Studies of the representation of interatomic distances in molecules and crystal as sum of atomic radii

The electron diffraction investigation of the following compounds has been carried out: sulfur, sulfur nitride, realgar, arsenic trisulfide, spiropentane, dimethyltrisulfide, cis and trans lewisite, methylal, and ethylene glycol.

The crystal structures of the following salts have been determined by x-ray diffraction: silver molybdateand hydrazinium dichloride.

Suggested revisions of the covalent radii for B, Si, P, Ge, As, Sn, Sb, and Pb have been made, and values for the covalent radii of Al, Ga, In, Ti, and Bi have been proposed.

The Schomaker-Stevenson revision of the additivity rule for single covalent bond distances has been used in conjunction with the revised radii. Agreement with experiment is in general better with the revised radii than with the former radii and additivity.

The principle of ionic bond character in addition to that present in a normal covalent bond has been applied to the observed structures of numerous molecules. It leads to a method of interpretation which is at least as consistent as the theory of multiple bond formation.

The revision of the additivity rule has been extended to double bonds. An encouraging beginning along these lines has been made, but additional experimental data are needed for clarification.

High resolution electron microscope studies of chromosomal fibers

Techniques are described for mounting and visualizing biological macromolecules for high resolution electron microscopy. Standard techniques are included in a discussion of new methods designed to provide the highest structural resolution. Methods are also discussed for handling samples on the grid, for making accurate size measurements at the 20 Å level, and for photographically enhancing image contrast.

The application of these techniques to the study of the binding of DNA polymerase to DNA is described. It is shown that the electron micrographs of this material are in agreement with the model proposed by Dr. Arthur Kornberg. A model is described which locates several active sites on the enzyme.

The chromosomal material of the protozoan tetrahymena has been isolated and characterized by biochemical techniques and by electron microscopy. This material is shown to be typical of chromatin of higher creatures.

Comparison with other chromatins discloses that the genome of tetrahymena is highly template active and has a relatively simple genetic construction.

High resolution electron microscope procedures developed in this work have been combined with standard biochemical techniques to give a comprehensive picture of the structure of interphase chromosome fibers. The distribution of the chromosomal proteins along its DNA is discussed.

I. Electron spin relaxation studies of manganese(II) complexes in acetonitrile. II. Nuclear spin relaxation studies of bromine in tetrabromomanganese(II) in acetonitrile

Magnetic resonance techniques have given us a powerful means for investigating dynamical processes in gases, liquids and solids. Dynamical effects manifest themselves in both resonance line shifts and linewidths, and, accordingly, require detailed analyses to extract desired information. The success of a magnetic resonance experiment depends critically on relaxation mechanisms to maintain thermal equilibrium between spin states. Consequently, there must be an interaction between the excited spin states and their immediate molecular environment which promote changes in spin orientation while excess magnetic energy is coupled into other degrees of freedom by non-radiative processes. This is well known as spin-lattice relaxation. Certain dynamical processes cause fluctuations in the spin state energy levels leading to spin-spin relaxation and, here again, the environment at the molecular level plays a significant role in the magnitude of interaction. Relatively few electron spin relaxation studies of solutions have been conducted and the present work is addressed toward the extension of our knowledge in this area and the retrieval of dynamical information from line shape analyses on a time scale comparable to diffusion controlled phenomena.

Specifically, the electron spin relaxation of three Mn⁺²3d⁵ complexes, Mn(CH₃CN)₆⁺², MnCl₄^-2 in acetonitrile has been studied in considerable detail. The effective spin Hamiltonian constants were carefully evaluated under a wide range of experimental conditions. Resonance widths of these Mn⁺² complexes were studied in the presence of various excess ligand ions and as a function of concentration, viscosity, temperature and frequency (X-band, ~9.5 Ԍ Hz and K-band, ~35 Ԍ Hz).

A number of interesting conclusions were drawn from these studies. For the Et₄NCl-₄^-2 system several relaxation mechanisms leading to resonance broadening were observed. One source appears to arise through spin-orbit interactions caused by modulation of the ligand field resulting from transient distortions of the complex imparted by solvent fluctuations in the immediate surroundings of the paramagnetic ion. An additional spin relaxation was assigned to the formation of ion pairs [Et₄N⁺…MnCl₄^-2] and it was possible to estimate the dissociation constant for this specie in acetonitrile.

The Bu₄NBr-MnBr₄^-2 study was considerably more interesting. As in the former case, solvent fluctuations and ion-pairing of the paramagnetic complex [Bu₄N⁺…MnBr₄^-2] provide significant relaxation for the electronic spin system. Most interesting, without doubt, is the onset of a new relaxation mechanism leading to resonance broadening which is best interpreted as chemical exchange. Thus, assuming that resonance widths were simply governed by electron spin state lifetimes, we were able to extract dynamical information from an interaction in which the initial and final states are the same

MnBr₄^-2 + Br^- = MnBr₄^-2 + Br^-.

The bimolecular rate constants were obtained at six different temperatures and their magnitudes suggested that the exchange is probably diffusion controlled with essentially a zero energy of activation. The most important source of spin relaxation in this system stems directly from dipolar interactions between the manganese 3d⁵ electrons. Moreover, the dipolar broadening is strongly frequency dependent indicating a deviation between the transverse and longitudinal relaxation times. We are led to the conclusion that the 3d⁵ spin states of ion-paired MnBr₄^-2 are significantly correlated so that dynamical processes are also entering the picture. It was possible to estimate the correlation time, ^Td, characterizing this dynamical process.

In Part II we study nuclear magnetic relaxation of bromine ions in the MnBr4-2-Bu4NBr-acetonitrile system. Essentially we monitor the 79Br and 81Br linewidths in response to the [MnBr4-2]/[Br-] ratio with the express purpose of supporting our contention that exchange is occurring between "free" bromine ions in the solvent and bromine in the first coordination sphere of the paramagnetic anion. The complexity of the system elicited a two-part study: (1) the linewidth behavior of Bu4NBr in anhydrous CH3CN in the absence of MnBr4-2 and (2) in the presence of MnBr4-2. It was concluded in study (1) that dynamical association, Bu4NBr k1= Bu4N+ + Br-, was modulating field-gradient interactions at frequencies high enough to provide an estimation of the unimolecular rate constant, k1. A comparison of the two isotopic bromine linewidth-mole fraction results led to the conclusion that quadrupole interactions provided the dominant relaxation mechanism. In study (2) the "residual" bromine linewidths for both 79Br and 81Br are clearly controlled by quadrupole interactions which appear to be modulated by very rapid dynamical processes other than molecular reorientation. We conclude that the "residual" linewidth has its origin in chemical exchange and that bromine nuclei exchange rapidly between a "free" solvated ion and the paramagnetic complex, MnBr4-2.

Mechanistic studies of a model reaction for enzymatic hydroxylation

A study has been made of the reaction mechanism of a model system for enzymatic hydroxylation. The results of a kinetic study of the hydroxylation of 2-hydroxyazobenzene derivatives by cupric ion and hydrogen peroxide are presented. An investigation of kinetic orders indicates that hydroxylation proceeds by way of a coordinated intermediate complex consisting of cupric ion and the mono anions of 2-hydroxyazobenzene and hydrogen peroxide. Studies with deuterated substrate showed the absence of a primary kinetic isotope effect and no evidence of an NIH shift. The effect of substituents on the formation of intermediate complexes and the overall rate of hydroxylation was studied quantitatively in aqueous solution. The combined results indicate that the hydroxylation step is only slightly influenced by ring substitution. The substituent effect is interpreted in terms of reaction by a radical path or a concerted mechanism in which the formation of ionic intermediates is avoided. The reaction mechanism is discussed as a model for enzymatic hydroxylation.

Studies of response to earthquake ground motion

A study is made of the accuracy of electronic digital computer calculations of ground displacement and response spectra from strong-motion earthquake accelerograms. This involves an investigation of methods of the preparatory reduction of accelerograms into a form useful for the digital computation and of the accuracy of subsequent digital calculations. Various checks are made for both the ground displacement and response spectra results, and it is concluded that the main errors are those involved in digitizing the original record. Differences resulting from various investigators digitizing the same experimental record may become as large as 100% of the maximum computed ground displacements. The spread of the results of ground displacement calculations is greater than that of the response spectra calculations. Standardized methods of adjustment and calculation are recommended, to minimize such errors.

Studies are made of the spread of response spectral values about their mean. The distribution is investigated experimentally by Monte Carlo techniques using an electric analog system with white noise excitation, and histograms are presented indicating the dependence of the distribution on the damping and period of the structure. Approximate distributions are obtained analytically by confirming and extending existing results with accurate digital computer calculations. A comparison of the experimental and analytical approaches indicates good agreement for low damping values where the approximations are valid. A family of distribution curves to be used in conjunction with existing average spectra is presented. The combination of analog and digital computations used with Monte Carlo techniques is a promising approach to the statistical problems of earthquake engineering.

Methods of analysis of very small earthquake ground motion records obtained simultaneously at different sites are discussed. The advantages of Fourier spectrum analysis for certain types of studies and methods of calculation of Fourier spectra are presented. The digitizing and analysis of several earthquake records is described and checks are made of the dependence of results on digitizing procedure, earthquake duration and integration step length. Possible dangers of a direct ratio comparison of Fourier spectra curves are pointed out and the necessity for some type of smoothing procedure before comparison is established. A standard method of analysis for the study of comparative ground motion at different sites is recommended.

Field and Laboratory Studies of Atmospheric Organic Aerosol

This thesis is the culmination of field and laboratory studies aimed at assessing processes that affect the composition and distribution of atmospheric organic aerosol. An emphasis is placed on measurements conducted using compact and high-resolution Aerodyne Aerosol Mass Spectrometers (AMS). The first three chapters summarize results from aircraft campaigns designed to evaluate anthropogenic and biogenic impacts on marine aerosol and clouds off the coast of California. Subsequent chapters describe laboratory studies intended to evaluate gas and particle-phase mechanisms of organic aerosol oxidation.

The 2013 Nucleation in California Experiment (NiCE) was a campaign designed to study environments impacted by nucleated and/or freshly formed aerosol particles. Terrestrial biogenic aerosol with > 85% organic mass was observed to reside in the free troposphere above marine stratocumulus. This biogenic organic aerosol (BOA) originated from the Northwestern United States and was transported to the marine atmosphere during periodic cloud-clearing events. Spectra recorded by a cloud condensation nuclei counter demonstrated that BOA is CCN active. BOA enhancements at latitudes north of San Francisco, CA coincided with enhanced cloud water concentrations of organic species such as acetate and formate.

Airborne measurements conducted during the 2011 Eastern Pacific Emitted Aerosol Cloud Experiment (E-PEACE) were aimed at evaluating the contribution of ship emissions to the properties of marine aerosol and clouds off the coast of central California. In one study, analysis of organic aerosol mass spectra during periods of enhanced shipping activity yielded unique tracers indicative of cloud-processed ship emissions (m/z 42 and 99). The variation of their organic fraction (f₄₂ and f₉₉) was found to coincide with periods of heavy (f₄₂ > 0.15; f₉₉ > 0.04), moderate (0.05 < f₄₂ < 0.15; 0.01 < f₉₉ < 0.04), and negligible (f₄₂ < 0.05; f₉₉ < 0.01) ship influence. Application of these conditions to all measurements conducted during E-PEACE demonstrated that a large fraction of cloud droplet (72%) and dry aerosol mass (12%) sampled in the California coastal study region was heavily or moderately influenced by ship emissions. Another study investigated the chemical and physical evolution of a controlled organic plume emitted from the R/V Point Sur. Under sunny conditions, nucleated particles composed of oxidized organic compounds contributed nearly an order of magnitude more cloud condensation nuclei (CCN) than less oxidized particles formed under cloudy conditions. The processing time necessary for particles to become CCN active was short ( < 1 hr) compared to the time needed for particles to become hygroscopic at sub-saturated humidity ( > 4 hr).

Laboratory chamber experiments were also conducted to evaluate particle-phase processes influencing aerosol phase and composition. In one study, ammonium sulfate seed was coated with a layer of secondary organic aerosol (SOA) from toluene oxidation followed by a layer of SOA from α-pinene oxidation. The system exhibited different evaporative properties than ammonium sulfate seed initially coated with α-pinene SOA followed by a layer of toluene SOA. This behavior is consistent with a shell-and-core model and suggests limited mixing among different SOA types. Another study investigated the reactive uptake of isoprene epoxy diols (IEPOX) onto non-acidified aerosol. It was demonstrated that particle acidity has limited influence on organic aerosol formation onto ammonium sulfate seed, and that the chemical system is limited by the availability of nucleophiles such as sulfate.

Flow tube experiments were conducted to examine the role of iron in the reactive uptake and chemical oxidation of glycolaldehyde. Aerosol particles doped with iron and hydrogen peroxide were mixed with gas-phase glycolaldehyde and photochemically aged in a custom-built flow reactor. Compared to particles free of iron, iron-doped aerosols significantly enhanced the oxygen to carbon (O/C) ratio of accumulated organic mass. The primary oxidation mechanism is suggested to be a combination of Fenton and photo-Fenton reactions which enhance particle-phase OH radical concentrations.

Studies of temperature sensitive mutants of polyoma virus

Polyoma virus can undergo two different types of interactions with susceptible cells; one type of interaction leads to the production of new infectious virus and eventual cell death while the other leads to a neoplastically transformed cell which is able to continue to divide under conditions that inhibit the multiplication of uninfected normal cells. In order to study the viral genes involved in both of these virus-cell interactions the isolation of temperature sensitive mutants of polyoma virus was undertaken.

Two strains (TS-a, TS-b) which were temperature sensitive in their plaque forming ability at 38.5˚C, but not at 31.5˚C, were isolated from a mutagenized stock of the polyoma wild type virus (PY). TS-a was studied in further detail.

TS-a grown at 31.5˚C was found to be indistinguishable from PY in a number of physical characteristics including the heat sensitivity of the completed viral components. TS-a was inhibited in its ability to produce infectious virus in mouse cells when incubated at 38.5˚C; this inhibition could be overcome by infection with high multiplicities.

The nature of the intracellular temperature sensitive step of TS-a was analysed to some degree. It was found that this step occurs after uncoating of the infecting virus particles and about the time of new viral DNA synthesis. New infectious viral DNA does not appear to be made at the nonpermissive temperature; in contrast noninfectious capsids are made at 38.5˚C, but in amounts smaller than a full yield, such as made by TS-a at 31.5˚C or by PY at both the high and low temperature.

TS-a has also been found to be temperature sensitive in its transforming ability in vitro. Cells transformed at 31.5˚C by TS-a retain their transformed characteristics upon cultivation at 38.5˚C. Thus the temperature sensitive function seems to be important for the initiation of transformation, but not essential for the maintenance of the transformed state. TS-a also appears to be temperature sensitive in the production of tumors in newborn hamsters.

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.

Experimental and theoretical studies of the electrothermal instability in a nonequilibrium plasma

Experimental and theoretical studies have been made of the electrothermal waves occurring in a nonequilibrium MHD plasma. These waves are caused by an instability that occurs when a plasma having a dependence of conductivity on current density is subjected to crossed electric and magnetic fields. Theoretically, these waves were studied by developing and solving the equations of a steady, one-dimensional nonuniformity in electron density. From these nonlinear equations, predictions of the maximum amplitude and of the half width of steady waves could be obtained. Experimentally, the waves were studied in a nonequilibrium discharge produced in a potassium-seeded argon plasma at 2000°K and 1 atm. pressure. The behavior of such a discharge with four different configurations of electrodes was determined from photographs, photomultiplier measurements, and voltage probes. These four configurations were chosen to produce steady waves, to check the stability of steady waves, and to observe the manifestation of the waves in a MHD generator or accelerator configuration.

Steady, one-dimensional waves were found to exist in a number of situations, and where they existed, their characteristics agreed with the predictions of the steady theory. Some extensions of this theory were necessary, however, to describe the transient phenomena occurring in the inlet region of a discharge transverse to the gas flow. It was also found that in a discharge away from the stabilizing effect of the electrodes, steady waves became unstable for large Hall parameters. Methods of prediction of the effective electrical conductivity and Hall parameter of a plasma with nonuniformities caused by the electrothermal waves were also studied. Using these methods and the values of amplitude predicted by the steady theory, it was found that the measured decrease in transverse conductivity of a MHD device, 50 per cent at a Hall parameter of 5, could be accounted for in terms of the electrothermal instability.

Studies of chemical speciation in naturally anoxic basins

The chemical speciation of both metals and non-metals, the use of polarographic techniques, and application to the study of the chemistry of anoxic waters are considered. In the first part of the paper unfamiliar terminology is explained and then an example of simple lake chemistry is presented to illustrate why the concept of speciation is necessary.

I. The crystal structure of potassium bis(tricyanovinyl)amine. II. Nuclear magnetic resonance studies of alkali halide solutions. III. Elucidation of the intramolecular hydrogen bond in acetylacetone by the deuterium isotope effect on the chemical shift of the bridge hydrogen

Part I

Potassium bis-(tricyanovinyl) amine, K⁺N[C(CN)=C(CN)₂]₂^-, crystallizes in the monoclinic system with the space group Cc and lattice constants, a = 13.346 ± 0.003 Å, c = 8.992 ± 0.003 Å, B = 114.42 ± 0.02°, and Z = 4. Three dimensional intensity data were collected by layers perpendicular to b* and c* axes. The crystal structure was refined by the least squares method with anisotropic temperature factor to an R value of 0.064.

The average carbon-carbon and carbon-nitrogen bond distances in –C-CΞN are 1.441 ± 0.016 Å and 1.146 ± 0.014 Å respectively. The bis-(tricyanovinyl) amine anion is approximately planar. The coordination number of the potassium ion is eight with bond distances from 2.890 Å to 3.408 Å. The bond angle C-N-C of the amine nitrogen is 132.4 ± 1.9°. Among six cyano groups in the molecule, two of them are bent by what appear to be significant amounts (5.0° and 7.2°). The remaining four are linear within the experimental error. The bending can probably be explained by molecular packing forces in the crystals.

Part II

The nuclear magnetic resonance of ⁸¹Br and ¹²⁷I in aqueous solutions were studied. The cation-halide ion interactions were studied by studying the effect of the Li⁺, Na⁺, K⁺, Mg⁺⁺, Cs⁺ upon the line width of the halide ions. The solvent-halide ion interactions were studied by studying the effects of methanol, acetonitrile, and acetone upon the line width of ⁸¹Br and ¹²⁷I in the aqueous solutions. It was found that the viscosity plays a very important role upon the halide ions line width. There is no specific cation-halide ion interaction for those ions such as Mg⁺⁺, Di⁺, Na⁺, and K⁺, whereas the Cs⁺ - halide ion interaction is strong. The effect of organic solvents upon the halide ion line width in aqueous solutions is in the order acetone ˃ acetonitrile ˃ methanol. It is suggested that halide ions do form some stable complex with the solvent molecules and the reason Cs⁺ can replace one of the ligands in the solvent-halide ion complex.

Part III

An unusually large isotope effect on the bridge hydrogen chemical shift of the enol form of pentanedione-2, 4(acetylacetone) and 3-methylpentanedione-2, 4 has been observed. An attempt has been made to interpret this effect. It is suggested from the deuterium isotope effect studies, temperature dependence of the bridge hydrogen chemical shift studies, IR studies in the OH, OD, and C=O stretch regions, and the HMO calculations, that there may probably be two structures for the enol form of acetylacetone. The difference between these two structures arises mainly from the electronic structure of the π-system. The relative population of these two structures at various temperatures for normal acetylacetone and at room temperature for the deuterated acetylacetone were calculated.

Upconversion and fluorescence spectral studies of Er3+/Yb3+-codoped Bi(2)Q(3)-GeO2-Ga(2)Q(3)-Na2O glasses

The absorption spectra and upconversion fluorescence spectra of Er3+/-Yb3+-codoped natrium-gallium-germanium-bismuth glasses are measured and investigated. The intense green (533 and 549 nm) and red (672 nm) emission bands were simultaneously observed at room temperature. The quadratic dependence of the green and red emission on excitation power indicates that the two-photon absorption processes occur. The influence of Ga2C3 on upconversion intensity is investigated. The intensity of green emissions increases slowly with increasing Ga2O3 content, while the intensity of red emission increases significantly. The possible upconversion mechanisms for these glasses have also been discussed. The maximum phonon energy of the glasses determined based on the infrared (IR) spectral analysis is as low as 740 cm(-1). The studies indicate that Bi2O3-GeO2-Ga2O3-Na2O glasses may be potential materials for developing upconversion optical devices (c) 2006 Published by Elsevier B.V.