Organic Structure Determination
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1 rganic Structure etermination The Beginning structure determined by chemical methods Me -glucose (1891) morphine (1925) strychnine (1948)
2 rganic Structure etermination ommon Spectroscopic Methods 1. uclear Magnetic Resonance (MR) - framework 2. Infrared Spectroscopy (IR) functional groups 3. Ultraviolet Spectroscopy (UV-Vis) conjugation 4. Mass Spectrometry (MS) molecular weight; chemical formula
3 rganic Structure etermination Spectroscopic etermination 38 Me Me 26 Me l Me Me niizalactam A Abe, 2015 spirastrellolide A (Anderson, 2001) Me Me Me Me Me ciguatoxin (Yasumoto, 1989)
4 rganic Structure etermination Bullvalene a fluxional molecule Ault J. hem. Ed. 2001, 78, 924. bullvalene etc. etc. etc. etc. interchange by ope rearrangement; 1,209,600 distinct structures;
5 rganic Structure etermination Stereochemistry of the Vinylcyclopropane Rearangement Baldwin J. Am. hem. Soc. 1994, 116, Δ (si + sr = 63%) ar = 13% ai = 24% (ar + ai = 37%) sr = 23% si = 40% biradical vs. concerted mechanism? determination of product distribution and rate constants support biradical process
6 rganic Structure etermination etermination of Peptide Secondary Structure Kessler J. Am. hem. Soc. 2001, 123, Br Ph 3 model hexapeptide
7 rganic Structure etermination Binding Studies icolaou, hazin, Gomez-Paloma J. Am. hem. Soc. 1998, 120, head to tail oligosaccharide dimer Me I S Me Me calicheamicin γ1 S S S Me Me
8 rganic Structure etermination Mistakes an appen amphidinolide A reported structure revised structure halipeptin A Me Me Me S Me reported structure revised structure
9 rganic Structure etermination Mistakes an appen hexacyclinol Me Me reported structure revised structure isolation: Gräfe J. Antibiotics 2002, st synthesis: Lalaire Angew. hem., Int. Ed. 2006, 45, MR prediction: Rychnovsky rg. Lett. 2006, 8, nd synthesis: Porco Angew. hem., Int. Ed. 2006, 45, retraction: Angew. hem., Int. Ed. 2012, 51,
10 rganic Structure etermination Mistakes an appen In YUR Lab 2 Me R iels-alder 2 Me R 2 Me R iels-alder 2 Me R original report: J. Am. hem. Soc. 1988, 110, 631. revision: Tetrahedron Lett. 1989, 30, 433 Et Me Si Me Pd cat. Et SiMe 2 Ph Et SiMe 2 Ph original report: J. Am. hem. Soc. 1997, 119, 698. revision: Tetrahedron Lett. 2001, 42, 3775
11 rganic Structure etermination Structure Proof!
12 rganic Structure etermination General Approach (Empirical Formula) Molecular Weight Molecular Formula (units of unsaturation) Functional Groups Structural Features (fragments à connectivity à stereochemistry) Final Structure?
13 Empirical Formula Elemental Analysis also known as combustion analysis provides quantitive information on atom types à relative percentages use to calculate empirical formula (gives lowest integer ratio of atoms present) how does it work? Δ x y z + 2 x 2 + ( y / 2 ) 2 known mass excess measure quantites of each formed general procedure 1. weigh compound exactly (2-5 mg) 2. wrap it in tin cup 3. place in vacuum chamber 4. evacuate air, then fill with 2 5. drop into 1000 furnace ( 2 atmosphere) 6. measure what comes off by G ( 2, 2, 2 )
14 Empirical Formula report Elemental Analysis % oxygen then determined by difference: % = 100% % % = 24.6%
15 rganic Structure etermination Elemental Analysis unknown compound à determine empirical formula sample: 64.6% 10.8% 24.6% 1. convert % to mole fraction: 2. convert grams to moles: assume 100g of sample, then 64.6% = 64.6g 10.8% = 10.8g 24.6% = 24.6g 64.6g / (12.01g/mol) = 5.38 moles 10.8g / (1.01 g/mol) = 10.7 moles 24.6g / (16.00 g/mol) = 1.54 moles 3. determine empirical formula: from above divide by smallest # convert to whole # ratio if needed à note: empirical formula is T the same as molecular formula!
16 rganic Structure etermination Elemental Analysis known compound à proof of purity 2 Et hemical Formula: Elemental Analysis:, 59.14;, 7.09;, reported as: Anal. alcd for :, 59.14%;, 7.09%. Found:, 59.03%;, 7.12%. error: 0.4 mass %
17 rganic Structure etermination Molecular Weight / Molecular Formula Low Resolution Mass Spectrometry (LRMS) MW determined to the nearest amu back to unknown: 64.6%, 10.8%, 24.6% à MW = 130; supports molecular formula vs , etc. parent ion!
18 rganic Structure etermination Molecular Weight / Molecular Formula Low Resolution Mass Spectrometry (LRMS) MW determined to the nearest amu LRMS alone? à can determine MW to nearest amu MW = 130; less certainty à many possible formulas Rule of 13 (Pavia section 1.5) à help to identify possible formula EXTREMELY TEIUS
19 rganic Structure etermination Molecular Weight / Molecular Formula Low Resolution Mass Spectrometry (LRMS) MW determined to the nearest amu LRMS alone? MW = 130; less certainty à many possible formulas rule of 13? on-line formula calculators: text book Tables: Silverstein Spectrometric Identification of rganic ompounds. hapter 2, Appendix A. Formula Masses (FM) for Various ombinatinos of arbon, ydrogen, itrogen and xygen. McLafferty, Turecek Interpretation of Mass Spectra, Table A.7 ommon elemental compositions of molecular ions.
20 rganic Structure etermination Molecular Weight / Molecular Formula igh Resolution Mass Spectrometry (RMS) MW determined to four decimal places use mass obtained to determine possible formulas in absence of elemental analysis formula calculators, tables in text to suggest possibilities as with LRMS MW = 130 (Silverstein, Appendix A)
21 rganic Structure etermination Molecular Weight / Molecular Formula RMS Rates: ld ominion University SMI! itrogen Rule if molecule has odd # of, molecular mass will be an odd number if molecule has even # of, molecular mass will be an even number MW: MW: 102
22 rganic Structure etermination Units of Unsaturation also known as Index of ydrogen eficiency, Unsaturation umber, etc. indicates number of p bonds and/or rings present in the molecule Saturated Alkane = n 2n+2 (n = # of carbons) saturated alkane ( n 2n+2 ) loss of 2 when add π bond or form ring units of unsaturation = expected (saturated) observed 2
23 rganic Structure etermination Units of Unsaturation units of unsaturation = expected (saturated) observed 2 example 1: 7 14 à 1 unit of unsaturation à one ring or 1 double bond example 2: 9 12 à 4 units of unsaturation à one ring, 3 double bond?
24 rganic Structure etermination Units of Unsaturation incorporation of elements other than & can influence calculation units of unsaturation = expected (saturated) observed 2 oxygen: no change to calculation (ignore ); also ignore S 7 14 à calculate as above so: (16-14)/2 à 1 unsaturation halogen: replace each X by an 7 13 Br à 7 14 so: (16-14)/2 à 1 unsaturation nitrogen: replace each by ; do same for P and B 7 13 à 8 14 so: (18-14)/2 à 2 unsaturation
25 rganic Structure etermination Units of Unsaturation: examples # l 2 X ignore 8 14 units of unsaturation = = 2 # ignore units of unsaturation = = 3 # P P units of unsaturation = = 12
26 The Electromagnetic Spectrum gamma rays x-rays ultraviolet (UV) visible Infrared (IR) microwaves radiowaves short wavelength high frequency high energy long wavelength low frequency low energy wavelength (λ): distance from one wave maxima to the next frequency (υ): number of maxima that pass by a point in a given time amplitude: height of wave measured from midpoint to maxima wavelengths of interest UV visible IR radiowaves nm nm µm 1-5 m an relate frequency (υ) to energy E = hυ Planck's constant: h = 6.63 x J s
27 Spectroscopy and the Electromagnetic Spectrum gamma rays x-rays ultraviolet (UV) visible Infrared (IR) microwaves radiowaves 1. uclear Magnetic Resonance (MR) radio waves à nuclear spin transitions EM radiation 2. Infrared Spectroscopy (IR) infrared radiations à bond vibrations 3. Ultraviolet Spectroscopy (UV-Vis) ultraviolet (visable) radiation à electronic transitions 4. Mass Spectrometry (MS) molecule bombarded with high energy electons
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