Development of a systems analysis approach for resolving the structure of biodegrading soil systems

An experimental and mathematical method is developed for the microbial systems analysis of polyaromatic hydrocarbon (PAH)-degrading mixed cultures in PAH-contaminated “town gas” soil systems. Frequency response is the primary experimental and data analysis tool used to probe the structure of these complicated systems. The objective is to provide a fundamental protocol for evaluating the performance of specific mixed microbial cultures on specific soil systems by elucidating the salient system variables and their interactions. Two well-described reactor systems, a constant volume stirred tank reactor (CSTR) and a plug flow differential volume reactor, are used in order to remove performance effects that are related to reactor type as opposed to system structure. These two reactor systems are well-defined systems that can be described mathematically and represent the two extremes of one potentially important system variable, macroscopic mass transfer. The experimental and mathematical structure of the protocol is described, experimental data is presented, and data analysis is demonstrated for the stripping, sorption, and biodegradation of napththalene.     

Synthesis and Characterization of Ge(II), Sn(II), and Pb(II) Monoamides with -NH2 Ligands

The synthesis and characterization of the first divalent germanium, tin, and lead monoamide derivatives of the parent amide group -NH(2) are presented. They have the general formula (ArMNH(2))(2) (M = Ge, Ar = Ar'(C(6)H(3)-2,6-Pr(i)(2)) or Ar* (C(6)H(3)-2,6(C(6)H(2)-2,4,6-Pr(i)(3))); M = Sn, Ar = Ar*; M = Pb, Ar = Ar*). For germanium and tin, they were obtained by reacting the corresponding terphenyl halides of the group 14 elements with liquid ammonia in diethyl ether. The lead amide derivative (Ar*PbNH(2))(2) was synthesized by reaction of LiNH(2) with Ar*PbBr in diethyl ether. The compounds were characterized by IR and multinuclear NMR spectroscopies and by X-ray crystallography in the case of the (Ar'GeNH(2))(2) or (Ar*SnNH(2))(2) derivatives. They possess dimeric structures with two -NH(2) groups bridging the germanium and tin centers. For lead, the reaction with ammonia led to isolation of a stable ammine complex of formula Ar*PbBr(NH(3)) which was characterized by IR and NMR spectroscopies and by X-ray crystallography. It is the first structural characterization of a divalent lead ammine complex.     

Metal Cyanide Ions Mx(CN)y]+,- in the gas phase: M = Fe,Co, Ni,Zn, Cd,Hg, Fe + Ag,Co + Ag

The generation of metal cyanide ions in the gas phase by laser ablation of M(CN)(2) (M = Co, Ni, Zn, Cd, Hg), Fe(III)[Fe(III)(CN)(6)] x xH(2)O, Ag(3)[M(CN)(6)] (M = Fe, Co), and Ag(2)[Fe(CN)(5)(NO)] has been investigated using Fourier transform ion cyclotron resonance mass spectrometry. Irradiation of Zn(CN)(2) and Cd(CN)(2) produced extensive series of anions, [Zn(n)(CN)(2n+1)](-) (1 < or = n < or = 27) and [Cd(n)(CN)(2n+1)](-) (n = 1, 2, 8-27, and possibly 29, 30). Cations Hg(CN)(+) and [Hg(2)(CN)(x)](+) (x = 1-3), and anions [Hg(CN)(x)](-) (x = 2, 3), are produced from Hg(CN)(2). Irradiation of Fe(III)[Fe(III)(CN)(6)] x xH(2)O gives the anions [Fe(CN)(2)](-), [Fe(CN)(3)](-), [Fe(2)(CN)(3)](-), [Fe(2)(CN)(4)](-), and [Fe(2)(CN)(5)](-). When Ag(3)[Fe(CN)(6)] is ablated, [AgFe(CN)(4)](-) and [Ag(2)Fe(CN)(5)](-) are observed together with homoleptic anions of Fe and Ag. The additional heterometallic complexes [AgFe(2)(CN)(6)](-), [AgFe(3)(CN)(8)](-), [Ag(2)Fe(2)(CN)(7)](-), and [Ag(3)Fe(CN)(6)](-) are observed on ablation of Ag(2)[Fe(CN)(5)(NO)]. Homoleptic anions [Co(n)(CN)(n+1)](-) (n = 1-3), [Co(n)(CN)(n+2)](-) (n = 1-3), [Co(2)(CN)(4)](-), and [Co(3)(CN)(5)](-) are formed when anhydrous Co(CN)(2) is the target. Ablation of Ag(3)[Co(CN)(6)] yields cations [Ag(n)(CN)(n-1)](+) (n = 1-4) and [Ag(n)Co(CN)(n)](+) (n = 1, 2) and anions [Ag(n)(CN)(n+1)](-) (n = 1-3), [Co(n)(CN)(n-1)](-) (n = 1, 2), [Ag(n)Co(CN)(n+2)](-) (n = 1, 2), and [Ag(n)Co(CN)(n+3)](-) (n = 0-2). The Ni(I) species [Ni(n)(CN)(n-1)](+) (n = 1-4) and [Ni(n)(CN)(n+1)](-) (n = 1-3) are produced when anhydrous Ni(CN)(2) is irradiated. In all cases, CN(-) and polyatomic carbon nitride ions C(x)N(y)(-) are formed concurrently. On the basis of density functional calculations, probable structures are proposed for most of the newly observed species. General structural features are low coordination numbers, regular trigonal coordination stereochemistry for d(10) metals but distorted trigonal stereochemistry for transition metals, the occurrence of M-CN-M and M(-CN-)(2)M bridges, addition of AgCN to terminal CN ligands, and the occurrence of high spin ground states for linear [M(n)(CN)(n+1)](-) complexes of Co and Ni.     

New approach to molecular docking and its application to virtual screening of chemical databases

This paper describes the validation of a molecular docking method and its application to virtual database screening. The code flexibly docks ligand molecules into rigid receptor structures using a tabu search methodology driven by an empirically derived function for estimating the binding affinity of a protein-ligand complex. The docking method has been tested on 70 ligand-receptor complexes for which the experimental binding affinity and binding geometry are known. The lowest energy geometry produced by the docking protocol is within 2.0 A root mean square of the experimental binding mode for 79% of the complexes. The method has been applied to the problem of virtual database screening to identify known ligands for thrombin, factor Xa, and the estrogen receptor. A database of 10,000 randomly chosen "druglike" molecules has been docked into the three receptor structures. In each case known receptor ligands were included in the study. The results showed good separation between the predicted binding affinities of the known ligand set and the database subset.     

Vibrationally resolved rate coefficients and branching fractions in the dissociative recombination of O2+

We have studied the dissociative recombination of the first three vibrational levels of O(2) (+) in its electronic ground X (2)Pi(g) state. Absolute rate coefficients, cross sections, quantum yields and branching fractions have been determined in a merged-beam experiment in the heavy-ion storage ring, CRYRING, employing fragment imaging for the reaction dynamics. We present the absolute total rate coefficients as function of collision energies up to 0.4 eV for five different vibrational populations of the ion beam, as well as the partial (vibrationally resolved) rate coefficients and the branching fractions near 0 eV collision energy for the vibrational levels v=0, 1, and 2. The vibrational populations used were produced in a modified electron impact ion source, which has been calibrated using Cs-O(2)(+) dissociative charge transfer reactions. The measurements indicate that at low collision energies, the total rate coefficient is weakly dependent on the vibrational excitation. The calculated thermal rate coefficient at 300 K decreases upon vibrational excitation. The partial rate coefficients as well as the partial branching fractions are found to be strongly dependent on the vibrational level. The partial rate coefficient is the fastest for v=0 and goes down by a factor of two or more for v=1 and 2. The O((1)S) quantum yield, linked to the green airglow, increases strongly upon increasing vibrational level. The effects of the dissociative recombination reactions and super elastic collisions on the vibrational populations are discussed.     

Studies Related to Biological Detoxification of Kraft Pulp Mill Effluent. IV.The Biodegradation of 14-Chlorodehydroabietic Acid with Mortierella isabellina

One of the fish-toxic chlorinated resin acids, 14-chlorodehydroabietic acid ( 5 ), found in kraft mill effluent is examined. When exposed to the fungus Mortierella isabellina, 5 is converted into a number of hydroxylated derivatives which show low levels of toxicity to fish. These biotransformation products were isolated and characterized.     

An example of a nuclear space in infinite dimensional holomorphy

LetU be an open subset of a complex locally convex spaceE, andH(U) the space of holomorphic functions fromU toC. If the dualE′ ofE is nuclear with respect to the topology generated by the absolutely convex compact subsets ofE, then it is shown thatH(U) endowed with the compact open topology is a nuclear space. In particular, ifE is the strong dual of a Fréchet nuclear space, thenH(U) is a Fréchet nuclear space.     

A study of electronic structures of Pt3M (M=Ti,V,Cr,Fe,Co,Ni) polycrystalline alloys with valence-band photoemission spectroscopy

The surface valence-band densities of states (DOS) of Pt(3)M (M=Ti,V,Cr,Fe,Co,Ni) polycrystalline alloys were investigated with ultraviolet photoemission spectroscopy. Upon annealing the ion-sputter-cleaned alloys at high temperatures, the observed valence-band DOS spectra clearly show the modified electronic structures on the surfaces suggesting the surface segregation of Pt as predicted in thermodynamic models. The measured d-band centers and widths for the annealed alloy surfaces show qualitatively the same trend as predicted by density-functional-theory calculations based on the model of a Pt "skin" on the topmost surface layer and a subsurface layer enriched in the 3d transition metal.     

Sensitive and high-throughput analyses of purine metabolites by dynamic pH junction multiplexed capillary electrophoresis: a new tool for metabolomic studies.

On-line sample preconcentration by a dynamic pH junction in conjunction with multiplexed capillary electrophoresis (CE) and UV detection represents a sensitive and high-throughput format for future metabolomic research, such as purine analysis. The optimization of purine focusing can be rapidly assessed by systematically altering the sample matrix properties, such as the buffer co-ion, pH and ionic strength using a 96-capillary array format. This method permits focusing of large sample injection volumes, resulting in over a 50-fold improvement in the concentration sensitivity. The limit of detection (S/N = 3) for purine metabolites was less than 8.0 x 10(-8) M under optimum conditions when using UV absorbance. Dynamic pH junction multiplexed CE demonstrated excellent linearity over a hundred-fold concentration range, as well as low inter-capillary precision in terms of normalized migration times and peak areas. The potential for clinically relevant high-throughput analyses of micromolar amounts of purine metabolites in urine was also demonstrated.