About

Mark Johnson is the Arthur T. Kemp Professor of Chemistry and a member of the Yale faculty since 1985. His research interests are centered on physical chemistry, specifically the mechanisms of complex synthetic pathways at the molecular level. He combines multi-dimensional laser spectroscopies, reaction dynamics, cryogenic ion chemistry, and bioanalytical methodologies to access transient species in solution, expanding the scope of chemistry addressed in his work. His laboratory develops and utilizes sophisticated instrumentation, including a new class of spectrometers that integrate FTIR-like capabilities with mass spectrometry, to study chemical processes with high precision. Professor Johnson's work involves understanding chemical processes in condensed phases by extracting key species directly from solutions, freezing them into well-defined geometries, and characterizing the potential energy surfaces that govern reactions. His research projects include structural characterization of host-guest linkages in supramolecular chemistry, photochemical conversion of intermediates in catalytic transformations of CO2 and H2O into solar fuels, and elucidation of micro-hydration regimes involved in charge translocation and covalent bond formation. His approach often involves close collaboration with inorganic, organic synthesis, and chemical biology groups, and his laboratory designs custom instruments to meet these scientific challenges. Throughout his career, he has been recognized with numerous honors, including election to the National Academy of Sciences, fellowships in major scientific societies, and awards for his contributions to molecular spectroscopy and physical chemistry.

Research topics

• Chemistry
• Chemical physics
• Physics
• Stereochemistry
• Chromatography
• Physical chemistry
• Materials science
• Photochemistry
• Crystallography
• Organic chemistry

Selected publications

• Cryogenic Ion Kinetics and Thermodynamics in a Temperature-Controlled, Radiofrequency Ion Trap: A Case Study of the “Tag Isomers” Adopted by the Py-CH₂-COOH⁺·D₂ Cation

  The Journal of Physical Chemistry Letters · 2025-08-20 · 2 citations

  articleSenior authorCorresponding

  Two spectroscopically distinct isomers of the Py-CH2-COOH+ cation are formed upon D2 condensation in a cryogenic radiofrequency ion trap. This provides a useful platform upon which to elucidate the bimolecular kinetics that underlie the temperature-dependent distribution of the isomers. This equilibrium is maintained by isomer interconversion reactions involving collisions with D2 molecules present at low pressure in the trap. The rates are determined by measuring the transient population recoveries after one of the isomers is selectively removed by resonant vibrational excitation with a 5 ns infrared laser. The correlated spectral response of the two isomers yields a direct experimental measurement of the relative optical cross sections of the D2-bound and free fundamental transitions of the OH group on the acid. The reaction thermochemistry is extracted using van ’t Hoff analysis of the temperature-dependent isomer populations.

  PublisherDOI

• Structural Insight into ESI+-Generated Ions of Oxazolochlorin Derivatives Using Cryogenic Infrared Ion Spectroscopy

  Journal of the American Society for Mass Spectrometry · 2025-12-15

  articleCorresponding

  Oxazolochlorins are synthetic porphyrinoids that are distinguished from regular tetrapyrrolic pigments by the presence of an oxazoline moiety in place of a pyrrole. They are amenable to electrospray ionization mass spectrometric analysis. Ionization can take place via protonation, the loss of an alkoxy side chain forming an α-oxacarbocation, or in the case of oxazolochlorinato metal complexes by (formal) oxidation of the metal center. Structural aspects of the ions were studied by using cryogenic ion vibrational spectroscopy. Comparison of the vibrational band patterns generated using density-functional theory calculations with the experimental spectra indicates that it is possible to distinguish specific protonation sites as well as oxazolochlorin constitutional macrocycle isomers. Information is also obtained regarding the nature of the alkoxy side chains on the protonated oxazolochlorins. Lastly, we explore how centrally coordinated metal ions (Ni2+ and Ag2+, both square planar coordinated divalent metals) influence the vibrational band patterns displayed by the macrocycles. This study provides a proof of concept that cryogenic infrared ion spectroscopy is suitable to expand our structural understanding of the ions formed by porphyrinoids under electrospray conditions.

  PublisherDOI

• Characterization of Two Positional Isomers of the Cs ⁺ Gly Complex Using Two-Color, IR–IR Photobleaching of the Cryogenically Cooled Ions

  The Journal of Physical Chemistry A · 2025-12-10

  articleSenior authorCorresponding

  and the glycine scaffold. In one isomer, the ion attaches to the oxygen atoms of the carboxyl group whereas in the other it docks to the amino nitrogen and the carbonyl oxygen. Attachment to the acid headgroup yields a very diffuse absorption associated the OH group engaged in a strong intramolecular H-bond that closes a 5 membered ring. The band assignments, rearrangement pathways and electrostatic distortion of the electron density distributions in the glycine scaffold by the proximal ion are explored with electronic structure calculations and anharmonic theory.

  PublisherDOI

• Microcanonical kinetics of water-mediated proton transfer in microhydrated 4-aminobenzoic acid

  Science · 2025-09-11 · 4 citations

  articleSenior authorCorresponding

  Isolated cluster systems can help to elucidate the molecular level description of water-mediated proton transfer. Protonation of neutral 4-aminobenzoic acid (4ABA) occurs at the acid ( O -protomer) and amine ( N -protomer) functionalities, yielding two distinct species with relative energies dependent on the degree of hydration. Here, we measured the rates of intramolecular proton transfer in 4ABAH + ·(H 2 O) 6 ions upon protomer-selective vibrational excitation of initially cold (6 K) cluster ions isolated in a cryogenic ion trap. Interconversion rates were observed on the microsecond time scale. These results quantify the kinetics of proton transfers in the context of a closed, finite system at well-defined internal energies and therefore provide experimental benchmarks for theoretical efforts that are being developed to treat relatively slow, highly cooperative solvent-mediated chemical processes.

  PublisherDOI

• Isomers and band assignments in the cryogenic vibrational spectrum of the binary complex between water and protonated formic acid using two color, IR–IR photobleaching and H/D isotopic substitution

  The Journal of Chemical Physics · 2025-06-02 · 2 citations

  articleSenior author

  Protonated formic acid (PFA) is purported to be the active species in the catalytic activation of condensation reactions at the acidic interface of microdroplets. Here, we investigate the fundamental interaction between PFA and water with cryogenic ion vibrational spectroscopy of the binary PFA-H2O complexes generated via electrospray ionization followed by buffer gas cooling to about 20 K. The patterns displayed by the isomer-specific IR spectra of D2-tagged PFA-H2O indicate that two distinct, non-interconverting rotamers are present at low temperatures based on the cis and trans structures of the HCO2H2+ core ion. Both of these occur with the water molecule attached to the OH that is in a cis-configuration relative to the CH group (denoted E), but differ in the E vs Z (cis vs trans relative to the CH group) orientation of the spectator OH. This assignment scheme corrects a previous theoretical analysis that invoked a scenario in which structures with E- and Z-bound water molecules interconvert at low (20 K) temperatures. Isomer-specific bands arising from the OH stretches and water bending modes are deconvoluted using isotopomer-specific spectroscopy of the complexes with partial H/D exchange. The dependence of the nominal shared proton OH stretch frequency on the deuteration of the tethered water confirms strong coupling between this mode and the water bending fundamental.

  PublisherDOI

• Dynamics of Protonated Oxalate from Machine-Learned Simulations and Experiment: Infrared Signatures, Proton Transfer Dynamics and Tunneling Splittings

  ArXiv.org · 2025-08-08

  preprintOpen access

  The infrared spectroscopy and proton transfer dynamics together with the associated tunneling splittings for H/D-transfer in oxalate are investigated using a machine learning-based potential energy surface (PES) of CCSD(T) quality, calibrated against the results of new spectroscopic measurements. Second order vibrational perturbation calculations (VPT2) very successfully describe both the framework and H-transfer modes compared with the experiments. In particular, a new low-intensity signature at 1666 cm$^{-1}$ was correctly predicted from the VPT2 calculations. An unstructured band centered at 2940 cm$^{-1}$ superimposed on a broad background extending from 2600 to 3200 cm$^{-1}$ is assigned to the H-transfer motion. The broad background involves a multitude of combination bands but a major role is played by the COH-bend. For the deuterated species, VPT2 and molecular dynamics simulations provide equally convincing assignments, in particular for the framework modes. Finally, based on the new PES the tunneling splitting for H-transfer is predicted as $Δ_{\rm H} = 35.0$ cm$^{-1}$ from ring polymer instanton calculations using higher-order corrections. This provides an experimentally accessible benchmark to validate the computations, in particular the quality of the machine-learned PES.

  PublisherOA PDFDOI

• The Onset for Vibrationally Induced, Intramolecular Proton Transfer at Three Water Molecules in Microhydrated 4-Aminobenzoic Acid

  The Journal of Physical Chemistry Letters · 2025-05-19 · 6 citations

  articleOpen accessSenior authorCorresponding

  Protonation of 4-aminobenzoic acid occurs at either the amino group (the N-protomer, N) or at the carboxylic acid C═O group (the O-protomer or O). N lies higher in energy than O in the isolated ion but becomes the more stable of the 4ABAH+·(H2O)n clusters in the size range n ∼ 5. We report the size-dependent onset of intramolecular proton transfer upon vibrational excitation of cold (20 K), size-selected 4ABAH+·(H2O)n clusters in a cryogenically cooled ion trap. The onset occurs with three water molecules, which are retained after protomer interconversion. While we do not definitively identify a mechanism for the transfer, path integral molecular dynamics simulations indicate that it may proceed by proton shuttling across a bridge of at least three water molecules. By capturing protomer interconversion in a closed, finite system with well-defined internal energy, we provide a useful benchmark for furthering our understanding of water-mediated proton transport.

  PublisherOA PDFDOI

• Mechanism of a Halogen Exchange Reaction in Water: Catalysis by Aqueous Media

  ACS Central Science · 2025-03-04 · 1 citations

  articleOpen access

  Reactions of Cl–, Br–, and I– ions in seawater with incoming molecules from the gas phase are of major atmospheric importance, but their mechanisms are mostly unknown. In this study, using ab initio molecular dynamics (AIMD) simulations, the microscopic mechanism of the halogen exchange reaction in water, HOCl + I– → HOI + Cl–, is unraveled. The main findings are as follows: (1) The reaction proceeds through a halogen-bonded isomer of the complex of HOCl with I–, which is present in water and has a significant lifetime. The hydrogen-bonded isomer of the complex seems to play no role in the reaction. (2) Several water molecules act to catalyze the reaction through a Grotthuss-like mechanism that is totally different from that of halogen exchange in the gas phase. These results may have important implications for the chemistry of seawater, in particular for other reactions involving halogenated species.

  PublisherOA PDFDOI

• Dynamics of protonated oxalate from machine-learned simulations and experiment: infrared signatures, proton transfer dynamics and tunneling splittings

  Physical Chemistry Chemical Physics · 2025-01-01 · 4 citations

  articleOpen access

  The infrared spectroscopy and proton transfer dynamics together with the tunneling splittings for H/D-transfer in oxalate are investigated using a machine learning-based potential energy surface (PES) of CCSD(T) quality, calibrated against new spectroscopic measurements.

  PublisherOA PDFDOI

• A Longitudinal Assessment of Resident and New Graduate Well-Being According to Length of Training: A Report From the Length of Training Pilot in Family Medicine

  Family Medicine · 2024-04-15 · 2 citations

  articleOpen access1st author

  Background & Objectives: No prior studies have examined how length of training may influence wellness. As part of the Length of Training Pilot (LoTP), we explored resident and new graduate well-being according to program year and length of training in 3- and 4-year family medicine residency training programs. METHODS: Two surveys captured data included in these analyses. One was a resident survey that included the Mayo Clinic physician-expanded Well-Being Index (eWBI) administered annually during the In-Training Examination (2014-2019). The second was administered to graduates 1 year after completion of training between 2016 and 2022 and included the same well-being questions. Response rates ranged between 77.7% and 96.8%. RESULTS: The eWBI summary scores for burnout were highest in postgraduate year 1 (PGY1) and did not differ statistically according to length of training (PGY1: 2.02 in 3-year [3YR] programs vs 1.93 in 4-year [4YR] programs, P=.55; postgraduate year 2 [PGY2]: 2.42 in 3YR programs vs 2.38 in 4YR programs, P=.83; postgraduate year 3 [PGY3]: 2.18 in 3YR programs vs 2.28 in 4YR programs, P=.59; and 2.34 in postgraduate year 4 [PGY4] for those in 4YR programs), though some statistical differences were noted for three items. New graduates' eWBI summary scores before the COVID-19 pandemic were 1.77 among 3YR graduates and 1.66 among 4YR graduates (P=.59). These scores were higher during COVID-19 at 1.89 for 3YR graduates and 2.02 for 4YR graduates (P=.62). Length of training was not associated with differences in well-being before or during COVID-19. CONCLUSIONS: We found no associations between length of training and physician well-being during training or among new graduates before or during COVID-19.

  PublisherOA PDFDOI

Recent grants

• U.S.-Japan Cooperative Research: Chemical Reactions of Microclusters in Gas Phase and Interaction with Surfaces

  NSF · $21k · 1991–1994

• MRI: Development of a hybrid mass spectrometry platform with mass-selective optical spectroscopy of cryogenic ions

  NSF · $500k · 2018–2021

• Spectroscopic characterization of elementary species in water-mediated chemistry using size-selected clusters

  NSF · $508k · 2006–2009

• Structural characterization of organometallic reaction intermediates and vibrational mechanics of water cages with temperature-controlled cryogenic ion spectroscopy

  NSF · $520k · 2015–2019

• Spectroscopic Signatures of Divalent Metal ion Binding to Anionic Surfactants and Local Mechanics of Embedded Groups in Two-Dimensional Water Networks Through Cryogenic Cluster

  NSF · $405k · 2019–2023

Frequent coauthors

• Kenneth D. Jordan

  University of Pittsburgh

  87 shared

• Gary H. Weddle

  Fairfield University

  81 shared

• Nathan I. Hammer

  University of Mississippi

  72 shared

• Joseph Roscioli

  Aerodyne Research

  67 shared

• Eric G. Diken

  Smiths Detection (United States)

  65 shared

• Anne B. McCoy

  University of Washington

  60 shared

• Patrick Ayotte

  50 shared

• William H. Robertson

  The University of Texas at El Paso

  47 shared

Labs

• Johnson LabPI

Awards & honors

• NSF Presidential Young Investigator (1987)
• Camille and Henry Dreyfus: Distinguished New Faculty (1985)
• Teacher-Scholar (1990)
• Professeur Invité, Université de Paris-Sud (1988 & 1994)
• Invited Lecturer by The Chemical Society of Brazil (1997)