Direct Observation of a Roaming Intermediate and Its Dynamics.

Chemical reactions are often characterized by their transition state, which defines the critical geometry the molecule must pass through to move from reactants to products. Roaming provides an alternative picture, where in a dissociation reaction, the bond breaking is frustrated and a loosely bound intermediate is formed. Following bond breaking, the two partners are seen to roam around each other at distances of several Ångstroms, forming a loosely bound, and structurally ill-defined, intermediate that can subsequently lead to reactive or unreactive collisions. Here, we present a direct and time-resolved experimental measurement of roaming. By measuring the photoelectron spectrum of UV-excited acetaldehyde with a femtosecond extreme ultraviolet pulse, we captured spectral signatures of all of the key reactive structures, including that of the roaming intermediate. This provided a direct experimental measurement of the roaming process and allowed us to identify the time scales by which the roaming intermediate is formed and removed and the electronic potential surfaces upon which roaming proceeds.

A multiphoton ionisation photoelectron imaging study of thiophene.

Thiophene is a prototype for the excited state photophysics that lies at the heart of many technologies within the field of organic electronics. Here, we report a multiphoton ionisation photoelectron imaging study of gas-phase thiophene using a range of photon energies to excite transitions from the ground electronic state to the first two electronically excited singlet states, from the onset of absorption to the absorption maximum. Analysis of the photoelectron spectra and angular distributions reveal features arising from direct photoionisation from the ground electronic state, and resonance-enhanced photoionisation via the electronically excited singlet states. The first two ionisation energies from the ground electronic state were confirmed to be 8.8 eV (adiabatic) and 9.6 eV (vertical). The ionisation energies from the first two electronically excited singlet states were found to be 3.7 eV (adiabatic) and 4.4 eV (vertical).

The "simple" photochemistry of thiophene.

The static gas-phase ("simple") ultraviolet absorption spectrum of thiophene is investigated using a combination of a vibronic coupling model Hamiltonian with multi-configuration time-dependent Hartree quantum dynamics simulations. The model includes five states and all 21 vibrations, with potential surfaces calculated at the complete active space with second-order perturbation level of theory. The model includes terms up to eighth-order to describe the diabatic potentials. The resulting spectrum is in excellent agreement with the experimentally measured spectrum of Holland et al. [Phys. Chem. Chem. Phys. 16, 21629 (2014)]. The, until now not understood, spectral features are assigned, with a combination of strongly coupled vibrations and vibronic coupling between the states giving rise to a progression of triplets on the rising edge of the broad spectrum. The analysis of the underlying dynamics indicates that population transfer between all states takes place on a sub-100 fs timescale, with ring-opening occurring at longer times. The model thus provides a starting point for further investigations into the complicated photo-excited dynamics of this key hetero-aromatic molecule.

Transcripts associated with chronic lung allograft dysfunction in transbronchial biopsies of lung transplants.

Transplanted lungs suffer worse outcomes than other organ transplants with many developing chronic lung allograft dysfunction (CLAD), diagnosed by physiologic changes. Histology of transbronchial biopsies (TBB) yields little insight, and the molecular basis of CLAD is not defined. We hypothesized that gene expression in TBBs would reveal the nature of CLAD and distinguish CLAD from changes due simply to time posttransplant. Whole-genome mRNA profiling was performed with microarrays in 498 prospectively collected TBBs from the INTERLUNG study, 90 diagnosed as CLAD. Time was associated with increased expression of inflammation genes, for example, CD1E and immunoglobulins. After correcting for time, CLAD manifested not as inflammation but as parenchymal response-to-wounding, with increased expression of genes such as HIF1A, SERPINE2, and IGF1 that are increased in many injury and disease states and cancers, associated with development, angiogenesis, and epithelial response-to-wounding in pathway analysis. Fibrillar collagen genes were increased in CLAD, indicating matrix changes, and normal transcripts were decreased-dedifferentiation. Gene-based classifiers predicted CLAD with AUC 0.70 (no time-correction) and 0.87 (time-corrected). CLAD related gene sets and classifiers were strongly prognostic for graft failure and correlated with CLAD stage. Thus, in TBBs, molecular changes indicate that CLAD primarily reflects severe parenchymal injury-induced changes and dedifferentiation.

Molecular phenotyping of rejection-related changes in mucosal biopsies from lung transplants.

Diagnosing lung transplant rejection currently depends on histologic assessment of transbronchial biopsies (TBB) with limited reproducibility and considerable risk of complications. Mucosal biopsies are safer but not histologically interpretable. Microarray-based diagnostic systems for TBBs and other transplants suggest such systems could assess mucosal biopsies as well. We studied 243 mucosal biopsies from the third bronchial bifurcation (3BMBs) collected from seven centers and classified them using unsupervised machine learning algorithms. Using the expression of a set of rejection-associated transcripts annotated in kidneys and validated in hearts and lung transplant TBBs, the algorithms identified and scored major rejection and injury-related phenotypes in 3BMBs without need for labeled training data. No rejection or injury, rejection, late inflammation, and recent injury phenotypes were thus scored in new 3BMBs. The rejection phenotype correlated with IFNG-inducible transcripts, the hallmarks of rejection. Progressive atrophy-related changes reflected by the late inflammation phenotype in 3BMBs suggest widespread time-dependent airway deterioration, which was especially pronounced after two years posttransplant. Thus molecular assessment of 3BMBs can detect rejection in a previously unusable biopsy format with potential utility in patients with severe lung dysfunction where TBB is not possible and provide unique insights into airway deterioration. ClinicalTrials.gov NCT02812290.

The role of vibronic coupling in the electronic spectroscopy of maleimide: a multi-mode and multi-state quantum dynamics study.

The first two excitation bands below 7 eV in the electronic absorption spectrum of maleimide are investigated using a model Hamiltonian including four low-lying singlet excited states within the manifold of 24 vibrational modes. The role of non-adiabatic effects is studied and shines light on both the broad, inter-state coupling-dominated spectral band as well as the fine-structured, not-so-strong coupled band. Calculations have been performed using the Multiconfigurational Time-Dependent Hartree (MCTDH) wavepacket propagation method as well as its multilayer version (ML-MCTDH) using a quadratic vibronic coupling (QVC) Hamiltonian model where parameters are obtained from fitting adiabatic potential energy surfaces computed by ab initio methods. The quantum dynamics calculations provide information on the relaxation dynamics and the vibrational modes involved. Already with a low-order vibronic coupling model and only a few modes being considered, a quantitative agreement with the experimental spectrum is obtained. However, it is found that all modes need to be considered to get a full picture of the photo-excited relaxation dynamics of this molecule.

Shining light on the electronic structure and relaxation dynamics of the isolated oxyluciferin anion.

Firefly bioluminescence is exploited widely in imaging in the biochemical and biomedical sciences; however, our fundamental understanding of the electronic structure and relaxation processes of the oxyluciferin that emits the light is still rudimentary. Here, we employ photoelectron spectroscopy and quantum chemistry calculations to investigate the electronic structure and relaxation of a series of model oxyluciferin anions. We find that changing the deprotonation site has a dramatic influence on the relaxation pathway following photoexcitation of higher lying electronically excited states. The keto form of the oxyluciferin anion is found to undergo internal conversion to the fluorescent S1 state, whereas we find evidence to suggest that the enol and enolate forms undergo internal conversion to a dipole bound state, possibly via the fluorescent S1 state. Partially resolved vibrational structure points towards the involvement of out-of-plane torsional motions in internal conversion to the dipole bound state, emphasising the combined electronic and structural role that the microenvironment plays in controlling the electronic relaxation pathway in the enzyme.

Photodissociation dynamics of methyl iodide probed using femtosecond extreme ultraviolet photoelectron spectroscopy.

Femtosecond pump-probe photoelectron spectroscopy measurements using an extreme ultraviolet probe have been made on the photodissociation dynamics of UV (269 nm) excited CH3I. The UV excitation leads to population of the 3Q0 state which rapidly dissociates. The dissociation is manifested as shifts in the measured photoelectron kinetic energy that map the extending C-I bond. The increased energy available in the XUV probe relative to a UV probe means the dynamics are followed over the chemically important region as far as C-I bond lengths of approximately 4 Å.

Photodissociation dynamics of CH3I probed via multiphoton ionisation photoelectron spectroscopy.

The dissociation dynamics of CH3I is investigated on the red (269 nm) and blue (255 nm) side of the absorption maximum of the A-band. Using a multiphoton ionisation probe in a time-resolved photoelectron imaging experiment we observe very different dynamics at the two wavelengths, with significant differences in the measured lifetime and dynamic structure. The differences are explained in terms of changes in excitation cross-sections of the accessible 3Q0 and 1Q1 states and the subsequent dynamics upon each of them. The measurements support the existing literature on the rapid dissociation dynamics on the red side of the absorption maximum at 269 nm which is dominated by the dynamics along the 3Q0 state. At 255 nm we observe similar dynamics along the 3Q0 state but also a significant contribution from the 1Q1 state. The dynamics along the 1Q1 potential show a more complex structure in the photoelectron spectrum and a significantly increased lifetime, indicative of a more complex reaction pathway.

Photoelectron Imaging and Quantum Chemistry Study of Phenolate, Difluorophenolate, and Dimethoxyphenolate Anions.

Phenolates and their substituted analogues are important molecular motifs in many biological molecules, including the family of fluorescent proteins based on green fluorescent protein. We have used a combination of anion photoelectron velocity-map imaging measurements and quantum chemistry calculations to probe the electronic structure of the phenolate anion and difluoro- and dimethoxy-substituted analogues. We report vertical detachment energies (VDEs) and quantify the photoelectron angular distributions. The VDEs for phenolate (2.26 ± 0.03 eV, 3.22 ± 0.02 eV) are in agreement with high-resolution measurements, whereas the values for the substituted analogues (2.61 ± 0.03 eV for difluorophenolate; ∼2.35 eV for dimethoxyphenolate) are new measurements. We also report adiabatic excitation energies (AEEs) of anion resonances and discuss their contributions to the overall photoelectron angular distributions. The AEE of the lowest lying resonance in phenolate (∼3.36 eV) is consistent with previous measurements, whereas the value for the next resonance (∼3.7 eV) is a new measurement. The AEEs of the resonances in the substituted analogues (∼3.74 eV for difluorophenolate; ∼3.4 and 3.74 eV for dimethoxyphenolate) are new measurements.

Review: The transcripts associated with organ allograft rejection.

The molecular mechanisms operating in human organ transplant rejection are best inferred from the mRNAs expressed in biopsies because the corresponding proteins often have low expression and short half-lives, while small non-coding RNAs lack specificity. Associations should be characterized in a population that rigorously identifies T cell-mediated (TCMR) and antibody-mediated rejection (ABMR). This is best achieved in kidney transplant biopsies, but the results are generalizable to heart, lung, or liver transplants. Associations can be universal (all rejection), TCMR-selective, or ABMR-selective, with universal being strongest and ABMR-selective weakest. Top universal transcripts are IFNG-inducible (eg, CXCL11 IDO1, WARS) or shared by effector T cells (ETCs) and NK cells (eg, KLRD1, CCL4). TCMR-selective transcripts are expressed in activated ETCs (eg, CTLA4, IFNG), activated (eg, ADAMDEC1), or IFNG-induced macrophages (eg, ANKRD22). ABMR-selective transcripts are expressed in NK cells (eg, FGFBP2, GNLY) and endothelial cells (eg, ROBO4, DARC). Transcript associations are highly reproducible between biopsy sets when the same rejection definitions, case mix, algorithm, and technology are applied, but exact ranks will vary. Previously published rejection-associated transcripts resemble universal and TCMR-selective transcripts due to incomplete representation of ABMR. Rejection-associated transcripts are never completely rejection-specific because they are shared with the stereotyped response-to-injury and innate immunity.

A photoelectron imaging and quantum chemistry study of the deprotonated indole anion.

Indole is an important molecular motif in many biological molecules and exists in its deprotonated anionic form in the cyan fluorescent protein, an analogue of green fluorescent protein. However, the electronic structure of the deprotonated indole anion has been relatively unexplored. Here, we use a combination of anion photoelectron velocity-map imaging measurements and quantum chemistry calculations to probe the electronic structure of the deprotonated indole anion. We report vertical detachment energies (VDEs) of 2.45 ± 0.05 eV and 3.20 ± 0.05 eV, respectively. The value for D0 is in agreement with recent high-resolution measurements whereas the value for D1 is a new measurement. We find that the first electronically excited singlet state of the anion, S1(ππ*), lies above the VDE and has shape resonance character with respect to the D0 detachment continuum and Feshbach resonance character with respect to the D1 continuum.

Role of Photoisomerization on the Photodetachment of the Photoactive Yellow Protein Chromophore.

The photocycle of photoactive yellow protein (PYP) is initiated by a photoinduced trans-cis isomerization around a C═C bond in the chromophore that lies at the heart of the protein; however, in addition to the desired photochemical pathway, the chromophore can undergo competing electronic relaxation processes. Here we combine gas-phase anion photoelectron spectroscopy and quantum chemistry calculations to investigate how locking the C═C bond in the chromophore controls the competition between these electronic relaxation processes following photoexcitation in the range 400-310 nm. We find evidence to suggest that preventing trans-cis isomerization effectively turns off internal conversion to the ground electronic state and enhances electron emission from the first electronically excited state.

Electronic structure and dynamics of torsion-locked photoactive yellow protein chromophores.

The photocycle of photoactive yellow protein (PYP) begins with small-scale torsional motions of the chromophore leading to large-scale movements of the protein scaffold triggering a biological response. The role of single-bond torsional molecular motions of the chromophore in the initial steps of the PYP photocycle are not fully understood. Here, we employ anion photoelectron spectroscopy measurements and quantum chemistry calculations to investigate the electronic relaxation dynamics following photoexcitation of four model chromophores, para-coumaric acid, its methyl ester, and two analogues with aliphatic bridges hindering torsional motions around the single bonds adjacent to the alkene group. Following direct photoexcitation of S1 at 400 nm, we find that both single bond rotations play a role in steering the PYP chromophore through the S1/S0 conical intersection but that rotation around the single bond between the alkene moiety and the phenoxide group is particularly important. Following photoexcitation of higher lying electronic states in the range 346-310 nm, we find that rotation around the single bond between the alkene and phenoxide groups also plays a key role in the electronic relaxation from higher lying states to the S1 state. These results have potential applications in tuning the photoresponse of photoactive proteins and materials with chromophores based on PYP.

Photoelectron spectroscopy of isolated luciferin and infraluciferin anions in vacuo: competing photodetachment, photofragmentation and internal conversion.

The electronic structure and excited-state dynamics of the ubiquitous bioluminescent probe luciferin and its furthest red-shifted analogue infraluciferin have been investigated using photoelectron spectroscopy and quantum chemistry calculations. In our electrospray ionization source, the deprotonated anions are formed predominantly in their phenolate forms and are directly relevant to studies of luciferin and infraluciferin as models for their unstable oxyluciferin and oxyinfraluciferin emitters. Following photoexcitation in the range 357-230 nm, we find that internal conversion from high-lying excited states to the S1(1ππ*) state competes efficiently with electron detachment. In infraluciferin, we find that decarboxylation also competes with direct electron detachment and internal conversion. This detailed spectroscopic and computational study defines the electronic structure and electronic relaxation processes of luciferin and infraluciferin and will inform the design of new bioluminescent systems and applications.

Controlling electron emission from the photoactive yellow protein chromophore by substitution at the coumaric acid group.

Understanding how the interactions between a chromophore and its surrounding protein control the function of a photoactive protein remains a challenge. Here, we present the results of photoelectron spectroscopy measurements and quantum chemistry calculations aimed at investigating how substitution at the coumaryl tail of the photoactive yellow protein chromophore controls competing relaxation pathways following photoexcitation of isolated chromophores in the gas phase with ultraviolet light in the range 350-315 nm. The photoelectron spectra are dominated by electrons resulting from direct detachment and fast detachment from the 2(1)ππ* state but also have a low electron kinetic energy component arising from autodetachment from lower lying electronically excited states or thermionic emission from the electronic ground state. We find that substituting the hydrogen atom of the carboxylic acid group with a methyl group lowers the threshold for electron detachment but has very little effect on the competition between the different relaxation pathways, whereas substituting with a thioester group raises the threshold for electron detachment and appears to 'turn off' the competing electron emission processes from lower lying electronically excited states. This has potential implications in terms of tuning the light-induced electron donor properties of photoactive yellow protein.

The atomistic structure of yttria stabilised zirconia at 6.7 mol%: an ab initio study.

Yttria stabilized zirconia (YSZ) is an important oxide ion conductor used in solid oxide fuel cells, oxygen sensing devices, and for oxygen separation. Doping pure zirconia (ZrO2) with yttria (Y2O3) stabilizes the cubic structure against phonon induced distortions and this facilitates high oxide ion conductivity. The local atomic structure of the dopant is, however, not fully understood. X-ray and neutron diffraction experiments have established that, for dopant concentrations below 40 mol% Y2O3, no long range order is established. A variety of local structures have been suggested on the basis of theoretical and computational models of dopant energetics. These studies have been restricted by the difficulty of establishing force field models with predictive accuracy or exploring the large space of dopant configurations with first principles theory. In the current study a comprehensive search for all symmetry independent configurations (2857 candidates) is performed for 6.7 mol% YSZ modelled in a 2 × 2 × 2 periodic supercell using gradient corrected density functional theory. The lowest energy dopant structures are found to have oxygen vacancy pairs preferentially aligned along the 〈210〉 crystallographic direction in contrast to previous results which have suggested that orientation along the 〈111〉 orientation is favourable. Analysis of the defect structures suggests that the Y3+-Ovac interatomic separation is an important parameter for determining the relative configurational energies. Current force field models are found to be poor predictors of the lowest energy structures. It is suggested that the energies from a simple point charge model evaluated at unrelaxed geometries is actually a better descriptor of the energy ordering of dopant structures. Using these observations a pragmatic procedure for identifying low energy structures in more complicated material models is suggested. Calculation of the oxygen vacancy migration activation energies within the lowest energy 〈210〉 oriented structures gives results consistent with experimental observations.

Chemical Descriptors of Yttria-Stabilized Zirconia at Low Defect Concentration: An ab Initio Study.

Yttria-stabilized zirconia (YSZ) is an important oxide ion conductor with applications in solid oxide fuel cells (SOFCs) and oxygen sensing devices. Doping the cubic phase of zirconia (c-ZrO2) with yttria (Y2O3) is isoelectronic, as two Zr(4+) ions are replaced by two Y(3+) ions, plus a charge compensating oxygen vacancy (Ovac). Typical doping concentrations include 3, 8, 10, and 12 mol %. For these concentrations, and all below 40 mol %, no phase with long-range order has been observed in either X-ray or neutron diffraction experiments. The prediction of local defect structure and the interaction between defects is therefore of great interest. This has not been possible to date as the number of possible defect topologies is very large and to perform reliable total energy calculations for all of them would be prohibitively expensive. Previous theoretical studies have only considered a selection of representative structures. In this study, a comprehensive search for low-energy defect structures using a combined classical modeling and density functional theory approach is used to identify the low-energy isolated defect structures at the dilute limit, 3.2 mol %. Through analysis of energetics computed using the best available Born-Mayer-Huggins empirical potential model, a point charge model, DFT, and a local strain energy estimated in the harmonic approximation, the main chemical and physical descriptors that correlate to the low-energy DFT structures are discussed. It is found that the empirical potential model reproduces a general trend of increasing DFT energetics across a series of locally strain relaxed structures but is unreliable both in predicting some incorrect low-energy structures and in finding some metastable structures to be unstable. A better predictor of low-energy defect structures is found to be the total electrostatic energy of a simple point charge model calculated at the unrelaxed geometries of the defects. In addition, the strain relaxation energy is estimated effectively in the harmonic approximation to the imaginary phonon modes of undoped c-ZrO2 but is found to be unimportant in determining the low-energy defect structures. These results allow us to propose a set of easily computed descriptors that can be used to identify the low-energy YSZ defect structures, negating the combinatorial complexity and number of defect structures that need to be considered.

Controlling radical formation in the photoactive yellow protein chromophore.

To understand how photoactive proteins function, it is necessary to understand the photoresponse of the chromophore. Photoactive yellow protein (PYP) is a prototypical signaling protein. Blue light triggers trans-cis isomerization of the chromophore covalently bound within PYP as the first step in a photocycle that results in the host bacterium moving away from potentially harmful light. At higher energies, photoabsorption has the potential to create radicals and free electrons; however, this process is largely unexplored. Here, we use photoelectron spectroscopy and quantum chemistry calculations to show that the molecular structure and conformation of the isolated PYP chromophore can be exploited to control the competition between trans-cis isomerization and radical formation. We also find evidence to suggest that one of the roles of the protein is to impede radical formation in PYP by preventing torsional motion in the electronic ground state of the chromophore.

The kinetics and product state distributions from gas-phase reactions of small atomic and molecular cations with C2H4, C2H3F, 1,1-C2H2F2, C2HF3 and C2F4.

The reactions of twenty one gas-phase cations with C2H3F, 1,1-C2H2F2, C2HF3 and C2F4 have been studied in a selected ion flow tube at 298 K. The cations are both atomic and molecular with recombination energies in the range 6-22 eV, and the kinetics and branching ratios into product ions are revealed for all the reactions. These data, together with that from an earlier study of reactions of C(x)F(y)(+) with these four fluorinated ethenes (J. Phys. Chem. A., 2012, 116, 8119), are compared with the reactions of these ions with C2H4, where available. Nearly all the reactions have a rate coefficient close to the collisional value calculated by either Langevin or modified average dipole orientation theories. The products of the reactions of N(+) and N2(+) with C2H4 are found to be anomalous, compared to their reactions with the four fluorinated ethenes. The branching ratios into product cations are compared with those from a high resolution (ca. 0.002 eV) photoionisation (hν = 10-22 eV) study of C2H3F, 1,1-C2H2F2, C2HF3 and C2F4 (Phys. Chem. Chem. Phys., 2012, 14, 3935) in order to gauge the importance of electron transfer in ion-molecule reactions. The higher the recombination energy of the cation, the better the agreement between the two sets of product branching ratios. Where there is disagreement at lower recombination energies, it appears that there is more fragmentation of the products in the photoionisation experiment compared to the ion-molecule reactions.