Modeling of H2 and H2/CH4 Moderate-Pressure Microwave Plasma Used for Diamond Deposition

One-dimensional transport models of moderate-pressure H ₂ and H ₂ /CH ₄ plasmas obtained in a diamond deposition microwave reactor are presented. These models describe the plasma as a thermochemically nonequilibrium flow with three different energy modes. The solution of the one-dimensional plasma transport equations enabled the estimation of plasma species concentrations and temperatures on the axis of the reactor. As far as pure H ₂ plasmas are concerned, results showed that the model predictions of gas and vibration temperatures are in good agreement with experimental measurements. The model also yields a relatively good qualitative prediction of the variations of H-atom mole fraction with the power density absorbed by the plasma. The results obtained for H ₂ /CH ₄ discharges showed that the model prediction on the variations of H-atom mole fraction with methane percentage in the discharge is in good qualitative agreement with experimental results. They also showed that methane is rapidly converted to acetylene before reaching the discharge zone. The concentrations of neutral hydrocarbon species in the reactor are mainly governed by thermal chemistry. The addition of methane strongly affects the ionization kinetics of the plasma. Three major ions are generally obtained in H ₂ /CH ₄ plasmas: C ₂ H ₂ ⁺ , C ₂ H ₃ ⁺ , and C ₂ H ₅ ⁺ . The relative predominance of these ions depends on the considered plasma region and on the discharge conditions. The ionic species concentrations are also mainly governed by chemistry, except very near the substrate surface. Finally the use of this transport model along with the surface chemistry model of Goodwin ⁽¹⁾ enabled us to estimate the diamond growth rate for several discharge conditions.     

Configurational entropy of polyethylene and other linear polymers

The configurational entropy of the polyethylene chain at the melting points calculated in two ways. In both calculations, tetrahedral angles and discrete trans and gauche arrangements of all bonds are assumed, and trans bonds are assumed more stable than gauche by energy U₁. First, calculations are made on chains of up to N = 18 bonds, disallowing all configurations having overlapping atoms, and the result is extrapolated to large N. Second, a calculation is made directly for long chains, with overlaps excluded only over every short chain segment. The results are in almost exact agreement, suggesting that the second method can be safely used with other molecules. The calculated configurational entropy is in line with that suggested by the entropy of fusion, assuming the chains to acquire a configurational freedom in the melt which approaches that of independent chains.     

Adsorption of <Emphasis Type="Italic">n</Emphasis>-Butanol from Aqueous Solutions on an Sn-Ga Electrode in the Absence of a Metal-Water Chemisorption Interaction

Data on the dependence of the differential capacitance on potential at the Sn-Ga/H₂O interface in 0.05 M solutions of Na₂SO₄ with various additives of n-butanol are obtained by a bridge method at a frequency of 420 Hz and a temperature of 32°C. In the region of potentials studied, the chemisorption interaction (Sn-Ga)-H₂O is completely absent. The adsorption parameters of n-butanol are obtained by a method of a regression analysis of these data. The data obtained are compared with similar data on various hydrophobic electrodes. Shown is that, on the Sn-Ga and Pb-Ga electrodes, whose “electronic” capacitance is similar, the free energies of adsorption of n-butanol are also similar but differ from the adsorption energy on electrodes of Hg, Bi-Ga, and Tl-Ga. The results that are obtained on an Sn-Ga electrode nicely fit a general correlation dependence between the reciprocal value of the electronic capacitance of various electrodes in the absence of a metal-water chemisorption interaction, (C _m ⁻¹ ), and the free energies of adsorption of molecules of n-butanol on these, ΔG _A ⁰ . The dependence of the free energies of adsorption of molecules of n-butanol in the absence of a metal-water chemisorption interaction on the magnitude of the electronic capacitance of the metal confirms the assumption that we had put forth previously that it is necessary to introduce corrections to criteria of hydrophilicity of metals based on a comparison of quantities ΔG _A ⁰ and potentials of cathodic peak of adsorption-desorption E _des, which are expressed in a rational scale. With the obtained correlation relationships taken into account, criteria of hydrophilicity are suggested, which take into account these correlation relationships.__________Translated from Elektrokhimiya, Vol. 41, No. 7, 2005, pp. 884–892.Original Russian Text Copyright © 2005 by Emets, Damaskin.     

Light scattering from spherulitic materials

The azimuthal angular dependence of the depolarized component of the light scattered from spherulitic materials is derived by an algebraic method that avoids the difficult angular integrations of the usual approach. The result appears as a sum of products of two factors, a molecular factor, that depends only on the structure and the scattering angle θ, and a geometrical factor that depends only on the azimuthal angle ? and the scattering angle θ. The molecular factors are evaluated for models of spherulitic structure that assume a constant tilt of the optical polarizability tensor. The radial distribution, in principle, is arbitrary, and an evaluation for the layered spherulite is made. If the tilt angle is ω when the azimuthal patterns depend only on a linear combination of P₂(cos ω) and P₄(cos ω), where P_n(x) is the Legendre polynomial of order n. In our theory the V_H scattering pattern is a four-leaf clover whose axes are restricted by the theory to be at either 0 or 45° to the polarization directions.     

Construction and Analysis of Lifson?Roig Models for the Helical Conformations of α‐Peptides

New forms of Lifson? Roig algorithms are introduced for modeling stabilities of helices formed by polypeptides derived from α‐amino acids. The principles of constructing and generalizing these algorithms are developed, and their application to modeling of circular dichroism ellipticities and protection factors derived from H/D exchange of α‐peptide backbone amide residues are critically reviewed. With the aim of comparing the properties of structured conformations formed by α‐ and β‐peptides, the intrinsic limitations of Lifson? Roig algorithms and their underlying assumptions are analyzed. Lifson? Roig state sums that provide easy structural analysis are generated by new algorithms based on products of 8×8 and 16×16 matrices, and a simple protocol is introduced for generating new state sums that are tailored for specific purposes. The N‐ and C‐capping of highly helical α‐peptides by means of tailored helix‐stabilizing templates is shown to result in helical conformational manifolds that approach those of helical β‐peptides in conformational homogeneity.     

The Implications of (2S,4S)‐Hydroxyproline 4‐O‐Glycosylation for Prolyl Amide Isomerization

The conformations of peptides and proteins are often influenced by glycans O‐linked to serine (Ser) or threonine (Thr). (2S,4R)‐4‐Hydroxyproline (Hyp), together with L ‐proline (Pro), are interesting targets for O‐glycosylation because they have a unique influence on peptide and protein conformation. In previous work we found that glycosylation of Hyp does not affect the N‐terminal amide trans/cis ratios (K_trans/cis) or the rates of amide isomerization in model amides. The stereoisomer of Hyp—(2S,4S)‐4‐hydroxyproline (hyp)—is rarely found in nature, and has a different influence both on the conformation of the pyrrolidine ring and on K_trans/cis. Glycans attached to hyp would be expected to be projected from the opposite face of the prolyl side chain relative to Hyp; the impact this would have on K_trans/cis was unknown. Measurements of ³J coupling constants indicate that the glycan has little impact on the C^γ‐endo conformation produced by hyp. As a result, it was found that the D ‐galactose residue extending from a C^γ‐endo pucker affects both K_trans/cis and the rate of isomerization, which is not found to occur when it is projected from a C^γ‐exo pucker; this reflects the different environments delineated by the proline side chain. The enthalpic contributions to the stabilization of the trans amide isomer may be due to disruption of intramolecular interactions present in hyp; the change in enthalpy is balanced by a decrease in entropy incurred upon glycosylation. Because the different stereoisomers—Hyp and hyp—project the O‐linked carbohydrates in opposite spatial orientations, these glycosylated amino acids may be useful for understanding of how the projection of a glycan from the peptide or protein backbone exerts its influence.     

Isobaric thermal behavior of glasses during uniform cooling and heating: Dependence of the characteristic temperatures on the relative contributions of temperature and structure to the rate of recovery. II. A one-parameter model approach

Isobaric variations of the characteristic temperatures T_g and T_max, obtained on uniform cooling and heating of glasses, are investigated in terms of their dependence on the relevant experimental variables, using a single retardation time model. The corresponding partial derivatives of T_g and T_max are derived as functions of the partition parameter x (ranging between zero and unity), which determines the relative contributions of temperature and structure to the retardation time. It is shown that the variation of T_g with the cooling rate is independent of x. In contrast, T_max critically depends on x, and its value as well as those of its three partial derivatives are linear functions of x^?1. The variations of T_max are analyzed in terms of a set of reduced variables, leading to simple reduction rules between any two of the experimental variables when the third is kept invariant. The reduction rules are further substantiated by investigating the behavior of glasses in two-step thermal cycles, which result in a unique set of inter-relationships between any pair of the partial derivatives of T_max, whatever the value of x. The results are discussed in terms of their relevance to the behavior of real glasses.     

Energy Transfer of Peptide Ions Colliding with a Self‐Assembled Monolayer Surface. The Influence of Peptide Ion Size

Atomistic dynamics of protonated polyglycine, gly_n‐H⁺ (n = 3, 5, and 7), colliding with a fluorinated octanethiol self‐assembled monolayer (F‐SAM) surface has been studied by trajectory calculations. The effects of peptide size on the collision processes and energy transfer efficiencies are emphasized and discussed in detail. The simulations show that the fraction of trapping, which is related to the soft‐landing process, dramatically drops with the increase in collision energy, but gently increases with the peptide size. The average energy transfer to the peptide ion's internal degrees of freedom, ΔE_int, is compared with previous experiments. The limiting probability P_o of energy transfer to the surface is given by fitting a function of P_oexp(–b/E_i). Our results suggest that the efficiencies of energy transfer are less dependent on the masses, even the categories of the peptide ions, and are determined by the character of the surfaces.     

Experimental criterion for the crystallization regime in polymer crystals grown from dilute solution: Possible limitation due to fractionation

By integration of equations previously derived by Frank, the growth rate of polymer crystals is shown to be dependent on their size, provided that the persistence length L_p or the kinetic length L_k = (2g/i)^1/2 are significantly larger than the primary nucleus. A new method of decorating the fold surface (isochronous decoration) allows the measurement of the quasi-instantaneous growth rate of very small crystals obtained from dilute xylene solution of a sharp polyethylene fraction of moderate molecular weight (M_w = 17,000, M_w/M_n = 1.11). Although the theory predicts that the growth rate increases with the size of the crystals as long as its dimension is smaller than the persistence length and/or the kinetic length, such an increase is not observed experimentally with the sharp PE fraction presently used. Therefore it appears that both the kinetic length and the (hypothetical) persistence length are beyond the resolution limit of electron microscopy and that crystallization occurs in the polynucleation regime. An upper bound is obtained for the rate g at which a locally new layer spreads in two directions on the substrate. The rate is lower than is estimated by the commonly Accepted theories. These theories lead also to an abnormally high value for the lateral surface free energy. The possibility that the observed initial linearity of the growth-rate curve may results from a balance of opposite effects (an increase with the size of the crystals on the one hand, a decrease with decreasing concentration and possible fractionation on the other) is thoroughly examined and ruled out. In fact, it must be stressed that at the early beginning of crystallization, negligible parts of the sample are crystallized and it is only at the end of crystallization that these effects appear. The fall in the growth rate as crystallization ends is due neither to progressive exhaustion of the solution alone nor to a depletion of the concentration by diffusion for this sharp fraction of low-molecular-weight PE. The major effect comes from fractionation. This segregation of the various molecular weights is predicted on the basis of a simple model and is verified by gel permeation chromatography (GPC). The fact that in such a sharp fraction significant fractionation occurs precludes any accurate determination of the supercooling and of the concentration of the polymer actually crystallizing. Subtle differences in the molecular weight distributions may result in significant variation of the growth rate. In conclusion, as the data used in the first part of this work were obtained with only a small percentage of the dissolved polymer sample crystallized, the observed constancy of the growth rate does not result from mutual compensation of opposite effects, and our conclusions about crystallization regime, order of magnitude of the kinetic and persistence lengths, and value of the rate of lateral spreading of a secondary nucleus are well founded.     

Konformative Beweglichkeit Flexibler Ringsysteme—X. Untersuchungen mit Hilfe der Protonenresonanz-Spektroskopie. Substituentenabhängigkeit der Ringinversion bei 1.3-Dioxanen, 1.3-Dithianen und 1.3-Oxathianen

Activation energies E_α and free enthalpies of activation ΔG? were determined by NMR for the ring inversions of nineteen 1.3-dioxanes, 1.3-dithianes and 1.3-oxathianes and their methyl-substituted derivatives. The rate constant k of the chair to chair-inversion of these rings depend on the number and positions of the substituents. In substituted 1.3-dioxanes k is lower than in 1.3-dioxane itself if two geminal CH₃-groups are situated in position 5. However, k becomes higher when the geminal CH₃-groups are in positions 2 or 4. The rate constants are particularly high for 4.4.6.6-tetramethyl-1.3-dioxane. A similar dependence of k on substituents has been observed in the oxathianes, while with 1.3-dithianes only a small influence is noticed. The effect of the methyl substituents in positions 2 or 4 in 1.3-dioxanes can be explained by assuming that the chair conformation is deformed by 1.3-interactions. In 1.3-dithianes such 1.3-interactions are expected to be smaller because of the larger C? S bond length. For 1.3-oxathianes the dependence of k on the substituents is more difficult to understand since these molecules are not symmetrical.     

Studies in nuclear magnetic resonance—XII: Complete analysis of the proton spectra of tert-butylcyohexane-3,3,4,4,5,5-d6 and -3,3,5,5-d4

Accurate parameters for the two title compounds have been obtained by the aid of a spectral subtraction technique in conjunction with analysis by LAOCN3. It is observed that J_{1eq, 6eq} and J_{1ax, 2ax} are abnormally large and small, respectively, and the significance of these and other coupling constants are discussed in terms of the probable geometry of tert-butylcyclohexane. The tert-butyl group affects the chemical shifts of the 4-protons, indicating that tert-butylcyclohexyl derivatives are poor models for fixed conformers of monosubstituted cyclohexanes. The deuterium isotope effects on proton chemical shifts appear to be influenced by the same factors as proton-proton coupling constants.     

Kinetic model for tensile deformation of polymers. Part IV: Effect of polydispersity

A previously introduced molecular model for tensile deformation of solid, flexible chain polymers is used to study the effect of the molecular weight distribution on the strain at break, or maximum draw ratio. The parameters in the model are chosen to represent melt-crystallized linear polyethylene. We focus, in particular, on the relation between the maximum draw ratio and two distribution characteristics: theM _t molecular weight average, first introduced by Graessley, and the polydispersity ratioM _z /M _w . For a log-normal molecular weight distribution, an increase in polydispersity at constantM _t leads to a broadening of the optimum rate (or temperature) window for achieving maximum elongation, but is accompanied, however, by a substantial decrease in the maximum attainable draw ratio. Studies on the deformation of systems having a bimodal molecular weight distribution indicate that blends made ofequal weight fractions of long and short chains exhibit an unexpectedly high elongation at break. These results are explained in terms of the model and possible technological implications are discussed.Dedicated to Professor Hans-Henning Kausch on the occasion of his 60th birthday.     

Resonance revisited: A consideration of the calculation of cyclic conjugation energies

A homomolecular differential bond separation reaction may be defined as the difference between the conventional bond separation reactions involving the unsaturated system and its saturated counterpart. Such a reaction is homomolecular in that the basic molecular structures involved are the same on both sides of the reaction. The type of homodesmotic reaction that also conserves structure in this way may be termed a homomolecular homodesmotic reaction. Both types of homomolecular reactions are readily related to hydrogenation reactions and, more importantly, to each other. Δ B(n), the energy of the homomolecular differential bond separation reaction involving a system with n double bonds, and H(n), the corresponding homomolecular homodesmotic reaction, are related by: where h(1) and h(e) are the hydrogenation energies of the system's monoene and of ethylene, respectively. Both types of reactions yield measures of cyclic conjugation energies that for certain classifications of molecules are simply related to each other. Consideration of extra conjugation in the monoenes allows a ready interpretation of those cases in which a simple classification is not obtained. Ab initio calculations illustrating these effects have been carried out on a variety of molecules including many five- and six-membered ring systems using second order Møller-Plesset and density functional approaches. © 1997 by John Wiley & Sons, Inc.     

Raman Spectroscopy and Ab-Initio Model Calculations on Ionic Liquids

A review of the recent developments in the study and understanding of room temperature ionic liquids are given. An intimate picture of how and why these liquids are not crystals at ambient conditions is attempted, based on evidence from crystallographical results combined with vibrational spectroscopy and ab-initio molecular orbital calculations. A discussion is given, based mainly on some recent FT-Raman spectroscopic results on the model ionic liquid system of 1-butyl-3-methylimidazolium ([C₄ mim][X]) salts. The rotational isomerism of the [C₄ mim]⁺ cation is described: the presence of anti and gauche conformers that has been elucidated in remarkable papers by Hamaguchi et al. Such presence of a conformational equilibrium seems to be a general feature of the room temperature liquids. Then the “localized structure features” that apparently exist in ionic liquids are described. It is hoped that the structural resolving power of Raman spectroscopy will be appreciated by the reader. It is of remarkable use on crystals of known different conformations and on the corresponding liquids, especially in combination with modern quantum mechanics calculations. It is hoped that these interdisciplinary methods will be applied to many more systems in the future. A few examples will be discussed.     

Atomic and bond properties in functionalized esters and amides

The properties of various atomic groups of molecules containing a carbonyl unit (XCOY) consisting of an ester (Y=OR) or amide function (Y=NHR) in different molecular environments (X=H, Me, Et, OH, OMe, NH₂, NHMe, F, Cl), as well as their influence on the properties of the alkyl chain (R=C₈H₁₇) in the molecule, were analyzed by use of the theory of atoms in molecules (AIM). To this end, the main atomic and bond properties for each atom in 18 carbonyl compounds of the aforementioned types were determined on the basis of 6-31++G**//6-31G* wave functions. The properties of the C and O atoms in the carbonyl group, and those of their bonds, are directly related to the nature and electronegativity of the X substituent and to the character of the Y group. The nature of the C Y bond and the properties of the Y group are also dependent on the proximity of the X group. Based on the precision with which integrated properties were determined, assessed by L(Ω), the properties of the methylene groups of the R chain located in α and β with respect to Y are essentially dependent on the nature of Y and, to a lesser extent, on that of X. The methylene group in γ with respect to Y exhibits a dependence on the nature of the latter that vanishes in more distinct groups; therefore, the methylene in ε can be assimilated to one in an alkane. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 1444–1454, 1999     

ESR-Spektren von CuN4-Chromophoren II: Komplexe mit Ammoniak, Äthylendiamin,Biguanid, N-Trifluoracetimidoyl-trifluoracetamidin,N-Trichloracetimidoyl-trichloracetamidin,Tetraaza-undecan,Hexamethyl-tetraaza-cyclotetradecan und -cyclotetra decadien in Einkristallen

The ESR spectra of eight copper complexes with two groups of nitrogen ligands have been measured in the solid state. The first group includes the σ-bonding ligands ammonia, ethylenediamine, 1,4,8,11-tetraaza-undecane, and the macrocyclic hexamethyl-1,4,8,11-tetraazacyclotetradecane of CURTIS . Ligands of the second group are biguanide, the CF₃ and CCl₃ derivatives of acetimidoyl-acetamidine, and hexamethyl-1, 4,8,11-tetraazacyclotetradecadiene. Single crystals of the parent Pt^II, Ni^II, or Zn^II compounds were used as host lattices and magnetic diluents. The spectra of the chromophores CuN₄, showing resolved hyperfine structure due to copper and nitrogen nuclear spins, are fitting a Spin-Hamiltonian on the basis of virtual site symmetry D_4h. The parameters g∥, g?, A∥, and A? were used to derive delocalization coefficients in terms of the LCAO-MO model introduced by MAKI and MC GARVEY . The comparative study clearly reveals that no reliable information on π-bonding is provided by application of this model. The results on σ-bonding ligands are particularly valuable in showing that the simple LCAO-MO model cannot account for the attenuation of spin orbit coupling due to σ-bonding in a physically meaningful way. Our results are qualitatively in agreement with AMMETER'S explanation of this phenomenon in terms of a virtual expansion of the d-shell in antibonding orbitals.     

Distribution function for the radius of gyration for theta chains attached at one end to an impenetrable surface

Chains that are unperturbed by the intramolecular excluded volume effect are examined in the free state and under conditions where one of the ends is attached to an impenetrable surface. The density of the attachment of the chains to the surface is so low that interchain interactions can be ignored. The shapes of the distribution functions for the squared end-to-end distance, r², and squared radius of gyrations, s², are evaluated in both situations. As is well-known from previous work, attachment of the chains to the impenetrable surface produces an increase in 〈r²〉 and (to a lesser extent) 〈s²〉. It also narrows the distribution function for r². There is, however, no detectable effect on the shape of the distribution function for s². The narrowing of the distribution function for r², coupled with the absence of any effect on the shape of the distribution function for s², is rationalized with a very simple model.     

Polymer swelling. XXV. Structure‐affinity correlation studies that involve poly(styrene‐co‐divinylbenzene) exposed to acetylenic liquids

The adsorption parameters (α) established for the monosubstituted acetylenic liquids in this investigation are consistent with expectation based on analogies with the log α_f = log α_i ‐ D_s(N_f − N_i) relationships reported earlier for the many homologous series of liquids ZR, in which Z is a functional group having strong affinity for the pendent phenyl group of polystyrene and R is an alkyl substituent that is varied systematically. The order of relative Z‐affinities, based on α for the respective ZCH₂CH₃ molecules, confirm that the nature of Z is the major factor that affects α and that electronic and steric contributions from R are modifying effects, which are reflected in D_s. Comparisons of the results observed for HCC(CH₂)_nZ′ liquids with those for HCC(CH₂)_nH and with analogous pairs of Z(CH₂)_nZ′ series confirm that Z′ at the other end of the polymethylene chain can have a moderate positive effect or a marked negative effect on α, depending on whether the mode of adsorption to pendent phenyl groups is mono‐ or bidentate. This study also confirms that a sharp reversal in the roles played by the molecules participating in the adsorption process occurs when all of the hydrogen atoms covalently bonded to the center of unsaturation are replaced by alkyl substituents. © 1999 John Wiley & Sons, Inc. J Polym Sci B: Polym Phys 37: 2611–2633, 1999     

The influence of the solvent on the conformational energy differences due to the anomeric effect

The solvation free energy ΔG^sol of molecules exhibiting the anomeric effect is computed in an approach that considers a continuous distribution for the solvent. A partition of ΔG^sol into separately evaluated contributions confirms that changes in the energy of the systems due to changes in conformation of the solute are ruled by the electrostatic contribution. A comparison with the “exact” values indicates that the approximate expression for the electrostatic contribution to ΔG^sol are not accurate enough to permit a proper modeling of the solvent influence on the anomeric effect. The systems are composed of methanediol, methoxymethanol, dimethoxymethane, and 2-methoxytetrahydropyran in carbon tetrachloride, chloroform, acetone, and water. The calculations have been performed at the SCF level with the STO -3G and 4–31G basis sets.