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Publications

Structures and fragmentation pathways of size-selected, D2-tagged ammonium/methylammonium bisulfate clusters

Christopher J. Johnson, Mark A. Johnson
Journal:J. Phys. Chem. A
Volume:117
Issue:50
Year:2013
Pages:13265
Research Areas: Atmospheric Chemistry | Hydrogen Predissociation
ABSTRACT

Origin of the diffuse vibrational signature of a cyclic intramolecular proton bond: anharmonic analysis of protonated 1,8-disubstituted naphthalene ions

Andrew F. DeBlase, Steven Bloom, Thomas Lectka, Kenneth D. Jordan, Anne B. McCoy, and Mark A. Johnson
Journal:J. Chem. Phys.
Volume:139
Issue:
Year:2013
Pages:024301
Research Areas: Shared Proton
ABSTRACT

Aggregation of Small Molecules: From Dimers to Crystals 

Gautam Desiraju, Mark A. Johnson, and Wolfram Sander
Journal:ChemPhysChem
Volume:14
Issue:
Year:2013
Pages:631-633
Research Areas:
ABSTRACT

Isolation and Characterization of a Peroxo Manganese(III) Dioxygen Reaction Intermediate Using Cryogenic Ion Vibrational Predissociation Spectroscopy

Arron B. Wolk, Christopher M. Leavitt, Joseph A. Fournier, Michael Z. Kamrath, Gayan Wijeratneb, Timothy A. Jackson and Mark A. Johnson
Journal:Int. J. Mass. Spectrom.
Volume:354-355
Issue:
Year:2013
Pages:33-38
Research Areas:
ABSTRACT

We apply cryogenic ion vibrational predissociation (CIVP) spectroscopy to characterize the O2 attachment motif in a prototypical peroxo manganese (III) reaction intermediate. In this approach, species are extracted from solution using electrospray ionization and cooled in a 30 K ion trap.  The infrared spectrum is then obtained by monitoring the photoinduced evaporation of a single, weakly bound N2 molecule as a function of laser wavelength.  Because the resulting CIVP action spectrum is linear in laser fluence, the pattern of well-resolved transitions can be directly compared with harmonic spectra calculated for predicted local minima using density functional theory (DFT).  The assignment of the O–O stretching band derived from the activated O2 ligand is established by following the evolution of the bands with 18O2 substitution, and the energy of this transition indicates that O2 is bound side-on to the Mn center. The successful application of CIVP to this class of compounds opens the way for sensitive spectroscopic characterization of weakly abundant species in complex solution environments.

Quantifying intrinsic ion-driven conformational changes in diphenylacetylene supramolecular switches with cryogenic ion vibrational spectroscopy

Arron Wolk, Etienne Garand, Ian Jones, Andrew Hamilton, and Mark Johnson
Journal:J. Phys. Chem. A
Volume:117
Issue:29
Year:2013
Pages:5962-5969
Research Areas: Hydrogen Predissociation
ABSTRACT

We report how two flexible diphenylacetylene (DPA) derivatives distort to accommodate both cationic and anionic partners in the binary X±·DPA series with X = TMA+ (tetramethyl ammonium), Na+, Cl‾, Br‾, and I‾. This is accomplished through theoretical analysis of X±·DPA∙2D2 vibrational spectra, acquired by predissociation of the weakly bound D2 adducts formed in a 10K ion trap.  DPA binds the weakly coordinating TMA+ ion with an arrangement similar to the neutral compound, while the smaller Na+ ion breaks all intramolecular H-bonds yielding a structure akin to the transition state for interconversion of the two conformations in neutral DPA. Halides coordinate to the urea NH donors in a bidentate H-bonded configuration analogous to the single intramolecular H-bonded motif identified at high chloride concentrations in solution. Three positions of the “switch” are thus identified in the intrinsic ion accommodation profile that differ by the number of intramolecular H-bonds (0,1 or 2) at play. 

Vibrational Predissociation Spectoscopy of Ar-Tagged, Trisubstituted Silyl Cations

Andrew F. DeBlase, Michael T. Scerba, Thomas Leckta, and Mark A. Johnson
Journal:Chem. Phys. Lett.
Volume:568–569
Issue:DOI: 10.1016/j.cplett.2013.03.002
Year:2013
Pages:9–13
Research Areas: Argon Predissociation
ABSTRACT

Characterization of an activated iridium water splitting catalyst using infrared photodissociation of H2 tagged ions

Etienne Garand, Joseph A. Fournier, Michael Z. Kamrath, Nathan D. Schley, Robert H. Crabtree, and Mark A. Johnson
Journal:Phys. Chem. Chem. Phys.
Volume:14
Issue:29
Year:2012
Pages:10109-10113
Research Areas: Hydrogen Predissociation | Organometallic Catalysts
ABSTRACT

We report the vibrational predissociation spectra of two related organometallic half-sandwich iridium species which have been recently reported as activated intermediates in the context of homogenous water oxidation. These compounds are extracted from solution into a cryogenic photofragmentation mass spectrometer and “tagged” with weakly bound H2 molecules that do not significantly perturb the intrinsic structures of the ions. The resulting spectra display very sharp ([similar]5 cm−1), well-resolved bands that provide a stringent test for electronic structure calculations, and are accurately recovered by harmonic predictions for the bare species. The spectra reveal subtle distortions of the ligand structure when a solvent molecule (acetonitrile) is directly coordinated with the metal center.

Isomer-specific IR-IR double resonance spectroscopy of D2-tagged protonated dipeptides prepared in a cryogenic ion trap

Christopher M. Leavitt, Arron B. Wolk, Joseph A. Fournier, Michael Z. Kamrath, Etienne Garand, Michael J. Van Stipdonk, and Mark A. Johnson
Journal:J. Phys. Chem. Lett.
Volume:3
Issue:9
Year:2012
Pages:1099-1105
Research Areas: Double Resonance | Hydrogen Predissociation | Peptide Conformation
ABSTRACT

Isomer-specific vibrational predissociation spectra are reported for the gas-phase GlySarH+ and SarSarH+ [Gly = glycine; Sar = sarcosine] ions prepared by electrospray ionization and tagged with weakly bound D2 adducts using a cryogenic ion trap. The contributions of individual isomers to the overlapping vibrational band patterns are completely isolated using a pump–probe photochemical hole-burning scheme involving two tunable infrared lasers and two stages of mass selection (hence IR2MS2). These patterns are then assigned by comparison with harmonic (MP2/6-311+G(d,p)) spectra for various possible conformers. Both systems occur in two conformations based on cis and trans configurations with respect to the amide bond. In addition to the usual single intramolecular hydrogen bond motif between the protonated amine and the nearby amide oxygen atom, cis-SarSarH+ adopts a previous unreported conformation in which both amino NH's act as H-bond donors. The correlated red shifts in the NH donor and C═O acceptor components of the NH···O═C linkage to the acid group are unambiguously assigned in the double H-bonded conformer.

Vibrational Fano resonances in dipole-bound anions

Stephen T. Edwards, Mark A. Johnson, and John C. Tully
Journal:J. Chem. Phys.
Volume:136
Issue:15
Year:2012
Pages:154305
Research Areas: Argon Predissociation | Halide Solvation
ABSTRACT

This paper explores Fano resonances due to non-adiabatic coupling of vibrational modes and the electron continuum in dipole-bound anions. We adopt a simple one-electron model consisting of a point dipole and an auxiliary potential to represent the electron interaction with the neutral core. Nuclear motion is added by assuming that harmonic vibrations modulate the dipole moment. When the model is parameterized to simulate key features of the water tetramer anion, the resultant photodetachment lineshape closely resembles that observed experimentally and analyzed as a Fano resonance with a parameter q close to −1. Other parameterizations are explored for the model and it is found that large changes in the auxiliary potential are required to change the sign of q. This is consistent with the experimental finding that q is negative for all water cluster sizes studied.

Vibrational manifestations of strong non-Condon effects in the H3O+·X3(X = Ar, N2, CH4, H2O) complexes: A possible explanation for the intensity in the “association band” in the vibrational spectrum of water

Anne B. McCoy, Timothy L. Guasco, Christopher M. Leavitt, Solveig G. Olesen and Mark A. Johnson
Journal:Phys. Chem. Chem. Phys.
Volume:14
Issue:20
Year:2012
Pages:7205-7214
Research Areas: Cationic Water | Supersonic Jet Expansion
ABSTRACT

The harmonic approximation provides a powerful approach for interpreting vibrational spectra. In this treatment, the energy and intensity of the 3N − 6 normal modes are calculated using a quadratic expansion of the potential energy and a linear expansion of the dipole moment surfaces, respectively. In reality, transitions are often observed that are not accounted for by this approach (e.g. combination bands, overtones, etc.), and these transitions arise from inherent anharmonicities present in the system. One interesting example occurs in the vibrational spectrum of H2O(l), where a band is observed near 2000 cm−1 that is commonly referred to as the “association band”. This band lies far from the expected bend and stretching modes of the water molecule, and is not recovered at the harmonic level. In a recent study, we identified a band in this spectral region in gas-phase clusters involving atomic and molecular adducts to the H3O+ ion. In the current study we probe the origins of this band through a systematic analysis of the argon-predissociation spectra of H3O+·X3 where X = Ar, CH4, N2 or H2O, with particular attention to the contributions from the non-linearities in the dipole surfaces, often referred to as non-Condon effects. The spectra of the H3O+ clusters all display strong transitions between 1900–2100 cm−1, and theoretical modeling indicates that they can be assigned to a combination band involving the HOH bend and frustrated rotation of H3O+ in the solvent cage. This transition derives its oscillator strength entirely from strong non-Condon effects, and we discuss its possible relationship to the association band in the spectrum of liquid water.

Characterization of Highly Unusual NH+–O Hydrogen Bonding to Ester Ether Oxygen Atoms through Spectroscopic and Computational Studies

Michael T. Scerba, Andrew F. DeBlase, Steven Bloom, Travis Duddin, Mark A. Johnson, and Thomas Lectka
Journal:J. Phys. Chem. A
Volume:116
Issue:14
Year:2012
Pages:3556
Research Areas: Cationic H-Bond | Hydrogen Predissociation
ABSTRACT

We characterize a highly unusual, charged NH–O hydrogen bond formed within esters of 8-(dimethylamino)naphthalen-1-ol in which an ammonium ion serves as an intramolecular hydrogen bond donor to spatially proximate ester ether oxygen atoms. Infrared spectroscopic analysis of the ester carbonyl frequencies demonstrates significant blue-shifting when ether hydrogen bonding is possible, in stark contrast to the more commonly observed red shift that occurs upon hydrogen bonding to the ester carbonyl oxygen. The intrinsic behavior of the linkage (i.e., in which counterions and solvent effects are eliminated) is provided by vibrational predissociation spectroscopy of the isolated gas-phase cations complexed with weakly bound D2 molecules.

Structural characterization of electron-induced proton transfer in the formic acid dimer anion, (HCOOH)2, with vibrational and photoelectron spectroscopies

Helen K. Gerardi, Andrew F. DeBlase, Christopher M. Leavitt, Xiaoge Su, Kenneth D. Jordan, Anne B. McCoy, and Mark A. Johnson
Journal:J. Chem. Phys.
Volume:136
Issue:13
Year:2012
Pages:134318
Research Areas: Electron-Induced Proton Transfer | Supersonic Jet Expansion
ABSTRACT

The (HCOOH)2 anion, formed by electron attachment to the formic acid dimer (FA2), is an archetypal system for exploring the mechanics of the electron-induced proton transfer motif that is purported to occur when neutral nucleic acid base-pairs accommodate an excess electron [K. Aflatooni, G. A. Gallup, and P. D. Burrow, J. Phys. Chem. A 102, 6205 (1998); J. H. Hendricks, S. A. Lyapustina, H. L. de Clercq, J. T. Snodgrass, and K. H. Bowen, J. Chem Phys. 104, 7788 (1996); C. Desfrancois, H. Abdoul-Carime, and J. P. Schermann, J. Chem Phys. 104, 7792 (1996)]. The FA2 anion and several of its H/D isotopologues were isolated in the gas phase and characterized using Ar-tagged vibrational predissociation and electron autodetachment spectroscopies. The photoelectron spectrum of the FA2 anion was also recorded using velocity-map imaging. The resulting spectroscopic information verifies the equilibrium FA2 geometry predicted by theory which features a symmetrical, double H-bonded bridge effectively linking together constituents that most closely resemble the formate ion and a dihydroxymethyl radical. The spectroscopic signatures of this ion were analyzed with the aid of calculated anharmonic vibrational band patterns.

Determination of Noncovalent Docking by Infrared Spectroscopy of Cold Gas-Phase Complexes

Etienne Garand, Michael Z. Kamrath, Peter A. Jordan, Arron B. Wolk, Christopher M. Leavitt, Anne B. McCoy, Scott J. Miller, and Mark A. Johnson
Journal:Science
Volume:335
Issue:6069
Year:2012
Pages:694-698
Research Areas: Catalysis | Double Resonance | Electrospray Ionization | Peptide Conformation
ABSTRACT

Multidentate, noncovalent interactions between small molecules and biopolymer fragments are central to processes ranging from drug action to selective catalysis. We present a versatile and sensitive spectroscopic probe of functional groups engaged in hydrogen bonding in such contexts. This involves measurement of the frequency changes in specific covalent bonds upon complex formation, information drawn from otherwise transient complexes that have been extracted from solution and conformationally frozen near 10 kelvin in gas-phase clusters. Resonances closely associated with individual oscillators are easily identified through site-specific isotopic labeling, as demonstrated by application of the method to an archetypal system involving a synthetic tripeptide known to bind biaryl substrates through tailored hydrogen bonding to catalyze their asymmetric bromination. With such data, calculations readily converge on the plausible operative structures in otherwise computationally prohibitive, high-dimensionality landscapes.

Bottom-Up View of Water Network-Mediated CO2 Reduction Using Cryogenic Cluster Ion Spectroscopy and Direct Dynamics Simulations

Kristin J. Breen, Andrew F. DeBlase, Timothy L. Guasco, Vamsee K. Voora, Kenneth D. Jordan, Takashi Nagata, and Mark A. Johnson
Journal:J. Phys. Chem. A
Volume:116
Issue:3
Year:2012
Pages:903-912
Research Areas: Argon Predissociation | CO2 Reduction
ABSTRACT

The transition states of a chemical reaction in solution are generally accessed through exchange of thermal energy between the solvent and the reactants. As such, an ensemble of reacting systems approaches the transition state configuration of reactant and surrounding solvent in an incoherent manner that does not lend itself to direct experimental observation. Here we describe how gas-phase cluster chemistry can provide a detailed picture of the microscopic mechanics at play when a network of six water molecules mediates the trapping of a highly reactive “hydrated electron” onto a neutral CO2 molecule to form a radical anion. The exothermic reaction is triggered from a metastable intermediate by selective excitation of either the reactant CO2 or the water network, which is evidenced by the evaporative decomposition of the product cluster. Ab initio molecular dynamics simulations of energized CO2•(H2O)6 clusters are used to elucidate the nature of the network deformations that mediate intracluster electron capture, thus revealing the detailed solvent fluctuations implicit in the Marcus theory for electron-transfer kinetics in solution.

Water

Robert G. Bryant, Mark A. Johnson, and Peter J. Rossky
Journal:Acc. Chem. Res.
Volume:45
Issue:18
Year:2012
Pages:1-2
Research Areas: Hydrated Electron
ABSTRACT

Water, as the most abundant molecule on the earth’s surface and in our own bodies, is ubiquitous in terrestrial chemical processes. These processes range from conventional solution reactions, to critical atmospheric reactions enabled by the presence of water clusters, to the myriad of biological chemical transformations. The role of water in biology includes most fundamentally its essential participation in dictating structure, including protein secondary and tertiary structure, the spontaneous formation of membranes, and the recognition of polynucleotide sequences in transcription...