Making the collective knowledge of chemistry open and machine actionable

Jablonka, K.M., Patiny, L. & Smit, B. (2022). “Making the collective knowledge of chemistry open and machine actionable.” Nature Chemistry 14, 365–376.

Abstract: Large amounts of data are generated in chemistry labs—nearly all instruments record data in a digital form, yet a considerable proportion is also captured non-digitally and reported in ways non-accessible to both humans and their computational agents. Chemical research is still largely centred around paper-based lab notebooks, and the publication of data is often more an afterthought than an integral part of the process. Here we argue that a modular open-science platform for chemistry would be beneficial not only for data-mining studies but also, well beyond that, for the entire chemistry community. Much progress has been made over the past few years in developing technologies such as electronic lab notebooks that aim to address data-management concerns. This will help make chemical data reusable, however it is only one step. We highlight the importance of centring open-science initiatives around open, machine-actionable data and emphasize that most of the required technologies already exist—we only need to connect, polish and embrace them.

Webinar: Forensic Techniques for Differentiating PFAS Sources

Dec 9, 2021, 11 am CST
Register here.

Join SERDP and ESTCP for a webinar featuring DoD-funded research efforts to develop methods for differentiating between the sources of per- and polyfluoroalkyl substances (PFAS) detected in impacted water. Specifically, investigators will discuss two approaches for differentiating between aqueous film-forming foam (AFFF) and non-AFFF sources.

Dr. Christopher Higgins (Colorado School of Mines) will discuss an approach that uses liquid chromatography with tandem mass spectrometry (LC-MS/MS) to measure specific PFAS compounds and a database of sources with PFAS chemical signatures. Then, Dr. David Sedlak (University of California, Berkeley) will present on using the total oxidizable precursor (TOP) analysis to measure PFAS and using advanced statistical tools to inform PFAS source forensics.

Draft Method 1633: Analysis of Per- and Polyfluoroalkyl Substances (PFAS) in Aqueous, Solid, Biosolids, and Tissue Samples by LC-MS/MS

Download the document.

Method 1633 is for use in the Clean Water Act (CWA) for the determination of the per- and
polyfluoroalkyl substances (PFAS) in Table 1 in aqueous, solid (soil, biosolids, sediment) and tissue
samples by liquid chromatography/mass spectrometry (LC-MS/MS).

Microplastics quantified with crime scene adhesive tape

Read the full story at The Engineer.

Adhesive tape designed to recover trace evidence from crimes scenes is being adopted to analyse microplastics, an effort that could prove more efficient than removal by filtration.

Webinar: PFAS Technical Support and Scientific Advancements

Aug 18, 2021 2-3 pm CDT
Register here.

The versatility of the family of perfluoroalkyl and polyfluoroalkyl substances (PFAS) for use in many
industrial and manufacturing applications as well as consumer products has led to thousands of PFAS
compounds being used for decades. These substances are highly persistent, difficult to break down, and bioaccumulate in living organisms over time. There are significant scientific challenges to understanding their distribution in the environment. Foremost is the lack of accredited laboratory methods to measure the presence for all but a relatively few of the PFAS that are in use.

Research chemists in EPA’s Office of Research and Development (ORD) have pioneered non-targeted
analytical methods (NTA) to identify the presence of a much larger number of PFAS compounds in environmental samples beyond the 30 or so that can be currently quantitated.

This webinar shares examples of EPA ORD projects conducted in collaboration with and designed by States and Tribes to use ORD’s expertise to identify and improve the understanding of what PFAS are present within various media in local areas of concern. Projects range from environmental sampling around manufacturing facilities to evaluation of the effectiveness of well and wastewater treatment.

CWA Analytical Methods for Per- and Polyfluorinated Alkyl Substances (PFAS)

In collaboration with the U.S. Department of Defense, EPA is developing analytical methods to test for PFAS in wastewater as well as surface water, groundwater, leachate, soil, sediment, biosolids, and fish tissue. Forty PFAS are currently the subject of analytical method development.

Method development includes single- and multi-laboratory testing. Following single-laboratory validation, which demonstrates proof of concept, a multi-laboratory validation will be conducted to further determine method viability. EPA anticipates that multi-laboratory validation for this method will be finalized in 2021.

Nontargeted mass-spectral detection of chloroperfluoropolyether carboxylates in New Jersey soils

Washington, JW, et al (2020). “Nontargeted mass-spectral detection of chloroperfluoropolyether carboxylates in New Jersey soils.” Science 368(6495), 1103-1107.

Perfluorocarbons’ path into soils

Covering carbon chains with fluorines has produced a variety of useful nonstick coatings. However, growing concern about the toxicity and extraordinary environmental persistence of the underlying compounds is spurring a search for alternatives. The precise structure of these next-generation alternatives often remains a trade secret. Washington et al. sampled soils in New Jersey and then used mass spectrometry to assign plausible structures—incorporating chlorine and ether segments into the CF2 chain—to compounds that appear to have emanated from their manufacture (see the Policy Forum by Gold and Wagner). The data can inform in-depth studies of these compounds’ environmental transport and persistence.

Abstract: The toxicity and environmental persistence of anthropogenic per- and poly-fluoroalkyl substances (PFAS) are of global concern. To address legacy PFAS concerns in the United States, industry developed numerous replacement PFAS that commonly are treated as confidential information. To investigate the distribution of PFAS in New Jersey, soils collected from across the state were subjected to nontargeted mass-spectral analyses. Ten chloroperfluoropolyether carboxylates were tentatively identified, with at least three congeners in all samples. Nine congeners are ≥(CF2)7. Distinct chemical formulas and structures, as well as geographic distribution, suggest airborne transport from an industrial source. Lighter congeners dispersed more widely than heavier congeners, with the most widely dispersed detected in an in-stock New Hampshire sample. Additional data were used to develop a legacy-PFAS fingerprint for historical PFAS sources in New Jersey.

Confronting Racism in Chemistry Journals

Read the editorial in ACS Sustainable Chemistry & Engineering.

We confront the terrible reality that systemic racism and discrimination impacts the daily personal and professional lives of many members of the scientific community and broader society. In the U.S., the brutal killing of George Floyd while in police custody is one of the most recent examples of the centuries of systemic violence suffered by Black Americans. This moment and its aftermath lay bare the legacies of racism and its exclusionary practices.

Let us be clear: we, the Editors, Staff, and Governance Members of ACS Publications condemn the tragic deaths of Black people and stand in solidarity with Black members of the science and engineering community. Moreover, ACS condemns racism, discrimination, and harassment in all forms. We will not tolerate practices and viewpoints that exclude or demean any member of our community. Despite these good intentions, we recognize that our community has not done enough to provide an environment for Black chemists to thrive.

A Critical Review of Extraction and Identification Methods of Microplastics in Wastewater and Drinking Water

Dounia Elkhatib and Vinka Oyanedel-Craver (2020). “A Critical Review of Extraction and Identification Methods of Microplastics in Wastewater and Drinking Water.” Environmental Science & Technology, online ahead of print.

Abstract: This critical review analyzes methodologies used to collect, quantify, and characterize microplastics in both wastewater and drinking water. Researchers used different techniques at all stages, from collection to characterization, for quantifying microplastics in urban water systems. This represents a barrier to comprehensively assess the current loads of microplastic and to compare the results obtained by such assessments. The compiled studies address microplastic contamination using four types of sample collection techniques, four methods for processing samples, and four techniques for characterizing microplastics. This results in significant discrepancies in each of the following: (1) reported concentrations in both wastewater effluents and drinking water, (2) microplastic characteristics (i.e., size, color, shape, and composition), and (3) quality control and assurance procedures. Finally, this review qualitatively evaluated the reports by the completeness of their data based on a ranking system using five criteria: sample collection, sample processing, quality control, identification technique, and results. The results of this ranking system clarify disparities between the studies.

Webinar: Submicron non-contact IR spectroscopy and simultaneous Raman in life sciences, microplastics, polymers, contaminant ID and more

May 20, 2020, 10 am CDT
Register here.

This webinar will introduce the new breakthrough technique, Optical Photothermal IR (O-PTIR) Spectroscopy, describe how it solves major limitations with IR Spectroscopy and how it can be coupled with Raman spectroscopy. O-PTIR spectroscopy is an optical IR spectroscopy technique which provides:

  • submicron resolution
  • high quality absorption spectra in non-contact reflection mode without scatter/dispersion artifacts
  • water compatible IR measurements

O-PTIR and IR+Raman applications will be discussed in a broad range of fields such as life sciences, particulates/microplastics, polymers and failure/defect analysis.

Since O-PTIR uses a visible probe to detect IR absorption, it offers the breakthrough ability to obtain simultaneous Raman spectroscopy from the same sample spot, at the same time and with the same spatial resolution. This can provide complementary and confirmatory analysis in a variety of applications. Learn how now, for the first-time live cells can be measured in water, with submicron IR spatial resolution, with IR+Raman spectral information, allowing for cellular metabolism and drug uptake studies for example.

Professor Ji-Xin Cheng of Boston University is the co-inventor of O-PTIR. He is one of the world’s leading vibrational spectroscopy researchers, having previously co-invented CARS, while doing his post-doctoral work with Prof Sunny Xie of Harvard. Prof Cheng has recently received several prestigious awards for his research including the Lippincott Award and the Pittcon Spectroscopy Award.