The Role of Torsion/Torsion Coupling in the Vibrational Spectrum of Cis−Cis HOONO

A three-dimensional model of the vibrational dynamics of HOONO is investigated. This model focuses on the couplings between the OH stretch vibration and the two torsions. The model is based on electronic energies, calculated at the CCSD(T)/cc-pVTZ level of theory and basis and dipole moment functions calculated at the CCSD/aug-cc-pVDZ level. The resulting points were fit to explicit functional forms, and the energies, wave functions, and intensities were evaluated using an approach in which the OH stretching motion was adiabatically separated from the torsional modes. It is found that the HOON torsion is strongly coupled to both the OONO torsion and OH stretch. Despite this, many of the conclusions that were drawn from earlier two-dimensional treatments, which did not include the OONO torsion, hold up on a semiquantitative level. In addition, we use this model to investigate the assignment of recently reported matrix isolated spectra of HOONO and DOONO. Finally, by comparing the results of this three-dimensional calculation to two-dimensional calculations and to the results of second-order perturbation theory, we investigate the question of how one determines the size of the reduced-dimensional system that is needed to describe the vibrational spectrum of molecules, like HOONO, that contain several large amplitude motions

Role of OH-stretch/torsion coupling and quantum yield effects in the first OH overtone spectrum of cis-cis HOONO

A joint theoretical and experimental investigation is undertaken to study the effects of OH-stretch/HOON torsion coupling and of quantum yield on the previously reported first overtone action spectrum of cis-cis HOONO (peroxynitrous acid). The minimum energy path along the HOON dihedral angle is computed at the coupled cluster singles and doubles with perturbative triples level with correlation consistent polarized quadruple zeta basis set, at the structure optimized using the triple zeta basis set (CCSD(T)/cc-pVQZ//CCSD(T)/cc-pVTZ). The two-dimensional ab initio potential energy and dipole moment surfaces for cis-cis HOONO are calculated as functions of the HOON torsion and OH bond length about the minimum energy path at the CCSD(T)/cc-pVTZ and QCISD/AUG-cc-pVTZ (QCISD—quadratic configuration interaction with single and double excitation and AUG-augmented with diffuse functions) level of theory/basis, respectively. The OH-stretch vibration depends strongly on the torsional angle, and the torsional potential possesses a broad shelf at ~90°, the cis-perp conformation. The calculated electronic energies and dipoles are fit to simple functional forms and absorption spectra in the region of the OH fundamental and first overtone are calculated from these surfaces. While the experimental and calculated spectra of the OH fundamental band are in good agreement, significant differences in the intensity patterns are observed between the calculated absorption spectrum and the measured action spectrum in the 2nuOH region. These differences are attributed to the fact that several of the experimentally accessible states do not have sufficient energy to dissociate to OH+NO2 and therefore are not detectable in an action spectrum. Scaling of the intensities of transitions to these states, assuming D0=82.0 kJ/mol, is shown to produce a spectrum that is in good agreement with the measured action spectrum. Based on this agreement, we assign two of the features in the spectrum to Delta n=0 transitions (where n is the HOON torsion quantum number) that are blue shifted relative to the origin band, while the large peak near 7000 cm^–1 is assigned to a series of Delta n=+1 transitions, with predominant contributions from torsionally excited states with substantial cis-perp character. The direct absorption spectrum of cis-cis HOONO (6300–6850 cm^–1) is recorded by cavity ringdown spectroscopy in a discharge flow cell. A single band of HOONO is observed at 6370 cm^–1 and is assigned as the origin of the first OH overtone of cis-cis HOONO. These results imply that the origin band is suppressed by over an order of magnitude in the action spectrum, due to a reduced quantum yield. The striking differences between absorption and action spectra are correctly predicted by the calculations

Exploring the relationships between anharmonicity and OH bond lengths in hydrogen bonded complexes

In this talk we explore the effects of anharmonicity on the zero-point averaged OH bond lengths in hydrogen bonded complexes. Clusters with as many as six HF molecules or water molecules are explored as well as protonated water clusters and complexes of water clusters with F$^-$, Cl$^-$, Br$^-$ and OH$^-$. It is shown that there is a universal correlation between the vibrationally averaged OH or HF bond length and the anharmonc OH or HF stretch frequency. This relationship provides an extension to previously investigated correlations between the equilibrium bond lengths and harmonic frequencies and allows one to anticipate OH or HF bond lengths based on measured frequencies. In addition, differences between the $R_z$ and $R_0$ structures are discussed within the context of these weakly bound complexes

PROGRESS TOWARDS THE ACCURATE CALCULATION OF ANHARMONIC VIBRATIONAL STATES OF FLUXIONAL MOLECULES AND CLUSTERS WITHOUT A POTENTIAL ENERGY SURFACE

Author Institution: Department of Chemistry, The Ohio State University, Columbus, OH 43210The accurate calculation of anharmonic vibrational states of highly fluxional systems is complicated by the need to first obtain the full-dimensional potential energy surface(PES). Although commonly exploited as a way around this problem, grid-based methodologies scale exponentially with system size while reduced dimensional approaches are highly system dependent, both in terms of the details of their application and in terms of their suitability. Moreover, the achievement of converged variational calculations of highly anharmonic systems is complicated by the necessity of using a very large basis and hence the construction and diagonalization of enormous Hamiltonian matrices. We report here our recent efforts to develop an algorithm capable of accurately calculating anharmonic vibrational energies, even for very floppy systems, without first obtaining a PES and using only a handful of basis functions per degree of freedom. More specifically, the potential energy and G-matrix elements are calculated on a set of points obtained from a Monte Carlo sampling of the most important regions of configuration space, allowing for a significant reduction in the number of required sampling points. The Hamiltonian matrix is then constructed using an evolving basis which, with each iteration, captures the effect of building $\mathbf{H}$ from an ever-expanding basis despite the fact that the actual dimensionality of $\mathbf{H}$ is fixed throughout the calculation. This latter property of the algorithm also greatly reduces the size of basis needed for the calculation relative to more traditional variational approaches. The results obtained from the application of our method to several test systems, including ion water complexes, will be reported along with its observed convergence properties

Photoelectron spectroscopy of the hydroxymethoxide anion, H 2 C(OH)O −

We report the negative ion photoelectron spectroscopy of the hydroxymethoxide anion, H2C(OH)O − . The photoelectron spectra show that 3.49 eV photodetachment produces two distinct electronic states of the neutral hydroxymethoxy radical (H2C(OH)O · ). The H2C(OH)O · ground state (X˜ 2A) photoelectron spectrum exhibits a vibrational progression consisting primarily of the OCO symmetric and asymmetric stretches, the OCO bend, as well as combination bands involving these modes with other, lower frequency modes. A high-resolution photoelectron spectrum aids in the assignment of several vibrational frequencies of the neutral H2C(OH)O · radical, including an experimental determination of the H2C(OH)O · 2ν12 overtone of the H–OCO torsional vibration as 220(10) cm−1 . The electron affinity of H2C(OH)O · is determined to be 2.220(2) eV. The low-lying A˜ 2A excited state is also observed, with a spectrum that peaks ∼0.8 eV above the X˜ 2A state origin. The A˜ 2A state photoelectron spectrum is a broad, partially resolved band. Quantum chemical calculations and photoelectron simulations aid in the interpretation of the photoelectron spectra. In addition, the gas phase acidity of methanediol is calculated to be 366(2) kcal mol−1 , which results in an OH bond dissociation energy, D0(H2C(OH)O–H), of 104(2) kcal mol−1 , using the experimentally determined electron affinity of the hydroxymethoxy radical

Cavity Ringdown Spectroscopy of the Hydroxy-Methyl-Peroxy Radical

We report vibrational and electronic spectra of the hydroxy-methyl-peroxy radical (HOCH_2OO^• or HMP), which was formed as the primary product of the reaction of the hydroperoxy radical, HO_2^•, and formaldehyde, HCHO. The ν_1 vibrational (OH stretch) spectrum and the à ← X electronic spectrum of HMP were detected by infrared cavity ringdown spectroscopy (IR-CRDS), and assignments were verified with density functional calculations. The HMP radical was generated in reactions of HCHO with HO_2^•. Free radical reactions were initiated by pulsed laser photolysis (PLP) of Cl_2 in the presence of HCHO and O_2 in a flow reactor at 300–330 Torr and 295 K. IR-CRDS spectra were measured in mid-IR and near-IR regions over the ranges 3525–3700 cm^(–1) (ν_1) and 7250–7800 cm^(–1) (à ← X) respectively, at a delay time 100 μs after photolysis. The ν_1 spectrum had an origin at 3622 cm^(–1) and exhibited partially resolved P- and R-branch contours and a small Q-branch. At these short delay times, spectral interference from HOOH and HCOOH was minimal and could be subtracted. From B3LYP/6-31+G(d,p) calculations, we found that the anharmonic vibrational frequency and band contour predicted for the lowest energy conformer, HMP-A, were in good agreement with the observed spectrum. In the near-IR, we observed four well spaced vibronic bands, each with partially resolved rotational contours. We assigned the apparent origin of the à ← X electronic spectrum of HMP at 7389 cm^(–1) and two bands to the blue to a progression in ν15′, the lowest torsional mode of the à state (ν_(15′) = 171 cm^(–1)). The band furthest to the red was assigned as a hot band in ν^(15″), leading to a ground state torsional frequency of (ν^(15″) = 122 cm^(–1)). We simulated the spectrum using second order vibrational perturbation theory (VPT2) with B3LYP/6-31+G(d,p) calculations at the minimum energy geometries of the HMP-A conformer on the X and à states. The predictions of the electronic origin frequency, torsional frequencies, anharmonicities, and rotational band contours matched the observed spectrum. We investigated the torsional modes more explicitly by computing potential energy surfaces of HMP as a function of the two dihedral angles τ_(HOCO) and τ_(OOCO). Wave functions and energy levels were calculated on the basis of this potential surface; these results were used to calculate the Franck–Condon factors, which reproduced the vibronic band intensities in the observed electronic spectrum. The transitions that we observed all involved states with wave functions localized on the minimum energy conformer, HMP-A. Our calculations indicated that the observed near-IR spectrum was that of the lowest energy X state conformer HMP-A, but that this conformer is not the lowest energy conformer in the à state, which remains unobserved. We estimated that the energy of this lowest conformer (HMP-B) of the à state is E_0 (Ã, HMP-B) ≈ 7200 cm^(–1), on the basis of the energy difference E_0(HMP-B) – E_0(HMP-A) on the à state computed at the B3LYP/6-31+G(d,p) level

Glycan shifting on hepatitis C virus (HCV) E2 glycoprotein is a mechanism for escape from broadly neutralizing antibodies

Hepatitis C virus (HCV) infection is a major cause of liver disease and hepatocellular carcinoma. Glycan shielding has been proposed to be a mechanism by which HCV masks broadly neutralizing epitopes on its viral glycoproteins. However, the role of altered glycosylation in HCV resistance to broadly neutralizing antibodies is not fully understood. Here, we have generated potent HCV neutralizing antibodies hu5B3.v3 and MRCT10.v362 that, similar to the previously described AP33 and HCV1, bind to a highly conserved linear epitope on E2. We utilize a combination of in vitro resistance selections using the cell culture infectious HCV and structural analyses to identify mechanisms of HCV resistance to hu5B3.v3 and MRCT10.v362. Ultra deep sequencing from in vitro HCV resistance selection studies identified resistance mutations at asparagine N417 (N417S, N417T and N417G) as early as 5 days post treatment. Comparison of the glycosylation status of soluble versions of the E2 glycoprotein containing the respective resistance mutations revealed a glycosylation shift from N417 to N415 in the N417S and N417T E2 proteins. The N417G E2 variant was glycosylated neither at residue 415 nor at residue 417 and remained sensitive to MRCT10.v362. Structural analyses of the E2 epitope bound to hu5B3.v3 Fab and MRCT10.v362 Fab using X-ray crystallography confirmed that residue N415 is buried within the antibody–peptide interface. Thus, in addition to previously described mutations at N415 that abrogate the β-hairpin structure of this E2 linear epitope, we identify a second escape mechanism, termed glycan shifting, that decreases the efficacy of broadly neutralizing HCV antibodies