Branched Chain Molecules Research Articles

Interstellar branched chain molecules: A theoretical-rotational study

Interstellar branched chain molecules: A theoretical-rotational study

Astrochemical model to study the abundances of branched carbon-chain molecules in a hot molecular core with realistic binding energies

ABSTRACT Straight-chain (normal-propyl cyanide, $\rm {n-C_3H_7CN}$) and branched-chain (iso-propyl cyanide, $\rm {i-C_3H_7CN}$) alkyl cyanides are recently identified in the massive star-forming regions (Sgr B2(N) and Orion). These branched-chain molecules indicate that the key amino acids (side-chain structures) may also be present in a similar region. The process by which this branching could propagate towards the higher order (butyl cyanide, $\rm {C_4H_9CN}$) is an active field of research. Since the grain catalysis process could have formed a major portion of these species, considering a realistic set of binding energies are indeed essential. We employ quantum chemical calculations to estimate the binding energy of these species considering water as a substrate because water is the principal constituent of this interstellar ice. We find significantly lower binding energy values for these species than were previously used. It is noticed that the use of realistic binding energy values can significantly change the abundance of these species. The branching is more favourable for the higher order alkyl cyanides with the new binding energies. With the inclusion of our new binding energy values and one essential destruction reaction ($\rm {i-C_3H_7CN+H \rightarrow CH_3C(CH_3)CN + H_2}$, having an activation barrier of 947 K), abundances of $\rm {t-C_4H_9CN}$ dramatically increased.

Surface pre-ignition measurements of fuel components and their mixtures

A closed loop temperature controlled glow-plug has been used to control the incidence of surface pre-ignition of n-pentane, iso-pentane, n-heptane, iso-octane, ethanol, cyclohexane, ethyl-benzene, toluene and xylene, and four representative mixtures of these components. Statistical data on the incidence of pre-ignition compared with spark ignition has been derived from the in-cylinder maximum pressure, and the glow-plug temperature has been characterised on a cycle-by-cycle basis.The alkanes and alcohols were found to be rather susceptible to surface pre-ignition, with the straight chained molecules having a higher pre-ignition tendency than branched chain molecules. The pre-ignition tendency of ring-structured components depends on the length of the attached chain, with shorter side-chain molecules (xylene, toluene) being less susceptible to pre-ignition than longer side-chain molecules like ethyl-benzene; cyclohexane was more susceptible to pre-ignition than any of the aromatic fuels. A higher glow-plug temperature was found to be needed for pre-igniting stoichiometric or rich mixtures, and this was attributed to the weaker mixture having a higher compression index and a lower specific heat capacity.

C5H9N isomers: pointers to possible branched chain interstellar molecules

The astronomical observation of isopropyl cyanide further stresses the link between the chemical composition of the ISM and molecular composition of the meteorites in which there is a dominance of branched chain amino acids as compared to the straight. However, observations of more branched chain molecules in ISM will firmly establish this link. In the light of this, we have considered C5H9N isomeric group in which the next higher member of the alkyl cyanide and other branched chain isomers belong. High-level quantum chemical calculations have been employed in estimating accurate energies of these isomers. From the results, the only isomer of the group that has been astronomically searched, n-butyl cyanide is not the most stable isomer and therefore, which might explain why its search could only yield upper limits of its column density without a successful detection. Rather, the two most stable isomers of the group are the branched chain isomers, tert-butylnitrile and isobutyl cyanide. Based on the rotational constants of these isomers, it is found that the expected intensity of tert-butylnitrile is the maximum among this isomeric group. Thus, this is proposed as the most probable candidate for astronomical observation. A simple LTE (Local thermodynamic equilibrium) modelling has also been carried out to check the possibility of detecting tert-butyl cyanide in the millimetre-wave region.

Three new branched chain equations of state based on Wertheim's perturbation theory

In this work, we present three new branched chain equations of state (EOS) based on Wertheim's perturbation theory. The first represents a slightly approximate general branched chain solution of Wertheim's second order perturbation theory (TPT2) for athermal hard chains, and the second represents the extension of first order perturbation theory with a dimer reference fluid (TPT1-D) to branched athermal hard chain molecules. Each athermal branched chain EOS was shown to give improved results over their linear counterparts when compared to simulation data for branched chain molecules with the branched TPT1-D EOS being the most accurate. Further, it is shown that the branched TPT1-D EOS can be extended to a Lennard-Jones dimer reference system to obtain an equation of state for branched Lennard-Jones chains. The theory is shown to accurately predict the change in phase diagram and vapor pressure which results from branching as compared to experimental data for n-octane and corresponding branched isomers.

From mono- to polytopic interactions via hydrogen bonds — Capacitive sensor studies

Supra molecular materials can be generated via hydrogen bonding between monomers. This leads either to “monotopic” molecules as well as self-assemblies of a restricted number of complementary components as “di-” or “polytopic” molecules with more than one functional unit. The latter structures grow spontaneously by self organization and in principle consist of repeatedly branched chain molecules analogous to dendrimers. When disturbing these aggregates by analyte molecules (e.g. volatile organic compounds), the supra molecular structures break down leading to a pronounced change in dielectric behavior that is detectable with inter digital capacitors. “Monotopic”-materials show linear behavior with increasing analyte concentration whereas “polytopic” molecules lead to properties resembling a threshold sensor.

Distribution and development of the highly specialized lipids in the sound reception systems of dolphins

Fat bodies in the heads of toothed whales, which serve to transmit and receive sound, represent extraordinary examples of physiological specialization in adipose tissues among mammals, yet we know surprisingly little about their biochemical composition. We describe the spatial distributions and development of unusual endogenous lipids (branched-chain ["iso"] molecules and wax esters) in the mandibular fat bodies of bottlenose dolphins (Tursiops truncatus) using an ontogenetic series (fetus to adult; n = 10). Although concentrations of iso-acids, iso-alcohols and waxes were lower in younger dolphins than in adults, the same relative spatial arrangement was present in all age classes, implying a set "pattern" of acoustic lipid distribution that is established very early in life. In all age classes, a small region of blubber overlying the lateral region contained unusually high concentrations of iso-acids, exhibiting a tenfold increase over "normal" adjacent blubber. Being chemically more similar to the acoustic fat bodies, this region may serve as an entry point for sound into the head. Developmental accumulations of some iso-acids and iso-alcohols occurred more rapidly than others, implying that not only are the spatial distributions of branched-chain molecules under extremely fine-scale control, but the regulatory mechanisms controlling acoustic lipid synthesis are also highly complex.

Molecular dynamics study on the phase diagrams of linear and branched chain molecules

The particle transfer molecular dynamics is used to study the phase equilibria of linear and branched chain molecules. The scaling of the critical temperature versus chain length is obtained and the critical densities are found to decrease with increasing chain length, which are in agreement with the results of experiment and theory. The phase diagrams of the linear and the branched chain molecules nearly overlap with each other. Moreover, the radial distribution functions of linear and branched chain molecules in gas phase are very similar, but in the liquid phase, they are different for different kinds of chains.

Nonequilibrium molecular dynamics of the rheological and structural properties of linear and branched molecules. Simple shear and poiseuille flows; instabilities and slip

Nonequilibrium molecular-dynamics simulations are performed for linear and branched chain molecules to study their rheological and structural properties under simple shear and Poiseuille flows. Molecules are described by a spring-monomer model with a given intermolecular potential. The equations of motion are solved for shear and Poiseuille flows with Lees and Edward's [A. W. Lees and S. F. Edwards, J. Phys. C 5, 1921 (1972)] periodic boundary conditions. A multiple time-scale algorithm extended to nonequilibrium situations is used as the integration method, and the simulations are performed at constant temperature using Nose-Hoover [S. Nose, J. Chem. Phys. 81, 511 (1984)] dynamics. In simple shear, molecules with flow-induced ellipsoidal shape, having significant segment concentrations along the gradient and neutral directions, exhibit substantial flow resistance. Linear molecules have larger zero-shear-rate viscosity than that of branched molecules, however, this behavior reverses as the shear rate is increased. The relaxation time of the molecules is associated with segment concentrations directed along the gradient and neutral directions, and hence it depends on structure and molecular weight. The results of this study are in qualitative agreement with other simulation studies and with experimental data. The pressure (Poiseuille) flow is induced by an external force F(e) simulated by confining the molecules in the region between surfaces which have attractive forces. Conditions at the boundary strongly influence the type of the slip flow predicted. A parabolic velocity profile with apparent slip on the wall is predicted under weakly attractive wall conditions, independent of molecular structure. In the case of strongly attractive walls, a layer of adhered molecules to the wall produces an abrupt distortion of the velocity profile which leads to slip between fluid layers with magnitude that depends on the molecular structure. Finally, the molecular deformation under flow depends on the attractive force of the wall, in such a way that molecules are highly deformed in the case of strong attracting walls.

Structure and Volumetric Properties of Linear and Triarm Star Polyethylenes from Atomistic Monte Carlo Simulation Using New Internal Rearrangement Moves

A number of elementary Monte Carlo moves are introduced for branched chain molecules. More specifically, branch point flip brings about a displacement in space of a branch point and its neighboring atoms in the molecule without change in the connectivity. Furthermore, branch point slithering allows for branch point displacement along the backbone; in this case, the size of the branches involved is changed. Finally, the flip move is extended to a dimer and is further generalized to an n-mer segment. The new Monte Carlo moves are used together with previously developed moves for the study of structure and volumetric properties of melts composed of symmetric triarm star polyethylenes of different arm lengths in a united atom representation. It is shown that the new moves result in very efficient relaxation of the macromolecules and, in particular, of their branch points. Comparisons are made against simulation results and experimental data for linear and branched polyethylene. The agreement between experimental data and Monte Carlo simulation for the melt density is good in all cases.

Thermodynamic properties and phase equilibria of branched chain fluids using first- and second-order Wertheim’s thermodynamic perturbation theory

We present an extension of the statistical associating fluid theory (SAFT) for branched chain molecules using Wertheim’s first- and second-order thermodynamic perturbation theory with a hard-sphere reference fluid (SAFT-B). Molecules are formed by hard spherical sites which are tangentially bonded. Linear chains are described as freely jointed monomeric units, whereas branched molecules are modeled as chains with a different number of articulation points, each of them formed by three arms. In order to calculate the vapor–liquid equilibria of the system, we have considered attractive interactions between the segments forming the chain at the mean-field level of van der Waals. The Helmholtz free energy due to the formation of the chain is explicitly separated into two contributions, one accounting for the formation of the articulation tetramer, and a second one due to the formation of the chain arms. The first term is described by the second-order perturbation theory of Phan et al. [J. Chem. Phys. 99, 5326 (1993)], which has been proven to predict the thermodynamic properties of linear chain fluids in a similar manner to Wertheim’s approach. The formation of the chain arms is calculated at Wertheim’s first-order perturbation level. The theory is used to study the effect of the chain architecture on the thermodynamic properties and phase equilibria of chain molecules. The equation predicts the general trends of the compressibility factor and vapor–liquid coexistence curve of the system with the branching degree, in qualitative agreement with molecular simulation results for similar models. Finally, SAFT-B is applied to predict the critical properties of selected light alkanes in order to assess the accuracy of the theory. Experimental trends of the critical temperature of branched alkanes are qualitatively captured by this simple theory.

Quasi-Hamiltonian equations of motion for internal coordinate molecular dynamics of polymers

Conventional molecular dynamics simulations macromolecules require long computational times because the most interesting motions are very slow compared with the fast oscillations of bond lengths and bond angles that limit the integration time step. Simulation of dynamics in the space of internal coordinates, that is with bond lengths, bond angles and torsions as independent variables, gives a theoretical possibility to eliminate all uninteresting fast degrees of freedom from the system. This paper presents a new method for internal coordinate molecular dynamics simulations of macromolecules. Equations of motion are derived which are applicable to branched chain molecules with any number of internal degrees of freedom. Equations use the canonical variables and they are much simpler than existing analogs. In the numerical tests the internal coordinate dynamics are compared with the traditional Cartesian coordinate molecular dynamics in simulations a 56 residue globular protein. It is shown that the traditional and internal coordinate dynamics require the same time step size for the same accuracy and that in the standard geometry approximation of amino acids, that is with fixed bond lengths, bond angles and rigid aromatic groups, the characteristic step size is 4 fsec, that is two times higher than with fixed bond lengths only. The step size can be increased up to 11 fsec when rotation of hydrogen atoms is suppressed.

Friction at the Atomic Scale

Considering the current race to manufacture machine components with astoundingly small dimensions, what is today considered fundamental research on the atomic scale may give way tomorrow to direct applications. For instance, the authors now know why substances made of branched-chain molecules make better lubricant than straight-chain molecules, even though the branched-chain one are, in bulk form, more viscous. (They remain as a liquid under greater forces than do the straight-chained molecules and thus are better able to keep two solid surfaces from touching.) Nanotribologists working with known contact geometries may one day help chemists understand friction-induced reaction taking place on surfaces or aid materials scientists in designing substances that resist wear. As the need to conserve both energy and raw materials becomes more urgent, physicists` rush to understand basic frictional processes can be expected only to accelerate.

Group-contribution theory for adsorption of gas mixtures on solid surfaces

Equilibrium properties are derived for multicomponent mixtures of complex molecules adsorbed on a nonuniform surface. A model of localized adsorption of simple and branched chain molecules on a patchwise heterogeneous adsorbent is analyzed in terms of lattice statistics. The principal results are obtained by applying Guggenheim's lattice theory of solutions to gas adsorption. Interactions among adsorbed molecules on each patch are treated in the Bragg-Williams approximation. Explicitly accounting for the physical and chemical structure of the adsorbate molecules is the primary improvement over conventional lattice-gas theories. The analysis accounts for adsorbent heterogeneity, molecular size differences of the mixture components, and polyfunctionality of the adsorbate molecules (i.e. different types of functional groups within a molecule), all of which can contribute to nonideal behavior of adsorbed solutions. The theory may provide a basis for developing a group-contribution method of estimating thermodynamic properties for wide classes of adsorbed mixtures from limited experimental data, similar to familiar methods for liquid solutions.

Laboratory studies of the influence of thin organic films on the neutralization reaction of H 2SO 4 aerosol with ammonia

The neutralization reaction of micro-encapsulated sulfuric acid aerosol with gaseous ammonia has been investigated. Experimental parameters were: influence of different coating substances, coating thickness, relative humidity and reaction time. The reaction of H 2SO 4 aerosol with NH 3 was measured as a function of time by chemical characterization of the particulate and gaseous phase before and after mixing of the reactants in a flow reactor. A remarkable decrease in the reaction rate was observed, depending on molecular structure of the organic coating substance and the thickness of coating. Straight chain molecules like n-hexadecane and n-hexadecanol strongly retard the reaction. Branched chain molecules as coating showed no significant effect, probably because of their inability to form tight films. Naturally occurring organic coating substances affect the neutralization, too. The mass transport resistance of the films investigated are interpreted in terms of the accommodation and reaction coefficient.

Statistical thermodynamics of association colloids. I. Lipid bilayer membranes

Step-weighted random walks (modified Markov chain statistics) combined with a self-consistent-field approximation form the basic concepts of a Flory–Huggins-type of theory to describe the lipid bilayer.1 The purpose of the present paper is to extend this model by incorporating the rotational isomeric state scheme, both for linear and branched chain molecules. Only three measurable interaction energy parameters of a Flory–Huggins-type are required, namely for the head group tail, the head group water, and the tail water contacts. In addition, the theory needs one energy parameter for the internal trans/gauche transition energy of the chain. Results of this self-consistent-field (SCF) theory are given for membranes formed by lecithin-like molecules. With respect to earlier work, more detailed insight is obtained in the behavior of the lipid bilayer above the gel to liquid phase transition temperature. Equilibrium conditions are formulated. Segment density profiles and solvent distributions are calculated. It is shown that the two apolar tails of the lecithin do not behave identically. The tail next to the head group is lifted slightly more out of the membrane than the other tail. The well-known balance of forces, responsible for membrane formation is analyzed. We found that the repulsive tail head interaction, often ignored in theories, is essential for the stability of association colloids.

INFLUENCE OF IN SITU TWO-PHASE POLYMERS ON AGGREGATE STABILIZATION IN VARIOUS TEXTURED NORTH DAKOTA SOILS

Two-phase in situ condensation polymers formed from amine and aldehyde monomers were tested on three differing soil textures for aggregating effectiveness and were compared to polyvinyl alcohol treated soils. The amine and aldehyde monomers differed in functionality (number of amines or carbonyl groups participating in the cross-linking polymerization reaction), molecular structure (branched versus straight chains and the number of polar structural groups) and molecular weight. Straight-chained molecules were more effective in aggregating soil than branched-chain molecules if a certain critical molecular weight was exceeded. The branched-chained and lower molecular weight molecules were less plastic. The number of polar monomer structural groups, notably ether, alcohol and amide oxygen, capable of bonding to clay particles determined aggregation effectiveness. PVA was effective at 0.1% concentration; two-phase polymers with long straight chains were effective at 5.0% by weight. Key words: Microaggregates, macroaggregates, amine, aldehyde, polyvinyl alcohol

Computer experiments on branched-chain molecules

Computer experiments on branched-chain molecules

ChemInform Abstract: MOLECULAR STRUCTURE OF EXPANDED LIQUID SELENIUM UP TO 1400°C

AbstractDer statische Strukturfaktor S(Q) und die Paarkorrelationsfunktion g(R) des flüssigen Se werden neutronendiffraktometrisch im Temp.‐Bereich 600‐1400°C bei Drücken bis zu 300 bar bestimmt.

Molecular Structure of Expanded Liquid Selenium up to 1400 °C

AbstractThe static structure factor, S (Q), and the pair correlation function, g (R), of liquid selenium have been investigated by neutron diffraction in the temperature range from 600°C to 1400°C at pressures up to 300 bar. Within this temperature range the intramolecular bond length increases slightly from 2.37 Å to 2.38 Å and the coordination number of nearest neighbors decreases from 2.0 to 1.8. From these findings and especially from the detailed analysis of the shape of the first peak of g (R) we conclude that the structural data give no indication for the existence of a significant concentration (≥ 1019 cm−3) of threefold coordinated sites (branched chain molecules) in liquid selenium at elevated temperatures. For the intermolecular distance distribution in the range 2.8 ≤ R ≤ 4.4 Å a continuous decrease up to a minimum around 1200°C is observed. This indicates a denser packing of small linear chain molecules with increasing temperature.