Introduction to Ionic Mechanisms Part I: Fundamentals of Bronsted-Lowry Acid-Base Chemistry
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Choosing Buffers Based on Pka in Many Experiments, We Need a Buffer That Maintains the Solution at a Specific Ph. We May Need An
Choosing buffers based on pKa In many experiments, we need a buffer that maintains the solution at a specific pH. We may need an acidic or a basic buffer, depending on the experiment. The Henderson-Hasselbalch equation can help us choose a buffer that has the pH we want. pH = pKa + log([conj. base]/[conj. acid]) With equal amounts of conjugate acid and base (preferred so buffers can resist base and acid equally), then … pH = pKa + log(1) = pKa + 0 = pKa So choose conjugates with a pKa closest to our target pH. Chemistry 103 Spring 2011 Example: You need a buffer with pH of 7.80. Which conjugate acid-base pair should you use, and what is the molar ratio of its components? 2 Chemistry 103 Spring 2011 Practice: Choose the best conjugate acid-base pair for preparing a buffer with pH 5.00. What is the molar ratio of the buffer components? 3 Chemistry 103 Spring 2011 buffer capacity: the amount of strong acid or strong base that can be added to a buffer without changing its pH by more than 1 unit; essentially the number of moles of strong acid or strong base that uses up all of the buffer’s conjugate base or conjugate acid. Example: What is the capacity of the buffer solution prepared with 0.15 mol lactic acid -4 CH3CHOHCOOH (HA, Ka = 1.0 x 10 ) and 0.20 mol sodium lactate NaCH3CHOHCOO (NaA) and enough water to make 1.00 L of solution? (from previous lecture notes) 4 Chemistry 103 Spring 2011 Review of equivalence point equivalence point: moles of H+ = moles of OH- (moles of acid = moles of base, only when the acid has only one acidic proton and the base has only one hydroxide ion). -
The Strongest Acid Christopher A
Chemistry in New Zealand October 2011 The Strongest Acid Christopher A. Reed Department of Chemistry, University of California, Riverside, California 92521, USA Article (e-mail: [email protected]) About the Author Chris Reed was born a kiwi to English parents in Auckland in 1947. He attended Dilworth School from 1956 to 1964 where his interest in chemistry was un- doubtedly stimulated by being entrusted with a key to the high school chemical stockroom. Nighttime experiments with white phosphorus led to the Headmaster administering six of the best. He obtained his BSc (1967), MSc (1st Class Hons., 1968) and PhD (1971) from The University of Auckland, doing thesis research on iridium organotransition metal chemistry with Professor Warren R. Roper FRS. This was followed by two years of postdoctoral study at Stanford Univer- sity with Professor James P. Collman working on picket fence porphyrin models for haemoglobin. In 1973 he joined the faculty of the University of Southern California, becoming Professor in 1979. After 25 years at USC, he moved to his present position of Distinguished Professor of Chemistry at UC-Riverside to build the Centre for s and p Block Chemistry. His present research interests focus on weakly coordinating anions, weakly coordinated ligands, acids, si- lylium ion chemistry, cationic catalysis and reactive cations across the periodic table. His earlier work included extensive studies in metalloporphyrin chemistry, models for dioxygen-binding copper proteins, spin-spin coupling phenomena including paramagnetic metal to ligand radical coupling, a Magnetochemi- cal alternative to the Spectrochemical Series, fullerene redox chemistry, fullerene-porphyrin supramolecular chemistry and metal-organic framework solids (MOFs). -
A Guide to Acids, Acid Strength, and Concentration
A GUIDE TO ACIDS, ACID STRENGTH, AND CONCENTRATION What’s the difference between acid strength and concentration? And how does pH fit in with these? This graphic explains the basics. CH COOH HCl H2SO4 HNO3 H3PO4 HF 3 H2CO3 HYDROCHLORIC ACID SULFURIC ACID NITRIC ACID PHOSPHORIC ACID HYDROFLUORIC ACID ETHANOIC ACID CARBONIC ACID pKa = –7 pKa = –2 pKa = –2 pKa = 2.12 pKa = 3.45 pKa = 4.76 pKa = 6.37 STRONGER ACIDS WEAKER ACIDS STRONG ACIDS VS. WEAK ACIDS ACIDS, Ka AND pKa CONCENTRATION AND pH + – The H+ ion is transferred to a + A decrease of one on the pH scale represents + [H+] [A–] pH = –log10[H ] a tenfold increase in H+ concentration. HA H + A water molecule, forming H3O Ka = pKa = –log10[Ka] – [HA] – – + + A + + A– + A + A H + H H H H A H + H H H A Ka pK H – + – H a A H A A – + A– A + H A– H A– VERY STRONG ACID >0.1 <1 A– + H A + + + – H H A H A H H H + A – + – H A– A H A A– –3 FAIRLY STRONG ACID 10 –0.1 1–3 – – + A A + H – – + – H + H A A H A A A H H + A A– + H A– H H WEAK ACID 10–5–10–3 3–5 STRONG ACID WEAK ACID VERY WEAK ACID 10–15–10–5 5–15 CONCENTRATED ACID DILUTE ACID + – H Hydrogen ions A Negative ions H A Acid molecules EXTREMELY WEAK ACID <10–15 >15 H+ Hydrogen ions A– Negative ions Acids react with water when they are added to it, The acid dissociation constant, Ka, is a measure of the Concentration is distinct from strength. -
Superacid Chemistry
SUPERACID CHEMISTRY SECOND EDITION George A. Olah G. K. Surya Prakash Arpad Molnar Jean Sommer SUPERACID CHEMISTRY SUPERACID CHEMISTRY SECOND EDITION George A. Olah G. K. Surya Prakash Arpad Molnar Jean Sommer Copyright # 2009 by John Wiley & Sons, Inc. All rights reserved Published by John Wiley & Sons, Inc., Hoboken, New Jersey Published simultaneously in Canada No part of this publication may be reproduced, stored in a retrieval system, or transmitted in any form or by any means, electronic, mechanical, photocopying, recording, scanning, or otherwise, except as permitted under Section 107 or 108 of the 1976 United States Copyright Act, without either the prior written permission of the Publisher, or authorization through payment of the appropriate per-copy fee to the Copyright Clearance Center, Inc., 222 Rosewood Drive, Danvers, MA 01923, (978) 750-8400, fax (978) 750-4470, or on the web at www.copyright.com. Requests to the Publisher for permission should be addressed to the Permissions Department, John Wiley & Sons, Inc., 111 River Street, Hoboken, NJ 07030, (201) 748-6011, fax (201) 748-6008, or online at http://www.wiley.com/go/permission. Limit of Liability/Disclaimer of Warranty: While the publisher and author have used their best efforts in preparing this book, they make no representations or warranties with respect to the accuracy or completeness of the contents of this book and specifically disclaim any implied warranties of merchantability or fitness for a particular purpose. No warranty may be created or extended by sales representatives or written sales materials. The advice and strategies contained herein may not be suitable for your situation. -
Reactivity Landscape of Pyruvate Under Simulated Hydrothermal Vent
Reactivity landscape of pyruvate under simulated SEE COMMENTARY hydrothermal vent conditions Yehor Novikova and Shelley D. Copleyb,c,1 aDepartment of Chemistry and Biochemistry, bDepartment of Molecular, Cellular, and Developmental Biology, and cCooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, CO 80309 Edited by Paul G. Falkowski, Rutgers, The State University of New Jersey, New Brunswick, NJ, and approved June 14, 2013 (received for review March 14, 2013) Pyruvate is an important “hub” metabolite that is a precursor for concentrations of many components (4). Fig. 1 shows an example in amino acids, sugars, cofactors, and lipids in extant metabolic net- which the availability of catalysts for different steps in a network works. Pyruvate has been produced under simulated hydrother- results in significantly different network topologies and accumu- mal vent conditions from alkyl thiols and carbon monoxide in the lation of different products. Network topology also depends on the presence of transition metal sulfides at 250 °C [Cody GD et al. set of reagents available and the concentrations of those reagents. K (2000) Science 289(5483):1337–1340], so it is plausible that pyru- For example, the network depicted in Fig. 1 would form only and M H J M vate was formed in hydrothermal systems on the early earth. We if no were available, and would form only and if the concentration of H were very high (assuming equal rate constants report here that pyruvate reacts readily in the presence of transi- D tion metal sulfide minerals under simulated hydrothermal vent for the partitioning of between the two possible pathways). -
Drugs and Acid Dissociation Constants Ionisation of Drug Molecules Most Drugs Ionise in Aqueous Solution.1 They Are Weak Acids Or Weak Bases
Drugs and acid dissociation constants Ionisation of drug molecules Most drugs ionise in aqueous solution.1 They are weak acids or weak bases. Those that are weak acids ionise in water to give acidic solutions while those that are weak bases ionise to give basic solutions. Drug molecules that are weak acids Drug molecules that are weak bases where, HA = acid (the drug molecule) where, B = base (the drug molecule) H2O = base H2O = acid A− = conjugate base (the drug anion) OH− = conjugate base (the drug anion) + + H3O = conjugate acid BH = conjugate acid Acid dissociation constant, Ka For a drug molecule that is a weak acid The equilibrium constant for this ionisation is given by the equation + − where [H3O ], [A ], [HA] and [H2O] are the concentrations at equilibrium. In a dilute solution the concentration of water is to all intents and purposes constant. So the equation is simplified to: where Ka is the acid dissociation constant for the weak acid + + Also, H3O is often written simply as H and the equation for Ka is usually written as: Values for Ka are extremely small and, therefore, pKa values are given (similar to the reason pH is used rather than [H+]. The relationship between pKa and pH is given by the Henderson–Hasselbalch equation: or This relationship is important when determining pKa values from pH measurements. Base dissociation constant, Kb For a drug molecule that is a weak base: 1 Ionisation of drug molecules. 1 Following the same logic as for deriving Ka, base dissociation constant, Kb, is given by: and Ionisation of water Water ionises very slightly. -
Infrared Spectroscopy of Protonated Acetic Acid
Probing Elusive Cations: Infrared Spectroscopy of Protonated Acetic Acid Julia A. Davies,a) Nicholas A. Besley,b) Shengfu Yanga) and Andrew M. Ellisa),* a) Department of Chemistry, University of Leicester, University Road, Leicester, LE1 7RH, UK b) School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, UK *Corresponding author: Email: [email protected] Manuscript submitted to The Journal of Physical Chemistry Letters 1 Abstract Protonated carboxylic acids, (RCOOH)H+, are the initial intermediates in acid-catalyzed (Fischer) esterification reactions. However the identity of the isomeric form is under debate. Surprisingly, no optical spectra have been reported for any isomer of the protonated carboxylic acid monomer, despite it being a fundamental organic cation. Here, we address these issues by using a new approach to prepare cold He-tagged cations of protonated acetic acid (AA), which entails electron ionization of helium nanodroplets containing metastable dimers of AA. The protonated species is subsequently probed using infrared photodissociation spectroscopy and, following a comparison with calculations, we identify the two isomers whose roles are debated in Fischer esterification. These are the carbonyl-protonated E,Z isomer and the metastable hydroxyl-protonated isomer. Our technique provides a novel approach that can be applied to other elusive ionic species. TOC Graphic 2 The mechanism of the acid-catalyzed (Fischer) esterification of carboxylic acids was first explored in detail in the 1930s.1,2 This early mechanistic work suggested that initial protonation occurs at the hydroxyl oxygen atom. In the case of an acetic acid monomer (AA), this leads to formation of the structure labelled as prot-OH in Figure 1. -
Protonation Patterns in Reduced and Oxidized Forms of Electron Transfer Proteins
Protonation patterns in reduced and oxidized forms of electron transfer proteins Dissertation For the award of the degree “doctor rerum naturalium” Division of Mathematics and Natural Sciences of the Georg-August-Universit¨at G¨ottingen submitted by Plamen Dobrev from Harmanli G¨ottingen 2012 Prof. Dr. Helmut Grubm¨uller (Reviewer) Department of Theoretical and Computational Biophysics, Max Planck In- stitute for Biophysical Chemistry G¨ottingen Prof. Dr. Marcus M¨uller (Reviewer) Institute for Theoretical Physics, Georg August University G¨ottingen Prof. Dr. Claudia Steinem Institute for Organic and Biomolecular Chemistry, Georg August University G¨ottingen Date of the oral examination: 08.05.2012 1 It is declared that the presented thesis has been written independently and with no other sources and aids than quoted. G¨ottingen, 10.04.2012 Plamen Dobrev 2 Contents 1 Introduction 6 2 Theory and Methods 13 2.1 Moleculardynamics........................ 13 2.2 pKa calculations of an acid in solution . 15 2.3 Free Energy calculation of deprotonation of an amino acid in MDsimulation .......................... 17 2.4 pKa calculation of ionizable groups in proteins using constant pHMD .............................. 19 2.5 Construction of the model compounds and the titratable amino acidsintheprotein ........................ 23 2.5.1 Residues with Carboxyl titratable group . 24 2.5.2 Histidine . 26 2.5.3 Tyrosine.......................... 27 2.5.4 Modelcompounds.. .. 27 2.6 Keeping the simulation box neutral upon protonation or de- protonation ............................ 29 2.6.1 Thechangeoftheionicstrength. 29 2.6.2 Restraing the coupled water molecules and the entropy change due tothe restraining potential . 30 3 2.6.3 Distance between the titrating site and the coupled watermolecule ..................... -
Intact Carbonic Acid Is a Viable Protonating Agent for Biological Bases
Intact carbonic acid is a viable protonating agent for biological bases Daniel Aminova, Dina Pinesa, Philip M. Kieferb, Snehasis Daschakrabortyb,1, James T. Hynesb,c,2, and Ehud Pinesa,2 aDepartment of Chemistry, Ben-Gurion University of the Negev, 84105 Beer-Sheva, Israel; bDepartment of Chemistry, University of Colorado Boulder, Boulder, CO 80309-0215; and cPASTEUR, Départmente de Chimie, Ecole Normale Supérieure, PSL Research University, Sorbonne Université, UPMC Université Paris 06, CNRS, 75005 Paris, France Contributed by James T. Hynes, August 28, 2019 (sent for review June 3, 2019; reviewed by Graham R. Fleming and Sharon Hammes-Schiffer) Carbonic acid H2CO3 (CA) is a key constituent of the universal CA/ plasma’s buffer capacity and about 53% of the whole blood ca- bicarbonate/CO2 buffer maintaining the pH of both blood and the pacity (16, 17) and, as the blood’s “front-line” buffer, is extremely oceans. Here we demonstrate the ability of intact CA to quantita- important for human physiology (7, 8). It is regulated in the body by tively protonate bases with biologically-relevant pKas and argue one of nature’s most efficient enzymes, carbonic anhydrase (18, 19). that CA has a previously unappreciated function as a major source − It is crucial that the very large HCO3 concentration (26 through of protons in blood plasma. We determine with high precision the 28 mM) (1, 2, 7–9) in equilibrium with CA makes CA a permanent = − + + temperature dependence of pKa(CA), pKa(T) 373.604 16,500/T factor in the plasma, with an equilibrium 2–3 μM concentration, 56.478 ln T. -
Characterization of the Acidity of Sio2-Zro2 Mixed Oxides
Characterization of the acidity of SiO2-ZrO2 mixed oxides Citation for published version (APA): Bosman, H. J. M. (1995). Characterization of the acidity of SiO2-ZrO2 mixed oxides. Technische Universiteit Eindhoven. https://doi.org/10.6100/IR436698 DOI: 10.6100/IR436698 Document status and date: Published: 01/01/1995 Document Version: Publisher’s PDF, also known as Version of Record (includes final page, issue and volume numbers) Please check the document version of this publication: • A submitted manuscript is the version of the article upon submission and before peer-review. There can be important differences between the submitted version and the official published version of record. People interested in the research are advised to contact the author for the final version of the publication, or visit the DOI to the publisher's website. • The final author version and the galley proof are versions of the publication after peer review. • The final published version features the final layout of the paper including the volume, issue and page numbers. Link to publication General rights Copyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights. • Users may download and print one copy of any publication from the public portal for the purpose of private study or research. • You may not further distribute the material or use it for any profit-making activity or commercial gain • You may freely distribute the URL identifying the publication in the public portal. -
Methylation Deficiency Disrupts Biological Rhythms from Bacteria To
ARTICLE https://doi.org/10.1038/s42003-020-0942-0 OPEN Methylation deficiency disrupts biological rhythms from bacteria to humans ✉ Jean-Michel Fustin 1,16,18 , Shiqi Ye1,18, Christin Rakers 2, Kensuke Kaneko3, Kazuki Fukumoto1, Mayu Yamano1, Marijke Versteven4, Ellen Grünewald5, Samantha J. Cargill5, T. Katherine Tamai 6, Yao Xu7, Maria Luísa Jabbur7, Rika Kojima8, Melisa L. Lamberti9, Kumiko Yoshioka-Kobayashi10, David Whitmore 11, 1234567890():,; Stephanie Tammam12, P. Lynne Howell 12,13, Ryoichiro Kageyama10, Takuya Matsuo14, Ralf Stanewsky 4, Diego A. Golombek9, Carl Hirschie Johnson7, Hideaki Kakeya 3, Gerben van Ooijen 5 & ✉ Hitoshi Okamura15,17 The methyl cycle is a universal metabolic pathway providing methyl groups for the methy- lation of nuclei acids and proteins, regulating all aspects of cellular physiology. We have previously shown that methyl cycle inhibition in mammals strongly affects circadian rhythms. Since the methyl cycle and circadian clocks have evolved early during evolution and operate in organisms across the tree of life, we sought to determine whether the link between the two is also conserved. Here, we show that methyl cycle inhibition affects biological rhythms in species ranging from unicellular algae to humans, separated by more than 1 billion years of evolution. In contrast, the cyanobacterial clock is resistant to methyl cycle inhibition, although we demonstrate that methylations themselves regulate circadian rhythms in this organism. Mammalian cells with a rewired bacteria-like methyl cycle are protected, like cyanobacteria, from methyl cycle inhibition, providing interesting new possibilities for the treatment of methylation deficiencies. 1 Graduate School of Pharmaceutical Sciences, Laboratory of Molecular Metabology, Kyoto University, Kyoto, Japan. -
The Role of Protonation States in Ligand-Receptor Recognition and Binding Marharyta Petukh Clemson University
Clemson University TigerPrints Publications Physics and Astronomy 5-2013 The Role of Protonation States in Ligand-Receptor Recognition and Binding Marharyta Petukh Clemson University Shannon Stefl Clemson University Emil Alexov Clemson University, [email protected] Follow this and additional works at: https://tigerprints.clemson.edu/physastro_pubs Part of the Biological and Chemical Physics Commons Recommended Citation Please use publisher's recommended citation. This Article is brought to you for free and open access by the Physics and Astronomy at TigerPrints. It has been accepted for inclusion in Publications by an authorized administrator of TigerPrints. For more information, please contact [email protected]. NIH Public Access Author Manuscript Curr Pharm Des. Author manuscript; available in PMC 2013 May 30. NIH-PA Author ManuscriptPublished NIH-PA Author Manuscript in final edited NIH-PA Author Manuscript form as: Curr Pharm Des. 2013 ; 19(23): 4182–4190. The Role of Protonation States in Ligand-Receptor Recognition and Binding Marharyta Petukh1, Shannon Stefl1, and Emil Alexov1 1Computational Biophysics and Bioinformatics, Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA Abstract In this review we discuss the role of protonation states in receptor-ligand interactions, providing experimental evidences and computational predictions that complex formation may involve titratable groups with unusual pKa’s and that protonation states frequently change from unbound to bound states. These protonation changes result in proton uptake/release, which in turn causes the pH-dependence of the binding. Indeed, experimental data strongly suggests that almost any binding is pH-dependent and to be correctly modeled, the protonation states must be properly assigned prior to and after the binding.