New pyridine carboxamide ligands and their complexation to copper(II). X-Ray crystal structures of mono-, di, tri- and tetranuclear copper complexes

Seven new pyridine dicarboxamide ligands H2L(1-7) have been synthesised from condensation reactions involving pyridine-2,6-dicarboxylic acid (H2dipic), pyridine-2,6-dicarbonyl dichloride or 2,6-diaminopyridine with heterocyclic amine or carboxylic acid precursors. Crystallographic analyses of N,N'-bis(2-pyridyl)pyridine-2,6-dicarboxamide monohydrate (H2L8 x H2O), N,N'-bis[2-(2-pyridyl)methyl]pyridine-2,6-dicarboxamide and N,N'-bis[2-(2-pyridyl)ethyl]pyridine-2,6-dicarboxamide monohydrate revealed extensive intramolecular hydrogen bonding interactions. 2,6-Bis(pyrazine-2-carboxamido)pyridine (H2L6) and 2,6-bis(pyridine-2-carboxamido)pyridine (H2L7) reacted with copper(II) acetate monohydrate to give tricopper(II) complexes [Cu3(L)2(mu2-OAc)2]. X-Ray crystallography confirmed deprotonation of the amidic nitrogen atoms and that the (L6,7)2- ligands and acetate anions hold three copper(II) ions in approximately linear fashion. H2L8. Reacted with copper(II) tetrakis(pyridine) perchlorate to give [Cu(L8)(OH2)]2 x 2H2O, in which (L8)2- was tridentate through the nitrogen atoms of the central pyridine ring and the deprotonated carboxamide groups at one copper centre, with one of the terminal pyridyl rings coordinating to the other copper atom in the dimer. The corresponding reaction using H2L7 gave [Cu3(L7)2(py)2][ClO4]2, which transformed during an attempted recrystallisation from ethanol under aerobic conditions to a tetracopper(II) complex [Cu4(L7)2(L7-O)2].     

The [M?OH]+ ions of m- and p-ethylnitrobenzene: A common structure?

The structures of the [M? OH]⁺ ions of m- and pethylnitrobenzene have been compared by measurements of metastable ion spectra, collisional activation spectra, kinetic energy releases and critical energies for the formation of these ions and their subsequent decomposition. Normalized rates of fragmentation of metastable molecular ions and metastable [M? OH]⁺ ions have been compared for ion lifetimes up to 30 μs. The energy measurements fail to distinguish between the structures of the [M? OH]⁺ ions, but the normalized fragmentation rates and the collisional activation spectra show their structures to be different.     

A top-down LC-FTICR MS-based strategy for characterizing oxidized calmodulin in activated macrophages

A liquid chromatography-mass spectrometry (LC-MS)-based approach for characterizing the degree of nitration and oxidation of intact calmodulin (CaM) has been used to resolve ～250 CaM oxiforms using only 500 ng of protein. The analysis was based on high-resolution data of the intact CaM isoforms obtained by Fourier-transform ion cyclotron resonance mass spectrometry (FTICR MS) coupled with an on-line reversed-phase LC separation. Tentative identifications of post-translational modifications (PTMs), such as oxidation or nitration, have been assigned by matching observed protein mass to a database containing all theoretically predicted oxidation products of CaM and verified through a combination of tryptic peptide information (generated from bottom-up analyses) and on-line collisionally induced dissociation (CID) tandem mass spectrometry (MS/MS) at the intact protein level. The reduction in abundance and diversity of oxidatively modified CaM (i.e., nitrated tyrosines and oxidized methionines) induced by macrophage activation has been explored and semiquantified for different oxidation degrees (i.e., no oxidation, moderate, and high oxidation). This work demonstrates the power of the top-down approach to identify and quantify hundreds of combinations of PTMs for single protein target such as CaM and implicate competing repair and peptidase activities to modulate cellular metabolism in response to oxidative stress.     

Trace LC/MS/MS quantitation of 17β‐estradiol as a biomarker for selective estrogen receptor modulator activity in the rat brain

A sensitive LC/MS/MS method has been developed by derivatization of 17β‐estradiol (E2) with dansyl chloride to quantitate 17β‐E2 in female rat serum. The use of E2‐d₅ minimized interferences from endogenous 17β‐E2 in order to achieve a limit of quantitation (LOQ) of 2.5 pg/ml using 150 µl of female rat serum. The recovery of the dansyl derivative was 95% or greater in quality control samples. The intra and interday assay precision was better than 8.2 and 6.2%, respectively, with accuracies ranging from 97 to 101% in the quality control samples. The assay was used for the quantitation of serum E2 as a biomarker for the estrogen receptor (ER) antagonist activity of small molecule SERMs (selective estrogen receptor modulators) in the female rat brain. The study revealed that a statistically significant upregulation of serum 17β‐E2 occurred for rats dosed with SERMs that are known to penetrate the brain and disrupt the hypothalamic‐pituitary‐ovarian (HPO) axis. Variations in 17β‐E2 in ascending dose studies also correlated with the corresponding trends in CYP17a1 levels, an mRNA biomarker for ovarian hyperstimulation. This biomarker assay has provided a useful screen for medicinal chemistry optimization to produce SERMs that do not interfere with negative feedback of estrogens on the brain and for biological hypothesis testing. Copyright © 2009 John Wiley & Sons, Ltd.     

Lithol Red: a systematic structural study on salts of a sulfonated azo pigment

The first systematic series of single-crystal diffraction structures of azo lake pigments is presented (Lithol Red with cations=Mg(II), Ca(II), Sr(II), Ba(II), Na(I) and Cd(II)) and includes the only known structures of non-Ca examples of these pigments. It is shown that these commercially and culturally important species show structural behaviour that can be predicted from a database of structures of related sulfonated azo dyes, a database that was specifically constructed for this purpose. Examples of the successful structural predictions from the prior understanding of the model compounds are that 1) the Mg salt is a solvent-separated ion pair, whereas the heavier alkaline-earth elements Ca, Sr and Ba form contact ion pairs, namely, low-dimensional coordination complexes; 2) all of the Lithol Red anions exist as the hydrazone tautomer and have planar geometries; and 3) the commonly observed packing mode of alternating inorganic layers and organic bilayers is as expected for an ortho-sulfonated azo species with a planar anion geometry. However, the literature database of dye structures has no predictive use for organic solvate structures, such as that of the observed Na Lithol Red DMF solvate. Interestingly, the Cd salt is isostructural with the Mg salt and not with the Ca salt. It is also observed that linked eight-membered [MOSO](2) rings are the basic coordination motif for all of the known structures of Ca, Sr and Ba salts of sulfonated azo pigments in which competing carboxylate groups are absent.     

Quenching of tryptophan fluorescence in various proteins by a series of small nickel complexes

A series of twelve anionic, cationic, and neutral nickel(II) complexes have been synthesized and characterized. The interaction of these complexes with bovine serum albumin (BSA), human serum albumin (HSA), lysozyme (Lyso), and tryptophan (Trp) has been studied using steady-state fluorescence spectroscopy. Dynamic and static quenching constants have been calculated, and the role played in quenching by the ligand and complex charge investigated. The nickel complexes showed selectivity towards the different proteins based on the environment surrounding the Trp residue(s). Only small neutral complexes with hydrophobic ligands effectively quenched protein fluorescence via static quenching, with association constants ranging from 10(2) M(-1) (free Trp) to 10(10) M(-1) (lysozyme), indicating a spontaneous and thermodynamically favorable interaction. The number of binding sites, on average, was determined to be one in BSA, HSA and free Trp, and two in lysozyme.     

Evidence of impurities in thiolated single-stranded DNA oligomers and their effect on DNA self-assembly on gold

The diversity of techniques used in the synthesis, treatment, and purification of the single-stranded DNA oligomers containing a thiol anchor group (SH-ssDNA) has led to a significant variation in the purity of commercially available SH-ssDNA. In this work, we use X-ray photoelectron spectroscopy (XPS) and time-of-flight secondary ion mass spectrometry (ToF-SIMS) to study how the impurities present in commercially synthesized SH-ssDNA oligomers affected the structure of the resulting DNA films on Au. XPS results indicate that two of the purchased SH-ssDNA oligomers contain excess carbon and sulfur. The molecular fragmentation patterns obtained with ToF-SIMS were used to determine the identity of several contaminants in the DNA films, including poly(dimethylsiloxane) (PDMS), lipid molecules, and sulfur-containing molecules. In particular, the ToF-SIMS results determined that the excess sulfur detected by XPS was due to the presence of dithiothreitol, a reductant often used to cleave disulfide precursors. Furthermore, we found that the SH-ssDNA self-assembly process is affected by the presence of these contaminants. When relatively pure SH-ssDNA is used to prepare the DNA films, the P, N, O, and C atomic percentages were observed by XPS to increase over a 24-h time period. In contrast, surfaces prepared using SH-ssDNA containing higher levels of contaminants did not follow this trend. XPS result indicates that, after the initial SH-ssDNA adsorption, the remaining material incorporated into these films was due to contamination.     

Synthesis, structure determination, and spectroscopic/computational characterization of a series of Fe(II)-thiolate model complexes: implications for Fe-S bonding in superoxide reductases

A combined synthetic/spectroscopic/computational approach has been employed to prepare and characterize a series of Fe(II)-thiolate complexes that model the square-pyramidal [Fe(II)(N(His))(4)(S(Cys))] structure of the reduced active site of superoxide reductases (SORs), a class of enzymes that detoxify superoxide in air-sensitive organisms. The high-spin (S = 2) Fe(II) complexes [(Me(4)cyclam)Fe(SC(6)H(4)-p-OMe)]OTf (2) and [FeL]PF(6) (3) (where Me(4)cyclam = 1,4,8,11-tetramethylcyclam and L is the pentadentate monoanion of 1-thioethyl-4,8,11-trimethylcyclam) were synthesized and subjected to structural, magnetic, and electrochemical characterization. X-ray crystallographic studies confirm that 2 and 3 possess an N(4)S donor set similar to that found for the SOR active site and reveal molecular geometries intermediate between square pyramidal and trigonal bipyramidal for both complexes. Electronic absorption, magnetic circular dichroism (MCD), and variable-temperature variable-field MCD (VTVH-MCD) spectroscopies were utilized, in conjunction with density functional theory (DFT) and semiemperical INDO/S-CI calculations, to probe the ground and excited states of complexes 2 and 3, as well as the previously reported Fe(II) SOR model [(L(8)py(2))Fe(SC(6)H(4)-p-Me)]BF(4) (1) (where L(8)py(2) is a tetradentate pyridyl-appended diazacyclooctane macrocycle). These studies allow for a detailed interpretation of the S-->Fe(II) charge transfer transitions observed in the absorption and MCD spectra of complexes 1-3 and provide significant insights into the nature of Fe(II)-S bonding in complexes with axial thiolate ligation. Of the three models investigated, complex 3 exhibits an absorption spectrum that is particularly similar to the one reported for the reduced SOR enzyme (SOR(red)), suggesting that this model accurately mimics key elements of the electronic structure of the enzyme active site; namely, highly covalent Fe-S pi- and sigma-interactions. These spectral similarities are shown to arise from the fact that 3 contains an alkyl thiolate tethered to the equatorial cyclam ring, resulting in a thiolate orientation that is very similar to the one adopted by the Cys residue in the SOR(red) active site. Possible implications of our results with respect to the electronic structure and reactivity of SOR(red) are discussed.     

Theoretical analysis of the anomalous spectral splitting of tetracene in 4He droplets

We present a theoretical analysis of the electronic absorption spectra of tetracene in (4)He droplets based on many-body quantum simulations. Using the path integral ground state approach, we calculate one- and two-body reduced density matrices of the most strongly localized He atoms near the molecule surface and use these to investigate the helium ground-state quantum coherence and correlations when tetracene is in its electronic ground and excited states. We identify a trio of quasi-one-dimensional, strongly localized atoms adsorbed along the long axis of the molecule that show some quantum coherence among themselves but far less with the remaining solvating helium. We evaluate the single-particle natural orbitals of the localized He atoms by diagonalization of the one-body density matrix and use these to construct single- and many-particle solvating helium basis states with which the zero-phonon spectral features of the tetracene-(4)He(N) absorption spectrum are then calculated. The absorption spectrum resulting from the three-body density matrix for the strongly bound trio of helium atoms is in very good agreement with the experimental data, accounting quantitatively for the anomalous splitting of the zero-phonon line [Hartmann, M.; Lindinger, A.; Toennies, J. P.; Vilesov, A. F. Chem. Phys. 1998, 239, 139; Krasnokutski, S.; Rouillé, G.; Huisken, F. Chem. Phys. Lett. 2005, 406, 386]. Our results indicate that the combination of strong localization and the quasi-one-dimensional nature of trios of helium atoms adsorbed along the long axis of tetracene leads to a quantum coherent, yet highly correlated ground state for the helium density closest to the molecule. The spectroscopic analysis shows that this feature accounts quantitatively for the anomalous splittings and hitherto unexplained fine structure observed in the absorption spectra of tetracene and suggests that it may be responsible for the corresponding zero-phonon splittings in other quasi-one-dimensional planar aromatic molecules.     

Synthesis and formulation of self-immolative PEG-aryl azide block copolymers and click-to-release reactivity with trans-cyclooctene

Self-immolative aryl azides can react with trans-cyclooctenes (TCO), triphenylphosphines or hydrogen sulfide (H₂S) to activate prodrugs, imaging probes and drug delivery systems. To date, the synthesis of polymers containing these aryl azide self-immolative linkers and their reactivity with a strained alkene (i.e., in a bioorthogonal reaction) has not been explored. Also, due to the instability of aryl azides towards light and high temperatures, the polymerization methods compatible with aryl azides are limited. Through systematic investigation of the reversible addition-fragmentation chain transfer (RAFT) and atom transfer radical polymerization (ATRP) methods, a self-immolative PEG-aryl azide block copolymer (PEG₄₅-b-ABOC₂₈ 2 ) and a non-responsive 4-fluoroaryl block copolymer (PEG₄₅-b-FBOC₂₄ 3 ) was prepared. ATRP provided the desired polymers in a highly controlled manner, whereas the RAFT conditions led to higher levels of aryl azide polymer degradation. The ATRP derived polymers 2 and 3 were formulated into nanoparticles of approximately 200 nm diameter, and particle triggering was demonstrated by the [3+2]-cycloaddition reaction of TCO with PEG₄₅-b-ABOC₂₈ 2 in solution (pure polymer) and as a formulated nanoparticle. Preliminary in vitro cell viability studies suggested that the stimuli-responsive aryl azide polymers/nanoparticles are not cytotoxic up to 200 μg/ml concentrations.