12.S: Structure Determination - Mass Spectrometry and Infrared Spectroscopy (Summary)
- Page ID
- 211001
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\(\newcommand{\avec}{\mathbf a}\) \(\newcommand{\bvec}{\mathbf b}\) \(\newcommand{\cvec}{\mathbf c}\) \(\newcommand{\dvec}{\mathbf d}\) \(\newcommand{\dtil}{\widetilde{\mathbf d}}\) \(\newcommand{\evec}{\mathbf e}\) \(\newcommand{\fvec}{\mathbf f}\) \(\newcommand{\nvec}{\mathbf n}\) \(\newcommand{\pvec}{\mathbf p}\) \(\newcommand{\qvec}{\mathbf q}\) \(\newcommand{\svec}{\mathbf s}\) \(\newcommand{\tvec}{\mathbf t}\) \(\newcommand{\uvec}{\mathbf u}\) \(\newcommand{\vvec}{\mathbf v}\) \(\newcommand{\wvec}{\mathbf w}\) \(\newcommand{\xvec}{\mathbf x}\) \(\newcommand{\yvec}{\mathbf y}\) \(\newcommand{\zvec}{\mathbf z}\) \(\newcommand{\rvec}{\mathbf r}\) \(\newcommand{\mvec}{\mathbf m}\) \(\newcommand{\zerovec}{\mathbf 0}\) \(\newcommand{\onevec}{\mathbf 1}\) \(\newcommand{\real}{\mathbb R}\) \(\newcommand{\twovec}[2]{\left[\begin{array}{r}#1 \\ #2 \end{array}\right]}\) \(\newcommand{\ctwovec}[2]{\left[\begin{array}{c}#1 \\ #2 \end{array}\right]}\) \(\newcommand{\threevec}[3]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \end{array}\right]}\) \(\newcommand{\cthreevec}[3]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \end{array}\right]}\) \(\newcommand{\fourvec}[4]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \\ #4 \end{array}\right]}\) \(\newcommand{\cfourvec}[4]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \\ #4 \end{array}\right]}\) \(\newcommand{\fivevec}[5]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \\ #4 \\ #5 \\ \end{array}\right]}\) \(\newcommand{\cfivevec}[5]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \\ #4 \\ #5 \\ \end{array}\right]}\) \(\newcommand{\mattwo}[4]{\left[\begin{array}{rr}#1 \amp #2 \\ #3 \amp #4 \\ \end{array}\right]}\) \(\newcommand{\laspan}[1]{\text{Span}\{#1\}}\) \(\newcommand{\bcal}{\cal B}\) \(\newcommand{\ccal}{\cal C}\) \(\newcommand{\scal}{\cal S}\) \(\newcommand{\wcal}{\cal W}\) \(\newcommand{\ecal}{\cal E}\) \(\newcommand{\coords}[2]{\left\{#1\right\}_{#2}}\) \(\newcommand{\gray}[1]{\color{gray}{#1}}\) \(\newcommand{\lgray}[1]{\color{lightgray}{#1}}\) \(\newcommand{\rank}{\operatorname{rank}}\) \(\newcommand{\row}{\text{Row}}\) \(\newcommand{\col}{\text{Col}}\) \(\renewcommand{\row}{\text{Row}}\) \(\newcommand{\nul}{\text{Nul}}\) \(\newcommand{\var}{\text{Var}}\) \(\newcommand{\corr}{\text{corr}}\) \(\newcommand{\len}[1]{\left|#1\right|}\) \(\newcommand{\bbar}{\overline{\bvec}}\) \(\newcommand{\bhat}{\widehat{\bvec}}\) \(\newcommand{\bperp}{\bvec^\perp}\) \(\newcommand{\xhat}{\widehat{\xvec}}\) \(\newcommand{\vhat}{\widehat{\vvec}}\) \(\newcommand{\uhat}{\widehat{\uvec}}\) \(\newcommand{\what}{\widehat{\wvec}}\) \(\newcommand{\Sighat}{\widehat{\Sigma}}\) \(\newcommand{\lt}{<}\) \(\newcommand{\gt}{>}\) \(\newcommand{\amp}{&}\) \(\definecolor{fillinmathshade}{gray}{0.9}\)Concepts & Vocabulary
- Spectroscopy describes several techniques used by chemists to understand chemical structures and bonds.
12.2 Mass Spectrometry of Small Molecules - Magnetic Sector Instruments
- Mass spectrometers consist of an ion source, mass analyzer and dectector.
- There are several common ion sources including electron ionization and chemical ionization.
- Upon ionization, a molecular ion is formed (the molecule after losing a single electron) which will break into smaller pieces (fragments).
- Fragments that are charged will appear in the mass spectrum and are helpful in identifying the parent molecule.
- The most abundant ion in a mass spectrum is called the base peak.
- The ion with the same mass as the parent molecule is called the molecular ion.
- Isotopes of carbon and hydrogen lead to common M+1 peaks.
- The x-axis of a mass spectrum is m/z - the mass to charge ratio, which in practice equals the mass of the ion.
12.3 Interpreting Mass Spectra
- Uncharged particles do not appear in mass spectra.
- The y-axis of a mass spectrum is the relative abundance, with the base peak set at 100 as the most abundant ion.
- Abundance of ions is related to their stability.
12.4 Mass Spectrometry of Some Common Functional Groups
12.5 Mass Spectrometry in Biological - Time-of-flight (TOF) Instruments
12.6 Spectroscopy and the Electromagnetic Spectrum
- Electromagnetic radiation is composed of waves where shorter wavelengths correspond to higher energy radiation.
- Electromagnetic radiation can also be thought of as a stream of particles called photons.
- The electromagnetic spectrum is made up of many types of radiation including infrared, ultraviolet, and visible lights as well as x-rays, gamma rays, microwaves, and radio waves.
- Molecular spectroscopy works by exposing a chemical sample to electromagnetic radiation. It will only absorb radiation with energy that corresponds to some excited state, while all other energies will pass through unabsorbed.
- When infrared radiation is absorbed, molecules will move to a higher vibrational energy state.
- Examples of molecular vibrations include bending and stretching of bonds. These vibrations can be symmetric or asymmetric.
- In general, more polar bonds have stronger IR absorption.
- IR spectra typically use wavenumbers (cm-1) as units for the x-axis.
- The y-axis for IR spectra is usually % transmittance, with 100% at the top of the spectrum and absorbances looking like valleys (or downward peaks).
12.8 Interpreting Infrared Spectra
- Functional groups have standard regions within the IR spectrum where they absorb.
- The general regions include hydrogen bonding (O-H and N-H), carbon-hydrogen bonds, triple bonds, carbonyls, alkenes, and fingerprint region.
Skills to Master
- Skill 12.1 Determine specific atoms from mass spectra based on molecular ion and M+2 peaks (N, Cl, Br).
- Skill 12.2 Interpret mass spectra fragments - recognizing common fragments.
- Skill 12.3 Interpret infrared spectra to determine functional groups that are present or absent.
Memorization Tasks (MT)
- MT 12.1 Memorize common mass spectra fragments.
- MT 12.2 Memorize common functional group regions in infrared spectroscopy.