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Comments on homework

Comments on homework. Lots of “Index of Hydrogen Deficiency” Math errors Matching arrows with HR MS data & Molecular formulas Following instructions: -typed & chemdraw work -Not applying rules for fragmentation -Not providing mechanisms

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Comments on homework

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  1. Comments on homework • Lots of “Index of Hydrogen Deficiency” Math errors • Matching arrows with HR MS data & Molecular formulas • Following instructions: • -typed & chemdraw work • -Not applying rules for fragmentation • -Not providing mechanisms • Poor mechanism presentations (Review arrow pushing) • Some organizational problems in “presentation” of homework

  2. Parent ion: m/z 150

  3. 1.6 Match each of the exact masses to the following mass spectra. (A–W) Note that two compounds have the same exact mass, and you will need to consider the CI mass spectrum when given: (a) 56.0264, (b) 73.0896, (c) 74.0363, (d) 89.0479, (e) 94.0535, (f) 96.0572, (g) 98.0736, (h) 100.0893, (i) 102.0678, (j) 113.0845, (k) 114.1043, (l) 116.0841, (m) 116.1206, (n) 122.0733, (o) 122.0733, (p)126.1041, (q) 138.0687, (r) 150.0041, (s) 152.0476, (t) 156.9934, (u) 161.9637, (v) 169.9735, (w) 208.0094.

  4. (r) 150.0041 -78.9183 = 71.0858

  5. 71.0858 C5H11

  6. C5H11Br IHD = 0 Therefore it is a pentylbromide isomer A propyl radical [M - 43] [M - 29] [M –Br] or [M -79] m/z 71 = m/z 107 = C2H4Br+ m/z 121 = C3H6Br+

  7. Fragmentation mechanisms must be consistent with valences of atoms -radical & cation chemistry

  8. Some helpful hints: • Draw hydrogens in. • Use proper arrow pushing –exactly like in mechanisms. • Gas phase radical cations have plenty of energy to rearrange and fragment.

  9. M-1 m/z 39, C3H3+ [M -17] or [M-OH] M M+1

  10. M-1 m/z 39, C3H3+ [M -17] or [M-OH] M

  11. Chapter 2: Infrared Spectroscopy

  12. Electromagnetic Energy: Light E = hυ h: Planck constant h = 6.626x10-34 J.s υ=c/λ Duality wave/particle of the light

  13. Infrared Spectroscopy • The vibrational IR extends from 2.5 x 10-6 m (2.5 m) to 2.5 x 10-5 m (25 m). • The frequency of IR radiation is commonly expressed in wavenumbers. • Wavenumber: The number of waves per centimeter, with units cm-1 • Expressed in wavenumbers, the vibrational IR extends from 4000 cm-1 to 400 cm -1

  14. Molecular vibrations • Fundamental stretching and bending vibrations for a methylene group.

  15. Molecular Vibrations • Consider two covalently bonded atoms as two vibrating masses connected by a spring. • The total energy is proportional to the frequency of vibration; E = hnwhere h is Planck’s constant. • The frequency of a stretching vibration is given by an equation derived from Hooke’s law. K = a force constant, which is a measure of bond strength, m = reduced mass of the two atoms, (m1m2)/(m1 + m2), where m is the mass of the atoms in amu.

  16. Potential energy diagrams. Curve 1, harmonic oscillator. Curve 2, anharmonic oscillator

  17. Molecular Vibrations • From this equation, we see that the peak position of a stretching vibration • is proportional to the strength of the vibrating bond. • is inversely proportional the masses of the atoms connected by the bond. • The intensity of absorption depends primarily on the polarity of the vibrating bond.

  18. i)   Stretching frequencies are higher than corresponding bending frequencies. (It is easier to bend a bond than to stretch or compress it.)ii)   Bonds to hydrogen have higher stretching frequencies than those to heavier atoms.iii)   Triple bonds have higher stretching frequencies than corresponding double bonds, which in turn have higher frequencies than single bonds.

  19. Comparison Beetween Dispersion Spectrometer and FTIR Dispersion Spectrometer To separate IR light, a grating is used. Detector Grating Slit In order to measure an IR spectrum, the dispersion Spectrometer takes several minutes. Also the detector receives only a few % of the energy of original light source. Sample To select the specified IR light, A slit is used. Light source FTIR An interferogram is first made by the interferometer using IR light. Fixed CCM In order to measure an IR spectrum, FTIR takes only a few seconds. Moreover, the detector receives up to 50% of the energy of original light source. (much larger than the dispersion spectrometer.) Detector B.S. Sample Moving CCM The interferogram is calculated and transformed into a spectrum using a Fourier Transform (FT). IR Light source

  20. Figure 16-9 Single- and double-beam spectra of atmospheric water vapor and CO2. In the lower, single-beam trace, the absorption of atmospheric gases is apparent. The top, double-beam trace shows that the reference beam compensates nearly perfectly for this absorption and allows a stable 100% T baseline to be obtained. (From J. D. Ingle Jr. and S. R. Crouch, Spectrochemical Analysis, p. 409. Englewood Cliffs, NJ: Prentice-Hall, 1988. With permission.)

  21. IR Source Sources of continuous radiation  A hot material emits a continuum of radiation. Blackbody (no envelope): intensity highest near 5000 cm-1; about 100 times lower near 500 cm-1. a) Nichrome coilheated electrically to 1100oC and a black oxide film forms. Simple, robust, reliable, long lifetime.

  22. Figure 16-4 Specpral distribution of energy from a Nernst glower operated at approximately 2200 K.

  23. Interferometer produces plot of intensity vs time during 1 scan (interferogram).Interference of beams occurs from fixed and moving mirrors. Mirror moves to create path difference between 2 beams Transmits 50%, reflects 50% At t=0, zero path difference between 2 beams for monochromatic radiation; constructive interference; maximum signal at detector.At a later time, path difference = /2; destructive interference; minimum signal. Later on, …. …maximum signal. So interferogram is a cosine wave.

  24. Interference is a superpositioning of waves FTIR seminar Relationship between light source spectrum and the signal output from interferometer Light source spectrum Signal output from interference wave I Az • Monochromatic • light • Dichroiclight • Continuous • spectrum light u Wavenumber Time t S I SAz u Wavenumber Time t I(t) b (u) Time t u Wavenumber All intensities are standardized.

  25. Centreburst grows when more frequencies are present One frequency Three frequencies Many frequencies

  26. Peak width When band is broader, interferogram wings decay faster: more frequencies give more chance of cancellation

  27. Relation between spectrum and interferogram. 3 interferogram parameters important: A, P, T

  28. Fourier Transform Single strength Fourier transform SB 400 4000 Wavenumber[cm-1] Optical path difference [x] (Interferogram) (Single beam spectrum) Time axis by FFT Wavenumber

  29. Schematic of steps in spectrum collection End of scan from (i) white light source or (ii) centreburst Background spectrum

  30. Advantages of FT-instrument over dispersive one • Fellgett advantage • All frequencies are measured simultaneously. Typical scan times are only a few seconds. • 2. Jacquinot advantage • The energy throughput is higher for any resolution, giving a higher signal:noise ratio. • 3. Connes advantage • The laser wavelength is used as a reference for the calculation of band positions, and is precise. • 4. Stray light • This only comes from aliasing and can be prevented. • 5. Resolution • This is constant for the whole spectral range • 6. Robustness • FT instruments only have 1 moving part

  31. Instrument scanning Signal: noise ratio, S/N  (measurement time)0.5 S/N  (no. of scans)0.5 How many scans do I need to reduce the noise in 1 scan by a factor of 4? Often 1 scan of sample is ratiod against 1 scan of (empty) background. In the ranges 70-35%T and 0-35%T normally the ratio of background:sample scans is increased to 1:2 and 1:4 respectively. When the energy throughput is reduced by a factor of x for the sample spectrum, x times more scans are required.

  32. Resolution

  33. Sample preparation Methods • Transmission • Solids: KBr Pellet • Liquids: NaCl Plates Quick press KBr pellet press

  34. Instrumental Setup: Attenuated Total Reflectance (ATR) Technique • IR radiation passes through (IRE-internal reflection element) crystal and hits sample at a 45 degree angle • IRE made of high refractive index material (zinc selenide, diamond, germanium • Incident radiation penetrates into sample (~1 micrometer) where it can be absorbed • Attenuated radiation is reflected

  35. Sample preparation Methods ATR • Liquids and solids loaded directly onto crystal • Arm Applies pressure to solids for uniform contact with crystal • PSI can be controlled

  36. Transmission vs. ATR ATR Advantages • High Quality Spectrum for qualitative analysis • Minimal sample preparation • Non destructive • Time efficient • Spectra not affected by sample thickness • Radiation penetrates only a few micrometers • Highly reproducible results • Wide variety of sample types • Threads, yarns, fabrics, fibers, pastes, powders, suspensions, polymers, rubbers

  37. ATR forensic applications • Drug analysis • Fiber analysis • Paint chip analysis • Ink analysis • Paper analysis • Biological analysis

  38. Spectra Comparison • Resulting peaks from ATR are very similar in intensity and wavelength to transmittance technique Koulis, Cynthia, et. al. Comparison of Transmission and Internal Reflection Infrared Spectra of Cocaine. Journal of Forensic Sciences, 2001.

  39. ATR Peak Shift • Small variations in peak intensity and position occur: • Carbonyl band Absorption of cocaine shows ATR peak shift Koulis, Cynthia, et. al. Comparison of Transmission and Internal Reflection Infrared Spectra of Cocaine. Journal of Forensic Sciences, 2001.

  40. C-H Stretch occurs around 3000 cm-1. In alkanes (except strained ring compounds), sp3 C-H absorption always occurs at frequencies less than 3000 cm-1 (3000-2840 cm-l). Methylene groups have a characteristic bending absorption of approximately 1465 cm-1. Methyl groups have a characteristic bending absorption of approximately 1375 cm-1. The bending (rocking) motion associated with four or more CH2 groups in an open chain occurs at about 720 cm-1 (called a long-chain band).

  41. =C-H Stretch for sp2 C-H occurs at values between 3100-3010 cm-1. =C-H Out-of-plane (oop) bending occurs in the range 1000-650 cm-1. Stretch occurs at 1660-1600 cm-1; often conjugation moves C=C stretch to lower frequencies and increases the intensity.Symmetrically substituted bonds (e.g., 2,3-dimethyl-2-butene) do not absorb in the infrared (no dipole change).Symmetrically disubstituted (trans) double bonds are often vanishingly weak in absorption; cis are stronger.

  42. Alkene isomers =CH bend =CH bend

  43. Aromatics C–H stretch from 3100-3000 cm-1 overtones, weak, from 2000-1665 cm-1 C–C stretch (in-ring) from 1600-1585 cm-1 C–C stretch (in-ring) from 1500-1400 cm-1 C–H "oop" from 900-675 cm-1

  44. Alkynes

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