DOCSLIB.ORG

Extraction of Chemical Structures and Reactions from the Literature

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Extraction of Chemical Structures and Reactions from the Literature DEPARTMENT OF CHEMISTRY Extraction of chemical structures and reactions from the literature Daniel Mark Lowe Pembroke College This dissertation is submitted for the degree of Doctor of Philosophy June 2012 Disclaimer This dissertation is the result of my own work and includes nothing which is the outcome of work done in collaboration except where specifically indicated in the text. This dissertation does not exceed the word limit (60000) set by the Chemistry Degree Committee. I Abstract The ever increasing quantity of chemical literature necessitates the creation of automated techniques for extracting relevant information. This work focuses on two aspects: the conversion of chemical names to computer readable structure representations and the extraction of chemical reactions from text. Chemical names are a common way of communicating chemical structure information. OPSIN (Open Parser for Systematic IUPAC Nomenclature), an open source, freely available algorithm for converting chemical names to structures was developed. OPSIN employs a regular grammar to direct tokenisation and parsing leading to the generation of an XML parse tree. Nomenclature operations are applied successively to the tree with many requiring the manipulation of an in-memory connection table representation of the structure under construction. Areas of nomenclature supported are described with attention being drawn to difficulties that may be encountered in name to structure conversion. Results on sets of generated names and names extracted from patents are presented. On generated names, recall of between 96.2% and 99.0% was achieved with a lower bound of 97.9% on precision with all results either being comparable or superior to the tested commercial solutions. On the patent names OPSIN’s recall was 2-10% higher than the tested solutions when the patent names were processed as found in the patents. The uses of OPSIN as a web service and as a tool for identifying chemical names in text are shown to demonstrate the direct utility of this algorithm. A software system for extracting chemical reactions from the text of chemical patents was developed. The system relies on the output of ChemicalTagger, a tool for tagging words and identifying phrases of importance in experimental chemistry text. Improvements to this tool required to facilitate this task are documented. The structure of chemical entities are where possible determined using OPSIN in conjunction with a dictionary of name to structure relationships. Extracted reactions are atom mapped to confirm that they are chemically consistent. 424,621 atom mapped reactions were extracted from 65,034 organic chemistry USPTO patents. On a sample of 100 of these extracted reactions chemical entities were identified with 96.4% recall and 88.9% precision. Quantities could be associated with reagents in 98.8% of cases and 64.9% of cases for products whilst the correct role was assigned to chemical entities in 91.8% of cases. Qualitatively the system captured the essence of the reaction in 95% of cases. This system is expected to be useful in the creation of searchable databases of reactions from chemical patents and in facilitating analysis of the properties of large populations of reactions. II Acknowledgements I would like to thank my supervisors, Professor Robert Glen and Professor Peter Murray-Rust, for their guidance and advice. I would also like to thank Dr Peter Corbett, for his initial work on the OPSIN codebase which was the precursor to the system that I developed, Dr Lezan Hawizy for her work on ChemicalTagger and many useful discussions on extending it, Dr David Jessop for his paragraph classifier, Albina Asadulina for her contribution to fused ring nomenclature support and Dr Sam Adams for many fruitful discussions on cheminformatics algorithms. I would also like to thank my colleagues at the Unilever Centre for providing such an enjoyable working environment. I am very grateful to Boehringer Ingelheim for funding my research. III Table of Contents Disclaimer ...................................................................................................................................... I Abstract ......................................................................................................................................... II Table of Contents ......................................................................................................................... IV Glossary ..................................................................................................................................... XIII Chapter 1 Introduction ................................................................................................................. 1 1.1 Where can text mining be performed? .............................................................................. 3 1.2 What can be text mined? ................................................................................................... 4 1.3 Overview of research project ............................................................................................. 4 Chapter 2 Tools and Methods ...................................................................................................... 6 2.1 XML ..................................................................................................................................... 6 2.2 Chemical Markup Language ............................................................................................... 7 2.3 SMILES................................................................................................................................. 8 2.4 InChI .................................................................................................................................. 10 2.5 Formal grammars .............................................................................................................. 11 2.6 Automata .......................................................................................................................... 12 2.7 Regular expressions .......................................................................................................... 14 2.8 OSCAR4 ............................................................................................................................. 15 2.9 ChemicalTagger ................................................................................................................ 18 2.10 Apache Maven ................................................................................................................ 22 2.11 Distributed version control ............................................................................................. 25 2.12 Continuous integration testing ....................................................................................... 26 IV Chapter 3 Conversion of Chemical Names to Structures ........................................................... 28 3.1 Introduction ...................................................................................................................... 28 3.1.1 History of systematic nomenclature.......................................................................... 28 3.1.1 Classes of chemical name .......................................................................................... 29 3.1.2 General construction of systematic names ............................................................... 29 3.1.3 History of programmatic name to structure conversion ........................................... 31 3.1.4 Current solutions ....................................................................................................... 32 3.2 Development and implementation of OPSIN ................................................................... 34 3.2.1 Strategy for development of OPSIN .......................................................................... 34 3.2.2 Architecture ............................................................................................................... 34 3.2.3 Pre-processing ........................................................................................................... 35 3.2.4 Tokenisation and parsing ........................................................................................... 36 3.2.4.1 Introduction ........................................................................................................ 36 3.2.4.2 Tokenisation algorithm ....................................................................................... 37 3.2.4.3 Looking up tokens in the lexicon ........................................................................ 40 3.2.4.4 Generation of parses .......................................................................................... 42 3.2.4.5 Drawbacks of a regular grammar ....................................................................... 44 3.2.4.6 Right to left parsing ............................................................................................ 44 3.2.4.7 XML generation .................................................................................................. 45 3.2.5 CAS index name uninversion ..................................................................................... 45 3.2.6 Chemical word rule assignment ................................................................................ 47 3.2.7 Component generation ............................................................................................
Load more

Recommended publications
  • IR-3 Elements and Groups of Elements (March 04)
    1 IR-3 Elements and Groups of Elements (March 04) CONTENTS IR-3.1 Names and symbols of atoms IR-3.1.1 Systematic nomenclature and symbols for new elements IR-3.2 Indication of mass, charge and atomic number using indexes (subscripts and superscripts) IR-3.3 Isotopes IR-3.3.1 Isotopes of an element IR-3.3.2 Isotopes of hydrogen IR-3.4 Elements (or elementary substances) IR-3.4.1 Name of an element of infinite or indefinite molecular formula or structure IR-3.4.2 Name of allotropes of definite molecular formula IR-3.5 Allotropic modifications IR-3.5.1 Allotropes IR-3.5.2 Allotropic modifications constituted of discrete molecules IR-3.5.3 Crystalline allotropic modifications of an element IR-3.5.4 Solid amorphous modifications and commonly recognized allotropes of indefinite structure IR-3.6 Groups of elements IR-3.6.1 Groups of elements in the Periodic Table and their subdivisions IR-3.6.2 Collective names of groups of like elements IR-3.7 References IR-3.1 NAMES AND SYMBOLS OF ATOMS The origins of the names of some chemical elements, for example antimony, are lost in antiquity. Other elements recognised (or discovered) during the past three centuries were named according to various associations of origin, physical or chemical properties, etc., and more recently to commemorate the names of eminent scientists. In the past, some elements were given two names because two groups claimed to have discovered them. To avoid such confusion it was decided in 1947 that after the existence of a new element had been proved beyond reasonable doubt, discoverers had the right to IUPACsuggest a nameProvisional to IUPAC, but that only Recommendations the Commission on Nomenclature of Inorganic Chemistry (CNIC) could make a recommendation to the IUPAC Council to make the final Page 1 of 9 DRAFT 2 April 2004 2 decision.
    [Show full text]
  • Retention Indices for Frequently Reported Compounds of Plant Essential Oils
    Retention Indices for Frequently Reported Compounds of Plant Essential Oils V. I. Babushok,a) P. J. Linstrom, and I. G. Zenkevichb) National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA (Received 1 August 2011; accepted 27 September 2011; published online 29 November 2011) Gas chromatographic retention indices were evaluated for 505 frequently reported plant essential oil components using a large retention index database. Retention data are presented for three types of commonly used stationary phases: dimethyl silicone (nonpolar), dimethyl sili- cone with 5% phenyl groups (slightly polar), and polyethylene glycol (polar) stationary phases. The evaluations are based on the treatment of multiple measurements with the number of data records ranging from about 5 to 800 per compound. Data analysis was limited to temperature programmed conditions. The data reported include the average and median values of retention index with standard deviations and confidence intervals. VC 2011 by the U.S. Secretary of Commerce on behalf of the United States. All rights reserved. [doi:10.1063/1.3653552] Key words: essential oils; gas chromatography; Kova´ts indices; linear indices; retention indices; identification; flavor; olfaction. CONTENTS 1. Introduction The practical applications of plant essential oils are very 1. Introduction................................ 1 diverse. They are used for the production of food, drugs, per- fumes, aromatherapy, and many other applications.1–4 The 2. Retention Indices ........................... 2 need for identification of essential oil components ranges 3. Retention Data Presentation and Discussion . 2 from product quality control to basic research. The identifi- 4. Summary.................................. 45 cation of unknown compounds remains a complex problem, in spite of great progress made in analytical techniques over 5.
    [Show full text]
  • Substrate Selectivity Profiling of the Human Monoamine Transporters
    DISSERTATION Titel der Dissertation Substrate Selectivity Profiling of the Human Monoamine Transporters Verfasst von Amir Seddik, B.Sc., M.Sc. angestrebter akademischer Grad Doktor der Naturwissenschaften (Dr. rer. nat.) Wien, 2015 Studienkennzahl lt. Studienblatt: A 796 610 449 Dissertationsgebiet lt. Studienblatt: Pharmazie, DK: Molecular Drug Targets Betreut von: Univ.-Prof. Mag. Dr. Gerhard F. Ecker A. Seddik - Substrate Selectivity Profiling of the Human Monoamine Transporters A. Seddik - Substrate Selectivity Profiling of the Human Monoamine Transporters Acknowledgement Hereby I would like to express my sincere gratitude to Prof. Gerhard F. Ecker, who has integrated me into the scientific community by letting me join his research group. I am thankful for his training during all these years, which has formed me into a very independent researcher. I thank him for his time and support and I admire his ambitions and interest for integrating students on European and international level. It has been an honor to work at the pharmaceutical department of the University of Vienna in this beautiful city. Gerhard, thank you for the great time. My gratitude goes out to Michael Freissmuth and my co-supervisor Harald H. Sitte with whom we had very successful collaborations and I thank them for giving me the opportunity to learn the experimental methods. I acknowledge the support from the MolTag program, to which I have applied for in the first place. The consortium has proven that collaboration between groups of different expertise is educative and beneficial to publish in world-class journals. I thank Steffen Hering, Gerhard Ecker, Marko Mihovilovic, Margot Ernst, Doris Stenitzer and Sophia Khom for devoting their time to the management of the project.
    [Show full text]
  • An Analysis of Electrophilic Aromatic Substitution: a “Complex Approach” PCCP
    Volume 23 Number 9 7 March 2021 Pages 5033–5682 PCCP Physical Chemistry Chemical Physics rsc.li/pccp ISSN 1463-9076 PERSPECTIVE Janez Cerkovnik et al . An analysis of electrophilic aromatic substitution: a “complex approach” PCCP View Article Online PERSPECTIVE View Journal | View Issue An analysis of electrophilic aromatic substitution: a ‘‘complex approach’’† Cite this: Phys. Chem. Chem. Phys., a a b 2021, 23, 5051 Nikola Stamenkovic´, Natasˇa Poklar Ulrih and Janez Cerkovnik * Electrophilic aromatic substitution (EAS) is one of the most widely researched transforms in synthetic organic chemistry. Numerous studies have been carried out to provide an understanding of the nature of its reactivity pattern. There is now a need for a concise and general, but detailed and up-to-date, overview. The basic principles behind EAS are essential to our understanding of what the mechanisms underlying EAS are. To date, textbook overviews of EAS have provided little information about the Received 5th October 2020, mechanistic pathways and chemical species involved. In this review, the aim is to gather and present the Accepted 21st December 2020 up-to-date information relating to reactivity in EAS, with the implication that some of the key concepts DOI: 10.1039/d0cp05245k will be discussed in a scientifically concise manner. In addition, the information presented herein suggests certain new possibilities to advance EAS theory, with particular emphasis on the role of modern Creative Commons Attribution-NonCommercial 3.0 Unported Licence. rsc.li/pccp
    [Show full text]
  • Evaluating Small Molecule Microscopic and Macroscopic Pka
    bioRxiv preprint doi: https://doi.org/10.1101/2020.10.15.341792; this version posted October 15, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 1 Overview of the SAMPL6 pK a Challenge: 2 Evaluating small molecule microscopic and 3 macroscopic pK a predictions 4 Mehtap Işık (ORCID: 0000-0002-6789-952X)1,2*, Ariën S. Rustenburg (ORCID: 0000-0002-3422-0613)1,3, Andrea 5 Rizzi (ORCID: 0000-0001-7693-2013)1,4, M. R. Gunner (ORCID: 0000-0003-1120-5776)6, David L. Mobley (ORCID: 6 0000-0002-1083-5533)5, John D. Chodera (ORCID: 0000-0003-0542-119X)1 7 1Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, 8 New York, NY 10065, United States; 2Tri-Institutional PhD Program in Chemical Biology, Weill Cornell Graduate 9 School of Medical Sciences, Cornell University, New York, NY 10065, United States; 3Graduate Program in 10 Physiology, Biophysics, and Systems Biology, Weill Cornell Medical College, New York, NY 10065, United States; 11 4Tri-Institutional PhD Program in Computational Biology and Medicine, Weill Cornell Graduate School of Medical 12 Sciences, Cornell University, New York, NY 10065, United States; 5Department of Pharmaceutical Sciences and 13 Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States; 6Department of 14 Physics, City College of New York, New York NY 10031 15 *For correspondence: 16 [email protected] (MI) 17 18 Abstract 19 K The prediction of acid dissociation constants (p a) is a prerequisite for predicting many other properties of a small molecule, 20 such as its protein-ligand binding affinity, distribution coefficient (log D), membrane permeability, and solubility.
    [Show full text]
  • Open Data, Open Source, and Open Standards in Chemistry: the Blue Obelisk Five Years On" Journal of Cheminformatics Vol
    Oral Roberts University Digital Showcase College of Science and Engineering Faculty College of Science and Engineering Research and Scholarship 10-14-2011 Open Data, Open Source, and Open Standards in Chemistry: The lueB Obelisk five years on Andrew Lang Noel M. O'Boyle Rajarshi Guha National Institutes of Health Egon Willighagen Maastricht University Samuel Adams See next page for additional authors Follow this and additional works at: http://digitalshowcase.oru.edu/cose_pub Part of the Chemistry Commons Recommended Citation Andrew Lang, Noel M O'Boyle, Rajarshi Guha, Egon Willighagen, et al.. "Open Data, Open Source, and Open Standards in Chemistry: The Blue Obelisk five years on" Journal of Cheminformatics Vol. 3 Iss. 37 (2011) Available at: http://works.bepress.com/andrew-sid-lang/ 19/ This Article is brought to you for free and open access by the College of Science and Engineering at Digital Showcase. It has been accepted for inclusion in College of Science and Engineering Faculty Research and Scholarship by an authorized administrator of Digital Showcase. For more information, please contact [email protected]. Authors Andrew Lang, Noel M. O'Boyle, Rajarshi Guha, Egon Willighagen, Samuel Adams, Jonathan Alvarsson, Jean- Claude Bradley, Igor Filippov, Robert M. Hanson, Marcus D. Hanwell, Geoffrey R. Hutchison, Craig A. James, Nina Jeliazkova, Karol M. Langner, David C. Lonie, Daniel M. Lowe, Jerome Pansanel, Dmitry Pavlov, Ola Spjuth, Christoph Steinbeck, Adam L. Tenderholt, Kevin J. Theisen, and Peter Murray-Rust This article is available at Digital Showcase: http://digitalshowcase.oru.edu/cose_pub/34 Oral Roberts University From the SelectedWorks of Andrew Lang October 14, 2011 Open Data, Open Source, and Open Standards in Chemistry: The Blue Obelisk five years on Andrew Lang Noel M O'Boyle Rajarshi Guha, National Institutes of Health Egon Willighagen, Maastricht University Samuel Adams, et al.
    [Show full text]
  • A Java-Based Platform for Evolutionary De Novo Molecular Design
    Article MoleGear: A Java-Based Platform for Evolutionary De Novo Molecular Design Yunhan Chu and Xuezhong He * Department of Chemical Engineering, Norwegian University of Science and Technology, N-7491 Trondheim, Norway; [email protected] * Correspondence: [email protected]; Tel.: +47-73593942 Received: 25 March 2019; Accepted: 10 April 2019; Published: 11 April 2019 Abstract: A Java-based platform, MoleGear, is developed for de novo molecular design based on the chemistry development kit (CDK) and other Java packages. MoleGear uses evolutionary algorithm (EA) to explore chemical space, and a suite of fragment-based operators of growing, crossover, and mutation for assembling novel molecules that can be scored by prediction of binding free energy or a weighted-sum multi-objective fitness function. The EA can be conducted in parallel over multiple nodes to support large-scale molecular optimizations. Some complementary utilities such as fragment library design, chemical space analysis, and graphical user interface are also integrated into MoleGear. The candidate molecules as inhibitors for the human immunodeficiency virus 1 (HIV-1) protease were designed by MoleGear, which validates the potential capability for de novo molecular design. Keywords: de novo design; evolutionary algorithm; drug molecules; fitness; multi-objective function 1. Introduction Computational chemistry plays an important role in the design of new drug-like molecules [1– 5], catalysts [6–8], and novel solvents of ionic liquids [9–11]. De novo molecular design has been an active research area of drug design/discovery over the last decades, and many approaches such as LUDI [12], LEA3D [13], Flux [14,15], and pharmacophore-linked fragment virtual screening (PFVS) [16] have been developed by using protein and ligand structures.
    [Show full text]
  • Cylinder Valve Selection Quick Reference for Valve Abbreviations
    SHERWOOD VALVE COMPRESSED GAS PRODUCTS Appendix Cylinder Valve Selection Quick Reference for Valve Abbreviations Use the Sherwood Cylinder Valve Series Abbreviation Chart on this page with the Sherwood Cylinder Valve Selection Charts found on pages 73–80. The Sherwood Cylinder Valve Selection Chart are for reference only and list: • The most commonly used gases • The Compressed Gas Association primary outlet to be used with each gas • The Sherwood valves designated for use with this gas • The Pressure Relief Device styles that are authorized by the DOT for use with these gases PLEASE NOTE: The Sherwood Cylinder Valve Selection Charts are partial lists extracted from the CGA V-1 and S-1.1 pamphlets. They can change without notice as the CGA V-1 and S-1.1 pamphlets are amended. Sherwood will issue periodic changes to the catalog. If there is any discrepancy or question between these lists and the CGA V-1 and S-1.1 pamphlets, the CGA V-1 and S-1.1 pamphlets take precedence. Sherwood Cylinder Valve Series Abbreviation Chart Abbreviation Sherwood Valve Series AVB Small Cylinder Acetylene Wrench-Operated Valves AVBHW Small Cylinder Acetylene Handwheel-Operated Valves AVMC Small Cylinder Acetylene Wrench-Operated Valves AVMCHW Small Cylinder Acetylene Handwheel-Operated Valves AVWB Small Cylinder Acetylene Wrench-Operated Valves — WB Style BV Hi/Lo Valves with Built-in Regulator DF* Alternative Energy Valves GRPV Residual Pressure Valves GV Large Cylinder Acetylene Valves GVT** Vertical Outlet Acetylene Valves KVAB Post Medical Valves KVMB Post Medical Valves NGV Industrial and Chrome-Plated Valves YVB† Vertical Outlet Oxygen Valves 1 * DF Valves can be used with all gases; however, the outlet will always be ⁄4"–18 NPT female.
    [Show full text]
  • Electrooxidation Enables Highly Regioselective Dearomative Annulation of Indole and Benzofuran Derivatives
    ARTICLE https://doi.org/10.1038/s41467-019-13829-4 OPEN Electrooxidation enables highly regioselective dearomative annulation of indole and benzofuran derivatives Kun Liu1, Wenxu Song1, Yuqi Deng1, Huiyue Yang1, Chunlan Song1, Takfaoui Abdelilah1, Shengchun Wang 1, Hengjiang Cong 1, Shan Tang1 & Aiwen Lei1* 1234567890():,; The dearomatization of arenes represents a powerful synthetic methodology to provide three-dimensional chemicals of high added value. Here we report a general and practical protocol for regioselective dearomative annulation of indole and benzofuran derivatives in an electrochemical way. Under undivided electrolytic conditions, a series of highly functio- nalized five to eight-membered heterocycle-2,3-fused indolines and dihydrobenzofurans, which are typically unattainable under thermal conditions, can be successfully accessed in high yield with excellent regio- and stereo-selectivity. This transformation can also tolerate a wide range of functional groups and achieve good efficiency in large-scale synthesis under oxidant-free conditions. In addition, cyclic voltammetry, electron paramagnetic resonance (EPR) and kinetic studies indicate that the dehydrogenative dearomatization annulations arise from the anodic oxidation of indole into indole radical cation, and this process is the rate- determining step. 1 College of Chemistry and Molecular Sciences, Institute for Advanced Studies (IAS), Wuhan University, Wuhan 430072, P. R. China. *email: aiwenlei@whu. edu.cn NATURE COMMUNICATIONS | (2020) 11:3 | https://doi.org/10.1038/s41467-019-13829-4 | www.nature.com/naturecommunications 1 ARTICLE NATURE COMMUNICATIONS | https://doi.org/10.1038/s41467-019-13829-4 reaking the aromatic systems of electron-rich arenes or fused indolines (Fig. 1a)39–44. Therefore, it is highly appealing to heteroarenes provides three-dimensional chemicals of high develop efficient approaches to allow for their preparation.
    [Show full text]
  • Colorimetric Sugar Sensing Using Boronic Acid-Substituted Azobenzenes
    Materials 2014, 7, 1201-1220; doi:10.3390/ma7021201 OPEN ACCESS materials ISSN 1996-1944 www.mdpi.com/journal/materials Review Colorimetric Sugar Sensing Using Boronic Acid-Substituted Azobenzenes Yuya Egawa *, Ryotaro Miki and Toshinobu Seki Faculty of Pharmaceutical Sciences, Josai University, Keyakidai, Sakado, Saitama 350-0295, Japan; E-Mails: [email protected] (R.M.); [email protected] (T.S.) * Author to whom correspondence should be addressed; E-Mail: [email protected]; Tel.: +81-49-271-7686; Fax: +81-49-271-7714. Received: 30 November 2013; in revised form: 13 January 2014 / Accepted: 28 January 2014 / Published: 14 February 2014 Abstract: In association with increasing diabetes prevalence, it is desirable to develop new glucose sensing systems with low cost, ease of use, high stability and good portability. Boronic acid is one of the potential candidates for a future alternative to enzyme-based glucose sensors. Boronic acid derivatives have been widely used for the sugar recognition motif, because boronic acids bind adjacent diols to form cyclic boronate esters. In order to develop colorimetric sugar sensors, boronic acid-conjugated azobenzenes have been synthesized. There are several types of boronic acid azobenzenes, and their characteristics tend to rely on the substitute position of the boronic acid moiety. For example, o-substitution of boronic acid to the azo group gives the advantage of a significant color change upon sugar addition. Nitrogen-15 Nuclear Magnetic Resonance (NMR) studies clearly show a signaling mechanism based on the formation and cleavage of the B–N dative bond between boronic acid and azo moieties in the dye.
    [Show full text]
  • Study of Photo-Induced Dichroism in Sudan III Doped in Poly(Methyl Methacrylate) Thin Films B
    Vol. 127 (2015) ACTA PHYSICA POLONICA A No. 3 Study of Photo-Induced Dichroism in Sudan III Doped in Poly(Methyl Methacrylate) Thin Films B. Abbasa;* and Y.T. Salmanb aAtomic Energy Commission, P.O. Box 6091, Damascus, Syria bPhysics Department, Faculty of Science, Damascus University, Damascus, Syria (Received December 4, 2013; in nal form December 10, 2014) Linear dichroism, dichroic ratio, contrast ratio and order parameters of Sudan III/PMMA guesthost thin lms have been investigated with visible polarized laser light. Dichroism increased in an exponential fashion with increase of the pump intensity. Light-induced dichroism and polar order of the dye molecules within the polymer network were reversible. These parameters showed fast increase in their values in an exponential fashion as the pumping process takes place. Also, they decay rapidly in an exponential fashion when the pump light is cut o. Photoisomerisation and polar orientation are dependent on both the molecular structure of the dye and polymer. Two forms of Sudan III molecules (trans and cis) are responsible for the interaction with laser light and forming an anisotropic structure inside the PMMA/Sudan III lms. However, there is another set of forms of the dye (keto and enol) has to be considered, which may contribute to dichroism. DOI: 10.12693/APhysPolA.127.780 PACS: 78.20.Ek, 33.55.+b, 78.66.Qn 1. Introduction Sudan III in solvents and doped in polymeric lms using the Z-scan technique. Multiple diraction rings were ob- Photoinduced optical anisotropy in polymer/organic served when the dye doped in both the liquid and solid dyes systems is the subject of intensive care and inves- media was exposed to a diode-pumped Nd:YAG laser tigations [1].
    [Show full text]
  • Evolution of Refrigerants Mark O
    This is an open access article published under an ACS AuthorChoice License, which permits copying and redistribution of the article or any adaptations for non-commercial purposes. pubs.acs.org/jced Review (R)Evolution of Refrigerants Mark O. McLinden* and Marcia L. Huber Cite This: J. Chem. Eng. Data 2020, 65, 4176−4193 Read Online ACCESS Metrics & More Article Recommendations *sı Supporting Information ABSTRACT: As we enter the “fourth generation” of refrigerants, we consider the evolution of refrigerant molecules, the ever- changing constraints and regulations that have driven the need to consider new molecules, and the advancements in the tools and property models used to identify new molecules and design equipment using them. These separate aspects are intimately intertwined and have been in more-or-less continuous development since the earliest days of mechanical refrigeration, even if sometimes out-of-sight of the mainstream refrigeration industry. We highlight three separate, comprehensive searches for new refrigerantsin the 1920s, the 1980s, and the 2010sthat sometimes identified new molecules, but more often, validated alternatives already under consideration. A recurrent theme is that there is little that is truly new. Most of the “new” refrigerants, from R-12 in the 1930s to R- 1234yf in the early 2000s, were reported in the chemical literature decades before they were considered as refrigerants. The search for new refrigerants continued through the 1990s even as the hydrofluorocarbons (HFCs) were becoming the dominant refrigerants in commercial use. This included a return to several long-known natural refrigerants. Finally, we review the evolution of the NIST REFPROP database for the calculation of refrigerant properties.
    [Show full text]