Preferential binding of peptides to graphene edges and planes

Peptides identified from combinatorial peptide libraries have been shown to bind to a variety of abiotic surfaces. Biotic-abiotic interactions can be exploited to create hybrid materials with interesting electronic, optical, or catalytic properties. Here we show that peptides identified from a combinatorial phage display peptide library assemble preferentially to the edge or planar surface of graphene and can affect the electronic properties of graphene. Molecular dynamics simulations and experiments provide insight into the mechanism of peptide binding to the graphene edge.     

Characterization of N-acetyltryptophan degradation products in concentrated human serum albumin solutions and development of an automated high performance liquid chromatography-mass spectrometry method for their quantitation

N-acetyltryptophan (NAT) has long been used as a stabilizer in some protein solutions, such as human serum albumin, to prevent oxidative protein degradation. However, the fate of NAT has not been discussed in literature. Two NAT degradation products have been observed in concentrated albumin solutions (20% and 25%) and identified as 1-acetyl-3a-hydroxy-1,2,3,3a,8,8a-hexahydropyrrolo[2,3-b]indole-2-carboxylic acid and 1-acetyl-3a,8a-dihydroxy-1,2,3,3a,8,8a-hexahydropyrrolo[2,3-b]indole-2-carboxylic acid. To monitor the levels of these two previously unidentified NAT degradation products in concentrated albumin solutions, a fully automated method, incorporating online size exclusion chromatography (SEC) trapping and reversed-phase high performance liquid chromatography-mass spectrometry (HPLC-MS) with multiple reaction monitoring (MRM) analysis, has been developed and validated for their quantitative analysis. The method does not require an internal standard. The only sample manipulation is to obtain an albumin concentration of 4% in all standards and test HPLC samples. A limit of quantitation (LOQ) as low as 20 ng/mL has been achieved for both compounds. This method can readily be adopted for the quantitative determination of other small molecules in concentrated protein solutions.     

Conformationally rigid aromatic amino acids as potential building blocks for abiotic foldamers

This communication describes the development of conformationally constrained unnatural aromatic amino acids, constructed on rigid backbone wherein the carboxyl and amino groups project in two dimensions (planes) on the aromatic framework. Such a feature offers the possibility of design and development of conformationally ordered synthetic oligomers with intriguing structural architectures distinct from those classically observed. Furthermore, such amino acids will have the potential to extend the conformational space available for foldamer design with diverse backbone conformation and structural architectures.     

Thiacalix[4]arene based reconfigurable molecular switches: set-reset memorized sequential device

The fluorescent chemosensors 3, 5 and 7 based on thiacalix[4]arene bearing naphthyl groups have been designed and synthesized. The optical chemosensor 3 based on a thiacalix[4]arene of cone conformation behaves as "turn-on" optical chemosensor for Fe(3+) and F(-) ions. However, chemosensors 5 and 7 based on a thiacalix[4]arene of 1,3-alternate conformation demonstrate "turn-on" optical behaviour for Hg(2+), F(-) ions (with receptor 5 as turn-on for K(+) ions also) and "turn-off" behaviour for Fe(3+) ions. The simultaneous presence of Fe(3+) and Hg(2+) or K(+) or F(-) ions results in formulation of reversible "on-off" switches. Various molecular logic gates developed in response to molecular switching between these chemical inputs have been integrated into sequential logic circuits with memory function in a feedback loop which mimics "set-reset" molecular level information processing device.     

Reactivity of acyclic (pentadienyl)iron(1+) cations: synthetic studies directed toward the frondosins

A short, 4-step route to the scaffold of frondosin A and B is reported. The [1-methoxycarbonyl-5-(2',5'-dimethoxyphenyl)pentadienyl]Fe(CO)(3)(+) cation was prepared in two steps from (methyl 6-oxo-2,4-hexadienoate)Fe(CO)(3). Reaction of this cation with isopropenyl Grignard or cyclohexenyllithium reagents affords (2-alkenyl-5-aryl-1-methoxycarbonyl-3-pentene-1,5-diyl)Fe(CO)(3) along with other addition products. Oxidative decomplexation of these (pentenediyl)iron complexes, utilizing CuCl(2), affords 6-aryl-3-methoxycarbonyl-1,4-cycloheptadienes via the presumed intermediacy of a cis-divinylcyclopropane.     

Optical chemosensor for Ag+, Fe3+, and cysteine: information processing at molecular level

A thiacalix[4]arene based chemosensor 3 bearing two pyrene groups has been synthesized which demonstrates ratiometric sensing with Ag(+) and fluorescence quenching with Fe(3+) ions in mixed aqueous media. The 'in situ' prepared Ag(+) and Fe(3+) complexes showed high selectivity toward cysteine. The molecular switching between three chemical inputs (Ag(+), Fe(3+), cysteine) results in various molecular logic gates which have been integrated sequentially to generate a sequential information processing device.     

Study of non-covalent interactions of luotonin A derivatives and the DNA minor groove as a first step in the study of their analytical potential as DNA probes

The interaction between DNA and several newly synthesized derivatives of the natural anticancer compound luotonin A has been studied. The results from our work reveal an effective and selective alkaloid/double-stranded DNA (ds-DNA) interaction. In the presence of increasing amounts of ds-DNA, a noticeable fluorescence quenching of the luotonin A derivatives under study was observed. However, this effect did not take place when single-stranded DNA (ss-DNA) was employed. The association constant alkaloids/ds-DNA was calculated by quantitation of such a quenching effect. The influence of other quenchers, namely Co²⁺ and Br⁻ on the native fluorescence of luotonin A and derivatives was also studied, and a remarkable quenching effect was observed for both ions. We have also investigated how by binding DNA the alkaloids could get protected from the external Co²⁺ and Br⁻ quenchers. The Stern–Volmer constants (K _SV) for Co²⁺ and Br⁻ quenching effect on the studied alkaloids were considerably reduced (10–50%) after incubation of the compounds in the presence of DNA with regard to the K _SV values in absence of DNA. An increase in the fluorescence anisotropy values of luotonins was also produced only in the presence of ds-DNA but not in the case of ss-DNA. To better characterize the nature of that interaction, viscosimetry assays and ethidium bromide displacement studies were conducted. With regard to DNA reference solutions, the viscosity of solutions containing DNA and luotonin A derivatives was reduced or not significantly increased. It was also observed that the studied compounds were unable to displace the intercalating agent ethidium bromide. All of these results, together with the obtained association constants values (K _ass = 2.2 × 10² – 1.3 × 10³), support that neither covalent nor intercalating interactions luotonin A derivatives/ds-DNA are produced, leading to the conclusion that these alkaloids bind ds-DNA through the minor groove. The specific changes in the fluorescence behavior of luotonin A and derivatives distinguishing between ss-DNA and ds-DNA binding, lead us to propose these compounds as attractive turn-off probes to detect DNA hybridization.     

An ?-uniform hybrid scheme for singularly perturbed delay differential equations

In this paper, a singularly perturbed delay differential equation of first order has been considered. The problem is solved by using a hybrid scheme on a Shishkin mesh. The difference scheme is shown to converge to the continuous solution uniformly with respect to the perturbation parameter. Truncation errors are obtained. Finally, numerical experiments are carried out on a test problem, confirming the effectiveness of the proposed technique.     

Crystallographic recognition controls peptide binding for bio-based nanomaterials

The ability to control the size, shape, composition, and activity of nanomaterials presents a formidable challenge. Peptide approaches represent new avenues to achieve such control at the synthetic level; however, the critical interactions at the bio/nano interface that direct such precision remain poorly understood. Here we present evidence to suggest that materials-directing peptides bind at specific time points during Pd nanoparticle (NP) growth, dictated by material crystallinity. As such surfaces are presented, rapid peptide binding occurs, resulting in the stabilization and size control of single-crystal NPs. Such specificity suggests that peptides could be engineered to direct the structure of nanomaterials at the atomic level, thus enhancing their activity.