Molecular Ions

• Type of physical science: Chemistry
• Field of study: Chemistry of molecules: types of molecules

Molecular ions are molecules that have gained or lost electrons, resulting in an unequal numbers of protons and electrons. Molecular ions are highly reactive, which makes them important participants in chemical systems.

Overview

Molecules consist of atoms, and atoms are composed of neutrons, positively charged protons, and negatively charged electrons. Atoms normally have an equal number of protons and electrons and have no overall charge. Neutral molecules have an equal number of protons and electrons in the total molecular system so that there is no net charge on the molecule. A molecular ion is formed when an electron is added to or removed from a neutral molecule so that the number of protons and the number of electrons is no longer equal.

If an electron is added to a neutral molecule, the resulting ion will have an overall charge of -1.

If two electrons are added to a neutral molecule, the ion produced will have an overall charge of -2. Negatively charged ions are called anions. If an electron is removed from a neutral molecule, the resulting ion will have an overall charge of +1. If two electrons are removed, then the overall charge becomes +2. Positively charged ions are called cations. The production of cations requires energy input to remove electrons, while generally, the formation of anions releases energy.

In the lower atmosphere of Earth, most of the molecules in the air, in liquids, and in solids are neutral molecules. Ions formed near ground level are highly reactive. Cations tend to acquire negatively charged electrons to return to a neutral state, while anions tend to give up electrons to return to a neutral molecule, depending on the chemical environment. Ions have short lifetimes at normal atmospheric pressure since they soon react with other molecules but can have long lifetimes when present at low atmospheric pressures. These conditions exist in the upper atmospheres of planets, in stellar atmospheres and plasmas, and in low-density plasmas used in industry, as well as in interstellar space. Ions in interstellar space can be detected on Earth using the experimental techniques of spectroscopy. In the laboratory, chemists can isolate and study ions by simulating the low-pressure, or near-vacuum, conditions of interstellar space. The two most widely used techniques for studying ions in the laboratory are mass spectrometry and high-resolution spectroscopy. Additional insight into molecular ion structure results from high-level ab initio molecular orbital calculations and successful semiempirical methods.

Mass spectrometry is one of the most widely used tools of the chemist. Physical chemists use mass spectrometers to study ion chemistry, while organic and analytical chemists use mass spectrometers primarily to understand the structure of molecules of interest. Molecular ions are the key to understanding both uses of these instruments. A mass spectrometer works in the following fashion. First, a sample substance is introduced into a sample compartment where the pressure is extremely low, typically around 10⁻⁶ to 10⁻⁹ atmospheres. The sample can be either in the gas, liquid, or solid phase. Then energy is supplied to the sample so that electrons are removed from the molecules and cations are formed. One common procedure is to bombard a gaseous sample with high-energy electrons. After this step, the ions are present in the gas phase, regardless of whether the sample originally was a solid, a liquid, or a gas. Some of the cations are only fragments of the original sample molecule. In the third step, an electric potential difference accelerates the positively charged ions into a flight tube section of the mass spectrometer. The accelerating voltages typically range in the kilovolt range, depending on the instrument. The ions are separated according to their mass-to-charge ratio in the fourth step. This is done in a variety of ways, such as using electric or magnetic fields, depending on the type of mass analyzer, so that ions are separated by their mass-to-charge ratio. All other ions collide with the walls of the mass spectrometer and are neutralized. Finally, ions that successfully pass through the mass-to-charge discriminating region collide with a detector, which measures the number of ions of each particular mass.

Consider the case of monitoring the level of carbon monoxide in the air by mass spectrometry. First, the sample, a molecule containing one carbon atom bound to one oxygen atom, must be introduced into the vacuum system. Then, energy is applied to the carbon monoxide molecules. Several ionic species are produced, including singly and doubly charged carbon monoxide cations, carbon atom cations, and oxygen atom cations. Next, a negative voltage is applied, which accelerates all the positively charged cations into the flight tube of the mass spectrometer. In the fourth step, the ions are separated by their mass-to-charge ratio. Singly charged carbon ions have a mass-to-charge ratio of 12, singly charged oxygen cations have a mass-to-charge ratio of 16, and the carbon monoxide ratio is 28. Doubly charged carbon monoxide cations have a mass-to-charge ratio of 28:2, or 14. Thus, the spectrum at this point should consist of four peaks occurring at 12, 14, 16, and 28 for the carbon, doubly charged carbon monoxide, oxygen, and singly charged carbon monoxide cations, respectively. The intensities of these four peaks show the relative numbers of each type of cation formed by the energy source in the sample. Finally, it should be noted that isotope peaks are clearly discriminated by mass spectrometry. Since the relative abundance of carbon atoms with a mass of 12 exactly is 98.93 percent, and that of carbon atoms with a mass of 13 is 1.107 percent, the mass spectrum reveals three additional peaks of low intensity at masses 13, 14.5, and 29. The peak at 13 is the singly charged carbon-13 isotope, that at 14.5 is the doubly charged carbon monoxide peak for the carbon-13 isotope (mass-to-charge equals 29:2, or 14.5), and that at 29 is the singly charged carbon monoxide peak for the carbon-13 isotope.

Physical chemists studying carbon monoxide focus on the individual ions. By systematically lowering the energy input that produces the ions in the first place, the experimentalist can determine the energy required to remove one or two electrons from the original molecule. The reactivity of the cations can be studied by introducing a target gas in the flight tube of the mass spectrometer after the mass selection region so that products of ion-molecule collisions can be monitored.

With the 1980s came the birth of high-resolution spectroscopy of ions. These methods include microwave spectroscopy, laser magnetic resonance, laser spectroscopy of fast ion beams, laser-induced fluorescence, Fourier transform infrared spectroscopy, and tunable infrared laser spectroscopy. These techniques allow for the determination of bond lengths and bond angles for the molecular ion of interest, in other words, for the determination of the structure of the ion.

Interpretation of spectroscopic experiments is often difficult and has been aided by high-level ab initio calculations.

Ab initio calculations are extremely valuable for understanding the structure of small molecular ions. These calculations are performed by picking an appropriate model to describe the molecular system and then solving the Schrödinger equation. The geometries and energies of ions can then be predicted and used as an aid to interpreting experimental results.

John A. Pople and coworkers at Carnegie Mellon University produced an ab initio package called GAUSSIAN for the chemistry community. This series of programs is designed to take advantage of the computer power available at any given laboratory. For larger ions, semiempirical calculations are more practical and very useful. Semiempirical methods are based on a low-level ab initio model but are then fitted with experimental data so that calculations are fast and results are fairly accurate. The most successful semiempirical approaches, MINDO/3, MNDO, and AM1, have been developed by Michael J. S. Dewar and coworkers at the University of Texas, Austin. In 1989, a fourth method, PM3, was developed by James J. P. Stewart at the Air Force Academy. Stewart has produced a molecular orbital package, known as MOPAC, containing all four of these methods.

Applications

Mass spectrometry is a powerful tool for the chemist. It works because ions can be formed for most molecules and sorted out by their mass and charge. In the 1980s, new developments in instrumentation opened the study of large biological compounds by mass spectrometry. Molecular weights of biological molecules with masses well above 300,000 Da can be determined with a precision far greater than any of the standard biochemical techniques. In addition, Klaus Biemann at the Massachusetts Institute of Technology led efforts to sequence proteins by mass spectrometry.

Molecular ions located in interstellar clouds emit microwave and infrared radiation that can be detected on Earth. In 1970, a microwave line originating in outer space was routinely detected on Earth. These lines had never been observed in the laboratory by spectroscopy, so no one knew which molecule was producing this line. It was suggested that perhaps the line was coming from a singly charged triatomic cation, the hydrogen-carbon-oxygen plus one ion. This cation was too difficult to observe in the laboratory, so Henry F. Schaefer III and coworkers at the University of California, Berkeley, calculated the structure of this species and the position of the microwave line using ab initio molecular orbital theory. The theoretical line fit the one observed from interstellar space to 1 part in 500, and it was concluded that the proper ion had been identified. Five years later, advances in experimental instrumentation made it possible to study the hydrogen-carbon-oxygen cation in the laboratory, and the geometry of the ion was determined. The theoretical structure proved to be very accurate when compared with the structure obtained from the experiment.

In 1979, Richard J. Saykally, an experimental physical chemist at the University of California, Berkeley, embarked on the search for several simple polyatomic ions in the laboratory. While Saykally and coworkers looked at experimental results, Schaefer and coworkers provided the theoretical predictions of the structures and positions of the infrared lines for these species. This merger of infrared laser spectroscopy and ab initio calculations was extremely successful, as the experimental results were interpreted from the ab initio predictions.

Another example of a physical chemistry investigation of ion structure is the investigation of doubly charged ethane cations by mass spectrometry and quantum mechanical calculations. Thomas F. Moran, at Georgia Institute of Technology, and coworkers have made extensive use of doubly charged ion mass spectra. Their experiments, as well as experiments by other workers, indicate that doubly charged ethane cations are not present in the mass spectra of hydrocarbons. The structure of ethane is predicted to be stable by three separate ab initio calculations, yet it is not observed by mass spectrometry. In order to understand this result, the semiempirical method MNDO was used to chart the potential energy curves for the dissociation of the ethane cations into two fragment cations. Potential energy curves are calculated by systematically breaking the original molecule into two fragments and changing the distance between the fragments in small steps. The maximum height of the potential energy curve directly yields the energy required to dissociate the molecule into the two fragments. It was discovered that the energy required to dissociate the doubly charged ethane cation into various product cations was relatively small. Furthermore, the doubly charged ethane cations were produced in the mass spectrometer with so much energy that they spontaneously dissociated before they could traverse the mass spectrometer.

One of the simplest molecular cations in existence is the singly charged carbon-hydrogen ion. It was discovered in the Canadian laboratory of Gerhard Herzberg and reported in 1942. This small, reactive, radical ion is chemically very active in combustion reactions and atmospheric chemistry. It is believed to play a fundamental role in the creation of many small molecules within interstellar clouds. William Klemperer of Harvard University and P. M. Solomon of Columbia University made a detailed analysis of the interstellar processes involving the carbon-hydrogen cation. Their work, reported in the Astrophysical Journal in 1972, describes reactions that this molecular ion undergoes to produce molecules within interstellar clouds. This ion is believed to be important in the formation of CH, CO, CN, and several other molecular species. In 1980, Fred J. Grieman, Bruce H. Mahan, Anthony O’Keefe, and John S. Winn at the University of California, Berkeley, developed an experimental apparatus to measure the high-resolution spectrum of the carbon-hydrogen molecular fragment ion. They combined the techniques of spectroscopy with mass spectrometry in order to store ions long enough to observe their spectroscopic transitions. Their results showed that the lifetime of the ion agreed well with the value predicted from theory.

Negative ions, or anions, can be studied by mass spectrometry and spectroscopic methods as well. Anions are not as well studied as cations, but this will change as spectroscopists devise experiments capable of high-resolution studies of these negatively charged ions. Anions are studied in mass spectrometers using a variety of different techniques.

Context

Molecular ions were known to exist in the early part of the twentieth century. Mass spectrometric investigations of molecular ions commenced before 1920. In 1910, Francis William Aston became the assistant to Sir Joseph John Thomson, who won the 1906 Nobel Prize in Physics, working on positive rays, including studies that led to the mass spectrum of neon. This work allowed Thomson to deduce that neon existed as two isotopes. Aston perfected the mass spectroscope after World War I, which brought him the 1922 Nobel Prize in Chemistry. Arthur Jeffrey Dempster began the study of molecular ions in 1918 after the development of an improved mass spectrometer. Dempster published three papers in PHYSICAL REVIEW on this work in 1918, 1921, and 1922.

Molecular ions are important constituents in high-energy systems on Earth, such as flames, and in low-pressure systems, such as interstellar clouds. Combustion processes produce ions, which are difficult to study directly in a flame. Fortunately, the experimental techniques of mass spectrometry and high-resolution spectroscopy, along with theoretical quantum mechanical calculations, have made the study of ions an exciting research area in recent times.

Mass spectrometry is dependent on the ease of ionizing molecules so that the resultant ions can be separated from neutral molecules and identified by their characteristic mass-to-charge ratio. Advances in ionization sources and magnets have dramatically increased the range of problems that can be addressed by mass spectrometry. It cannot be overemphasized that technical progress in the 1970s and 1980s has made this technique much more powerful and much more accessible to researchers. Further advances are sure to come. For example, the use of superconducting magnets has improved mass resolution, though not by many orders of magnitude, and advances in instrumentation have enabled sensitive analysis of large molecules. Advances in Orbitrap mass spectrometry allow single molecular ions to be tracked for up to about 25 seconds, significantly improving mass resolution, signal-to-noise ratio, and measurement accuracy, and enabling detailed analysis of very large molecules such as proteins.

The study of molecular ions by high-resolution spectroscopy expanded significantly in the 1980s. Technological advances such as tunable lasers and improved ion beam techniques revolutionized the study of ions. Developments also include combining mass spectrometry with techniques such as X-ray spectroscopy and ion mobility, enabling detailed structural and electronic analysis of molecular ions in the gas phase. Accurate ab initio calculations of ions are extremely important to spectroscopists. It is possible to predict experimental results for a given ion from ab initio computations. In this way, theory can guide experiment. There are many examples of experimentalists identifying and characterizing ions based on theoretical predictions. Developments in artificial intelligence allow models to analyze millions of mass spectra and predict molecular structures from ion fragmentation patterns, significantly improving the interpretation of complex ion data.

This type of close interaction between theory and experiment will be more important in the future as larger ions have more complicated spectra. The theoretical knowledge of molecular structure will greatly aid spectroscopists. Finally, anions are characterized by spectroscopy so that the detailed high-resolution structures of cations, anions, and neutral molecules can be compared.

Principal terms

ANION: an ion with an overall negative charge (more electrons than protons)

CATION: an ion with an overall positive charge (more protons than electrons)

ELECTRONS: small negative charges, which are attracted to positively charged protons in nuclei; electrons are responsible for chemical bonds

ION: an atom or a molecule that is no longer neutral because of an unequal number of electrons and protons

MASS SPECTROMETRY: an experimental technique that allows for the determination of molecular mass by separating a stream of charged particles according to the mass-to-charge ratio

MASS-TO-CHARGE RATIO: the mass divided by the charge; this ratio identifies each peak in a mass spectrum

MOLECULE: a collection of atoms bonded together; normally neutral since it has an equal number of protons and electrons

POTENTIAL ENERGY CURVE: a plot of energy on the y-axis versus internuclear distance on the x-axis, calculated by quantum mechanics

PROTONS: positively charged particles in the nucleus, which attract negatively charged electrons; protons are much heavier than electrons

SPECTROSCOPY: experimental techniques for determining the geometry of molecules and ions; the way chemists “see” molecules and ions

Bibliography

Berkowitz, Joseph, and Karl-Ontjes Groeneveld, editors. Molecular Ions: Geometric and Electronic Structures. Plenum Press, 1983.

Bushuiev, R., et al. Self-Supervised Learning of Molecular Representations from Millions of Tandem Mass Spectra Using DreaMS. Nature Biotechnology, vol. 44, 2026, pp. 630–40, doi:10.1038/s41587-025-02663-3. Accessed 22 Apr. 2026.

Crowther, James G. The Cavendish Laboratory, 1874–1974. Science History, 1974.

Deslignière, E., et al. Ultralong Transients Enhance Sensitivity and Resolution in Orbitrap-Based Single-Ion Mass Spectrometry. Nature Methods, vol. 21, 2024, pp. 619–22, doi:10.1038/s41592-024-02207-8. Accessed 22 Apr. 2026.

Grant, E. R., and R. G. Cooks. “Mass Spectrometry and Its Use in Tandem with Laser Spectroscopy.” Science, vol. 250, no. 4977, 5 Oct. 1990, p. 61.

Heo, Jun, et al. “Capturing the Generation and Structural Transformations of Molecular Ions.” Nature, vol. 625, no. 7996, 2024, pp. 710–14, doi:10.1038/s41586-023-06909-5. Accessed 22 Apr. 2026.

Ihde, Aaron J. The Development of Modern Chemistry. Harper & Row, 1964.

Kung, Jocky C. K., et al. “X-Ray Spectroscopy Meets Native Mass Spectrometry: Probing Gas-Phase Protein Complexes.” Physical Chemistry Chemical Physics, vol. 27, 2025, pp. 13234–42, doi:10.1039/D5CP00604J. Accessed 22 Apr. 2026.

Offenhatz, Peter. Atomic and Molecular Theory. McGraw-Hill, 1970.

Thomson, George Paget. J. J. Thomson and the Cavendish Laboratory in His Day. Thomas Nelson, 1964.