Spectroscopy Vs Spectrometry

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Spectroscopy vs spectrometrySpectroscopyLatin specere“to look at”Greek skopia“to see”-metryGreek metria“process of measuring”Spectroscopy traditionally involves the absorption of some type ofenergy leading to an “excited state” that is subsequently emitted This returns the molecule to the initial state non-destructively.Energy of excitation is just enough to promote a ground state to anexcited state no more, no less because it is quantizedTypical examples: UV-vis, fluorescence, IR, NMRVersus typically destructive techniques (mass spec) or thosethat involve the scattering of radiation (X-ray crystallography)

Spectroscopic methods: what are the goals?Molecular information:Identity- Constitution: number and types of atoms in the molecule- Configuration: position of the atoms in space- Conformation: isomers derived from rotation about single bondsPurityDynamic information:Rates- follow functional group changes with in situ IR- UV-vis for enzyme kineticsEquilibria- temperature dependent NMR studies of interconverting isomersReaction progress- workup and measure an aliquot from a reaction

What information do we ultimately want?Molecular formulaFunctional group presenceCarbon skeletonPresence of heteroatomsPresence of “unsaturation” (rings, multiple bonds)Stereochemical relationshipsWhat are the available techniques to give this information?

Basically, this section is about solving puzzles.You must piece together bits of data (“givens”) such that themolecule is consistent with the data (“the story checks out”)Sometimes, the data will give direct insight, andOther times you must make leaps of faithDan has 2 eggs, Sue has 2 eggs.How many does Dan have?Vs.Dan and Sue have 4 eggs.How many does Dan have?The problem solving aspect makes this class a lot of fun,and very frustrating.

Similarities to logic problemsThere is no “right way” to approach these just as there is no “right way” to approachspectral interpretation. The best way to build proficiency is to do problems!I will show you what works for me along the way.

Crews, Rodríguez, Jaspars. Organic Structural Analysis Table 1.1

Timeline of available techniquesElemental analysis (combustion)Melting point, boiling pointChemical reactivity and degradation: derivativesUltraviolet-visible (UV-vis) - 1930sWoodward-Fieser Rules ca. 1941Circular dichroism 1960sInfrared (IR) - 1940sFunctional groups, molecular fingerprintsRaman spectroscopy 1960sMass spectrometry (MS) - 1950sMolecular weights, and observation of key fragmentsCharacteristic reactivity molecular fingerprintsNuclear magnetic resonance (NMR) - 1960sFourier Transform NMR 1970s2-D correlation spectroscopies 1980s

What energies are involved?E hν hc/λFrequencyHz or s-1Wavelengthmh: Planck’s constant (Js)c: speed of light (m/s)We can and will think of these units as s-100sof eVUV-vis100sof nmIR1000sof cm-1 to NMR100sof ppm

Step 1: obtain compound

Step 2: molecular formulaHaving the molecular formula will allow us to startmaking guesses of the structure(or more regally, proposing structures)How? By drawing constitutional isomers!(this was not simply an exercise in busy work)How do we obtain a molecular formula?Falzone, Townsend and Tovar will not always be aroundoo give you one on an exam

Elemental Analysis: Empirical formulaePavia et al, Introduction to Spectroscopy

ProblemWhat is the formula of our molecule?C7H14O2?C14H28O4?C21H42O6? ?

Types of mass and their decimal needsUnit Mass vs. exact mass:SWK Chapter 1 Appendix AUnit mass: integral valuesC 12O 16e.g. 55C 2H 3N 2C 3H 3OC 3H 5NC 4H 755.029755.018455.042255.0548A high resolution exactmass determination is nowacceptable to verify identityand to establish purity!Silverstein,Spectrometric Identificationof Organic CompoundsMolecular weight for stoichiometry:two decimalsbased on natural abundancea weighted valueC 12.011 (12C 98.9 13C 1.1%)O 15.9994Exact mass: four decimalsweight of a specific isotope12C 12.000013C 13.0033616O 15.994918O 17.9992

Basics of mass spectrometryUsing a mass spectrometer, we will ionize an analyte and thenDetect it (the details of this will not be covered here).In one typical example, the molecule is bombarded with high energyElectrons, that cause an electron to be ejected from the analyte.(called “electron impact” mass spec)In mass spec, we can only detect charged speciesThe energy of this impact renders the ionized molecule subject toFragmentation chemistries leading to smaller but still charged structures

Electron impact MSHigh energy (ca. 70 eV) electrons bombard a vaporized analyteThis collision strips an electron from the analyteM e–- M 2 e–(M is the “molecular ion”)The ionization potential of most organics is ca. 15 eV,so the M has a lot of excess energyRecall that a covalent bond is ca. 3-10 eV this excess energyleads to bond cleavages and molecular rearrangements.How likely is the observation of M ?Can anything useful be deduced from these reactions?

Relative energies, apologies to a flyThis is IRThis is UV-visThis is MS

The mass spectrumMolecularionBase peakSWKFragment ions:Characteristic for a particularfunctional group or compound![M-16] or[M-NH2]

Predicting molecular formulaeIf we don’t know the identity of the analyte, we can use the M inmany situations to start our search for a molecular formula.“Rule of 13” given that this is an organic chemistry course, it isfair to assume that we will have at least a CH group 13 amuObserve M , divide it by 13. The integral portion of the quotient (n)defines the number of CH groups to give (CH)nThe remainder (m) (remember your long division) is added to theformula as extra hydrogens giving CnHn mM 78 78/13 6 C6H6 is a candidate formulaM 92 92/13 7r1 C7H8 is a candidate formula

HeteroatomsMake replacements from the hydrocarbon candidate formula onThe basis of unit mass equivalencies16Oreplaces CH4 (12 1 1 1 1)14Nreplaces CH235Clreplaces C2H11 etcM 108 108/13 8r4 C8H12OR C7H8O C8H12 - CH4 OOR C5H1O3 OR This gives possible molecular formulae, we need other data tonarrow down our choices

Hydrogen deficiencyConsider the following:Ethylene isdeficient 1 moleculeof hydrogenHH3CCH3HH H2HH3CCH3Deficient 4 moleculesHHHHaka “degreesof unsaturation” H2OCyclohexane isdeficient 1 moleculeDeficient 1 molecule

INDEX OF HYDROGEN DEFICIENCY for the molecular formula αwβxγyδz:Index (z) – (w/2) (y/2) 1Where α represents all monovalent atoms (H, D, halogen), β divalent (O, S),γ trivalent (N, P) and δ tetravalent (C, Si, Sn).Linear alkanes: CnH2n 2 hexane C6H14 2n 2 is the maximum # of HDivalent (such as oxygen): consider hexanol, butyl ethyl ether C6H14O no change in HTrivalent (nitrogen): consider hexyl amine C6H15N add one H to maxMonovalent (halides): hexyl bromide C6H13Br less one H to maxThen, subtract existing protons in the formula each less one HBut first divide by 2 (one H2 has 2 H!)It can’t be negative without violating standard valenciesIt can’t be used for charged species

Example C7H7NOMono:Di:Tri:Tetra:HONCw 7x 1y 1z 7Hydrogen deficiency 7 - (7/2) (1/2) 1 5OPossibilities:OHNH2NOH2NNeed other data to determine, but this gives us a start

Issues in interpretationYou may not always have the luxury of knowing a molecular formulaand will need to use mass spectrometry to determine the mass.M ?zyM orImpurity?xBaseand M Vs.zyxAre we seeing the true molecular ion, or simply a large fragment?Does the absence of a molecular ion imply that the desired/expectedcompound is not present in the analyte?When in doubt, use multiple ionization techniques!

Isotopes in mass spectrometryRemember, we are presumably looking at individual molecules,So we must consider isotopic abundance!“C” 12.011 12.00000(0.989) 13.00336(0.011)12C 12.00000 (ca. 98.9%)13C 13.00336 (ca. 1.1%) a one-unit differenceSo, there is a one percent chance of a 13C being in a given molecule,And a .01% chance of two 13C and 12C4H 7:M 5512C 13CH :37M 5612C 13C H :22 7m/zM 57If my powerpoint skillswere any good,the intensitiesof these should beca 1: 0.01: 0.0001

More pronounced isotopic effectsS:32S(100)33S34S(4.4)M 2 (noticeable!)(100)29Si30Si(3.35)M 2MSi:28SiMCl:35Cl79BrMSWK(5.1)M 1(100)37Cl(100)81BrMBr:(0.78)M 1(32.5)M 2(98)M 2“relative intensities”in parentheses(equal intensities!)

EI-MS Ionization and fragmentationSince EI provides high probabilities of fragment formation,We will refer to this often in our discussion of fragmentatione–M M What is the fate of this ion?2 e–persists? leads to molecular iondecomposition pathways? Gas phase organic chemistryWhere does the electron come from? Molecular “hot spots” asmost likely sources for an ionizable electronheteroatoms, pi-systems, or even sigma bonds!consider where these electrons are relative to vacuum– e–Delocalized: no indication of charge locationvacvacvacOLocalized: explicit assignment of radicals and ionsO

Typical bond cleavagesKEEP PROPER TRACK OF ELECTRONS!CAREFUL ACCOUNTING IS KEY!Notice how these two suggestions are written in all caps.1) HomolyticR COO CH3Silent!(neutral)R CC RC ROUse proper arrownotation:Full vs barbedDetected[M-15] Oor more compactly .2) HeterolyticR CH3CC RR CC R Detected[M-C2H4] H3CSilent!(neutral)stepwise .

General molecular ion lifetimesThe lifetimes of typical ions are on the order of 10-5 sbut within this range there are some general structural trendsto guide us to predict the likelihood of fragmentation for a moleculewith particular functional groupsHighChance:AromaticsConjugated alkene and alkyneSulfidesUnbranched boxylic acids (– CO2)Branched hydrocarbons (stable cations)Alcohols (– H2O)

General comments1) Gas phase! Assume unimolecular decompositionand no collisions among fragments or ions(except CI of course!)2) Remember atomic valences and oxidation states!OOneutralcharged3) When guessing the arrow pushing for ion formation,fragment ion stability trumps fragment radical stability CH3 CH3Secondary cationPrimary radicalPrimary cationSecondary radical

Alkane fragmentation 1: linear, branchedOnly options are C-C and C-H σ bond ruptureC-C:orConsider dodecane and methyl undecane C12H26 MW 17029C2H557C4H985C6H13154371CH3 C3H7 C5H11127C9H9CRJ6.1871C5H11

Alkane fragmentation 2: cyclic97C6H13Hm/z 97H Hm/z 97HH-shiftH HHHHm/z 69HHHHm/z 69HHm/z 41allyl cationCRJ6.18

Alkene fragmentation: 1-hepteneHaH homo-homom/z 422 Cation:HaHH H Hahomo-heterom/z 56HVsH-shift HHm/z 70CRJ6.191 cation: m/z 41allyl cationThe most stable initial intermediateneed not be formed preferentiallyif a less stable structure can lead toa highly stabilized fragment!

Alkene EI-MS: fingerprint for MW 98CRJ Fig 6.19

Alkyne and arene fragmentationHHRHRR H HHH2CHm/z 39Halso, [M-H](how?)HHHH m/z 91CRJ 8.14,15

Isomeric alkanolsSWK Fig 1.18

Aliphatic and aromatic ethersSWK Fig 1.20, 1.21

Spectroscopy vs spectrometry Spectroscopy . The problem solving aspect makes this class a lot of fun, and very frustrating. . “Rule of 13” given that this is an organic chemistry course, it is fair

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