Supramolecular Templating in Thermodynamically Controlled Synthesis
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Towards Life Originating De-Novo
Diplomarbeit Towards Life originating de-novo: Strategies how Compartmentalization could be induced by a synthetic Self-Replicator Ausgefuhrt¨ zum Zwecke der Erlangung des akademischen Grades der Diplom-Ingeneurin (Dipl.-Ing.) im Rahmen des Studiums Technische Chemie unter der Leitung von Univ.Prof. Dipl.-Ing. Dr. (tech) Johannes Frohlich¨ Institut fur¨ Angewandte Synthesechemie Technische Universitat¨ Wien und Prof. Dr. Sijbren Otto Stratingh Institut fur¨ Systemchemie Universitat¨ Groningen Eingereicht an der Technischen Universitat¨ Wien Institut fur¨ Angewandte Synthesechemie Die approbierte gedruckte Originalversion dieser Diplomarbeit ist an der TU Wien Bibliothek verfügbar. The approved original version of this thesis is available in print at TU Wien Bibliothek. von Anna-Patricia Wolf, BSc. 1302118 Wien, am 23. April 2020 Unterschrift Verfasserin Die approbierte gedruckte Originalversion dieser Diplomarbeit ist an der TU Wien Bibliothek verfügbar. The approved original version of this thesis is available in print at TU Wien Bibliothek. Die approbierte gedruckte Originalversion dieser Diplomarbeit ist an der TU Wien Bibliothek verfügbar. The approved original version of this thesis is available in print at TU Wien Bibliothek. "Der Mensch braucht ein Ziel!" - Heinz Tauscher Die approbierte gedruckte Originalversion dieser Diplomarbeit ist an der TU Wien Bibliothek verfügbar. The approved original version of this thesis is available in print at TU Wien Bibliothek. DECLARATIONONOATH statutory declaration I declare that I have written this thesis independently, that I have not used other than the declared sources or resources, and that I have explicitly marked all material, which has been quoted either literally or by content from the used sources. eidesstattliche erklärung Ich erkläre an Eides statt, dass ich die vorliegende Arbeit selbstständig verfasst, andere als die angegebenen Quellen oder Hilfsmittel nicht benutzt und die den benutzten Quellen wörtlich und inhaltlich entnommenen Stellen als solche kenntlich gemacht habe. -
Sodium Borohydride (Nabh4) Itself Is a Relatively Mild Reducing Agent
1770 Vol. 35 (1987) Chem. Pharm. Bull. _35( 5 )1770-1776(1987). Reactions of Sodium Borohydride. IV.1) Reduction of Aromatic Sulfonyl Chlorides with Sodium Borohydride ATSUKO NOSE and TADAHIRO KUDO* Daiichi College of Pharmaceutical Sciences, 22-1 Tamagawa-cho, Minami-ku, Fukuoka 815, Japan (Received September 12, 1986) Aromatic sulfonyl chlorides were reduced with sodium borohydride in tetrahydrofuran at 0•Ž to the corresponding sulfinic acids in good yields. Further reduction proceeded when the reaction was carried out under reflux in tetrahydrofuran to give disulfide and thiophenol derivatives via sulfinic acid. Furthermore, sulfonamides were reduced with sodium borohydride by heating directly to give sulfide, disulfide and thiophenol derivatives, and diphenyl sulfone was reduced under similar conditions to give thiophenol and biphenyl. Keywords reduction; sodium borohydride; aromatic sulfonyl chloride; sulfonamide; sulfone; aromatic sulfinic acid; disulfide; sulfide; thiophenol Sodium borohydride (NaBH4) itself is a relatively mild reducing agent which is extensively used for the selective reduction of the carbonyl group of ketone, aldehyde and (carboxylic) acid halide derivatives. In the previous papers, we reported that NaBI-14 can reduce some functional groups, such as carboxylic anhydrides,2) carboxylic acids3) and nitro compounds.1) As a continuation of these studies, in the present paper, we wish to report the reduction of aromatic sulfonyl chlorides, sulfinic acids and sulfonamides with NaBH4. Many methods have been reported for the reduction of sulfonyl chlorides to sulfinic acids, such as the use of sodium sulfite,4a-d) zinc,5) electrolytic reduction,6) catalytic reduction,7) magnesium,8) sodium amalgam,9) sodium hydrogen sulfite,10) stannous chlo- TABLE I. -
Olefin Metathesis in Peptidomimetics, Dynamic Combinatorial Chemistry, and Molecular Imprinting
OLEFIN METATHESIS IN PEPTIDOMIMETICS, DYNAMIC COMBINATORIAL CHEMISTRY, AND MOLECULAR IMPRINTING By TAMMY KARRIE CHENG LOW A DISSERTATION PRESENTED TO THE GRADUATE SCHOOL OF THE UNIVERSITY OF FLORIDA IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY UNIVERSITY OF FLORIDA 2006 The views expressed in this dissertation are those of the author and do not reflect the official policy or position of the United States Air Force, Department of Defense, or the U.S. Government. This dissertation is dedicated to my parents for their unconditional love and support. ACKNOWLEDGEMENTS My sincere gratitude goes out to the many individuals who have supported me throughout the years. I first like to thank the Air Force Academy for giving me the opportunity to pursue my Ph.D. I look forward to returning and working in a wonderful teaching environment. Special thanks go to Lt Col Ron Furstenau, a mentor and role model, who taught me a lot about being a good instructor and inspired me to teach. I would like to extend my sincere appreciation to my research advisor, Dr. Eric Enholm, for his support, patience, understanding, and invaluable help. He provided me all the necessary guidance to complete my dissertation, and allowed me the research freedom to develop my own ideas. Most importantly, he is a caring person who was always concerned for my family, especially during the monstrous hurricane season of 2004 in Florida. He has been a great advisor and I will never forget his encouragement and kindness. I would like to thank my committee members for their constructive feedback and advice. -
N* Interactions Modulate the Properties of Cysteine Residues
n →π* Interactions Modulate the Properties of Cysteine Residues and Disulfide Bonds in Proteins The MIT Faculty has made this article openly available. Please share how this access benefits you. Your story matters. Citation Kilgore, Henry R. and Ronald T. Raines. “n →π* Interactions Modulate the Properties of Cysteine Residues and Disulfide Bonds in Proteins.” Journal of the American Chemical Society 140 (2018): 17606-17611 © 2018 The Author(s) As Published https://dx.doi.org/10.1021/JACS.8B09701 Publisher American Chemical Society (ACS) Version Author's final manuscript Citable link https://hdl.handle.net/1721.1/125597 Terms of Use Article is made available in accordance with the publisher's policy and may be subject to US copyright law. Please refer to the publisher's site for terms of use. HHS Public Access Author manuscript Author ManuscriptAuthor Manuscript Author J Am Chem Manuscript Author Soc. Author Manuscript Author manuscript; available in PMC 2019 May 21. Published in final edited form as: J Am Chem Soc. 2018 December 19; 140(50): 17606–17611. doi:10.1021/jacs.8b09701. n➝π* Interactions Modulate the Properties of Cysteine Residues and Disulfide Bonds in Proteins Henry R. Kilgore and Ronald T. Raines* Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States Abstract Noncovalent interactions are ubiquitous in biology, taking on roles that include stabilizing the conformation of and assembling biomolecules, and providing an optimal environment for enzymatic catalysis. Here, we describe a noncovalent interaction that engages the sulfur atoms of cysteine residues and disulfide bonds in proteins—their donation of electron density into an antibonding orbital of proximal amide carbonyl groups. -
Validation of a Methodology to Determine Benzene, Toluene
M. L. Gallego-Diez et al.; Revista Facultad de Ingeniería, No. 79, pp. 138-149, 2016 Revista Facultad de Ingeniería, Universidad de Antioquia, No. 79, pp. 138-149, 2016 Validation of a methodology to determine Benzene, Toluene, Ethylbenzene, and Xylenes concentration present in the air and adsorbed in activated charcoal passive samplers by GC/ FID chromatography Validación de una metodología para la determinación de la concentración de Benceno, Tolueno, Etilbenceno y Xilenos, presentes en muestras aire y adsorbidos en captadores pasivos de carbón activado, mediante cromatografía GC/FID Mary Luz Gallego-Díez1*, Mauricio Andrés Correa-Ochoa2, Julio César Saldarriaga-Molina2 1Facultad de Ingeniería, Universidad de Antioquia. Calle 67 # 53- 108. A. A. 1226. Medellín, Colombia. 2Grupo de Ingeniería y Gestión Ambiental (GIGA), Facultad de Ingeniería, Universidad de Antioquia. Calle 67 # 53- 108. A. A. 1226. Medellín, Colombia. ARTICLE INFO ABSTRACT: This article shows the validation of the analytical procedure which allows Received August 28, 2015 determining concentrations of Benzene (B), Toluene (T), Ethylbenzene (E), and Xylenes (X) Accepted April 02, 2016 -compounds known as BTEX- present in the air and adsorbed by over activated charcoal by GC-FID using the (Fluorobenzene) internal standard addition as quantification method. In the process, reference activated charcoal was employed for validation and coconut -base granular charcoal (CGC) for the construction of passive captors used in sample taken in external places or in environmental air. CGC material was selected from its recovering capacity of BTEX, with an average of 89.1% for all analytes. In this research, BTEX presence KEYWORDS in air samples, taken in a road of six lines and characterized for having heavy traffic, in Validation, activated Medellín city (Antioquia, Colombia), was analyzed. -
Sijbren Otto Is Awarded a TA-NEWPOL Grant Highlights By
116 March 2016 Sijbren Otto is awarded a TA-NEWPOL grant Sijbren Otto is awarded a 250.000 TA-NEWPOL grant. These grants aim at developing new polymer materials which meet the social and industrial need for sustainability and multifunctionali- ty. Self -synthesizing gels This research aims to develop new gels that form from simple building blocks. The build-up process can be controlled so that the gels have the desired structure and properties. The investiga- tors wish to apply the resulting materials as media for the growth of cells in three dimensions. Highlights by Prof. dr. Jan B.F.N.Engberts Three organic chemists from the Technical University of Munich wrote an interesting re- view about self-assembled supramolecular structures that can be used as catalysts for re- actions that occur via cationic transition states. Such catalysts are highly necessary since otherwise the cationic transition states may be attacked by counterions and/or solvent molecules. The supramolecular structures contain aromatic, hydrophobic reaction pockets and make it possible to perform cationic reactions outside the scope of standard solution chemistry. A number of such processes have been discussed in some detail. However, se- veral problems have still to be solved and a variety of new host structures have to be desig- ned and prepared. Such structures should be easily obtainable, tailored towards a particu- lar transformation and highly modifiable. Catti, L., Zhang, Q., Tiefenbacher, K., Synthesis 2016, 48, 313. SN2 nucleophilic substitution processes are significantly dependent on nucleophile, sol- vent and the leaving group. Physical-organic chemists from Institutes in Austria and Hun- gary argue that the role of the leaving group on the reaction dynamics has remained rather unclear. -
THIOL OXIDATION a Slippery Slope the Oxidation of Thiols — Molecules RSH Oxidation May Proceed Too Predominates
RESEARCH HIGHLIGHTS Nature Reviews Chemistry | Published online 25 Jan 2017; doi:10.1038/s41570-016-0013 THIOL OXIDATION A slippery slope The oxidation of thiols — molecules RSH oxidation may proceed too predominates. Here, the maximum of the form RSH — can afford quickly for intermediates like RSOH rate constants indicate the order − − − These are many products. From least to most to be spotted and may also afford of reactivity: RSO > RS >> RSO2 . common oxidized, these include disulfides intractable mixtures. Addressing When the reactions are carried out (RSSR), as well as sulfenic (RSOH), the first problem, Chauvin and Pratt in methanol-d , the obtained kinetic reactions, 1 sulfinic (RSO2H) and sulfonic slowed the reactions down by using isotope effect values (kH/kD) are all but have (RSO3H) acids. Such chemistry “very sterically bulky thiols, whose in the range 1.1–1.2, indicating that historically is pervasive in nature, in which corresponding sulfenic acids were no acidic proton is transferred in the been very disulfide bonds between cysteine known to be isolable but were yet rate-determining step. Rather, the residues stabilize protein structures, to be thoroughly explored in terms oxidations involve a specific base- difficult to and where thiols and thiolates often of reactivity”. The second problem catalysed mechanism wherein an study undergo oxidation by H2O2 or O2 in was tackled by modifying the model acid–base equilibrium precedes the order to protect important biological system, 9-mercaptotriptycene, by rate-determining nucleophilic attack − − − structures from damage. Among including a fluorine substituent to of RS , RSO or RSO2 on H2O2. the oxidation products, sulfenic serve as a spectroscopic handle. -
Thiol-Disulfide Exchange in Human Growth Hormone Saradha Chandrasekhar Purdue University
Purdue University Purdue e-Pubs Open Access Dissertations Theses and Dissertations January 2015 Thiol-Disulfide Exchange in Human Growth Hormone Saradha Chandrasekhar Purdue University Follow this and additional works at: https://docs.lib.purdue.edu/open_access_dissertations Recommended Citation Chandrasekhar, Saradha, "Thiol-Disulfide Exchange in Human Growth Hormone" (2015). Open Access Dissertations. 1449. https://docs.lib.purdue.edu/open_access_dissertations/1449 This document has been made available through Purdue e-Pubs, a service of the Purdue University Libraries. Please contact [email protected] for additional information. i THIOL-DISULFIDE EXCHANGE IN HUMAN GROWTH HORMONE A Dissertation Submitted to the Faculty of Purdue University by Saradha Chandrasekhar In Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy August 2015 Purdue University West Lafayette, Indiana ii To my parents Chandrasekhar and Visalakshi & To my fiancé Niranjan iii ACKNOWLEDGEMENTS I would like to thank Dr. Elizabeth M. Topp for her tremendous support, guidance and valuable suggestions throughout. The successful completion of my PhD program would not have been possible without her constant encouragement and enthusiasm. Through the last five years, I’ve learned so much as a graduate student in her lab. My thesis committee members: Dr. Stephen R. Byrn, Dr. Gregory T. Knipp and Dr. Weiguo A. Tao, thank you for your time and for all your valuable comments during my oral preliminary exam. I would also like to thank Dr. Fred Regnier for his suggestions with the work on human growth hormone. I am grateful to all my lab members and friends for their assistance and support. I would like to especially thank Dr. -
In Situ Chemical Oxidation of Carbon Disulfide Using Activated Persulfate
In Situ Chemical Oxidation of Carbon Disulfide Using Activated Persulfate Ian Ross Ph.D., FMC Environmental Solutions Mark O‟Neill & Jeff Burdick, ARCADIS Saipem Innovation Award 2012 Presentation Outline Introduction to CS2 The state of the art for remediation of CS2 Project Background The approach: R&D Treatability Trials –Laboratory proof of concept Field Pilot Trials Full scale remediation Carbon Disulfide -Properties • Carbon disulphide (CS2) has been widely used as a solvent • It is generated in small quantities by natural processes, (stagnant water bodies). • It is highly volatile and extremely flammable, having a wider explosive range in air than hydrogen and a lower ignition energy. (LEL 1%) • Odour of rotting cabbages/ radishes. • Boiling point 38 oC • Specific Gravity 1.26 • Water solubility 2.3 g/L 1946 Site Layout 1995 Site Layout CS2 Remediation „State of the Art‟ 2008 Removal of CS2 DNAPL-contaminated soils after in situ mixing with bentonite slurry to stabilise the CS2 saturated material. Stabilised material was excavated and removed to approved off-site landfill Permeable Reactive Barrier (PRB) “funnel and gate” system comprising a bentonite wall directing groundwater flow to two reactive zero-valent iron “gates” in which dissolved-phase CS2 reacts to yield innocuous end-products. In situ techniques Hot Water and Co-Solvent Flushing tested at lab scale Bentonite Stabilised Dig & Dump Increased Volume for Hazardous Waste Disposal Demolition of Houses Utilities Disruption Lorries in Residential Neighbourhood Sustainability -
Protein Folding Guides Disulfide Bond Formation
Protein folding guides disulfide bond formation Meng Qina,b, Wei Wanga,1, and D. Thirumalaib,1 aNational Laboratory of Solid State Microstructure, Department of Physics, and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China; and bBiophysics Program, Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742 Edited by Harold A. Scheraga, Cornell University, Ithaca, NY, and approved June 26, 2015 (received for review February 25, 2015) The Anfinsen principle that the protein sequence uniquely deter- Here, we investigate the coupling between conformational folding mines its structure is based on experiments on oxidative refolding of and disulfide bond formation by creating a novel way to mimic the a protein with disulfide bonds. The problem of how protein folding effect of disulfide bond formation and rupture in coarse-grained drives disulfide bond formation is poorly understood. Here, we have (CG) molecular simulations, which have proven useful in a number – solved this long-standing problem by creating a general method of applications (15 18). As a case study, we use the 58-residue bo- – for implementing the chemistry of disulfide bond formation and vine pancreatic trypsin inhibitor (BPTI) with three S Sbondsinthe rupture in coarse-grained molecular simulations. As a case study, native state to illustrate the key structural changes that occur during the folding reaction. The pioneering experiments of Creighton (9) we investigate the oxidative folding of bovine pancreatic trypsin – inhibitor (BPTI). After confirming the experimental findings that the seemed to indicate that nonnative disulfide species (19 22) are obligatory for productive folding to occur (for a thoughtful analysis, multiple routes to the folded state contain a network of states see ref. -
Famelabnl Audience Award Goes to Groningen!
136 May 2018 FameLabNL audience award goes to Groningen! Photo courtesy of Joost Weddepohl Last week the national final of FameLab was held in Utrecht. FameLab is the big- gest science communication competition in the world. The idea behind FameLab is that young scientists (students, PhD’s, postdocs and starting professors) have to present a scientific topic to an audience of laymen in under 3 minutes without using powerpoint. This year the audience award was awarded to Marcel Eleveld, who gave a presen- tation about the Eigen paradox of the origin of life (“Machinery for accurate (molecular) self-replication needs a lot of information to be encoded - but how do you obtain such machinery before the associated information can be accurately co- pied?”). Marcel is a Nanoscience master student who is working in the group of Sijbren Otto. The jury award was awarded to Jair Santanna (assistant professor at the TU Twen- te) who spoke about DDoS attacks and how they can be prevented. Stratingh Institute for Chemistry Newsletter nr 136 - May 2018 1 Sijbren Otto wins prestigious Royal Society of Chemistry Award Professor of Systems Chemistry Sijbren Otto is the 2018 re- cipient of the Royal Society of Chemistry (UK) Supramole- cular Chemistry Award. This biennial award is in recogni- tion of Otto’s contribution to the science of molecular net- works and systems chemistry. The main theme of his cur- rent work is chemical evolution. As recipient of the award, Otto will give a number of lectures in Britain. ‘I feel very honoured to receive this award’, says Otto. -
Supplementary Information for Disulfide
Electronic Supplementary Material (ESI) for Chemical Communications This journal is © The Royal Society of Chemistry 2012 Supplementary Information for Disulfide- and terminal alkyne-functionalized magnetic silica particles for enrichment of azido glycopeptides Sheng Wang, Wenxian Xie, Xiu Zhang Xia Zou and Yan Zhang* Ministry of Education Key Laboratory of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240,China *: corresponding author. Email: [email protected] Electronic Supplementary Material (ESI) for Chemical Communications This journal is © The Royal Society of Chemistry 2012 1. Experimental Section 1.1 Chemicals and reagents FeCl3·6H2O, sodium acetate, sodium citrate, sodium ascorbate, 28% NH3·H2O, triethylamine(TEA), KBr, CuSO4, NaCl, MnCl2, were bought from Sinopharm Chemical Reagent (Shanghai, China). Tetrahydrofuran (THF), ethanol, methanol and ethylene glycol were bought from Yangyuan Chemical (Changshu, China). 3-aminopropyltriethoxysilane (APTES), glutaric anhydride, 6-heptynoic acid, 1-(3-dimethylaminopropyl)-3- ethylcarbodiimide hydrochloride (EDC·HCl, or EDC); were bought from Aladdin Reagent (Shanghai, China). Tetraethylorthosilicate (TEOS), cystamine dihydrochloride, NH4HCO3, trifluoroacetic acid (TFA), DL-Dithiothreitol solution (DTT, 1M), Iodoacetamide (IAA), Tris[(1-benzyl-1H-1,2,3-triazol-4-yl)methyl]amine (TBTA), sodium dodecyl sulfate (SDS), Triton X100 were bought from Sigma (St. Louis, MO). Tris(hydroxymethyl)aminomethane (Tris) and Tris(2-carboxyethyl)phosphine hydrochloride (TCEP) were bought from Bio Basic Inc. Bovine serum albumin (BSA) was bought from Pierece. Sequencing grade trypsin was bought from Promega. 2,5 Dihydroxybenzoic acid (DHB) was from Bruker Daltonics (Bremen, Germany). HPLC grade acetonitrile (ACN) were from Merck. UDP-N-azidoacetylgalactosamine (UDP-GalNAz) was from by Shanghai Institute of Organic Chemistry,Chinese Academy of Sciences.