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.

I. Studies on bacteriophage DNA's and minicircular DNA's in M. lysodeikticus and E. coli 15. II. Flow dichroism of DNA solutions

Part I

Chapter 1.....A physicochemical study of the DNA molecules from the three bacteriophages, N1, N5, and N6, which infect the bacterium, M. lysodeikticus, has been made. The molecular weights, as measured by both electron microscopy and sedimentation velocity, are 23 x 10⁶ for N5 DNA and 31 x 10⁶ for N1 and N6 DNA's. All three DNA's are capable of thermally reversible cyclization. N1 and N6 DNA's have identical or very similar base sequences as judged by membrane filter hybridization and by electron microscope heteroduplex studies. They have identical or similar cohesive ends. These results are in accord with the close biological relation between N1 and N6 phages. N5 DNA is not closely related to N1 or N6 DNA. The denaturation T_m of all three DNA's is the same and corresponds to a (GC) content of 70%. However, the buoyant densities in CsCl of Nl and N6 DNA's are lower than expected, corresponding to predicted GC contents of 64 and 67%. The buoyant densities in Cs₂SO₄ are also somewhat anomalous. The buoyant density anomalies are probably due to the presence of odd bases. However, direct base composition analysis of N1 DNA by anion exchange chromatography confirms a GC content of 70%, and, in the elution system used, no peaks due to odd bases are present.

Chapter 2.....A covalently closed circular DNA form has been observed as an intracellular form during both productive and abortive infection processes in M. lysodeikticus. This species has been isolated by the method of CsC1-ethidium bromide centrifugation and examined with an electron microscope.

Chapter 3.....A minute circular DNA has been discovered as a homogeneous population in M. lysodeikticus. Its length and molecular weight as determined by electron microscopy are 0.445 μ and 0.88 x 10⁶ daltons respectively. There is about one minicircle per bacterium.

Chapter 4.....Several strains of E. coli 15 harbor a prophage. Viral growth can be induced by exposing the host to mitomycin C or to uv irradiation. The coliphage 15 particles from E. coli 15 and E, coli 15 T^- appear as normal phage with head and tail structure; the particles from E. coli 15 TAU are tailless. The complete particles exert a colicinogenic activity on E.coli 15 and 15 T^-, the tailless particles do not. No host for a productive viral infection has been found and the phage may be defective. The properties of the DNA of the virus have been studied, mainly by electron microscopy. After induction but before lysis, a closed circular DNA with a contour length of about 11.9 μ is found in the bacterium; the mature phage DNA is a linear duplex and 7.5% longer than the intracellular circular form. This suggests the hypothesis that the mature phage DNA is terminally repetitious and circularly permuted. The hypothesis was confirmed by observing that denaturation and renaturation of the mature phage DNA produce circular duplexes with two single-stranded branches corresponding to the terminal repetition. The contour length of the mature phage DNA was measured relative to φX RFII DNA and λ DNA; the calculated molecular weight is 27 x 10⁶. The length of the single-stranded terminal repetition was compared to the length of φX 174 DNA under conditions where single-stranded DNA is seen in an extended form in electron micrographs. The length of the terminal repetition is found to be 7.4% of the length of the nonrepetitious part of the coliphage 15 DNA. The number of base pairs in the terminal repetition is variable in different molecules, with a fractional standard deviation of 0.18 of the average number in the terminal repetition. A new phenomenon termed "branch migration" has been discovered in renatured circular molecules; it results in forked branches, with two emerging single strands, at the position of the terminal repetition. The distribution of branch separations between the two terminal repetitions in the population of renatured circular molecules was studied. The observed distribution suggests that there is an excluded volume effect in the renaturation of a population of circularly permuted molecules such that strands with close beginning points preferentially renature with each other. This selective renaturation and the phenomenon of branch migration both affect the distribution of branch separations; the observed distribution does not contradict the hypothesis of a random distribution of beginning points around the chromosome.

Chapter 5....Some physicochemical studies on the minicircular DNA species in E. coli 15 (0.670 μ, 1.47 x 10⁶ daltons) have been made. Electron microscopic observations showed multimeric forms of the minicircle which amount to 5% of total DNA species and also showed presumably replicating forms of the minicircle. A renaturation kinetic study showed that the minicircle is a unique DNA species in its size and base sequence. A study on the minicircle replication has been made under condition in which host DNA synthesis is synchronized. Despite experimental uncertainties involved, it seems that the minicircle replication is random and the number of the minicircles increases continuously throughout a generation of the host, regardless of host DNA synchronization.

Part II

The flow dichroism of dilute DNA solutions (A₂₆₀≈0.1) has been studied in a Couette-type apparatus with the outer cylinder rotating and with the light path parallel to the cylinder axis. Shear gradients in the range of 5-160 sec.^-1 were studied. The DNA samples were whole, "half," and "quarter" molecules of T4 bacteriophage DNA, and linear and circular λb₂b₅c DNA. For the linear molecules, the fractional flow dichroism is a linear function of molecular weight. The dichroism for linear A DNA is about 1.8 that of the circular molecule. For a given DNA, the dichroism is an approximately linear function of shear gradient, but with a slight upward curvature at low values of G, and some trend toward saturation at larger values of G. The fractional dichroism increases as the supporting electrolyte concentration decreases.

Part I: Latent heat of vaporization of n-decane. Part II: Heat and mass transfer from a cylinder placed in a turbulent air stream - Sherwood and Frössling numbers as a function of free stream turbulence level and Reynolds number

Part I

The latent heat of vaporization of n-decane is measured calorimetrically at temperatures between 160° and 340°F. The internal energy change upon vaporization, and the specific volume of the vapor at its dew point are calculated from these data and are included in this work. The measurements are in excellent agreement with available data at 77° and also at 345°F, and are presented in graphical and tabular form.

Part II

Simultaneous material and energy transport from a one-inch adiabatic porous cylinder is studied as a function of free stream Reynolds Number and turbulence level. Experimental data is presented for Reynolds Numbers between 1600 and 15,000 based on the cylinder diameter, and for apparent turbulence levels between 1.3 and 25.0 per cent. n-heptane and n-octane are the evaporating fluids used in this investigation.

Gross Sherwood Numbers are calculated from the data and are in substantial agreement with existing correlations of the results of other workers. The Sherwood Numbers, characterizing mass transfer rates, increase approximately as the 0.55 power of the Reynolds Number. At a free stream Reynolds Number of 3700 the Sherwood Number showed a 40% increase as the apparent turbulence level of the free stream was raised from 1.3 to 25 per cent.

Within the uncertainties involved in the diffusion coefficients used for n-heptane and n-octane, the Sherwood Numbers are comparable for both materials. A dimensionless Frössling Number is computed which characterizes either heat or mass transfer rates for cylinders on a comparable basis. The calculated Frössling Numbers based on mass transfer measurements are in substantial agreement with Frössling Numbers calculated from the data of other workers in heat transfer.