Dibenzothiophene and Open Access

This blog focuses on desulfurization. But that focus is just a pretext for a more important effort … the effort to improve our ability to find useful technology information on the Web.

To that end, this post presents both a particular free full text article on dibenzothiophene, and tips on how to find open access articles on desulfurization in particular, and technology in general.

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"This is a very exciting time in scholarly publishing. Now that the “fight” for open access has more or less been won, we are able to move beyond open access and work to create a new ecosystem and infrastructure for scholarly publications and communications."
Dr. Caroline Sutton, Co-Founder of Co-Action Publishing and Director at Infrastructure Services for Open Access (IS4OA), on open access publishing becoming more established and her plans for expanding its reach. 
source: https://www.editage.com/insights/he-said-she-said-10-great-quotes-from-experts-in-scholarly-publishing-in-2014
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Here is a recent Open Access article …

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RSC Advances, Issue 18, 2019, Issue in Progress
Hydrodesulfurization of dibenzothiophene using Pd-promoted Co–Mo/Al2O3 and Ni–Mo/Al2O3 catalysts coupled with ionic liquids at ambient operating conditions
Yaseen Muhammad,ab   Ata Ur Rahman,b   Haroon Ur Rashid,a   Maria Sahibzada,c   Sidra Subhanab  and   Zhangfa Tong*a 
Author affiliations
*  Corresponding authors
a  School of Chemistry and Chemical Engineering, Key Laboratory of Petrochemical Resource Processing and Process Intensification Technology, Guangxi University, P. R. China
E-mail: zhftong@sina.com  
b  Institute of Chemical Sciences, University of Peshawar, Peshawar, Pakistan
c  Department of Chemistry, Umea University, Umea, Sweden
Abstract
Sulfur compounds in fuel oils are a major source of atmospheric pollution. This study is focused on the hydrodesulfurization (HDS) of dibenzothiophene (DBT) via the coupled application of 0.5 wt% Pd-loaded Co–Mo/Al2O3 and Ni–Mo/Al2O3 catalysts with ionic liquids (ILs) at ambient temperature (120 °C) and pressure (1 MPa H2). The enhanced HDS activity of the solid catalysts coupled with [BMIM]BF4, [(CH3)4N]Cl, [EMIM]AlCl4, and [(n-C8H17)(C4H9)3P]Br was credited to the synergism between hydrogenation by the former and extractive desulfurization and better H2 transport by the latter, which was confirmed by DFT simulation. The Pd-loaded catalysts ranked highest by activity i.e. Pd–Ni–Mo/Al2O3 > Pd–Co–Mo/Al2O3 > Ni–Mo/Al2O3 > Co–Mo/Al2O3. With mild experimental conditions of 1 MPa H2 pressure and 120 °C temperature and an oil : IL ratio of 10 : 3.3, DBT conversion was enhanced from 21% (by blank Ni–Mo/Al2O3) to 70% by Pd–Ni–Mo/Al2O3 coupled with [(n-C8H17)(C4H9)3P]Br. The interaction of polarizable delocalized bonds (in DBT) and van der Waals forces influenced the higher solubility in ILs and hence led to higher DBT conversion. The IL was recycled four times with minimal loss of activity. Fresh and spent catalysts were characterized by FESEM, ICP-MS, EDX, XRD, XPS and BET surface area techniques. GC-MS analysis revealed biphenyl as the major HDS product. This study presents a considerable advance to the classical HDS processes in terms of mild operating conditions, cost-effectiveness, and simplified mechanization, and hence can be envisaged as an alternative approach for fuel oil processing.
Graphical abstract: Hydrodesulfurization of dibenzothiophene using Pd-promoted Co–Mo/Al2O3 and Ni–Mo/Al2O3 catalysts coupled with ionic liquids at ambient operating conditions
1.  Introduction
Organosulfur compounds leading to the production of deleterious and hazardous sulfur oxides, i.e. SOx, from the combustion of fuel oils has led to the permissible limits of sulfur becoming much more stringent over the years.1 Among the many desulfurization approaches, such as oxidative desulfurization,2 biodesulfurization3 and extractive desulfurization,4 hydrodesulfurization (HDS) ranks higher, attributed to its diverse nature, high practicability and efficiency.5 HDS generally utilizes a Co or Ni sulfide phase added to Mo impregnated over Al2O3-supported catalysts.6–8 Furthermore, incorporation of a third promoter metal, i.e. Pt, Pd, and Ir, can further enhance the HDS activity of classical catalysts.5,9,10 Despite its efficient and versatile nature, HDS suffers from complex mechanization, poor safety and harsh temperature (380–400 °C) and pressure (8 MPa) operating conditions.11–13 Similarly, expensive catalytic promoters like Pt, Pd, and Ir further add to the uncontrolled process costs. Thus, an HDS process operated at mild temperature and pressure over a low-cost catalyst without compromising on the process efficiency could offer an alternative route for fuel oil processing.
Apart from HDS, a newer approach to fuel oil desulfurization research is extraction using ionic liquids (ILs).14,15 Aspects such as ease of synthesis, high recycling ability, low volatility, high thermal stability and environmental friendliness are credited for the widespread application of ILs.16 However, few studies on the integrated application of ILs with solid catalysts have been reported in hydrogenation reactions,17 which emphasizes that ILs coupled with solid catalysts should be tested for HDS of fuel oils.
In previous work, we reported 52% dibenzothiophene (DBT) conversion in a HDS process with a mild operating temperature and pressure by the coupled application of selected ILs with Ce–Ni–Mo/Al2O3 catalysts.18 However, to further improve the efficiency of solid catalyst-coupled ILs HDS processes, more exploration is required for new types of catalysts and ILs.
Pd has been reported as a more promising promoter for classical HDS catalysts than many of its counterparts, e.g. Ir and Ru.19,20 However, to our knowledge, no studies on the HDS of DBT coupled with ILs using Pd-promoted Co–Mo/Al2O3 and Ni–Mo/Al2O3 catalysts at mild operating conditions have been reported so far. Extractive desulfurization by ILs can augment the hydrogenation by solid catalysts in their blended application at mild operating conditions. Low Pd loading and mild operating conditions can concomitantly lead to cost-effectiveness and process safety. Thus, in this work, HDS of DBT was performed at 120 °C temperature and 1 MPa H2 pressure over low (0.5 wt%) Pd-loaded Co–Mo/Al2O3 and Ni–Mo/Al2O3 sulfide phase catalysts coupled with selected ILs. The fresh and spent catalysts were characterized by X-ray photoelectron spectroscopy (XPS), field emission scanning electron microscopy (FESEM), inductively coupled plasma mass spectrometry (ICP-MS), energy dispersive X-ray (EDX), X-ray diffraction (XRD) and BET surface area techniques. The reaction products were quantitatively and qualitatively analyzed via high-pressure liquid chromatography (HPLC) and gas chromatography coupled with mass spectrometry (GC-MS), respectively, and a suitable reaction mechanism was proposed.
Read the free full text source: https://pubs.rsc.org/en/content/articlelanding/2019/ra/c9ra00095j#!divAbstract
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TIP: Google® open access journals to find useful information on how to find and browse free full text technology literature. Browse the following to understand the philosophy and publishing mechanisms behind open access. For example …

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FROM WIKIPEDIA
Open access (OA) is a mechanism by which research outputs are distributed online, free of cost or other barriers, and, in its most precise meaning, with the addition of an open license applied to promote reuse.
Academic articles (as historically seen in print-based academic journals) have been the main focus of the movement. Conventional (non-open access) journals cover publishing costs through access tolls such as subscriptions, site licenses or pay-per-view charges. Open access can be applied to all forms of published research output, including peer-reviewed and non peer-reviewed academic journal articles, conference papers, theses, book chapters, and monographs.
Open access research does not require payment to access articles, and is instead funded through other means. The main routes to open access are:
Open access journals ('gold' open access): The publisher of the journal makes all articles and related content available for free on the journal's website.
Hybrid open access journals:[21] partially funded by subscriptions, and only provide open access for those individual articles for which the authors (or research sponsor) pay a publication fee[22]
Self-archiving ('green' open access): After peer review by a journal, the author posts the same content the journal will be publishing to a website controlled by the author, the research institution that funded or hosted the work, or which has been set up as a central open access repository.
Advantages and disadvantages of open access have generated considerable discussion amongst researchers, academics, librarians, university administrators, funding agencies, government officials, commercial publishers, editorial staff and society publishers. Reactions of existing publishers to open access journal publishing have ranged from moving with enthusiasm to a new open access business model, to experiments with providing as much free or open access as possible, to active lobbying against open access proposals. There are many publishers that started up as open access-only publishers, such as PLOS, Hindawi Publishing Corporation, Frontiers in... journals, MDPI and BioMed Central.

Visit https://en.wikipedia.org/wiki/Open_access to read the full text of this instructive article.
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Learn more about Open Access from the following …

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SPARC (the Scholarly Publishing and Academic Resources Coalition) works to enable the open sharing of research outputs and educational materials in order to democratize access to knowledge, accelerate discovery, and increase the return on our investment in research and education. As a catalyst for action, SPARC focuses on collaborating with other stakeholders—including authors, publishers, libraries, students, funders, policymakers and the public—to build on the opportunities created by the Internet, promoting changes to both infrastructure and culture needed to make open the default for research and education.
The key to SPARC’s success is the commitment of our members to support and shape our initiatives. Our 200+ members are primarily academic and research libraries located in the U.S. and Canada, who use the resources and support provided by SPARC to actively promote Open Access to scholarly articles, the open sharing of research data, and the creation and adoption of Open Educational Resources on their campuses.
Research provides the foundation of modern society. Research leads to breakthroughs, and communicating the results of research is what allows us to turn breakthroughs into better lives—to provide new treatments for disease, to implement solutions for challenges like global warming, and to build entire industries around what were once just ideas.
However, our current system for communicating research is crippled by a centuries old model that hasn’t been updated to take advantage of 21st century technology:
1. Governments provide most of the funding for research—hundreds of billions of dollars annually—and public institutions employ a large portion of all researchers.
2. Researchers publish their findings without the expectation of compensation. Unlike other authors, they hand their work over to publishers without payment, in the interest of advancing human knowledge.
3. Through the process of peer review, researchers review each other’s work for free.
4. Once published, those that contributed to the research (from taxpayers to the institutions that supported the research itself) have to pay again to access the findings. Though research is produced as a public good, it isn’t available to the public who paid for it.
Our current system for communicating research uses a print-based model in the digital age. Even though research is largely produced with public dollars by researchers who share it freely, the results are hidden behind technical, legal, and financial barriers. These artificial barriers are maintained by legacy publishers and restrict access to a small fraction of users, locking out most of the world’s population and preventing the use of new research techniques.
This fundamental mismatch between what is possible with digital technology—an open system for communicating research results in which anyone, anywhere can contribute—and our outdated publishing system has led to the call for Open Access.
Open Access is the free, immediate, online availability of research articles combined with the rights to use these articles fully in the digital environment. Open Access is the needed modern update for the communication of research that fully utilizes the Internet for what it was originally built to do—accelerate research.
Read more at: https://sparcopen.org/open-access/
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Another article you might want to peruse is …

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Why Open Access Matters
Most publishers own the rights to the articles in their journals. Anyone who wants to read the articles must pay to access them. Anyone who wants to use the articles in any way must obtain permission from the publisher and is often required to pay an additional fee.
Although many researchers can access the journals they need via their institution and think that access is free, in reality it is not. The institution has often been involved in lengthy negotiations around the price of their site license and reuse of this content is limited.
Paying for access to journals makes sense in the world of print publishing, where providing articles to each reader requires the production of physical copies of articles, but in the online world, with distribution as wide as the internet's reach, it makes much less sense.
How It Works at PLOS
PLOS applies the Creative Commons Attribution (CC BY) license to works we publish. This license was developed to facilitate Open Access—namely, free immediate access to, and unrestricted reuse of, original works of all types. Under this license, authors agree to make articles legally available for reuse, without permission or fees, for virtually any purpose. Anyone may copy, distribute or reuse these articles, as long as the author and original source are properly cited. Additionally, the journal platform that PLOS uses to publish research articles is Open Source.
source: https://www.plos.org/open-access
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OK, so if you want to browse Open Access Journals, how do you find them? Here are a couple of resources …

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DOAJ (Directory of Open Access Journals)
DOAJ is a community-curated online directory that indexes and provides access to high quality, open access, peer-reviewedjournals. DOAJ is independent. All funding is via donations, 40% of which comes from sponsors and 60% from members andpublisher members. All DOAJ services are free of charge including being indexed in DOAJ. All data is freely available.
DOAJ operates an education and outreach program across the globe, focussing on improving the quality of applications submitted.
source: https://doaj.org/
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Open Access Directory
The Open Access Directory (OAD) is a compendium of simple factual lists about open access (OA) to science and scholarship, maintained by the OA community at large. By bringing many OA-related lists together in one place, OAD makes it easier for everyone to discover them, use them for reference, and update them. The easier they are to maintain and discover, the more effectively they can spread useful, accurate information about OA. To see what we have, browse the table of contents below, browse the table of categories, or use the search box in near the upper right corner. To help the cause, just register and start editing. If you have any questions, see our help section or drop us a line.
OAD is a wiki and we count on our users to keep these lists accurate, comprehensive, and up to date. Our goal is for the OA community itself to maintain the lists with little intervention from the editors or editorial board. We welcome your contributions to the lists, ideas for new lists, and comments to help us improve. Please contact us or use the discussion tabs on individual pages. The OAD is hosted by the School of Library and Information Science at Simmons College and supervised by an independent editorial board.
source: http://oad.simmons.edu/oadwiki/Main_Page
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You Are So Transparent (And That’s a Good Thing)

From politics to Facebook, transparency is on all our minds. And science, of course, depends on transparency to advance.

A big barrier to transparency in scientific research is the cost of viewing peer reviewed articles. A simple Google® Scholar search on a topic of your choosing will result in thousands of articles, many of which you might want to read. Unfortunately, to review an article requires payment of $30 or more. Who can afford that?

The mission of open access sites like PLOS-Public Library of Science (http://journals.plos.org/) is to breach the cost barrier and promote the free flow of peer reviewed research.

Granted, the focus of PLOS seems to be on medical research. And yet, even so, an article by ExxonMobil researchers Prosset and Hedgpeth, is a part of the trove of treasures in this collection.

Viva transparency!

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Effects of bioturbation on environmental DNA migration through soil media
Christopher M. Prosser & Bryan M. Hedgpeth
PLOS  Published: April 24, 2018 • https://doi.org/10.1371/journal.pone.0196430
Contributed equally to this work with: Christopher M. Prosser, Bryan M. Hedgpeth
Roles: Conceptualization, Methodology, Writing
* E-mail: Christopher.m.prosser@exxonmobil.com
ORCID: http://orcid.org/0000-0002-5209-1878  Bryan M. Hedgpeth
Affiliation: ExxonMobil Biomedical Sciences Incorporated, Annandale, NJ, United States of America  
Abstract
Extracting and identifying genetic material from environmental media (i.e. water and soil) presents a unique opportunity for researchers to assess biotic diversity and ecosystem health with increased speed and decreased cost as compared to traditional methods (e.g. trapping). The heterogeneity of soil mineralogy, spatial and temporal variations however present unique challenges to sampling and interpreting results. Specifically, fate/transport of genetic material in the terrestrial environment represents a substantial data gap. Here we investigate to what degree, benthic fauna transport genetic material through soil. Using the red worm (Eisenia fetida), we investigate how natural movement through artificial soil affect the transport of genetic material. All experiments were run in Frabill® Habitat® II worm systems with approximately 5 cm depth of artificial soil. We selected an ªexoticº source of DNA not expected to be present in soil, zebrafish (Danio rerio) tissue. Experiment groups contained homogenized zebrafish tissue placed in a defined location combined with a varying number of worms (10, 30 or 50 worms per experimental group). Experimental groups comprised two controls and three treatment groups (representing different worm biomass) in triplicate. A total of 210 soil samples were randomly collected over the course of 15 days to investigate the degree of genetic transfer, and the rate of detection. Positive detections were identified in 14% - 38% of samples across treatment groups, with an overall detection rate of 25%. These findings highlight two important issues when utilizing environmental DNA for biologic assessments. First, benthic fauna are capable of redistributing genetic material through a soil matrix. Second, despite a defined sample container and abundance of worm biomass, as many as 86% of the samples were negative. This has substantial implications for researchers and managers who wish to interpret environmental DNA results from terrestrial systems. Studies such as these will aid in future study protocol design and sample collection methodology. Introduction Accurate biodiversity assessments are a central component to compliance with environmental regulations. In the United States, for example, environmental impact statements under the National Environmental Policy Act require extensive baseline information on biodiversity. Similarly, quantitative biodiversity assessments are important for assessing the progress of habitat reclamation efforts. However, traditional biodiversity monitoring relies on direct (ex. traps, sightings) or indirect (ex. tracks, calls) observation of organisms. Especially true for direct methods such as trapping or netting, these activities are often time consuming, expensive, and impractical in remote or hard to reach regions. Over the past decade, technological advances have resulted in the ability to detect the presence of organisms through amplification of environmental DNA (eDNA). eDNA is a generic term collectively referring to all genetic material that can be extracted from environmental media. Examples are extracellular DNA fragments, hair, feces, blood, free microbial cells, pollen or any other source by which cells and/or tissue may enter the environment [1]. Due to high precision, species-specific detection and low rates of false positives, eDNA has been increasingly utilized for an array of studies including biodiversity assessments, mapping of species distributions, and detection of invasive and endangered species [1±5]. DNA-based ecosystem monitoring can have distinct advantages over traditional sampling methods, including being less invasive/less destructive than trapping/netting. Sampling only environmental media (water, soil, sediment), reduces stress and danger of entrapment of valuable (e.g. endangered) species in nets or snares. The DNA sequencing of bulk material containing the DNA of dozens or hundreds of species would have been cost-prohibitive with older low throughput DNA sequencing platforms (e.g. Sanger sequencing). However, with next generation DNA sequencers (NGS), which use high-throughput technologies such as massively parallel sequencing, it is now possible to generate millions of DNA reads from bulk material in a short period of time [6]. Additionally, newer DNA sequencing technologies boast low detection limits (10−8 ng/μL) allowing for low levels of genetic material to be amplified and sequenced. To date, the majority of eDNA studies have focused on aquatic and/or wetland systems [3, 7±9]. This is most likely due to methodological advantages of sampling aquatic media. For example, lotic and lentic systems provide defined boundaries within which to sample and relatively large volumes of water (as large as several liters) can be filtered to concentrate available genetic material. In contrast to eDNA analysis from aquatic/marine systems, there is generally a paucity of data from terrestrial habitats. Soil matrices present unique challenges that are not encountered in aquatic systems. For example, the volume of soil used in extractions is typically a limiting factor (~0.25g soil per extraction). Additionally, little is known on eDNA fate and mobility in terrestrial systems over time and space (i.e. once deposited, there is little data to predict transport and/or persistence). A non-detect may be a false-negative if in fact the complexity of soil matrix precludes homogenous distribution of genetic material thus limiting spatial area from which it can be detected. As compared to aqueous media, the chemical complexity and reactivity of soils displays a greater degree of spatial and temporal heterogeneity, raising questions about eDNA mobility in soils. Soil mineralogy (e.g. clay, sand, silt) and subsequent mixtures (e.g. silty clays) will greatly influence the amount of surface reactive particles present, and thus the adsorption of genetic material within that matrix [10]. Physicochemical interactions influencing eDNA mobility within the soil matrix are highly variable and will depend on DNA fragment size, soil mineralogy, hydrophobicity, pH and ionic strength [11]. Persistence of eDNA in soils has also received limited attention and is incompletely understood. The presence of clay and soil colloids has been suggested to prohibit enzymatic degradation of genetic material thus potentially prolonging its availability for detection [12,13]. In anoxic environments, such as lake sediment, eDNA has been recovered dating back thousands of years [14]. Conversely, eDNA can also be taken up by bacteria as a source of nutrition expediting its removal from the environment [10]. Such uncertainties have led to wide estimates in persistence ranging from days to years in the top 15 cm of soil [15]. To date, few field studies have been conducted specifically focused on eDNA extraction from soil. However, in recent years researchers have investigated soil samples from natural wetland habitats [16] as well as in more spatially defined zoos and parks [17]. Fahner et al. [16] investigated large-scale plant monitoring using DNA metabarcoding. Researchers collected core samples from the Ramsar designated Peace-Athabasca Delta in Wood Buffalo National Park, Alberta, Canada with the goal of identifying standard DNA markers designed to evaluate floral biodiversity. An important approach in this study was the targeting of full length amplicons (400±900 base pairs), demonstrating this length is not so extensively degraded to preclude their use in biodiversity assessment. Andersen et al. [17] investigated a fundamental relationship between known species abundance and detectable levels of eDNA. Researchers isolated and amplified eDNA from known species in safari parks, zoological gardens, and farms and found that detectable eDNA generally reflected the diversity of animals on the landscape. However, these researchers reported patchy detection (as low as 31%) from soil surface. Researchers also reported eDNA extraction efficiency was inversely proportional to organic carbon content of the soil. The vast majority of studies to date have focused on the presence/absence of DNA in the environment; however, such studies do little to investigate eDNA fate and transport. While there are some exceptions in aquatic systems (i.e. [8]), there is a noticeable data gap investigating such effects in terrestrial systems. While the deposition of genetic material through normal processes (e.g. hair loss) is generally accepted, the degree to which physical (e.g. wind/rain) and biological (bioturbation) processes disseminate genetic material through terrestrial media are not well understood. As eDNA continues to grow as a tool for use in ecological assessments, a fundamental understanding of detection rate, and the risk of false negatives in terrestrial media will bolster data interpretation. Given the paucity of data related to eDNA fate and transport within terrestrial environments, the scope of this study focused on whether bioturbation will transport eDNA through soil. Our study was designed to investigate if normal biotic activity (e.g. the natural movement of worms through soil) would transport detectable levels of genetic material from a single, well defined depositional source, to adjacent areas. The redworm (Eisenia fetida) was used in controlled laboratory experiments to examine if, and to what degree bioturbation moves DNA from a single deposition source through soil. 
source: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0196430
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Here are some excerpts from the PLOS Web site …

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Founded in 2001 as an alternative to the growing constraints of traditional scientific publishing, the Public Library of Science (PLOS) rapidly evolved into a driving force in the Open Access movement.
source: https://www.plos.org/history
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Your Research, Our Resources
QUALITY  Scientists that peer review and serve on editorial boards for PLOS are experts committed to reporting, ethics and publishing guidelines. This means every article published with PLOS is the most robust it can be.
SPEED  From submission to acceptance, PLOS publishing processes are tightly focused to eliminate unnecessary publication delays.
INFLUENCE  Policymakers, educators, journalists and organizations around the world turn to trustworthy research published in PLOS journals. In 2017, nearly 4,000 research articles were covered by news sources such as the BBC, NPR, The New York Times and The Guardian. That's a 15% increase from our 2016 coverage.
OPEN ACCESS FOR MAXIMUM IMPACT  PLOS research attracts more than 15 million article views per month. Articles are immediately and freely available under a Creative Commons Attribution License (CC BY).
ARTICLE-LEVEL METRICS (ALMS)  PubMed, Scopus, Web of Science and Google Scholar feature PLOS articles. At PLOS, all these sources feed into ALMs to help demonstrate the influence of your work.
DATA AVAILABLITY  Authors commit to making the data underlying their conclusions fully available, when at all possible. This enables validation, replication and reproducibility—all increasing the value of research. source: source: https://www.plos.org/why-publish-with-plos 
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TIP: Search the PLOS Web (http://journals.plos.org/plosone/) using whatever term you are interested in … like, for example, desulfurization. Then read to your heart’s content.