The organometallic chemistry of the Ru(001) surface

The organometallic chemistry of the hexagonally close-packed Ru(001) surface has been studied using electron energy loss spectroscopy and thermal desorption mass spectrometry. The molecules that have been studied are acetylene, formamide and ammonia. The chemistry of acetylene and formamide has also been investigated in the presence of coadsorbed hydrogen and oxygen adatoms.

Acetylene is adsorbed molecularly on Ru(001) below approximately 230 K, with rehybridization of the molecule to nearly sp^3 occurring. The principal decomposition products at higher temperatures are ethylidyne (CCH_3) and acetylide (CCH) between 230 and 350 K, and methylidyne (CH) and surface carbon at higher temperatures. Some methylidyne is stable to approximately 700 K. The preadsorption of hydrogen does not alter the decomposition products of acetylene, but reduces the saturation coverage and also leads to the formation of a small amount of ethylene (via an η^2-CHCH_2 species) which desorbs molecularly near 175 K. Preadsorbed oxygen also reduces the saturation coverage of acetylene but has virtually no effect on the nature of the molecularly chemisorbed acetylene. It does, however, lead to the formation of an sp^2-hybridized vinylidene (CCH_2) species in the decomposition of acetylene, in addition to the decomposition products that are formed on the clean surface. There is no molecular desorption of chemisorbed acetylene from clean Ru(001), hydrogen-presaturated Ru(001), or oxygen-presaturated Ru(001).

The adsorption and decomposition of formamide has been studied on clean Ru(001), hydrogen-presaturated Ru(001), and Ru(001)-p(1x2)-O (oxygen adatom coverage = 0.5). On clean Ru(001), the adsorption of low coverages of formamide at 80 K results in CH bond cleavage and rehybridization of the carbonyl double bond to produce an η^2 (C,O)-NH_2CO species. This species is stable to approximately 250 K at which point it decomposes to yield a mixture of coadsorbed carbon monoxide, ammonia, an NH species and hydrogen adatoms. The decomposition of NH to hydrogen and nitrogen adatoms occurs between 350 and 400 K, and the thermal desorption products are NH_3 (-315 K), H_2 (-420 K), CO (-480 K) and N_2 (-770 K). At higher formamide coverages, some formamide is adsorbed molecularly at 80 K, leading both to molecular desorption and to the formation of a new surface intermediate between 300 and 375 K that is identified tentatively as η^1(N)-NCHO. On Ru(001)- p(1x2)-O and hydrogen-presaturated Ru(001), formamide adsorbs molecularly at 80 K in an η^1(O)- NH_2CHO configuration. On the oxygen-precovered surface, the molecularly adsorbed formamide undergoes competing desorption and decomposition, resulting in the formation of an η^2(N,O)-NHCHO species (analogous to a bidentate formate) at approximately 265 K. This species decomposes near 420 K with the evolution of CO and H_2 into the gas phase. On the hydrogen precovered surface, the Η^1(O)-NH_2CHO converts below 200 K to η^2(C,O)-NH_2CHO and η^2(C,O)-NH^2CO, with some molecular desorption occurring also at high coverage. The η^2(C,O)-bonded species decompose in a manner similar to the decomposition of η^2(C,O)-NH_2CO on the clean surface, although the formation of ammonia is not detected.

Ammonia adsorbs reversibly on Ru(001) at 80 K, with negligible dissociation occurring as the surface is annealed The EEL spectra of ammonia on Ru(001) are very similar to those of ammonia on other metal surfaces. Off-specular EEL spectra of chemisorbed ammonia allow the v(Ru-NH_3) and ρ(NH_3) vibrational loss features to be resolved near 340 and 625 cm^(-1), respectively. The intense δ_g (NH_3) loss feature shifts downward in frequency with increasing ammonia coverage, from approximately 1160 cm^(-1) in the low coverage limit to 1070 cm^(-1) at saturation. In coordination compounds of ammonia, the frequency of this mode shifts downward with decreasing charge on the metal atom, and its downshift on Ru(001) can be correlated with the large work function decrease that the surface has previously been shown to undergo when ammonia is adsorbed. The EELS data are consistent with ammonia adsorption in on-top sites. Second-layer and multilayer ammonia on Ru(001) have also been characterized vibrationally, and the results are similar to those obtained for other metal surfaces.

The electrocatalytic and stoichiometric oxidation chemistry of binuclear ruthenium complexes incorporating the anionic tripod ligand {(η5-C5H5)Co[P(OCH3)2(=O)]3}-

The anionic tripod ligand NaLoMe (L_(oMe) - = [(η^5-C_5H_5)Co{P(O)(OCH_3)_2}_3]^-) reacts with RuO_4 in a biphasic reaction mixture of 1% H_2SO_4 and CCI_4 to afford [(L_(oMe) (HO)Ru^(IV) (µ-O)_2Ru ^(IV)(OH)(L_(oMe)] (1), which is treated with aqueous CF_3S0_3H to generate [(L_(oMe)(H_2O)Ru^(IV) (µ-O)_2R^(IV) (OH_2)(L_(oMe)][CF_3SO_3]_2 ([H_21][CF_3SO_3]_2). Addition of iodosobenzene to an acetonitrile solution of this salt yields [(L_(oMe)(O)Ru^v(µ-0)2Ru^v-(O)(_(LoMe)] (2). The dimer 1 can be reduced chemically or electrochemically to the Ru^(III)- Ru^(III) dimers [(L_(oMe)(H_20)Ru^(III) (µ-OH)_2Ru^(III) (OH_2)(L_(oMe)) ]^2+ and [(L_(oMe)) ^(III) (µ-0Hh(µ-0H2)Ru^(III) (L_(oMe)]^2+ which interconvert in aqueous media. Two electron processes dominate both the bulk chemistry and the electrochemistry of 1. Among these processes are the quasi-reversible Ru^(IV) - Ru^(IV)/Ru^(III)- Ru^(III) and Ru^(III)- Ru^(III)/ Ru^(II)- Ru^(II) reductions and a largely irreversible Ru^(V) - Ru^(V)/ Ru^(IV) - Ru^(IV)/oxidation. The dioxo dimer 2 oxidizes alcohols and aldehydes in organic media to afford 1 and the corresponding aldehydes and acids. Analogously, the Ru^(V) - Ru^(V)/ Ru^(IV)- Ru^(IV) redox wave mediates the electrooxidation of alcohols and aldehydes in aqueous buffer. In this system, substrates can be oxidized completely to CO_2. The kinetic behavior of these oxidations was examined by UV-vis and chronoamperometry, respectively, and the chemistry is typical of metal-oxo complexes, indicating that electronic coupling between two metal centers does not dramatically affect the metal-oxo chemistry. Dimer [H_21]^(2+) also reacts with alcohols, aldehydes, and triphenylphosphine in CH_3CN to afford Ru^(III)- Ru^(III) products including [(L_(oMe))CH_3CN) Ru^(III) (µ-OH)_2 Ru^(III) (NCCH_3)( L_(oMe))][CF_3SO_3]2 (characterized by X-ray crystallography) and the corresponding organic products. Reaction of 1 with formaldehyde in aqueous buffer quantitatively affords the triply bridged dimer [(L_(oMe)Ru^(III) (µ-OH)2- (µ-HCOO) Ru^(III) (L_(oMe)][CF_3SO_3] (characterized by X-ray crystallography). This reaction evidently proceeds by two parallel inner-sphere pathways, one of which is autocatalytic. Neither pathway exhibits a primary isotope effect suggesting the rate determining process could be the formation of an intermediate, perhaps a Ru^(IV) - Ru^(IV) formate adduct. The Ru^(III)- Ru^(III)formate adduct is easily oxidized to the Ru^(IV) - Ru^(IV) analog [(L_(oMe)Ru^(IV)(µ-OH)_2-(µ-HCOO) Ru^(IV) (L_(oMe)][CF_3SO_3], which, after isolation, reacts slowly with aqueous formaldehyde to generate free formate and the Ru^(III)- Ru^(III) formate adduct. These dimers function as catalysts for the electrooxidation of formaldehyde at low anodic potentials (+0.0 V versus SCE in aqueous buffer, pH 8.5) and enhance the activity of Nafion treated palladium/carbon heterogeneous fuel cell catalysts.

Novel roles of the SRP RNA in co-translational protein targeting

The signal recognition particle (SRP) and its receptor (SR) are universally conserved protein machineries that deliver nascent peptides to their proper destination. The SRP RNA is a universally conserved and essential component of SRP, which serves as the “catalyst” of the protein targeting cycle. The SRP RNA accelerates SRP-SR complex formation at the beginning of the protein targeting reaction, and triggers GTP hydrolysis and SRP-SR complex disassembly at the end. Here we combined biochemical and biophysical approaches to investigate the molecular mechanism of the functions of the SRP RNA. We found that two functional ends in the SRP RNA mediate distinct functions. The tetraloop end facilitates initial assembly of SRP and SR by mediating an electrostatic interaction with the Lys399 receptor, which ensures efficient and accurate substrate targeting. At the later stage of the SRP cycle, the SRP-SR complex relocalizes ~ 100 Angstrom to the 5’,3’-distal end of the RNA, a conformation crucial for GTPase activation and cargo handover. These results, combined with recent structural work, elucidate the functions of the SRP RNA during the protein targeting reaction.

Application of microwave diagnostics to copper chloride and carbon dioxide lasers

Part A

A problem restricting the development of the CuCl laser has been the decrease in output power with increases of tube temperature above 400°C. At that temperature the CuCl vapor pressure is about .1 torr. This is a small fraction of the buffer gas pressure (He at 10 torr).

The aim of the project was to measure the peak radiation temperature (assumed related to the mean energy of electrons) in the laser discharge as a function of the tube temperature. A 24 gHz gated microwave radiometer was used.

It was found that at the tube temperatures at which the output power began to deteriorate, the electron radiation temperature showed a sharp increase (compared with radiation temperature in pure buffer).

Using the above result, we have postulated that this sudden increase is a result of Penning ionization of the Cu atoms. As a consequence of this process the number of Cu atoms available for lasing decrease.

PART B

The aim of the project was to study the dissociation of CO₂ in the glow discharge of flowing CO₂ lasers.

A TM₀₁₁ microwave (3 gHz) cavity was used to measure the radially averaged electron density n_e and the electron-neutral collision frequency in the laser discharge. An estimate of the electric field is made from these two measurements. A gas chromatograph was used to measure the chemical composition of the gases after going through the discharge. This instrument was checked against a mass spectrometer for accuracy and sensitivity.

Several typical laser mixtures were .used: CO₂-N₂-He (1,3,16), (1,3,0), (1,0,16), (1,2,10), (1,2,0), (1,0,10), (2,3,15), (2,3,0), (2,0,15), (1,3,16)+ H₂O and pure CO₂. Results show that for the conditions studied the dissociation as a function of the electron density is uniquely determined by the STP partial flow rate of CO₂, regardless of the amount of N₂ and/or He present. The presence of water vapor in the discharge decreased the degree of dissociation.

A simple theoretical model was developed using thermodynamic equilibrium. The electrons were replaced in the calculations by a distributed heat source.

The results are analyzed with a simple kinetic model.

Zirconocenes as models for homogeneous Ziegler-Natta olefin polymerization catalysts

Using density functional theory, we studied the fundamental steps of olefin polymerization for zwitterionic and cationic Group IV ansa-zirconocenes and a neutral ansa- yttrocene. Complexes [H₂E(C₅H₄)₂ZrMe]ⁿ (n = 0: E = BH₂ (1), BF₂ (2), AlH₂(3); n = +: E = CH₂(4), SiH₂(5)) and H₂Si(C₅H₄)₂YMe were used as computational models. The largest differences among these three classes of compounds were the strength of olefin binding and the stability of the β-agostic alkyl intermediate towards β-hydrogen elimination. We investigated the effect of solvent on the reaction energetics for land 5. We found that in benzene the energetics became very similar except that a higher olefin insertion barrier was calculated for 1. The calculated anion affinity of [CH₃BF₃]^- was weaker towards 1 than 5. The calculated olefin binding depended primarily on the charge of the ansa linker, and the olefin insertion barrier was found to decrease steadily in the following order: [H₂C(C₅H₄)₂ZrMe]⁺ > [F₂B(C₅H₄)₂ZrMe] ≈ [H₂B(C₅H₄)₂ZrMe] > [H₂Si(C₅H₄)₂ZrMe]⁺ > [H₂Al(C₅H₄)₂ZrMe].

We prepared ansa-zirconocene dicarbonyl complexes Me₂ECp₂Zr(CO)₂ (E = Si, C), and t-butyl substituted complexes (t-BuCp)₂Zr(CO)₂, Me₂E(t-BuCp)₂Zr(CO)₂ (E = Si, C), (Me₂Si)₂(t-BuCp)₂Zr(CO)₂ as well as analogous zirconocene complexes. Both the reduction potentials and carbonyl stretching frequencies follow the same order: Me₂SiCp₂ZrCl₂> Me₂CCp₂ZrCl₂> Cp₂ZrCl₂> (Me₂Si)₂Cp₂ZrCl₂. This ordering is a result of both the donating abilities of the cyclopentadienyl substituents and the orientation of the cyclopentadiene rings. Additionally, we prepared a series of analogous cationic zirconocene complexes [LZrOCMe₃][MeB(C₆F₅)₃] (L = CP₂, Me₂SiCp₂, Me₂CCP₂, (Me₂Si)₂Cp₂) and studied the kinetics of anion dissociation. We found that the enthalpy of anion dissociation increased from 10.3 kcal•mol^-1 to 17.6 kcal•mol^-1 as exposure of the zirconium center increased.

We also prepared series of zirconocene complexes bearing 2,2-dimethyl-2-sila-4-pentenyl substituents (and methyl-substituted olefin variants). Methide abstraction with B(C₆F₅) results in reversible coordination of the tethered olefin to the cationic zirconium center. The kinetics of olefin dissociation have been examined using NMR methods, and the effects of ligand variation for unlinked, singly [SiMe₂]-linked and doubly [SiMe₂]-linked bis(cyclopentadienyl) arrangements has been compared (ΔG‡ for olefin dissociation varies from 12.8 to 15.6 kcal•mol^-1). Methide abstraction from 1,2-(SiMe₂)₂(η⁵-C₅H₃)₂Zr(CH₃)-(CH₂CMe₂CH₂CH = CH₂) results in rapid β-allyl elimination with loss of isobutene yielding the allyl cation [{1,2-(SiMe₂)₂(η⁵-C₅H₃)₂Zr(η³-CH₂CH=CH₂)]⁺.

A ratiometric-based measure of gene co-expression

Current measures of global gene expression analyses, such as correlation and mutual information-based approaches, largely depend on the degree of association between mRNA levels and to a lesser extent on variability. I develop and implement a new approach, called the Ratiometric method, which is based on the coefficient of variation of the expression ratio of two genes, relying more on variation than previous methods. The advantage of such modus operandi is the ability to detect possible gene pair interactions regardless of the degree of expression dispersion across the sample group. Gene pairs with low expression dispersion, i.e., their absolute expressions remain constant across the sample group, are systematically missed by correlation and mutual information analyses. The superiority of the Ratiometric method in finding these gene pair interactions is demonstrated in a data set of RNA-seq B-cell samples from the 1000 Genomes Project Consortium. The Ratiometric method renders a more comprehensive recovery of KEGG pathways and GO-terms.

Combustion of CS₂/O₂ in a laminar mixing layer and processes in the CO chemical laser

The combustion of CS₂ and O₂ in a free burning laminar mixing layer at low pressure was investigated using emission spectroscopy. The temperature fields, CO vibrational distributions, and CO concentrations were measured. The data indicate that vibration ally excited CO was produced in the mixing layer flames, but that there were no vibrational population inversions. In comparison with the CS₂/O₂ premixed flames, the mixing layer flames favored greater production of COS and CO₂. Computer modeling was used to study the mechanisms responsible for the production of COS and CO₂, and to study how the branching chain mechanism responsible for production of CO affects the behavior of the mixing layer flame. The influences of the gas additives, N₂O, COS, and CNBr, were also investigated.

Influence of composition on the structure, electric and magnetic properties of Pd-Mn-P and Pd-Co-P amorphous alloys

The influence of composition on the structure and on the electric and magnetic properties of amorphous Pd-Mn-P and Pd-Co-P prepared by rapid quenching techniques were investigated in terms of (1) the 3d band filling of the first transition metal group, (2) the phosphorus concentration effect which acts as an electron donor and (3) the transition metal concentration.

The structure is essentially characterized by a set of polyhedra subunits essentially inverse to the packing of hard spheres in real space. Examination of computer generated distribution functions using Monte Carlo random statistical distribution of these polyhedra entities demonstrated tile reproducibility of the experimentally calculated atomic distribution function. As a result, several possible "structural parameters" are proposed such as: the number of nearest neighbors, the metal-to-metal distance, the degree of short-range order and the affinity between metal-metal and metal-metalloid. It is shown that the degree of disorder increases from Ni to Mn. Similar behavior is observed with increase in the phosphorus concentration.

The magnetic properties of Pd-Co-P alloys show that they are ferromagnetic with a Curie temperature between 272 and 399°K as the cobalt concentration increases from 15 to 50 at.%. Below 20 at.% Co the short-range exchange interactions which produce the ferromagnetism are unable to establish a long-range magnetic order and a peak in the magnetization shows up at the lowest temperature range . The electric resistivity measurements were performed from liquid helium temperatures up to the vicinity of the melting point (900°K). The thermomagnetic analysis was carried out under an applied field of 6.0 kOe. The electrical resistivity of Pd-Co-P shows the coexistence of a Kondo-like minimum with ferromagnetism. The minimum becomes less important as the transition metal concentration increases and the coefficients of ℓn T and T^2 become smaller and strongly temperature dependent. The negative magnetoresistivity is a strong indication of the existence of localized moment.

The temperature coefficient of resistivity which is positive for Pd- Fe-P, Pd-Ni-P, and Pd-Co-P becomes negative for Pd-Mn-P. It is possible to account for the negative temperature dependence by the localized spin fluctuation model and the high density of states at the Fermi energy which becomes maximum between Mn and Cr. The magnetization curves for Pd-Mn-P are typical of those resulting from the interplay of different exchange forces. The established relationship between susceptibility and resistivity confirms the localized spin fluctuation model. The magnetoresistivity of Pd-Mn-P could be interpreted in tenns of a short-range magnetic ordering that could arise from the Rudennan-Kittel type interactions.

Part I. Electric birefringence studies of deoxyribonucleic acids. Part II. Selective dissociation of nucleohistone complexes

Part I

The electric birefringence of dilute DNA solutions has been studied in considerable detail and on a large number of samples, but no new and reliable information was discovered concerning the tertiary structure of DNA. The large number of variables which effect the birefringence results is discussed and suggestions are made for further work on the subject.

The DNA molecules have been aligned in a rapidly alternating (10 to 20 kc/sec) square wave field confirming that the orientation mechanism is that of counterion polarization. A simple empirical relation between the steady state birefringence, Δn_st, and the square of the electric field, E, has been found: Δn_st = E²/(a E² + b), where a = 1/Δn_s and b = (E²/Δn_st)_E→o. Δn_s is the birefringence extrapolated to infinite field strength.

The molecules show a distribution of relaxation times from 10^-4 to 0.2 sec, which is consistent with expectations for flexible coil molecules. The birefringence and the relaxation times decrease with increasing salt concentrations. They also depend on the field strength and pulse duration in a rather non-reproducible manner, which may be due in part to changes in the composition of the solution or in the molecular structure of the DNA (other than denaturation). Further progress depends on the development of some control over these effects.

Part II

The specificity of the dissociation of reconstituted and native deoxyribonucleohistones (DNH) by monovalent salt solutions has been investigated. A novel zone ultracentrifugation method is used in which the DNH is sedimented as a zone through a preformed salt gradient, superimposed on a stabilizing D₂O (sucrose) density gradient. The results, obtained by scanning the quartz sedimentation tubes in a spectrophotometer, were verified by the conventional, preparative sedimentation technique. Procedures are discussed for the detection of microgram quantities of histones, since low concentrations must be used to prevent excessive aggregation of the DNH.

The data show that major histone fractions are selectively dissociated from DNH by increasing salt concentrations: Lysine rich histone (H I) dissociates gradually between 0.1 and 0.3 F, slightly lysine rich histone (H II) dissociates as a narrow band between 0.35 and 0.5 F, and arginine rich histone (H III, H IV) dissociates gradually above 0.5 F NaClO₄.

The activity of the partially dissociated, native DNH in sustaining RNA synthesis, their mobility and their unusual heat denaturation and renaturation behavior are described. The two-step melting behavior of the material indicates that the histones are non-randomly distributed along the DNA, but the implications are that the uncovered regions are not of gene-size length.