Gut flora metagenomic analysis coupled with metabolic and deep immune profiling in chronic kidney disease.

BACKGROUND AND HYPOTHESIS: Perturbation of gut microbiota has been linked to chronic kidney disease (CKD), which was correlated with a sophisticated milieu of metabolic and immune dysregulation. METHODS: To clarify the underlying host-microbe interaction in CKD, we performed multi-omics measurements, including systems-level gut microbiome, targeted serum metabolome, and deep immunotyping, in a cohort of patients and non-CKD controls. RESULTS: Our analyses on functional profiles of gut microbiome showed a decrease in the diversity and abundance of carbohydrate-active enzyme (CAZyme) genes but an increase in the abundance of antibiotic resistance, nitrogen cycling enzyme, and virulence factor genes in CKD. Moreover, models generated using measurements of serum metabolites (amino acids, bile acids, and short-chain fatty acids) or immunotypes were predictive of renal impairment but less so than many of functional profiles derived from gut microbiota, with the CAZyme genes being the top performing model to accurately predict early stage of diseases. In addition, co-occurrence analyses revealed coordinated host-microbe relationships in CKD. Specifically, the highest fractions of significant correlations were identified with circulating metabolites by several taxonomic and functional profiles of gut microbiome, while immunotype features were moderately associated with the abundance of microbiome-encoded metabolic pathways and serum levels of amino acids (e.g. B cell cluster-tryptophan and B cell cluster-tryptophan metabolism). CONCLUSION: Overall, our multi-omics integration revealed several signatures of systems-level gut microbiome in robust associations with host-microbe co-metabolites and renal function, which may be of etiological and diagnostic implications in CKD.

Photodissociation Dynamics of CO-Forming Channels on the Ground-State Surface of Methyl Formate at 248 nm: Direct Dynamics Study and Assessment of Generalized Multicenter Impulsive Models.

The photodissociation dynamics of methyl formate in the electronic ground state S0, initiated by a 248 nm-wavelength laser, is studied by direct dynamics simulations. We analyze five channels, where four of them have as products CH3OH + CO, one leading to the formation of three fragments, H2CO + H2 + CO, and a channel characterized by a roaming transition state. The analysis of energy distribution among the degrees of freedom of the product and the comparison with experimental results previously published by other groups provide the ingredients to distinguish the examined dissociation pathways. The interpretation of the results proves that the characterization of dissociation mechanisms must rely on a dynamics approach involving multiple electronic states, including considerations on the features of the S1/S0 conical intersection. Here, we also assess the generalized multicenter impulsive model, GMCIM, that has been designed for dissociation processes with exit barriers, and the energy distribution in the products is predicted on the basis of information from the saddle points and the intrinsic reaction coordinates. Main features, advantages, limits, and future perspectives of the method are reported and discussed.

Vectorial imaging of the photodissociation of 2-bromobutane oriented via hexapolar state selection.

Molecular orientation techniques are becoming available in the study of elementary chemical processes, in order to highlight those structural and dynamical properties that would be concealed by random rotational motions. Recently successful orientation was achieved for asymmetric-top and chiral molecules of much larger complexity than hitherto. In this work, we report and discuss the correlation between the vectors' photofragment recoil velocity v, transition dipole moment µ, and permanent dipole moment d in a dissociation experiment on hexapole oriented 2-bromobutane, photoinitiated by a linearly polarized laser. The sliced ion images of the Br*(2P1/2) and Br(2P3/2) photofragments were acquired at 234.0 and 254.1 nm, respectively, by a (2 + 1) resonance-enhanced multiphoton ionization technique. A detailed analysis of the sliced ion images obtained at a tilting angle 45° of laser polarization provides information on the correlation of the three vectors, which are confined by two polar angles α and χ and one azimuthal angle φµd in the recoil frame. The sliced ion images of Br fragments eliminated individually from the enantiomers at 254.1 nm yield an asymmetric factor close to zero; for this reason the photofragment angular distributions do not show significant differences. The elimination of the Br* fragment at 234.0 nm is mainly correlated with a parallel transition, giving rise to a large anisotropy parameter of 1.85, and thus can be considered as a single state excitation. The resulting recoil frame angles are optimized to 163° ± 8° and 164° ± 1° for α and χ, respectively, whereas φµd is approaching 0° for the best fit. Since for the present molecule, the three vectors have an only slight spatial arrangement, the photofragment angular distributions of the two enantiomers do not show appreciable differences. Theoretical and computational simulations provide us the basis to state that oriented enantiomers can be discriminated on-the-fly in photodissociation processes even initiated by non-circularly polarized light, provided that the three vectors encountered above have specific three-dimensional arrangements. The fact that Br fragment elimination involves a multi-potential dissociation carries uncertainties in theoretical estimates of the vector direction. Therefore, this work represents a preliminary but significant step on the road to chiral discrimination on-the-fly, which is shown to be best propitiated in molecules where vectors are far from having degenerate mutual angular directions.

A generalized unimolecular impulsive model for curved reaction path.

This work aims to introduce a generalized impulsive model for unimolecular dissociation processes. This model allows us to take into account the curvature of the reaction path explicitly. It is a generalization of the previously developed multi-center impulsive model [P.-Y. Tsai and K.-C. Lin, J. Phys. Chem. A 119, 29 (2015)]. Several limitations of conventional impulsive models are eliminated by this study: (1) Unlike conventional impulsive models, in which a single molecular geometry is responsible for the impulse determination, the gradients on the whole dissociation path are taken into account. The model can treat dissociation pathways with large curvatures and loose saddle points. (2) The method can describe the vibrational excitation of polyatomic fragments due to the bond formation by multi-center impulse. (3) The available energy in conventional impulsive models is separated into uncoupled statistical and impulsive energy reservoirs, while the interplay between these reservoirs is allowed in the new model. (4) The quantum state correlation between fragments can be preserved in analysis. Dissociations of several molecular systems including the roaming pathways of formaldehyde, nitrate radical, acetaldehyde, and glyoxal are chosen as benchmarks. The predicted photofragment energy and vector distributions are consistent with the experimental results reported previously. In these examples, the capability of the new model to treat the curved dissociation path, loose saddle points, polyatomic fragments, and multiple-body dissociation is verified. As a cheaper computational tool with respect to ab initio on-the-fly direct dynamic simulations, this model can provide detailed information on the energy disposal, quantum state correlation, and stereodynamics in unimolecular dissociation processes.

Flexible or Robust Amorphous Photonic Crystals from Network-Forming Block Copolymers for Sensing Solvent Vapors.

Large-area and flexible amorphous photonic crystals (APCs) featuring interconnected network microstructures are fabricated using high-molecular-weight polystyrene- block-poly(methyl methacrylate) (PS-PMMA) block copolymers. Kinetically controlled microphase separation combining with synergistic weak incompatibility gives rise to short-range-order network microstructures, exhibiting noniridescent optical properties. Solubility-dependent solvatochromism with distinct responses to various organic solvent vapors is observed in the network-forming APC film. By taking advantage of photodegradation of the PMMA block, nanoporous network-forming films were prepared for subsequent template synthesis of robust SiO2- and TiO2-based APC films through sol-gel reaction. Consequently, refractive index contrast of the APC film was able to be manipulated, resulting in intensely enhanced reflectivity and increased response rate for detecting solvent vapor. With the integration of self-assembly and photolithography approaches, flexible and robust network-forming APC films with well-defined photopatterned textures are carried out. This can provide a novel means for the design of photopatterned organic or inorganic APC films for sensing solvent vapors.

Photodissociation of CH3CHO at 248 nm: identification of the channels of roaming, triple fragmentation and the transition state.

Quasi-classical trajectory (QCT) calculations are performed on the molecular products CO + CH4via the tight transition state (TS) and global minimum configurations. With the aid of this theoretical evidence, we have re-examined the experimental results published previously to clarify the controversial issue of photodissociation dynamics of CH3CHO at 248 nm. For the CO (v = 0 and 1) bimodal rotational distributions obtained previously [K.-C. Hung, P.-Y. Tsai, H.-K. Li, and K.-C. Lin, J. Chem. Phys., 2014, 140, 064313], the low-rotational (J) component is re-assigned to the contribution of triple fragmentation (H + CO + CH3), whereas the high-J component is ascribed to the CH3-roaming pathway. The H-roaming pathway is not found in the calculations. Further, the QCT results have confirmed that the CO vibrational population especially at higher states and the low-energy component of CH4 vibrational bimodality obtained experimentally are mainly produced following the TS pathway, which has never been identified before. While taking into account both the theoretical and experimental results, the ratio of the molecular products (CO(v = 1) + CH4) obtained by the triple fragmentation/roaming/TS processes is evaluated to be 0.23 : 1 : 0.29.

On the state selection of linear triatomic molecules by electrostatic hexapole fields.

Electrostatic hexapole state-selector is a versatile tool in experimental stereodynamics. The requirement of appropriate models to correctly predict the behavior of molecules in the hexapole motivated us to realize a treatment that predicts the Stark effect of linear triatomic molecules with rotational doublet states. Various perturbative approximations are conventionally adopted to obtain analytic Stark energy derivatives of a truncated Hamiltonian matrix, without utilizing numerical diagonalization of the full Hamiltonian matrix. By including both the low and high field effects, which were alternatively ignored in the analytical formulae of such approximate approaches, herein we demonstrate that the performance of hexapole state selector to linear triatomic molecules can be appropriately predicted via Van Vleck transformation. This method can provide analytic Stark energy derivatives that are acceptably in consistent with the ones obtained via numerical diagonalization of the full Hamiltonian matrix. Particularly, this work is suitable for v2 = 1 level of linear triatomic molecules, due to the following reasons: (1) the Stark energy derivative and the molecular orientation as a function of the electric field are expressed in analytical formulae, hence it is suitable for implementation without involving numerical diagonalization of the full Hamiltonian matrix; (2) a better prediction of the focusing curves with respect to conventional analytical treatments is provided, allowing a reliable determination of the selected state compositions and molecular orientation.

Hexapole-Oriented Asymmetric-Top Molecules and Their Stereodirectional Photodissociation Dynamics.

Molecular orientation is a fundamental requisite in the study of stereodirected dynamics of collisional and photoinitiated processes. In this past decade, variable hexapolar electric filters have been developed and employed for the rotational-state selection and the alignment of molecules of increasing complexity, for which the main difficulties are their mass, their low symmetry, and the very dense rotational manifold. In this work, for the first time, a complex molecule such as 2-bromobutane, an asymmetric top containing a heavy atom (the bromine), was successfully oriented by a weak homogeneous field placed downstream from the hexapolar filter. Efficiency of the orientation was characterized experimentally, by combining time-of-flight measurements and a slice-ion-imaging detection technique. The application is described to the photodissociation dynamics of the oriented 2-bromobutane, which was carried out at a laser wavelength of 234 nm, corresponding to the breaking of the C-Br bond. The Br photofragment is produced in both the ground Br ((2)P3/2) and the excited Br ((2)P1/2) electronic states, and both channels are studied by the slice imaging technique, revealing new features in the velocity and angular distributions with respect to previous investigations on nonoriented molecules.

Rovibrationally Excited Molecules on the Verge of a Triple Breakdown: Molecular and Roaming Mechanisms in the Photodecomposition of Methyl Formate.

For the photodissociation of the simplest of esters, methyl formate HCOOCH3, the energy threshold for triple fragmentation into H, CH3O, and CO was measured by previous ion-imaging experiments at a sequence of wavelengths. The translational energy features of product CO in the ground vibrational level (υ = 0) and for selected rotational states were characterized. In this integrated experimental and theoretical approach (i) the focus is at a laser energy barely below that threshold; (ii) Fourier-transform infrared emission spectroscopy measurements probe the rovibrational energy deposition in CO(υ) for υ > 0 and the emergence of the roaming phenomenon; (iii) accompanying quantum chemical calculations describe the selective rupture of bonds; and (iv) molecular dynamics simulations of dissociation are performed, introducing an approach explicitly involving outcomes from paths originated nonadiabatically through conical intersections. Quantitative information on energy disposal is provided: we found extensive vibrational excitation of CO, while rotational bands are colder and bimodal, due to contributions from direct and roaming modes.

Roaming as the dominant mechanism for molecular products in the photodissociation of large aliphatic aldehydes.

Photodissociation of isobutyraldehyde (C3H7CHO) at 248 nm is investigated using time-resolved Fourier-transform infrared emission spectroscopy to demonstrate the growing importance of the roaming pathway with increasing molecular size of aliphatic aldehydes. Each acquired CO rotational distribution from v = 1 to 4 is well characterized by a single Boltzmann rotational temperature from 637 to 750 K, corresponding to an average rotational energy of 5.9 ± 0.6 kJ mol(-1). The roaming signature that shows a small fraction of CO rotational energy disposal accompanied by a vibrationally hot C3H8 co-fragment is supported by theoretical prediction. The energy difference between the tight transition state (TS) and the roaming saddle point (SP) is found to be -27, 4, 15, 22, and 30 kJ mol(-1) for formaldehyde, acetaldehyde, propionaldehyde, isobutyraldehyde, and 2,2-dimethyl propanal, respectively. The roaming SP is stabilized by a larger alkyl moiety. It is suggested that the roaming photodissociation rate of aldehydes increasingly exceeds those via the tight TS, resulting in the dominance of the CO + alkane products, as the size of aldehydes becomes larger. Along with formaldehyde, acetaldehyde, and propionaldehyde, in this work isobutyraldehyde is further demonstrated that this aldehyde family with special functional group is the first case in the organic compound to follow predominantly a roaming dissociation pathway, as the molecular size becomes larger.

Insight into photofragment vector correlation by a multi-center impulsive model.

A multi-center impulsive model has been recently developed to characterize the dynamic feature of product energy distribution in photodissociation of formaldehyde, H2CO → CO + H2. (J. Phys. Chem. A, 2015, 119, 29) The model is extended to predict the vector correlations among transition dipole moment µ of the parent molecule, recoil velocity v and rotational angular momentum j of the fragments produced via the transition state (TS) and roaming path. The correlation results of µ-j, j-j and µ-v vectors of the fragments are consistent with those reported using quasi-classical trajectory simulation on the global potential energy surface. In contrast to the TS route, the vector properties via the roaming path are loosely correlated. This work offers an alternative method to study stereodynamics of the photodissociation process, and is conducive to clarifying the origin of photofragment vector correlation especially for the roaming pathway.

Characterization of molecular channel in photodissociation of SOCl2 at 248 nm: Cl2 probing by cavity ring-down absorption spectroscopy.

A primary elimination channel of the chlorine molecule in the one-photon dissociation of SOCl2 at 248 nm was investigated using cavity ring-down absorption spectroscopy (CRDS). By means of spectral simulation, the ratio of the vibrational population in the v = 0, 1, and 2 levels was evaluated to be 1 : (0.10 ± 0.02) : (0.009 ± 0.005), corresponding to a Boltzmann vibrational temperature of 340 ± 30 K. The Cl2 molecular channel was obtained with a quantum yield of 0.4 ± 0.2 from the X(1)A' ground state of SOCl2via internal conversion. The dissociation mechanism differs from a prior study where a smaller yield of <3% was obtained, initiated from the 2(1)A' excited state. Temperature-dependence measurements of the Cl2 fragment turn out to support our mechanism. With the aid of ab initio potential energy calculations, two dissociation routes to the molecular products were found, including one synchronous dissociation pathway via a three-center transition state (TS) and the other sequential dissociation pathway via a roaming-mediated isomerization TS. The latter mechanism with a lower energy barrier dominates the dissociation reaction.

Communication: photodissociation of CH3CHO at 308 nm: observation of H-roaming, CH3-roaming, and transition state pathways together along the ground state surface.

Following photodissociation of acetaldehyde (CH3CHO) at 308 nm, the CO(v = 1-4) fragment is acquired using time-resolved Fourier-transform infrared emission spectroscopy. The CO(v = 1) rotational distribution shows a bimodal feature; the low- and high-J components result from H-roaming around CH3CO core and CH3-roaming around CHO radical, respectively, in consistency with a recent assignment by Kable and co-workers (Lee et al., Chem. Sci. 5, 4633 (2014)). The H-roaming pathway disappears at the CO(v ≥ 2) states, because of insufficient available energy following bond-breaking of H + CH3CO. By analyzing the CH4 emission spectrum, we obtained a bimodal vibrational distribution; the low-energy component is ascribed to the transition state (TS) pathway, consistent with prediction by quasiclassical trajectory calculations, while the high-energy component results from H- and CH3-roamings. A branching fraction of H-roaming/CH3-roaming/TS contribution is evaluated to be (8% ± 3%)/(68% ± 10%)/(25% ± 5%), in which the TS pathway was observed for the first time. The three pathways proceed concomitantly along the electronic ground state surface.

Dynamical, spectroscopic and computational imaging of bond breaking in photodissociation: roaming and role of conical intersections.

Recent experimental and theoretical advances in the study of the dissociation of excited molecules are revealing unexpected mechanisms, when their outcomes are tackled by combining (i) space-time ion imaging of translational features, with (ii) spectroscopic probing of rotational and vibrational distributions; crucial is the assistance of (iii) the quantum chemistry of structural investigations of rearrangements of chemical bonds, and of (iv) the simulations of molecular dynamics to follow the evolution of selective bond stretching and breaking. Here we present results of such an integrated approach to methyl formate, HCOOCH3, the simplest of esters; the main focus is on the rotovibrationally excited CO (v=1) product and in general on the energy distribution in the fragments. Previous laser studies of dissociation into CO and CH3OH at a sequence of various wavelengths discovered signatures of a roaming mechanism by the late arrival of CO (v=0) products in time-of-flight ion imaging. Subsequent detailed investigations as a function of excitation energy provided the assessment of the threshold, which opens for triple breakdown into CO and further fragments H and CH3O, as spectroscopically characterized by ion imaging and FTIR respectively. Accompanying quantum mechanical electronic structure calculations and classical molecular dynamics simulations clarify the origin of these fragments through "roaming" pathways involving incipient radical intermediates at energies below the triple fragmentation threshold: a specific role is played by nonadiabatic transitions at a conical intersection between ground and excited states; alternative pathways focalize our attention to regions of the potential energy surfaces other than those in the neighbourhoods of saddle points along minimum energy paths: eventually this leads us to look for avenues in reaction kinetics beyond those of venerable transition state theories.

Insight into the photodissociation dynamical feature of conventional transition state and roaming pathways by an impulsive model.

Without the need to construct complicated potential energy surfaces, a multicenter impulsive model is developed to characterize the dynamical feature of conventional transition state (TS) and roaming pathways in the photodissociation of formaldehyde, H2CO → CO + H2. The photofragment energy distributions (PED) resulting from the roaming mechanism are found to closely correlate to a particular configuration that lies close to the edge of the plateau-like intrinsic reaction coordinate, whereas such a PED is associated with the configuration at the saddle point when the conventional TS pathway is followed. The evaluated PED results are consistent with those by experimental findings and quasi-classical trajectory calculations. Following impulsive analysis, the roaming pathway can be viewed as a consequence of energy transfer events between several vibrational modes. For H2CO, the available energy initially accumulated at the C-H bond is transferred to other transitional mode(s) via stretching-bending coupling, and finally to the HH stretching.

Directions of chemical change: experimental characterization of the stereodynamics of photodissociation and reactive processes.

This perspective article aims at accounting for the versatility of some current experimental investigations for exploring novel paths in chemical reactions. It updates a previous one [Phys. Chem. Chem. Phys., 2005, 5, 291] and is limited to work by the authors. The use of advanced molecular beam techniques together with a combination of modern tools for specific preparation, selection and detection permits us to discover new trends in reactivity in the gas phase as well as at interfaces. We specifically discuss new facets of stereodynamics, namely the effects of molecular orientation and alignment on reactive and photodissociation processes. Further topics involve roaming paths and triple fragmentation in photodissociation probed by imaging techniques, chirality effects in collisions and deviations from Arrhenius behavior in the temperature dependence of chemical reactions.

Molecular halogen elimination from halogen-containing compounds in the atmosphere.

Atmospheric halogen chemistry has drawn much attention, because the halogen atom (X) playing a catalytic role may cause severe stratospheric ozone depletion. Atomic X elimination from X-containing hydrocarbons is recognized as the major primary dissociation process upon UV-light irradiation, whereas direct elimination of the X2 product has been seldom discussed or remained a controversial issue. This account is intended to review the detection of X2 primary products using cavity ring-down absorption spectroscopy in the photolysis at 248 nm of a variety of X-containing compounds, focusing on bromomethanes (CH2Br2, CF2Br2, CHBr2Cl, and CHBr3), dibromoethanes (1,1-C2H4Br2 and 1,2-C2H4Br2) and dibromoethylenes (1,1-C2H2Br2 and 1,2-C2H2Br2), diiodomethane (CH2I2), thionyl chloride (SOCl2), and sulfuryl chloride (SO2Cl2), along with a brief discussion on acyl bromides (BrCOCOBr and CH2BrCOBr). The optical spectra, quantum yields, and vibrational population distributions of the X2 fragments have been characterized, especially for Br2 and I2. With the aid of ab initio calculations of potential energies and rate constants, the detailed photodissociation mechanisms may be comprehended. Such studies are fundamentally important to gain insight into the dissociation dynamics and may also practically help to assess the halogen-related environmental variation.

Photodissociation of CH3CHO at 248 nm by time-resolved Fourier-transform infrared emission spectroscopy: verification of roaming and triple fragmentation.

By using time-resolved Fourier-transform infrared emission spectroscopy, the HCO fragment dissociated from acetaldehyde (CH3CHO) at 248 nm is found to partially decompose to H and CO. The fragment yields are enhanced by the Ar addition that facilitates the collision-induced internal conversion. The channels to CH2CO + H2 and CH3CO + H are not detected significantly. The rotational population distribution of CO, after removing the Ar collision effect, shows a bimodal feature comprising both low- and high-rotational (J) components, sharing a fraction of 19% and 81%, respectively, for the vibrational state v = 1. The low-J component is ascribed to both roaming pathway and triple fragmentation. They are determined to have a branching ratio of <0.13 and >0.06, respectively, relative to the whole v = 1 population. The CO roaming is accompanied by a highly vibrational population of CH4 that yields a vibrational bimodality.

Photodissociation of Propionaldehyde at 248 nm: Roaming Pathway as an Increasingly Important Role in Large Aliphatic Aldehydes.

Time-resolved Fourier transform infrared emission spectroscopy is employed in the photolysis of propionaldehyde (CH3CH2CHO) at 248 nm to characterize the role of the roaming pathway. High-resolution spectra of CO are analyzed to yield a single Boltzmann rotational distribution for each vibrational level (ν = 1-4) with small rotational and large vibrational energy disposals. A roaming saddle point is found containing two far separated moieties of HCO and CH3CH2 with a weak interaction between them. Quasiclassical trajectory calculations on this configuration yield the CO energy flow behavior, consistent with the findings. The rate constant along the roaming pathway is evaluated to be larger by >1-2 orders of magnitude than those along tight transition state or three-body dissociation pathways. This work implies that the roaming mechanism plays an increasingly important role in aliphatic aldehydes as the molecular size becomes larger.