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Gas Phase Ion/Molecule Reactions As Studied by Fourier Transform Ion Cyclotron Resonance Mass Spectrometry

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INIS-mf—10165 GAS PHASE ION/MOLECULE REACTIONS AS STUDIED BY FOURIER TRANSFORM ION CYCLOTRON RESONANCE MASS SPECTROMETRY STEEN INGEMANN J0RGENSEN GAS PHASE ION/MOLECULE REACTIONS AS STUDIED BY FOURIER TRANSFORM ION CYCLOTRON RESONANCE MASS SPECTROMETRY ACADEMISCH PROEFSCHRIFT ter verkrijging van de graad van doctor in de Wiskunde en Natuurwetenschappen aan de Universiteit van Amsterdam, op gezag van de Rector Magnificus dr. D.W. Bresters, hoogleraar in de Faculteit der Wiskunde en Natuurwetenschappen, in het openbaar te verdedigen in de Aula der Universiteit (tijdelijk in het Wiskundegebouw, Roetersstraat 15) op woensdag 12 juni 1985 te 16.00 uur. door STEEN INGEMANN J0RGENSEN geboren te Kopenhagen 1985 Offsetdrukkerij Kanters B.V., Alblasserdam PROMOTOR: Prof. Dr. N.M.M. Nibbering Part of the work described in this thesis has been accomplished under the auspices of the Netherlands Foundation for Chemical Research (SON) with the financial support from the Netherlands Organization for the Advancement of Pure Research (ZWO). STELLINGEN 1. De door White e.a. getrokken conclusie, dat het cycloheptatrieen anion omlegt tot het benzyl anion in de gasfase, is onvoldoende ondersteund door de experimentele gegevens. R.L. White, CL. Wilkins, J.J. Heitkamp, S.W. Staley, J. Am. Chem. Soc, _105, 4868 (1983). 2. De gegeven experimentele methode voor de lithiëring van endo- en exo- -5-norborneen-2,3-dicarboximide is niet in overeenstemming met de ge- postuleerde vorming van een algemeen dianion van deze verbindingen. P.J. Garratt, F. Hollowood, J. Org. Chem., 47, 68 (1982). 3. De door Barton e.a. gegeven verklaring voor de observaties, dat O-alkyl- -S-alkyl-dithiocarbonaten reageren met N^-dimethylhydrazine onder vor- ming van ^-alkyl-thiocarbamaten en ^-alkyl-thiocarbazaten, terwijl al- koxythiocarbonylimidazolen uitsluitend £-alkyl-thiocarbazaten geven, is hoogst twijfelachtig. D.H.R. Barton, J. Boivin, S. Legreneur, W.B. Motherwell, J. Chem. Soc, Perkin Trans. I, 1005 (1984). 4. De toepasbaarheid van de Marcus theorie op de deprotonering van carbon- zuren in de gasfase met behulp van ab initio berekeningen houdt te wei- nig rekening met tot nu toe verkregen experimentele gegevens. S. Wolfe, Can. J. Chem., 62_, 1465 (1984). 5. Het zou interessant zijn een structuur te zien van een molecuul met een massa van 100 daltons en een polariseerbaarheid van 100 8 , die door Comisarow wordt voorgesteld als een typisch geval. M.B. Comisarow, Lect. Notes Chem., 31, 484 (1982). 6. Hoewel het idee van Li, dat "Surfaced Enhanced Raman Scattering" (SERS) door een gestimuleerd Raman effect verklaard zou kunnen worden, is zijn uitwerking, die gebaseerd is op een klassieke benadering en die als resultaat enkele vrij in te stellen parameters geeft, onvoldoende. K. Li, Surf. Science, JJ5., 513 (1982). 7. De door Mclver en medewerkers voorgestelde methode voor nauwkeurige me- tingen van massa's van ionen met behulp van FT-ICR is niet op een be- vredigende wijze getest. T.J. Francl, M.G. Sherman, R.L. Hunter, M.J. Locke, W.D. Bowers, R.T. Mclver, Jr., Int. J. Mass Spectrom. Ion Processes, 54, 189 (1983). 8. De door Ross e.a. verworven resultaten geven geen indicatie voor een electron overdrachts mechanisme tijdens de nitrering van naftaleen in een mengsel van zwavelzuur (56-60%) en salpeterzuur, dat ook een kata- lytische hoeveelheid salpeterigzuur bevat. D.R. Ross, K.D. Moran, R. Malhorta, J. Org. Chem., 4£, 2118 (1983). 9. In tegenstelling tot een bewering van Savéant en medewerkers is nog niet bewezen, dat de dimerisatie van radikaal anionen gevormd door electrochemisehe reductie van enkele inonogesubstitueerde anthracenen, verloopt via een eenvoudige koppelingsreactie. L. Amatore, J. Pinson, J.M. Savéant, J. Electroanal. Chem., 137, 143 (1982). J.M. Savéant, Acta Chem. Scand. BJ7, 365 (1983). 10. De toekenning van m/z 603 in het positieve ionen FAB spectrum van cis, + trans-((As)2Fe(CO)2(C(0)Me)(ETPB))BF^(C20H3QAs2Fe06P BF4~) aan het kation van dit complex is te betwijfelen, vanwege het ontbreken van isotoop pieken. B. Gregory, C.R. Jablonski, Y.P. Wang, J. Organomet. Chem., 26£, 74 (1984). Steen Ingemann Jdrgensen Amsterdam, 12 juni 1985 tilegnet Sonja og Asbjdrn VOORWOORD Bij de voltooiing van dit proefschrift wil ik graag mijn dank betuigen aan allen die op wetenschappelijke of sociale wijze hebben bijgedragen aan de totstandkoming ervan. In de eerste plaats wil ik mijn promotor Nico M.M. Nibbering bedanken voor de unieke gelegenheid die hij mij bood om onderzoek te verrichten op een zeer boeiend terrein van de scheikunde. Mijn (ex)collega's J.C. Kleingeld, L.J. de Koning en H. van der Wel wil ik graag bedanken voor de plezierige samenwerking tijdens mijn promotieperiode. De heren F.A. Pinkse, J.P.J. Brandt en K.J. Jansen bedank ik voor hun her- haaldelijke technische steun, die onmisbaar is geweest voor het uitvoeren van de experimenten. Aan mijn (ex)collega's van de massaspectrometrie groep: R. Bregman, J.W. Dal- linga, J.H.J. Dawson, R.H. Fokkens, E. Kluft, C.W.F. Kort, W. de Lange, W.P.M. Maas, T.A. Molenaar-Langeveld, A.J. Noest, R.P.H. Peerboom, H. Zappey en J.J. Zwinselman, bewaar ik plezierige herinneringen. I would like to thank V.M. Bierbaum, C.H. DePuy, J.J. Grabowski and S.A. Sul- livan for their contributions to part of the work described in this thesis, and M.L. Gross, 0. Hammerich, S. Hammerum, L. Jansen, P.v.R. Schleyer, H. Schwarz, R.R. Squires and G.H. Wegdam for stimulating discussions. Tenslotte wil ik E.H. Hoogeveen bedanken voor de wijze waarop zij dit proef- schrift heeft uitgetypt en J.W.H. Peeters voor het maken van tekeningen en foto's. LIST OF ABBREVIATIONS ADC Analog to Digital Converter ADO Average Dipole Orientation theory BDE Bond Dissociation Energy CID Collision Induced Dissociation CIMS Chemical Ionization Mass Spectrometry DMF N,N-Dimethylformamide DMNA N,N-Dimethyl-N-nitrosamine DMTF N,N-Dimethylthioformamide EA Electron Affinity FA Flowing Afterglow FT-ICR Fourier Transform Ion Cyclotron Resonance GC Gas Chromatography HPMS High Pressure Mass Spectrometry HSAB Hard and Soft Acids and Bases theory ICR Ion Cyclotron Resonance IE Ionization Energy MCA Methyl Cation Affinity MF Methyl Formate PA Proton Affinity PES " Photoelectron Spectroscopy RF Radio Frequency RRKM Rice-Ramsperger-Kassel-Marcus theory SIFT Selected Ion Flow Tube S/N Signal to Noise ratio NON-SI UNITS eV Electron Volt (96.485 kJ inch 0.0254 m D Debye (3.3356.10~30 Cm) erg 10~7 J CONTENTS INTRODUCTION CHAPTER 1. BASIC ASPECTS OF GAS PHASE ION/MOLECULE REACTIONS Introduction 4 Ion/molecule collision rate theory 5 Kinetic description and potential energy surface 8 Thermochemical quantities 11 References 14 CHAPTER 2. EXPERIMENTAL METHODS 18 Introduction 18 Basic principles and development of ICR spectroraetry 18 Fourier Transform Ion Cyclotron Resonance 20 Experimental procedure 26 Flowing Afterglow and Selected Ion Flow Tube 27 References 28 CHAPTER 3. NUCLEOPHILIC AROMATIC SUBSTITUTION IN THE GAS PHASE: THE IMPORTANCE OF F~ ION/MOLECULE COMPLEXES FORMED IN GAS PHASE REACTIONS BETWEEN NUCLEOPHILES AND SOME ALKÏL PENTAFLUOROPHENYL ETHERS 33 Introduction 33 Results 34 Primary negative ion formation from pentafluoroanisole 34 General reactivity of pentafluoroanisole 36 Oxygen nucleophiles 38 Sulfur nucleophiles 40 Nitrogen nucleophiles 40 Enolate anions 40 Allyl anions 42 Discussion 43 Charge-localized nucleophile 44 Enolate anions 50 Allyl anions 52 Conclusion 55 Materials 55 References 55 CHAPTER 4. GAS PHASE REACTIONS OF ANIONS WITH 2-, 3-, AND 4-FLUOROANISOLE 58 Introduction 58 Results 59 Acidities 62 Hydrogen-deuterium exchange reactions 62 Formation of C-.Ht.F" 62 S..2 substitution 62 IPSO substitution 64 Attack on the fluorine-bearing carbon atom 65 Discussion 66 Acidities 66 Formation of the C,H,,F~ ion 67 Hydrogen-deuterium exchange reactions 68 Nuclecphilic aromatic substitution 70 Competition between reaction channels 74 Conclusions 76 Materials 76 References 77 CHAPTER 5. GAS PHASE CHEMISTRY OF a-THIO CARBANIONS 80 Introduction 80 Results 81 CH SCH 81 86 Discussion 91 Ion structures 91 Acidities 93 Reactivity 96 Conclusion 97 Materials 97 References 97 CHAPTER 6. GAS PHASE REACTIONS OF ANIOHS WITH METHYL FORMATE AND N.N-DIMETHYLFORMAMIDE 100 Introduction 100 Results 101 General reactivity of methyl formate 101 General reactivity of N,N-dimethylformamide 108 Discussion 111 Methyl formate 111 a-Elimination 111 Carbonyl addition reactions 113 S..2 Reaction 115 N N,N-Dimethylformamide 115 a-Elimination 115 Carbonyl addition 116 References 117 CHAPTER 7. ON THE DIPOLE STABILIZED CARBANIONS DERIVED FROM METHYL FORMATE AND N,N-DIMETHYLFORMAMIDE 119 Introduction 119 Results 120 Methyl formate 120 N,N-Dimethylformamide 125 Discussion 129 Methyl formate 129 Acidities 129 Ion structures 130 N,N-Dimethylformamide 136 Acidities 136 Ion structures 137 Dipole stabilization 140 Conclusions 141 Materials 141 References 141 CHAPTER 8. GAS PHASE CHEMISTRY OF DIPOLE STABILIZED CARBANIONS DERIVED FROM N,N-DIMETHYLTHIOFORMAMIDE AND N,N- -DIMETHYL-N-NITROSAMINE 144 Introduction 144 Results 144 N,N-Dimethylthioformamide 144 N,N-Dimethyl-N-nitrosaraine 145 Discussion 148 Materials 151 References 152 CHAPTER 9. ISOMERIC C HgO~ IONS FORMED IN GAS PHASE REACTIONS OF ANIONS WITH 2,2-DIMETHYLPROPANAL AND 2,2-DIMETHYL- CYCLOPROPANOL 154 Introduction 154 Results 154 2,2-Dimethylpropanal 154 2,2-Dimethylcyclopropanol 157 Discussion 159 Acidities 159 Ion structures 160 Materials 163 References 163 SUMMARY 166 SAMENVATTING 169 INTRODUCTION The chemistry of ions in the gas phase i* 'an established but continuously expanding research field. This is refleered in several recently published monographs and reviews which cover fundamental and analytical aspects of the chemistry of positive as well as negative ions in the gas phase. Knowledge of the structure, stability and reactivity of gaseous ions is important partly because solvent molecules and counterions can exert a domi- nant influence on the chemistry of ions in solution.
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    Ch4206.qxd 03/15/2000 08:57 Page 166 166 Metal ions in ribozyme folding and catalysis Raven Hanna* and Jennifer A Doudna† Current research is reshaping basic theories regarding the state. This ‘two-metal-ion model’ became the standard to roles of metal ions in ribozyme function. No longer viewed as which subsequent experimental observations were com- strict metalloenzymes, some ribozymes can access alternative pared, and upon which most current theories are based. catalytic mechanisms depending on the identity and availability of metal ions. Similarly, reaction conditions can allow different Catalytic metal ions of the group I intron folding pathways to predominate, with divalent cations Of the large ribozymes, most is known about catalysis by the sometimes playing opposing roles. Tetrahymena thermophila group I intron, which performs a two- step transesterification reaction using a single active site. It is Addresses generally studied in multiple-turnover form, only executing Department of Molecular Biophysics and Biochemistry and †Howard the cleavage portion of the splicing reaction, where the Hughes Medical Institute, Yale University, 266 Whitney Ave, intron catalyzes nucleophilic attack of the 3′ hydroxyl of a New Haven, CT 06520, USA bound guanosine on a specific phosphodiester bond in a *e-mail: [email protected] †e-mail: [email protected] bound oligonucleotide substrate. Its tightly folded catalytic core positions divalent cations around the labile bond to sta- Current Opinion in Chemical Biology 2000, 4:166–170 bilize the transition state. Assembling details about the 1367-5931/00/$ — see front matter chemical environment of the active site is critical for under- © 2000 Elsevier Science Ltd.
  • The Synthesis and Characterisation of a New Tröger's Base Content

    The Synthesis and Characterisation of a New Tröger's Base Content

    Sys Rev Pharm 2020;11(7):319-323 A multifaceted review journal in the field of pharmacy The Synthesis and Characterisation of a New Tröger’s Base Content Methoxy Group Sadiq A. Karim1, Mohammed H. Said2, Jinan A. Abd3, Asim A. Balakit4, Ayad F. Alkaim5 1,2,5Chemistry department, College of Science for women, University of Babylon, Iraq. 3Department of Laser physics, College of Science for women, University of Babylon, Iraq. 4Pharmaceutical Chemistry department, College of Pharmacy, University of Babylon, Iraq. Corresponding author: [email protected] ABSTRACT Five Tröger’s base (TB) molecules were synthesized by reaction aniline’s Keywords: Tröger base, heterocyclic compounds, chirality derivatives which content a methoxy group with a supplement of methylene (dimethoxymethane (DMM)) in present trifluoroacetic acid (TFA) as a solvent Correspondence: and catalyst. This method afforded a good ratio product between 62% to 99%, Sadiq A. Karim1 all products were conforming by FTIR, HRMs, 1HNMR, 13CNMR, and XRD. 1,2,5Chemistry department, College of Science for women, University of Babylon, Iraq. Corresponding author: [email protected] INTRODUCTION collected by filtration and was dried in a vacuum oven at The first Tröger’s base was create in 1887 by Julius Tröger 50 °C for 2 h. during his Ph.D. studied, this compound was called Tröger base 1 (TB1) which from the condensation of methanal 1- Synthesis of 2,9-Dimethoxy-6H,12H-5,11- with 4-aminotoluene in HCl-catalysed media.1 The TB1 methanodibenzo[b,f](1,5)diazocine (TB-OCH3-1) (2,8-dimethyl-6H,12H-5,11- General procedure was followed using m-anisidine (9.1 methanodibenzo[b,f][1,5]diazocine) was conformed ml, 10.00 g, 81.20 mmol), DMM (10.8 ml, 9.269 g, 121.80 structure through chemical reaction by M.