Pentane Effect Research Articles

A stochastic method for asphaltene structure formulation from experimental data: avoidance of implausible structures.

This work presents a stochastic procedure designed to formulate a discrete set of molecular structures that, as a whole, adjust properly to experimental asphaltene data. This algorithm incorporates the pentane effect concept and Clar's sextet rule to the formulation process. The set of viable structures was constructed based on probability distribution functions obtained from experimental information and an isomer database containing all plausible configurations for a given number of rings, avoiding high-energy structures. This procedure was applied to a collection of experimental data from the literature. Ten sets, consisting of 5000 structures each, were obtained. Each set was then optimized. For the most accurate representation, four molecules were sufficient to properly reproduce the experimental input. The asphaltene system obtained is consistent with the reported molecular weight, number of aromatic rings and heteroatom content. Molecular dynamic simulations showed that the asphaltene representation adequately reproduced asphaltene aggregation behavior in toluene and n-heptane. In toluene, a single three-molecule aggregate was observed, and the majority of asphaltene molecules remained in a monomeric state. In n-heptane, aggregates containing up to four molecules were observed; both porous and compact aggregates were found. The asphaltene molecular representation obtained, which allows researchers to avoid inappropriate torsions in the molecule, is able to reproduce interplanar distances between aromatic cores of 4 Å or less for the aggregation state, as supported by experimental results.

A model-free temperature-dependent conformational study of n-pentane in nematic liquid crystals.

The proton NMR spectra of n-pentane orientationally ordered in two nematic liquid-crystal solvents are studied over a wide temperature range and analysed using covariance matrix adaptation evolutionary strategy. Since alkanes possess small electrostatic moments, their anisotropic intermolecular interactions are dominated by short-range size-and-shape effects. As we assumed for n-butane, the anisotropic energy parameters of each n-pentane conformer are taken to be proportional to those of ethane and propane, independent of temperature. The observed temperature dependence of the n-pentane dipolar couplings allows a model-free separation between conformer degrees of order and conformer probabilities, which cannot be achieved at a single temperature. In this way for n-pentane 13 anisotropic energy parameters (two for trans trans, tt, five for trans gauche, tg, and three for each of gauche+ gauche+, pp, and gauche+ gauche-, pm), the isotropic trans-gauche energy difference Etg and its temperature coefficient Etg(') are obtained. The value obtained for the extra energy associated with the proximity of the two methyl groups in the gauche+ gauche- conformers (the pentane effect) is sensitive to minute details of other assumptions and is thus fixed in the calculations. Conformer populations are affected by the environment. In particular, anisotropic interactions increase the trans probability in the ordered phase.

Adjacent Gauche Stabilization in Linear Alkanes: Implications for Polymer Models and Conformational Analysis

High-level ab initio quantum mechanical calculations are used to study various gauche conformational energies of n-pentane to n-decane. The destabilizing "pentane effect" (adjacent gauche states of opposite sign) for alkanes is confirmed, but the energies were found to depend slightly on chain length. In contrast, introducing an adjacent gauche of the same sign requires only 0.22-0.37 kcal/mol, approximately half of the single gauche state energy. This adjacent gauche stabilization should be taken into account when formulating or analyzing rotational isomeric models, carrying out conformational analysis, and developing force fields for alkanes, lipids, and related polymers.

An ab Initio Study on the Torsional Surface of Alkanes and Its Effect on Molecular Simulations of Alkanes and a DPPC Bilayer

Energies of 119 conformations of normal alkanes from butane to heptane were calculated at approximately the CCSD(T)/cc-pVQZ level. Energies of gauche (g) conformers relative to trans (t) decrease as chain length increases. In what is termed the "positive pentane effect", adjacent gauche conformers of the same sign are stabilized compared to nonadjacent conformers; e.g., for hexane the energies of tgt, tgg, and gtg are 0.600, 0.930, and 1.18 kcal/mol, respectively. Torsional terms in the CHARMM27 (C27) force field were fit to the calculated QM energies to yield a revised potential, C27r. Molecular dynamics simulations of normal alkanes (heptane, decane, tridecane, and pentadecane) with C27r yield higher populations of gauche states, increased transition rates, and improved agreement with experiment as compared to C27. In addition, C27r simulations of a hydrated DPPC lipid bilayer yield improved agreement with the experimental NMR deuterium order parameters for the aliphatic chain ends.

Tacticity induced molecular microstructure dependence of the configurational properties of metallocene-synthesized polypropylenes

Stereoblock polypropylene (PP) produced using metallocene catalysts consists of alternating stereoregular and stereoirregular sequences. Through a control of the isotactic and atactic sequence lengths, the Bernoullian replication probability and the rate of isomerization of the metallocene catalysts, polymeric chains of various molecular microstructures could be generated. The dependence of the microstructure on the various polymerization parameters is examined in terms of the isotactic pentad content, [mmmm]. The dependence of the physical properties of PP on the molecular microstructure induced by the chain tacticity was also investigated both experimentally and theoretically using Metropolis Monte Carlo techniques. It was shown that the intrinsic viscosity and the characteristic ratio of the polymer are greatly influenced by the stereoregularity of the polymeric chains, which was attributed to a possible steric hindrance between the neighbouring methyl side groups. Other configuration-dependent physical properties such as the radius of gyration, the persistence length and the molar stiffness function were also investigated for PP of different stereoregular microstructures. It was shown by examining the distribution of the dihedral angles that the pentane effect resulting from the steric hindrance of the side groups is the underlying principle for the microstructure dependence of the configurational properties of stereoblock PP.

A Raman spectroscopic study of the rotational isomerism of linear permethylated stannylsilanes Me3Sn(SiMe2)nSnMe3 with n=1, 2, 3, 4

Abstract The IR and Raman vibrational spectra of the methyl(trimethylstannyl)silanes Me 3 Sn(SiMe 2 ) n SnMe 3 with n =1 ( 1 ), 2 ( 2 ), 3 ( 3 ) and 4 ( 4 ) were recorded at various temperatures. Compound 2 consists of a mixture of two conformers, gauche (G) and anti (A), in the liquid state. By variable temperature Raman spectroscopy, the enthalpy difference Δ H = H gauche − H anti was determined from the relative intensities of the symmetric SiSn stretching bands as 0.8±0.3 kJ mol −1 . In the Raman spectrum of the crystalline solid, the lines of the G conformer disappear completely, facilitating the assignment of the fundamental vibrations for the A form. No indication of the presence of a third ( ortho ) conformer could be detected. HF-SCF ab initio calculations using electron core potentials for the heavy atoms predict the existence of three conformers on the potential surface. In the Raman spectra of 3 , the symmetric SiSn stretching vibration splits into three components, which can be assigned to the G + G + , GA and AA conformers. The G + G − rotamer could not be observed. As its energy is significantly larger than that for the other conformations due to repulsive four bond interactions between the SnMe 3 groups (pentane effect), the concentration in the equilibrium mixture is negligibly small. For 4 , eight (2 3 ) spectroscopically distinct (classical) conformations are possible. In the room temperature Raman spectrum, the SiSn stretching vibration consists of a line at 330 cm −1 with a broad shoulder at 320 cm −1 . In the solid (−60°C), a single rotamer (probably the all anti form) survives. Upon heating, several conformational states with higher energies are populated which could not be resolved by Raman spectroscopy.

Deuteron NMR study of a long-chain smectic liquid crystal: molecular order and dynamics.

Deuteron Zeeman (T(1Z)) and quadrupolar (T(1Q)) spin-lattice relaxation times and quadrupolar splittings were measured in the nematic and smectic A phases of a chain-deuterated 4-n-octyloxy-4'-cyanobiphenyl (8OCB-d17) at 15.1 and 46 MHz. To model the NMR observables, the so-called pentane effect is used to limit the number of possible conformations in the chain, and is found to be a good approximation. The additive potential method is employed to construct the potential of mean torque using the quadrupolar splittings. A decoupled model is used to describe correlated internal motions in the chain, which are independent of the molecular reorientation. The latter motion is treated using the small-step rotational diffusion model of Nordio (Tarroni and Zannoni), while the former motion is described using a master rate equation. In the nematic phase, order director fluctuations are found to be necessary. The relaxation data in both mesophases were treated using a global target method, and the derived motional parameters are acceptable in comparison with those found for 6OCB.

CC and CO bond conformations in 1,2-dimethoxyethane, bis-(2-methoxyethyl)ether and poly(ethyleneoxide): dependence on solvent and temperature

Data from 3 J HCCH and 3 J HCOC couplings in 1,2-dimethoxyethane and bis-(2-methoxyethyl)ether, plus 3 J HCCH in poly(ethylene oxide), have been obtained in five solvents by iterative fitting. The resulting proportions of gauche rotamers are higher than previous estimates, and higher still after allowance is made for the pentane effect. They fit well with gas phase electron diffraction data, with current gas phase theoretical calculations and with standard RIS parameters for the polymer, but less well with calculations for the liquid state. The influence of solvent arises more from variations in its H-bond donor properties than in its dielectric.

Correlated chain dynamics in the nematic phase of 4-cyano-4′-hexyloxybiphenyl

Abstract We report in this paper measurements of the Zeeman and Quadrupolar spin-lattice relaxation times at two different deuteron Larmor frequencies for the nematic phase of the perdeuteriated nematogen 6OCB. A model of correlated internal motion is used to account for both the quadrupolar splittings and the spectral densities of motion. The nematic mean field is constructed using the additive potential method, while the conformational transitions among the allowed configurations are described by a master equation. For modelling the quadrupolar splittings, we used 729 conformations, although this seemed impossible when the spectral densities were fitted by minimizing the sum of squares of per cent errors. The pentane effect has, therefore, been used to limit the size of the transition rate matrix in the master equation. We found that the dynamic model for liquid crystals proposed by one of us (1991, Phys. Rev. A, 43, 4310) is essentially correct for 6OCB.

Topological Index and Thermodynamic Properties. IV. Size Dependency of the Structure-Activity Correlation of Alkanes

Abstract Correlation coefficients between twelve thermodynamic properties (ΔS, ΔHf, ΔGf, bp, d, nD, Rm, Vm, pc, Tc, Vc, dc) of 624 isomers of nonane through dodecane and five different topological indices (Z, p3, w, p2, A3) were calculated, where the new index A3 is proposed to be defined as the half sum of the off-diagonal elements of the cube of the adjacency matrix A. These properties can be classified into several types, according to the behavior of the two correlation coefficients, ρ(Z) and ρ(p3), against the change of the size of molecules. ΔS and bp depend largely on Z, while d and nD on p3, irrespective of the size change of molecules. On the other hand, ΔHf of smaller alkanes is largely dependent on Z, but for larger alkanes it turns out to be a p3-dependent property. Various interesting behaviors of the structure-activity relationships including the “pentane effect” were observed and discussed.

Enumeration of normal hydrocarbon conformations

The conformational states of linear hydrocarbons as a function of internal energy are enumerated. The principal nonbonded interaction, the pentane effect, is assigned a finite energy, but other nonbonded interactions are neglected. Using a generating function technique several equivalent expressions are derived for N(n, n g, n p), the number of conformations of a chain with n rotatable bonds, n g gauche bonds and n p adjacent opposite rotations. A combinatorial interpretation for these expressions is given and the asymptotic behaviour is studied. A similar analysis is made for T(n, n p), the total number of states with a fixed number of pairs, but no restriction on n g. These results clarify and extend other recent work. A general framework for including other nonbonded interactions is constructed and illustrated. Finally it is shown that a relation between the generating function and the partition function gives an exact expression for the latter.

Derivation of the conformational density of states of a normal hydrocarbon

We consider conformational states of a saturated linear hydrocarbon, within the rotational isomeric approximation. The principal nonbonded interaction within the chain, the ‘‘pentane effect,’’ is assigned a finite energy; other nonbonded interactions are ignored. Within these approximations, we derive an exact closed expression for the conformational density of states. This result is compared to previous work. Some consequences of this result are examined.

Non-bonded interactions in the enumeration of normal hydrocarbon conformations

We enumerate conformational states of linear hydrocarbons as a function of internal energy, both analytically and by Monte Carlo simulation. The principal non-bonded interaction within the chain (the “pentane effect”) is accounted for simply. By a simple statistically mechanical calculation we demonstrate that the pentane effect is more important than previously believed in determining the thermally accessible conformations of a hydrocarbon chain.

Steric effects on the dynamical behaviour and 13C nuclear spin relaxation in flexible chain molecules

Steric effects on the dynamical behaviour and 13C nuclear spin relaxation in flexible chain molecules have been examined by simulating the random motions of n-hexylamine coordinated to Gd(FOD) 3 with several models by the Monte Carlo technique. The spectral density functions were calculated for the respective carbons of the hexyl group and power densities at the Larmor frequency were compared with experimental values of T 1M. Simulation models where the pentane effect is taken into considerations gave satisfactory results.

Conformational properties of isolated macromolecules

AbstractThe properties of many kinds of solid material (e.g., ionic crystals, quartz, etc.) appear to have only a tenuous correlation with those of the isolated individual atoms or molecules of which they are made. In macromolecular substances, however, thanks primarily to the great strength of covalent bonds, such correlations are strong and indeed essential to fundamental understanding of structure‐property relationships. With certain exceptions, such as polypeptides and polynucleotides with their remarkable helix‐coil transformations, the conformational properties of macromolecules in liquid or amorphous environment are only secondarily dependent on the nature or concentration of diluents; and in many cases the molecular conformation observed in the crystalline state is also the most stable conformation of the isolated chain. There are also strong correlations between the rates of conformational change for isolated macromolecules in dilute solution and various non‐equilibrium properties of polymeric substances in bulk.During the past decade, great progress has been made in the analysis and prediction of macromolecular conformations. Detailed accounts may be found in the books by VOLKENSTEIN, by BIRSTEIN and PTITSYN, and by FLORY. By combination of several types of experimental evidence with semi‐empirical and theoretical considerations, it has been possible to construct fairly reliable potential energies governing the conformations of a wide variety of chain molecules. An important simplifying feature of the results is that for many purposes it is sufficient to focus attention on the various minima of the potential energy, corresponding to the so‐called rotational‐isomeric states. Another essential feature is that as a rule one finds strong interdependence of the rotational states of adjoining bonds in the chain backbone; a simple example is found in the “pentane effect” for paraffin chains, which renders highly improbable the occurence of two successive gauche rotations of opposite sense. An important exception is seen in polyamides, where the essentially rigid planarity of the amide link allows independence of the rotations of the immediately adjacent bonds. Inclusion of other rigid or semi‐rigid elements in the chain backbone, such as the rings in cellulose and in terephthalate polyesters, leads to similar effects, but in detail each chain is sui generis. The conformations of chains bearing asymmetric centers (e.g., PVC, polypropylene) depends strongly on tacticity and stereoregularity.For the discussion of non‐equilibrium properties at a fundamental level, the maxima (barriers between minima) of the conformational potential energy also play an essential role, but at present most theories of viscoelasticity, for example, are based on less realistic models, such as beads‐and‐springs, random‐flight chain, KRATKY‐POROD wormlike chain, etc. The elaboration of these models and their relation to the detailed molecular structure is currently an active field of study.