Catalytic conversion of nitrogen to ammonia by an iron model complex

Threefold symmetric Fe phosphine complexes have been used to model the structural and functional aspects of biological N₂ fixation by nitrogenases. Low-valent bridging Fe-S-Fe complexes in the formal oxidation states Fe(II)Fe(II), Fe(II)/Fe(I), and Fe(I)/Fe(I) have been synthesized which display rich spectroscopic and magnetic behavior. A series of cationic tris-phosphine borane (TPB) ligated Fe complexes have been synthesized and been shown to bind a variety of nitrogenous ligands including N₂H₄, NH₃, and NH₂-. These complexes are all high spin S = 3/2 and display EPR and magnetic characteristics typical of this spin state. Furthermore, a sequential protonation and reduction sequence of a terminal amide results in loss of NH₃ and uptake of N₂. These stoichiometric transformations represent the final steps in potential N₂ fixation schemes.

Treatment of an anionic FeN₂ complex with excess acid also results in the formation of some NH₃, suggesting the possibility of a catalytic cycle for the conversion of N₂ to NH₃ mediated by Fe. Indeed, use of excess acid and reductant results in the formation of seven equivalents of NH₃ per Fe center, demonstrating Fe mediated catalytic N₂ fixation with acids and protons for the first time. Numerous control experiments indicate that this catalysis is likely being mediated by a molecular species.

A number of other phosphine ligated Fe complexes have also been tested for catalysis and suggest that a hemi-labile Fe-B interaction may be critical for catalysis. Additionally, various conditions for the catalysis have been investigated. These studies further support the assignment of a molecular species and delineate some of the conditions required for catalysis.

Finally, combined spectroscopic studies have been performed on a putative intermediate for catalysis. These studies converge on an assignment of this new species as a hydrazido(2-) complex. Such species have been known on group 6 metals for some time, but this represents the first characterization of this ligand on Fe. Further spectroscopic studies suggest that this species is present in catalytic mixtures, which suggests that the first steps of a distal mechanism for N₂ fixation are feasible in this system.

Observations of nitrogen and oxygen isotopes in the low energy cosmic rays

The isotopic composition of the enhanced low energy nitrogen and oxygen cosmic rays can provide information regarding the source of these particles. Using the Caltech Electron/Isotope Spectrometer aboard the IMP-7 satellite, a measurement of this isotopic composition was made. To determine the isotope response of the instrument, a calibration was performed, and it was determined that the standard range-energy tables were inadequate to calculate the isotope response. From the calibration, corrections to the standard range-energy tables were obtained which can be used to calculate the isotope response of this and similar instruments.

The low energy nitrogen and oxygen cosmic rays were determined to be primarily ^(14)N and ^(16)O. Upper limits were obtained for the abundances of the other stable nitrogen and oxygen isotopes. To the 84% confidence level the isotopic abundances are: ^(15)N/N ≤ 0.26 (5.6- 12.7 MeV/nucleon), ^(17)0/0 ≤ 0.13 (7.0- 11.8 MeV/nucleon), (18)0/0 ≤ 0.12 (7.0 - 11.2 MeV/nucleon). The nitrogen composition differs from higher energy measurements which indicate that ^(15)N, which is thought to be secondary, is the dominant isotope. This implies that the low energy enhanced cosmic rays are not part of the same population as the higher energy cosmic rays and that they have not passed through enough material to produce a large fraction of ^(15)N. The isotopic composition of the low energy enhanced nitrogen and oxygen is consistent with the local acceleration theory of Fisk, Kozlovsky, and Ramaty, in which interstellar material is accelerated to several MeV/nucleon. If, on the other hand, the low energy nitrogen and oxygen result from nucleosynthesis in a galactic source, then the nucleosynthesis processes which produce an enhancement of nitrogen and oxygen and a depletion of carbon are restricted to producing predominantly ^(14)N and ^(16)O.

I. The rate and mechanism of the vapor-phase reaction between water and parts-per-million concentrations of nitrogen dioxide. II. The rate and mechanism of the air oxidation of parts-per-million concentrations of nitric oxide in the presence of water vapor.

Part I

A study of the thermal reaction of water vapor and parts-per-million concentrations of nitrogen dioxide was carried out at ambient temperature and at atmospheric pressure. Nitric oxide and nitric acid vapor were the principal products. The initial rate of disappearance of nitrogen dioxide was first order with respect to water vapor and second order with respect to nitrogen dioxide. An initial third-order rate constant of 5.5 (± 0.29) x 10⁴ liter² mole^-2 sec^-1 was found at 25˚C. The rate of reaction decreased with increasing temperature. In the temperature range of 25˚C to 50˚C, an activation energy of -978 (± 20) calories was found.

The reaction did not go to completion. From measurements as the reaction approached equilibrium, the free energy of nitric acid vapor was calculated. This value was -18.58 (± 0.04) kilocalories at 25˚C.

The initial rate of reaction was unaffected by the presence of oxygen and was retarded by the presence of nitric oxide. There were no appreciable effects due to the surface of the reactor. Nitric oxide and nitrogen dioxide were monitored by gas chromatography during the reaction.

Part II

The air oxidation of nitric oxide, and the oxidation of nitric oxide in the presence of water vapor, were studied in a glass reactor at ambient temperatures and at atmospheric pressure. The concentration of nitric oxide was less than 100 parts-per-million. The concentration of nitrogen dioxide was monitored by gas chromatography during the reaction.

For the dry oxidation, the third-order rate constant was 1.46 (± 0.03) x 10⁴ liter² mole^-2 sec^-1 at 25˚C. The activation energy, obtained from measurements between 25˚C and 50˚C, was -1.197 (±0.02) kilocalories.

The presence of water vapor during the oxidation caused the formation of nitrous acid vapor when nitric oxide, nitrogen dioxide and water vapor combined. By measuring the difference between the concentrations of nitrogen dioxide during the wet and dry oxidations, the rate of formation of nitrous acid vapor was found. The third-order rate constant for the formation of nitrous acid vapor was equal to 1.5 (± 0.5) x 10⁵ liter² mole^-2 sec^-1 at 40˚C. The reaction rate did not change measurably when the temperature was increased to 50˚C. The formation of nitric acid vapor was prevented by keeping the concentration of nitrogen dioxide low.

Surface effects were appreciable for the wet tests. Below 35˚C, the rate of appearance of nitrogen dioxide increased with increasing surface. Above 40˚C, the effect of surface was small.

The rate and mechanism of the partial oxidation of acetaldehyde by PPM concentrations of nitrogen dioxide

The thermal reaction between nitrogen dioxide and acetaldehyde in the gas phase was investigated at room temperature and atmospheric pressure. The initial rate of disappearance of nitrogen dioxide was 1.00 ± 0.03 order with respect to nitrogen dioxide and 1.00 ± 0.07 order with respect to acetaldehyde. An initial second order rate constant of (8.596 ± 0.189) x 10^-3 1.mole^-1 sec^-1 was obtained at 22.0 ± 0.1 °C and a total pressure of one atmosphere. The activation energy of the reaction was 12,900 cal/mole in the temperature range between 22°C and 122°C.

The products of the reaction were nitric oxide, carbon dioxide, methyl nitrite, nitromethane and a trace amount of trans-dimeric nitrosomethane. The addition of nitric oxide increased the rate of formation of nitromethane and decreased the rate of formation of methyl nitrite. There were no measurable surface effects due to the addition of glass wool or glass beads to the reactor.

Reactants and products were analyzed by gas chromatography. A mechanism was proposed incorporating the principal features of the reaction.

The Flocculation of E. coli with Polyethyleneimine

A comprehensive study was made of the flocculation of dispersed E. coli bacterial cells by the cationic polymer polyethyleneimine (PEI). The three objectives of this study were to determine the primary mechanism involved in the flocculation of a colloid with an oppositely charged polymer, to determine quantitative correlations between four commonly-used measurements of the extent of flocculation, and to record the effect of varying selected system parameters on the degree of flocculation. The quantitative relationships derived for the four measurements of the extent of flocculation should be of direct assistance to the sanitary engineer in evaluating the effectiveness of specific coagulation processes.

A review of prior statistical mechanical treatments of absorbed polymer configuration revealed that at low degrees of surface site coverage, an oppositely- charged polymer molecule is strongly adsorbed to the colloidal surface, with only short loops or end sequences extending into the solution phase. Even for high molecular weight PEI species, these extensions from the surface are theorized to be less than 50 Å in length. Although the radii of gyration of the five PEI species investigated were found to be large enough to form interparticle bridges, the low surface site coverage at optimum flocculation doses indicates that the predominant mechanism of flocculation is adsorption coagulation.

The effectiveness of the high-molecular weight PEI species 1n producing rapid flocculation at small doses is attributed to the formation of a charge mosaic on the oppositely-charged E. coli surfaces. The large adsorbed PEI molecules not only neutralize the surface charge at the adsorption sites, but also cause charge reversal with excess cationic segments. The alignment of these positive surface patches with negative patches on approaching cells results in strong electrostatic attraction in addition to a reduction of the double-layer interaction energies. The comparative ineffectiveness of low-molecular weight PEI species in producing E. coli flocculation is caused by the size of the individual molecules, which is insufficient to both neutralize and reverse the negative E.coli surface charge. Consequently, coagulation produced by low molecular weight species is attributed solely to the reduction of double-layer interaction energies via adsorption.

Electrophoretic mobility experiments supported the above conclusions, since only the high-molecular weight species were able to reverse the mobility of the E. coli cells. In addition, electron microscope examination of the seam of agglutination between E. coli cells flocculation by PEI revealed tightly- bound cells, with intercellular separation distances of less than 100-200 Å in most instances. This intercellular separation is partially due to cell shrinkage in preparation of the electron micrographs.

The extent of flocculation was measured as a function of PEl molecular weight, PEl dose, and the intensity of reactor chamber mixing. Neither the intensity of mixing, within the common treatment practice limits, nor the time of mixing for up to four hours appeared to play any significant role in either the size or number of E.coli aggregates formed. The extent of flocculation was highly molecular weight dependent: the high-molecular-weight PEl species produce the larger aggregates, the greater turbidity reductions, and the higher filtration flow rates. The PEl dose required for optimum flocculation decreased as the species molecular weight increased. At large doses of high-molecular-weight species, redispersion of the macroflocs occurred, caused by excess adsorption of cationic molecules. The excess adsorption reversed the surface charge on the E.coli cells, as recorded by electrophoretic mobility measurements.

Successful quantitative comparisons were made between changes in suspension turbidity with flocculation and corresponding changes in aggregate size distribution. E. coli aggregates were treated as coalesced spheres, with Mie scattering coefficients determined for spheres in the anomalous diffraction regime. Good quantitative comparisons were also found to exist between the reduction in refiltration time and the reduction of the total colloid surface area caused by flocculation. As with turbidity measurements, a coalesced sphere model was used since the equivalent spherical volume is the only information available from the Coulter particle counter. However, the coalesced sphere model was not applicable to electrophoretic mobility measurements. The aggregates produced at each PEl dose moved at approximately the same vlocity, almost independently of particle size.

PEl was found to be an effective flocculant of E. coli cells at weight ratios of 1 mg PEl: 100 mg E. coli. While PEl itself is toxic to E.coli at these levels, similar cationic polymers could be effectively applied to water and wastewater treatment facilities to enhance sedimentation and filtration characteristics.

Kinetic investigations of heterogeneously catalyzed reactions on the Ru(001) and Pt(110)-(1x2) surfaces

The initial probabilities of activated, dissociative chemisorption of methane and ethane on Pt(110)-(1 x 2) have been measured. The surface temperature was varied from 450 to 900 K with the reactant gas temperature constant at 300 K. Under these conditions, we probe the kinetics of dissociation via trapping-mediated (as opposed to 'direct') mechanism. It was found that the probabilities of dissociation of both methane and ethane were strong functions of the surface temperature with an apparent activation energies of 14.4 kcal/mol for methane and 2.8 kcal/mol for ethane, which implys that the methane and ethane molecules have fully accommodated to the surface temperature. Kinetic isotope effects were observed for both reactions, indicating that the C-H bond cleavage was involved in the rate-limiting step. A mechanistic model based on the trapping-mediated mechanism is used to explain the observed kinetic behavior. The activation energies for C-H bond dissociation of the thermally accommodated methane and ethane on the surface extracted from the model are 18.4 and 10.3 kcal/mol, respectively.

The studies of the catalytic decomposition of formic acid on the Ru(001) surface with thermal desorption mass spectrometry following the adsorption of DCOOH and HCOOH on the surface at 130 and 310 K are described. Formic acid (DCOOH) chemisorbs dissociatively on the surface via both the cleavage of its O-H bond to form a formate and a hydrogen adatom, and the cleavage of its C-O bond to form a carbon monoxide, a deuterium adatom and an hydroxyl (OH). The former is the predominant reaction. The rate of desorption of carbon dioxide is a direct measure of the kinetics of decomposition of the surface formate. It is characterized by a kinetic isotope effect, an increasingly narrow FWHM, and an upward shift in peak temperature with Ɵ_T, the coverage of the dissociatively adsorbed formic acid. The FWHM and the peak temperature change from 18 K and 326 K at Ɵ_T = 0.04 to 8 K and 395 K at Ɵ_T = 0.89. The increase in the apparent activation energy of the C-D bond cleavage is largely a result of self-poisoning by the formate, the presence of which on the surface alters the electronic properties of the surface such that the activation energy of the decomposition of formate is increased. The variation of the activation energy for carbon dioxide formation with Ɵ_T accounts for the observed sharp carbon dioxide peak. The coverage of surface formate can be adjusted over a relatively wide range so that the activation energy for C-D bond cleavage in the case of DCOOH can be adjusted to be below, approximately equal to, or well above the activation energy for the recombinative desorption of the deuterium adatoms. Accordingly, the desorption of deuterium was observed to be governed completely by the desorption kinetics of the deuterium adatoms at low Ɵ_T, jointly by the kinetics of deuterium desorption and C-D bond cleavage at intermediate Ɵ_T, and solely by the kinetics of C-D bond cleavage at high Ɵ_T. The overall branching ratio of the formate to carbon dioxide and carbon monoxide is approximately unity, regardless the initial coverage Ɵ_T, even though the activation energy for the production of carbon dioxide varies with Ɵ_T. The desorption of water, which implies C-O bond cleavage of the formate, appears at approximately the same temperature as that of carbon dioxide. These observations suggest that the cleavage of the C-D bond and that of the C-O bond of two surface formates are coupled, possibly via the formation of a short-lived surface complex that is the precursor to to the decomposition.

The measurement of steady-state rate is demonstrated here to be valuable in determining kinetics associated with short-lived, molecularly adsorbed precursor to further reactions on the surface, by determining the kinetic parameters of the molecular precursor of formaldehyde to its dissociation on the Pt(110)-(1 x 2) surface.

Overlayers of nitrogen adatoms on Ru(001) have been characterized both by thermal desorption mass spectrometry and low-energy electron diffraction, as well as chemically via the postadsorption and desorption of ammonia and carbon monoxide.

The nitrogen-adatom overlayer was prepared by decomposing ammonia thermally on the surface at a pressure of 2.8 x 10^(-6) Torr and a temperature of 480 K. The saturated overlayer prepared under these conditions has associated with it a (√247/10 x √247/10)R22.7° LEED pattern, has two peaks in its thermal desorption spectrum, and has a fractional surface coverage of 0.40. Annealing the overlayer to approximately 535 K results in a rather sharp (√3 x √3)R30° LEED pattern with an associated fractional surface coverage of one-third. Annealing the overlayer further to 620 K results in the disappearance of the low-temperature thermal desorption peak and the appearance of a rather fuzzy p(2x2) LEED pattern with an associated fractional surface coverage of approximately one-fourth. In the low coverage limit, the presence of the (√3 x √3)R30° N overlayer alters the surface in such a way that the binding energy of ammonia is increased by 20% relative to the clean surface, whereas that of carbon monoxide is reduced by 15%.

A general methodology for the indirect relative determination of the absolute fractional surface coverages has been developed and was utilized to determine the saturation fractional coverage of hydrogen on Ru(001). Formaldehyde was employed as a bridge to lead us from the known reference point of the saturation fractional coverage of carbon monoxide to unknown reference point of the fractional coverage of hydrogen on Ru(001), which is then used to determine accurately the saturation fractional coverage of hydrogen. We find that ƟSAT/H = 1.02 (±0.05), i.e., the surface stoichiometry is Ru : H = 1 : 1. The relative nature of the method, which cancels systematic errors, together with the utilization of a glass envelope around the mass spectrometer, which reduces spurious contributions in the thermal desorption spectra, results in high accuracy in the determination of absolute fractional coverages.

Palladium-Catalyzed Decarboxylative and Decarbonylative Transformations in the Synthesis of Fine and Commodity Chemicals

Decarboxylation and decarbonylation are important reactions in synthetic organic chemistry, transforming readily available carboxylic acids and their derivatives into various products through loss of carbon dioxide or carbon monoxide. In the past few decades, palladium-catalyzed decarboxylative and decarbonylative reactions experienced tremendous growth due to the excellent catalytic activity of palladium. Development of new reactions in this category for fine and commodity chemical synthesis continues to draw attention from the chemistry community.

The Stoltz laboratory has established a palladium-catalyzed enantioselective decarboxylative allylic alkylation of β-keto esters for the synthesis of α-quaternary ketones since 2005. Recently, we extended this chemistry to lactams due to the ubiquity and importance of nitrogen-containing heterocycles. A wide variety of α-quaternary and tetrasubstituted α-tertiary lactams were obtained in excellent yields and exceptional enantioselectivities using our palladium-catalyzed decarboxylative allylic alkylation chemistry. Enantioenriched α-quaternary carbonyl compounds are versatile building blocks that can be further elaborated to intercept synthetic intermediates en route to many classical natural products. Thus our chemistry enables catalytic asymmetric formal synthesis of these complex molecules.

In addition to fine chemicals, we became interested in commodity chemical synthesis using renewable feedstocks. In collaboration with the Grubbs group, we developed a palladium-catalyzed decarbonylative dehydration reaction that converts abundant and inexpensive fatty acids into value-added linear alpha olefins. The chemistry proceeds under relatively mild conditions, requires very low catalyst loading, tolerates a variety of functional groups, and is easily performed on a large scale. An additional advantage of this chemistry is that it provides access to expensive odd-numbered alpha olefins.

Finally, combining features of both projects, we applied a small-scale decarbonylative dehydration reaction to the synthesis of α-vinyl carbonyl compounds. Direct α-vinylation is challenging, and asymmetric vinylations are rare. Taking advantage of our decarbonylative dehydration chemistry, we were able to transform enantioenriched δ-oxocarboxylic acids into quaternary α-vinyl carbonyl compounds in good yields with complete retention of stereochemistry. Our explorations culminated in the catalytic enantioselective total synthesis of (–)-aspewentin B, a terpenoid natural product featuring a quaternary α-vinyl ketone. Both decarboxylative and decarbonylative chemistries found application in the late stage of the total synthesis.

Part I: The abortive infection of bacteriophage øx174 at low temperatures. Part II: The early stages in the process of infection by bacteriophage øx174

Part I

The infection of E. coli by ΦX174 at 15°C is abortive; the cells are killed by the infection but neither mature phage nor SS (single-stranded) DNA are synthesized. Parental RF (replicative form) is formed and subsequently replicated at 15°C. The RF made at 15°C shows normal infectivity and full competence to act as precursor to progeny SS DNA after an increase in temperature to 37°C. The investigations suggest that all of the proteins required for SS DNA synthesis and phage maturation are present in the abortive infection at 15°C.

Three possible causes are suggested for the abortive infection at 15°C: (a) A virus-coded protein whose role is essential to the infection is made at 15°C and assumes its native conformation, but its rate of activity is too low at this temperature to sustain the infection process. (b) Virus maturation may involve the formation of a DNA-protein complex and conformational changes which have an energy threshold infrequently reached at 15°C. (c) A host-coded protein present in uninfected cells, and whose activity is essential to the infection at all temperatures, but not to the host at 15°C, is inactive at 15°C. An hypothesis of this type is offered which proposes that the temperature-limiting factor in SS DNA synthesis in vivo may reflect a temperature-dependent property of the host DNA polymerase.

Part II

Three distinct stages are demonstrated in the process whereby ΦX174 invades its host: (1) Attachment: The phage attach to the cell in a manner that does not irreversibly alter the phage particle and which exhibits "single-hit" kinetics. The total charge on the phage particle is demonstrated to be important in determining the rate at which stable attachment is effected. The proteins specified by ΦX cistrons II, III and VII play roles, which may be indirect, in the attachment reaction. (2) Eclipse: 'The attached phage undergo a conformational change. Some of the altered phage particles spontaneously detach from the cell (in a non-infective form) while the remainder are more tightly bound to the cell. The altered phage particles detached (spontaneously or chemically) from such complexes have at least 40% of their DNA extruded from the phage coat. It is proposed that this particle is, or derives from, a direct intermediate in the penetration of the viral DNA.

The kinetics for the eclipse of attached phage particles are first-order with respect to phage concentration and biphasic; about 85% of the phage eclipse at one rate (k = 0.86 min^-1) and the remainder do so at a distinctly lesser rate (k = 0.21 min^-1).

The eclipse event is very temperature-dependent and has the relatively high Arrhenius activation energy of 36.6 kcal/mole, indicating the cooperative nature of the process. The temperature threshold for eclipse is 17 to 18°C.

At present no specific ΦX cistron is identified as affecting the eclipse process. (3) DNA penetration: A fraction of the attached, eclipsed phage particles corresponding in number to the plaque-forming units complete DNA penetration. The penetrated DNA is found in the cell as RF, and the empty phage protein coat remains firmly attached to the exterior of the cell. This step is inhibited by prior irradiation of the phage with relatively high doses of UV light and is insensitive to the presence of KCN and NaN₃. Temporally excluded superinfecting phages do not achieve DNA penetration.

Both eclipsed phage particles and empty phage protein coats may be dissociated from infected cells; some of their properties are described.

Rydberg states of diatomic and polyatomic molecules using model potentials

A simple model potential is used to calculate Rydberg series for the molecules: nitrogen, oxygen, nitric oxide, carbon monoxide, carbon dioxide, nitrogen dioxide, nitrous oxide, acetylene, formaldehyde, formic acid, diazomethane, ketene, ethylene, allene, acetaldehyde, propyne, acrolein, dimethyl ether, 1, 3-butadiene, 2-butene, and benzene. The model potential for a molecule is taken as the sum of atomic potentials, which are calibrated to atomic data and contain no further parameters. Our results agree with experimentally measured values to within 5-10% in all cases. The results of these calculations are applied to many unresolved problems connected with the above molecules. Some of the more notable of these problems are the reassignment of states in carbon monoxide, the first ionization potential of nitrogen dioxide, the interpretation of the V state in ethylene, and the mystery bands in substituted ethylenes, the identification of the R and R’ series in benzene and the determination of the orbital scheme in benzene from electron impact data.