Facilitating chemical and biochemical experiments with electronic microcontrollers and single-board computers

Prabhu, Gurpur Rakesh D.; Yang, Tung‐Han; Hsu, Chun-Yao; Shih, Chun-Pei; Chang, Chao‐Kai; Liao, Pei-Han; Ni, Hsiang-Ting; Urban, Pawel L.

doi:10.1038/s41596-019-0272-1

Cited by 34 publications

(39 citation statements)

References 53 publications

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“…The control unit of PENVOC was developed using inexpensive electronic modules (Figure S2), following the recent trend in the prototyping of instruments for chemistry research ( cf. refs − ). A graphical user interface (Figure S3) coded in the Processing software (version 3.5.4, Cambridge, MA, USA) is used to control the system.…”

Section: Methodsmentioning

confidence: 99%

Robotized Noncontact Open-Space Mapping of Volatile Organic Compounds Emanating from Solid Specimens

Bakar

Urban

2021

Anal. Chem.

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Analysis of volatile organic compounds (VOCs) is normally preceded by sample homogenization and solvent extraction. This methodology does not provide spatial resolution of the analyzed VOCs in the examined matrix. Here, we present a robotized pen-shaped probe for open-space sampling and mapping of VOCs emanating from solid specimens (dubbed “PENVOC”). The system combines vacuum-assisted suction probe, mass spectrometry, and robotic handling of the probe. The VOCs are scavenged from the sample surface by a gentle hydrodynamic flow of air sustained by a vacuum pump. The sampled gas is transferred to the proximity of corona discharge in an atmospheric pressure chemical ionization source of a tandem mass spectrometer. The PENVOC has been attached to a robotic arm to enable unattended scanning of flat surfaces. The specimens can be placed away from the mass spectrometer during the scan. The robotized PENVOC has been characterized using chemical standards (benzaldehyde, limonene, 2-nonanone, and ethyl octanoate). The limits of detection are in the range from 2.33 × 10–5 to 2.68 × 10–4 mol m–2. The platform has further been used for mapping of VOCs emanating from a variety of specimens: flowers, glove exposed to smoke, fuel stains, worn medical face mask, worn clothing, cheese, ham, and fruits. The chemical maps show unique distributions of the VOCs on the scanned surfaces. Obtaining comparable results (VOC maps) using other techniques (e.g., repetitive headspace sampling prior to offline analysis) would be time-consuming. The presented mapping technique may find applications in environmental, forensic, and food science.

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Section: Methodsmentioning

confidence: 99%

Robotized Noncontact Open-Space Mapping of Volatile Organic Compounds Emanating from Solid Specimens

Bakar

Urban

2021

Anal. Chem.

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“…Simple experimental tasks can easily be automated using microcontrollers or single board computers with only a few lines of Python or Arduino (C++) code. 92 While short linear scripts and hardcoded variables may suffice in some applications, robust and reusable software is needed to meet the reproducibility expectations of work that is to be classed as scientific research. Contrary to the expectation that digitization and automation should lead to increased reproducibility, code from many academic software projects does not execute, even just a few years after initial publication.…”

Section: Automation Of Chemistrymentioning

confidence: 99%

Chemputation and the Standardization of Chemical Informatics

Hammer

Leonov

Bell

et al. 2021

JACS Au

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The explosion in the use of machine learning for automated chemical reaction optimization is gathering pace. However, the lack of a standard architecture that connects the concept of chemical transformations universally to software and hardware provides a barrier to using the results of these optimizations and could cause the loss of relevant data and prevent reactions from being reproducible or unexpected findings verifiable or explainable. In this Perspective, we describe how the development of the field of digital chemistry or chemputation, that is the universal code-enabled control of chemical reactions using a standard language and ontology, will remove these barriers allowing users to focus on the chemistry and plug in algorithms according to the problem space to be explored or unit function to be optimized. We describe a standard hardware (the chemical processing programming architecture—the ChemPU) to encompass all chemical synthesis, an approach which unifies all chemistry automation strategies, from solid-phase peptide synthesis, to HTE flow chemistry platforms, while at the same time establishing a publication standard so that researchers can exchange chemical code (χDL) to ensure reproducibility and interoperability. Not only can a vast range of different chemistries be plugged into the hardware, but the ever-expanding developments in software and algorithms can also be accommodated. These technologies, when combined will allow chemistry, or chemputation, to follow computation—that is the running of code across many different types of capable hardware to get the same result every time with a low error rate.

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“…Lipase-catalyzed ester hydrolysis is known to induce pH changes [39] , [40] . Here, we demonstrate the use of our fluorometric probe in monitoring ester hydrolysis catalyzed by different amounts of immobilized lipase.…”

Section: Validation and Characterizationmentioning

confidence: 99%