hosts (Wurster's thiacrown ethers L1 and L2, respectively) were prepared and studied as Hg(II) ionophores. The distinct electrochemical properties of the two hosts allowed for the formation of a coordination compound with the ortho-Wurster's thiacrown ether but not the para isomer. In the latter case, the Hg(II) ion served as an oxidant in an electron-transfer reaction with the host. Solutions of the Hg(II) complex of L2 were studied by 13C NMR spectroscopy and cyclic voltammetry and revealed a strong interaction between the redox-active phenylenediamine subunit and the bound metal cation. An X-ray analysis confirmed the participation of the three macrocyclic S atoms and both phenylenediamine N atoms in the stabilization of the complex.

Journal Article↗
PubMed2006

Tunable columnar mesophases utilizing C2 symmetric aromatic donor-acceptor complexes.

Derivatives of relatively electron rich 1,5-dialkoxynaphthalene (Dan) donors and relatively electron deficient 1,4,5,8-naphthalenetetracarboxylic diimide (Ndi) acceptors have been exploited in the folding and self-assembly of a variety of complex molecular systems in solution. Here, we report the use of Dan and Ndi derivatives to direct assembly of extended columns with alternating face-centered stacked structure in the solid state. A variety of 1:1 Dan:Ndi mixtures produced mesophases that were found to be stable over temperature ranges extending up to 110 degrees C. Analysis of these mesophases indicates mixtures with soft/plastic crystal phases and a few mixtures with the thermodynamic properties of true liquid crystals, all composed of alternating donor-acceptor columns within. Importantly, a correspondence was found between the clearing and crystallization points of the mesophase mixtures and the melting/clearing points of the component Ndi and Dan units, respectively. This correspondence enables the predictable tuning of mesophase phase transition temperatures. The study of sterically hindered derivatives led to a set of mixtures in which a dramatic and sudden color change (deep red to yellow) was observed upon crystallization of the mesophase due to a phase separation of the component donor and acceptor units.

Biomimetic Materials↗
PubMed2006

Polyhydroxylated sapphyrins: multisite non-metallic catalysts for activated phosphodiester hydrolysis.

Enhanced hydrolysis rates for the cleavage of bis(4-nitrophenyl)phosphate (BNPP), a model phosphodiester, may be achieved by using appropriately designed ditopic receptors containing the known phosphate-binding nucleus, sapphyrin, attached covalently to suitably oriented polyhydroxyl subunits. Evidence for the interaction between sapphyrin and BNPP comes from solid-state X-ray diffraction analysis of a diprotonated dihydroxylated sapphyrin-BNPP complex and from solution-phase (31)P NMR spectroscopic binding studies. The sapphyrins described in this paper may have a role to play as oligonucleotide cleavage agents.

Catalysis↗
PubMed2005

Wurster's thiacrown ethers: synthesis, properties, and Pt(II)-coordination chemistry.

Two isomeric redox-responsive azathiacrown ethers, based on p-phenylenediamine, have been synthesized in traditional crown (L1) and crownophane (L2) architectures. Each of these "Wurster's crowns" was designed to target the encapsulation of transition or heavy metal ions. The solid-state structures of these ligands show binding cavities defined by three exocyclic sulfur atoms and either a N donor atom (L1) or the electron-rich pi face of the phenylenediamine subunit (L2). The ability of these ligands to form complexes with platinum(II) was investigated by various techniques including 1H NMR spectroscopy, electrospray mass spectrometry, cyclic voltammetry, and single-crystal X-ray analysis. The traditional crown geometry proved to be better at forming stable endocyclic complexes with Pt(II) than the crownophane geometry. The square-planar Pt(II) crown complex includes direct bonding to the redox center (Pt1-N1 = 2.125 angstroms and Pt1-S(av) = 2.278 angstroms) with concomitant polarization of the phenylenediamine moiety. This results in the crown complex oxidizing 916 mV more anodically than the free ligand. In contrast, modest shifts in the oxidation potential of the crownophane isomer indicate poor interaction between the redox center and complexed Pt(II) ion.

Journal Article↗
PubMed2005

Calix[n]bispyrrolylbenzenes: synthesis, characterization, and preliminary anion binding studies.

A series of novel calixpyrrole-like macrocycles, calix[n]bis(pyrrol-2-yl)benzene (calix[n]BPBs, n=2-4) 9 a-11 a, have been synthesized by means of the TFA-catalyzed condensation reaction of bis(pyrrol-2-yl)benzene 8 a with acetone. Calix[2]BPB 9 a represents an expanded version of calix[4]pyrrole in which two of the four meso bridges are replaced by benzene rings. By contrast, systems 10 a and 11 a, which bear great considerable to calixbipyrroles 2 and 3, represent higher homologues of the basic calix[n]BPB motif. Solution-phase anion binding studies, carried out by means of (1)H NMR spectroscopic titrations in [D2]dichloromethane and isothermal titration calorimetry (ITC) in 1,2-dichloroethane, reveal that 9 a binds typical small anions with substantially higher affinities than 1, even though the same number of hydrogen bonding donor groups are found in both compounds. The basic building block for 9 a, benzene dipyrrole 8 a, also displays a higher affinity for anions than the building block for 1, dimethyldipyrromethane 16. Structural studies, carried out by single-crystal X-ray diffraction analyses, are consistent with the solution-phase results and reveal that 9 a is able to stabilize complexes with chloride and nitrate in the solid state. Structures of the PF6- and NO3- complexes of 10 a were also solved as were those of the acetone adduct of 9 a and the ethyl acetate adduct of 11 a.

Anions↗
PubMed2005

Anion-binding behavior of hybrid calixpyrroles.

Hybrid calixpyrrole systems are calixpyrrole-like macrocycles that are based on more than one type of small molecule building block. Structurally, these "mixed-breed" macrocycles differ from calixpyrroles in that some pyrrolic units in the latter are replaced by other hetereocyclic units such as furan, thiophene, bipyrrole, and bithiophene. Although several such systems have been reported in recent years, only a few have been studied as possible anion receptors. In this paper, the results of detailed anion binding studies involving several prototypic systems are reported. Taken in concert, these results highlight the fact that some hybrid systems, including compounds 2-5, display anion affinities that are considerably weaker than those of the parent system 1. On the other hand, they also show that compounds 6-8 are good receptors for "Y-shaped" anions, such as carboxylates, and that they bind these species with high affinity. These findings are strongly supported by solid-state structural studies, which reveal an interesting "cross binding mode" for the binding of carboxylate anions by the bis-thiophene, bis-pyrrole system 7.

Anions↗
PubMed2005

Molecular evolution of duplicated ray finned fish HoxA clusters: increased synonymous substitution rate and asymmetrical co-divergence of coding and non-coding sequences.

In this study the molecular evolution of duplicated HoxA genes in zebrafish and fugu has been investigated. All 18 duplicated HoxA genes studied have a higher non-synonymous substitution rate than the corresponding genes in either bichir or paddlefish, where these genes are not duplicated. The higher rate of evolution is not due solely to a higher non-synonymous-to-synonymous rate ratio but to an increase in both the non-synonymous as well as the synonymous substitution rate. The synonymous rate increase can be explained by a change in base composition, codon usage, or mutation rate. We found no changes in nucleotide composition or codon bias. Thus, we suggest that the HoxA genes may experience an increased mutation rate following cluster duplication. In the non-Hox nuclear gene RAG1 only an increase in non-synonymous substitutions could be detected, suggesting that the increased mutation rate is specific to duplicated Hox clusters and might be related to the structural instability of Hox clusters following duplication. The divergence among paralog genes tends to be asymmetric, with one paralog diverging faster than the other. In fugu, all b-paralogs diverge faster than the a-paralogs, while in zebrafish Hoxa-13a diverges faster. This asymmetry corresponds to the asymmetry in the divergence rate of conserved non-coding sequences, i.e., putative cis-regulatory elements. These results suggest that the 5' HoxA genes in the same cluster belong to a co-evolutionary unit in which genes have a tendency to diverge together.

Animals↗
PubMed2004

Calix[4]phyrins. Effect of peripheral substituents on conformational mobility and structure within a series of related systems.

A new, stepwise synthesis of calix[4]phyrins is described. It relies on the condensation of a ketone with pyrrole to form a dipyrromethane containing a quaternary carbon center that is subsequently condensed with an aromatic aldehyde. This methodology, in contrast to the previous rational approach described by this group (involving formation of a trisubstituted dipyrromethane via the condensation of an aldehyde with pyrrole, followed by condensation of this dipyrromethane with acetone), allows for a variety of bulky, ketone-derived substituents to be incorporated into the meso-like positions. The resulting systems, while all containing the same central macrocyclic core, display conformational properties that reflect the nature of these meso-like substituents; these conformational features were independently assessed by X-ray diffraction analysis, NMR spectroscopy, and quantum chemical calculations.

Calixarenes↗
PubMed2004

Thermodynamic analysis of receptors based on guanidinium/boronic acid groups for the complexation of carboxylates, alpha-hydroxycarboxylates, and diols: driving force for binding and cooperativity.

The thermodynamics of guanidinium and boronic acid interactions with carboxylates, alpha-hydroxycarboxylates, and diols were studied by determination of the binding constants of a variety of different guests to four different hosts (7-10). Each host contains a different combination of guanidinium groups and boronic acids. The guests included molecules with carboxylate and/or diol moieties, such as citrate, tartrate, and fructose, among others. The Gibbs free energies of binding were determined by UV/Vis absorption spectroscopy, by use of indicator displacement assays. The receptor based on three guanidinium groups (7) was selective for the tricarboxylate guest. The receptors that incorporated boronic acids (8-10) had higher affinities for guests that included alpha-hydroxycarboxylate and catechol moieties over guests containing only carboxylates or alkanediols. Isothermal titration calorimetry revealed the enthalpic and entropic contributions to the Gibbs free energies of binding. The binding of citrate and tartrate was investigated with hosts 7-10, for which all the binding events were exothermic, with positive entropy. Because of the selectivity of hosts 8-10, a simple boronic acid (14) was also investigated and determined to be selective for alpha-hydroxycarboxylates and catechols over amino acids and alkanediols. Further, the cooperativity of 8 and 9 in binding tartrate was also investigated, revealing little or no cooperativity with 8, but negative cooperativity with 9. A linear entropy/enthalpy compensation relationship for all the hosts 7-10, 14, and the carboxylate-/diol-containing guests was also obtained. This relationship indicates that increasing enthalpy of binding is offset by similar losses in entropy for molecular recognition involving guanidinium and boronic acid groups.

Binding Sites↗
PubMed2004

Octaethylporphyrin and expanded porphyrin complexes containing coordinated BF2 groups.

In contrast to octaethylporphyrin, which forms a very labile bis-BF(2) complex, treatment of the hexa- and octapyrrolic expanded porphyrins amethyrin and [32]octaphyrin with BF(3).Et(2) under standard reaction and work-up conditions gives rise to stable, non-labile mono- and bis-BF(2) complexes; these were readily characterised by, inter alia, X-ray diffraction analyses.

Boron Compounds↗
PubMed2003

Water soluble sapphyrins: potential fluorescent phosphate anion sensors.

As part of an ongoing effort to study the anion binding properties of sapphyrins in various media, a number of previously reported water solubilized sapphyrins were studied in methanol and in buffered, neutral aqueous solutions and found to undergo self-aggregation under these solution phase conditions. The nature of the species produced as the result of self-aggregation and the processes leading to their formation were studied via UV-vis absorbance and fluorescence spectroscopy. In previous work (V. Král, H. Furuta, K. Shreder, V. Lynch, and J. L. Sessler, J. Am. Chem. Soc. 1996, 118 1595-1607) it was found that the addition of phosphate-type anions to water soluble sapphyrins at pH 6.1 gives rise to visible spectroscopic changes consistent with the binding to the aggregated form and the concurrent formation of an anion-bound dimer with effective equilibrium constants on the order of 100-300 M(-1). In this study we show that at high phosphate-to-sapphyrin ratios in neutral, buffered aqueous solutions further deaggregation occurs to produce an anion-bound monomeric form. This highly fluorescent species is formed with effective equilibrium constants on the order of 6-19 M(-1) leading to considerations that sapphyrins could function as fluorescent phosphate anion sensors. In an effort to modulate the deaggregation properties, several new sapphyrin derivatives bearing two meso aryl substituents were prepared and studied. The aggregation properties of these latter systems were analyzed in methanol and, in the case of one water solublized system, in neutral aqueous media. In analogy to what was observed for the beta-alkyl substituted sapphyrins, H-type aggregates were seen for the water solubilized meso-substituted system in aqueous media. However, in contrast to the H-type dimers seen in the case of the meso-free systems in methanol, J-type dimers were observed in the case of the sapphyrins bearing two meso substituents in this solvent. The effective dimerization constants of several of the meso-diaryl sapphyrins were determined in methanol as were their pKa values in aqueous media. The solid state structure of the bis HBr salt of one of the meso-diaryl sapphyrins, specifically 10,15-bis(3,5-di-tert-butylphenyl)-3,22-diethyl-2,23-dimethylsapphyrin, was also determined and found to show elements in common with those of previously reported sapphyrin derivatives. In particular, the two counter anions were found to be hydrogen bound above and below the diprotonated sapphyrin plane.

Anions↗
PubMed2003

The first liquid-crystalline, expanded porphyrins.

Aliphatic derivatives of hydrazinophyrin, a new type of tetrapyrrolic macrocycle prepared by the condensation of 2,5-diformylpyrroles with hydrazine, exhibit liquid crystalline properties as judged from polarising optical microscopy; these hydrazinophyrins appear to be the first mesogens derived from an expanded porphyrin core.

Journal Article↗