Synteza oraz właściwości fizykochemiczne bis-interkalatorów naftalimidowych

Wydział Chemii

Nowe metody wyznaczania parametru asymetrii tensora gradientu pola elektrycznego w spektroskopii NQR i ich zastosowanie do badania układów nieuporządkowanych

Wydział Fizyki

Grignard Reaction - Synthesis of Substituted Benzoic Acids

A convenient preparation of substituted benzoic acids from Grignard additions to solid carbon dioxide. Students create a library of carboxylic acids by using differentially substituted, commercially available aryl bromides, which can be used as the starting materials for a multistep synthesis. This is a modification and improvement of a very popular undergraduate organic chemistry experiment.

New insights into Hoogsteen base pairs in DNA duplexes from a structure-based survey.

Hoogsteen (HG) base pairs (bps) provide an alternative pairing geometry to Watson-Crick (WC) bps and can play unique functional roles in duplex DNA. Here, we use structural features unique to HG bps (syn purine base, HG hydrogen bonds and constricted C1'-C1' distance across the bp) to search for HG bps in X-ray structures of DNA duplexes in the Protein Data Bank. The survey identifies 106 A•T and 34 G•C HG bps in DNA duplexes, many of which are undocumented in the literature. It also uncovers HG-like bps with syn purines lacking HG hydrogen bonds or constricted C1'-C1' distances that are analogous to conformations that have been proposed to populate the WC-to-HG transition pathway. The survey reveals HG preferences similar to those observed for transient HG bps in solution by nuclear magnetic resonance, including stronger preferences for A•T versus G•C bps, TA versus GG steps, and also suggests enrichment at terminal ends with a preference for 5'-purine. HG bps induce small local perturbations in neighboring bps and, surprisingly, a small but significant degree of DNA bending (∼14°) directed toward the major groove. The survey provides insights into the preferences and structural consequences of HG bps in duplex DNA.

15N NMR relaxation data reveal significant chemical exchange broadening in the alpha-domain of human α-lactalbumin

Human alpha-lactalbumin (alpha-LA), a 123-residue calcium-binding protein, has been studied using (15)N NMR relaxation methods in order to characterize backbone dynamics of the native state at the level of individual residues. Relaxation data were collected at three magnetic field strengths and analyzed using the model-free formalism of Lipari and Szabo. The order parameters derived from this analysis are generally high, indicating a rigid backbone. A total of 46 residues required an exchange contribution to T(2); 43 of these residues are located in the alpha-domain of the protein. The largest exchange contributions are observed in the A-, B-, D-, and C-terminal 3(10)-helices of the alpha-domain; these residues have been shown previously to form a highly stable core in the alpha-LA molten globule. The observed exchange broadening, along with previous hydrogen/deuterium amide exchange data, suggests that this part of the alpha-domain may undergo a local structural transition between the well-ordered native structure and a less-ordered molten-globule-like structure.

Immobilisation of heavy metal in cement-based solidification/stabilisation: a review

Heavy metal-bearing waste usually needs solidification/stabilization (s/s) prior to landfill to lower the leaching rate. Cement is the most adaptable binder currently available for the immobilisation of heavy metals. The selection of cements and operating parameters depends upon an understanding of chemistry of the system. This paper discusses interactions of heavy metals and cement phases in the solidification/stabilisation process. It provides a clarification of heavy metal effects on cement hydration. According to the decomposition rate of minerals, heavy metals accelerate the hydration of tricalcium silicate (C3S) and Portland cement, although they retard the precipitation of portlandite due to the reduction of pH resulted from hydrolyses of heavy metal ions. The chemical mechanism relevant to the accelerating effect of heavy metals is considered to be H+ attacks on cement phases and the precipitation of calcium heavy metal double hydroxides, which consumes calcium ions and then promotes the decomposition Of C3S. In this work, molecular models of calcium silicate hydrate gel are presented based on the examination of Si-29 solid-state magic angle spinning/nuclear magnetic resonance (MAS/NMR). This paper also reviews immobilisation mechanisms of heavy metals in hydrated cement matrices, focusing on the sorption, precipitation and chemical incorporation of cement hydration products. It is concluded that further research oil the phase development during cement hydration in the presence of heavy metals and thermodynamic modelling is needed to improve effectiveness of cement-based s/s and extend this waste management technique. (C) 2008 Elsevier Ltd. All rights reserved.

Novel inclusion complex of ibuprofen tromethamine with cyclodextrins: Physico-chemical characterization

Guest-host interactions of ibuprofen tromethamine salt (Ibu.T) with native and modified cyclodextrins (CyDs) have been investigated using several techniques, namely phase solubility diagrams (PSDs), proton nuclear magnetic resonance (H-1 NMR), differential scanning calorimetry (DSC), Fourier transform infrared spectroscopy (FT-IR), X-ray powder diffractometry (XRPD). scanning-electron microscopy (SEM) and molecular mechanics (MM). From the analysis of PSD data (A(L)-type) it is concluded that the anionic tromethamine salt of ibuprofen (pK(a) = 4.55) forms 1: 1 soluble complexes with all CyDs investigated in buffered water at pH 7.0, while the neutral form of Ibu forms an insoluble complex with beta-CyD (B-S-type) in buffered water at pH 2.0. Ibu.T has a lower tendency to complex with beta-CyD (K-11 = 58 M-1 at pH 7.0) compared with the neutral Ibu (K-11 = 4200 M (1)) in water. Complex formation of Ibu.T with beta-CyD (Delta G degrees = -20.4 kJ/mol) is enthalpy driven (Delta H degrees = -22.9 kJ/mol) and is accompanied by a small unfavorable entropy (Delta S degrees = -8.4 J/mol K) change. H-1 NMR studies and MM computations revealed that, on complexation, the hydrophobic central benzene ring of lbu.T and part of the isobutyl group reside within the beta-CyD cavity leaving the peripheral groups (carboxylate, tromethamine and methyl groups) located near the hydroxyl group networks at either rim of beta-CyD. PSD, H-1 NMR, DSC, FT-IR, XRPD, SEM and MM studies confirmed the formation of Ibu.T/beta-CyD inclusion complex in solution and the solid state. (C) 2009 Elsevier B.V. All rights reserved.

Characterisation of products of tricalcium silicate hydration in the presence of heavy metals

The hydration of tricalcium silicate (C(3)S) in the presence of heavy metal is very important to cement-based solidification/stabilisation (s/s) of waste. In this work, tricalcium silicate pastes and aqueous suspensions doped with nitrate salts of Zn(2+), Pb(2+), Cu(2+) and Cr(3+) were examined at different ages by X-ray powder diffraction (XRD), thermal analysis (DTA/TG) and (29)Si solid-state magic angle spinning/nuclear magnetic resonance (MAS/NMR). It was found that heavy metal doping accelerated C(3)S hydration, even though Zn(2+) doping exhibited a severe retardation effect at an early period of time of C(3)S hydration. Heavy metals retarded the precipitation of portlandite due to the reduction of pH resulted from the hydrolysis of heavy metal ions during C(3)S hydration. The contents of portlandite in the control, Cr(3+)-doped, Cu(2+)-doped, Pb(2+)-doped and Zn(2+)-doped C(3)S pastes aged 28 days were 16.7, 5.5, 5.5, 5.5, and <0.7%, respectively. Heavy metals co-precipitated with calcium as double hydroxides such as (Ca(2)Cr(OH)(7).3H(2)O, Ca(2)(OH)(4)4Cu(OH)(2).2H(2)O and CaZn(2)(OH)(6).2H(2)O). These compounds were identified as crystalline phases in heavy metal doping C(3)S suspensions and amorphous phases in heavy metal doping C(3)S pastes. (29)Si NMR data confirmed that heavy metals promoted the polymerisation of C-S-H gel in 1-year-old of C(3)S pastes. The average numbers of Si in C-S-H gel for the Zn(2+)-doped, Cu(2+)-doped, Cr(3+)-doped, control, and Pb(2+)-doped C(3)S pastes were 5.86, 5.11, 3.66, 3.62, and 3.52. And the corresponding Ca/Si ratios were 1.36, 1.41, 1.56, 1.57 and 1.56, respectively. This study also revealed that the presence of heavy metal facilitated the formation of calcium carbonate during C(3)S hydration process in the presence of carbon dioxide.

Self-lubricating silicone elastomer biomaterials

Silicone has a relatively high coefficient of friction and silicone medical devices therefore lack inherent lubricity, leading to pain on device insertion and potential tissue trauma. In this study, higher molecular weight tetra(alkoxy) silanes, particularly tetra(oleyloxy) silane, have been used as crosslinkers in the condensation cure of a hydroxy end-functionalised linear poly(dimethylsiloxane). The resulting elastomers displayed a persistent lubricous surface of oleyl alcohol, and coefficients of friction (static and dynamic) approaching zero. Chemical structures of the synthesised silanes and surface alcohol exudate were confirmed by nuclear magnetic resonance spectroscopy. Mechanical properties of the elastomers, which were chemically identical to conventionally cured systems, suggested that an 80/20 mixture of tetra(oleyloxy) silane and tetra(propoxysilane) gave the best compromise between desirable mechanical and frictional properties.

Stability of 5-aminolevulinic acid in novel non-aqueous gel and patch-type systems intended for topical application.

Aminolevulinic acid (ALA) stability within topical formulations intended for photodynamic therapy (PDT) is poor due to dimerisation to pyrazine-2,5-dipropionic acid (PY). Most strategies to improve stability use low pH vehicles, which can cause cutaneous irritancy. To overcome this problem, a novel approach is investigated that uses a non-aqueous vehicle to retard proton-induced charge separation across the 4-carbonyl group on ALA and lessen nucleophilic attack that leads to condensation dimerisation. Bioadhesive anhydrous vehicles based on methylvinylether-maleic anhydride copolymer patches and poly(ethyleneglycol) or glycerol thickened poly(acrylic acid) gels were formulated. ALA stability fell below pharmaceutically acceptable levels after 6 months, with bioadhesive patches stored at 5°C demonstrating the best stability by maintaining 86.2% of their original loading. Glycerol-based gels maintained 40.2% in similar conditions. However, ALA loss did not correspond to expected increases in PY, indicating the presence of another degradative process that prevented dimerisation. Nuclear magnetic resonance (NMR) analysis was inconclusive in respect of the mechanism observed in the patch system, but showed clearly that an esterification reaction involving ALA and both glycerol and poly(ethyleneglycol) was occurring. This was especially marked in the glycerol gels, where only 2.21% of the total expected PY was detected after 204 days at 5°C. Non-specific esterase hydrolysis demonstrated that ALA was recoverable from the gel systems, further supporting esterified binding within the gel matrices. It is conceivable that skin esterases could duplicate this finding upon topical application of the gel and convert these derivatives back to ALA in situ, provided skin penetration is not affected adversely.

Elucidation of the interactions between the transcription factor E2A and the transcriptional co-activator CBP/p300

E2A is a transcription factor that plays a particularly critical role in lymphopoiesis. The chromosomal translocation 1;19, disrupts the E2A gene and results in the expression of the fusion oncoprotein E2A-PBX1, which is implicated in acute lymphoblastic leukemia. Both E2A and E2A-PBX1 contain two activation domains, AD1 and AD2, which comprise conserved ΦxxΦΦ motifs where Φ denotes a hydrophobic amino acid. These domains function to recruit transcriptional co-activators and repressors, including the histone acetyl transferase CREB binding protein (CBP) and its paralog p300. The PCET motif within E2A AD1 interacts with the KIX domain of CBP/p300, the disruption of which abrogates the transcriptional activation by E2A and the transformative properties of E2A-PBX1. The generation of a peptide-based inhibitor targeting the PCET:KIX interaction would serve useful in further assessing the role of E2A and E2A-PBX1 in lymphopoiesis and leukemogenesis. An interaction between E2A AD2 and the KIX domain has also been recently identified, and the TAZ domains of CBP/p300 have been shown to interact with several transcription factors that contain ΦxxΦΦ motifs. Thus the design of an inhibitor of the E2A:CBP/p300 interaction requires the full complement of interactions between E2A and the various domains of CBP/p300 to be elucidated. Here, we have used nuclear magnetic resonance (NMR) spectroscopy to determine that AD2 interacts with KIX at the same site as PCET, which indicates that the E2A:KIX interaction can be disrupted by targeting a single binding site. Using an iterative synthetic peptide microarray approach, a peptide with the sequence DKELQDLLDFSLQY was derived from PCET to interact with KIX with higher affinity than the wild type sequence. This peptide now serves as a lead molecule for further development as an inhibitor of the E2A:CBP/p300 interaction. Fluorescence anisotropy, peptide microarray technology, and isothermal titration calorimetry were employed to characterize interactions between both TAZ domains of CBP/p300 and the PCET motif and AD2 of E2A. Alanine substitution of residues within PCET demonstrated that the ΦxxΦΦ motif is a key mediator of these interactions, analogous to the PCET:KIX interaction. These findings now inform future work to establish possible physiological roles for the E2A:TAZ1 and E2A:TAZ2 interactions.

Hapten synthesis and antibody production for the development of a melamine immunoassay

The incorporation of melamine into food products is banned but its misuse has been widely reported in both animal feeds and food. The development of a rapid screening immunoassay for monitoring of the substance is an urgent requirement. Two haptens of melamine were synthesized by introducing spacer arms of different lengths and structures on the triazine ring of the analyte molecular structure. 6-Aminocaproic acid and 3-mercaptopropionic acid were reacted with 2-chloro-4,6-diamino-1,3,5-triazine (CAAT) to produce hapten 1[3-(4,6-diamino-1,6-dihydro-1,3,5-triazin-2-ylamino) hexanoic acid] and hapten 2[3-(4,6-diamino-1,6-dihydro-1,3,5-triazin-2-ylthio) propanoic acid]. respectively. The molecular structures of the two haptens were identified by I H nuclear magnetic resonance spectrometry, mass spectrometry and infrared spectrometry. An immunogen was prepared by coupling hapten 1 to bovine serum albumin (BSA). Two plate coating antigens were prepared by coupling both haptens to egg ovalbumin (OVA). A competitive indirect enzyme-linked immunosorbent assay (ciELISA) was developed to evaluate homogeneous and heterogeneous assay formats. The results showed that polyclonal antibodies with high titers were obtained, and the heterogeneous immunoassay format demonstrated a better performance with an IC50 of 70.6 ng mL(-1), a LOD of 2.6 ng mL(-1) and a LOQ of 7.6 ng mL(-1). Except for cyromazine, no obvious cross-reactivity to common compounds was found. The data showed that the hapten synthesis was successful and the resultant antisera could be used in an immunoassay for the rapid and sensitive detection of this banned chemical. (C) 2010 Elsevier B.V. All rights reserved.

Metabolic profile changes in the testes of mice with streptozotocin-induced type 1 diabetes mellitus

Contrary to the traditional view, recent studies suggest that diabetes mellitus has an adverse influence on male reproductive function. Our aim was to determine the effect of diabetes on the testicular environment by identifying and then assessing perturbations in small molecule metabolites. Testes were obtained from control and streptozotocin-induced diabetic C57BL/6 mice, 2, 4 and 8 weeks post-treatment. Diabetic status was confirmed by glycated haemoglobin, non-fasting blood glucose, physiological condition and body weight. A novel extraction procedure was utilized to obtain protein free, low-molecular weight, water soluble extracts which were then assessed using H-1 nuclear magnetic resonance spectroscopy. Principal component analysis of the derived profiles was used to classify any variations, and specific metabolites were identified based on their spectral pattern. Characteristic metabolite profiles were identified for control and type 1 diabetic animals with the most distinctive being from mice with the largest physical deterioration and loss of body weight. Eight streptozotocin-treated animals did not develop diabetes and displayed profiles similar to controls. Diabetic mice had decreases in creatine, choline and carnitine and increases in lactate, alanine and myo-inositol. Betaine levels were found to be increased in the majority of diabetic mice but decreased in a few animals with severe loss of body weight and physical condition. The association between perturbations in a number of small molecule metabolites known to be influential in sperm function, with diabetic status and physiological condition, adds further impetus to the proposal that diabetes influences important spermatogenic pathways and mechanisms in a subtle and previously unrecognized manner.

Biosynthetic Chlorination of the Piperazate Residue in Kutzneride Biosynthesis by KthP

Kutznerides 2 and 8 of the cyclic hexadepsipeptide family of antifungal natural products from the soil actinomycete Kutzneria sp. 744 contain two sets of chlorinated residues, a 6,7-dichlorohexahydropyrroloindole moiety derived from dichlorotryptophan and a 5-chloropiperazate moiety, as well as a methylcyclopropylglycine residue that may arise from isoleucine via a cryptic chlorination pathway. Previous studies identified KtzD, KtzQ and KtzR as three halogenases in the kutzneride pathway but left no candidate for installing the CS chlorine on piperazate. On the basis of analysis of the complete genome sequence of Kutzneria, we now identify a fourth halogenase in the pathway whose gene is separated from the defined kutzneride cluster by 12 open reading frames. KthP (kutzneride halogenase for piperazate) is a mononuclear nonheme iron halogenase that acts on the piperazyl ring tethered by a thioester linkage to the holo forms of thiolation domains. MS analysis of the protein-bound product confirmed chlorination of the piperazate framework from the (3S)- but not the (3R)-piperazyl-S-pantetheinyl thiolation proteins. After thioesterase-mediated release, nuclear magnetic resonance was used to assign the free imino acid as (3S,5S)-5-chloropiperazate, distinct from the 3S,5R stereoisomer reported in the mature kutznerides. These results demonstrate that a fourth halogenase, KthP, is active in the kutzneride biosynthetic pathway and suggest further processing of the (3S,5S)-5-chloropiperazate during subsequent incorporation into the kutzneride depsipeptide frameworks.

Geophysical and geochemical survey of a large marine pockmark on the Malin Shelf, Ireland

Marine pockmarks are a specific type of seabed geological setting resembling craters or pits and are considered seabed surface expressions of fluid flow in the subsurface. A large composite pockmark on the Malin Shelf, off the northern coast of Ireland was surveyed and ground truthed to assess its activity and investigate fluid related processes in the subsurface. Geophysical (including acoustic and electromagnetic) data confirmed the subsurface presence of signatures typical of fluids within the sediment. Shallow seismic profiling revealed a large shallow gas pocket and typical gas related indicators such as acoustic blanking and enhanced reflectors present underneath and around the large pockmark. Sulphate profiles indicate that gas from the shallow reservoir has been migrating upwards, at least recently. However, there are no chimney structures observed in the sub-bottom data and the migration pathways are not apparent. Electromagnetic data show slightly elevated electrical conductivity on the edges of the pockmarks and a drop below regional levels within the confines of the pockmark, suggesting changes in physical properties of the sediment. Nuclear Magnetic Resonance (NMR) experiments were employed to characterize the organic component of sediments from selected depths. Very strong microbial signatures were evident in all NMR spectra but microbes outside the pockmark appear to be much more active than inside. These observations coincide with spikes in conductivity and the lateral gas bearing body suggesting that there is an increase in microbial activity and biomass when gas is present.