Anne B. McCoy

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

Ties That Bind Almost by definition, effective catalysts bind their substrates for a very short time—releasing them quickly after helping them react and then moving on to bind new, as yet unreacted, substrates. This property engenders an efficient cycle, but it hinders study of the binding motif. Garand et al. (p. 694, published online 19 January; see the Perspective by Zwier) devised a technique to extract bound complexes from solution and freeze their conformations in cold, gas-phase clusters. Probing these clusters by vibrational spectroscopy in conjunction with theoretical calculations then allowed the sites of hydrogen bonding that hold the complexes together to be pinpointed. Conformationally freezing a weakly bound complex in the gas phase sheds light on its likely binding motifs in solution. 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.

Rate of Gas Phase Association of Hydroxyl Radical and Nitrogen Dioxide

Honing in on HONO2 Modeling air pollution requires knowledge of all the interrelated reactions occurring in the atmosphere. Among the most significant is the formation of nitric acid (HONO2) from OH and NO2 radicals. One sticking point in the study of this reaction has been the uncertainty in how often radicals link through an O-O rather than an O-N bond. Mollner et al. (p. 646) measured the partitioning coefficient, as well as the overall consumption rate of the radicals, with an array of highly sensitive spectroscopic techniques in the laboratory. The measurements yielded a well-defined rate constant for nitric acid formation, which was applied to the prediction of ozone levels in atmospheric simulations of the Los Angeles basin. Laboratory measurements of a critical atmospheric rate constant should improve predictions of tropospheric ozone formation. The reaction of OH and NO2 to form gaseous nitric acid (HONO2) is among the most influential in atmospheric chemistry. Despite its importance, the rate coefficient remains poorly determined under tropospheric conditions because of difficulties in making laboratory rate measurements in air at 760 torr and uncertainties about a secondary channel producing peroxynitrous acid (HOONO). We combined two sensitive laser spectroscopy techniques to measure the overall rate of both channels and the partitioning between them at 25°C and 760 torr. The result is a significantly more precise value of the rate constant for the HONO2 formation channel, 9.2 (±0.4) × 10−12 cm3 molecule−1 s−1 (1 SD) at 760 torr of air, which lies toward the lower end of the previously established range. We demonstrate the impact of the revised value on photochemical model predictions of ozone concentrations in the Los Angeles airshed.

Rotation–vibration interactions in highly excited states of SO2 and H2CO

Canonical Van Vleck perturbation theory (CVPT) is used to investigate rotation–vibration mixing of highly excited vibrational states of SO2 and H2CO. For SO2 we find a nearly complete separation of the rotational and vibrational degrees of freedom, even for J=12 and Evib=11 000 cm−1. In contrast, for H2CO we observe extensive mixing between rotational and vibrational degrees of freedom at similar rotational excitation but with Evib=8000 cm−1. Although a‐axis Coriolis coupling is pronounced, b‐ and c‐axis Coriolis couplings play an important additional role in mixing states with different Ka quantum numbers. The implementation of CVPT, the choice of internal coordinates, and the convergence of the results are discussed in detail.

How the Shape of an H-Bonded Network Controls Proton-Coupled Water Activation in HONO Formation

Its the Network Numerous reactions of small molecules and ions in the atmosphere take place in the confines of watery aerosols. Relph et al. (p. 308; see the Perspective by Siefermann and Abel) explored the specific influence of a water clusters geometry on the transformation of solvated nitrosonium (NO+) to nitrous acid (HONO). The reaction involves (O)N–O(H) bond formation with one water molecule, concomitant with proton transfer to additional, surrounding water molecules. Vibrational spectroscopy and theoretical simulations suggest that certain arrangements of the surrounding water network are much more effective than others in accommodating this charge transfer, and thus facilitating the reaction. Vibrational spectroscopy uncovers the role of a surrounding water network in the mediating reaction of a solvated ion. Many chemical reactions in atmospheric aerosols and bulk aqueous environments are influenced by the surrounding solvation shell, but the precise molecular interactions underlying such effects have rarely been elucidated. We exploited recent advances in isomer-specific cluster vibrational spectroscopy to explore the fundamental relation between the hydrogen (H)–bonding arrangement of a set of ion-solvating water molecules and the chemical activity of this ensemble. We find that the extent to which the nitrosonium ion (NO+)and water form nitrous acid (HONO) and a hydrated proton cluster in the critical trihydrate depends sensitively on the geometrical arrangement of the water molecules in the network. Theoretical analysis of these data details the role of the water network in promoting charge delocalization.

Diffusion Monte Carlo approaches for investigating the structure and vibrational spectra of fluxional systems

Recent advances in diffusion Monte Carlo (DMC) are reviewed within the context of the vibrational motions of systems that undergo large amplitude motions. Specifically, the authors describe the DMC approach for obtaining the ground state wave function and zero-point energy (ZPE) of the system of interest, as well as extensions to the method for evaluating probability amplitudes, rotational constants, vibrationally excited states and methods for obtaining vibrational spectra. The discussion is framed in terms of the properties of several systems of current experimental and theoretical interest, specifically complexes of neon atoms with OH or SH, , , and . The results of the DMC simulations provide the information necessary to characterize the extent of delocalization of the probability amplitudes, even in the ground vibrational states. Methods for evaluating expectation values and vibrationally excited states are explored, and, when possible, the results are compared with those from other approaches. Finally, the methods for evaluating intensities are described and existing and future challenges for the approach are reviewed. Contents PAGE 1. Introduction 78 2. Systems 79  2.1. Nen · XH complexes 79  2.2. and 80  2.3. 83 3. Ground state wave functions and energies 84  3.1. Theory 84  3.2. Results 86 4. Obtaining properties from DMC 89  4.1. Averaging by Pair Counting (AVPC) 89  4.2. Adiabatic DMC 89  4.3. Descendent weighting 91  4.4. Example 1 – Bond lengths in 91  4.5. Example 2 – Bond length distributions for and 91  4.6. Example 3 – Rotational constants 93 5. Excited states 96  5.1. Example 4 – The stretch fundamental in Ar3 99  5.2. Example 5 – The fundamentals in Ne2XH 100  5.3. Example 6 – Fundamental vibrations in and 102 6. Using DMC to interpret spectra 103 7. Summary and future prospects 104 Acknowledgements 105 References 105

Perturbative calculations of vibrational (J=0) energy levels of linear molecules in normal coordinate representations

Canonical Van Vleck perturbation theory is used to transform curvilinear and rectilinear normal coordinate vibrational Hamiltonians of HCN, C2H2, and CO2 to block‐diagonal effective Hamiltonians. Accurate energies as high as 11 000 cm−1 above the zero point are reported for all three molecules. In the absence of off‐diagonal coupling terms in the effective Hamiltonians, these two coordinate systems yield identical perturbative expansions for the vibrational energies. Only when coupling terms are introduced do differences between the calculated energies in the two representations become apparent. In CO2, where there is pronounced configuration interaction between nearly degenerate states, we find that the perturbative energies obtained from the curvilinear normal coordinate Hamiltonian are converging significantly faster than those obtained in the rectilinear normal coordinate representation.

Spectroscopic Study of the Ion-Radical H-Bond in H4O2

The primary event in the ionization of water involves rapid proton transfer, leading to charge localization on H(3)O(+) and the creation of a hydroxyl radical. We trap the nascent [H(3)O(+).(*)OH] exit channel intermediate in the bimolecular reaction by Ar-mediated ionization of the neutral water dimer and characterize the nature of this ion-radical complex using vibrational predissociation spectroscopy of the Ar-tagged species. The resulting bands involving the displacement of the bridging proton are broad and appear as a strong triplet centered around 2000 cm(-1). The observed band pattern is analyzed with theoretical calculations to identify the origin of the anhamonic effects evident in the spectrum. In the course of this work, expressions were derived for treating the coupling terms within a sinc-DVR. Although this level of treatment did not reveal the assignment of the triplet structure, its characteristic approximately 100 cm(-1) spacing suggests activity involving the frustrated rotation of the hydroxyl radical upon excitation of the bridging-proton vibration parallel to the heavy atom axis. The behavior of this system is considered in the context of that reported previously for the related H(5)O(2)(+), H(3)O(2)(-), and F(-).H(2)O complexes.

Quantum studies of the vibrations in H3O2− and D3O2−

The vibrations of H3O2- and D3O2- are investigated using diffusion Monte Carlo (DMC) and vibrational configuration-interaction approaches, as implemented in the program MULTIMODE. These studies use the potential surface recently developed by Huang et al. [ J. Am. Chem. Soc. 126, 5042 (2004)]. The focus of this work is on the vibrational ground state and fundamentals which occur between 100 and 3700 cm(-1). In most cases, excellent agreement is obtained between the fundamental frequencies calculated by the two approaches. This serves to demonstrate the power of both methods for treating this very anharmonic system. Based on the results of the MULTIMODE and DMC treatments, the extent and nature of the couplings in H3O2- and D3O2- are investigated.

Quantum and classical studies of vibrational motion of CH5+ on a global potential energy surface obtained from a novel ab initio direct dynamics approach.

We report a full dimensional, ab initio based potential energy surface for CH(5) (+). The ab initio electronic energies and gradients are obtained in direct-dynamics calculations using second-order Møller-Plesset perturbation theory with the correlation consistent polarized valence triple zeta basis. The potential energy and the dipole moment surfaces are fit using novel procedures that ensure the full permutational symmetry of the system. The fitted potential energy surface is tested by comparing it against additional electronic energy calculations and by comparing normal mode frequencies at the three lowest-lying stationary points obtained from the fit against ab initio ones. Well-converged diffusion Monte Carlo zero-point energies, rotational constants, and projections along the CH and HH bond lengths and the tunneling coordinates are presented and compared with the corresponding harmonic oscillator and standard classical molecular dynamics ones. The delocalization of the wave function is analyzed through comparison of the CH(5) (+) distributions with those obtained when all of the hydrogen atoms are replaced by (2)H and (3)H. The classical dipole correlation function is examined as a function of the total energy. This provides a further probe of the delocalization of CH(5) (+).

Infrared-driven unimolecular reaction of CH3CHOO Criegee intermediates to OH radical products

Breaking down a Criegee intermediate Ozones damaging role in the upper atmosphere is well known, but ozone is also quite active closer down to where we live. In particular, ozones run-ins with airborne unsaturated hydrocarbons, from natural or anthropogenic sources, produce even more-reactive OH radicals. Liu et al. used vibrational spectroscopy to study how OH emerges from a so-called Criegee intermediate formed when ozone attacks 2-butene. The results suggest that OH production is easier than current theory predicts. Science, this issue p. 1596 Spectroscopy in the laboratory elucidates key steps in ozone’s atmospheric reaction with unsaturated hydrocarbons. Ozonolysis of alkenes, an important nonphotolytic source of hydroxyl (OH) radicals in the troposphere, proceeds through energized Criegee intermediates that undergo unimolecular decay to produce OH radicals. Here, we used infrared (IR) activation of cold CH3CHOO Criegee intermediates to drive hydrogen transfer from the methyl group to the terminal oxygen, followed by dissociation to OH radicals. State-selective excitation of CH3CHOO in the CH stretch overtone region combined with sensitive OH detection revealed the IR spectrum of CH3CHOO, effective barrier height for the critical hydrogen transfer step, and rapid decay dynamics to OH products. Complementary theory provides insights on the IR overtone spectrum, as well as vibrational excitations, structural changes, and energy required to move from the minimum-energy configuration of CH3CHOO to the transition state for the hydrogen transfer reaction.