February 26, 2019
By Matt Binnington, Marketing & Communications Specialist
ACD/Labs is proud to support cutting-edge academic research, and every year hundreds of authors cite our software for its meaningful contributions to their novel findings. Here we’ve collected five of our favorite examples from 2018 (in chronological order), with a preference for open-access articles so that readers can investigate these intriguing applications of our software on their own. Read on!
- Reppas-Chrysovitsinos E, Sobek A, MacLeod M. (2018). In silico screening-level prioritization of 8468 chemicals produced in OECD countries to identify potential planetary boundary threats. B Environ Contam Tox, 100(1): 134-146.
Overview: Planetary boundaries represent nine environmental thresholds for various Earth system processes that denote a “safe operating space for humanity” (ex. climate change, ocean acidification, biosphere integrity, etc.). Many of these planetary boundaries may be threatened by chemical agents, which can be categorized by their shared physicochemical properties of concern. To identify potential planetary boundary threat candidates, a database containing 8,648 compounds produced within member countries of the Organisation for Economic Co-operation and Development (OECD) was screened for chemicals representing high exposure hazards.
Contribution of ACD/Labs Software: The 8,648 screening substances originated from the Screen-POP database[2,3] of compounds produced by OECD countries whose physicochemical properties resemble those of persistent organic pollutants (POPs) and persistent, bioaccumulative, and toxic (PBT) substances. Using ACD/Labs software, an initial screening exercise was conducted to eliminate records in the full Screen-POP DB (n = 12 619) that were likely to be ionized at environmentally relevant pH values (i.e. pKa < 5 or pKb > 8), which was performed by estimating pKa and pKb parameters using ACD/Percepta.
Notable Finding: “We successfully identified high scoring Screen-POP chemicals that have a high potential to be POP, very persistent and very bioaccumulative (vPvB), airborne persistent contaminant (APC), and/or waterborne persistent contaminant (WPC) candidates and we further proposed a scoring scheme that can be used to disentangle the complementary nature of these four profiles by focusing on the spatial range of their exposure potential.”
Learn more about ACD/Percepta.
- Pupier M, Nuzillard JM, Wist J, Schlörer NE, Kuhn S, Erdelyi M, et al. (2018). NMReDATA, a standard to report the NMR assignment parameters of organic compounds. Magn Reson Chem, 56: 703-715.
Overview: Despite the application of NMR to a wide variety of pursuits in small molecule characterization, no standard file format for NMR data currently exists. This manuscript introduces a standardized file format – NMReDATA (nuclear magnetic resonance extracted data) – to associate all NMR parameters extracted from 1D and 2D spectra of organic compounds (ex. chemical shifts, signal integrals, intensities, etc.) to the proposed chemical structure. This format is easily readable by both computers and humans, and provides a simple and efficient means for distributing, verifying, and cataloguing structural chemistry investigation NMR results.
Contribution of ACD/Labs Software: ACD/Labs employees Mikhail Elyashberg, Senior Expert, Molecular Spectroscopy, and Dimitris Argyropoulos, NMR Product Manager, are contributing authors to this publication, and ACD/Labs has committed to using the NMReDATA format in future product releases. In fact, manual and automatic verification processes for reported NMReDATA are already being introduced into the ACD/Spectrus analytical environment.
Notable Finding: “We believe that, in the future, all users of NMR data will have access to software packages allowing them to easily check chemical structures for consistency with all experimental data used for structure verification or elucidation. This shall significantly reduce the number of wrong structures published in chemical journals.”
Learn more about ACD/Labs’ NMR software solutions.
- Bergmann AJ, Points GL, Scott RP, Wilson G, Anderson KA. (2018). Development of quantitative screen for 1550 chemicals with GC/MS. Anal Bioanal Chem, 410: 3101-3110.
Overview: High-throughput analytical techniques are required to effectively monitor the environment for chemicals numbering in the hundreds of thousands, many without authentic standards. A cost-effective quantitative screening method is presented for 1,550 chemicals based on statistical modeling of responses paired with identification via deconvolution software. This technique shows promise as a downstream analytical approach for silicone wristband passive sampling epidemiological studies.
Contribution of ACD/Labs Software: The screening model, Many Analyte Screen Version 1500 (MASV 1500), represents an optimized multiple linear regression of GC/MS response by a variety of physicochemical properties: molecular weight, topical polar surface area, octanol-water partitioning coefficient and acid disassociation constant, among others. ACD/Percepta was used to obtain all relevant physchem parameters for the majority of the 1,550 chemicals that were catalogued in ChemSpider.
Notable Finding: “The source of input parameters can affect model results. We chose ACD/Labs as the primary source for the thoroughness of parameters available and consistency within this study. The Chemistry Dashboard from U.S. EPA is a platform for centralized chemical properties, including from ACD/Labs, and offers a parameter prediction with open quantitative structure activity relationship application (OPERA) modeling.”
Learn more about ACD/Percepta.
- Boateng BO, Fever M, Edwards D, Petersson P, Euerby MR, Sutcliffe OB. (2018). Chromatographic retention behavior, modelling, and optimization of a UHPLC-UV separation of the regioisomers of the novel psychoactive substance (NPS) methoxphenidine (MXP). J Pharm Biomed Anal, 153: 238-247.
Overview: Methoxphenidine (MXP) is an NPS that distorts perceptions, produces feelings of detachment, and induces a state of anesthesia by antagonizing ionotropic N-methyl-D-aspartate receptors in the CNS . Its three regioisomers (2-, 3-, 4-MXP) were investigated thoroughly to clarify their retention behavior and separation via LC/MS. Ultimately, a rapid and highly sensitive LC/MS friendly method (i.e. Rsmin > 5 within 4 min) was predicted and verified.
Contribution of ACD/Labs Software: LogD and pKa values for the MXP regioisomers were predicted using ACD/Percepta, while retention modelling and optimization was performed using ACD/Method Selection Suite. Using the non-linear models described in ACD/Method Selection Suite it was possible to predict MXP isomer retention with a high degree of certainty (<0.5%).
Notable Finding: “…a rapid and highly sensitive isocratic LC/MS friendly method (i.e. Rsmin > 5 within 4 min) was predicted and verified. The developed methodology should be highly suitable for the rapid, specific, and sensitive detection and control of these novel illicit drugs with bulk forensic samples.”
Learn more about ACD/Method Selection Suite.
- McEachran AD, Mansouri K, Newton SR, Beverly BEJ, Sobus JR, Williams AJ. (2018). A comparison of three liquid chromatography (LC) retention time prediction models. Talanta, 182: 371-379.
Overview: Chromatographic retention time (RT) prediction represents a valuable tool to reduce the number of unknown chemicals within an observed RT window for mixtures of environmental contaminants. This type of non-targeted analysis (NTA) was performed using three RT prediction models in order to compare their relative predictive ability and applicability.
Contribution of ACD/Labs Software: One of the three models used in the exercise was ACD/ChromGenius, which was compared to the EPI Suite logP-RT prediction model and an internally developed U.S. Environmental Protection Agency (EPA) product entitled OPERA-RT. For all calculations both ACD/ChromGenius and OPERA-RT outperformed EPI Suite logP-RT. They also performed similarly to one another across all exercises, with minor differences depending on the metric of interest.
Notable Finding: “OPERA-RT does not offer some of the benefits of the commercial tool ACD/ChromGenius, which has an intuitive user interface, an underpinning of multiple physicochemical prediction algorithms, and a knowledgebase containing training sets aggregated across multiple methods.”
Learn more about ACD/AutoChrom (the parent software package that includes ACD/ChromGenius).
References: Rockström J, Steffen W, Noone K, Persson Å, Chapin III FS, Lambin EF, et al. (2009). A safe operating space for humanity. Nature, 461 (24): 472-475.  Arnot JA, Brown TN, Wania F, Breivik K, McLachlan MS. (2012). Prioritizing chemicals and data requirements for screening-level exposure and risk assessment. Environ Health Perspect, 120: 1565-1570.  Breivik K, Arnot JA, Brown TN, McLachlan MS, Wania F. (2012). Screening organic chemicals in commerce for emissions in the context of environmental and human exposure. J Environ Monit, 14: 2028-2037.  Morris H, Wallach J. (2014). From PCP to MXE: a comprehensive review of the non-medicinal use of dissociative drugs. Drug Test Anal, 6 (7-8): 614-632.