Benzothienoquinolines: new one-pot synthesis and fluorescence studies of their interaction with DNA and polynucleotides

Revised version. "Available online 10 August 2014"In this work, we were able to obtain the benzothieno[3,2-b]quinoline 1 and benzothieno[2,3-c]quinoline 2 using a new one-pot procedure from the reaction of the commercially available 3-bromobenzo[b]thiophene-2-carbaldehyde with 2-aminophenylpinacolborane under Suzuki coupling conditions using a stereochemically hindered ligand, 2-(cyclohexylphosphane)biphenyl and Ba(OH)2.8H2O as the base. Fluorescence properties of the benzothieno[3,2-b]quinoline 1 and the benzothieno[2,3-c]quinoline 2 were studied in solvents of different polarity. Both compounds exhibit a solvent sensitive emission, compound 1 being less fluorescent (quantum yield < 0.05) than compound 2 (quantum yield between 0.04 and 0.10). The interaction of these compounds with salmon sperm DNA and synthetic double-stranded heteropolynucleotides, poly(dA–dT)•(dA–dT) and poly(dG–dC)•(dG–dC), was studied using spectroscopic methods, allowing the determination of the intrinsic binding constants and binding site sizes. The interaction of both compounds is stronger with adenine-thymine (A-T) base pairs. Compound 1 is the most intercalative in salmon sperm DNA (47%) and polynucleotides (46%-49% of intercalated molecules), while for compound 2, 41% is intercalated in salmon sperm DNA and only 8% in poly(dG–dC)•(dG–dC). Docking studies indicate that compound 1 interacts more strongly with DNA than compound 2, with a significant value of binding free energy in the case of intercalation. Minor groove binding is also very favorable and, probably, both mechanisms occur with a preponderance of intercalation in the case of compound 1. Overall, these results indicate that both benzothienoquinolines interact with nucleic acids by both intercalation and groove binding.Foundation for the Science and Technology (FCT, Portugal), for financial support to the Portuguese NMR network (PTNMR) and also to FEDER and QREN for financial support to the Research Centres, CFUM [Strategic Project PEst-C/FIS/UI0607/2013 (FCOMP-01-0124-FEDER-037291)] and CQ/UM [Strategic Project PEst-C/QUI/UI0686/2013 (FCOMP-01-0124-FEDER-037302)], and to the research project PTDC/QUI-QUI/111060/2009 (F-COMP-01-0124-FEDER-015603) also financed by COMPETE/QREN/EU. FCT, POPH-QREN and FSE are acknowledged for the PhD grants of A.R.O.R. (SFRH/BD/90949/2012) and M.S.D.C. (SFRH/BD/47052/2008), for the Post-Doc. Grant of R.C.C. (SFRH/BPD/68344/2010) and for support to MAP-Fis Doctoral Program

Modeling asphaltene precipitation in Algerian oilfields with the CPA EoS

One of the major flow assurance problems afflicting the oil industry is the asphaltene precipitation during the production, transportation and storage of oil. The precipitation of these heavy compounds is responsible for changes in crude oil properties, increases in oil viscosity, and formation of deposits that reduce oil production and disable equipment leading to significant operational costs. In Algeria, the deposition of asphaltene in res- ervoirs and pipelines is a severe problem. During production the depressurization of reservoir fluid and the variations of thermodynamic conditions create the need to frequently pig the lines and, in some cases, to inject solvents and dispersants to maintain the production. The understanding of the asphaltene behavior and the prediction of its deposition in flow conditions is crucial to implement appropriate strategies for the prevention or remediation, especially in the wellbore region. In this work we used the CPA EoS to describe the asphaltene phase envelope and predict the PT regions of stability for five Algerian live oils. The model provides a very good description of the experimental behavior of live oils without and with gas injection. The sensitivity to SARA analysis data and its effect on the asphaltene phase boundaries were also analyzed.BC Advanced Technologies Limited, Sonatrachpublishe

Quantum Link Prediction in Complex Networks

Predicting new links in physical, biological, social, or technological networks has a significant scientific and societal impact. Path-based link prediction methods utilize explicit counting of even and odd-length paths between nodes to quantify a score function and infer new or unobserved links. Here, we propose a quantum algorithm for path-based link prediction, QLP, using a controlled continuous-time quantum walk to encode even and odd path-based prediction scores. Through classical simulations on a few real networks, we confirm that the quantum walk scoring function performs similarly to other path-based link predictors. In a brief complexity analysis we identify the potential of our approach in uncovering a quantum speedup for path-based link prediction.Comment: Keywords: Complex Networks, Quantum Algorithms, Link Prediction, Social Networks, Protein-Protein Interaction Network

Using coarse-grained molecular dynamics to understand the effect of ionic liquids on the aggregation of Pluronic copolymer solutions

This study is aimed to enhance the understanding of the interaction between ionic liquids (ILs) and non-ionic Pluronic triblock copolymers in aqueous two-phase micellar systems (ATPMS) used for the selective separation/purification of hydrophobic biomolecules. The ILs allow a precise control of the cloud point phase separation temperature (CPT), particularly important when the stability of the molecule is highly dependent on temperature. The effect of choline-based ILs, with two different counter-anions, chloride and hexanoate, was evaluated using molecular dynamics simulations (MD) for F-68 and L-35 Pluronic aqueous solutions. The simulations revealed the role played by the anions during the Pluronic self-assembly, with choline chloride hindering Pluronic aggregation and the choline hexanoate favouring micelle formation and coalescence, in agreement with the experimental data. A detailed study of the accessible surface area of Pluronic showed a progressive dehydration of the Pluronic hydrophilic micelle corona in choline hexanoate mixtures promoting inter-micelle interactions and, consequently, micelle coalescence. With the addition of choline hexanoate, it was observed that the hydrophilic segments, which form the micelle corona, twisted towards the Pluronic micelle core. The electrostatic interaction is also shown to play a key role in this IL–Pluronic aqueous solution, as the hexanoate anions are accommodated in the Pluronic micelle core, while the choline cations are hosted by the Pluronic micelle corona, with the ions interacting with each other during the self-assembly process. In addition, a comparison study of F-68 and L-35 aqueous solutions shows that the IL impact depends on the length of the Pluronic hydrophilic segment. This work provides a realistic microscopic scenario of the complex interactions between Pluronic copolymers and ILs.This work was developed within the scope of the project CICECO-Aveiro Institute of Materials, UIDB/50011/2020 & UIDP/50011/2020, financed by national funds through the FCT/MEC and when appropriate co-financed by FEDER under the PT2020 Partnership Agreement. The authors acknowledge the research contract under the project CENTRO-01-0145- FEDER-000005: SusPhotoSolutions: Soluções Fotovoltaicas Sustentáveis. G. Pérez-Sánchez and N. Schaeffer acknowledge the national funds (OE), through FCT – Fundação para a Ciência e a Tecnologia, I. P., in the scope of the framework contract foreseen in the numbers 4, 5 and 6 of the article 23, of the Decree-Law 57/2016, of August 29th, changed by Law 57/2017, of July 19th. A. M. Lopes acknowledges the support from the State of São Paulo Research Foundation (FAPESP/Brazil, processes #2017/10789-1 and #2018/10799-0). J. F. B. Pereira also acknowledges FAPESP through the project 2014/16424-7.publishe

Novel insights into biomass delignification with acidic deep eutectic solvents: a mechanistic study of β-O-4 ether bond cleavage and the role of the halide counterion in the catalytic performance

The development of innovative technologies for an efficient, yet eco-friendly, biomass delignification is required to achieve higher sustainability than traditional processes. In this context, the use of deep eutectic solvents (DES) for the delignification process could fulfil these requirements and stands today as a promising alternative. This work focus on understanding the fundamental chemistry behind the cleavage of B-O-4 ether bond present in 2-phenoxy-1-phenylethanol (PPE), a lignin model compound, with three acidic DES, including Propionic acid/Urea (PA:U), Lactic acid/Choline Chloride (LA:ChCl) and p-Toluenesulphonic acid/Choline chloride (pTSA:ChCl). The acidic nature of each DES influenced the efficiency of PPE cleavage and determined the extent of further side reactions of cleavage products. Although PA:U (2:1) demonstrated ability to dissolve lignin, it is unable to cleave B-O-4 ether linkage in PPE. On the other hand, LA:ChCl (10:1) allowed PPE cleavage, but an esterification between the PPE and lactic acid as well as oligomerization of lactic acid were detected. Among examined solvents, pTSA:ChCl (1:1) demonstrated the highest performance on the PPE cleavage, although the high acidity of this system lead to condensation of cleavage products at prolonged time. The presence of water decreases the ability of DES for the cleavage, but the extension of undesired side reactions was also reduced. Finally, the analysis of intermediates and products of the reactions allowed the identification of a chlorinated species of PPE that precedes the cleavage reaction. A kinetic study using pTSA:ChCl (1:1) and pTSA:ChBr (1:1) was performed to unveil the role of the halide counterion present in DES on the cleavage of <2=2 ether bond and a new reaction mechanism was herein proposed and supported by density functional theory (DFT) calculations.Altri ñ Celbi, Buckman, Crown Van Gelder, CTP, DS Smith Paper, ESKA, Essity, Holmen, ISPT, Mayr-Melnhof Eerbeek, Mets‰ Fibre, Mid Sweden University, Mondi, Omya, The Navigator Company, Sappi, Essity, Smurfit Kappa, Stora Enso, Eindhoven University of Technology, University of Aveiro, University of Twente, UPM, Valmet Technologies Oy, Voith Paper, VTT Technical Research Centre of Finland Ltd, WEPA and Zellstoff Pols.in publicatio

Repurposing kraft black liquor as reductant for enhanced lithium-ion battery leaching

The economic advantages of H2SO4 make it the acid of choice for the hydrometallurgical treatment of waste lithium-ion batteries (LIBs). However, to facilitate the full dissolution of the higher valency metal oxides present in the cathode black mass, a suitable reducing agent is required. Herein, the application of industrial black liquor (BL) obtained from the Kraft pulping for papermaking is investigated as a renewable reducing agent for the enhanced leaching of transition metals from LIB powder with H2SO4. The addition of acidified BL to H2SO4 significantly improved the leaching efficiency for a range of LIB cathode chemistries, with the strongest effect observed for manganese-rich active material. Focusing on NMC111 (LiMnxCoyNizO2) material, a linear correlation between the BL concentration and the leaching yield of Mn was obtained, with the best overall leaching efficiencies being achieved for 2.0 mol L-1 H2SO4 and 50 vol % of BL at 353 K. A quasi-total degradation of oxygenated and aromatic groups from the BL during NMC111 dissolution was observed after leaching, suggesting that these chemical groups are essential for LIB reduction. Finally, the leached transition metals could be easily recovered by pH adjustment and oxalic acid addition, closing the resource loop and fostering resource efficiency.This work was developed within the scope of the project CICECOAveiro Institute of Materials, UIDB/50011/2020, UIDP/50011/2020 & LA/P/0006/2020, financed by national funds through the FCT/MEC (PIDDAC). This work was further supported by national funds through FCT/MCTES (PIDDAC): LSRE-LCM, UIDB/50020/2020 (DOI: 10.54499/UIDB/50020/2020) and UIDP/50020/2020 (DOI: 10.54499/ UIDP/50020/2020); and ALiCE, LA/P/0045/2020 (DOI: 10.54499/LA/ P/0045/2020). Ana R.F. Carreira acknowledges FCT for the Ph.D. grant SFRH/BD/143612/2019. Nicolas Schaeffer acknowledges the national funds (OE), through FCT-Fundação para a Ciência e a Tecnologia, in the scope of the framework contract foreseen in the numbers 4, 5, and 6 of the article 23, of the Decree-Law 57/2016, of August 29th, changed by Law57/2017, of July 19th. André M. da Costa Lopes acknowledges his research contract funded by the Fundação para a Ciência e Tecnologia (FCT) and project CENTRO04-3559-FSE-000095-Centro Portugal Regional Operational Programme (Centro2020), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (ERDF).publishe

Kraft lignin solubility and its chemical modification in deep eutectic solvents

Lignin stands as a promising raw material to produce commodities and specialty chemicals, yet its poor solubility remains a big challenge. Recently, deep eutectic solvents (DES) have been proposed as sustainable solvents with high potential to dissolve and valorize lignin. In the present study, the ability of DES based on cholinium chloride ([Ch]Cl) combined with alcohols and carboxylic acids as hydrogen bond donors (HBDs) to dissolve kraft lignin and to change its chemical structure was examined. The influence of the chemical nature of HBDs, water content, and HBD:hydrogen bond acceptor (HBA) molar ratio on the solubility of kraft lignin in DES was studied (313.15 K). The kraft lignin solubility was enhanced by increasing both the HBD’s carbon chain length and the molar ratio, with [Ch]Cl:HEXA (1,6-hexanediol) and [Ch]Cl:MaleA (maleic acid) being the best studied solvents for kraft lignin dissolution, while the addition of water was a negative factor. The thermal treatments (393.15 K) of kraft lignin show that carboxylic acid-based DES promote chemical modifications to kraft lignin, including the disruption of several C–O covalent type bonds (e.g., β-O-4, α-O-4 and α-O-α), while alcohol-based DES were found to be nonderivatizing solvents maintaining the lignin chemical structure. These results show the versatility of DES, which, depending on their chemical nature, may offer distinct strategies for lignin valorization.publishe

Fast and efficient method to evaluate the potential of eutectic solvents to dissolve lignocellulosic components

The application of eutectic solvents (ESs) in lignocellulosic biomass fractionation has been demonstrated as a promising approach to accomplish efficient and environmentally friendly biomass valorization. In general, ESs are a combination of two components, a hydrogen-bonding donor and a hydrogen-bonding acceptor, in which the melting point of the mixture is lower than that of the individual components. However, there are plenty of possible combinations to form ESs with the potential to apply in biomass processing. Therefore, the development of fast and effective screening methods to find combinations capable to dissolve the main biomass components—namely cellulose, hemicelluloses, and lignin—is highly required. An accurate and simple technique based on optical microscopy with or without polarized lenses was used in this study to quickly screen and monitor the dissolution of cellulose, xylose (a monomer of hemicelluloses), and lignin in several ESs. The dissolution of these solutes were investigated in different choline-chloride-based ESs (ChCl:UREA, ChCl:PROP, ChCl:EtGLY, ChCl:OXA, ChCl:GLY, ChCl:LAC). Small amounts of solute and solvent with temperature control were applied and the dissolution process was monitored in real time. The results obtained in this study showed that cellulose was insoluble in these ESs, while lignin and xylose were progressively dissolved.publishe

Use of ionic liquids and deep eutectic solvents in polysaccharides dissolution and extraction processes towards sustainable biomass valorization

A shift to a bioeconomy development model has been evolving, conducting the scientific community to investigate new ways of producing chemicals, materials and fuels from renewable resources, i.e., biomass. Specifically, technologies that provide high performance and maximal use of biomass feedstocks into commodities with reduced environmental impact have been highly pursued. A key example comprises the extraction and/or dissolution of polysaccharides, one of the most abundant fractions of biomass, which still need to be improved regarding these processes' efficiency and selectivity parameters. In this context, the use of alternative solvents and the application of less energy-intensive processes in the extraction of polysaccharides might play an important role to reach higher efficiency and sustainability in biomass valorization. This review debates the latest achievements in sustainable processes for the extraction of polysaccharides from a myriad of biomass resources, including lignocellulosic materials and food residues. Particularly, the ability of ionic liquids (ILs) and deep eutectic solvents (DESs) to dissolve and extract the most abundant polysaccharides from natural sources, namely cellulose, chitin, starch, hemicelluloses and pectins, is scrutinized and the efficiencies between solvents are compared. The interaction mechanisms between solvent and polysaccharide are described, paving the way for the design of selective extraction processes. A detailed discussion of the work developed for each polysaccharide as well as the innovation degree and the development stage of dissolution and extraction technologies is presented. Their advantages and disadvantages are also identified, and possible synergies by integrating microwave- and ultrasound-assisted extraction (MAE and UAE) or a combination of both (UMAE) are briefly described. Overall, this review provides key information towards the design of more efficient, selective and sustainable extraction and dissolution processes of polysaccharides from biomass.publishe