Resonance Raman and DFT studies of tetra-tert-butyl porphine: Assignment of strongly enhanced distortion modes in a ruffled porphyrin

The free-base form of tetra-tert-butyl porphine (TtBP), which has extremely bulky meso substituents, is severely distorted from planarity, with a ruffling angle of 65.5degrees. The resonance Raman spectrum of TtBP (lambda(ex) = 457.9 nm) and its d(2), d(8), and d(10) isotopomers have been recorded, and while the spectra show high-frequency bands similar to those observed for planar meso-substituted porphyrins, there are several additional intense bands in the low-frequency region. Density functional calculations at the B3-LYP/6-31G(d) level were carried out for all four isotopomers, and calculated frequencies were scaled using a single factor of 0.98. The single factor scaling approach was validated on free base porphine where the RMS error was found to be 14.9 cm(-1). All the assigned bands in the high-frequency (> 1000 cm(-1)) region of TtBP were found to be due to vibrations similar in character to the in-plane skeletal modes of conventional planar porphyrins. In the low-frequency region, two of the bands, assigned as nu(8) (ca. 330 cm(-1)) and nu(16) (ca. 540 cm(-1)), are also found in planar porphyrins such as tetra-phenyl porphine (TPP) and tetra-iso-propyl porphine (IPP). Of the remaining three very strong bands, the lowest frequency band was assigned as gamma(12) (pyr swivel, obsd 415 cm(-1), calcd 407 cm(-1) in do). The next band, observed at 589 cm-1 in the do compound (calcd 583 cm(-1)), was assigned as a mode whose composition is a mixture of modes that were previously labeled gamma(13) (gamma(CmCaHmCa)) andy gamma(11) (pyr fold(asym)) in NiOEP. The final strong band, observed at 744 cm(-1) (calcd 746 cm(-1)), was assigned to a mode whose composition is again a mixture of gamma(11) and gamma(13), although here it is gamma(11) rather than gamma(13) which predominates. These bands have characters and positions similar to those of three of the four porphyrin ring-based, weak bands that have previously been observed for NiTPP. In addition there are several weaker bands in the TtBP spectra that are also

A Density Functional Theory Study on the Active Center of Fe-Only Hydrogenase: Characterization and Electronic Structure of the Redox States

We have carried out extensive density functional theory (DFT) calculations for possible redox states of the active center in Fe-only hydrogenases. The active center is modeled by [(H(CH(3))S)(CO)(CN(-))Fe(p)(mu-DTN)(mu-CO)Fe(d)(CO)(CN(-))(L)](z) (z is the net charge in the complex; Fe(p)= the proximal Fe, Fe(d) = the distal Fe, DTN = (-SCH(2)NHCH(2)S-), L is the ligand that bonds with the Fed at the trans position to the bridging CO). Structures of possible redox states are optimized, and CO stretching frequencies are calculated. By a detailed comparison of all the calculated structures and the vibrational frequencies with the available experimental data, we find that (i) the fully oxidized, inactive state is an Fe(II)-Fe(II) state with a hydroxyl (OH(-)) group bonded at the Fe(d), (ii) the oxidized, active state is an Fe(II)-Fe(l) complex which is consistent with the assignment of Cao and Hall (J. Am. Chem. Soc. 2001, 123, 3734), and (iii) the fully reduced state is a mixture with the major component being a protonated Fe(l)-Fe(l) complex and the other component being its self-arranged form, Fe(II)-Fe(II) hydride, Our calculations also show that the exogenous CO can strongly bond with the Fe(II)-Fe(l) species, but cannot bond with the Fe(l)-Fe(l) complex. This result is consistent with experiments that CO tends to inhibit the oxidized, active state, but not the fully reduced state. The electronic structures of all the redox states have been analyzed. It is found that a frontier orbital which is a mixing state between the e(g) of Fe and the 2pi of the bridging CO plays a key role concerning the reactivity of Fe-only hydrogenases: (1) it is unoccupied in the fully oxidized, inactive state, half-occupied in the oxidized, active state, and fully occupied in the fully reduced state; (ii) the e(g)-2pi orbital is a bonding state, and this is the key reason for stability of the low oxidation states, such as Fe(l)-Fe(l) complexes; and (iii) in the e(g)-2pi orbital more charge accumulates between the bridging CO and the Fe(d) than between the bridging CO and the Fe(p), and the occupation increase in this orbital will enhance the bonding between the bridging CO and the Fe(d), leading to the bridging-CO shift toward the Fe(d).

Analysis of DNA processing reactions in bacterial conjugation by using suicide oligonucleotides

Protein TrwC is the conjugative relaxase responsible for DNA processing in plasmid R388 bacterial conjugation. TrwC has two catalytic tyrosines, Y18 and Y26, both able to carry out cleavage reactions using unmodified oligonucleotide substrates. Suicide substrates containing a 30-Sphosphorothiolate linkage at the cleavage site displaced TrwC reaction towards covalent adducts and thereby enabled intermediate steps in relaxase reactions to be investigated. Two distinct covalent TrwC–oligonucleotide complexes could be separated from noncovalently bound protein by SDS–PAGE. As observed by mass spectrometry, one complex contained a single, cleaved oligonucleotide bound to Y18, whereas the other contained two cleaved oligonucleotides, bound to Y18 and Y26. Analysis of the cleavage reaction using suicide substrates and Y18F or Y26F mutants showed that efficient Y26 cleavage only occurs after Y18 cleavage. Strand-transfer reactions carried out with the isolated Y18–DNA complex allowed the assignment of specific roles to each tyrosine. Thus, only Y18 was used for initiation. Y26 was specifically used in the second transesterification that leads to strand transfer, thus catalyzing the termination reaction that occurs in the recipient cell.

An electrochemical study of PCl3 and POCl3 in the room temperature ionic liquid [C(4)mpyrr][N(Tf)(2)]

Voltammetric studies of PCl3 and POCl3 have not been reported in the literature to date, probably due to the instability of these molecules in conventional aprotic solvents giving unstable and irreproducible results. From a previous study [Amigues et al. Chem. Commun. 2005, 1-4], it was found that ionic liquids have the ability to offer a uniquely stable solution phase environment for the study of these phosphorus compounds. Consequently, the electrochemistry of PCl3 and POCl3 has been studied by cyclic voltammetry on a gold microelectrode in the ionic liquid [C(4)mpyrr][N(Tf)(2)] (1-butyl-1-methylpyrrolidinium bis(trifluoromethylsulfonyl) imide). For both compounds, reduction and oxidation waves were observed and a tentative assignment of the waves is given. For PCl3, the reduction was thought to proceed via the following mechanism: PCl3 + e(-) h reversible arrow PCl3-, PCl3- reversible arrow Cl- + (PCl2)-Cl-center dot, (and) Cl- + PCl3 h PCl4-. For POCl3, the suggested reduction mechanism was analogous to that of PCl3: POCl3 + e(-) reversible arrow POCl3-, POCl3- reversible arrow Cl- + (POCl2)-O-center dot, and Cl- + POCl3 h POCl4-. In both cases (PCl2)-Cl-center dot and (POCl2)-O-center dot are likely to engage in further reactions. Potential step microdisk chronoamperometry was carried out on the reductive waves of PCl3 and POCl3 to measure diffusion coefficients and number of electrons transferred. It was found that the diffusion of PCl3 was unusually slow (3.1 x 10(-12) m(2) s(-1)): approximately 1 order of magnitude less than that for POCl3 (2.2 x 10(-11) m(2) s(-1)). For both PCl3 and POCl3, a

The temperature dependence of the adsorption of NO on Pt{211}: A RAIRS and DFT investigation

RAIRS experiments have been performed to investigate the adsorption of NO on Pt{211}. Results show that adsorption is complex and strongly temperature dependent. At 307 K, three bands are seen at saturation with frequencies of 1801, 1609, and 1576 cm(-1). However, at 120 K only two bands, at 1688 and 1620 cm(-1), are observed. To help with the assignment of these vibrational bands, DFT calculations were also performed. The calculations show that a bridged NO species, bonded to the step edge, is the most stable species on the surface and gives rise to the band observed at 1610-1620 cm(-1). The calculations also suggest that the temperature dependence of NO adsorption on Ptf{211} can be assigned to NO dissociation which occurs at room temperature but not at 120 K. In particular, the RAIRS band observed at 1801 cm(-1), which is observed on adsorption at 307 K but not at 120 K, is tentatively assigned to the formation of an O-NO complex. This species forms when a NO molecule bonds on top of an O atom, which results from the dissociation of NO on the Pt{211} surface at room temperature.

Assignment methods for incidence calculus

Incidence calculus is a mechanism for probabilistic reasoning in which sets of possible worlds, called incidences, are associated with axioms, and probabilities are then associated with these sets. Inference rules are used to deduce bounds on the incidence of formulae which are not axioms, and bounds for the probability of such a formula can then be obtained. In practice an assignment of probabilities directly to axioms may be given, and it is then necessary to find an assignment of incidence which will reproduce these probabilities. We show that this task of assigning incidences can be viewed as a tree searching problem, and two techniques for performing this research are discussed. One of these is a new proposal involving a depth first search, while the other incorporates a random element. A Prolog implementation of these methods has been developed. The two approaches are compared for efficiency and the significance of their results are discussed. Finally we discuss a new proposal for applying techniques from linear programming to incidence calculus.

Suggested Binding Mechanism of the HIV-gp120 to its CD4 Receptor

The molecular recognition and attachment of the CD4 molecule and the HIV envelope glycoprotein (gp120) might be described as a consecutive three-step molecular recognition process. 1. (a) Long range interaction: electrostatic pre-orientation, 2. (b) short range interaction: electronic attachment followed by a ‘Locking-in’ (via aromatic ring orientation) and 3. (c) internal interaction (induced fit): conformational readjustment of the protein molecules. On the basis of the preliminary investigations (X-ray structures of CD4 and biological studies of CD4 and gp120 point mutants) we described a computational model. This approach consists of empirical calculations as well as ab initio level of quantum chemistry. The conformational analysis of the wild type and mutant CD4 molecules was supported by molecular mechanics and dynamics (Amber force field). The latter analysis involves the application of a novel method, the Amino Acid Conformation Assignment of Proteins (ACAP) software, developed for the notation of secondary protein structures. According to the cardinal role of the electrostatic factors during this interaction, several ab initio investigations were performed for better understanding of the recognition process on submolecular level. Using the above mentioned computational model, we could interpret the basic behaviours and predict some additional features of CD4-gp120 interaction, in spite of the missing gp120 X-ray structure.

Methodological considerations in reserve system selection: a case study of Malagasy Lemurs.

Although data quality and weighting decisions impact the outputs of reserve selection algorithms, these factors have not been closely studied. We examine these methodological issues in the use of reserve selection algorithms by comparing: (1) quality of input data and (2) use of different weighting methods for prioritizing among species. In 2003, the government of Madagascar, a global biodiversity hotspot, committed to tripling the size of its protected area network to protect 10% of the country’s total land area. We apply the Zonation reserve selection algorithm to distribution data for 52 lemur species to identify priority areas for the expansion of Madagascar’s reserve network. We assess the similarity of the areas selected, as well as the proportions of lemur ranges protected in the resulting areas when different forms of input data were used: extent of occurrence versus refined extent of occurrence. Low overlap between the areas selected suggests that refined extent of occurrence data are highly desirable, and to best protect lemur species, we recommend refining extent of occurrence ranges using habitat and altitude limitations. Reserve areas were also selected for protection based on three different species weighting schemes, resulting in marked variation in proportional representation of species among the IUCN Red List of Threatened Species extinction risk categories. This result demonstrates that assignment of species weights influences whether a reserve network prioritizes maximizing overall species protection or maximizing protection of the most threatened species.

Microsatellite standardization and evaluation of genotyping error in a large multi-partner research programme for conservation of Atlantic salmon (Salmo salar L.).

Microsatellite genotyping is a common DNA characterization technique in population, ecological and evolutionary genetics research. Since different alleles are sized relative to internal size-standards, different laboratories must calibrate and standardize allelic designations when exchanging data. This interchange of microsatellite data can often prove problematic. Here, 16 microsatellite loci were calibrated and standardized for the Atlantic salmon, Salmo salar, across 12 laboratories. Although inconsistencies were observed, particularly due to differences between migration of DNA fragments and actual allelic size ('size shifts'), inter-laboratory calibration was successful. Standardization also allowed an assessment of the degree and partitioning of genotyping error. Notably, the global allelic error rate was reduced from 0.05 ± 0.01 prior to calibration to 0.01 ± 0.002 post-calibration. Most errors were found to occur during analysis (i.e. when size-calling alleles; the mean proportion of all errors that were analytical errors across loci was 0.58 after calibration). No evidence was found of an association between the degree of error and allelic size range of a locus, number of alleles, nor repeat type, nor was there evidence that genotyping errors were more prevalent when a laboratory analyzed samples outside of the usual geographic area they encounter. The microsatellite calibration between laboratories presented here will be especially important for genetic assignment of marine-caught Atlantic salmon, enabling analysis of marine mortality, a major factor in the observed declines of this highly valued species.

Electrochemistry of Hg(II) Salts in Room-Temperature Ionic Liquids

The electrochemistry of HgCl(2) and [Hg(NTf(2))(2)] ([NTf(2)](-) = bis-{(trifluoromethyl)sulfonyl}imide) has been studied in room temperature ionic liquids. It has been found that the cyclic voltammetry of Hg(II) is strongly dependent on a number of factors (e.g., concentration, anions present in the mixture, and nature of the working electrode) and differs from that found in other media. Depending on conditions, the cyclic voltammetry of Hg(II) can give rise to one, two, or four reduction peaks, whereas the reverse oxidative scans show two to four peaks. Diffuse reflectance UV-vis spectroscopy and X-ray powder diffraction have been used to aid the assignment of the voltammetric waves.

Down with MNE-centric theories! Market entry and expansion as the bundling of MNE and local assets

Both Anderson and Gatignon and the Uppsala internationalization model see the initial mode of foreign market entry and subsequent modes of operation as unilaterally determined by multinational enterprises (MNEs) arbitraging control and risk and increasing their commitment as they gain experience in the target market. OLI and internalization models do recognize that foreign market entry requires the bundling of MNE and complementary local assets, which they call location or country-specific advantages, but implicitly assume that those assets are freely accessible to MNEs. In contrast to both of these MNE-centric views, I explicitly consider the transactional characteristics of complementary local assets and model foreign market entry as the optimal assignment of equity between their owners and MNEs. By looking at the relative efficiency of the different markets in which MNE and complementary local assets are traded, and at how these two categories of assets match, I am able to predict whether equity will be held by MNEs or by local firms, or shared between them, and whether MNEs will enter through greenfields, brownfields, or acquisitions. The bundling model I propose has interesting implications for the evolution of the MNE footprint in host countries, and for the reasons behind the emergence of Dragon MNEs.

Identification and molecular analysis of cable pilus biosynthesis genes in Burkholderia cepacia

Burkholderia cepacia is an opportunistic respiratory pathogen in cystic fibrosis patients. One highly transmissible and virulent clone belonging to genomovar IIIa expresses pili with unique cable morphology, which enable the bacterium to bind cytokeratin 13 in epithelial cells. The cblA gene, encoding the major pilin subunit, is often used as a DNA marker to identify potentially virulent isolates. The authors have now cloned and sequenced four additional genes, cblB, cblC, cblD and cblS, in the pilus gene cluster. This work shows that the products of the first four genes of the cbl operon, cblA, cblB, cblC and cblD, are sufficient for pilus assembly on the bacterial surface. Deletion of cblB abrogated pilus assembly and compromised the stability of the CblA protein in the periplasm. In contrast, deletion of cblD resulted in no pili, but there was no effect on expression and stability of the CblA protein subunit. These results, together with protein sequence homologies, predicted structural analyses, and the presence of typical amino acid motifs, are consistent with the assignment of functional roles for CblB as a chaperone that stabilizes the major pilin subunit in the periplasm, and CblD as the initiator of pilus biogenesis. It is also shown that expression of Cbl pili in Escherichia coli is not sufficient to mediate the binding of bacteria to the epithelial cell receptor cytokeratin 13, and that B. cepacia still binds to cytokeratin 13 in the absence of Cbl pili, suggesting that additional bacterial components are required for effective binding.

The structures of four bombesins and their cloned precursor-encoding cDNAs from acid-solvated skin secretion of the European yellow-bellied toad, Bombina variegata

Four different bombesins (bombesin, His(6)-bombesin, Phe(13)-bombesin and Asp(2)-, Phe(4)-SAP-bombesin) have been identified by a systematic sequencing study of peptides in reverse phase HPLC fractions of the skin secretion of the European yellow-bellied toad, Bombina variegata, that had been solvated in 0.1% (v/v) aqueous trifluoroacetic acid (TFA) and stored frozen at -20°C for 12 years. By using a 3'- and 5'-RACE PCR strategy, the corresponding biosynthetic precursor-encoding cDNAs of all four peptides were cloned from a cDNA library made from the same long-term frozen, acid-solvated skin secretion sample following thawing and lyophilization. Canonical bombesin and His(6)-bombesin are classical bombesin sub-family members, whereas Phe(13)-bombesin and Asp(2)-, Phe(4)-SAP-bombesin, belong to the litorin/ranatensin sub-family of bombesin-like peptides (BLPs). Assignment of these peptides to respective sub-families, was based upon both their primary structural similarities and their comparative pharmacological activities. An interesting observation in this study, was that the nucleotide sequences of the open-reading frames of cloned cDNAs encoding bombesin and its His(6)-substituted analog, were identical except for a single base that was responsible for the change observed at the position 6 residue in the mature peptide from Asn to His. In contrast, the precursor cDNA nucleotide sequences encoding the Phe(13)-bombesins, exhibited 53 base differences. The pharmacological activities of synthetic replicates of each bombesin were compared using two different mammalian smooth muscle preparations and all four peptides were found to be active. However, there were significant differences in their relative potencies.

Electron paramagnetic resonance studies of the neutral nitrogen vacancy in diamond

Despite the numerous experimental and theoretical studies on the negatively charged nitrogen vacancy center (NV-) in diamond and the predictions that the neutral nitrogen vacancy center (NV0) should have an S=1/2 ground state, NV0 has not previously been detected by electron paramagnetic resonance (EPR). We report new EPR data on a trigonal nitrogen-containing defect in diamond with an S=3/2 excited state populated via optical excitation. Analysis of the spin Hamiltonian parameters and the wavelength dependence of the optical excitation leads to assignment of this S=3/2 state to the (4)A(2) excited state of NV0. This identification, together with an examination of the electronic structure of the NV centers in diamond, provides a plausible explanation for the lack of observation (to date) of an EPR signal from the NV0 ground state.