1
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DeYong AE, Trinidad JC, Pohl NLB. An identification method to distinguish monomeric sugar isomers on glycopeptides. Analyst 2023; 148:4438-4446. [PMID: 37555458 DOI: 10.1039/d3an01036h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/10/2023]
Abstract
A one-step protocol for the automated flow synthesis of protected glycosylated amino acids is described using pumps with open-source controls in overall yields of 21-50%. The resulting glycosylated amino acids could be used directly in solid-phase peptide synthesis (SPPS) protocols to quickly produce glycopeptide standards. Access to a variety of stereoisomers of the sugar enabled the development of an LC-MS/MS protocol that can distinguish between peptides modified with carbohydrates having the same exact mass. This method could definitively identify fucose in an O-glycosylation site on the transmembrane protein, Notch1.
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Affiliation(s)
- Ashley E DeYong
- Chemistry, Indiana University, 212 S Hawthorne Dr., Bloomington, IN 47405, USA.
| | - Jonathan C Trinidad
- Chemistry, Indiana University, 212 S Hawthorne Dr., Bloomington, IN 47405, USA.
| | - Nicola L B Pohl
- Chemistry, Indiana University, 212 S Hawthorne Dr., Bloomington, IN 47405, USA.
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2
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Bai J, Cao L, Mosbach S, Akroyd J, Lapkin AA, Kraft M. From Platform to Knowledge Graph: Evolution of Laboratory Automation. JACS AU 2022; 2:292-309. [PMID: 35252980 PMCID: PMC8889618 DOI: 10.1021/jacsau.1c00438] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Indexed: 05/19/2023]
Abstract
High-fidelity computer-aided experimentation is becoming more accessible with the development of computing power and artificial intelligence tools. The advancement of experimental hardware also empowers researchers to reach a level of accuracy that was not possible in the past. Marching toward the next generation of self-driving laboratories, the orchestration of both resources lies at the focal point of autonomous discovery in chemical science. To achieve such a goal, algorithmically accessible data representations and standardized communication protocols are indispensable. In this perspective, we recategorize the recently introduced approach based on Materials Acceleration Platforms into five functional components and discuss recent case studies that focus on the data representation and exchange scheme between different components. Emerging technologies for interoperable data representation and multi-agent systems are also discussed with their recent applications in chemical automation. We hypothesize that knowledge graph technology, orchestrating semantic web technologies and multi-agent systems, will be the driving force to bring data to knowledge, evolving our way of automating the laboratory.
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Affiliation(s)
- Jiaru Bai
- Department
of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, United Kingdom
| | - Liwei Cao
- Department
of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, United Kingdom
| | - Sebastian Mosbach
- Department
of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, United Kingdom
- Cambridge
Centre for Advanced Research and Education in Singapore (CARES), CREATE Tower #05-05, 1 Create Way, 138602 Singapore
| | - Jethro Akroyd
- Department
of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, United Kingdom
- Cambridge
Centre for Advanced Research and Education in Singapore (CARES), CREATE Tower #05-05, 1 Create Way, 138602 Singapore
| | - Alexei A. Lapkin
- Department
of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, United Kingdom
- Cambridge
Centre for Advanced Research and Education in Singapore (CARES), CREATE Tower #05-05, 1 Create Way, 138602 Singapore
| | - Markus Kraft
- Department
of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, United Kingdom
- Cambridge
Centre for Advanced Research and Education in Singapore (CARES), CREATE Tower #05-05, 1 Create Way, 138602 Singapore
- School
of Chemical and Biomedical Engineering, Nanyang Technological University, 62 Nanyang Drive, 637459 Singapore
- The
Alan Turing Institute, London NW1 2DB, United Kingdom
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3
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Yalamanchili S, Nguyen T, Zsikla A, Stamper G, DeYong AE, Florek J, Vasquez O, Pohl NLB, Bennett CS. Automated, Multistep Continuous‐Flow Synthesis of 2,6‐Dideoxy and 3‐Amino‐2,3,6‐trideoxy Monosaccharide Building Blocks. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202109887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
| | - Tu‐Anh Nguyen
- Chemistry Tufts University 62 Talbot Ave Medford MA 02145 USA
| | | | - Gavin Stamper
- Chemistry Indiana University 800 E Kirkwood Ave Bloomington IN 47405 USA
| | - Ashley E. DeYong
- Chemistry Indiana University 800 E Kirkwood Ave Bloomington IN 47405 USA
| | - John Florek
- Chemistry Tufts University 62 Talbot Ave Medford MA 02145 USA
| | - Olivea Vasquez
- Chemistry Tufts University 62 Talbot Ave Medford MA 02145 USA
| | - Nicola L. B. Pohl
- Chemistry Indiana University 800 E Kirkwood Ave Bloomington IN 47405 USA
| | - Clay S. Bennett
- Chemistry Tufts University 62 Talbot Ave Medford MA 02145 USA
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4
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Yalamanchili S, Nguyen TA, Zsikla A, Stamper G, DeYong AE, Florek J, Vasquez O, Pohl NLB, Bennett CS. Automated, Multistep Continuous-Flow Synthesis of 2,6-Dideoxy and 3-Amino-2,3,6-trideoxy Monosaccharide Building Blocks. Angew Chem Int Ed Engl 2021; 60:23171-23175. [PMID: 34463017 PMCID: PMC8511145 DOI: 10.1002/anie.202109887] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Indexed: 12/31/2022]
Abstract
An automated continuous flow system capable of producing protected deoxy-sugar donors from commercial material is described. Four 2,6-dideoxy and two 3-amino-2,3,6-trideoxy sugars with orthogonal protecting groups were synthesized in 11-32 % overall yields in 74-131.5 minutes of total reaction time. Several of the reactions were able to be concatenated into a continuous process, avoiding the need for chromatographic purification of intermediates. The modular nature of the experimental setup allowed for reaction streams to be split into different lines for the parallel synthesis of multiple donors. Further, the continuous flow processes were fully automated and described through the design of an open-source Python-controlled automation platform.
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Affiliation(s)
| | - Tu-Anh Nguyen
- Chemistry, Tufts University, 62 Talbot Ave, Medford, MA 02145
| | | | - Gavin Stamper
- Chemistry, Indiana University, 800 E Kirkwood Ave, Bloomington, IN, 47405
| | - Ashley E. DeYong
- Chemistry, Indiana University, 800 E Kirkwood Ave, Bloomington, IN, 47405
| | - John Florek
- Chemistry, Tufts University, 62 Talbot Ave, Medford, MA 02145
| | - Olivea Vasquez
- Chemistry, Tufts University, 62 Talbot Ave, Medford, MA 02145
| | - Nicola L. B. Pohl
- Chemistry, Indiana University, 800 E Kirkwood Ave, Bloomington, IN, 47405
| | - Clay S. Bennett
- Chemistry, Tufts University, 62 Talbot Ave, Medford, MA 02145
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5
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Hsu CY, Prabhu GRD, Urban PL. Telechemistry 2.0: Remote monitoring of fluorescent chemical reactions. HARDWAREX 2021; 10:e00244. [PMID: 35607687 PMCID: PMC9123467 DOI: 10.1016/j.ohx.2021.e00244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 09/16/2021] [Accepted: 10/25/2021] [Indexed: 06/15/2023]
Abstract
Implementation of the Internet-of-Things in chemistry research has the potential to improve research methodologies. Here, we describe a cloud-integrated real-time laboratory monitoring system for: (i) monitoring reactions involving fluorescent chemical species, and (ii) monitoring laboratory environment for safety purpose. A probe-type fluorescence detection system has been constructed to monitor reactions that involve fluorescent molecules. This device incorporates an in-house-built 3D-printed probe, two optical fibers, a light-emitting diode, a photoresistor, and a microcontroller board (MCB). The MCB relays experimental data to a single-board computer (SBC), which then uploads the data to a cloud-based platform (ThingSpeak) for data storage and visualization. The SBC is also connected to auxiliary sensors to measure relative alcohol vapor concentration, temperature, and humidity at different locations in the laboratory. The device has been validated and tested for its performance by monitoring a fluorescent chemical reaction (synthesis of fluorescent gold nanoclusters) for a period of 12 h.
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Affiliation(s)
- Chun-Yao Hsu
- Department of Chemistry, National Tsing Hua University, 101, Section 2, Kuang-Fu Rd., Hsinchu 30013, Taiwan
| | - Gurpur Rakesh D. Prabhu
- Department of Chemistry, National Tsing Hua University, 101, Section 2, Kuang-Fu Rd., Hsinchu 30013, Taiwan
| | - Pawel L. Urban
- Department of Chemistry, National Tsing Hua University, 101, Section 2, Kuang-Fu Rd., Hsinchu 30013, Taiwan
- Frontier Research Center on Fundamental and Applied Sciences of Matters, National Tsing Hua University, 101, Section 2, Kuang-Fu Rd., Hsinchu 30013, Taiwan
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6
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7
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Raju CM, Yu KC, Shih CP, Elpa DP, Prabhu GRD, Urban PL. Catalytic Oxygenation-Mediated Extraction as a Facile and Green Way to Analyze Volatile Solutes. Anal Chem 2021; 93:8923-8930. [PMID: 34143609 DOI: 10.1021/acs.analchem.1c01354] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Sparging-based methods have long been used to liberate volatile organic compounds (VOCs) from liquid sample matrices prior to analysis. In these methods, a carrier gas is delivered from an external source. Here, we demonstrate "catalytic oxygenation-mediated extraction" (COME), which relies on biocatalytic production of oxygen occurring directly in the sample matrix. The newly formed oxygen (micro)bubbles extract the dissolved VOCs. The gaseous extract is immediately transferred to a separation or detection system for analysis. To start COME, dilute hydrogen peroxide is injected into the sample supplemented with catalase enzyme. The entire procedure is performed automatically-after pressing a "start" button, making a clapping sound, or triggering from a smartphone. The pump, valves, and detection system are controlled by a microcontroller board. For quality control and safety purposes, the reaction chamber is monitored by a camera linked to a single-board computer, which follows the enzymatic reaction progress by analyzing images of foam in real time. The data are instantly uploaded to the internet cloud for retrieval. The COME apparatus has been coupled on-line with the gas chromatography electron ionization mass spectrometry (MS) system, atmospheric pressure chemical ionization (APCI) MS system, and APCI ion-mobility spectrometry system. The three hyphenated variants have been tested in analyses of complex matrices (e.g., fruit-based drinks, whiskey, urine, and stored wastewater). In addition to the use of catalase, COME variants using crude potato pulp or manganese(IV) dioxide have been demonstrated. The technique is inexpensive, fast, reliable, and green: it uses low-toxicity chemicals and emits oxygen.
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Affiliation(s)
- Chamarthi Maheswar Raju
- Department of Chemistry, National Tsing Hua University, 101, Section 2, Kuang-Fu Rd., Hsinchu 30013, Taiwan
| | - Kai-Chiang Yu
- Department of Chemistry, National Tsing Hua University, 101, Section 2, Kuang-Fu Rd., Hsinchu 30013, Taiwan
| | - Chun-Pei Shih
- Department of Chemistry, National Tsing Hua University, 101, Section 2, Kuang-Fu Rd., Hsinchu 30013, Taiwan
| | - Decibel P Elpa
- Department of Chemistry, National Tsing Hua University, 101, Section 2, Kuang-Fu Rd., Hsinchu 30013, Taiwan.,Department of Applied Chemistry, National Yang Ming Chiao Tung University, 1001 University Road, Hsinchu 30010, Taiwan
| | - Gurpur Rakesh D Prabhu
- Department of Chemistry, National Tsing Hua University, 101, Section 2, Kuang-Fu Rd., Hsinchu 30013, Taiwan
| | - Pawel L Urban
- Department of Chemistry, National Tsing Hua University, 101, Section 2, Kuang-Fu Rd., Hsinchu 30013, Taiwan.,Frontier Research Center on Fundamental and Applied Sciences of Matters, National Tsing Hua University, 101, Section 2, Kuang-Fu Rd., Hsinchu 30013, Taiwan
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8
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Redekop EA, Johansson N, Kokkonen E, Urpelainen S, Lopes da Silva F, Kaipio M, Nieminen HE, Rehman F, Miikkulainen V, Ritala M, Olsbye U. Synchronizing gas injections and time-resolved data acquisition for perturbation-enhanced APXPS experiments. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2021; 92:044101. [PMID: 34243480 DOI: 10.1063/5.0039957] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 03/15/2021] [Indexed: 06/13/2023]
Abstract
An experimental approach is described in which well-defined perturbations of the gas feed into an Ambient Pressure X-ray Photoelectron Spectroscopy (APXPS) cell are fully synchronized with the time-resolved x-ray photoelectron spectroscopy data acquisition. These experiments unlock new possibilities for investigating the properties of materials and chemical reactions mediated by their surfaces, such as those in heterogeneous catalysis, surface science, and coating/deposition applications. Implementation of this approach, which is termed perturbation-enhanced APXPS, at the SPECIES beamline of MAX IV Laboratory is discussed along with several experimental examples including individual pulses of N2 gas over a Au foil, a multi-pulse titration of oxygen vacancies in a pre-reduced TiO2 single crystal with O2 gas, and a sequence of alternating precursor pulses for atomic layer deposition of TiO2 on a silicon wafer substrate.
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Affiliation(s)
- Evgeniy A Redekop
- Department of Chemistry, Centre for Materials Science and Nanotechnology (SMN), University of Oslo, Oslo 0371, Norway
| | | | - Esko Kokkonen
- MAX IV Laboratory, Lund University, SE-221 00 Lund, Sweden
| | - Samuli Urpelainen
- Nano and Molecular Systems Research Unit, University of Oulu, FI-90014 Oulu, Finland
| | | | - Mikko Kaipio
- Department of Chemistry, University of Helsinki, FI-00014 Helsinki, Finland
| | | | - Foqia Rehman
- Department of Physics, Lund University, SE-221 00 Lund, Sweden
| | - Ville Miikkulainen
- Department of Chemistry, University of Helsinki, FI-00014 Helsinki, Finland
| | - Mikko Ritala
- Department of Chemistry, University of Helsinki, FI-00014 Helsinki, Finland
| | - Unni Olsbye
- Department of Chemistry, Centre for Materials Science and Nanotechnology (SMN), University of Oslo, Oslo 0371, Norway
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9
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Davis JJ, Foster SW, Grinias JP. Low-cost and open-source strategies for chemical separations. J Chromatogr A 2021; 1638:461820. [PMID: 33453654 PMCID: PMC7870555 DOI: 10.1016/j.chroma.2020.461820] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 12/12/2020] [Accepted: 12/14/2020] [Indexed: 12/18/2022]
Abstract
In recent years, a trend toward utilizing open access resources for laboratory research has begun. Open-source design strategies for scientific hardware rely upon the use of widely available parts, especially those that can be directly printed using additive manufacturing techniques and electronic components that can be connected to low-cost microcontrollers. Open-source software eliminates the need for expensive commercial licenses and provides the opportunity to design programs for specific needs. In this review, the impact of the "open-source movement" within the field of chemical separations is described, primarily through a comprehensive look at research in this area over the past five years. Topics that are covered include general laboratory equipment, sample preparation techniques, separations-based analysis, detection strategies, electronic system control, and software for data processing. Remaining hurdles and possible opportunities for further adoption of open-source approaches in the context of these separations-related topics are also discussed.
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Affiliation(s)
- Joshua J Davis
- Department of Chemistry & Biochemistry, Rowan University, Glassboro, NJ 08028, United States
| | - Samuel W Foster
- Department of Chemistry & Biochemistry, Rowan University, Glassboro, NJ 08028, United States
| | - James P Grinias
- Department of Chemistry & Biochemistry, Rowan University, Glassboro, NJ 08028, United States.
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10
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Neyt NC, Riley DL. Application of reactor engineering concepts in continuous flow chemistry: a review. REACT CHEM ENG 2021. [DOI: 10.1039/d1re00004g] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The adoption of flow technology for the manufacture of chemical entities, and in particular pharmaceuticals, has seen rapid growth over the past two decades with the technology now blurring the lines between chemistry and chemical engineering.
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Affiliation(s)
- Nicole C. Neyt
- Faculty of Natural and Agricultural Sciences
- Department of Chemistry
- University of Pretoria
- South Africa
| | - Darren L. Riley
- Faculty of Natural and Agricultural Sciences
- Department of Chemistry
- University of Pretoria
- South Africa
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11
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Abstract
With the rapid development of high technology, chemical science is not as it used to be a century ago. Many chemists acquire and utilize skills that are well beyond the traditional definition of chemistry. The digital age has transformed chemistry laboratories. One aspect of this transformation is the progressing implementation of electronics and computer science in chemistry research. In the past decade, numerous chemistry-oriented studies have benefited from the implementation of electronic modules, including microcontroller boards (MCBs), single-board computers (SBCs), professional grade control and data acquisition systems, as well as field-programmable gate arrays (FPGAs). In particular, MCBs and SBCs provide good value for money. The application areas for electronic modules in chemistry research include construction of simple detection systems based on spectrophotometry and spectrofluorometry principles, customizing laboratory devices for automation of common laboratory practices, control of reaction systems (batch- and flow-based), extraction systems, chromatographic and electrophoretic systems, microfluidic systems (classical and nonclassical), custom-built polymerase chain reaction devices, gas-phase analyte detection systems, chemical robots and drones, construction of FPGA-based imaging systems, and the Internet-of-Chemical-Things. The technology is easy to handle, and many chemists have managed to train themselves in its implementation. The only major obstacle in its implementation is probably one's imagination.
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Affiliation(s)
- Gurpur Rakesh D Prabhu
- Department of Chemistry, National Tsing Hua University, 101, Section 2, Kuang-Fu Road, Hsinchu, 30013, Taiwan.,Department of Applied Chemistry, National Chiao Tung University, 1001 University Road, Hsinchu, 300, Taiwan
| | - Pawel L Urban
- Department of Chemistry, National Tsing Hua University, 101, Section 2, Kuang-Fu Road, Hsinchu, 30013, Taiwan.,Frontier Research Center on Fundamental and Applied Sciences of Matters, National Tsing Hua University, 101, Section 2, Kuang-Fu Road, Hsinchu, 30013, Taiwan
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