Non-associated Molecules Research Articles

Predicting PC-SAFT pure-component parameters by machine learning using a molecular fingerprint as key input

In this work, a machine learning (ML)-approach was developed to predict pure-component parameters for the Perturbed-Chain Statistical Associating Fluid Theory (PC-SAFT) for non-associating molecules using a deep neural network. Extended-connectivity fingerprints (ECFP) were used as key inputs for the neural network to achieve flexible and easily available non-experimental representations of a chemical molecule. A detailed analysis of bit collisions during the ECFP generation was performed to obtain the optimal ECFP initial bit lengths creating possible inputs for neural networks to be trained. Three ECFP initial bit lengths (210, 212, 214) were used to train three neural networks. The results show that the neural networks using ECFP initial bit lengths of 212 and 214 achieve high prediction accuracy (AARD < 5 %) for original (literature) PC-SAFT pure-component parameters. Moreover, correlations for homologous series of PC-SAFT pure-component parameters were adapted by the neural networks trained. Further validation was performed comparing calculations of physical properties (vapor pressure, saturation liquid density) using ML-predicted PC-SAFT pure-component parameters to experimental data. Being a predictive ML-approach, the neural networks of this work can be used in early process synthesis to obtain PC-SAFT pure-component parameters without experimental data.

Modeling of the Interfacial Behavior of Carbon Dioxide + Methyl Myristate, Carbon Dioxide + Palmitate, and Carbon Dioxide + Methyl Myristate + Methyl Palmitate Mixtures Using CPA-EOS and Gradient Theory

This work presents the vapor–liquid equilibrium and the interfacial behavior modeling of binary and ternary CO $$_2$$ + ester mixtures, with the cubic plus association equation of state (CPA-EOS) combined with the density gradient theory. The binary mixtures, CO $$_2$$ + methyl myristate and CO $$_2$$ + methyl palmitate, were studied at temperatures from 313.15 K to 333.15 K, considering the ester molecules as non-associating and the carbon dioxide as non-associating or self-associating (2B scheme) molecule. Phase behavior was predicted with binary interaction parameters adjusted from binary mixture phase equilibrium experimental data. Results show than there are some points better represented by the associating scheme, but the overall trend shows that the CPA-EOS with the non-associating scheme for all the molecules is the best option for describing the phase equilibrium and calculating the interfacial tension for the CO $$_2$$ + ester binary mixtures. For this reason, the CO $$_2$$ + methyl myristate + methyl palmitate mixture at 313.15 K was modeled only with non-associating fluids. The AAD% for the calculated interfacial tensions, considering non-associating molecules in the mixture is 9.7 % for the CO $$_2$$ + methyl myristate mixture, 15.1 % for the CO $$_2$$ + methyl palmitate mixture, and 7.9 % for the CO $$_2$$ + methyl myristate + methyl palmitate mixture.

Modeling the Critical and Phase Equilibrium Properties of Pure Fluids and Mixtures with the Crossover Cubic-Plus-Association Equation of State

The cubic-plus-association (CPA) equation of state (EoS) is unable to correctly describe the vapor–liquid critical behavior of pure fluids and mixtures because of its classical behavior. In fact, the traditional parametrization procedure (i.e., matching the saturated pressure and liquid density curves far from the critical point) causes an overprediction of the critical pressures and temperatures of pure components. Besides, the deviations with respect to experimental data are even larger for systems containing hydrogen-bonding species, in comparison to systems composed of nonassociating molecules. To improve the representation of the thermodynamic properties of fluids in near-critical regions with CPA, we have applied White’s recursive procedure to introduce density fluctuations in the classical model, allowing the correct description of the nonanalytical behavior of real fluids close to the critical point. The resulting model (i.e., the crossover CPA (CCPA) EoS) is capable of accurately representing the phase behavior of fluids, specifically normal alkanes and alcohols, carbon dioxide, and water as well as some of their binary mixtures, far away from and close to the critical region. This is shown by the comparison of the results obtained from CCPA and classical EoS with the experimental data.

Evaluation of the polar contribution in the SAFT-VR Mie equation of state for simultaneous correlation of condensed-phase density, condensed-phase speed of sound, saturated density and saturated pressure of pure polar fluids

Polar forces affect significantly the thermodynamic properties and phase equilibria of pure fluids. In this work, the original SAFT-VR Mie equation of state was modified by the introduction of an explicit term to account for multipolar effects. Two approaches were evaluated: the Polar SAFT-VR Mie (PSAFT-VR Mie) and the Truncated Polar SAFT-VR Mie (tPSAFT-VR Mie). For non-associating molecules the agreement between experimental data and model predictions are very good. The tPSAFT-VR Mie equation of state presented better results than the SAFT-VR Mie and PSAFT-VR Mie models correlating condensed-phase density, condensed-phase speed of sound, saturated density and saturated pressure with lower deviations. For associating molecules the results obtained with the tPSAFT-VR Mie model were equivalent to the ones obtained with the SAFT-VR Mie equation of state. In order to the tPSAFT-VR Mie model better predict second-derivative thermodynamic properties, such as the speed of sound and the isobaric heat capacity, some information about this type of property must be used in the pure components parameters regression. All evaluated models predicted similar values for the second virial coefficient.

Concentration and solvent induced micellization of F68 tri-block copolymer

The Fourier transform infrared spectroscopy is used to study the binary mixtures of F68/water and F68/p-xylene. The results show that in aqueous solution the wavenumbers of the two bands associated to the O-H and C-O-C vibrations are inversely proportional. This can be explained by the fact that the dehydrated methylene groups approach by the hydrophobic interaction to form hydrophobic cores, which lead to a breakdown of the hydrogen bond between water and C-O-C. The spectrum associated to the binary mixture F68/p-xylene show that F68 exists as nonassociated molecules (unimers) at room temperature. The results of the ternary mixtures of the F68/p-xylene/water show a change in the spectra on the level of the vibrations of the O-H and C-O-C groups which is attributed to the change of structure following the variation of the concentration from unimers to large aggregates.

A Hard Convex Core Yukawa Equation of State for Nonassociated Chain Molecules

The compressibility factor of nonassociated chain molecules composed of hard convex core Yukawa segments was derived with SAFT-VR and an extension of the Barker-Henderson perturbation theory for convex bodies. The temperature-dependent chain and dispersion compressibility factors were derived using the Yukawa potential. The effects of temperature, packing fraction, and segment number on the compressibility factor were investigated for chains of the prolate sphereocylinder segments. A comparison of hard core Yukawa chain compressibility factor values and hard chain compressibility factor values showed that the type of interaction potential has more effect on those chain molecules with higher segment numbers. The results demonstrated that in reduced temperatures 1.4 and 2.4, the Yukawa chain of the compressibility factor is insensitive to temperature, while the dispersion term of the compressibility factor changes remarkably with the temperature. The derived equation of state can fairly predict the SAFT-VR results of the hard sphere core chain molecules in the limit of α = 1.

Predicting Fluid Viscosity of Nonassociating Molecules

Previous work by the author demonstrated that a new predictive corresponding-states viscosity model, based on entity Chapman–Enskog scaling, correlated pure n-alkane component viscosity data with entity scaled residual entropy. With five fitting constants, a 5.2% average absolute relative deviation (AARD) was obtained over the entire fluid region for a group of 17 n-alkanes, ranging from methane to 1280 Mw linear polyethylene. The work reported here demonstrates that this same model and fitting constants predicts fluid viscosity of other molecular classifications over a wide range of temperature and pressure. Molecular structure was incorporated to improve the predictability of the earlier corresponding-states viscosity model. With the inclusion of molecular structure, an AARD of 6.6% was obtained over the entire fluid region for ten classifications of nonassociating molecules and a wide range of temperature (60–800 K) and pressure (1–46 800 atm). Thus, a predictive corresponding-states fluid viscosity mo...

Predictive Corresponding-States Viscosity Model for the Entire Fluid Region: n-Alkanes

Previous work by the author demonstrated a novel approach for correlating the scaled self-diffusion coefficient, viscosity, and thermal conductivity with the residual entropy over the entire fluid region. It is shown here that a new entity-based scaled viscosity model correlates pure n-alkane components to a single semilogarithmic line with the entity residual entropy. With five fitting parameters, a 5.2% group average of the absolute relative deviations (AADs) is obtained over the entire fluid region for a group of 17 n-alkanes, ranging from methane to linear polyethylene with a molecular weight of 1280 g/mol. It was also found that these same five fitting parameters predict the fluid viscosity of some other alkanes, ethers, and olefins. Thus, the entity-based scaling approach introduced here provides a predictive corresponding-states model for fluid viscosity of nonassociating molecules and is a practical approach to determining viscosity in process engineering, product engineering, oil and gas reservoir engineering, pipelines, and fracking applications. This entity-based scaled viscosity-entity residual entropy model is particularly useful in the critical region and at high pressures because the traditional saturated liquid and saturated vapor viscosity component correlations are not applicable.

Vapour–liquid equilibrium of binary systems containing pentafluorochemicals from 363 to 413 K: Measurement and modelling with Peng–Robinson and three SAFT-like equations of states

New sets of data are provided to characterize the phase equilibrium of new mixtures containing fluorochemicals and show their potential in energy recovery applications, as industrial heat pumps. Isothermal Vapour–Liquid Equilibrium data have been measured for R245fa + isopentane, and R365mfc + isopentane systems. Measurements were performed for four isotherms with pressure from 0.4 to 2.9 MPa. The data are correlated using different models (Peng–Robinson, PC-SAFT, polar PC-SAFT and SAFT-VR equations of state) and all four approaches can accurately describe the VLE. A very good description of the VLE for the pure components and the mixtures can be obtained by representing the R245fa and R365mfc molecules either as non-polar associating compounds or as non-associating dipolar molecules. To confirm the experimental values of the dipoles used in polar PC-SAFT, we performed DFT calculations of the permanent dipoles of the molecules and a good agreement with the experimental values is found for R245fa, while two different values corresponding to two different conformations were found for R365mfc.

Microscopic dynamics of supercooled low weight alcohols

Dynamical properties of low weight alcohols have been analyzed both in the liquid and the supercooled states. Realistic interatomic potential models for methanol and ethanol have been used. The influence of temperature on the hydrogen-bonded structure has been undertaken. Remarkable similarities have been obtained in both systems. Velocity autocorrelation functions have been evaluated for molecules participating in zero, one, and two hydrogen bonds at a wide range of temperatures. A backscattering area preceded by a shoulder has been identified as a signature of this function when evaluated for the subset of molecules that participate in two hydrogen bonds. Memory functions have also been evaluated. Their initial decay depends only slightly upon temperature. A more marked temperature dependence is observed for the nonassociated molecules. For them, reasonable agreement with the mode-coupling approach predictions has been encountered.

Phase stability analysis using the PC-SAFT equation of state and the tunneling global optimization method

Phase stability calculation is a very important topic in phase equilibrium modeling. Usually the phase stability problem is solved by minimization of the tangent plane distance (TPD) function, the sign of the objective function at its global minimum indicating the state of the mixture at given conditions. The TPD function is non-convex and may be highly non-linear, many phase stability problems being really challenging. The tunneling global optimization method had been successfully used for solving a variety of phase equilibrium problems, including stability, with cubic equations of state (EoS). In this work, we test the ability of the tunneling method to solve the phase stability problem for more complex EoS like PC-SAFT. Calculations are performed for several benchmark problems, for mixtures of non-associating molecules, from binaries to multicomponent. In one example, the mixture contains hydrogen sulphide, for which the three parameters required by the PC-SAFT EoS were unavailable in the literature. These parameters, as well as the binary interaction parameter (BIP) between hydrogen sulphide and methane, were calculated based on experimental data.

Uniform polymer in synthetic polymer chemistry

AbstractThe preparation of uniform polymers and their use in fundamental polymer chemistry are reviewed. A typical method of preparation is a combination of living polymerization and supercritical fluid chromatography separation. Synthetic uniform polymers allow us to solve ambiguous problems in polymer chemistry due to molecular weight distribution and are of significant importance for studies on structure–property relationships. A close inspection of an isotactic uniform chloral oligomer with a symmetrical chemical structure reveals that oligomers are the first examples of stable atropisomers of aldehyde oligomers and that their chiroptical properties are due only to their helical geometries. A molecular‐level understanding of the mechanism and stoichiometry of the association process of polymer molecules is possible only with uniform polymers, and stereocomplex formation between isotactic and syndiotactic poly(methyl methacrylate)s in acetone has vigorously been studied by size exclusion chromatography (SEC) and NMR. End‐functionalized uniform polymers have enabled us to prepare uniform polymer architectures, such as block, graft, comb, and star polymers. A uniform stereoblock poly(methyl methacrylate) with an isotactic (methyl methacrylate)46‐syndiotactic (methyl methacrylate)46 structure shows a single SEC peak in chloroform but three peaks in acetone, which are ascribable to intermolecularly and intramolecularly associated complexes and nonassociated molecules. A three‐arm star polymer with one isotactic chain and two syndiotactic chains shows a peculiar SEC behavior in acetone due to a braid type of intramolecular stereocomplex formation. © 2003 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 42: 416–431, 2004

Exploring the reciprocal relationship between immunity and inflammation in chronic inflammatory arthritis.

Experimental models seeking to explore how susceptible individuals develop rheumatoid arthritis (RA) propose that genetic and environmental factors shape a complex series of molecular and cellular interactions leading to a chronic inflammatory response. T lymphocytes and MHC class II genes have featured prominently in these models. More recent studies have suggested that perpetuation of inflammation in a disease-susceptible host might occur through failure to down-regulate the inflammatory process. One prediction from this model is that effective mechanisms of immunoregulation might be most easily investigated in non-susceptible individuals. However, this has been difficult to study in man. Based on the observation that extended MHC haplotypes are strongly associated with RA in different ethnic groups, I have explored the function of human MHC-encoded genes in transgenic mice using two different experimental approaches. First, by comparing the molecular interactions between disease-associated or non-associated HLA-DR4 molecules and CD4+ T lymphocytes, it has been possible to gain insight into how immune responses in non-susceptible individuals might differ from T-cell responses observed in a susceptible host. This has been achieved using transgenic mice expressing RA disease-associated and non-associated human HLA class II molecules. Secondly, the effects of prolonged exposure of T cells to the proinflammatory cytokine tumour necrosis factor alpha (TNF) have been studied in vitro and in vivo, focusing on T-cell receptor (TCR) signalling and effector responses. In studies of HLA class II transgenic mice, the major differences between disease-associated and non-associated alleles in terms of T-cell responses occur at the level of presentation of antigenic peptides, and the sustained expression of inflammatory cytokines such as TNF. Chronic exposure of T cells to inflammatory cytokines such as TNF induces a phenotype which resembles RA synovial T cells, including the induction of non-deletional and reversible hyporesponsiveness to TCR ligation and uncoupling of proximal TCR signal transduction pathways. The experimental findings are consistent with a model in which HLA class II-driven inflammatory cytokine expression uncouples TCR signalling pathways in the susceptible host in such a way as to profoundly suppress proliferative and immunoregulatory cytokine responses, while at the same time promoting cell survival and effector responses.

Dynamic rheology of agar gels: theory and experiments. Part II: gelation behavior of agar sols and fitting of a theoretical rheological model

A theoretical rheological model for agar gels, based on the bead spring model for linear flexible random coils and the model for crosslinked polymers, is successfully fitted to experimental gelation curves obtained over a wide range of cooling rates (0.5–20°Cmin−1) and agar concentration (1–3wt%). The theoretical gelation temperature, Tgelmodel increases with increasing agar concentration and decreasing cooling rate. The intrinsic net association rate increases significantly with increasing cooling rate. This increase is related to the higher probability of association of the non-associated agar molecules at higher cooling rates.

The associating Martin–Hou (AMH) equation of state: II. Applications of the AMH EOS to associating compounds and mixtures

The associating Martin–Hou equation of state (AMH EOS) has been developed in our previous work. The present work is an extension of the work. Emphasis is given on calculations of pure-component properties, vapor–liquid equilibria for mixtures containing associating and non-associating molecules and excess enthalpies for mixtures of alcohol–hydrocarbon. The result shows the method is reliable.

A study of associating Lennard–Jones chains by a new reference radial distribution function

A new radial distribution function (RDF) for the Lennard–Jones (LJ) fluid is derived around the LJ potential size ( σ). The theoretically based RDF is completely analytical and real. Comparisons with computer simulation data at various conditions indicate that the RDF is very accurate at r<1.2 σ, and the accuracy is consistent from low to high densities. The new RDF is utilized to study associating LJ chains by combining with Wertheim's first-order perturbation theory. The resulting equation of state is tested against computer simulation data for second virial coefficient and pressure of LJ chains, and for pressure and the fraction of non-associating molecules in associating LJ chains. The calculated results indicate that the new equation of state is very satisfactory and its performance is comparable to several empirical equations reported in the literature. Another feature of the new equation of state is that both chain bonding and association sites are adjustable for practical purposes.

Immune response of HLA-DQ8 transgenic mice to peptides from the third hypervariable region of HLA-DRB1 correlates with predisposition to rheumatoid arthritis.

The major histocompatibility complex class II genes play an important role in the genetic predisposition to many autoimmune diseases. In the case of rheumatoid arthritis (RA), the human leukocyte antigen (HLA)-DRB1 locus has been implicated in the disease predisposition. The "shared epitope" hypothesis predicts that similar motifs within the third hypervariable (HV3) regions of some HLA-DRB1 alleles are responsible for the class II-associated predisposition to RA. Using a line of transgenic mice expressing the DQB1*0302/DQA1*0301 (DQ8) genes in the absence of endogenous mouse class II molecules, we have analyzed the antigenicity of peptides covering the HV3 regions of RA-associated and nonassociated DRB1 molecules. Our results show that a correlation exists between proliferative response to peptides derived from the HV3 regions of DRB1 chains and nonassociation of the corresponding alleles with RA predisposition. While HV3 peptides derived from nonassociated DRB1 molecules are highly immunogenic in DQ8 transgenic mice, all the HV3 peptides derived from RA-associated DRB1 alleles fail to induce a DQ8-restricted T-cell response. These data suggest that the role of the "shared epitope" in RA predisposition may be through the shaping of the T-cell repertoire.

Diffusion of pseudo-planar molecules: an experimental evaluation of the molecular effects on diffusion

Limiting mutual-diffusion coefficients of non-associated pseudo-planar molecules, ranging from benzene to anthracene, in various solvents have been measured at 298.2 K using the chromatographic peak-broadening method. For the non-associated solutes studied, there exists a linear relationship between the reciprocal of the diffusion coefficients and the molecular volume of the solutes. The diffusivities are found to be insensitive to the mass and dipole moment of the solute molecules. The data of the pseudo-planar molecules are compared with those of the pseudo-spherical solutes reported in the literature. The effects of molecular shape on diffusion are discussed.

Isolation and characterization of 5T4, a tumour‐associated antigen

The monoclonal antibody (MAb) 5T4 defines a human trophoblast antigen marker with a restricted pattern of expression in normal adult tissues but this antigen is expressed on a variety of carcinomas. The purification of 5T4 antigenic molecules is described from term syncytiotrophoblast by a combination of lectin- and immunoaffinity chromatography and gel filtration giving up to 10,000-fold purification with 70% yield. The antigen is carried by non-associated glycoprotein molecules with an apparent molecular weight of 72 kDa on SDS-PAGE and a neutral pI. Removal of N-linked sugars by N-glycanase reveals a core protein of 42 kDa. Treatment with enzymes that cleave O-linked sugars does not substantially alter the molecular size. The native 5T4 molecules are very resistant to proteolysis until the N-linked sugars are removed or the glycoprotein is denatured and reduced. Glycopeptides generated by these approaches will be suitable for amino acid sequencing.

The Effects of Heparin on the Physicochemical Properties of Reconstituted Collagen

Pepsin-solubilized bovine dermal collagen was reconstituted in 0.02 M sodium phosphate(pH 7.2), concentrated to 30-40 mg/ml, and adjusted to physiological ionic strength by addition of sodium chloride. These preparations, at 4-15 °C, are fibrillar suspensions composed of fibrils of varying diameters and nonassociated molecules. Addition of heparin to these suspensions promoted a dose-dependent increase in average fibril diameter as measured by turbidimetry and electron microscopic analyses. These effects were relatively specific for heparin and heparin-like glycosaminoglycans. Chondroitin sulfate and hyaluronic acid had little or no effect on fibrillar diameters under these conditions, whereas dermatan sulfate had an intermediate effect on fibrillar reorganization. Differential scanning calorimetry revealed that addition of optimal concentrations of heparin generated fibrils of higher stability and that this effect was associated with the disappearance of structures of lower stability, including nonassociated molecules and thin fibrils. Light microscopic analyses of the fibrillar collagen/heparin matrix showed it to be a more open network of distinct collagen fibers than was observed with the fibrillar collagen preparation alone. Binding experiments indicated that heparin bound to fibrillar collagen in a saturable fashion with a Kd of approximately 4 × 10-7 M. Creep experiments provided evidence that the addition of heparin to fibrillar collagen suspensions greatly reduces the gelation phenomenon that is normally observed when such suspensions are warmed to 37°C. These differences in fibrillar architecture may be in part responsible for differences noted in the biological response to fibrillar collagen and fibrillar collagen/heparin implants in vivo (McPherson et al., 1988).