Influence of 5-N-carboxamide modifications on the thermodynamic stability of oligonucleotides.

We have recently shown that the incorporation of modified nucleotides such as 5-N-carboxamide-deoxyuridines into random nucleic acid libraries improves success rates in SELEX experiments and facilitates the identification of ligands with slow off-rates. Here we report the impact of these modifications on the thermodynamic stability of both duplexes and intramolecular 'single-stranded' structures. Within duplexes, large, hydrophobic naphthyl groups were destabilizing relative to the all natural DNA duplex, while the hydrophilic groups exhibited somewhat improved duplex stability. All of the significant changes in stability were driven by opposing contributions from the enthalpic and entropic terms. In contrast, both benzyl and naphthyl modifications stabilized intramolecular single-stranded structures relative to their natural DNA analogs, consistent with the notion that intramolecular folding allows formation of novel, stabilizing hydrophobic interactions. Imino proton NMR data provided evidence that elements of the folded structure form at temperatures well below the Tm, with a melting transition that is distinctly less cooperative when compared to duplex DNA. Although there are no data to suggest that the unmodified DNA sequences fold into structures similar to their modified analogs, this still represents clear evidence that these modifications impart thermodynamic stability to the folded structure not achievable with unmodified DNA.

Chemical Equilibria and Kinetics in Aqueous Solutions of Zymonic Acid.

The chemistry of pyruvic acid is of great interest due to its essential role in metabolism for all life and its role in atmospheric chemistry. Pyruvic acid under a wide range of conditions, including normal storage conditions, will spontaneously dimerize to form zymonic acid. We isolated zymonic acid and, using a variety of 1D and 2D NMR techniques, identified it as a single structure as a solid or dissolved in DMSO. When in aqueous solution, however, we identified a mixture of five different tautomers and hydrates in equilibrium with each other with no single dominant form. The kinetics of this conversion were studied in situ via NMR. The reactivity of the tautomers and hydrates in aqueous solution is investigated and discussed in terms of aqueous reaction mechanisms. There is strong evidence for a direct, reversible conversion from an enol to a geminal diol without passing through a ketone intermediate, which implies the reversible addition of water across a double bond under ambient conditions. Additionally, there is evidence for a base catalyzed lactone ring formation, which is in essence a base catalyzed esterification reaction. The equilibrium between pyruvic acid and its oligomers in aqueous solution is of consequence in the natural environment.

Photochemistry of aqueous pyruvic acid.

The study of organic chemistry in atmospheric aerosols and cloud formation is of interest in predictions of air quality and climate change. It is now known that aqueous phase chemistry is important in the formation of secondary organic aerosols. Here, the photoreactivity of pyruvic acid (PA; CH3COCOOH) is investigated in aqueous environments characteristic of atmospheric aerosols. PA is currently used as a proxy for α-dicarbonyls in atmospheric models and is abundant in both the gas phase and the aqueous phase (atmospheric aerosols, fog, and clouds) in the atmosphere. The photoreactivity of PA in these phases, however, is very different, thus prompting the need for a mechanistic understanding of its reactivity in different environments. Although the decarboxylation of aqueous phase PA through UV excitation has been studied for many years, its mechanism and products remain controversial. In this work, photolysis of aqueous PA is shown to produce acetoin (CH3CHOHCOCH3), lactic acid (CH3CHOHCOOH), acetic acid (CH3COOH), and oligomers, illustrating the progression from a three-carbon molecule to four-carbon and even six-carbon molecules through direct photolysis. These products are detected using vibrational and electronic spectroscopy, NMR, and MS, and a reaction mechanism is presented accounting for all products detected. The relevance of sunlight-initiated PA chemistry in aqueous environments is then discussed in the context of processes occurring on atmospheric aerosols.

Photoinitiated synthesis of self-assembled vesicles.

The aqueous photochemistry of 2-oxooctanoic acid (a single-tailed surfactant) results in the synthesis of a double-tailed surfactant product followed by spontaneous self-assembly into vesicles. The photochemical mechanism is detailed here, and the reaction products are identified using mass spectrometry. Then, the self-assembled vesicles are characterized using dynamic light scattering, fluorescence microscopy, and NMR. Further, their stability over time and in the presence of MgCl2 salt is demonstrated. This work contributes to membrane evolution through the provision of a prebiotic route for the synthesis of plausible membrane components and subsequent self-assembly of a primitive enclosure.

Nanoscale structure-activity relationships, mode of action, and biocompatibility of gold nanoparticle antibiotics.

The emergence of resistance to multiple antimicrobial agents by pathogenic bacteria has become a significant global public health threat. Multi-drug-resistant (MDR) Gram-negative bacteria have become particularly problematic, as no new classes of small-molecule antibiotics for Gram-negative bacteria have emerged in over two decades. We have developed a combinatorial screening process for identifying mixed ligand monolayer/gold nanoparticle conjugates (2.4 nm diameter) with antibiotic activity. The method previously led to the discovery of several conjugates with potent activity against the Gram-negative bacterium Escherichia coli. Here we show that these conjugates are also active against MDR E. coli and MDR Klebsiella pneumoniae. Moreover, we have shown that resistance to these nanoparticles develops significantly more slowly than to a commercial small-molecule drug. These results, combined with their relatively low toxicity to mammalian cells and biocompatibility in vivo, suggest that gold nanoparticles may be viable new candidates for the treatment of MDR Gram-negative bacterial infections.

Photochemical kinetics of pyruvic acid in aqueous solution.

Pyruvic acid in the atmosphere is found in both the gas and aqueous phases, and its behavior gives insight into that of other α-keto acids. Photolysis is a significant degradation pathway for this molecule in the environment, and in aqueous solution the major photoproducts are higher-molecular-weight compounds that may contribute to secondary organic aerosol mass. The kinetics of the aqueous-phase photolysis of pyruvic acid under aerobic and anaerobic conditions was investigated in order to calculate the first-order rate constant, Jaq, in solution. Analysis of the exponential decay of pyruvic acid was performed by monitoring both pyruvic acid and its photolytic products over the course of the reaction by (1)H NMR spectroscopy. Detection of major and minor products in the 0.1, 0.05, and 0.02 M pyruvic acid photolyses clearly demonstrates that the primary reaction pathways are highly dependent on the initial pyruvic acid concentration and the presence of dissolved oxygen. The Jaq values were calculated with approximations based on the dominant pathways for limiting cases of the mechanism. Finally, a model study using the calculated rate constants demonstrates the importance of aqueous-phase photolysis as a sink for pyruvic acid in the atmosphere, compared with gas-phase photolysis and OH oxidation.

Inclusion compound based approach to arrays of artificial dipolar molecular rotors: bulk inclusions.

We examine the insertion of two dipolar molecular rotors as guests into a host, tris(o-phenylenedioxy)cyclotriphosphazine (TPP, 1), using differential scanning calorimetry, solid-state NMR, powder X-ray diffraction, and dielectric spectroscopy. The rotors are 1-(4'-n-pentylbiphenyl-4-yl)-12-(2,3-dichlorophenyl)-p-dicarba-closo-dodecaborane and 1,12-bis(2,3-dichlorophenyl)-p-dicarba-closo-dodecaborane. Both enter the bulk even though their nominal diameter exceeds the nominal channel diameter and although a closely related rotor, 1-n-hexadecyl-12-(2,3-dichlorophenyl)-p-dicarba-closo-dodecaborane, is known to produce a surface inclusion compound. Rotational barriers of 5.4-9.3 kcal/mol were found for the dichlorophenyl rotator contained within the TPP channel. Clearly, van der Waals diameters in themselves do not suffice to predict TPP channel entry. It is suggested that the efficacy of the p-carborane stopper is reduced by the presence of the two relatively bulky adjacent benzene rings, which help to stretch the channel, and by the axial direction of its axis, which prevents the attached rotator from contributing to the stopping action.

Sunlight-initiated chemistry of aqueous pyruvic acid: building complexity in the origin of life.

Coupling chemical reactions to an energy source is a necessary step in the origin of life. Here, we utilize UV photons provided by a simulated sun to activate aqueous pyruvic acid and subsequently prompt chemical reactions mimicking some of the functions of modern metabolism. Pyruvic acid is interesting in a prebiotic context due to its prevalence in modern metabolism and its abiotic availability on early Earth. Here, pyruvic acid (CH3COCOOH, a C3 molecule) photochemically reacts to produce more complex molecules containing four or more carbon atoms. Acetoin (CH3CHOHCOCH3), a C4 molecule and a modern bacterial metabolite, is produced in this chemistry as well as lactic acid (CH3CHOHCOOH), a molecule which, when coupled with other abiotic chemical reaction pathways, can provide a regeneration pathway for pyruvic acid. This chemistry is discussed in the context of plausible environments on early Earth such as near the ocean surface and atmospheric aerosol particles. These environments allow for combination and exchange of reactants and products of other reaction environments (such as shallow hydrothermal vents). The result could be a contribution to the steady increase in chemical complexity requisite in the origin of life.

Inclusion compound based approach to arrays of artificial dipolar molecular rotors. A surface inclusion.

We describe an approach to regular triangular arrays of dipolar molecular rotors based on insertion of dipolar rotator carrying shafts as guests into channels of a host, tris(o-phenylenedioxy)cyclotriphosphazene (TPP). The rotor guests can either enter the bulk of the host or stay at or near the surface, if a suitable stopper is installed at the end of the shaft. Differential scanning calorimetry, solid-state NMR, and powder X-ray diffraction were used to examine the insertion of a dipolar rotor synthesized for the purpose, 1-n-hexadecyl-12-(2,3-dichlorophenyl)-p-dicarba-closo-dodecaborane, and it was found that it forms a surface inclusion compound. Rotational barriers from 1.2 to 9 kcal/mol were found by dielectric spectroscopy and were attributed to rotors inserted into the surface to different degrees, some rubbing the surface as they turn.

Three serendipitous pathways in E. coli can bypass a block in pyridoxal-5'-phosphate synthesis.

Bacterial genomes encode hundreds to thousands of enzymes, most of which are specialized for particular functions. However, most enzymes have inefficient promiscuous activities, as well, that generally serve no purpose. Promiscuous reactions can be patched together to form multistep metabolic pathways. Mutations that increase expression or activity of enzymes in such serendipitous pathways can elevate flux through the pathway to a physiologically significant level. In this study, we describe the discovery of three serendipitous pathways that allow synthesis of pyridoxal-5'-phosphate (PLP) in a strain of E. coli that lacks 4-phosphoerythronate (4PE) dehydrogenase (PdxB) when one of seven different genes is overexpressed. We have characterized one of these pathways in detail. This pathway diverts material from serine biosynthesis and generates an intermediate in the normal PLP synthesis pathway downstream of the block caused by lack of PdxB. Steps in the pathway are catalyzed by a protein of unknown function, a broad-specificity enzyme whose physiological role is unknown, and a promiscuous activity of an enzyme that normally serves another function. One step in the pathway may be non-enzymatic.

A dimethyl ketal-protected benzoin-based linker suitable for photolytic release of unprotected peptides.

Photolabile 3',5'-dimethoxybenzoin-based linkers are advantageous for a variety of solid-phase synthetic procedures and manipulations of biomolecules because UV irradiation in aqueous media provides fast and essentially quantitative release of tethered molecules, while generating unreactive side products. Practical applications of previously reported linkers are compromised to some extent by the 1,3-dithiane protection of the benzoin carbonyl group and the lengthy synthesis. We have extended the group of photocleavable 3',5'-dimethoxybenzoin-based linkers by designing and synthesizing a linker in which the carbonyl group is protected as a dimethyl ketal. This protection is compatible with commonly used esterification and amide bond formation techniques, including the Fmoc/tBu strategy for solid phase peptide synthesis, is stable under mild acidic conditions, and can be quantitatively removed in <5 min by 3% TFA in dichloromethane. Irradiation of beads carrying peptides attached to the linker at 350 nm in aqueous or partially aqueous media affords >90% release after 30 min. The linker was synthesized from commercially available starting materials in five steps with an overall yield of 40% and without any column chromatography purification. Additionally, we developed a route to a dithiane-protected linker that requires only two steps and proceeds in 65% yield, a significant improvement over previous synthetic routes.

Pretransitional orientational ordering of a calamitic liquid crystal by helical nanofilaments of a bent-core mesogen.

Mixtures of 8CB (a calamitic mesogen) and NOBOW (P-9-O-PIMB, a bent-core mesogen) have been investigated using differential scanning calorimetry, nuclear magnetic resonance spectroscopy, and freeze fracture transmission electron microscopy. On cooling the isotropic mixture, the NOBOW component phase separates, forming a dilute, random network of helical nanofilaments in the B4 phase with isotropic 8CB material filling the interstitial volume. At lower temperature, but still far above the bulk isotropic-nematic transition of pure 8CB, a significant fraction of the 8CB becomes prealigned on the filament surfaces. We propose that this pretransitional ordering is induced by short-range interactions of the polar 8CB molecules with the NOBOW filaments, leading to the formation of an adsorbed film of orientationally frozen 8CB around each filament.

LiCB(11)(CH(3))(12)-catalyzed radical polymerization of isobutylene: highly branched polyisobutylene and an isobutylene-ethyl acrylate copolymer.

In the presence of LiCB(11)Me(12) catalyst and a nonoxidizing radical initiator, isobutylene undergoes radical chain polymerization in an inert solvent at ambient temperature and pressure to give a new highly branched form of polyisobutylene. Copolymerization with ethyl acrylate is also possible.

New type of Li ion conductor with 3D interconnected nanopores via polymerization of a liquid organic electrolyte-filled lyotropic liquid-crystal assembly.

A new type of polymer electrolyte material for Li ion transport has been developed. This material is based on a polymerizable lyotropic (i.e., amphiphilic) liquid crystal (1) that forms a type-II bicontinuous cubic (Q(II)) phase with the common liquid electrolyte, propylene carbonate (PC), and its Li salt solutions. The resulting cross-linked, solid-liquid nanocomposite has an ordered, three-dimensional interconnected network of phase-separated liquid PC nanochannels and exhibits a room-temperature ion conductivity of 10(-4) to 10(-3) S cm(-1) when formed with 15 wt % 0.245 M LiClO(4)-PC solution. This value approaches that of conventional gelled poly(ethylene oxide)-based electrolytes blended with larger amounts of higher-concentration Li salt solutions. It is also similar to that of a bulk 0.245 M LiClO(4)-PC solution measured using the same AC impedance methods. Preliminary variable-temperature ion conductivity and NMR DOSY studies showed that liquidlike diffusion is present in the Q(II) nanochannels and that good ion conductivity ( approximately 10(-4) S cm(-1)) and PC mobility are retained down to -35 degrees C (and lower). This type of stable, liquidlike ion conductivity over a broad temperature range is typically not exhibited by conventional gelled-polymer- or liquid-crystal-based electrolytes, making this new material potentially valuable for enabling Li ion batteries that can operate more efficiently over a wider temperature range.

A novel method for conjugating the terminal amine of peptide ligands to cholesterol: synthesis iRGD-cholesterol.

AIM: Conventional conjugation reactions often involve the use of activated PEG as a linker, but concerns about PEG-mediated reduction in intracellular delivery and enhanced immunogenicity have generated interest in developing methods that eliminate the need for a PEG linker. MATERIALS & METHODS: Reaction conditions were identified that specifically couples the terminal amine of a cyclic iRGD peptide (CRGDRGPDC) to the hydroxyl moiety of cholesterol through a short carbamate linker. RESULTS & CONCLUSION: Using this method for synthesizing iRGD-cholesterol, peptide ligands can be incorporated into lipid-based delivery systems, thereby eliminating concerns about adverse reactions to PEG. Toxicity and stability data indicate low toxicity and adequate serum stability at low ligand levels.

Pyridine ligand rotation in self-assembled trigonal prisms. Evidence for intracage solvent vapor bubbles.

The rate of interconversion of the two inequivalent edges of the pyridine rings in the trigonal prism 3c, self-assembled from 3 equiv of the star connector, tetrakis[4-(4-pyridylethynyl)phenyl]cyclobutadienecyclopentadienylcobalt, and 6 equiv of a platinum linker, cis-(Me3P)2Pt(2+) 2 TfO(-), was determined by DNMR in nitromethane. It exhibits a highly unusual bilinear Eyring plot. In the low temperature regime, the activation enthalpy DeltaH(double dagger) is approximately 12 kcal/mol and an activation entropy DeltaS(double dagger) ranges from approximately -15 to approximately 0 cal/mol x K as a function of the nature and concentration of the anions present. The reaction is attributed to hindered rotation of the pyridine rings about the Pt-N bond, facilitated by a tight pairing with a counterion. Above a counterion-dependent limiting temperature, DeltaH(double dagger) and DeltaS(double dagger) change abruptly to approximately 35 kcal/mol and approximately 60 cal/mol x K, respectively. The changes largely compensate, such that the reactions have comparable rates in the two regimes, both amenable to DNMR measurement, but their mechanisms clearly differ. Several kinetic models for the involvement of ion pairing equilibria fit the observed data nearly equally well, and they all contain a reaction step with high DeltaH(double dagger) and DeltaS(double dagger) values in the high-temperature regime. Its mechanism is proposed to involve a counterion-assisted reversible dissociation of one or two adjacent Pt-N bonds, followed by nearly free rotation of the terminal pyridine ring or rings and subsequent bond reclosure, which is similar to the last presumed step in the initial prism assembly. An interpretation of the very high DeltaS(double dagger) value is suggested by molecular dynamics calculations: at equilibrium, there is a bubble of gaseous nitromethane solvent inside the prism, and it collapses when the prism opens as the transition state is reached. A simple calculation of the entropy of cavitation provides quantitative support for this tentative proposal. The presence of such voids might be generally important for the formation and properties of self-assembled cages.

Coordination-driven face-directed self-assembly of trigonal prisms. Face-based conformational chirality.

The coordination-driven self-assembly of four different trigonal prisms from 3 equiv of one of four different tetrapyridyl star connectors and 6 equiv of a platinum linker dication in nitromethane is presented. This face-directed approach affords high yields without template assistance. The prisms have been characterized by multinuclear and DOSY NMR and dual ESI-FT-ICR mass spectrometry. The use of a conformationally chiral star connector leads to a conformationally chiral prism when connector arm ends attached to a vertex have a strongly correlated twist sense and chirality is communicated across polyhedral faces, edges, and vertices. Molecular mechanics results suggest that in the smallest prism 3d collective effects dominate and the all-P and all-M conformers are strongly favored. NMR data prove that the two edges of the pyridine rings in the triflate salts of 3a-3d are distinct. An Eyring plot of rates obtained from line-shape analysis and 1-D EXCHSY NMR yields an activation enthalpy DeltaH(double dagger) of approximately 12 kcal/mol and activation entropy DeltaS(double dagger) of approximately -15 cal/mol x K for the edge interconversion process, compatible with pyridine rotation around the Pt-N bond. For 3c, this behavior is observed only up to approximately 318 K. At higher temperatures, the Eyring plot is again linear but follows a very different straight line, with a DeltaH(double dagger) of approximately 35 kcal/mol and DeltaS(double dagger) of approximately 60 cal/mol x K. This highly unusual result is further investigated and discussed in the following companion paper.

Effect of Conformational Chirality on Optical Activity Observed in a Smectic of Achiral, Bent-Core Molecules.

Smectics of achiral, tilted bent-core liquid crystal molecules are chiral, but their optical activity is generally small. Here, we study the effect of conformational chirality on optical activity in smectic phases of an achiral, bent-core mesogen, W513. The neat material has a modulated B4 phase, which appears dark under crossed polarizers and shows no observable optical rotation under decrossed polarizers. However, mixtures of W513 with a rod-like mesogen, 8CB, show a conventional B4 phase, in which distinct left- and right-handed chiral domains with opposite optical activity are observed. The optical behavior of the mixtures is consistent with NMR results, which show a splitting of the carbonyl peak of the bent-core molecules into two, indicating a twisted conformation between the two molecular arms of the bent-core molecules as in conventional B4 materials.