Ab initio investigation of structure and cohesive energy of crystalline urea

The structure and cohesive energy of crystalline urea have been investigated at the ab initio level of calculation. The performance of different Hamiltonians in dealing with a hydrogen-bonded molecular crystal as crystalline urea is assessed. Detailed calculations carried out by adopting both HF and some of the most popular DFT methods in solid-state chemistry are reported. Local, gradient-corrected, and hybrid functionals have been adopted: SVWN, PW91, PBE, B3LYP, and PBE0. First, a 6-31G(d,p) basis set has been adopted, and then the basis set dependence of computed results has been investigated at the B3LYP level. All calculations were carried out by using a development version of the periodic ab initio code CRYSTAL06, which allows full optimization of lattice parameters and atomic coordinates. With the 6-31G(d,p) basis set, structural features are well reproduced by hybrid methods and GGA. LDA gives lattice parameters and hydrogen-bond distances that are too small relative to experiment, while at the HF level the opposite trend is observed. Results show that hybrid methods are more accurate than HF and both LDA and GGA functionals, with a trend in the computed properties similar to that of hydrogen-bonded molecular complexes. When BSSE and ZPE are taken into account, all methods, except LDA, give computed cohesive energies that are underestimated with respect to the experimental sublimation enthalpy. Dispersion energy, not properly taken into account by DFT methods, plays a crucial role. Such a deficiency also affects dramatically the computed crystalline structure, especially when large basis sets are adopted. We show that this is an artifact due to the BSSE. Indeed, with small basis sets the BSSE gives an extra-binding that compensates for the missing dispersion forces, thus yielding structures in fortuitous agreement with experiment.     

Unusual metal ion selectivities of the highly preorganized tetradentrate ligand 1,10-phenanthroline-2,9-dicarboxamide: a thermodynamic and fluorescence study

Some metal ion complexing properties of the ligand PDAM (1,10-phenanthroline-2,9-dicarboxamide) in aqueous solution are reported. Using UV-visible spectroscopy to follow the intense π-π* transitions of PDAM as a function of metal ion concentration, log K(1) values in 0.1 M NaClO(4) and at 25 °C are, for Cu(II), 3.56(5); Ni(II), 3.06(5); Zn(II), 3.77(5); Co(II), 3.8(1); Mg(II), 0.1(1); Ca(II), 1.94(4); and Ba(II), 0.7(1). For more strongly bound metal ions, competition reactions between PDAM and EDTA (ethylenedinitrilo-tetraacetic acid) or tetren (1,4,7,10,13-pentaazatridecane), monitored following the UV spectrum of PDAM, gave the following log K(1) values in 0.1 M NaClO(4) and at 25 °C: Cd(II), 7.1(1); Pb(II), 5.82(5); In(III), 9.4(1); and Bi(III), 9.4(1). The very low log K(1)(PDAM) values for small metal ions such as Cu(II) or Zn(II) are unprecedented for a phen-based ligand (phen = 1,10-phenanthroline), which is rationalized in terms of the low basicity of the N donors of the ligand (pK(a) = 0.6) and the fact that PDAM has a best-fit size corresponding to large metal ions of ionic radius ~1.0 ?. Large metal ions with ionic radius ≥1.0 ? show large increases in log K(1) relative to their phen complexes, which in turn produces unparalleled selectivities, such as a 3.5 log units greater log K(1)(PDAM) for Cd(II) than for Cu(II). PDAM shows strong fluorescence in aqueous solution, suggesting that its carboxamide groups do not produce a fluorescence-quenching photon-induced electron transfer (PET) effect. Only Ca(II) produces a weak CHEF (chelation enhanced fluorescence) effect with PDAM, while all other metal ions tested produce a decrease in fluorescence, a CHEQ (chelation enhanced quenching effect). The production of the CHEQ effect is rationalized in terms of the idea that coordination of metal ions to PDAM stabilizes a canonical form of the carboxamide groups that promotes a PET effect.     

The Cytotoxic Effect of α-Synuclein Aggregates

Parkinson's disease is a neurodegenerative disorder involving a functional protein, α-synuclein, whose primary function is related to vesicle trafficking. However, α-synuclein is prone to form aggregates, and these inclusions, known as Lewy bodies, are the hallmark of Parkinson's disease. α-synuclein can alter its conformation and acquire aggregating capacity, forming aggregates containing β-sheets. This protein's pathogenic importance is based on its ability to form oligomers that impair synaptic transmission and neuronal function by increasing membrane permeability and altering homeostasis, generating a deleterious effect over cells. First, we establish that oligomers interfere with the mechanical properties of 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) membrane, as demonstrated by nanoindentation curves. In contrast, nanoindentation revealed that the α-synuclein monomer's presence leads to a much more resistant lipid bilayer. Moreover, the oligomers’ interaction with cell membranes can promote lactate dehydrogenase (LDH) release, suggesting the activation of cytotoxic events.     

Electrophysiological Responses of Bactrocera kraussi (Hardy) (Tephritidae) to Rectal Gland Secretions and Headspace Volatiles Emitted by Conspecific Males and Females

Pheromones are biologically important in fruit fly mating systems, and also have potential applications as attractants or mating disrupters for pest management. Bactrocera kraussi (Hardy) (Diptera: Tephritidae) is a polyphagous pest fruit fly for which the chemical profile of rectal glands is available for males but not for females. There have been no studies of the volatile emissions of either sex or of electrophysiological responses to these compounds. The present study (i) establishes the chemical profiles of rectal gland contents and volatiles emitted by both sexes of B. kraussi by gas chromatography–mass spectrometry (GC–MS) and (ii) evaluates the detection of the identified compounds by gas chromatography–electroantennogram detection (GC–EAD) and –electropalpogram detection (GC–EPD). Sixteen compounds are identified in the rectal glands of male B. kraussi and 29 compounds are identified in the rectal glands of females. Of these compounds, 5 were detected in the headspace of males and 13 were detected in the headspace of females. GC–EPD assays recorded strong signals in both sexes against (E,E)-2,8-dimethyl-1,7-dioxaspiro[5.5]undecane, 2-ethyl-7-mehtyl-1,6-dioxaspiro[4.5]decane isomer 2, (E,Z)/(Z,E)-2,8-dimethyl-1,7-dioxaspiro[5.5]undecane, and (Z,Z)-2,8-dimethyl-1,7-dioxaspiro[5.5]undecane. Male antennae responded to (E,E)-2,8-dimethyl-1,7-dioxaspiro[5.5]undecane, 2-methyl-6-pentyl-3,4-dihydro-2H-pyran, 6-hexyl-2-methyl-3,4-dihydro-2H-pyran, 6-oxononan-1-ol, ethyl dodecanoate, ethyl tetradecanoate and ethyl (Z)-hexadec-9-enoate, whereas female antennae responded to (E,E)-2,8-dimethyl-1,7-dioxaspiro[5.5]undecane and 2-methyl-6-pentyl-3,4-dihydro-2H-pyran only. These compounds are candidates as pheromones mediating sexual interactions in B. kraussi.     

Highly efficient antibody-catalyzed deuteration of carbonyl compounds

Antibody 38C2 efficiently catalyzes deuterium-exchange reactions at the alpha position of a variety of ketones and aldehydes, including substrates that have a variety of sensitive functional groups. In addition to the regio- and chemoselectivity of these reactions, the catalytic rates (kcat) and rate-enhancement values (kcat/kun) are among the highest values ever observed with catalytic antibodies. Comparison of the substrate range of the catalytic antibody with highly evolved aldolase enzymes, such as rabbit-muscle aldolase, highlights the much broader practical scope of the antibody, which accepts a wide range of substrates. The hydrogen-exchange reaction was used for calibration and mapping of the antibody active site. Isotope-exchange experiments with cycloheptanone reveal that the formation of the Schiff base species (as concluded from the 16O/18O exchange rate at the carbonyl oxygen) is much faster than the formation of the enamine intermediate (as concluded from the H/D exchange rate), and both steps are faster than the antibody-catalyzed aldol addition reaction.     

A recommended and verified procedure for in situ tryptic digestion of formalin‐fixed paraffin‐embedded tissues for analysis by matrix‐assisted laser desorption/ionization imaging mass spectrometry

Matrix‐assisted laser desorption/ionization imaging mass spectrometry (MALDI IMS) is a molecular imaging technology uniquely capable of untargeted measurement of proteins, lipids, and metabolites while retaining spatial information about their location in situ. This powerful combination of capabilities has the potential to bring a wealth of knowledge to the field of molecular histology. Translation of this innovative research tool into clinical laboratories requires the development of reliable sample preparation protocols for the analysis of proteins from formalin‐fixed paraffin‐embedded (FFPE) tissues, the standard preservation process in clinical pathology. Although ideal for stained tissue analysis by microscopy, the FFPE process cross‐links, disrupts, or can remove proteins from the tissue, making analysis of the protein content challenging. To date, reported approaches differ widely in process and efficacy. This tutorial presents a strategy derived from systematic testing and optimization of key parameters, for reproducible in situ tryptic digestion of proteins in FFPE tissue and subsequent MALDI IMS analysis. The approach describes a generalized method for FFPE tissues originating from virtually any source.     

Copper + nickel-in-charcoal (Cu-Ni/C): a bimetallic, heterogeneous catalyst for cross-couplings

A new heterogeneous catalyst composed of copper and nickel oxide particles supported within charcoal has been developed. It catalyzes cross-couplings that traditionally use palladium, nickel, or copper, including Suzuki-Miyaura reactions, Buchwald-Hartwig aminations, vinylalane alkylations, etherifications of aryl halides, aryl halide reductions, asymmetric conjugate reductions of activated olefins, and azide-alkyne "click" reactions.     

Copolymerization of ethylene and non-conjugated diene using homogenous catalyst

Ethylene and different amounts of 1,7-octadiene were copolymerized using the metallocene catalyst system ethylidene-bis(fluorenyl) zirconium dichloride and methylaluminoxane (MAO) at both 50 and 90 °C. The catalyst activity has slightly increased with the addition of low amounts of the diene in relation to the homopolymerization of ethylene. The obtained polymers were characterized according to their melting temperature (T_m) and crystallinity degree (x_c) by differential scanning calorimetry (DSC). Weight-average molecular weight (M_w) and polydispersity were determined by gel permeation chromatography (GPC). Diene contents in the copolymer were obtained through the FTIR spectroscopy. The results indicated that at polymerization temperature of 90 °C, crosslinking bonds in the obtained copolymers were low, differently from what was observed at 50 °C. The diene content in the copolymer achieved more than 3 mol% and the comonomer conversion was around 15%. Moreover, the obtained copolymers have M_w around 100,000 and large polydispersity.     

Reactions of lignin in chlorine dioxide bleaching of kraft pulps

The reactions between chlorine dioxide and the residual lignin in oxygen-bleached softwood kraft pulps have been studied. In a first series, isolated lignin samples have been subjected to chlorine dioxide oxidation at different pH values and subsequently analysed by oxidative degradation and elemental analysis. Different analytical techniques have also been employed to follow the gradual chemical changes in lignins isolated from kraft pulps after each of the bleaching stages in the OD(EOP)DD sequence. The results demonstrate that, in order to minimize chlorination of the lignin, the first chlorine dioxide stage should be carried out at a pH around or above three. At this pH level, a high degree of lignin oxidation is also achieved. A certain (mono)-chlorination of the lignin in the first D stage cannot be avoided, but this chlorine is to a large extent removed in the later bleaching stages. The efficient and non-selective oxidation of the various phenolic lignin end groups by chlorine dioxide is clearly illustrated by the analytical data. Moreover,¹³C NMR reveals that reduced lignin structures formed during the kraft cook survive the oxidative bleaching stages to a large extent.     

A four coordinate parent imide via a titanium nitridyl

Treatment of d(1) [(nacnac)TiCl(Ntol(2))] with NaN(3) results in NaCl formation and N(2) ejection to yield the first four coordinate, parent imide [(nacnac)Ti=NH(Ntol(2))] (nacnac(-)=[ArNC(CH(3))](2)CH, Ar = 2,6-iPr(2)C(6)H(3), tol = 4-CH(3)C(6)H(4)).