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A mass spectrometry instrument with a photographic readout. In the 1919 apparatus described in Chapter V: The Mass-Spectrograph, a gas discharge produced positive ions. Two narrow slits formed a ribbon beam in a vacuum; plates applied an electric field to spread it, an aperture selected part of it, and a magnetic field bent it oppositely. Focusing reduced the spread caused by differing ion speeds, concentrating a given mass-to-charge ratio into a line on a photographic plate.

The observed quantity was line displacement from a fiducial spot. Known reference lines calibrated displacement against mass-to-charge ratio; repeated exposures with changed magnetic field tested the calibration. Evacuation limited collisions. Comparing line shapes with narrow and wide apertures helped distinguish geometric broadening from photographic spreading. Finite slit widths, plate response, and overlapping molecular or multiply charged ions limited interpretation. See Chapter V: The Mass-Spectrograph (§§33–40: apparatus and photographic procedure; §§43 and 45–46: calibration, aperture comparisons, and accuracy).

In Mass spectra and isotopes by Francis William Aston (Nobel lecture, 12 December 1922), the reported neon lines at 20 and 22 have companions at 10 and 11 from doubly charged ions. That paired pattern and comparison with reference lines support different atomic masses within one chemical element, rather than an atomic mass concentrated at the bulk average. The lecture also describes an earlier failed separation by distillation and partial separation by diffusion, showing why the focused mass spectrum supplied stronger evidence. These numbers used a historical oxygen-based reference scale. The lecture's whole-number rule was an empirical approximation at its stated accuracy, not the modern exact definition $A=Z+N$.^[ref]

Mass spectrometry separates and detects ions according to mass-to-charge ratio. It can distinguish isotopes which belong to the same chemical element but have different atomic masses. The instrument measures ions: interpreting the result as a neutral atomic mass requires accounting for Electron removal and its ionization energy. For a singly positive ion in its ground state, $m_{+}=m_{\mathrm{a}}-m_e+I/c^2$, where $m_e$ is the Electron rest mass, $I$ is the ionization energy, and $c$ is the speed of light.

For a simple illustrative analyzer, positive ions of mass $m$ and electric charge $q=ze$ gain kinetic energy $qV=m{v}^2/2$ across an electric potential difference $V$ before entering a transverse uniform magnetic field $B$. The Lorentz force supplies centripetal acceleration, soAt fixed $V$ and $B$, the measured bending radius $r$ separates mass-to-charge ratios, not masses independently of electric charge. This ideal model assumes negligible initial kinetic energy and speeds small compared with the speed of light; the historical focusing mass spectrograph used the geometry described below.

In the International Union of Pure and Applied Chemistry (IUPAC) mass spectrometry convention, a molecular ion is formed by removing or adding one or more Electrons to a molecule without fragmentation of its molecular structure.^[ref] For example, removing one Electron from intact water gives ${\mathrm{H}}_2{\mathrm{O}}^{\bullet +}$: two hydrogen and one oxygen chemical atom, total electric charge $+e$, and an unpaired Electron, hence a radical cation. Atom inventory, net electric charge, and electronic state are separate pieces of information. Hydronium, ${\mathrm{H}}_3{\mathrm{O}}^{+}$, has a different inventory; it is a polyatomic ion, rather than the molecular ion obtained by electron removal from water.

A molecule, using the International Union of Pure and Applied Chemistry (IUPAC) convention, is an electrically neutral entity containing two or more chemical atoms. Its constituents form a bound unit through chemical bonds; merely drawing a boundary around neighboring particles does not make a molecule. The neutrality requirement concerns total electric charge, not the absence of internal charge separation: water is a polar molecule with zero total electric charge.^[ref]

One water molecule, ${\mathrm{H}}_2\mathrm{O}$, contains two hydrogen and one oxygen chemical atom. One molecular oxygen molecule, ${\mathrm{O}}_2$, contains two oxygen chemical atoms; a molecule need not contain different chemical elements. One carbon dioxide molecule, $\mathrm{C}{\mathrm{O}}_2$, contains one carbon and two oxygen chemical atoms. The molecular formula records these inventories, while molecular geometry describes their arrangement. Water and carbon dioxide are chemical compounds; molecular oxygen is a form of one chemical element.

Ordinary crystalline sodium chloride, $\mathrm{NaCl}$, contains an extended arrangement of sodium cations $\mathrm{N}{\mathrm{a}}^{+}$ and chlorine anions $\mathrm{C}{\mathrm{l}}^{-}$. Its formula unit specifies one of each for compositional accounting, without selecting a unique isolated pair. Bulk neutrality therefore does not imply a material consists of neutral molecules. This statement concerns the ionic crystal; the physical state and conditions matter when deciding what particles a chemical formula represents.^[ref]

A polyatomic ion is a charged bound group of chemical atoms, such as hydronium, ${\mathrm{H}}_3{\mathrm{O}}^{+}$. A molecular ion formed by removing an Electron from intact water, ${\mathrm{H}}_2{\mathrm{O}}^{\bullet +}$, retains the same atom inventory but has net electric charge $+e$. Neither satisfies the neutral-molecule definition. Distinguishing these entities makes molecular count and amount of substance and mass spectrometry interpretable: say whether the count is of chemical atoms, neutral molecules, ions, or formula units.

The useful surprise is that a molecule can be treated as one particle for motion and counting while retaining internal structure. Its molar mass connects a particle inventory to bulk mass; molecular rotation and molecular vibration reveal internal organization. The continuum approximation uses bulk fields in place of individual molecular positions and motions.