To Some, 'Click Chemistry' Is Simply a Relabelling of Standard Organic
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Ethanol Production from Hydrolyzed Kraft Pulp by Mono- and Co-Cultures of Yeasts: the Challenge of C6 and C5 Sugars Consumption
energies Article Ethanol Production from Hydrolyzed Kraft Pulp by Mono- and Co-Cultures of Yeasts: The Challenge of C6 and C5 Sugars Consumption Rita H. R. Branco, Mariana S. T. Amândio, Luísa S. Serafim and Ana M. R. B. Xavier * CICECO–Aveiro Institute of Materials, Chemistry Department, University of Aveiro, Campus Universitario de; Santiago, 3810-193 Aveiro, Portugal; [email protected] (R.H.R.B.); [email protected] (M.S.T.A.); luisa.serafi[email protected] (L.S.S.) * Correspondence: [email protected]; Tel.: +351-234-370-716 Received: 27 December 2019; Accepted: 4 February 2020; Published: 8 February 2020 Abstract: Second-generation bioethanol production’s main bottleneck is the need for a costly and technically difficult pretreatment due to the recalcitrance of lignocellulosic biomass (LCB). Chemical pulping can be considered as a LCB pretreatment since it removes lignin and targets hemicelluloses to some extent. Chemical pulps could be used to produce ethanol. The present study aimed to investigate the batch ethanol production from unbleached Kraft pulp of Eucalyptus globulus by separate hydrolysis and fermentation (SHF). Enzymatic hydrolysis of the pulp resulted in a glucose yield of 96.1 3.6% and a xylose yield of 94.0 7.1%. In an Erlenmeyer flask, fermentation of the ± ± hydrolysate using Saccharomyces cerevisiae showed better results than Scheffersomyces stipitis. At both the Erlenmeyer flask and bioreactor scale, co-cultures of S. cerevisiae and S. stipitis did not show significant improvements in the fermentation performance. The best result was provided by S. cerevisiae alone in a bioreactor, which fermented the Kraft pulp hydrolysate with an ethanol yield of 0.433 g g 1 and a volumetric ethanol productivity of 0.733 g L 1 h 1, and a maximum ethanol · − · − · − concentration of 19.24 g L 1 was attained. -
Read the Book of Abstracts
2o21 ONLINE May 10- 12 2021 International Symposium on SupraBiomolecular Systems 2021 Table of Contents TBD 1 Prof. Andreas Herrmann TBD 2 Prof. Rachel O’Reilly Tackling challenges in nanomedicine with responsive supramolecular polymers and advanced mi- croscopy 3 Dr. Silvia Pujals, Mr. Edgar Fuentes, Dr. Lorenzo Albertazzi Water Soluble Nanotubular Architectures from Amphiphilic Dinucleobases 4 Dr. Fatima Aparicio, Ms. Paula Blue Chamorro, Dr. Raquel Chamorro, Prof. David Gonzalez-Rodriguez Glyconucleolipids as new drug delivery systems for Parkinson’s disease treatment 5 Mr. Anthony Cunha, Dr. Alexandra Gaubert, Prof. Philippe Barthélémy, Dr. Benjamin Dehay, Dr. Laurent Latxague Membraneless compartments based on intrinsically disordered proteins: from biology towards new pro- tein materials 6 Prof. Paolo Arosio Low Molecular Weight Oleogel formation via unique keto-enol-type nucleolipid supramolecular assembly 8 Mr. Arthur KLUFTS-EDEL, Ms. Bérangère Dessane, Dr. Aladin Hamoud, Dr. Geoffrey Prévot, Dr. Antoine Lo- quet, Dr. Brice Kauffmann, Prof. Philippe Barthélémy, Prof. Sylvie Crauste-Manciet, Dr. Valérie Desvergnes Multi-responsive supramolecular fibers from peptide-based amphiphiles 9 Mr. Edgar Fuentes, Dr. Marieke Gerth, Dr. Jose Augusto Berrocal, Dr. Carlo Matera, Prof. Pau Gorostiza, Prof. Ilja Voets, Dr. Silvia Pujals, Dr. Lorenzo Albertazzi Electrostatic Protein Assemblies Towards Biohybrid Photoactive Materials 10 Dr. Eduardo Anaya-Plaza, Prof. Mauri Kostiainen Exploring Polyoxometalates as Non-destructive Staining Agents for Contrast-Enhanced Microfocus Com- puted Tomography of Biological Tissues 11 Ms. Sarah Vangrunderbeeck, Mr. Sébastien De Bournonville, Mrs. Hong Giang T. Ly, Prof. Wim De Borggraeve, Prof. Tatjana Parac-Vogt, Prof. Greet Kerckhofs Hydrogels with Photo-Switchable Stiffness: A Tool to Mimic Extra Cellular Matrix 13 Prof. -
Synthesis of Organometallic PNA Oligomers by Click Chemistry
Supplementary Material (ESI) for Chemical Communications This journal is (c) The Royal Society of Chemistry 2008 1 Supporting Information: Synthesis of organometallic PNA oligomers by click chemistry Gilles Gasser, Nina Hüsken, S. David Köster and Nils Metzler-Nolte* Department of Inorganic Chemistry I – Bioinorganic Chemistry, Faculty of Chemistry and Biochemistry, Ruhr-University Bochum Universitätsstrasse 150; 44801 Bochum, Germany Fax: +49 (0)234 – 32 14378; E-Mail: [email protected] Table of contents I. Experimental Section a) Materials 2 b) Instrumentation and methods 2 c) Peptide Nucleic Acid synthesis 2 d) Synthesis, characterisation and NMR spectra of Fmoc-1-OtBu, Fmoc-1-OH, Fmoc-2-OtBu and 3 3 e) Characterisation of PNA1-4 10 f) Synthesis and characterisation of Fc-PNA1-3 and Fc2-PNA4 10 II. MALDI-TOF Spectra a) Figure 5: MALDI-TOF mass spectrum of Fc-PNA1 11 b) Figure 6: MALDI-TOF mass spectrum of Fc-PNA2 12 c) Figure 7: MALDI-TOF mass spectrum of Fc-PNA3 12 d) Figure 8: MALDI-TOF mass spectrum of Fc2-PNA4 13 III. References 13 Supplementary Material (ESI) for Chemical Communications This journal is (c) The Royal Society of Chemistry 2008 2 I. Experimental Section a) Materials. All chemicals were of reagent grade quality or better, obtained from commercial suppliers and used without further purification. Solvents were used as received or dried over 4 Å molecular sieves. b) Instrumentation and methods. 1H and 13C NMR spectra were recorded in deuterated solvents on a Bruker DRX 400 spectrometer at 30°C. The chemical shifts, δ, are reported in ppm (parts per million). -
Professor of Chemistry
Bruce C. Gibb FRSC Professor of Chemistry Department of Chemistry Tulane University New Orleans, LA 70118, USA Tel: (504) 862 8136 E-mail: [email protected] Website: http://www.gibbgroup.org Twitter: @brucecgibb Research Interests: Aqueous supramolecular chemistry: understanding how molecules interact in water: from specific ion- pairing and the hydrophobic effect, to protein aggregation pertinent to neurodegenerative disorders. Our research has primarily focused on: 1) novel hosts designed to probe the hydrophobic, Hofmeister, and Reverse Hofmeister effects, and; 2) designing supramolecular capsules as yocto-liter reaction vessels and separators. Current efforts to probe the hydrophobic and Hofmeister effects include studies of the supramolecular properties of proteins. Professional Positions: Visiting Professor, Wuhan University of Science and Technology as a Chair Professor of Chutian Scholars Program (2015-2018) Professor of Chemistry, Tulane University, New Orleans, USA (2012-present). University Research Professor, University of New Orleans, USA (2007-2011). Professor of Chemistry, University of New Orleans, USA (2005-2007). Associate Professor of Chemistry, University of New Orleans, USA (2002-2005). Assistant Professor of Chemistry, University of New Orleans, USA, (1996-2002). Education: Postdoctoral Work Department of Chemistry, New York University. Synthesis of Carbonic Anhydrase (CA) mimics with Advisor: Prof. J. W. Canary, (1994-1996). Department of Chemistry, University of British Columbia, Canada De Novo Protein development. Advisor: Prof. J. C. Sherman (1993-1994). Ph.D. Robert Gordon’s University, Aberdeen, UK. Synthesis and Structural Examination of 3a,5-cyclo-5a- Androstane Steroids. Advisors: Dr. Philip J. Cox and Dr. Steven MacManus (1987-92) . B.Sc. with Honors in Physical Sciences Robert Gordon’s University, Aberdeen, UK. -
Article Metric to 'Green' Chemistry – Which Are the Best?
View Article Online / Journal Homepage / Table of Contents for this issue Metrics to ‘green’ chemistry—which are the best? David J. C. Constable,a Alan D. Curzonsb and Virginia L. Cunninghama a GlaxoSmithKline Pharmaceuticals, 2200 Renaissance Boulevard, King of Prussia, PA 19406, USA. E-mail: [email protected] b GlaxoSmithKline Pharmaceuticals, Southdownview Way, Worthing, West Sussex, UK BN14 8NQ Received 26th June 2002 First published as an Advance Article on the web 17th October 2002 A considerable amount has been written about the use of metrics to drive business, government and communities towards more sustainable practices. A number of metrics have also been proposed over the past 5U10 years to make chemists aware of the need to change the methods used for chemical syntheses and chemical processes. This paper explores several metrics commonly used by chemists and compares and contrasts these metrics with a new metric known as reaction mass efficiency. The paper also uses an economic analysis of four commercial pharmaceutical processes to understand the relationship between metrics and the most important cost drivers in these processes. Selected metrics used in the past autoclaved cell mass have some environmental impacts of one kind or another that would need to be evaluated and ad- A considerable number of publications have been written about dressed. the use of metrics to drive business, government and commu- nities towards more sustainable practices. The reader is referred elsewhere for a discussion of what metrics have -
Comparative Analysis of Click Chemistry Mediated Activity-Based Protein Profiling in Cell Lysates
Molecules 2013, 18, 12599-12608; doi:10.3390/molecules181012599 OPEN ACCESS molecules ISSN 1420-3049 www.mdpi.com/journal/molecules Communication Comparative Analysis of Click Chemistry Mediated Activity-Based Protein Profiling in Cell Lysates Yinliang Yang, Xiaomeng Yang and Steven H. L. Verhelst * Lehrstuhl für Chemie der Biopolymere, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, Germany; E-Mails: [email protected] (Y.Y.); [email protected] (X.Y.) * Author to whom correspondence should be addressed; E-Mail: [email protected]; Tel.: +49-8161-713505; Fax: +49-8161-714404. Received: 26 June 2013; in revised form: 7 August 2013 / Accepted: 26 September 2013 / Published: 11 October 2013 Abstract: Activity-based protein profiling uses chemical probes that covalently attach to active enzyme targets. Probes with conventional tags have disadvantages, such as limited cell permeability or steric hindrance around the reactive group. A tandem labeling strategy with click chemistry is now widely used to study enzyme targets in situ and in vivo. Herein, the probes are reacted in live cells, whereas the ensuing detection by click chemistry takes place in cell lysates. We here make a comparison of the efficiency of the activity-based tandem labeling strategy by using Cu(I)-catalyzed and strain-promoted click chemistry, different ligands and different lysis conditions. Keywords: activity-based probes; cathepsins; click chemistry; proteases; protein modification 1. Introduction Within chemical biology, site specific protein modification by covalent small molecule probes is a powerful and often used technique to interrogate biomolecular interactions and protein function. The introduction of covalent small molecule probes can be based on different types of chemistries: probes may be incorporated by the use of exogenous or endogenous enzymes [1,2], or they can contain an intrinsic reactivity such as an electrophile or photocrosslinker that by itself forms a covalent bond to the target proteins [3–5]. -
Sufex-Enabled, Agnostic Discovery of Covalent Inhibitors of Human Neutrophil Elastase
SuFEx-enabled, agnostic discovery of covalent inhibitors of human neutrophil elastase Qinheng Zhenga,1, Jordan L. Woehlb,1, Seiya Kitamurab, Diogo Santos-Martinsc, Christopher J. Smedleyd, Gencheng Lia, Stefano Forlic, John E. Mosesd, Dennis W. Wolanb,2, and K. Barry Sharplessa,2 aDepartment of Chemistry, The Scripps Research Institute, La Jolla, CA 92037; bDepartment of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037; cDepartment of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037; and dLa Trobe Institute for Molecular Science, La Trobe University, Bundoora, Melbourne, VIC 3086, Australia Contributed by K. Barry Sharpless, July 23, 2019 (sent for review July 9, 2019; reviewed by Peng R. Chen and Lei Wang) Sulfur fluoride exchange (SuFEx) has emerged as the new gener- unique ensemble of factors between the naturally folded protein ation of click chemistry. We report here a SuFEx-enabled, agnostic and its correct partner probe’s latent S–F electrophilic site. approach for the discovery and optimization of covalent inhibi- When the perfect S–F probe for a given protein encounters the tors of human neutrophil elastase (hNE). Evaluation of our ever- denatured form of the latter, there is no detectable reaction (24, growing collection of SuFExable compounds toward various bio- 33). In fact, in our experience with many S–F capture probes and logical assays unexpectedly revealed a selective and covalent hNE various denatured proteins, even including entire denatured inhibitor: benzene-1,2-disulfonyl fluoride. Synthetic derivatization proteomes, is that misfolded proteins simply do not react with of the initial hit led to a more potent agent, 2-(fluorosulfonyl)phenyl S–F electrophiles at all (24). -
Applications of Click Chemistry Themed Issue
This article was published as part of the Applications of click chemistry themed issue Guest editors Professors M.G. Finn and Valery Fokin Please take a look at the issue 4 table of contents to access other reviews in this themed issue CRITICAL REVIEW www.rsc.org/csr | Chemical Society Reviews Click chemistry with DNAw Afaf H. El-Sagheerab and Tom Brown*a Received 1st September 2009 First published as an Advance Article on the web 9th February 2010 DOI: 10.1039/b901971p The advent of click chemistry has led to an influx of new ideas in the nucleic acids field. The copper catalysed alkyne–azide cycloaddition (CuAAC) reaction is the method of choice for DNA click chemistry due to its remarkable efficiency. It has been used to label oligonucleotides with fluorescent dyes, sugars, peptides and other reporter groups, to cyclise DNA, to synthesise DNA catenanes, to join oligonucleotides to PNA, and to produce analogues of DNA with modified nucleobases and backbones. In this critical review we describe some of the pioneering work that has been carried out in this area (78 references). Introduction Azides and unactivated alkynes are almost entirely un- reactive towards the functional groups normally encountered Click chemistry was developed to provide a simple method to join in nature; they react only with each other. together organic molecules in high yields under mild conditions The triazole unit is extremely stable, and is not toxic. 3 and in the presence of a diverse range of functional groups. The In this review we describe the use of click chemistry across best example of this new class of extremely efficient chemical the nucleic acids field, focusing on synthetic strategies and I reactionsistheCu catalysed [3+2] azide–alkyne cycloaddition briefly describing some important practical applications. -
PEO/PEG, Click Chemistry, Hydralink
H10E Innovative conjugation & labeling solutions / biochemistry methods and reagents from Interchim CHEMISTRIES | FUNCTIONALIZATION | NANOMATERIALS | LABELING ● Hydrazone Chemistry reagents (HyNic/4FB) (PH) • Bio-Orthogonal • Controllable activation: UV-traceable • Stable activation: flexible Uses HyNic ligators and aldehyde ligators, to activate i.e. amines (SANH), or nucleic acids (with amidite-Alkynes). HyNic and Aldehyde groups react to form a stable hydrazine bond, in bioorthogonal and highly specific way. ● Standard Click Chemistry reagents (PH) • Chemoselective Uses alkyne ligators and azide ligators, to activate i.e. amines (ZL5530 & ZL5540), or nucleic acids (with amidite-Alkynes). Alkyne and Azide react in presence of Copper(II)- TBTA complex FY2780 , in bioorthogonal and highly specific way ● Copper-free Click Chemistry reagents (DBCO reagents) (PH) • DBCO reagents make easier Click reactions • no more need catalyzer! • no toxic by-products Use cyclooctynes ligators (DBCO) and azide ligators, to activate i.e. amines or other biomolecules. DBCO and azide partners react directly (SPAAC reaction), in bioorthogonal and highly specific way. ● Readilink Rapid Protein Labeling Kits (Buccutite based) (PH) • Click-chemistry like base technology (use Buccutite-FOL/MTA reagents) • Selective – easy (no final desalting step) 1+1/2hr procedure • Available with mFluor dyes for FCM, iFLuor dyes, APC, APC-Cy5.5 Tandem, PE-Cy5 Tandem, PE-Cy5.5 Tandem, PE-Texas Red Tandem, trFluor™ Eu & Tb, HRP, Proteins conjugation. Use Baccutite FOL/MTA reagents as partners for a highly specific reaction. Also ReadiLink Kits using SE method, available with more labels ● Staudinger Chemistry (TriArylPhosphine reagents) (PH) • Chemoselective • not toxic • ideal for In-vivo and metabolic labelings Use an appropriate substituted triaryl phosphine and an azide to form an amide bond. -
High Performance Liquid Chromatography Method Development and Chemometric Analysis of Ecstasy and Cocaine
institlüld ictterkcnny TeicneoUiochti institute lyit (.«Ulf C*»n«lon of Technology High performance liquid chromatography method development and chemometric analysis of ecstasy and cocaine Kim McFadden Supervisors Dr. B. F. Carney, Letterkenny Institute of Technology Dr. D. O'Driscoll, Forensic Science Laboratory, Dublin Submitted to Higher bducation and Training Awards Council (HETAC) in fulfilment for the requirements for the degree of Doctor of Philosophy HPLC method development & chemomelric analysis of ecstasy & cocaine Declaration I hereby declare that the work herein, submitted for Ph.D. in Analytical Science at Letterkenny Institute of Technology, is the result of my own investigation, except where reference is made to published literature. I also certify that the material submitted in this thesis has not been previously submitted for any other qualification. Kim McFadden 1 HPLC method development & chemometric analysis of ecstasy & cocaine Table of Contents Declaration 1 Abstract 5 List of Abbreviations 7 List of Figures 10 List of Tables 14 List of Presentations and Publications 16 Acknowledgments 18 Chapter 1: Literature review. 19 1.1. Introduction. 20 1.2. Drugs of abuse. 21 1.2.1. Narcotics. 22 1.2.2. Depressants. 24 1.2.3. Stimulants. 24 1.2.4. Hallucinogens. 25 1.2.5. Ecstasy. 26 1.2.6. Cocaine. 31 1.3. Current analytical techniques for forensic drug analysis. 34 1.3.1. Spectrometric methods. 34 1.3.2. Chromatographic methods. 36 1.4. Fundamentals of High Performance Liquid Chromatography. 40 1.4.1. Chromatographic interactions. 40 1.4.2. Mobile phase. 41 1.4.3. The column. 42 1.4.4. -
New Deoxyribozymes for the Native Ligation of RNA
molecules Article New Deoxyribozymes for the Native Ligation of RNA Carolin P. M. Scheitl 1, Sandra Lange 2 and Claudia Höbartner 1,* 1 Institute of Organic Chemistry, University of Würzburg, Am Hubland, 97074 Würzburg, Germany; [email protected] 2 Agricultural Center, BASF SE, Speyerer Str 2, 67117 Limburgerhof, Germany; [email protected] * Correspondence: [email protected] Academic Editors: Michael Smietana, Stellios Arseniyadis and Sabine Müller Received: 29 July 2020; Accepted: 10 August 2020; Published: 11 August 2020 Abstract: Deoxyribozymes (DNAzymes) are small, synthetic, single-stranded DNAs capable of catalyzing chemical reactions, including RNA ligation. Herein, we report a novel class of RNA ligase deoxyribozymes that utilize 50-adenylated RNA (50-AppRNA) as the donor substrate, mimicking the activated intermediates of protein-catalyzed RNA ligation. Four new DNAzymes were identified by in vitro selection from an N40 random DNA library and were shown to catalyze the intermolecular linear RNA-RNA ligation via the formation of a native 30-50-phosphodiester linkage. The catalytic activity is distinct from previously described RNA-ligating deoxyribozymes. Kinetic analyses revealed the optimal incubation conditions for high ligation yields and demonstrated a broad RNA substrate scope. Together with the smooth synthetic accessibility of 50-adenylated RNAs, the new DNA enzymes are promising tools for the protein-free synthesis of long RNAs, for example containing precious modified nucleotides or fluorescent labels for biochemical and biophysical investigations. Keywords: RNA ligation; DNA catalysis; in vitro selection; deoxyribozyme 1. Introduction DNA is best known in the form of the famous Watson-Crick double helix of two antiparallel phosphodiester single strands held together by hydrogen bonding and stacking interactions of complementary A–T and G–C base pairs. -
Click Chemistry: New Protocol for the Labeling and Modification of Biomolecules
Click Chemistry: new protocol for the labeling and modification of biomolecules Click Chemistry is a reaction between azide and alkyne yielding covalent product - 1,5-disubstituted 1,2,3-triazole. This process is also known as CuAAC - Cu catalyzed alkyne azide cycloaddition. Click Chemistry is based on copper catalysis. The catalyst is often introduced as Cu-TBTA complex. Among the vast variety of organic reactions, Click Chemistry has been selected as a conjugation chemistry reaction because of several advantages. • It is very selective. Click Chemistry reaction takes place only between azide and alkyne components. It is does not interfere with most any other organic groups present in DNA and proteins being labeled, such as amino and carboxy groups. • There are no azides and alkynes in native biomolecules. These groups should be specially introduced into DNA and proteins. Alkyne-containing DNA can be prepared with alkyne phosphoramidite during standard oligo synthesis. Proteins labeled with azide and alkyne can be made using azide activated ester and alkyne activated ester. • Click Chemistry takes place in water. Aqueous DMSO, DMF, acetonitrile, alcohols, or pure water and buffers can be used for the reaction. The reaction is biocompatible and can take place in living cells. • Reaction is quick and quantitative. Click Chemistry is a tool that allows preparation of nanomols of conjugates in diluted solutions. • The reaction is pH-insensitive. Unlike reaction of NHS esters with amines, and some other conjugation chemistries, there is no need to control pH in reaction mixture. There is no need to add any special buffer, acid or base - Click Chemistry works well in pH interval of 4-11.