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12.S: Structure Determination - Mass Spectrometry and Infrared Spectroscopy (Summary)

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    Concepts & Vocabulary

    12.1 Introduction

    • 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.

    12.7 Infrared Spectroscopy

    • 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.

    12.9 Infrared Spectra of Some Common Functional Groups

    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.

    12.S: Structure Determination - Mass Spectrometry and Infrared Spectroscopy (Summary) is shared under a CC BY-SA 4.0 license and was authored, remixed, and/or curated by Layne Morsch.