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Publications

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...

Characterizing the Intramolecular H-bond and Secondary Structure in Methylated GlyGlyH+ with H2 Predissociation Spectroscopy

Christopher M. Leavitt, Arron B. Wolk, Michael Z. Kamrath, Etienne Garand, Michael J. Van Stipdonk, and Mark A. Johnson
Journal:J. Am. Soc. Mass Spectrom.
Volume:22
Issue:11
Year:2011
Pages:1941-1952
Research Areas: Electrospray Ionization | Peptide Conformation
ABSTRACT

We report vibrational predissociation spectra of the four protonated dipeptides derived from glycine and sarcosine, GlyGlyH+•(H2)1,2, GlySarH+•(D2)2, SarGlyH+•(H2)2, and SarSarH+•(D2)2, generated in a cryogenic ion trap. Sharp bands were recovered by monitoring photoevaporation of the weakly bound H2 (D2) molecules in a linear action regime throughout the 700–4200 cm–1 range using a table-top laser system. The spectral patterns were analyzed in the context of the low energy structures obtained from electronic structure calculations. These results indicate that all four species are protonated on the N-terminus, and feature an intramolecular H-bond involving the amino group. The large blue-shift in the H-bonded N–H fundamental upon incorporation of a methyl group at the N-terminus indicates that this modification significantly lowers the strength of the intramolecular H-bond. Methylation at the amide nitrogen, on the other hand, induces a significant rotation (~110o) about the peptide backbone.

NH+–F Hydrogen Bonding in a Fluorinated “Proton Sponge” Derivative: Integration of Solution, Solid-State, Gas-Phase, and Computational Studies

Michael T. Scerba, Christopher M. Leavitt, Matthew E. Diener, Andrew F. DeBlase, Timothy L. Guasco, Maxime A. Siegler, Nathaniel Bair, Mark A. Johnson, and Thomas Lectka
Journal:J. Org. Chem
Volume:76
Issue:19
Year:2011
Pages:7975-7984
Research Areas: Electrospray Ionization | Hydrogen Predissociation | Shared Proton
ABSTRACT

We report detailed studies on the characterization of an intramolecular NH–F hydrogen bond formed within a fluorinated “proton sponge” derivative. An ammonium ion, generated from 8-fluoro-N,N-dimethylnaphthalen-1-amine, serves as a charged hydrogen bond donor to a covalently bound fluorine appropriately positioned on the naphthalene skeleton. Potentiometric titrations of various N,N-dimethylnaphthalen-1-amines demonstrate a significant increase in basicity when hydrogen bonding is possible. X-ray crystallography reveals that NH–F hydrogen bonding in protonated 8-fluoro-N,N-dimethylnaphthalen-1-amine is heavily influenced by ion pairing in the solid state; bifurcated and trifurcated hydrogen bonds are formed depending on the counterion utilized. Compelling evidence of hydrogen bonding in the 8-fluoro-N,N-dimethylnaphthyl-1-ammonium cation is provided by gas-phase cryogenic vibrational photodissociation spectroscopy. Solution-phase infrared spectroscopy provides complementary results, and the frequencies of the N–H stretching mode in both phases are in excellent agreement with the computed vibrational spectra. NMR analysis of protonated 8-fluoro-N,N-dimethylnaphthalen-1-amine demonstrates significant H–F coupling between the N–H hydrogen and fluorine that cannot be attributed to long-range, through-bond interactions; the couplings correlate favorably with calculated values. The results obtained from these experiments are congruent with the formation of an NH–F hydrogen bond upon protonation of 8-fluoro-N,N-dimethylnaphthalen-1-amine.

Unraveling the Anomalous Solvatochromic Response of the Formate Ion Vibrational Spectrum: An Infrared, Ar-Tagging Study of the HCO2¯, DCO2¯, and HCO2¯·H2O Ions

Helen K. Gerardi, Andrew F. DeBlase, Xiaoge Su, Kenneth D. Jordan, Anne B. McCoy, and Mark A. Johnson
Journal:J. Phys. Chem. Lett.
Volume:2
Issue:19
Year:2011
Pages:2437-2441
Research Areas: Argon Predissociation
ABSTRACT

Reductive activation offers an attractive synthetic route for conversion of CO2 to transportable fuels, a process that often involves creation of the formate ion as an intermediate. We carry out an Ar-tagging infrared spectroscopic study of isolated HCO2¯ and its first hydrate, HCO2¯•H2O, and analyze the resulting band patterns with electronic structure and vibrationally anharmonic calculations. Strong vibronic interactions and intramolecular mode couplings are identified that are responsible for the deceptively complex solvation behavior of this familiar ion. In particular, the CH stretch fundamental is found to be anomalously low in energy in the isolated ion and to dramatically blue shift (by hundreds of cm–1) upon solvation. These two effects are traced to the large dependence of the electronic wave function on the CH bond length, reminiscent of the classic curve-crossings that dominate the dissociation behavior of neutral salt molecules.

The Importance of NO+(H2O)4 in the Conversion of NO+(H2O)n to H3O+(H2O)n: I. Kinetics Measurements and Statistical Rate Modeling

Nicole Eyet, Nicholas S. Shuman, Albert A. Viggiano, Jürgen Troe, Rachael A. Relph, Ryan P. Steele, and Mark A. Johnson
Journal:J. Phys. Chem. A
Volume:115
Issue:26
Year:2011
Pages:7582-7590
Research Areas: Kinetics
ABSTRACT

The kinetics for conversion of NO+(H2O)n to H3O+(H2O)n has been investigated as a function of temperature from 150 to 400 K. In contrast to previous studies, which show that the conversion goes completely through a reaction of NO+(H2O)3, the present results show that NO+(H2O)4 plays an increasing role in the conversion as the temperature is lowered. Rate constants are derived for the clustering of H2O to NO+(H2O)1–3 and the reactions of NO+(H2O)3,4 with H2O to form H3O+(H2O)2,3, respectively. In addition, thermal dissociation of NO+(H2O)4 to lose HNO2 was also found to be important. The rate constants for the clustering increase substantially with the lowering of the temperature. Flux calculations show that NO+(H2O)4 accounts for over 99% of the conversion at 150 K and even 20% at 300 K, although it is too small to be detectable. The experimental data are complimented by modeling of the falloff curves for the clustering reactions. The modeling shows that, for many of the conditions, the data correspond to the falloff regime of third body association.

Tuning the intermolecular proton bond in the H5O2+ ‘Zundel ion’ scaffold

S.G. Olesen, T.L. Guasco, J.R. Roscioli, and M.A. Johnson
Journal:Chem. Phys. Lett.
Volume:509
Issue:4-6
Year:2011
Pages:89-95
Research Areas: Argon Predissociation | Protonated Water Clusters
ABSTRACT

The Zundel ion, H2O•H+•H2O, provides a versatile scaffold with which to explore the quantum structure of the intermolecular proton bond (IPB). This information is encoded in the vibrational frequencies adopted by the shared proton, νsp, which are observed to follow a remarkably similar trend as the exterior OH groups are sequentially solvated or are replaced by methyl substituents. In effect, solvents H-bonding to exterior OH groups act to increase the proton affinity of the water to which they are bound in a roughly additive fashion. We discuss this behavior in the context of the extreme sensitivity of IPBs to their solvation environments.

Unraveling Anharmonic Effects in the Vibrational Predissociation Spectra of H5O2+ and Its Deuterated Analogues

Timothy L. Guasco, Mark A. Johnson, and Anne B. McCoy
Journal:J. Phys. Chem. A
Volume:115
Issue:23
Year:2011
Pages:5847-5858
Research Areas: Argon Predissociation | Protonated Water Clusters
ABSTRACT

The nature of anharmonic couplings in the H5O2+ “Zundel” ion and its deuterated isotopologues is investigated through comparison of their measured and calculated vibrational spectra. This follows a recent study in which we reported spectra for H5O2+, D5O2+, and D4HO2+ from 600 to 4000 cm−1, as well as H4DO2+ in the OH and OD stretching regions [ J. Phys. Chem. B 2008, 112, 321]. While the assignments of the higher-energy transitions associated with the fundamentals of the exterior OH and OD motions are relatively straightforward, difficulties arise in the assignment of the lower-frequency regions that involve displacement of the bridging proton, especially for the isotopically mixed species. Here we revisit the Ar-tagged isotopomers, and report the low energy action spectrum of H4DO2+ for the first time, as well as present significantly improved spectra for the D4HO2+ and D5O2+ systems. Band assignments are clarified in several cases using IR−IR hole-burning. We then investigate the physical origin of the anharmonic effects encoded in these spectra using a recently developed technique in which the anharmonic frequencies and intensities of transitions (involving up to two quanta of excitation) are evaluated using the ground state probability amplitudes [ J. Phys. Chem. A 2009, 113, 7346] obtained from diffusion Monte Carlo simulations. This approach has the advantage that it is applicable to low-symmetry systems [such as (HDO)H+(OH2)] that are not readily addressed using highly accurate methods such as the multiconfigurational time-dependent Hartree (MCTDH) approach. Moreover, it naturally accommodates an intuitive evaluation of the types of motion that contribute oscillator strength in the various regions of the spectrum, even when the wave function is intrinsically not separable as a product of low-dimensional approximate solutions. Spectra for H5O2+, D5O2+, H4DO2+, and D4HO2+ that are calculated by this approach are shown to be in excellent agreement with the measured spectra for these species, leading to reassignments of two of the bands in the intramolecular bending region of D4HO2+

Vibrational Characterization of Simple Peptides Using Cryogenic Infrared Photodissociation of H2-Tagged, Mass-Selected Ions

Michael Z. Kamrath, Etienne Garand, Peter A. Jordan, Christopher M. Leavitt, Arron B. Wolk, Michael J. Van Stipdonk, Scott J. Miller, and Mark A. Johnson
Journal:J. Am. Chem. Soc.
Volume:133
Issue:16
Year:2011
Pages:6440-6448
Research Areas: Electrospray Ionization | Hydrogen Predissociation
ABSTRACT

We present infrared photodissociation spectra of two protonated peptides that are cooled in a 10 K quadrupole ion trap and “tagged” with weakly bound H2 molecules. Spectra are recorded over the range of 600−4300 cm−1 using a table-top laser source, and are shown to result from one-photon absorption events. This arrangement is demonstrated to recover sharp (Δν 6 cm−1) transitions throughout the fingerprint region, despite the very high density of vibrational states in this energy range. The fundamentals associated with all of the signature N−H and C═O stretching bands are completely resolved. To address the site-specificity of the C═O stretches near 1800 cm−1, we incorporated one 13C into the tripeptide. The labeling affects only one line in the complex spectrum, indicating that each C═O oscillator contributes a single distinct band, effectively “reporting” its local chemical environment. For both peptides, analysis of the resulting band patterns indicates that only one isomeric form is generated upon cooling the ions initially at room temperature into the H2 tagging regime.

Vibrational predissociation spectroscopy of the H2-tagged mono- and dicarboxylate anions of dodecanedioic acid

Michael Z. Kamrath, Rachael A. Relph, Timothy L. Guasco, Christopher M. Leavitt, and Mark A. Johnson
Journal:Int. J. Mass. Spectrom.
Volume:300
Issue:2-3
Year:2011
Pages:91-98
Research Areas: Electrospray Ionization | Hydrogen Predissociation
ABSTRACT

Vibrational predissociation spectroscopy of the HOOC(CH2)10COO and OOC(CH2)10COO anions is carried out by predissociation of weakly bound H2 molecules. The HOOC(CH2)10COO (H2)2 andOOC(CH2)10COO (H2)10 cluster ions are formed by H2 attachment to the electrospray-generated bare ions in an ion trap cooled to below 20 K using a closed cycle helium cryostat. The photofragmentation behavior indicates that the H2 binding energy is about 600 cm−1, which is similar in strength to that found in Ar-tagged ions. The spectra indicate that the monoanion adopts a cyclic structure through the formation of an asymmetrical, internal anionic H-bond.

Vibrational predissociation spectroscopy and theory of Ar-tagged, protonated Imidazole (Im) Im1–3H+·Ar clusters

Helen K. Gerardi, George H. Gardenier, Usha Viswanathan, Scott M. Auerbach, and Mark A. Johnson
Journal:Chem. Phys. Lett.
Volume:501
Issue:4-6
Year:2011
Pages:172-178
Research Areas: Argon Predissociation
ABSTRACT

We report vibrational predissociation spectra and theoretical analysis of the Ar-tagged cluster ions of imidazole, Im1–3H+•Ar. The frequencies of the external N–H stretches are observed to incrementally blue-shift toward that of neutral imidazole upon addition of the second and third Im molecules, consistent with the calculated behavior of the Im3H+ complex in which the excess charge is symmetrically shared by two internal N–H–N hydrogen bonds. A very strong, symmetrical doublet near 1000 cm−1 is observed for the Im2H+ complex and attributed to the parallel bridging proton displacement based on anharmonic frequency calculations.

Vibrational Predissociation Spectrum of the Carbamate Radical Anion, C5H5N-CO2, Generated by Reaction of Pyridine with (CO2)m

Michael Z. Kamrath, Rachael A. Relph, and Mark A. Johnson
Journal:J. Am. Chem. Soc.
Volume:2010
Issue:44
Year:2010
Pages:15508-15511
Research Areas: Argon Predissociation
ABSTRACT

We report the vibrational predissociation spectrum of C5H5N-CO2, a radical anion which is closely related to the key intermediates postulated to control activation of CO2 in photoelectrocatalysis with pyridine (Py). The anion is prepared by the reaction of Py vapor with (CO2)m clusters carried out in an ionized, supersonic entrainment ion source. Comparison with the results of harmonic frequency calculations establishes that this species is a covalently bound molecular anion derived from the corresponding carbamate, C5H5N-CO2(H+). These results confirm the structural assignment inferred in an earlier analysis of the cluster distributions and photoelectron spectra of the mixed Pym(CO2)n complexes [J. Chem. Phys. 2000113 (2), 596−601]. The spectra of the (CO2)m (m = 5 and 7) clusters are presented for the first time in the lower energy range (1000−2400 cm−1), which reveal several of the fundamental modes that had only been characterized previously by their overtones and combination bands. Comparison of these new spectra with those displayed by Py(CO2)nsuggests that a small fraction of the Py(CO2)n ions are trapped entrance channel reaction intermediates in which the charge remains localized on the (CO2)m part of the cluster.

Isolating the Spectral Signatures of Individual Sites in Water Networks Using Vibrational Double-Resonance Spectroscopy of Cluster Isotopomers

Timothy L. Guasco, Ben M. Elliott, Mark A. Johnson, Jing Ding, and Kenneth D. Jordan
Journal:J. Phys. Chem. Lett.
Volume:1
Issue:15
Year:2010
Pages:2396-2401
Research Areas: Double Resonance | Hydrated Electron | Isomer Selective
ABSTRACT

We report the spectral signatures of water molecules occupying individual sites in an extended H-bonding network using mass-selective, double-resonance vibrational spectroscopy of isotopomers. The scheme is demonstrated on the water heptamer anion, (H2O)7¯, where we first randomly incorporate a single, intact D2O molecule to create an ensemble of isotopomers. The correlation between the two OD stretching frequencies and that of the intramolecular DOD bending transition is then revealed by photochemical modulation of the isotopomer population responsible for particular features in the vibrational spectrum. The observed patterns confirm the assignment of the dominant doublet, appearing most red-shifted from the free OD stretch, to a single water molecule attached to the network in a double H-bond acceptor (AA) arrangement. The data also reveal the unanticipated role of accidentally overlapping transitions, where the highest-energy OD stretch, for example, occurs with its companion OD stretch obscured by the much stronger AA feature.

Downsizing the hydrated electron's lair

Kenneth D. Jordan and Mark A. Johnson
Journal:Science
Volume:329
Issue:5987
Year:2010
Pages:42-43
Research Areas: Feature | Hydrated Electron
ABSTRACT

The hydrated electron is a key reactive intermediate in many chemical reactions, including those responsible for the biological effects of radiation. When water molecules (or molecules dissolved in it) encounter radiation, they ionize and emit electrons that can react with biomolecules, often in deleterious ways. Despite being so reactive, these electrons can have appreciable lifetimes because they are stabilized by surrounding water molecules. The hydrated electron, eaq, has been understood for more than 50 years in terms of a cavity model in which the electron is excluded from regions where the water molecules have appreciable electron density, and the void or cavity it occupies is stabilized by the interaction of the charge with the dielectric medium outside the void (13). On page 65 of this issue, Larsen et al. (4) challenge both of these traditional views with a new model in which theeaq not only penetrates the charge distribution of the water molecules but also is associated with a region of enhanced water density rather than a cavity. The electron wave function is distributed like tentacles that wrap around and between the water molecules.

Tribute to W. Carl Lineberger

Anne B. McCoy and Mark A. Johnson
Journal:J. Phys. Chem. A
Volume:114
Issue:3
Year:2010
Pages:1225-1226
Research Areas: Feature
ABSTRACT

Survey of Ar-Tagged Predissociation and Vibrationally Mediated Photodetachment Spectroscopies of the Vinylidene Anion, C2H2−
Helen K. Gerardi, Kristin J. Breen, Timothy L. Guasco, Gary H. Weddle, George H. Gardenier, Jennifer E. Laaser, and Mark A. Johnson
Journal:J. Phys. Chem. A
Volume:114
Issue:3
Year:2010
Pages:1592-1601
Research Areas: Argon Predissociation | Photoelectron Spectroscopy
ABSTRACT

We report predissociation spectra of Ar-tagged C2H2 and C2D2 anions, and explore vibrationally mediated photodetachment from various vibrational levels of the bare C2H2 ion using velocity-map imaging. Intense photodetachment resonances are observed in the C−H stretching region that are strongly correlated with vibrational hot bands in the anion photoelectron spectra, indicating that one-color, resonant two-photon photodetachment (R2PD) is complicated by excitation of vibrationally excited states with autodetaching upper levels embedded in the continuum. Isolation of the R2PD spectrum was achieved using a two-color, IR−IR scheme in which vibrational excitation and photodetachment were carried out in two separate laser interaction regions.