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Welcome to the McCoy group website where you can learn about the fun we have studying anharmonicity and large amplitude motion! Have a look at Anne’s research, learn a little bit about her and the rest of the group, catch up on the group’s news and recent publications, and be sure to check out the group’s photo page. To learn more about the methods we use, check out our References page on the group GitHub, as well as the Python packages group members have developed for these methods.
Research topics
- Physics
- Mathematics
- Computer Science
- Artificial Intelligence
- Geometry
- Biochemical engineering
- Crystallography
- Nanotechnology
- Engineering
- Materials science
- Quantum mechanics
- Chemical physics
- Chemistry
Selected publications
The Journal of Physical Chemistry A · 2026-04-14
articleSenior authorCorrespondingThe spectra of CH5+ and its deuterated analogues are challenging to interpret due to the very flat potential surface and the highly delocalized ground state wave function. In this work, an approach is developed to model the spectra of CH5+ and CH4D+. In this approach, several thousand geometries are sampled from the ground-state probability density, which is evaluated using diffusion Monte Carlo. For each structure, the potential energy is minimized with respect to the five CH bond lengths, and the frequencies and intensities for the five 1–0 transitions involving the CH or CD stretching vibrations are then evaluated using a five-dimensional harmonically coupled anharmonic oscillator model and a sum of one-dimensional cuts through the dipole moment surface. This information is used to obtain the spectrum by two approaches. To model the lower-resolution laser-induced reaction spectrum, the calculated spectrum is obtained by convoluting the spectra obtained at all of the sampled structures. To model the helium droplet spectrum, in which the individual CH vibrational transitions are resolved, the spectrum is obtained by averaging the Hamiltonian matrices and transition moment vectors over the sampled structures. We find that these approaches reproduce the reported spectra. Analysis of the helium droplet spectrum leads us to conclude that, in this environment, the isomerization of CH5+ in its ground state is restricted compared to the gas phase. Overall, this approach provides a simple and physically transparent way to connect fluxional structures to CH-stretch spectral patterns, and offers frameworks for interpreting future spectroscopic studies.
International Journal of Mass Spectrometry · 2026-04-11
articlePhysical Chemistry Chemical Physics · 2026-01-01
articleOpen accessWe report cryogenic ion vibrational spectroscopy of chloride, bromide, and iodide complexes with octa-methyl calix[4]pyrrole (omC4P) and with the tetra-α “four wall” 4-nitroaryl-extended calix[4]pyrrole (AEC4P).
ChemRxiv · 2026-05-22
articleOpen access1st authorCorrespondingA strategy is developed for evaluating spectra of anions of polycyclic aromatic hydrocarbon (PAH) molecules. The high symmetry of these systems and the similarity of the frequencies of the CH wagging and ring distortion vibrations result in normal modes that are highly mixed in character. This results in extensive mixing among the nearly degenerate states with energies in the 2600 to 3200 cm -1 region of the spectrum. When we generate vibrational modes that resemble localized CH stretching, CH wagging or ring distortion vibrations from linear combinations of the normal modes we find that the 2:1 Fermi resonances that couple the states with two quanta of excitation in the CH wagging vibration and one quantum of excitation in the corresponding CH stretching vibration are an order of magnitude or more larger than all of the other terms that couple these nearly degenerate states. The Fermi resonance coupling terms are evaluated for polar and Cartesian representations of the displacements of the hydrogen atom in the plane molecule for the anions of anthracene, pyrene, perylene and fluroanthene. We find the Fermi coupling constants to be nearly constant across all of the the CH bonds in these four ions, with values of 125 and 62 cm -1 for the Cartesian and polar representations of the Hamiltonian, respectively. When the polar coordinate representation of the displacements of the hydrogen atoms is used, the leading contribution to the Fermi coupling constant can be traced to the kinetic term in the Hamiltonian that involves the momentum of the wagging vibration, where the leading contribution to the effective mass is the moment of inertia of the CH bond. Using a Fermi coupling constant 62 cm1, along with a transferrable model for the anharmonicity of the states in this energy range with one ar two quanta of excitation, we can reproduce the recently reported spectra of these anions.
The Journal of Physical Chemistry A · 2026-03-05
articleSenior authorCorrespondingCryogenic Vibrational Spectroscopy of the Deprotonated Dimer of Phosphoric Acid
Refubium (Universitätsbibliothek der Freien Universität Berlin) · 2026-01-01
articleOpen accessPhosphate-containing molecules are ubiquitous in nature, where they play crucial roles in biochemical processes. Further, they are of technical importance, for example, in certain batteries and in fuel cells, where a unique property of phosphoric acid is exploited─its exceptionally high proton conductivity. Proton transport in phosphoric acid is known to involve proton shuttling; however, the elementary steps involved are not clear. To elucidate the hydrogen bonding preferences of phosphoric acid, we investigate the dihydrogen phosphate anion as well as the deprotonated dimer of phosphoric acid (H3PO4·H2PO4–) in the gas phase using infrared action spectroscopy in helium nanodroplets and infrared D2-tagging photodissociation spectroscopy, and the experimental spectra are compared to theoretical ones. Theory finds for H3PO4·H2PO4– two different structures that are predicted to be nearly isoenergetic. The comparison to the experimental spectra, however, allows for a clear assignment and structure identification. The resulting structure has an interesting binding motif, which might be of relevance to interactions of phosphoric acid in the condensed phase and which can serve as a benchmark for quantum chemical calculations.
Infrared Spectroscopy of Protonated Ethane in Helium Droplets
The Journal of Physical Chemistry Letters · 2026-05-04
articleCorrespondingProtonated saturated hydrocarbons like C2H7+ often have unique structures and multiple isomers, but they are notoriously difficult to study due to their short-lived nature and tendency to fragment or react to produce smaller ions. Here we report the infrared spectrum of protonated ethane (C2H7+) in helium droplets and of the weakly bound C2H5+–H2 complex. We found that C2H7+ could be formed by H3+ protonation of C2H6 molecules as well as ionization of methane dimers. The spectrum displayed in this work is in agreement with previous results obtained for the bridged isomer of protonated ethane in the gas phase. However, we could not identify the classical isomer with a pentacoordinated carbon atom. Anharmonic calculations, performed using second-order vibrational perturbation theory (VPT2) based on electronic structure calculations performed at the B2PLYP-D3/aug-cc-pVTZ level of theory/basis, corroborate our assignments and reveal that broad C2H7+ bands previously assigned to single fundamental CH3 stretches may be due to overlapping fundamental and combination bands.
ChemRxiv · 2026-05-11
articleOpen accessSenior authorThe CH stretching region of the infrared spectra of polycyclic aromatic hydrocarbon radical anions (2700-3100 cm-1) is characterized by complicated band patterns that defy straightforward assignments from harmonic calculations. We compare experimental infrared photodissociation spectra of Argon tagged anthracene, pyrene, perylene, and fluoranthene anions with spectra computed using different methods in the framework of vibrational perturbation theory, starting from electronic structure calculations based on density functional theory. We trace the complex behavior in the CH stretching region to Fermi interactions between levels with one vibrational quantum of CH stretching excitation and vibrational states with overall two quanta in lower frequency modes characterized by CH wagging, CC stretching, and CCC bending motions. The resulting vibrational states are strongly mixed in the basis of the harmonic normal modes. Taking all 2:1 Fermi resonances in the relevant frequency range into account typically results in the best agreement between theory and experiment.
Rotation, Vibration, Torsion Coupling Effects in the Spectrum of Dimethyl Sulfide
The Journal of Physical Chemistry A · 2026-04-01
articleCorrespondingThe room temperature, high-resolution (8–16 MHz) rovibrational absorption spectrum of low-pressure dimethyl sulfide [ J. Quant. Spectrosc. Radiat. Transfer 2025, 37, 109690] shows spectral congestion at transition energies as low as ∼1000 cm–1. The origin of this congestion is investigated theoretically by developing a rotation/torsion/vibration Hamiltonian and dipole moment surface that allow us to model the excitation of the methyl rocking vibrations that are excited in the experiment. The vibrations that are described by this Hamiltonian include the two torsions and the seven additional low-frequency vibrations with harmonic frequencies below 1100 cm–1. The effect of Coriolis coupling is minimized by defining a body-fixed embedding that satisfies the Eckart condition at the nine equivalent minima on the potential surface. The couplings between the torsions and vibrations, especially for those states excited in hot-band transitions, lead to substantial state mixing. Not only does this state mixing lead to spectral congestion due to intensity borrowing, it also leads to the quartet of transitions, which are associated with the torsional tunneling of the two methyl groups, becoming spectrally distinct at the experimental resolution. These combined effects lead to a model spectrum with similar levels of congestion as are observed experimentally, allowing us to deconvolute the various contributions to this low-energy spectral congestion. This analysis identifies torsion-induced vibrational mode mixing as the most important contributor to the observed spectral congestion.
ChemRxiv · 2025-08-27
articleOpen accessWe report cryogenic ion vibrational spectroscopy of the chloride, bromide, and iodide complexes of octa-methyl calix[4]pyrrole (omC4P) and α,α,α,α-isomer of the 4-nitro-aryl-extended calix[4]pyrrole (AEC4P). The experimentally determined infrared spectra are compared with those obtained using density functional theory calculations, providing molecular-level insights into the binding properties of these receptor-halide complexes. Halide binding is mainly driven by the symmetric interactions between the halide ion and the receptor’s four pyrrole NH groups. These interactions lock the receptors in cone conformation and are encoded in the NH stretching region of the infrared spectra of the complexes. In the case of the “four wall” AEC4P, the cone conformation receptor defines a deep, polar, aromatic cavity, which is closed at one end by the four converging pyrrole NHs. Upon inclusion of the halide (Cl−, Br−, or I−), we observed a redistribution of the negative charge of the bound anion into the meso-p-nitro-aryl groups of the receptor. The resulting electrostatic field pushes the ion deeper into the cavity of the AEC4P receptor. This contrasts with the more superficial binding geometry of the corresponding omC4P anionic complex, which lacks meso-aryl substituents. A detailed decomposition of the electrostatic forces from various parts of the meso-4-substituted aryl groups suggests design principles that could guide the development of other anion receptors with improved binding affinity and selectivity.
Recent grants
Theoretical Studies of Spectral Signatures of Large Amplitude Vibrational Motions
NSF · $500k · 2019–2023
NSF · $415k · 2016–2019
Exploring Spectral Signatures of Molecular Vibrations
NSF · $510k · 2022–2026
Theoretical Studies of Spectral Signatures of Large Amplitude Vibrational Motions
NSF · $615k · 2015–2019
Structure, Spectroscopy and Dynamics of Systems that Undergo Large Amplitude Motions
NSF · $455k · 2005–2011
Frequent coauthors
- 105 shared
Joan‐Emma Shea
University of California, Santa Barbara
- 96 shared
Sharon Hammes‐Schiffer
Yale University
- 91 shared
Gregory D. Scholes
Princeton University
- 89 shared
Martin T. Zanni
University of Wisconsin–Madison
- 88 shared
Prashant V. Kamat
University of Notre Dame
- 87 shared
Scott J. Miller
NextFlex
- 86 shared
Gustavo E. Scuseria
Rice University
- 85 shared
David L. Kaplan
Tufts University
Labs
Awards & honors
- Fellow of the American Physical Society (2007)
- Fellow of the American Chemical Society (2009)
- Fellow of the American Association for the Advancement of Sc…
- Elected to the Washington State Academy of Sciences (2019)
- Herschbach Medal (2025)
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