1 Functional Asymmetry and Chemical Reactivity of Csor Family Persulfide
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A Web-Based 3D Molecular Structure Editor and Visualizer Platform
Mohebifar and Sajadi J Cheminform (2015) 7:56 DOI 10.1186/s13321-015-0101-7 SOFTWARE Open Access Chemozart: a web‑based 3D molecular structure editor and visualizer platform Mohamad Mohebifar* and Fatemehsadat Sajadi Abstract Background: Chemozart is a 3D Molecule editor and visualizer built on top of native web components. It offers an easy to access service, user-friendly graphical interface and modular design. It is a client centric web application which communicates with the server via a representational state transfer style web service. Both client-side and server-side application are written in JavaScript. A combination of JavaScript and HTML is used to draw three-dimen- sional structures of molecules. Results: With the help of WebGL, three-dimensional visualization tool is provided. Using CSS3 and HTML5, a user- friendly interface is composed. More than 30 packages are used to compose this application which adds enough flex- ibility to it to be extended. Molecule structures can be drawn on all types of platforms and is compatible with mobile devices. No installation is required in order to use this application and it can be accessed through the internet. This application can be extended on both server-side and client-side by implementing modules in JavaScript. Molecular compounds are drawn on the HTML5 Canvas element using WebGL context. Conclusions: Chemozart is a chemical platform which is powerful, flexible, and easy to access. It provides an online web-based tool used for chemical visualization along with result oriented optimization for cloud based API (applica- tion programming interface). JavaScript libraries which allow creation of web pages containing interactive three- dimensional molecular structures has also been made available. -
Anaerobic Degradation of Methanethiol in a Process for Liquefied Petroleum Gas (LPG) Biodesulfurization
Anaerobic degradation of methanethiol in a process for Liquefied Petroleum Gas (LPG) biodesulfurization Promotoren Prof. dr. ir. A.J.H. Janssen Hoogleraar in de Biologische Gas- en waterreiniging Prof. dr. ir. A.J.M. Stams Persoonlijk hoogleraar bij het laboratorium voor Microbiologie Copromotor Prof. dr. ir. P.N.L. Lens Hoogleraar in de Milieubiotechnologie UNESCO-IHE, Delft Samenstelling promotiecommissie Prof. dr. ir. R.H. Wijffels Wageningen Universiteit, Nederland Dr. ir. G. Muyzer TU Delft, Nederland Dr. H.J.M. op den Camp Radboud Universiteit, Nijmegen, Nederland Prof. dr. ir. H. van Langenhove Universiteit Gent, België Dit onderzoek is uitgevoerd binnen de onderzoeksschool SENSE (Socio-Economic and Natural Sciences of the Environment) Anaerobic degradation of methanethiol in a process for Liquefied Petroleum Gas (LPG) biodesulfurization R.C. van Leerdam Proefschrift ter verkrijging van de graad van doctor op gezag van de rector magnificus van Wageningen Universiteit Prof. dr. M.J. Kropff in het openbaar te verdedigen op maandag 19 november 2007 des namiddags te vier uur in de Aula Van Leerdam, R.C., 2007. Anaerobic degradation of methanethiol in a process for Liquefied Petroleum Gas (LPG) biodesulfurization. PhD-thesis Wageningen University, Wageningen, The Netherlands – with references – with summaries in English and Dutch ISBN: 978-90-8504-787-2 Abstract Due to increasingly stringent environmental legislation car fuels have to be desulfurized to levels below 10 ppm in order to minimize negative effects on the environment as sulfur-containing emissions contribute to acid deposition (‘acid rain’) and to reduce the amount of particulates formed during the burning of the fuel. Moreover, low sulfur specifications are also needed to lengthen the lifetime of car exhaust catalysts. -
Inorganic Syntheses
INORGANIC SYNTHESES Volume 27 .................... ................ Board of Directors JOHN P. FACKLER, JR. Texas A&M University BODlE E. DOUGLAS University of Pittsburgh SMITH L. HOLT, JR. Oklahoma State Uniuersity JAY H. WORRELL University of South Florida RUSSELL N. GRIMES University of Virginia ROBERT J. ANGELIC1 Iowa State University Future Volumes 28 ROBERT J. ANGELIC1 Iowa State University 29 RUSSELL N. GRIMES University of Virginia 30 LEONARD V. INTERRANTE Rensselaer Polytechnic Institute 31 ALLEN H. COWLEY University of Texas, Austin 32 MARCETTA Y. DARENSBOURG Texas A&M University International Associates MARTIN A. BENNETT Australian National University, Canberra FAUSTO CALDERAZZO University of Pisa E. 0. FISCHER Technical University. Munich JACK LEWIS Cambridge University LAMBERTO MALATESTA University of Milan RENE POILBLANC University of Toulouse HERBERT W. ROESKY University of Gottingen F. G. A. STONE University of Bristol GEOFFREY WILKINSON Imperial College of Science and Technology. London AKlO YAMAMOTO Tokyo Institute 01 Technology. Yokohama Editor-in-Chief ALVIN P. GINSBERG INORGANIC SYNTHESES Volume 27 A Wiley-Interscience Publication JOHN WILEY & SONS New York Chichester Brisbane Toronto Singapore A NOTE TO THE READER This book has been electronically reproduced from digital idormation stored at John Wiley h Sons, Inc. We are phased that the use of this new technology will enable us to keep works of enduring scholarly value in print as long as there is a reasonable demand for them. The content of this book is identical to previous printings. Published by John Wiley & Sons, Inc. Copyright $? 1990 Inorganic Syntheses, Inc. All rights reserved. Published simultaneously in Canada. Reproduction or translation of any part of this work beyond that permitted by Section 107 or 108 of the 1976 United States Copyright Act without the permission of the copyright owner is unlawful. -
Polymer Chemistry
Polymer Chemistry View Article Online PAPER View Journal | View Issue Solution processible hyperbranched inverse- vulcanized polymers as new cathode materials Cite this: Polym. Chem., 2015, 6, 973 in Li–S batteries† Yangyang Wei,a Xiang Li,b Zhen Xu,a Haiyan Sun,a Yaochen Zheng,a,c Li Peng,a Zheng Liu,a Chao Gao*a and Mingxia Gao*b Soluble inverse-vulcanized hyperbranched polymers (SIVHPs) were synthesized via thiol–ene addition of polymeric sulfur (S8) radicals to 1,3-diisopropenylbenzene (DIB). Benefiting from their branched molecular architecture, SIVHPs presented excellent solubility in polar organic solvents with an ultrahigh concen- tration of 400 mg mL−1. After end-capping by sequential click chemistry of thiol–ene and Menschutkin quaternization reactions, we obtained water soluble SIVHPs for the first time. The sulfur-rich SIVHPs were employed as solution processible cathode-active materials for Li–S batteries, by facile fluid infiltration into conductive frameworks of graphene-based ultralight aerogels (GUAs). The SIVHPs-based cells showed high initial specific capacities of 1247.6 mA h g−1 with 400 charge–discharge cycles. The cells also demonstrated an excellent rate capability and a considerable depression of shuttle effect with stable cou- Received 24th September 2014, lombic efficiency of around 100%. The electrochemical performance of SIVHP in Li–S batteries over- Accepted 14th October 2014 whelmed the case of neat sulfur, due to the chemical fixation of sulfur. The combination of high DOI: 10.1039/c4py01055h solubility, structure flexibility, and superior electrochemical performance opens a door for the promising www.rsc.org/polymers application of SIVHPs. -
Integrated Multi-Selection Schemes for Complex Molecular Structures
Workshop on Molecular Graphics and Visual Analysis of Molecular Data (MolVA) (2019) J. Byška, M. Krone, and B. Sommer (Editors) MolFind – Integrated Multi-Selection Schemes for Complex Molecular Structures Robin Skånberg1;2, Mathieu Linares1;2, Martin Falk1;2, Ingrid Hotz1;2, and Anders Ynnerman1;2 1Scientific Visualization Group, Linköpings University, Sweden 2Swedish e-Science Research Centre (SeRC) Figure 1: Growing an initial selection of two residues along covalent bonds in a protein fibril. Abstract Selecting components and observing changes of properties and configurations over time is an important step in the analysis of molecular dynamics (MD) data. In this paper, we present a selection tool combining text-based queries with spatial selection and filtering. Morphological operations facilitate refinement of the selection by growth operators, e.g. across covalent bonds. The combination of different selection paradigms enables flexible and intuitive analysis on different levels of detail and visual depiction of molecular events. Immediate visual feedback during interactions ensures a smooth exploration of the data. We demonstrate the utility of our selection framework by analyzing temporal changes in the secondary structure of poly-alanine and the binding of aspirin to phospholipase A2. 1 Introduction In this paper, we present a selection framework for molecu- lar substructures embedded in the visual analytics tool VIA-MD “It is through the interactive manipulation of a visual in- [SLK∗18, KSH∗18]. The work is mostly targeted toward expert terface – the analytic discourse – that knowledge is con- users from the molecular simulation domain. The user-driven de- structed, tested, refined and shared.”[PSCO09] sign of the framework combines a large set of selection paradigms This is also true for the analysis of molecular dynamics (MD) in a flexible way while maintaining a simple and intuitive interface data and the generation of expressive visualization. -
Interdomain Zinc Site on Human Albumin SPECIAL FEATURE
Interdomain zinc site on human albumin SPECIAL FEATURE Alan J. Stewart*, Claudia A. Blindauer*, Stephen Berezenko†, Darrell Sleep†, and Peter J. Sadler*‡ *School of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, United Kingdom; and †Delta Biotechnology Ltd., Castle Court, Castle Boulevard, Nottingham NG7 1FD, United Kingdom Edited by Jack Halpern, University of Chicago, Chicago, IL, and approved December 20, 2002 (received for review October 30, 2002) Albumin is the major transport protein in blood for Zn2؉, a metal binds to the thiolate sulfur at Cys-34 (23). CD studies suggest ion required for physiological processes and recruited by various that the major Zn2ϩ site is also a secondary (weaker) binding drugs and toxins. However, the Zn2؉-binding site(s) on albumin is site for Cu2ϩ and Ni2ϩ (17). Early 113Cd NMR experiments ϩ ill-defined. We have analyzed the 18 x-ray crystal structures of hu- on BSA demonstrated the existence of two Cd2 -binding sites man albumin in the PDB and identified a potential five-coordinate (18), A and B. Competition experiments on bovine and HSAs ϩ Zn site at the interface of domains I and II consisting of N ligands (18, 19, 24) have shown that site A binds Zn2 more strongly ϩ from His-67 and His-247 and O ligands from Asn-99, Asp-249, and than Cd2 . NMR peaks A (130 ppm in phosphate buffer) and 113 H2O, which are the same amino acid ligands as those in the zinc B (24 ppm) were also observed when Cd was added to in- enzymes calcineurin, endonucleotidase, and purple acid phospha- tact human blood serum, although peak A was shifted down- tase. -
Python Module Index 79
mendeleev Documentation Release 0.9.0 Lukasz Mentel Sep 04, 2021 CONTENTS 1 Getting started 3 1.1 Overview.................................................3 1.2 Contributing...............................................3 1.3 Citing...................................................3 1.4 Related projects.............................................4 1.5 Funding..................................................4 2 Installation 5 3 Tutorials 7 3.1 Quick start................................................7 3.2 Bulk data access............................................. 14 3.3 Electronic configuration......................................... 21 3.4 Ions.................................................... 23 3.5 Visualizing custom periodic tables.................................... 25 3.6 Advanced visulization tutorial...................................... 27 3.7 Jupyter notebooks............................................ 30 4 Data 31 4.1 Elements................................................. 31 4.2 Isotopes.................................................. 35 5 Electronegativities 37 5.1 Allen................................................... 37 5.2 Allred and Rochow............................................ 38 5.3 Cottrell and Sutton............................................ 38 5.4 Ghosh................................................... 38 5.5 Gordy................................................... 39 5.6 Li and Xue................................................ 39 5.7 Martynov and Batsanov........................................ -
ADP-Ribosyl)Hydrolases: Structure, Function, and Biology
Downloaded from genesdev.cshlp.org on October 6, 2021 - Published by Cold Spring Harbor Laboratory Press SPECIAL SECTION: REVIEW (ADP-ribosyl)hydrolases: structure, function, and biology Johannes Gregor Matthias Rack,1,3 Luca Palazzo,2,3 and Ivan Ahel1 1Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom; 2Institute for the Experimental Endocrinology and Oncology, National Research Council of Italy, 80145 Naples, Italy ADP-ribosylation is an intricate and versatile posttransla- Diversification of NAD+ signaling is particularly apparent tional modification involved in the regulation of a vast in vertebrata, being linked to evolutionary optimization of variety of cellular processes in all kingdoms of life. Its NAD+ biosynthesis and increased (ADP-ribosyl) signaling complexity derives from the varied range of different (Bockwoldt et al. 2019). ADP-ribosylation is used by or- chemical linkages, including to several amino acid side ganisms from all kingdoms of life and some viruses chains as well as nucleic acids termini and bases, it can (Perina et al. 2014; Aravind et al. 2015) and controls a adopt. In this review, we provide an overview of the differ- wide range of cellular processes such as DNA repair, tran- ent families of (ADP-ribosyl)hydrolases. We discuss their scription, cell division, protein degradation, and stress re- molecular functions, physiological roles, and influence sponse to name a few (Bock and Chang 2016; Gupte et al. on human health and disease. Together, the accumulated 2017; Palazzo et al. 2017; Rechkunova et al. 2019). In ad- data support the increasingly compelling view that (ADP- dition to proteins, several in vitro observations strongly ribosyl)hydrolases are a vital element within ADP-ribosyl suggest that nucleic acids, both DNA and RNA, can be signaling pathways and they hold the potential for novel targets of ADP-ribosylation (Nakano et al. -
(12) United States Patent (10) Patent No.: US 6,545,171 B2 Krafczyk Et Al
USOO65451.71B2 (12) United States Patent (10) Patent No.: US 6,545,171 B2 Krafczyk et al. (45) Date of Patent: Apr. 8, 2003 (54) PROCESS FOR THE PRODUCTION OF (52) U.S. Cl. ....................................................... 556/427 YELLOW BIS(3-TRIALKOXYSILYALKYL) (58) Field of Search .......................................... 556/427 POLYSULEANES (56) References Cited (75) Inventors: Roland Krafczyk, Rheinfelden (DE); Ulrich Deschler, Sailauf (DE); Björn U.S. PATENT DOCUMENTS Treffeisen, Gundelfingen (DE) 6,140,524 A * 10/2000 Ichinohe et al. ............ 556/427 (73) Assignee: Degussa AG, Düsseldorf (DE) 6,384.256 B1 * 5/2002 Backer et al. .............. 556/427 * cited by examiner (*) Notice: Subject to any disclaimer, the term of this patent is extended or adjusted under 35 Primary Examiner Paul F. Shaver U.S.C. 154(b) by 0 days. (74) Attorney, Agent, or Firm-Smith, Gambrell & Russell, LLP (21) Appl. No.: 10/188,033 (57) ABSTRACT (22) Filed: Jul. 3, 2002 Process for the production of yellow bis(3-trialkoxy-silyl (65) Prior Publication Data alkyl)polysulfanes with an iodine color index of s 10 mg iodine/100 ml, in which an organic acid is added to neutral US 2003/00231.06 A1 Jan. 30, 2003 chloroalkyltrialkoxysilane and then reacted with Sodium (30) Foreign Application Priority Data polysulfide (NPS) or sodium sulfide (NaS) and Sulfur or sodium polysulfide (NPS) and NaS in alcohol. Jul. 6, 2001 (DE) ... - - - - - - - - - - - - - - - - - - - - - - - - 101 32939 (51) Int. Cl." ............................... C07F 7/08; CO7F 7/18 9 Claims, No Drawings US 6,545,171 B2 1 2 PROCESS FOR THE PRODUCTION OF An object of the present invention therefore is to provide YELLOW BIS(3-TRIALKOXYSILYALKYL) an alternative process by means of which a yellow bis(3- POLYSULEANES trialkoxysilylalkyl)polysulfane can be obtained and in which the additional use of aggressive chlorosilanes can be dispensed with. -
A Script to Highlight Hydrophobicity and Charge on Protein Surfaces
METHODS published: 13 October 2015 doi: 10.3389/fmolb.2015.00056 A script to highlight hydrophobicity and charge on protein surfaces Dominique Hagemans, Ianthe A. E. M. van Belzen, Tania Morán Luengo and Stefan G. D. Rüdiger * Cellular Protein Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, Netherlands The composition of protein surfaces determines both affinity and specificity of protein-protein interactions. Matching of hydrophobic contacts and charged groups on both sites of the interface are crucial to ensure specificity. Here, we propose a highlighting scheme, YRB, which highlights both hydrophobicity and charge in protein structures. YRB highlighting visualizes hydrophobicity by highlighting all carbon atoms that are not bound to nitrogen and oxygen atoms. The charged oxygens of glutamate and aspartate are highlighted red and the charged nitrogens of arginine and lysine are highlighted blue. For a set of representative examples, we demonstrate that YRB highlighting intuitively Edited by: Ophry Pines, visualizes segments on protein surfaces that contribute to specificity in protein-protein Hebrew University of Jerusalem, Israel interfaces, including Hsp90/co-chaperone complexes, the SNARE complex and a Reviewed by: transmembrane domain. We provide YRB highlighting in form of a script that runs using Paolo De Los Rios, the software PyMOL. Ecole Polytechnique Fédérale de Lausanne, Switzerland Keywords: protein-protein interaction, surface hydrophobicity, charge pairs, PyMOL, amino acid properties Eilika Weber-Ban, ETH Zurich, Switzerland *Correspondence: Introduction Stefan G. D. Rüdiger, Cellular Protein Chemistry, Bijvoet Protein-protein interactions underlie all processes in the cell. Specificity of protein-protein Center for Biomolecular Research, interactions is determined by matching of complementary functional groups with those of Utrecht University, Padualaan 8, 3584 CH Utrecht, Netherlands the opposite surface (Chothia and Janin, 1975; Eaton et al., 1995). -
Growth and Nitrogen Fixation Dynamics of Azotobacter Chroococcum in Nitrogen-Free and Omw Containing Medium
GROWTH AND NITROGEN FIXATION DYNAMICS OF AZOTOBACTER CHROOCOCCUM IN NITROGEN-FREE AND OMW CONTAINING MEDIUM A THESIS SUBMITTED TO THE GRADUATE SCHOOL OF NATURAL AND APPLIED SCIENCES OF THE MIDDLE EAST TECHNICAL UNIVERSITY BY GÜL )ø'AN SARIBAY IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF MASTER OF SCIENCE IN THE DEPARTMENT OF FOOD ENGINEERING DECEMBER 2003 Approval of the Graduate School of Natural and Applied Sciences. Prof. Dr. Canan Özgen Director I certify that this thesis satisfies all the requirements as a thesis for the degree of Master of Science. ¢¡¤£¦¥¨§ © ¡ § !¡¤"# Head of Department We certify that we have read this thesis and in our opinion it is fully adequate, in scope and quality, as a thesis for the degree of Master of Science in Food Engineering. 3 ABSTRACT GROWTH AND NITROGEN FIXATION DYNAMICS OF AZOTOBACTER CHROOCOCCUM IN NITROGEN-FREE AND OMW CONTAINING MEDIUM $%&¤'()%+*,¦-/.0¦13254¦%+6 M.Sc., Department of Food Engineering 789):;=<)>#?A@B;DCFEG;¤@H¨IJK; ILNM OP8QNLNMRSM+RST U December 2003, 68 Pages Olive Mill Wastewater (OMW), by-product of oil industry, is a dark liquid with a characteristic fetid smell, bitter taste and bright appearance; having a high pollution potential, creating serious problems in countries producing olive oil. Azotobacter chroococcum as a Nitrogen-fixing bacteria can bioremediate OMW, by degrading its toxic constituents. With the help of this detoxification process OMW can be used as biofertilizer. In this study, the dynamics of growth and nitrogen fixation at different physiological conditions and nutrient requirements of A. chroococcum in chemically defined N-free medium was determined. -
The Anticancer Drug Cisplatin Can Cross-Link the Interdomain Zinc Site on Human Albumin
Electronic Supplementary Material (ESI) for Chemical Communications This journal is © The Royal Society of Chemistry 2011 For submission to Chem. Commun. The Anticancer Drug Cisplatin Can Cross-link the Interdomain Zinc Site on Human Albumin Wenbing Hu, Qun Luo, Kui Wu, Xianchan Li, Fuyi Wang,* Yi Chen, Xiaoyan Ma, Jianping Wang, Jianan Liu, Shaoxiang Xiong, and Peter J. Sadler* Supporting Information 1. Experimental Section 2. Table S1 3. Figure S1-S7 Electronic Supplementary Material (ESI) for Chemical Communications This journal is © The Royal Society of Chemistry 2011 Experimental Section Materials. Recombinant human albumin (rHA) was kindly provided by Delta Biotechnology Ltd (Nottingham, UK) and extensively dialyzed against NH4HCO3 buffer (100 mM) and lyophilized before use. Trypsin (sequence grade) was purchased from Promega, guanidine hydrochloride from Amresco, selenocystamine dihydrochloride from Sigma, dithiothreitol (DTT) from Pierce, iodoacetamide and acetonitrile (HPLC grade) from Merck, trifluoroacetic acid (TFA) from Acros, and triethylammonium acetate buffer (TEAA) from Transgenomic. Microcon centrifugal filtration units with a 10 kDa molecular weight cut-off were purchased from Millipore. Aqueous solutions were prepared using MilliQ water (MilliQ Reagent Water System). HPLC-ESI-MS(/MS). Positive-ion electrospray ionization mass spectra were obtained on a Micromass Q-TOF mass spectrometer (Waters) coupled to a Waters CapLC HPLC system. The tryptic digests of rHA or platinated rHA were separated on a Symmetry-C18 column (10×5mm, 100Å, 3.5 μm, waters). Mobile phases were A: 95% H2O containing 4.9% acetonitrile and 0.1% formic acid, and B: 95% acetonitrile containing 4.9% H2O and 0.1% formic acid. The peptides were eluted with a 50 min linear gradient from 1% to 45 % of B at a rate of 30 μL min-1.