Naming Organic Compounds: Alkanes
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Side-Chain Liquid Crystal Polymers (SCLCP): Methods and Materials. an Overview
Materials 2009, 2, 95-128; doi:10.3390/ma2010095 OPEN ACCESS materials ISSN 1996-1944 www.mdpi.com/journal/materials Review Side-chain Liquid Crystal Polymers (SCLCP): Methods and Materials. An Overview Tomasz Ganicz * and Włodzimierz Stańczyk Centre of Molecular and Macromolecular Studies, Polish Academy of Science, Sienkiewicza 112, 90- 363 Łódź, Poland; E-Mail: [email protected] * Author to whom correspondence should be addressed; E-Mail: [email protected]; Tel. +48-42-684-71-13; Fax: +48-42-684-71-26 Received: 5 February 2009; in revised form: 3 March 2009 / Accepted: 9 March 2009 / Published: 11 March 2009 Abstract: This review focuses on recent developments in the chemistry of side chain liquid crystal polymers. It concentrates on current trends in synthetic methods and novel, well defined structures, supramolecular arrangements, properties, and applications. The review covers literature published in this century, apart from some areas, such as dendritic and elastomeric systems, which have been recently reviewed. Keywords: Liquid crystals, side chain polymers, polymer modification, polymer synthesis, self-assembly. 1. Introduction Over thirty years ago the work of Finkelmann and Ringsdorf [1,2] gave important momentum to synthesis of side chain liquid crystal polymers (SCLCPs), materials which combine the anisotropy of liquid crystalline mesogens with the mechanical properties of polymers. Although there were some earlier attempts [2], their approach of decoupling the motions of a polymer main chain from a mesogen, thus allowed side chain moieties to build up long range ordering (Figure 1). They were able to synthesize polymers with nematic, smectic and cholesteric phases via free radical polymerization of methacryloyl type monomers [3]. -
Common Names for Selected Aromatic Groups
More Nomenclature: Common Names for Selected Aromatic Groups Phenyl group = or Ph = C6H5 = Aryl = Ar = aromatic group. It is a broad term, and includes any aromatic rings. Benzyl = Bn = It has a -CH2- (methylene) group attached to the benzene ring. This group can be used to name particular compounds, such as the one shown below. This compound has chlorine attached to a benzyl group, therefore it is called benzyl chloride. Benzoyl = Bz = . This is different from benzyl group (there is an extra “o” in the name). It has a carbonyl attached to the benzene ring instead of a methylene group. For example, is named benzoyl chloride. Therefore, it is sometimes helpful to recognize a common structure in order to name a compound. Example: Nomenclature: 3-phenylpentane Example: This is Amaize. It is used to enhance the yield of corn production. The systematic name for this compound is 2,4-dinitro-6-(1-methylpropyl)phenol. Polynuclear Aromatic Compounds Aromatic rings can fuse together to form polynuclear aromatic compounds. Example: It is two benzene rings fused together, and it is aromatic. The electrons are delocalized in both rings (think about all of its resonance form). Example: This compound is also aromatic, including the ring in the middle. All carbons are sp2 hybridized and the electron density is shared across all 5 rings. Example: DDT is an insecticide and helped to wipe out malaria in many parts of the world. Consequently, the person who discovered it (Muller) won the Nobel Prize in 1942. The systematic name for this compound is 1,1,1-trichloro-2,2-bis-(4-chlorophenyl)ethane. -
The Role of Side-Chain Branch Position on Thermal Property of Poly-3-Alkylthiophenes
Polymer Chemistry The Role of Side-chain Branch Position on Thermal Property of Poly-3-alkylthiophenes Journal: Polymer Chemistry Manuscript ID PY-ART-07-2019-001026.R2 Article Type: Paper Date Submitted by the 02-Oct-2019 Author: Complete List of Authors: Gu, Xiaodan; University of Southern Mississippi, School of Polymer Science and Engineering Cao, Zhiqiang; University of Southern Mississippi, School of Polymer Science and Engineering Galuska, Luke; University of Southern Mississippi, School of Polymer Science and Engineering Qian, Zhiyuan; University of Southern Mississippi, School of Polymer Science and Engineering Zhang, Song; University of Southern Mississippi, School of Polymer Science and Engineering Huang, Lifeng; University of Southern Mississippi, School of Polymers and High Performance Materials Prine, Nathaniel; University of Southern Mississippi, School of Polymer Science and Engineering Li, Tianyu; Oak Ridge National Laboratory; University of Tennessee Knoxville He, Youjun; Oak Ridge National Laboratory Hong, Kunlun; Oak Ridge National Laboratory, Center for Nanophase Materials Science; Oak Ridge National Laboratory, Center for Nanophase Materials Science Page 1 of 13 PleasePolymer do not Chemistryadjust margins ARTICLE The Role of Side-chain Branch Position on Thermal Property of Poly-3-alkylthiophenes Received 00th January 20xx, a a a a a a Accepted 00th January 20xx Zhiqiang Cao, Luke Galuska, Zhiyuan Qian, Song Zhang, Lifeng Huang, Nathaniel Prine, Tianyu Li,b, c Youjun He,b Kunlun Hong,*b, c and Xiaodan Gu*a DOI: 10.1039/x0xx00000x Thermomechanical properties of conjugated polymers (CPs) are greatly influenced by both their microstructures and backbone structures. In the present work, to investigate the effect of side-chain branch position on the backbone’s mobility and molecular packing structure, four poly (3-alkylthiophene-2, 5-diyl) derivatives (P3ATs) with different side chains, either branched and linear, were synthesized by a quasi-living Kumada catalyst transfer polymerization (KCTP) method. -
Chapter 21 the Chemistry of Carboxylic Acid Derivatives
Instructor Supplemental Solutions to Problems © 2010 Roberts and Company Publishers Chapter 21 The Chemistry of Carboxylic Acid Derivatives Solutions to In-Text Problems 21.1 (b) (d) (e) (h) 21.2 (a) butanenitrile (common: butyronitrile) (c) isopentyl 3-methylbutanoate (common: isoamyl isovalerate) The isoamyl group is the same as an isopentyl or 3-methylbutyl group: (d) N,N-dimethylbenzamide 21.3 The E and Z conformations of N-acetylproline: 21.5 As shown by the data above the problem, a carboxylic acid has a higher boiling point than an ester because it can both donate and accept hydrogen bonds within its liquid state; hydrogen bonding does not occur in the ester. Consequently, pentanoic acid (valeric acid) has a higher boiling point than methyl butanoate. Here are the actual data: INSTRUCTOR SUPPLEMENTAL SOLUTIONS TO PROBLEMS • CHAPTER 21 2 21.7 (a) The carbonyl absorption of the ester occurs at higher frequency, and only the carboxylic acid has the characteristic strong, broad O—H stretching absorption in 2400–3600 cm–1 region. (d) In N-methylpropanamide, the N-methyl group is a doublet at about d 3. N-Ethylacetamide has no doublet resonances. In N-methylpropanamide, the a-protons are a quartet near d 2.5. In N-ethylacetamide, the a- protons are a singlet at d 2. The NMR spectrum of N-methylpropanamide has no singlets. 21.9 (a) The first ester is more basic because its conjugate acid is stabilized not only by resonance interaction with the ester oxygen, but also by resonance interaction with the double bond; that is, the conjugate acid of the first ester has one more important resonance structure than the conjugate acid of the second. -
Metabolic-Hydroxy and Carboxy Functionalization of Alkyl Moieties in Drug Molecules: Prediction of Structure Influence and Pharmacologic Activity
molecules Review Metabolic-Hydroxy and Carboxy Functionalization of Alkyl Moieties in Drug Molecules: Prediction of Structure Influence and Pharmacologic Activity Babiker M. El-Haj 1,* and Samrein B.M. Ahmed 2 1 Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, University of Science and Technology of Fujairah, Fufairah 00971, UAE 2 College of Medicine, Sharjah Institute for Medical Research, University of Sharjah, Sharjah 00971, UAE; [email protected] * Correspondence: [email protected] Received: 6 February 2020; Accepted: 7 April 2020; Published: 22 April 2020 Abstract: Alkyl moieties—open chain or cyclic, linear, or branched—are common in drug molecules. The hydrophobicity of alkyl moieties in drug molecules is modified by metabolic hydroxy functionalization via free-radical intermediates to give primary, secondary, or tertiary alcohols depending on the class of the substrate carbon. The hydroxymethyl groups resulting from the functionalization of methyl groups are mostly oxidized further to carboxyl groups to give carboxy metabolites. As observed from the surveyed cases in this review, hydroxy functionalization leads to loss, attenuation, or retention of pharmacologic activity with respect to the parent drug. On the other hand, carboxy functionalization leads to a loss of activity with the exception of only a few cases in which activity is retained. The exceptions are those groups in which the carboxy functionalization occurs at a position distant from a well-defined primary pharmacophore. Some hydroxy metabolites, which are equiactive with their parent drugs, have been developed into ester prodrugs while carboxy metabolites, which are equiactive to their parent drugs, have been developed into drugs as per se. -
Methyl Substitution Effects on the Proton Chemical Shifts in Benzene *
Methyl Substitution Effects on the Proton Chemical Shifts in Benzene * G. S. REDDY E. I. du Pont de Nemours & Company, Inc. Explosives Department, Eastern Laboratory, Gibbstown, New Jersey, U.S.A. (Z. Naturforschg. 21 a, 609—615 [1966] ; received 16 December 1965) Methyl substitution effects on aromatic and methyl proton chemical shifts in several mono-, di-, and trimethyl benzenes are studied. A new method for obtaining the changes in the ring proton chemical shifts from those of methyl proton shifts at the corresponding positions is used. The extra jr-electron densities in toluene are calculated using the already known relation between the jr-elec- tron densities and the proton shifts in aromatic systems. An inverse relationship is obtained between the ionization potentials and the total methyl effects on the chemical shifts in this series of com- pounds as one would expect. Dipole moment of toluene is calculated, and a reasonably good agree- ment is found between the experimentally observed and the calculated dipole moment. Several efforts have been made from time to Considerable work has also been done in estimat- time to study the substitution effects on chemical ing ir-electron densities from chemical shift meas- shifts and coupling constants. One of the earliest urements in unsaturated systems. This study in- attempts in this line are those of CAVANAUGH and volves extension of the substitution effects and also DAILEY 1 who tried to study the effect of multiple estimating jr-electron densities in methyl benzenes. methyl substitution in methane. They encountered Eight mono-, di-, and trimethyl substituted benzenes negative shifts contrary to expectations based on have been studied, and a new technique has been inductive and hyperconjugative effects of the methyl deployed to obtain the methyl substitution effects group which eventually was attributed to the an- on the chemical shifts of ring protons from proton isotropy effect of the added C — C bonds 2-7. -
Improved Prediction of Protein Side-Chain Conformations with SCWRL4 Georgii G
proteins STRUCTURE O FUNCTION O BIOINFORMATICS Improved prediction of protein side-chain conformations with SCWRL4 Georgii G. Krivov,1,2 Maxim V. Shapovalov,1 and Roland L. Dunbrack Jr.1* 1 Institute for Cancer Research, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, Pennsylvania 19111 2 Department of Applied Mathematics, Moscow Engineering Physics Institute (MEPhI), Kashirskoe Shosse 31, Moscow 115409, Russian Federation INTRODUCTION ABSTRACT The side-chain conformation prediction problem is an integral Determination of side-chain conformations is an component of protein structure determination, protein structure important step in protein structure prediction and protein design. Many such methods have prediction, and protein design. In single-site mutants and in closely been presented, although only a small number related proteins, the backbone often changes little and structure pre- 1 are in widespread use. SCWRL is one such diction can be accomplished by accurate side-chain prediction. In method, and the SCWRL3 program (2003) has docking of ligands and other proteins, taking into account changes remained popular because of its speed, accuracy, in side-chain conformation is often critical to accurate structure pre- and ease-of-use for the purpose of homology dictions of complexes.2–4 Even in methods that take account of modeling. However, higher accuracy at compara- changes in backbone conformation, one step in the process is recal- ble speed is desirable. This has been achieved in culation of side-chain conformation or ‘‘repacking.’’5 Because many a new program SCWRL4 through: (1) a new backbone conformations may be sampled in model refinements, backbone-dependent rotamer library based on side-chain prediction must also be very fast. -
Molecular Modelling Virtual Chemistry Resource Pymol Experiment Answer Sheet Well Done for Completing Our Pymol Experiment! We Really Hope You Enjoyed It!
#Outtheboxthinking Faculty of Natural & Mathematical Sciences Department of Chemistry Molecular Modelling Virtual Chemistry Resource PyMol Experiment Answer Sheet Well done for completing our PyMol experiment! We really hope you enjoyed it! Please make sure you have completed our post experiment questionnaire. https://kings.onlinesurveys.ac.uk/post-questionnaire-for-outtheboxthinking-resources Send us photos, comments, or thoughts to either our twitter or Instagram accounts using the hashtag #outtheboxthinking. We also encourage you to make a poster of your data and email it to us. Exploring how proteins are formed Press “Amino Acid” Q. What is the R group in the side chain of this amino acid? CH3- Methyl Group Q. Which amino acid is shown here? Alanine Press the button “ALA_ASP” and an additional amino acid will appear Q. What is the chemical formula of the side chain of the new amino acid? CH2COOH Q. What is the name of the second, new amino acid? Aspartic Acid or Aspartate Press the button “Bonded_Ala_Asp” Q. What colour(s) is the amide bond connecting the two amino acids? Blue and green. It is important to highlight the bond between the nitrogen of one amino acid and the carbonyl of the second amino acid and not any other bond (Figure 1). Figure 1: Arrow points to the amide bond formed between two amino acids. Page 1 of 8 Instagram: kclchemoutreach #outtheboxthinking Q. Which elements have been lost from each amino acid following their bonding? Amino acid 1:: Alanine has lost an oxygen and a hydrogen Amino acid 2: Aspartic Acid has lost a hydrogen If you are unsure why this is correct look at figure 2 and open the PyMol document again to visualise the bonding Figure 2: Reaction scheme for amino acid bonding, resulting in the formation of an amide bond and the loss of water. -
Amino Acid Recognition by Aminoacyl-Trna Synthetases
www.nature.com/scientificreports OPEN The structural basis of the genetic code: amino acid recognition by aminoacyl‑tRNA synthetases Florian Kaiser1,2,4*, Sarah Krautwurst3,4, Sebastian Salentin1, V. Joachim Haupt1,2, Christoph Leberecht3, Sebastian Bittrich3, Dirk Labudde3 & Michael Schroeder1 Storage and directed transfer of information is the key requirement for the development of life. Yet any information stored on our genes is useless without its correct interpretation. The genetic code defnes the rule set to decode this information. Aminoacyl-tRNA synthetases are at the heart of this process. We extensively characterize how these enzymes distinguish all natural amino acids based on the computational analysis of crystallographic structure data. The results of this meta-analysis show that the correct read-out of genetic information is a delicate interplay between the composition of the binding site, non-covalent interactions, error correction mechanisms, and steric efects. One of the most profound open questions in biology is how the genetic code was established. While proteins are encoded by nucleic acid blueprints, decoding this information in turn requires proteins. Te emergence of this self-referencing system poses a chicken-or-egg dilemma and its origin is still heavily debated 1,2. Aminoacyl-tRNA synthetases (aaRSs) implement the correct assignment of amino acids to their codons and are thus inherently connected to the emergence of genetic coding. Tese enzymes link tRNA molecules with their amino acid cargo and are consequently vital for protein biosynthesis. Beside the correct recognition of tRNA features3, highly specifc non-covalent interactions in the binding sites of aaRSs are required to correctly detect the designated amino acid4–7 and to prevent errors in biosynthesis5,8. -
2. Proteins Have Hierarchies of Structure
27 2. Proteins have Hierarchies of Structure Protein structure is usually described at four different levels (Fig. II.2.1). The first level, called the primary structure, describes the linear sequence of the amino acids in the chain. The different primary structures correspond to the different sequences in which the amino acids are covalently linked together. The secondary structure describes two common patterns of structural repetition in proteins: the coiling up into helices of segments of the chain, and the pairing together of strands of the chain into β-sheets. The tertiary structure is the next higher level of organization, the overall arrangement of secondary structural elements. The quaternary structure describes how different polypeptide chains are assembled into complexes. Figure II.2.1. Different levels of protein structure. A protein chain’s primary structure is its amino acid sequence. Secondary structure consists of the regular organization of helices and sheets. The example shown is a schematic representation of an α helix. Tertiary structure is a polypeptide chain’s three- dimensional native conformation, which often involves compact packing of secondary structure elements. The example given in the figure is a schematic drawing of one of the four polypeptide chains (subunits) of hemoglobin, the protein that transports oxygen in the blood. α-helices along the chain are represented as cylinders. N is the amino terminus and C is the carboxyl terminus of the polypeptide chain. Quaternary structure is the arrangement of multiple polypeptide chains (subunits) to form a functional biomolecular structure. The figure shows the quaternary arrangement of four subunits to form the functional hemoglobin molecule. -
Functional Groups Kimberly Hatch Harrison
Functional Groups Kimberly Hatch Harrison Functional groups are those small chemical species you see hanging off the outside of a molecule. Just a handful of these functional groups de- termine most of the chemical reactions that happen between biological molecules. If you memorize the chemical behavior of these functional groups, you’ll be able to predict what kinds of reactions biological molecules can do. You can’t open a lock with a screwdriver–the shape of a screwdriver is quite different from a key, which means it has a dif- ferent function. "Form determines function" is something you’ll hear over and over in biochemistry, and that’s because it’s true. The over- all 3-dimensional shape of a molecule allows it to fit into another molecule, like how a key fits into a lock. But not all keys are the same. You have to look closely at the teeth of a key to see which lock it can open. Similarly, you need to look at the details of the outside of a molecule to understand what kinds of chemical interactions it can do with other molecules. How the carbon skeleton of a biological molecule is folded up de- termines its general 3D shape. So that’s one level of understanding– this molecule looks like a key, this one looks like a lock, etc. But then you must look closer, at the surface details, to understand exactly which key, exactly what kind of lock. When you examine the outside of a biological molecule, you can identify which functional groups are standing out on its surface, like little flags. -
Organic Chemistry Nomenclature Guide
Chemistry 222 Organic Chemistry Nomenclature Guide Many molecules in organic chemistry can be named using alkyl groups. MEMORIZE THEM! Common Alkyl (R) Groups Number of Carbons Formula Name 1 -CH3 methyl 2 -CH2CH3 ethyl 3 -CH2CH2CH3 propyl 4 -CH2CH2CH2CH3 butyl 5 -CH2CH2CH2CH2CH3 pentyl 6 -CH2(CH2)4CH3 hexyl 7 -CH2(CH2)5CH3 heptyl 8 -CH2(CH2)6CH3 octyl 9 -CH2(CH2)7CH3 nonyl Alkyl groups are generically referred to as R-groups, where R could be a methyl group, ethyl group, octyl group, etc. Organic compounds are often lumped into families or classes of compounds. The classes we will study this term include the following: R H R O H R O R R X Alcohols Ethers Alkanes Cycloalkanes Alkyl Halides or haloalkanes O O C C C C R C R C R H Ketones Aldehydes Alkynes Alkenes Aromatics H O O O All of these families are detailed in the R N R C R C R C pages that follow. H O H O R NH2 Amides Amines Carboxylic Acids Esters Page IV-20-1 / Organic Chemistry Nomenclature Guide Alkanes Elemental Formula: CnH2n+2 H Nomenclature Guidelines: -yl on alkyl group, +ane to ending Notes: An alkane is an alkyl group plus a hydrogen, often referenced as R-H. H C H Alkanes contain only carbon and hydrogen atoms in long chains with no rings. Each 3 H carbon atom is sp hybridized. Alkanes make great fuels but are generally unreactive. methane, CH4 Example: CH4 - methane - is a methyl group plus a hydrogen (CH3-H) Example: C2H6 - ethane - is a ethyl group plus a hydrogen (CH3CH2-H) Cycloalkanes H Elemental Formula: CnH2n H Nomenclature Guidelines: cyclo+ -yl on alkyl group, +ane to ending C H Notes: Cycloalkanes are alkanes which form an internal ring within the H C C molecule.