Investigating Intramolecular H Atom Transfer Dynamics in ß-Diketones with Ultrafast Infrared Spectroscopies and Theoretical Modeling.

The vibrational signatures and ultrafast dynamics of the intramolecular H-bond in a series of ß-diketones are investigated with 2D IR spectroscopy and computational modeling. The chosen ß-diketones exhibit a range of H atom donor-acceptor distances and asymmetry along the H atom transfer coordinate that tunes the intramolecular H-bond strength. The species with the strongest H-bonds are calculated to have very soft H atom potentials, resulting in highly red-shifted OH stretch fundamental frequencies and dislocation of the H atom upon vibrational excitation. These soft potentials lead to significant coupling to the other normal mode coordinates and give rise to the very broad vibrational signatures observed experimentally. The 2D IR spectra in both the OH and OD stretch regions of the light and deuterated isotopologues reveal broadened and long-lived ground-state bleach signatures of the vibrationally hot molecules. Polarization-sensitive transient absorption measurements in the OH and OD stretch regions reveal notable isotopic differences in orientational dynamics. Orientational relaxation was measured to occur on ∼600 fs and ∼2 ps time scales for the light and deuterated isotopologues, respectively. The orientational dynamics are interpreted in terms of activated H/D atom transfer events driven by collective intramolecular structural rearrangements.

High-Resolution Photoelectron Spectroscopy of Vibrationally Excited Vinoxide Anions.

High-resolution photoelectron spectra of vibrationally pre-excited vinoxide anions (CH2CHO-) are reported using the recently developed IR-cryo-SEVI technique. This method is combined with a newly developed implementation of vibrational perturbation theory that can readily identify relevant anharmonic couplings among nearly degenerate vibrational states. IR-cryo-SEVI spectra are obtained by resonant infrared excitation of vinoxide anions via the fundamental C-O (ν4, 1566 cm-1) or isolated C-H (ν3, 2540 cm-1) stretching vibrations prior to photodetachment. Excitation of the ν4 mode leads to a well-resolved photoelectron spectrum that is in excellent agreement with a harmonic Franck-Condon simulation. Excitation of the higher-energy ν3 mode results in a more complicated spectrum that requires consideration of the calculated anharmonic resonances in both the anion and the neutral. From this analysis, information about the zeroth-order states that contribute to the nominal ν3 wave function in the anion is obtained. In the neutral, we observe anharmonic splitting of the ν3 fundamental into a polyad feature with peaks at 2737(22), 2 835(18), and 2910(12) cm-1, for which only the center frequency has been previously reported. Overall, 9 of the 12 fundamental frequencies of the vinoxy radical are extracted from the IR-cryo-SEVI and ground-state cryo-SEVI spectra, most of which are consistent with previous measurements. However, we provide a new estimate of the ν5 (CH2 scissoring) fundamental frequency at 1395(11) cm-1 and attribute the discrepancy with previously reported values to a Fermi resonance with the 2ν11 overtone (CH2 wagging).

A general expression for vibrational Hamiltonians expressed in oblique coordinates.

We examine the properties of oblique coordinates. The coordinates, introduced by Zúñiga et al. [J. Phys. B: At., Mol. Opt. Phys. 52, 055101, (2019)], reduce vibrational mode-mixing and enhance the quality of vibrational assignments in quantum mechanical investigations of two-dimensional model Hamiltonians. Oblique coordinates are obtained by making non-orthogonal rotations of the original coordinates that convert the matrix representation of the quadratic Hamiltonian operator into a block-diagonal matrix where the blocks are distinguished by the total quanta of vibrational excitation. Using techniques for the polar decomposition of matrices, we present a scheme for finding these coordinates for systems of arbitrary dimensions. Several molecular examples are presented that highlight the advantages of these coordinates.

Exploring Expansions of the Potential and Dipole Surfaces Used for Vibrational Perturbation Theory.

A scheme for evaluating expansions of the potential and dipole moment surfaces for vibrational perturbation theory is described. The approach is based on numerical differentiation of the Hessian in the coordinates of interest. It is shown that performing these calculations in internal coordinates generates expansions that are transferable among isotopologues of the molecule of interest. Additionally, re-expressing the expansion of the potential in terms of functions of the internal coordinates, for example, cosines of angles or exponential functions of the bond length displacements, provides expansions that can be used for higher-order perturbation theory calculations. The approach is explored and the results are discussed for water, HOD, ammonia, isomers of HNO3, and halogenated methane.

Fast Near Ab Initio Potential Energy Surfaces Using Machine Learning.

A machine-learning based approach for evaluating potential energies for quantum mechanical studies of properties of the ground and excited vibrational states of small molecules is developed. This approach uses the molecular-orbital-based machine learning (MOB-ML) method to generate electronic energies with the accuracy of CCSD(T) calculations at the same cost as a Hartree-Fock calculation. To further reduce the computational cost of the potential energy evaluations without sacrificing the CCSD(T) level accuracy, GPU-accelerated Neural Network Potential Energy Surfaces (NN-PES) are trained to geometries and energies that are collected from small-scale Diffusion Monte Carlo (DMC) simulations, which are run using energies evaluated using the MOB-ML model. The combined NN+(MOB-ML) approach is used in variational calculations of the ground and low-lying vibrational excited states of water and in DMC calculations of the ground states of water, CH5+, and its deuterated analogues. For both of these molecules, comparisons are made to the results obtained using potentials that were fit to much larger sets of electronic energies than were required to train the MOB-ML models. The NN+(MOB-ML) approach is also used to obtain a potential surface for C2H5+, which is a carbocation with a nonclassical equilibrium structure for which there is currently no available potential surface. This potential is used to explore the CH stretching vibrations, focusing on those of the bridging hydrogen atom. For both CH5+ and C2H5+ the MOB-ML model is trained using geometries that were sampled from an AIMD trajectory, which was run at 350 K. By comparison, the structures sampled in the ground state calculations can have energies that are as much as ten times larger than those used to train the MOB-ML model. For water a higher temperature AIMD trajectory is needed to obtain accurate results due to the smaller thermal energy. A second MOB-ML model for C2H5+ was developed with additional higher energy structures in the training set. The two models are found to provide nearly identical descriptions of the ground state of C2H5+.

A wave function correction-based approach to the identification of resonances for vibrational perturbation theory.

An approach for identifying resonances in vibrational perturbation theory calculations is introduced. This approach makes use of the corrections to the wave functions that are obtained from non-degenerate perturbation theory calculations to identify spaces of states that must be treated with degenerate perturbation theory. Pairs of states are considered to be in resonance if the magnitude of expansion coefficients in the corrections to the wave functions in the non-degenerate perturbation theory calculation is greater than a specified threshold, χmax. This approach is applied to calculations of the vibrational spectra of CH4, H2CO, HNO3, and cc-HOONO. The question of how the identified resonances depend on the value of χmax and how the choice of the resonance spaces affects the calculated vibrational spectrum is further explored for H2CO. The approach is also compared to the Martin test [J. M. L. Martin et al., J. Chem. Phys. 103, 2589-2602 (1995)] for calculations of the vibrational spectra of H2CO and cc-HOONO.

A flexible approach to vibrational perturbation theory using sparse matrix methods.

A sparse linear algebra based implementation of Rayleigh-Schrödinger vibrational perturbation theory is presented. This implementation allows for flexibility in the coordinates used to expand the vibrational Hamiltonian as well as the order to which the perturbation theory is performed. It also provides a powerful tool for investigating the origin of spectral intensity and transition frequencies. Specifically, this flexibility allows for the analysis of which terms in the expansions of the Hamiltonian and dipole surface lead to the largest corrections to the energies and transition intensities, and how these conclusions depend on the coordinates used for these expansions. Comparisons of corrections to transition frequencies are reported for the Morse oscillator when the potential is expanded in Δr and Morse coordinates as well as for water, water dimer, and peroxynitrous acid when the molecular Hamiltonians and dipole surfaces are expanded in Cartesian displacement coordinates and in the displacements of the bond-angle-dihedral internal coordinates. Further comparisons of the corrections to the transitions moments are made for H2O and (H2O)2. It is found that while the transition frequencies and intensities are independent of coordinate choice, a good choice of coordinates leads to a cleaner interpretation of the origins of the anharmonicities in these systems.

Infrared spectroscopic signature of a hydroperoxyalkyl radical (•QOOH).

Infrared (IR) action spectroscopy is utilized to characterize a prototypical carbon-centered hydroperoxyalkyl radical (•QOOH) transiently formed in the oxidation of volatile organic compounds. The •QOOH radical formed in isobutane oxidation, 2-hydroperoxy-2-methylprop-1-yl, •CH2(CH3)2COOH, is generated in the laboratory by H-atom abstraction from tert-butyl hydroperoxide (TBHP). IR spectral features of jet-cooled and stabilized •QOOH radicals are observed from 2950 to 7050 cm-1 at energies that lie below and above the transition state barrier leading to OH radical and cyclic ether products. The observed •QOOH features include overtone OH and CH stretch transitions, combination bands involving OH or CH stretch and a lower frequency mode, and fundamental OH and CH stretch transitions. Most features arise from a single vibrational transition with band contours well simulated at a rotational temperature of 10 K. In each case, the OH products resulting from unimolecular decay of vibrationally activated •QOOH are detected by UV laser-induced fluorescence. Assignments of observed •QOOH IR transitions are guided by anharmonic frequencies computed using second order vibrational perturbation theory, a 2 + 1 model that focuses on the coupling of the OH stretch with two low-frequency torsions, as well as recently predicted statistical •QOOH unimolecular decay rates that include heavy-atom tunneling. Most of the observed vibrational transitions of •QOOH are readily distinguished from those of the TBHP precursor. The distinctive IR transitions of •QOOH, including the strong fundamental OH stretch, provide a general means for detection of •QOOH under controlled laboratory and real-world conditions.

Electronic and mechanical anharmonicities in the vibrational spectra of the H-bonded, cryogenically cooled X- · HOCl (X=Cl, Br, I) complexes: Characterization of the strong anionic H-bond to an acidic OH group.

We report vibrational spectra of the H2-tagged, cryogenically cooled X- · HOCl (X = Cl, Br, and I) ion-molecule complexes and analyze the resulting band patterns with electronic structure calculations and an anharmonic theoretical treatment of nuclear motions on extended potential energy surfaces. The complexes are formed by "ligand exchange" reactions of X- · (H2O)n clusters with HOCl molecules at low pressure (∼10-2 mbar) in a radio frequency ion guide. The spectra generally feature many bands in addition to the fundamentals expected at the double harmonic level. These "extra bands" appear in patterns that are similar to those displayed by the X- · HOD analogs, where they are assigned to excitations of nominally IR forbidden overtones and combination bands. The interactions driving these features include mechanical and electronic anharmonicities. Particularly intense bands are observed for the v = 0 → 2 transitions of the out-of-plane bending soft modes of the HOCl molecule relative to the ions. These involve displacements that act to break the strong H-bond to the ion, which give rise to large quadratic dependences of the electric dipoles (electronic anharmonicities) that drive the transition moments for the overtone bands. On the other hand, overtone bands arising from the intramolecular OH bending modes of HOCl are traced to mechanical anharmonic coupling with the v = 1 level of the OH stretch (Fermi resonances). These interactions are similar in strength to those reported earlier for the X- · HOD complexes.

Coupling of torsion and OH-stretching in tert-butyl hydroperoxide. II. The OH-stretching fundamental and overtone spectra.

The vibrational spectra of gas phase tert-butyl hydroperoxide have been recorded in the OH-stretching fundamental and overtone regions (ΔvOH = 1-5) at room temperature using conventional Fourier transform infrared (ΔvOH = 1-3) and cavity ring-down (ΔvOH = 4-5) spectroscopy. In hydroperoxides, the OH-stretching and COOH torsion vibrations are strongly coupled. The double-well nature of the COOH torsion potential leads to tunneling splitting of the energy levels and, combined with the low frequency of the torsional vibration, results in spectra in the OH-stretching regions with multiple vibrational transitions. In each of the OH-stretching regions, both an OH-stretching and a stretch-torsion combination feature are observed, and we show direct evidence for the tunneling splitting in the OH-stretching fundamental region. We have developed two complementary vibrational models to describe the spectra of the OH-stretching regions, a reaction path model and a reduced dimensional local mode model, both of which describe the features of the vibrational spectra well. We also explore the torsional dependence of the OH-stretching transition dipole moment and show that a Franck-Condon treatment fails to capture the intensity in the region of the stretch-torsion combination features. The accuracy of the Franck-Condon treatment of these features improves with increasing ΔvOH.

Coupling of torsion and OH-stretching in tert-butyl hydroperoxide. I. The cold and warm first OH-stretching overtone spectrum.

The infrared (IR) spectrum of tert-butyl hydroperoxide (TBHP) in the region of the first OH-stretching overtone has been observed under jet-cooled and thermal (300 K, 3 Torr) conditions at ∼7017 cm-1. The jet-cooled spectrum is recorded by IR multiphoton excitation with UV laser-induced fluorescence detection of OH radical products, while direct IR absorption is utilized under thermal conditions. Prior spectroscopic studies of TBHP and other hydroperoxides have shown that the OH-stretch and XOOH (X = H or C) torsion vibrations are strongly coupled, resulting in a double well potential associated with the torsional motion about the OO bond that is different for each of the OH-stretching vibrational states. A low barrier between the wells on the torsional potential results in tunneling split energy levels, which leads to four distinct transitions associated with excitation of the coupled OH-stretch-torsion states. In order to interpret the experimental results, two theoretical models are used that include the OH-stretch-torsion coupling in TBHP. Both methods are utilized to compute the vibrational transitions associated with the coupled OH-stretch-torsion states of TBHP, revealing the underlying transitions that compose the experimentally observed features. A comparison between theory and experiment illustrates the necessity for treatments that include OH-stretch and COOH torsion in order to unravel the spectral features observed in the first OH-stretching overtone region of TBHP.

Age-related differences in IL-1 signaling and capsule serotype affect persistence of Streptococcus pneumoniae colonization.

Young age is a risk factor for prolonged colonization by common pathogens residing in their upper respiratory tract (URT). Why children present with more persistent colonization is unknown and there is relatively little insight into the host-pathogen interactions that contribute to persistent colonization. To identify factors permissive for persistent colonization during infancy, we utilized an infant mouse model of Streptococcus pneumoniae colonization in which clearance from the mucosal surface of the URT requires many weeks to months. Loss of a single bacterial factor, the pore-forming toxin pneumolysin (Ply), and loss of a single host factor, IL-1α, led to more persistent colonization. Exogenous administration of Ply promoted IL-1 responses and clearance, and intranasal treatment with IL-1α was sufficient to reduce colonization density. Major factors known to affect the duration of natural colonization include host age and pneumococcal capsular serotype. qRT-PCR analysis of the uninfected URT mucosa showed reduced baseline expression of genes involved in IL-1 signaling in infant compared to adult mice. In line with this observation, IL-1 signaling was important in initiating clearance in adult mice but had no effect on early colonization of infant mice. In contrast to the effect of age, isogenic constructs of different capsular serotype showed differences in colonization persistence but induced similar IL-1 responses. Altogether, this work underscores the importance of toxin-induced IL-1α responses in determining the outcome of colonization, clearance versus persistence. Our findings about IL-1 signaling as a function of host age may provide an explanation for the increased susceptibility and more prolonged colonization during early childhood.

Diffusion Monte Carlo Studies on the Detection of Structural Changes in the Water Hexamer upon Isotopic Substitution.

The ground-state structures of water hexamer and several deuterated variants are studied by using the diffusion Monte Carlo (DMC) method. We demonstrate that a recently developed guided DMC approach allows us to study these systems using substantially smaller ensembles than are required for standard DMC approaches. DMC calculations of the ground states of (H2O)6 and (D2O)6 using the MB-pol potential with 50 000 walkers and a 1 au time step show that for (H2O)6 the cage structure is 51 ± 7 cm-1 lower in energy than the prism structure. In the case of (D2O)6, the two structures have nearly equal energies (ΔE = 9 ± 11 cm-1). The structures of the singly substituted, (H2O)(D2O)5 and (H2O)5(D2O), variants of water hexamer are also explored to identify the impact of the location of the unique water molecule on the relative stability of the possible structure. The effect on the stability of the hydrogen bond on whether a hydrogen bond has an OD or OH bond as the donor is also explored.

The Role of Tunneling in the Spectra of H5+ and D5+ up to 7300 cm-1.

The spectra for H5+ and D5+ are extended to cover the region between 4830 and 7300 cm-1. These spectra are obtained using mass-selected photodissociation spectroscopy. To understand the nature of the states that are accessed by the transitions in this and prior studies, we develop a four-dimensional model Hamiltonian. This Hamiltonian is expressed in terms of the two outer H2 stretches, the displacement of the shared proton from the center of mass of these two H2 groups, and the distance between the H2 groups. This choice is motivated by the large oscillator strength associated with the shared proton stretch and the fact that the spectral regions that have been probed correspond to zero, one, and two quanta of excitation in the H2 stretches. This model is analyzed using an adiabatic separation of the H2 stretches from the other two vibrations and includes the non-adiabatic couplings between H2 stretch states with the same total number of quanta of excitation in the H2 stretches. Based on the analysis of the energies and wave functions obtained from this model, we find that when there are one or more quanta of excitation in the H2 stretches the states come in pairs that reflect tunneling doublets. The states accessed by the transitions in the spectrum with the largest intensity are assigned to the members of the doublets with requisite symmetry that are localized on the lowest-energy adiabat for a given level of H2 excitation.

Broad detection of bacterial type III secretion system and flagellin proteins by the human NAIP/NLRC4 inflammasome.

Inflammasomes are cytosolic multiprotein complexes that initiate host defense against bacterial pathogens by activating caspase-1-dependent cytokine secretion and cell death. In mice, specific nucleotide-binding domain, leucine-rich repeat-containing family, apoptosis inhibitory proteins (NAIPs) activate the nucleotide-binding domain, leucine-rich repeat-containing family, CARD domain-containing protein 4 (NLRC4) inflammasome upon sensing components of the type III secretion system (T3SS) and flagellar apparatus. NAIP1 recognizes the T3SS needle protein, NAIP2 recognizes the T3SS inner rod protein, and NAIP5 and NAIP6 recognize flagellin. In contrast, humans encode a single functional NAIP, raising the question of whether human NAIP senses one or multiple bacterial ligands. Previous studies found that human NAIP detects both flagellin and the T3SS needle protein and suggested that the ability to detect both ligands was achieved by multiple isoforms encoded by the single human NAIP gene. Here, we show that human NAIP also senses the Salmonella Typhimurium T3SS inner rod protein PrgJ and that T3SS inner rod proteins from multiple bacterial species are also detected. Furthermore, we show that a single human NAIP isoform is capable of sensing the T3SS inner rod, needle, and flagellin. Our findings indicate that, in contrast to murine NAIPs, promiscuous recognition of multiple bacterial ligands is conferred by a single human NAIP.

Neutrophils and Ly6Chi monocytes collaborate in generating an optimal cytokine response that protects against pulmonary Legionella pneumophila infection.

Early responses mounted by both tissue-resident and recruited innate immune cells are essential for host defense against bacterial pathogens. In particular, both neutrophils and Ly6Chi monocytes are rapidly recruited to sites of infection. While neutrophils and monocytes produce bactericidal molecules, such as reactive nitrogen and oxygen species, both cell types are also capable of synthesizing overlapping sets of cytokines important for host defense. Whether neutrophils and monocytes perform redundant or non-redundant functions in the generation of anti-microbial cytokine responses remains elusive. Here, we sought to define the contributions of neutrophils and Ly6Chi monocytes to cytokine production and host defense during pulmonary infection with Legionella pneumophila, responsible for the severe pneumonia Legionnaires' disease. We found that both neutrophils and monocytes are critical for host defense against L. pneumophila. Both monocytes and neutrophils contribute to maximal IL-12 and IFNγ responses, and monocytes are also required for TNF production. Moreover, natural killer (NK) cells, NKT cells, and γδ T cells are sources of IFNγ, and monocytes direct IFNγ production by these cell types. Thus, neutrophils and monocytes cooperate in eliciting an optimal cytokine response that promotes effective control of bacterial infection.

Primary Role for Toll-Like Receptor-Driven Tumor Necrosis Factor Rather than Cytosolic Immune Detection in Restricting Coxiella burnetii Phase II Replication within Mouse Macrophages.

Coxiella burnetii replicates within permissive host cells by employing a Dot/Icm type IV secretion system (T4SS) to translocate effector proteins that direct the formation of a parasitophorous vacuole. C57BL/6 mouse macrophages restrict the intracellular replication of the C. burnetii. Nine Mile phase II (NMII) strain. However, eliminating Toll-like receptor 2 (TLR2) permits bacterial replication, indicating that the restriction of bacterial replication is immune mediated. Here, we examined whether additional innate immune pathways are employed by C57BL/6 macrophages to sense and restrict NMII replication. In addition to the known role of TLR2 in detecting and restricting NMII infection, we found that TLR4 also contributes to cytokine responses but is not required to restrict bacterial replication. Furthermore, the TLR signaling adaptors MyD88 and Trif are required for cytokine responses and restricting bacterial replication. The C. burnetii NMII T4SS translocates bacterial products into C57BL/6 macrophages. However, there was little evidence of cytosolic immune sensing of NMII, as there was a lack of inflammasome activation, T4SS-dependent cytokine responses, and robust type I interferon (IFN) production, and these pathways were not required to restrict bacterial replication. Instead, endogenous tumor necrosis factor (TNF) produced upon TLR sensing of C. burnetii NMII was required to control bacterial replication. Therefore, our findings indicate a primary role for TNF produced upon immune detection of C. burnetii NMII by TLRs, rather than cytosolic PRRs, in enabling C57BL/6 macrophages to restrict bacterial replication.

Direct Probe of Vibrational Fingerprint and Combination Band Coupling.

Vibrational fingerprints and combination bands are a direct measure of couplings that control molecular properties. However, most combination bands possess small transition dipoles. Here we use multiple, ultrafast coherent infrared pulses to resolve vibrational coupling between CH3CN fingerprint modes at 918 and 1039 cm-1 and combination bands in the 2750-6100 cm-1 region via doubly vibrationally enhanced (DOVE) coherent multidimensional spectroscopy (CMDS). This approach provides a direct probe of vibrational coupling between fingerprint modes and near-infrared combination bands of large and small transition dipoles in a molecular system over a large frequency range.

Characterization of the Oxazolone and Macrocyclic Motifs in the bn (n = 2-5) Product Ions from Collision-Induced Dissociation of Protonated Oligoglycine Peptides with Isomer-Selective, Cryogenic Vibrational Spectroscopy.

Collision-induced dissociation (CID) of small, protonated peptides leads to the formation of b-type fragment ions that can occur with several structural motifs driven by different covalent intramolecular bonding arrangements. Here, we characterize the so-called "oxazolone" and "macrocycle" bn ion structures that occur upon CID of oligoglycine peptides (Gn) ions (n = 2-6). This is determined by acquiring the vibrational band patterns of the cryogenically cooled, D2-tagged bn ions obtained using isomer-selective, two-color IR-IR photobleaching and analyzing them with predicted (DFT) harmonic spectra for the candidate structures. Both oxazolone and macrocyclic isomers are formed by b4, whereas only oxazolone species are created for b2 and b3 and the macrocycle is created for b5. As such, n = 4 corresponds to the minimum size where both Oxa and MC forms are present.

TNF and type I IFN induction of the IRG1-itaconate pathway restricts Coxiella burnetii replication within mouse macrophages.

The intracellular Gram-negative bacterium Coxiella burnetii replicates within macrophages and causes a zoonotic disease known as Q fever. In murine macrophages, the cytokine tumor necrosis factor (TNF) is critical for restriction of intracellular C. burnetii replication. Here, we show that TNF collaborates with type I interferon (IFN) signaling for maximal control of C. burnetii. We found that TNF and type I IFN upregulate the expression of the metabolic enzyme immune responsive gene 1 (IRG1), also known as cis-aconitate decarboxylase 1 (ACOD1), and that IRG1 is required to restrict C. burnetii T4SS translocation and replication within macrophages. Further, we show that itaconic acid, the metabolic product of IRG1, restricts C. burnetii replication both intracellularly and in axenic culture. These data reveal that TNF and type I IFN upregulate the IRG1-itaconate pathway to restrict intracellular C. burnetii replication within murine macrophages.