Mass Spectrometry Notes (Part 1)

Mass Spectrometry and Infrared Spectroscopy (Part 1: Mass Spectrometry)

• Purpose of mass spectrometry (MS):

  • Determine molecular weight of organic molecules.

  • From the molecular weight, infer a molecular formula using the Rule of 13.

  • Use the mass spectrum to identify structural features and fragments of the molecule.

  • It is an analytical technique: the sample is destroyed in the process and cannot be recovered.

• Instrument: mass spectrometer (simplified depiction)

  • Sample is introduced into a vacuum chamber.

  • The sample is vaporized.

  • A high-energy electron beam ionizes the sample, causing fragmentation.

  • Resulting fragments can be positively charged, negatively charged, or neutral.

  • In this course, only positively charged fragments are detected by the detector.

  • Fragments travel through a tube/chamber to the detector, which records the signals.

• Mass spectrum basics

  • Output is a bar graph with:

  • y-axis: relative abundance (abundance of fragments, 0–100%).

  • x-axis: M/Z, the mass-to-charge ratio of detected ions.

  • In typical MS for organic molecules, the detected ions are positively charged; the x-axis values are the m/z of those ions.

  • The molecular ion (often denoted as $M^+$) is the ion formed when the original molecule loses one electron; its mass-to-charge ratio equals the molecular weight (assuming charge +1).

  • The molecular ion generally appears as the rightmost peak in the spectrum (largest m/z).

  • The base peak is the most abundant peak (highest signal on the y-axis). It does not have to be the molecular ion or the largest m/z.

• Conceptual visualization

  • The molecule you don’t know is disrupted into fragments in the MS; the spectrum shows those pieces as peaks. The goal is to piece together the original structure from the fragments and their masses.

  • Example visualization: a molecule is ionized and fragments break off parts (e.g., a circle, pentagon, rectangle), each fragment yields a peak corresponding to its mass-to-charge ratio.

• Example with benzamide (illustrative):

  • Molecular ion (M+) appears with an $m/z = 121$ (M+ = 121).

  • Fragment peaks shown in a spectrum: 44, 77, 105, and the molecular ion at 121.

  • The 77 peak is the base peak in this example, though the molecular ion at 121 is the rightmost peak.

  • Explanation: all detected fragments are positively charged; each peak’s position indicates the mass of that fragment, and its height indicates relative abundance.

• Key vocabulary recap

  • Mass spectrum: the data output from the mass spectrometer; a bar graph of abundance vs $M/Z$.

  • Molecular ion (M+): ion representing the original molecule minus one electron; its mass equals the molecule’s molecular weight (for +1 charge).

  • Base peak: the most abundant peak in the spectrum; it is not necessarily the molecular ion.

  • Mass-to-charge ratio $M/Z$: the x-axis of the spectrum; typically Z ≈ +1 for organic MS, so $M/Z \approx M$ for the observed fragments.

  • Fragment: any piece of the molecule after fragmentation; can be positively charged (detected) or neutral (not detected).

• What we can deduce from MS data

  • If the molecular ion mass is known, we know the original molecular weight.

  • The Rule of 13 helps generate a base molecular formula from a molecular ion mass.

  • The base formula can become the actual molecular formula after refinements (see IHD, nitrogen rule, halogen adjustments).

  • The presence of nitrogen or halogens can be inferred by rules and isotopic patterns (see below).

  • Fragments provide clues about structural features (e.g., common fragment masses correspond to functional groups).

  • Differences between peaks (M to M − X) reveal neutral losses, which imply fragments that were present but not detected.

• Rule of 13: deriving a base formula from the molecular ion mass

  • Let the molecular ion mass be $M$ (mass of the original molecule).

  • Compute the quotient and remainder for division by 13:

  • $\frac{M}{13}=CqHq+r$ with $Cq=quotient$ is the number of carbons and Hq = the number of hydrogen is the quotient +$r=$ remainder.

  • The base formula is:

  • number of carbons: $Cq$

  • number of hydrogens: $Hq$

    number of the remainder is: r

  • Example: If $M = 72$, then $\frac{72}{13}=5$ , so $q=5,\,h=5,r=7$ and the base formula is C5H12 (pentane).

  • Check the index of hydrogen deficiency (IHD) to validate the base formula.

  • IHD formula (general): $\mathrm{IHD} = \frac{2C + 2 + N - H - X}{2}$, where $C$ is carbons, $H$ hydrogens, $N$ nitrogens, and $X$ halogens.

  • If there are no nitrogens or halogens, this reduces to $\mathrm{IHD} = \frac{2C + 2 - H}{2}$.

  • For the pentane example: $C=5, H=12, N=0, X=0$, so $\mathrm{IHD} = \frac{2\cdot 5 + 2 - 12}{2} = 0$, meaning no rings or double bonds (consistent with a saturated acyclic hydrocarbon).

  • If the computed IHD is not a whole number or not zero, adjust the base formula to account for possible nitrogens or halogens:

  • Nitrogen rule: odd molecular ion mass often indicates an odd number of nitrogens. If the IHD is fractional, you may need to incorporate nitrogen by replacing a CH unit with an N unit while keeping the mass constant.

    • Practical adjustment: remove one C and two H (mass 14) and add one N (mass 14): this keeps the mass the same but changes the formula to include nitrogen.

    • Example: M = 71 → initial base: $q=5,h=5,r=6$ $C5H11$ IHD is fractional so you replace the 1 C and 2 H with N. The new base formula is C4H9N with a mass 71 and the IHD = 1 (valid).

  • Halogens: chlorine and bromine isotope patterns affect the spectrum and base formula adjustments are sometimes needed to accommodate halogens.

• Halogen isotope patterns in MS (how to detect Cl and Br)

  • Chlorine (Cl): major isotopes $^{35}\mathrm{Cl}$ and $^{37}\mathrm{Cl}$ with natural abundance roughly 3:1.

  • In MS, you’ll observe an M peak and an M+2 peak with relative intensities near a 3:1 ratio (M+2 is about one-third the height of M).

  • Example signature: M = 78, M+ = 78, M+2 = 80; the M+2 peak height ~ 1/3 of the M peak height indicates chlorine presence.

  • Bromine (Br): major isotopes $^{79}\mathrm{Br}$ and $^{81}\mathrm{Br}$ with nearly 1:1 natural abundance.

  • M and M+2 peaks have similar heights (roughly 50/50).

  • This 1:1 M to M+2 intensity pattern indicates bromine presence.

  • Practically, look for the presence of an M+2 peak and compare its height to the M peak to infer whether chlorine or bromine is present and in what proportion.

• Fragmentation information: identifying structural features from fragments

  • There exists a mass-to-charge (m/z) value associated with common fragments corresponding to known groups, listed in typical MS tables:

  • 15 → methyl group (CH3)

  • 43 → propyl group (C3H7) or related fragment

  • 91 → benzyl group (common aryl-alkyl fragment)

  • If a fragment is detected at a certain m/z, you can infer the presence of the corresponding functional group or substructure in the molecule.

  • Not all fragments are detected; some neutrals are lost and not detected. However, their presence can be inferred from differences between peaks:

  • If a peak at $m/z = M - X$ is observed, that indicates a neutral fragment of mass $X$ was lost.

  • Example: a loss of 40 mass units (M − 40) may indicate the loss of a particular neutral piece (e.g., a rectangle-shaped fragment in the visualization).

  • Using these neutral losses helps deduce the presence of substructures that were not directly observed as peaks.

• Summary of practical notes for interpretation

  • The molecular ion mass gives the molecular weight; use this in the Rule of 13 to propose a base formula.

  • The IHD check is essential to validate the base formula; if the IHD is not a whole number or not zero, adjust for heteroatoms (notably nitrogen) and/or halogens.

  • Halogens have characteristic isotope patterns that strongly aid identification (Cl: 3:1 ratio; Br: ~1:1 ratio).

  • Fragment masses provide clues to substructures; common fragments include 15 (methyl), 43 (propyl-related piece), 91 (benzyl-like fragment).

  • Differences between peaks reveal neutral losses; even unsubscribed fragments (neutrals) can be inferred from M − X values.

  • The base peak is not necessarily the molecular ion; it is simply the most abundant fragment peak.

• Connection to broader topics and upcoming content

  • This mass spectrometry analysis provides foundational tools for elucidating organic structures.

  • Infrared spectroscopy will be covered in the next capsule to supplement structural information with vibrational data.

• Quick list of key equations and references

  • Mass-to-charge axis: $M/Z$

  • Molecular ion corresponds to the molecular weight: $M^+ = \text{molar mass of original molecule}$

  • Rule of 13 base formula: let $\frac{M}{13}=CqHq+R$ with C=# of the quotient, H= # of the quotient and R= remainder

  • IHD (general): $\mathrm{IHD} = \frac{2C + 2 + N - H - X}{2}$

  • Nitrogen adjustment for fractional IHD: replace one C and 2 H with 1 N

  • Halogen isotope patterns:

  • Chlorine: M and M+2 peaks with ratio about $3:1$ for $^{35}\mathrm{Cl}$ and $^{37}\mathrm{Cl}$

  • Bromine: M and M+2 peaks with ratio about $1:1$ for $^{79}\mathrm{Br}$ and $^{81}\mathrm{Br}$