Estimation of Mixture Properties from First- and Second-Order Group Contributions with the UNIFAC Model

A new UNIFAC (extended model), to be called KT-UNIFAC, is proposed for estimation of mixture properties (activity coefficients and excess enthalpies) for vapor−liquid equilibrium from group contributions. Estimation is performed at two levels:  the basic level uses contributions from first-order simple groups, while the second level uses a small set of second-order groups having the first-order groups as building blocks. The role of the second-order groups is to consider, to some extent, the proximity effects and to distinguish among isomers. In the second-order UNIFAC model (Fluid Phase Equilib. 1999, 158, 349), the excess Gibbs function is calculated as a sum of a first-order combinatorial contribution, a first-order residual contribution, and a second-order residual contribution. The sets of first- and second-order groups have been revised and extended. The performance of this KT-UNIFAC model has been tested through correlation and prediction of vapor−liquid equilibria, infinite dilution activity coefficients, and excess enthalpies covering data involving 4413 binary mixtures and 27 ternary systems. Compared with some of the currently used versions of UNIFAC, the KT-UNIFAC model makes significant improvements in accuracy while providing a much wider range of applicability

Not from Scratch: Predicting Thermophysical Properties through Model-Based Transfer Learning Using Graph Convolutional Networks

In this study, a framework for the prediction of thermophysical properties based on transfer learning from existing estimation models is explored. The predictive capabilities of conventional group-contribution methods and traditional machine-learning approaches rely heavily on the availability of experimental datasets and their uncertainty. Through the use of a pretraining scheme, which leverages the knowledge established by other estimation methods, improved prediction models for thermophysical properties can be obtained after fine-tuning networks with more accurate experimental data. As our experiments show, for the case of critical properties of compounds, this pipeline not only improves the performance of the models on commonly found organic structures but can also help these models generalize to less explored areas of chemical space, where experimental data is scarce, such as inorganics and heavier organic compounds. Transfer learning from estimation models data also allows for graph-based deep learning models to create more flexible molecular features over a bigger chemical space, which leads to improved predictive capabilities and can give insights into the relationship between molecular structures and thermophysical properties. The generated molecular features can discriminate behavior discrepancy between isomers without the need of additional parameters. Also, this approach shows better robustness to outliers in experimental datasets

Experimental Measurement of Phase Equilibrium of Hydrate in Water + Ionic Liquid + CH₄ System

With the goal of discovering a more effective type of thermodynamic hydrate inhibitors (THIs), the phase equilibrium conditions of CH₄ hydrates were examined in the presence of morpholinium and piperidinium ionic liquids (ILs) at a mass fraction of 0.1. It was observed that the addition of ILs shifted the hydrate equilibrium conditions toward higher pressure and lower temperature compared with those of hydrates formed from pure water. Both cationic and anionic species influenced the equilibrium conditions of the CH₄ hydrate. The piperidinium ILs showed better inhibition effect than did the morpholinium ILs at the same species of counteranions. The result may be due to the more hydrophobic nature of piperidinium ILs, which have a higher affinity for CH₄ molecules. It was also seen that the inhibition effect of BF₄^– ions was stronger than that of Br^– ions for both piperidinium and morpholinium ILs. Thus, the inhibition effect became stronger in the order: <i>N</i>-ethyl-<i>N</i>-methylpiperidinium tetrafluoroborate ([EMPip]­[BF₄]) > <i>N</i>-ethyl-<i>N</i>-methylpiperidinium bromide ([EMPip]­[Br]) > <i>N</i>-ethyl-<i>N</i>-methylmorpholinium tetrafluoroborate ([EMMor]­[BF₄]) > <i>N</i>-ethyl-<i>N</i>-methylmorpholinium bromide ([EMMor]­[Br]). The best among these ILs had inhibition effectiveness comparable with ethylene glycol and triethylene glycol, which are used commercially as THIs

Thermal Stability and Isomerization Mechanism of <i>exo</i>-Tetrahydrodicyclopentadiene: Experimental Study and Molecular Modeling

Thermal stability and the primary initiation mechanism of exo-tetrahydrodicyclopentadiene (exo-THDCP, C10H16) were investigated in a batch-type reactor. The catalytic role of the stainless steel inside the reactor was eliminated by inserting a quartz flask. exo-THDCP decomposed at temperatures over 623 K and 1-cyclopentylcyclopentene (1-CPCP, C10H16) and 4-methyl-2,3,4,5,6,7-hexahydro-1H-indene (4-MHI, C10H16) were the primary decomposition products of exo-THDCP. C10 hydrocarbons were determined to be the major products. The amount of C5−C7 hydrocarbons, such as cyclopentene, benzene, and toluene, were relatively small. We performed the molecular modeling (MM) on some of the compounds, including 1-CPCP and 4-MHI produced from exo-THDCP to evaluate the activation energy and molecular structure of the intermediates. The experimental and MM results showed that 1-CPCP and 4-MHI were independently formed from exo-THDCP. The experimental results closely corresponded with the MM result; the products that were only minimally produced after the reaction had qualitatively higher activation energies than the other products

Drug-Eluting Microarrays for Cell-Based Screening of Chemical-Induced Apoptosis

Traditional high-throughput screening (HTS) is carried out in centralized facilities that require extensive robotic liquid and plate handling equipment. This model of HTS is restrictive as such facilities are not accessible to many researchers. We have designed a simple microarray platform for cell-based screening that can be carried out at the benchtop. The device creates a microarray of 2100 individual cell-based assays in a standard microscope slide format. A microarray of chemical-laden hydrogels addresses a matching array of cell-laden microwells thus creating a microarray of sealed microscale cell cultures each with unique conditions. We demonstrate the utility of the device by screening the extent of apoptosis and necrosis in MCF-7 breast cancer cells in response to exposure to a small library of chemical compounds. From a set of screens we produced a rank order of chemicals that preferentially induce apoptosis over necrosis in MCF-7 cells. Treatment with doxorubicin induced high levels of apoptosis in comparison with staurosporine, ethanol, and hydrogen peroxide, whereas treatment with 100 μM ethanol induced minimal apoptosis with high levels of necrosis. We anticipate broad application of the device for various research and discovery applications as it is easy to use, scalable, and can be fabricated and operated with minimal peripheral equipment

Image_1_The Effect of Environmental Enrichment on Glutathione-Mediated Xenobiotic Metabolism and Antioxidation in Normal Adult Mice.pdf

<p>Olfactory bulb (OB) plays an important role in protecting against harmful substances via the secretion of antioxidant and detoxifying enzymes. Environmental enrichment (EE) is a common rehabilitation method and known to have beneficial effects in the central nervous system. However, the effects of EE in the OB still remain unclear. At 6 weeks of age, CD-1® (ICR) mice were assigned to standard cages or EE cages. After 2 months, we performed proteomic analysis. Forty-four up-regulated proteins were identified in EE mice compared to the control mice. Gene Ontology analysis and Kyoto Encyclopedia of Genes and Genomes Pathway demonstrated that the upregulated proteins were mainly involved in metabolic pathways against xenobiotics. Among those upregulated proteins, 9 proteins, which participate in phase I or II of the xenobiotic metabolizing process and are known to be responsible for ROS detoxification, were validated by qRT-PCR. To explore the effect of ROS detoxification mediated by EE, glutathione activity was measured by an ELISA assay. The ratio of reduced glutathione to oxidized glutathione was significantly increased in EE mice. Based on a linear regression analysis, GSTM2 and UGT2A1 were found to be the most influential genes in ROS detoxification. For further analysis of neuroprotection, the level of iNOS and the ratio of Bax to Bcl-2 were significantly decreased in EE mice. While TUNEL⁺ cells were significantly decreased, Ki67⁺ cells were significantly increased in EE mice, implicating that EE creates an optimal state for xenobiotic metabolism and antioxidant activity. Taken together, our results suggested that EE protects olfactory layers via the upregulation of glutathione-related antioxidant and xenobiotic metabolizing enzymes, eventually lowering ROS-mediated inflammation and apoptosis and increasing neurogenesis. This study may provide an opportunity for a better understanding of the beneficial effects of EE in the OB.</p

Table_1_The Effect of Environmental Enrichment on Glutathione-Mediated Xenobiotic Metabolism and Antioxidation in Normal Adult Mice.pdf

<p>Olfactory bulb (OB) plays an important role in protecting against harmful substances via the secretion of antioxidant and detoxifying enzymes. Environmental enrichment (EE) is a common rehabilitation method and known to have beneficial effects in the central nervous system. However, the effects of EE in the OB still remain unclear. At 6 weeks of age, CD-1® (ICR) mice were assigned to standard cages or EE cages. After 2 months, we performed proteomic analysis. Forty-four up-regulated proteins were identified in EE mice compared to the control mice. Gene Ontology analysis and Kyoto Encyclopedia of Genes and Genomes Pathway demonstrated that the upregulated proteins were mainly involved in metabolic pathways against xenobiotics. Among those upregulated proteins, 9 proteins, which participate in phase I or II of the xenobiotic metabolizing process and are known to be responsible for ROS detoxification, were validated by qRT-PCR. To explore the effect of ROS detoxification mediated by EE, glutathione activity was measured by an ELISA assay. The ratio of reduced glutathione to oxidized glutathione was significantly increased in EE mice. Based on a linear regression analysis, GSTM2 and UGT2A1 were found to be the most influential genes in ROS detoxification. For further analysis of neuroprotection, the level of iNOS and the ratio of Bax to Bcl-2 were significantly decreased in EE mice. While TUNEL⁺ cells were significantly decreased, Ki67⁺ cells were significantly increased in EE mice, implicating that EE creates an optimal state for xenobiotic metabolism and antioxidant activity. Taken together, our results suggested that EE protects olfactory layers via the upregulation of glutathione-related antioxidant and xenobiotic metabolizing enzymes, eventually lowering ROS-mediated inflammation and apoptosis and increasing neurogenesis. This study may provide an opportunity for a better understanding of the beneficial effects of EE in the OB.</p

Selective Enrichment and Mass Spectrometric Identification of Nitrated Peptides Using Fluorinated Carbon Tags

Protein tyrosine nitration (PTN) is a post-translational modification that is related to several acute or chronic diseases. PTN introduces a nitro group in the ortho position of the phenolic hydroxyl group of tyrosine residues. PTN has been shown to be involved in the pathogenesis of inflammatory responses, cancers, and neurodegenerative and age-related disorders. Furthermore, it has been proposed that PTN regulates signal cascades related to nitric oxide (NO·) production and NO-mediated processes. Although nitrated proteins as markers of oxidative stress are confirmed by immunological assays in various affected cells or tissues, it is not known how many different types of proteins in living cells are nitrated. Since protein nitration is a low-abundance post-translational modification, development of an effective enrichment method for nitrated proteins is needed to detect nitrated peptides or proteins from the limited amount of pathophysiological samples. In the present study, we developed an enrichment method using specific chemical tagging. Nitroproteome profiling using chemical tagging and mass spectrometry was validated by model proteins. Furthermore, we successfully identified numerous nitrated proteins from the Huh7 human hepatoma cell line

Proteomic Analysis of the Aqueous Humor in Age-related Macular Degeneration (AMD) Patients

Age-related macular degeneration (AMD) can lead to irreversible central vision loss in the elderly. Although large number of growth factor pathways, including the vascular endothelial growth factor (VEGF), has been implicated in the pathogenesis of AMD, no study has directly assessed the whole proteomic composition in the aqueous humor (AH) among AMD patients. The AH contains proteins secreted from the anterior segment tissue, and these proteins may play an important role in the pathogenesis of AMD. Thus, comparisons between the AH proteomic profiles of AMD patients and non-AMD controls may lead to the verification of novel pathogenic proteins useful as potential clinical biomarkers. In this study, we used discovery-based proteomics and Multiple Reaction Monitoring Mass Spectrometry (MRM-MS) to analyze AH from AMD patients and AH from controls who underwent cataract surgery. A total of 154 proteins with at least two unique peptides were identified in the AH. Of these 154 proteins identified by discovery-based proteomics, 10 AH proteins were novel identifications. The protein composition in the AH was different between AMD patients and non-AMD controls. Subsequently, a systematic MRM-MS assay was performed in seven highly abundant differentially expressed proteins from these groups. Differential expression of three proteins was observed in the AH of AMD patients compared with that of cataract controls (<i>p</i> < 0.0312). Elucidation of the aqueous proteome will establish a foundation for protein function analysis and identify differentially expressed markers associated with AMD. This study demonstrates that integrated proteomic technologies can yield novel biomarkers to detect exudative AMD