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We investigated the signature of ultrafast hydrogen dynamics in Polarization-Averaged Molecular-Frame Photoelectron Angular Distributions and studied intramolecular hydrogen migrations by the spectra for CH3OH2+, C2H5OH2+ and C3H7OH2+.

The internal conversion from the optically bright S$_2$ ($^1$B$_{2\mathrm{u}}$, $\pi\pi^*$) state to the dark S$_1$ ($^1$B$_{3\mathrm{u}}$, n$\pi^*$) state in pyrazine is a standard benchmark for experimental and theoretical studies on ultrafast radiationless decay. Since 2008 a few theoretical groups have suggested significant contributions of other dark states S$_3$ ($^1$A$_\mathrm{u}$, n$\pi^*$) and S$_4$ ($^1$B$_{2\mathrm{g}}$, n$\pi^*$) to the decay of S$_2$. We have previously reported the results of nuclear wave packet simulations [Phys. Chem. Chem. Phys. 17, 2012 (2015)] and photoelectron spectrum calculations [Chem. Phys. 515, 704 (2018)] that support the conventional two-state picture. In this article, the two different approaches, i.e., wave packet simulation and photoelectron spectrum calculation are combined: We computed the time-resolved vacuum ultraviolet photoelectron spectrum and photoelectron angular distribution for the ionization of the wave packet transferred from S$_2$ to S$_1$. The present results reproduce almost all the characteristic features of the corresponding experimental time-resolved spectrum [T. Horio et al., J. Chem. Phys. 145, 044306 (2016)] such as a rapid change from a three-band to two-band structure. This further supports the existence and character of the widely accepted pathway (S$_2$ $\rightarrow$ S$_1$) of ultrafast internal conversion in pyrazine., Comment: 30 pages, 8 figures. This article has been submitted to The Journal of Chemical Physics

Velocity and angular distributions of photofragment CO2+ ions produced from mass-selected (CO2)2+ at 532 nm excitation were observed in an ion imaging experiment. The velocity distribution was assigned to two components, fast and slow velocity components, which was consistent with the previous study by Bowers et al. The anisotropy parameters of the angular distributions for the fast and slow velocity components were experimentally determined to be βfast = 1.52 ± 0.14 and βslow = 0.46 ± 0.10, respectively. In the theoretical approach, potential energy surfaces (PESs) of (CO2)2+ were calculated along two coordinates, the intermolecular distance and mutual orientations of the CO2 monomers. In addition, molecular dynamics simulations were performed. The visible transition of the most stable staggered structure of (CO2)2+ was attributed to 2Ag ← 2Bu by an excited state calculation. On the PES of the state, a potential well was found in which the two CO2 monomers lay side by side to each other, in addition to a repulsive slope along the intermolecular distance. The results of the simulations confirmed that the fragment CO2+ ions with fast velocity and large anisotropy originated from the rapid dissociation of (CO2)2+ on the repulsive slope. Meanwhile, the fragment CO2+ ions with slow velocity and small anisotropy were expected to emerge from statistical dissociation after large amplitude libration of CO2 molecules which was caused by the potential well in the excited state PES.

The photoinduced ring-opening reaction of 1,3-cyclohexadiene (CHD) to produce 1,3,5-hexatriene (HT) plays an essential role in the photobiological synthesis of vitamin D3 in the skin. This reaction follows the Woodward-Hoffmann rule, and C5-C6 bond rupture via an electronically excited state occurs with conrotatory motion of the end CH2 groups. However, it is noted that the photoexcited S1(π,π*) state of CHD is not electronically correlated with the ground state of HT, and the reaction must proceed via nonadiabatic transitions. In the present study, we have clearly observed the nonadiabatic reaction pathway via the doubly excited state of CHD using ultrafast extreme UV photoelectron spectroscopy. The results indicate that the reaction occurs in only 68 fs and creates product vibrational coherence. Extensive computational simulations support the interpretation of experimental results and provide further insights into the electronic dynamics in this paradigmatic electrocyclic ring-opening reaction.

Our recently developed trajectory surface hopping method uses numerical time derivatives of adiabatic potential gradients to estimate the nonadiabatic transition probability and the hopping direction. To demonstrate the practicality of the novel method, we applied it to the intermolecular photodissociation of a carbon dioxide dimer cation (CO

The photoinduced ring-opening reaction of 1,3-cyclohexadiene to produce 1,3,5-hexatriene is a well-known example of the Woodward-Hoffmann rule for stereochemical reactions governed by molecular orbital symmetry, and it plays an essential role in photobiological synthesis of vitamin D3 in the skin. Since the photoexcited 11B state of 1,3-cyclohexadiene is not electronically correlated to the ground state of 1,3,5-hexatriene, the reaction is expected to proceed via non-adiabatic transitions through a doubly excited 21A electronic state. However, spectroscopic observation of this elusive state has been difficult. Here we present the results of a photoelectron spectroscopy study using table-top ultrafast deep and extreme UV lasers, based on filamentation four-wave mixing and high-harmonic generation, which enabled us to arrest the 21A state. It is shown that the ring-opening reaction takes only 60 fs to complete, which is a considerably shorter time than previous experimental and theoretical estimates. The ballistic reaction creates vibrational coherence in the reaction products.

Extreme overproduction of gratuitous proteins can overload cellular protein production resources, leading to growth defects, a phenomenon known as the protein burden/cost effect. Genetic screening in the budding yeast Saccharomyces cerevisiae has isolated several dubious ORFs whose deletions mitigated the protein burden effect, but individual characterization thereof has yet to be delineated. We found that deletion of the YJL175W ORF yielded an N-terminal deletion of Swi3, a subunit of the SWI/SNF chromatin remodeling complex, and partial loss of function of Swi3. The deletion mutant showed a reduction in transcription of genes encoding highly expressed, secreted proteins and an overall reduction in translation. Mutations in the chromatin remodeling complex could thus mitigate the protein burden effect, likely by reallocating residual cellular resources used to overproduce proteins. This cellular state might also be related to cancer cells, as they frequently harbor mutations in the SWI/SNF complex.

The internal conversion of photo-excited pyrazine, which occurs rapidly on a time scale of about 20 fs, has long been considered to proceed via a conical intersection between the optically bright S2 (1B2u, ππ∗) and dark S1 (1B3u, nπ∗) states. Since 2008, several theoretical studies have raised the possibility that other dark states S3 (1Au, nπ∗) and S4 (1B2g, nπ∗) may participate dominantly in the early stage of the nonradiative decay of S2. To clarify this issue, being motivated by the recent pump–probe experiment by Horio et al. [J. Chem. Phys. 145 (2016) 044306], we calculated vacuum ultraviolet photoelectron spectra for ionization from each of the four excited states. Comparison was made with the measured time-resolved photoelectron spectrum exhibiting a temporally varying multi-band structure. We confirmed no contribution of S3 or S4 and thus the validity of the conventional two-state (S2 → S1) picture for ultrafast nonradiative transition in pyrazine.

A simple time-evolution method for nuclear quantum dynamics is proposed in which the wavefunction is expanded in terms of Gaussians placed at von Neumann unit cells in phase space, with an accuracy threshold parameter e. The wavepacket propagation is obtained by solving the equations of motion for expansion coefficients only. New Gaussians are added to the basis set when the change in wavefunction exceeds another threshold parameter δ (>e). From the application to model tunneling systems in one to three dimensions, the present Gaussian expansion approach is able to accurately evaluate the tunneling time and tunneling direction in multidimensional systems.

Coulomb explosion of diiodomethane CH2I2 molecules irradiated by ultrashort and intense X-ray pulses from SACLA, the Japanese X-ray free electron laser facility, was investigated by multi-ion coincidence measurements and self-consistent charge density-functional-based tight-binding (SCC-DFTB) simulations. The diiodomethane molecule, containing two heavy-atom X-ray absorbing sites, exhibits a rather different charge generation and nuclear motion dynamics compared to iodomethane CH3I with only a single heavy atom, as studied earlier. We focus on charge creation and distribution in CH2I2 in comparison to CH3I. The release of kinetic energy into atomic ion fragments is also studied by comparing SCC-DFTB simulations with the experiment. Compared to earlier simulations, several key enhancements are made, such as the introduction of a bond axis recoil model, where vibrational energy generated during charge creation processes induces only bond stretching or shrinking. We also propose an analytical Coulomb energy partition model to extract the essential mechanism of Coulomb explosion of molecules from the computed and the experimentally measured kinetic energies of fragment atomic ions by partitioning each pair Coulomb interaction energy into two ions of the pair under the constraint of momentum conservation. Effective internuclear distances assigned to individual fragment ions at the critical moment of the Coulomb explosion are then estimated from the average kinetic energies of the ions. We demonstrate, with good agreement between the experiment and the SCC-DFTB simulation, how the more heavily charged iodine fragments and their interplay define the characteristic features of the Coulomb explosion of CH2I2. The present study also confirms earlier findings concerning the magnitude of bond elongation in the ultrashort X-ray pulse duration, showing that structural damage to all but C–H bonds does not develop to a noticeable degree in the pulse length of ∼10 fs.

Biphenyl contains a direct bond between two phenyl functional groups, and the dihedral angle between the two phenyl groups has been discussed in terms of electronic and steric stabilization. Facile rotation about the C–C bond between the two phenyl components is expected to occur at high temperatures. Here, we report observations of the rotational dynamics of a biphenylene dirotor in a crystalline state in a novel molecular gyrotop. The structure and rotational dynamics of the rotor exhibit remarkable temperature dependence. In accordance with the amplification of the angular displacement of biphenylene inside a crystal with increasing temperature, the birefringence of the single crystal decreased.

Levulinic acid (LA) is a building block alternative to fermentable sugars derived from cellulosic biomass. Among LA catabolic processes in Pseudomonas putida KT2440, ligation of coenzyme A (CoA) to LA by levulinyl-CoA synthetase (LvaE) is known to be an initial enzymatic step in LA metabolism. To identify the genes involved in the first step of LA metabolism in Pseudomonas citronellolis LA18T, RNA-seq-based comparative transcriptome analysis was carried out for LA18T cells during growth on LA and pyruvic acid. The two most highly upregulated genes with LA exhibited amino acid sequence homologies to cation acetate symporter and 5-aminolevulinic acid dehydratase from Pseudomonas spp. Potential LA metabolic genes (lva genes) in LA18T that clustered with these two genes and were homologous to lva genes in KT2440 were identified, including lvaE2 of LA18T, which exhibited 35% identity with lvaE of KT2440. Using Escherichia coli cells with the pCold™ expression system, LvaE2 was produced and investigated for its activity toward LA. High performance liquid chromatography analysis confirmed that crude extracts of E. coli cells expressing the lvaE2 gene could convert LA to levulinyl-CoA in the presence of both HS-CoA and ATP. Phylogenetic analysis revealed that LvaE2 and LvaE formed a cluster with medium-chain fatty acid CoA synthetase, but they fell on different branches. Superimposition of LvaE2 and LvaE homology-based model structures suggested that LvaE2 had a larger tunnel for accepting fatty acid substrates than LvaE. These results indicate that LvaE2 is a novel levulinyl-CoA synthetase. Electronic supplementary material The online version of this article (10.1186/s13568-019-0853-y) contains supplementary material, which is available to authorized users.

The increasing availability of X-ray free-electron lasers (XFELs) has catalyzed the development of single-object structural determination and of structural dynamics tracking in real-time. Disentangling the molecular-level reactions triggered by the interaction with an XFEL pulse is a fundamental step towards developing such applications. Here we report real-time observations of XFEL-induced electronic decay via short-lived transient electronic states in the diiodomethane molecule, using a femtosecond near-infrared probe laser. We determine the lifetimes of the transient states populated during the XFEL-induced Auger cascades and find that multiply charged iodine ions are issued from short-lived (∼20 fs) transient states, whereas the singly charged ones originate from significantly longer-lived states (∼100 fs). We identify the mechanisms behind these different time scales: contrary to the short-lived transient states which relax by molecular Auger decay, the long-lived ones decay by an interatomic Coulombic decay between two iodine atoms, during the molecular fragmentation., X線照射で始まる超高速反応の観測に成功 --レントゲンによるX線の発見から120年で初--. 京都大学プレスリリース. 2019-05-28.

Theoretical studies indicated that ${\mathrm{C}}_{60}$ exposed to linearly polarized intense infrared pulses undergoes periodic cage structural distortions with typical periods around 100 fs ($1\text{ }\mathrm{fs}={10}^{\ensuremath{-}15}\text{ }\text{ }\mathrm{s}$). Here, we use the laser-driven self-imaging electron diffraction technique, previously developed for atoms and small molecules, to measure laser-induced deformation of ${\mathrm{C}}_{60}$ in an intense $3.6\text{ }\text{ }\ensuremath{\mu}\mathrm{m}$ laser field. A prolate molecular elongation along the laser polarization axis is determined to be $(6.1\ifmmode\pm\else\textpm\fi{}1.4)%$ via both angular- and energy-resolved measurements of electrons that are released, driven back, and diffracted from the molecule within the same laser field. The observed deformation is confirmed by density functional theory simulations of nuclear dynamics on time-dependent adiabatic states and indicates a nonadiabatic excitation of the ${h}_{g}(1)$ prolate-oblate mode. The results demonstrate the applicability of laser-driven electron diffraction methods for studying macromolecular structural dynamics in four dimensions with atomic time and spatial resolutions.

Velocity and angular distributions of photofragment CO2+ ions produced from mass-selected (CO2)2+ at 532 nm excitation were observed in an ion imaging experiment. The velocity distribution was assigned to two components, fast and slow velocity components, which was consistent with the previous study by Bowers et al. The anisotropy parameters of the angular distributions for the fast and slow velocity components were experimentally determined to be βfast = 1.52 ± 0.14 and βslow = 0.46 ± 0.10, respectively. In the theoretical approach, potential energy surfaces (PESs) of (CO2)2+ were calculated along two coordinates, the intermolecular distance and mutual orientations of the CO2 monomers. In addition, molecular dynamics simulations were performed. The visible transition of the most stable staggered structure of (CO2)2+ was attributed to C[combining tilde]2Ag ← X[combining tilde]2Bu by an excited state calculation. On the PES of the C[combining tilde] state, a potential well was found in which the two CO2 monomers lay side by side to each other, in addition to a repulsive slope along the intermolecular distance. The results of the simulations confirmed that the fragment CO2+ ions with fast velocity and large anisotropy originated from the rapid dissociation of (CO2)2+ on the repulsive slope. Meanwhile, the fragment CO2+ ions with slow velocity and small anisotropy were expected to emerge from statistical dissociation after large amplitude libration of CO2 molecules which was caused by the potential well in the excited state PES.

Our recently developed trajectory surface hopping method uses numerical time derivatives of adiabatic potential gradients to estimate the nonadiabatic transition probability and the hopping direction. To demonstrate the practicality of the novel method, we applied it to the intermolecular photodissociation of a carbon dioxide dimer cation (CO2)2+. Our simulations reproduced the measured velocity distribution of CO2+ fragments consisting of two (fast and slow) components and revealed that nonadiabatic transitions occur promptly toward the electronic ground state regardless of the fragment velocity. The structure of (CO2)2+ at optical excitation governs the fate of subsequent nonadiabatic dynamics leading to a fast or slow dissociation. Our method gave similar results to the fewest switches algorithm at lower computational expense. Our fast and robust surface hopping method is promising for the investigation of nonadiabatic dynamics in large and complex systems.

High-affinity H2 -oxidizing bacteria possessing group 5 [NiFe]-hydrogenase genes are important contributors to atmospheric hydrogen (H2 ) uptake in soil environments. Although previous studies reported the occurrence of a significant H2 uptake activity in vegetation, there has been no report on the identification and diversity of the responsible microorganisms. Here, we show the existence of plant-associated bacteria with the ability to consume atmospheric H2 that may be a potential energy source required for their persistence in plants. Detection of the gene hhyL - encoding the large subunit of group 5 [NiFe]-hydrogenase - in plant tissues showed that plant-associated high-affinity H2 -oxidizing bacteria are widely distributed in herbaceous plants. Among a collection of 145 endophytic isolates, 7 Streptomyces strains were shown to possess hhyL gene and exhibit high- or intermediate-affinity H2 uptake activity. Inoculation of Arabidopsis thaliana (thale cress) and Oryza sativa (rice) seedlings with selected isolates resulted in an internalization of the bacteria in plant tissues. H2 uptake activity per bacterial cells was comparable between plant and soil, demonstrating that both environments are favorable for the H2 uptake activity of streptomycetes. This study first demonstrated the occurrence of plant-associated high-affinity H2 -oxidizing bacteria and proposed their potential contribution as a sink for atmospheric H2 .

We studied the electronic and nuclear dynamics of I-containing organic molecules induced by intense hard X-ray pulses at the XFEL facility SACLA in Japan. The interaction with the intense XFEL pulse causes absorption of multiple X-ray photons by the iodine atom, which results in the creation of many electronic vacancies (positive charges) via the sequential electronic relaxation in the iodine, followed by intramolecular charge redistribution. In a previous study we investigated the subsequent fragmentation by Coulomb explosion of the simplest I-substituted hydrocarbon, iodomethane (CH3I). We carried out three-dimensional momentum correlation measurements of the atomic ions created via Coulomb explosion of the molecule and found that a classical Coulomb explosion model including charge evolution (CCE-CE model), which accounts for the concerted dynamics of nuclear motion and charge creation/charge redistribution, reproduces well the observed momentum correlation maps of fragment ions emitted after XFEL irradiation. Then we extended the study to 5-iodouracil (C4H3IN2O2, 5-IU), which is a more complex molecule of biological relevance, and confirmed that, in both CH3I and 5-IU, the charge build-up takes about 10 fs, while the charge is redistributed among atoms within only a few fs. We also adopted a self-consistent charge density-functional based tight-binding (SCC-DFTB) method to treat the fragmentations of highly charged 5-IU ions created by XFEL pulses. Our SCC-DFTB modeling reproduces well the experimental and CCE-CE results. We have also investigated the influence of the nuclear dynamics on the charge redistribution (charge transfer) using nonadiabatic quantum-mechanical molecular dynamics (NAQMD) simulation. The time scale of the charge transfer from the iodine atomic site to the uracil ring induced by nuclear motion turned out to be only ∼5 fs, indicating that, besides the molecular Auger decay in which molecular orbitals delocalized over the iodine site and the uracil ring are involved, the nuclear dynamics also play a role for ultrafast charge redistribution. The present study illustrates that the CCE-CE model as well as the SCC-DFTB method can be used for reconstructing the positions of atoms in motion, in combination with the momentum correlation measurement of the atomic ions created via XFEL-induced Coulomb explosion of molecules.

The studies of crystal structures with hydrogen bonds have been actively pursued because of their moderate stabilization energy for constructing unique structures. In this study, we synthesized a molecular conductor based on 2,6-bis(4-pyridyl)-1,4,5,8-tetrathiafulvalene (trans-TTF-py2). Two pyridyl groups were introduced into the TTF skeleton toward the structural exploration in TTF-based molecular conductors involved by hydrogen bonds. In the obtained molecular conductor, (trans-TTF-py2)1.5(PF6)&middot, EtOH, short contacts between the pyridyl group and the hydrogen atom of the TTF skeleton were observed, indicating that hydrogen bonding interactions were introduced in the crystal structure. Spectroscopic measurements and conductivity measurement revealed semiconducting behavior derived from &pi, stacked trans-TTF-py2 radical in the crystal structure. Finally, these results are discussed with the quantified hydrogen bonding stabilization energy, and the band calculation of the crystal obtained from density functional theory calculation.

In order to investigate dissociation dynamics of water molecules in a near-IR femtosecond intense laser pulse, we performed ab initio molecular dynamics calculations combined with the time-dependent adiabatic state approach. We showed that H+ is produced from H2O2+ not only by the two-body dissociation but also by the three-body dissociation and that the kinetic energy distributions of H+ for the two-body dissociation are in good agreement with the corresponding experimental data. We also performed time-dependent configuration interaction calculations to estimate the ionization probability of H2O2+ and confirmed that H2O2+ is ionized to H2O3+ by the charge-resonance enhanced ionization mechanism.

Pseudomonas citronellolis LA18T catabolizes levulinic acid (LA) from cellulosic biomass hydrolysate via acetyl-coenzyme A (acetyl-CoA) and propionyl-CoA. This study reports the 7.22-Mbp draft genome sequence of P. citronellolis LA18T., Pseudomonas citronellolis LA18T catabolizes levulinic acid (LA) from cellulosic biomass hydrolysate via acetyl-coenzyme A (acetyl-CoA) and propionyl-CoA. This study reports the 7.22-Mbp draft genome sequence of P. citronellolis LA18T. The draft genome sequence will aid the study of the LA catabolic pathway, which will allow for more applications of LA-utilizing bacteria.

Theoretical studies indicated that C_{60} exposed to linearly polarized intense infrared pulses undergoes periodic cage structural distortions with typical periods around 100 fs (1 fs=10^{-15} s). Here, we use the laser-driven self-imaging electron diffraction technique, previously developed for atoms and small molecules, to measure laser-induced deformation of C_{60} in an intense 3.6 μm laser field. A prolate molecular elongation along the laser polarization axis is determined to be (6.1±1.4)% via both angular- and energy-resolved measurements of electrons that are released, driven back, and diffracted from the molecule within the same laser field. The observed deformation is confirmed by density functional theory simulations of nuclear dynamics on time-dependent adiabatic states and indicates a nonadiabatic excitation of the h_{g}(1) prolate-oblate mode. The results demonstrate the applicability of laser-driven electron diffraction methods for studying macromolecular structural dynamics in four dimensions with atomic time and spatial resolutions.

International audience; We propose a modification to the nonadiabatic surface hopping calculation method formulated in a paper by Yu et al. [Phys. Chem. Chem. Phys. 16, 25883 (2014)], which is a multidimensional extension of the Zhu-Nakamura theory with a practical diabatic gradient estimation algorithm. In our modification, their diabatic gradient estimation algorithm, which is based on a simple interpolation of the adiabatic potential energy surfaces, is replaced by an algorithm using the numerical derivatives of the adiabatic gradients. We then apply the algorithm to several models of nonadiabatic dynamics, both analytic and ab initio models, to numerically demonstrate that our method indeed widens the applicability and robustness of their method. We also discuss the validity and limitations of our new nonadiabatic surface hopping method while considering in mind potential applications to excited-state dynamics of biomolecules or unconventional nonadiabatic dynamics such as radiation decay processes in ultraintense X-ray fields.ACKNOWLEDGMENTS

Despite their importance as a biofuel production platform, only a very limited number of butanol-tolerant bacteria have been identified thus far. Here, we extensively explored butanol- and isobutanol-tolerant bacteria from various environmental samples. A total of 16 aerobic and anaerobic bacteria that could tolerate greater than 2.0% (vol/vol) butanol and isobutanol were isolated. A 16S rRNA gene sequencing analysis revealed that the isolates were phylogenetically distributed over at least nine genera: Bacillus , Lysinibacillus , Rummeliibacillus , Brevibacillus , Coprothermobacter , Caloribacterium , Enterococcus , Hydrogenoanaerobacterium , and Cellulosimicrobium , within the phyla Firmicutes and Actinobacteria . Ten of the isolates were phylogenetically distinct from previously identified butanol-tolerant bacteria. Two relatively highly butanol-tolerant strains CM4A (aerobe) and GK12 (obligate anaerobe) were characterized further. Both strains changed their membrane fatty acid composition in response to butanol exposure, i.e., CM4A and GK12 exhibited increased saturated and cyclopropane fatty acids (CFAs) and long-chain fatty acids, respectively, which may serve to maintain membrane fluidity. The gene ( cfa ) encoding CFA synthase was cloned from strain CM4A and expressed in Escherichia coli . The recombinant E. coli showed relatively higher butanol and isobutanol tolerance than E. coli without the cfa gene, suggesting that cfa can confer solvent tolerance. The exposure of strain GK12 to butanol by consecutive passages even enhanced the growth rate, indicating that yet-unknown mechanisms may also contribute to solvent tolerance. Taken together, the results demonstrate that a wide variety of butanol- and isobutanol-tolerant bacteria that can grow in 2.0% butanol exist in the environment and have various strategies to maintain structural integrity against detrimental solvents.

In recent years, laser control of electrons in molecular system and condensed matter has attracted considerable attention with rapid progress in laser science and technology [. In particular, control of π-electron rotation in photo-induced chiral aromatic molecules has potential utility to the next-generation ultrafast switching devices. In this paper, we present a fundamental principle of generation of ultrafast coherent ring currents and the control in photo-induced aromatic molecules. This is based on quantum dynamics simulations of π-electron rotations and preparation of unidirectional angular momentum by ultrashort UV laser pulses properly designed. For this purpose, we adopt 2,5-dichloro [(3,6) pyrazinophane (DCPH) fixed on a surface, which is a real chiral aromatic molecule with plane chirality. Here π electrons can be rotated along the aromatic ring clockwise or counterclockwise by irradiation of a linearly polarized laser pulse with the properly designed photon polarization direction and the coherent ring current with the definite direction along the aromatic ring is prepared. This is contrast to ordinary ring current in an achiral aromatic ring molecule with degenerate electronic excited state, which is prepared by a circularly polarized laser [2]. In this case, π electrons rotate along the Z-axis of the laboratory coordinates, while for the present case electrons rotate along the z-axis in molecular Cartesian coordinates. It should be noted that signals originated from the coherent ring currents prepared by linearly polarized ultrashort UV lasers are specific to the chiral molecule of interest.

Levulinic acid (LA) is produced by the catalytic conversion of a variety of woody biomass. To investigate the potential use of desalting electrodialysis (ED) for LA purification, electrodialytic separation of levulinate from both reagent and cedar-derived LA solution (40-160 g L-1 ) was demonstrated. When using reagent LA solution with pH5.0-6.0, the recovery rates of levulinate ranged from 68 to 99%, and the energy consumption for recovery of 1 kg of levulinate ranged from 0.18 to 0.27 kWh kg-1 . With cedar-derived LA solution (pH6.0), good agreement in levulinate recovery (88-99%), and energy consumption (0.18-0.22 kWh kg-1 ) were observed in comparison to the reagent LA solutions, although a longer operation time was required due to some impurities. The application of desalting ED was favorable for promoting microbial utilization of cedar-derived LA. From 0.5 mol L-1 of the ED-concentrated sodium levulinate solution, 95.6% of levulinate was recovered as LA calcium salt dihydrate by crystallization. This is the first report on ED application for LA recovery using more than 20 g L-1 LA solutions (40-160 g L-1 ). © 2017 American Institute of Chemical Engineers Biotechnol. Prog., 33:448-453, 2017.

Burkholderia stabilis LA20W produces trehalose using levulinic acid (LA) as a substrate. Here, we report the 7.97-Mb draft genome sequence of B. stabilis LA20W, which will be useful in investigations of the enzymes involved in LA metabolism and the mechanism of LA-induced trehalose production.

Recently, molecular rotor systems have been emerging as a promising candidate of functional nanoscale devices. A macroscopic gyroscope like molecule in a crystalline solid is particularly unique owing to its variable physicochemical properties. Setaka et al. have achieved the synthesis of a novel crystalline molecular gyroscope characterized by a closed topology with a phenylene rotator encased in three long siloxaalkane spokes [Setaka, W.; et al. Chem. Lett.2007, 36, 1076]. We theoretically investigated the underlying mechanism of its rotational dynamics by utilizing the self-consistent-charge density-functional-based tight-binding (DFTB) method for crystal structures. We first found that the DFTB semiquantitatively reproduced the unit cell molecular geometries of all three stable X-ray structures under the periodic boundary condition. From the potential energy surface calculations, the activation barrier for phenylene rotation was estimated to be about 1.2 kcal/mol, which is much lower than those of oth...

The laser-polarization effects on nonadiabatically coupled π-electron rotation (ring current) and molecular vibration have been theoretically analyzed for aromatic molecules with quasi-degenerate excited states irradiated by an ultrashort laser pulse of arbitrary polarization. We first derived general formulations of the coherent electronic wave packet and expectation value of electronic angular momentum within a frozen-nuclei model. The relative quantum phase of the superposed quasi-degenerate states, which determines the oscillating behavior of angular momentum, can be manipulated by the ellipticity and orientation of the incident laser. Nuclear wave packet simulations with a model molecule confirmed the controllability of π-electron rotation, although the angular momentum is gradually reduced by nonadiabatic couplings. The amplitude of molecular vibration depends prominently on the orientation of linear polarization vectors rather than the helicity of circular polarization. The characteristic feature in vibrational amplitudes is attributed to the interference in nonadiabatic transition governed by the relative quantum phase between nuclear wave packets. This offers a new strategy for laser control of molecular vibrations through the wave packet interference in nonadiabatic transition.

Results of a theoretical study of ultrafast coherent dynamics of nonadiabatically coupled quasi-degenerate π -electronic excited states of molecules were presented. Analytical expressions for temporal behaviors of population and vibrational coherence were derived using a simplified model to clarify the quantum mechanical interferences between the two coherently excited electronic states, which appeared in the nuclear wavepacket simulations [M. Kanno, H. Kono, Y. Fujimura, S.H. Lin, Phys. Rev. Lett 104 (2010) 108302]. The photon-polarization direction of the linearly polarized laser, which controls the populations of the two quasi-degenerate electronic states, determines constructive or destructive interference. Features of the vibrational coherence transfer between the two coupled quasi-electronic states through nonadiabatic couplings are also presented. Information on both the transition frequency and nonadiabatic coupling matrix element between the two states can be obtained by analyzing signals of two kinds of quantum beats before and after transfer through nonadiabatic coupling.

Some 25 fungi, including at least 14 basidiomycetes, one ascomycete, and five anamorphic fungi were evaluated for their cellulose-degrading abilities in Difco potato dextrose broth or Difco malt extract broth cultures with cellulosic substrates (e.g., filter paper) in plastic Petri dishes. Among them, Peniophora sp. 06-13 and Phlebia sp. 99-335 reduced the dry weights of the whole cultures with these substrates more than the dry weights of the respective original substrates after 30 days of culture, showing definite cellulose degradation. In the cultures with more than 10 test fungi including Pycnoporus coccineus 84-117, such weight losses did not occur. This assay technique for the primary screening for cellulose degrading fungi is simple, inexpensive, reproducible and accurate.

Being motivated by the recent progress in attosecond laser technology, we theoretically explore the strategy of inducing ultrafast electron dynamics inherent to aromatic molecules, i.e., ring currents by means of polarized laser pulses. The main topic of discussion is how to control the direction of ring currents in an aromatic molecule of low symmetry, for which the design of an efficient control pulse cannot be achieved intuitively. We first consider a system with a single aromatic ring and show that coherent π-electron angular momentum, which oscillates with time, can be produced and controlled by a polarized laser pulse with its ellipticity and orientation properly chosen. Nonadiabatic couplings with molecular vibration gradually weaken the angular momentum, while the vibrational amplitude strongly depends on the polarization of incident light. This suggests the conversion of the polarization dependence of ring current into that of subsequent vibration, which may open a way to detect laser-driven ultrafast electron dynamics by vibrational spectroscopy. The laser-control scheme for the ring current is then extended to a molecule with two aromatic rings, which exhibits characteristic phenomena absent in that with a single ring. We demonstrate that two-dimensional switching of the direction of angular momentum is possible in such molecules. In addition, ring current can be localized at a specific ring by tailored lasers. The application of the present control method to polycyclic aromatic hydrocarbons will lead to the development of next-generation organic optical switching devices.

The dynamical behavior of H 2 + in near-infrared, intense laser fields (I > 1013 W/cm2 and λ > 700 nm) was discussed on the basis of the results of accurate electronic and nuclear wave packet propagation obtained by the application of the dual transformation method. Using “field-following” time-dependent adiabatic states defined as the eigenfunctions of the “instantaneous” electronic Hamiltonian including the dipole interaction with laser fields, we clarify the importance of the excited state dynamics in the ionization process. We also discuss the mechanism of ionization of H2 on the basis of the description of the multicofiguration time-dependent Hartree-Fock (MCTDHF) method.

High-affinity hydrogen (H2 )-oxidizing bacteria possessing group 5 [NiFe]-hydrogenase genes are important contributors to atmospheric H2 uptake in soil environments. Although previous studies reported the occurrence of a significant H2 uptake activity in vegetation, there has been no report on the identification and diversity of the responsible microorganisms. Here, we show the existence of plant-associated bacteria with the ability to consume atmospheric H2 that may be a potential energy source required for their persistence in plants. Detection of the gene hhyL - encoding the large subunit of group 5 [NiFe]-hydrogenase - in plant tissues showed that plant-associated high-affinity H2 -oxidizing bacteria are widely distributed in herbaceous plants. Among a collection of 145 endophytic isolates, seven Streptomyces strains were shown to possess hhyL gene and exhibit high- or intermediate-affinity H2 uptake activity. Inoculation of Arabidopsis thaliana (thale cress) and Oryza sativa (rice) seedlings with selected isolates resulted in an internalization of the bacteria in plant tissues. H2 uptake activity per bacterial cells was comparable between plant and soil, demonstrating that both environments are favourable for the H2 uptake activity of streptomycetes. This study first demonstrated the occurrence of plant-associated high-affinity H2 -oxidizing bacteria and proposed their potential contribution as atmospheric H2 sink.

We theoretically verified the participation of optically dark nπ* states other than S1 in ultrafast internal conversion of pyrazine. Contrary to a recent semiclassical study, our quantum dynamical calculations demonstrated that their contributions are negligible.

We have developed a method for describing the reaction dynamics of a polyatomic molecule in intense laser fields. First, the dynamical behavior of H2+ and H2 in near-infrared, intense laser fields ...

An obligately anaerobic bacterium, designated strain GK12T, was isolated from an anaerobic digester in Fukagawa, Hokkaido Prefecture, Japan. The cells of strain GK12Twere non-motile, non-spore-forming cocci that commonly occurred in chains. 16S rRNA gene sequence analysis revealed that strain GK12Twas affiliated with the familyErysipelotrichaceaein the phylumFirmicutesand showed 91.8 % sequence similarity to the most closely related species,Faecalicoccus acidiformans. The strain grew at 30–50 °C (optimally at 40 °C) and at pH 5.5–8.5 (optimally at pH 7.5). The main end product of glucose fermentation was lactate. Yeast extract was required for growth. The strain contained C14 : 0, C14 : 01,1-dimethoxyalkane (DMA), C16 : 0DMA and C18 : 0DMA as the major cellular fatty acids (>10 % of the total). The polar lipid profile was composed of phosphatidylglycerol, phosphatidylinositol and an unidentified phospholipid. The whole-cell sugars were galactose, rhamnose and ribose. The cell-wall murein contained alanine, glutamic acid, lysine, serine and threonine, but not diaminopimelic acid. The G+C content of the genomic DNA was 47.7 mol%. Based on phenotypic, phylogenetic and chemotaxonomic properties, a novel genus and species,Catenisphaera adipataccumulansgen. nov., sp. nov., is proposed to accommodate strain GK12T( = NBRC 108915T = DSM 25799T).

We theoretically investigated the mechanism of ultrafast nonradiative transition through conical intersections in photoexcited pyrazine by ab initio quantum dynamical calculations. This work was motivated by the recent theoretical and experimental studies that presented conflicting results: the former is the on-the-fly semiclassical surface hopping calculation combined with the time-dependent density functional theory, which showed that nonadiabatic transitions from the optically bright S2 ((1)B(2u), ππ*) state to the optically dark S3 ((1)A(u), nπ*) and S4 ((1)B(2g), nπ*) states take place predominantly at the initial stage of electronic relaxation [U. Werner et al., Chem. Phys., 2008, 349, 319]; the latter is the pump-probe photoelectron spectroscopic measurement, which reported the S2 lifetime (22 ± 3 fs) of nonradiative decay to the almost dark S1 ((1)B(3u), nπ*) state [Y.-I. Suzuki et al., J. Chem. Phys., 2010, 132, 174302]. We constructed adiabatic and diabatic potential energy surfaces of these ππ* and nπ* states using the multireference configuration interaction method and calculated their diabatic couplings within two-dimensional subspaces spanned by selected ground-state normal coordinates. Contrary to the surface hopping study, our nuclear wave packet simulations demonstrated that nonadiabatic transitions to the S3 and S4 states are so small that the conventional two-state (S1 and S2) picture is valid. Ultrafast internal conversion of pyrazine, which is deemed to proceed with a 22 fs lifetime, in fact consists of three consecutive steps: (i) the wave packet excited to the S2 state travels toward the S2-S1 conical intersection in 10 fs, (ii) the nonadiabatic transition to the S1 state progresses at a rapid rate corresponding to a transient lifetime of 7 fs, and (iii) intramolecular vibrational energy redistribution occurs in the S1 state in about 80 fs after optical excitation. To verify this prediction, time-resolved experiments with a resolution of several fs or shorter are desirable.

The present study was undertaken to examine the possible involvement of cortical gamma-aminobutyric acid (GABA) neuronal mechanisms in the regional differences of dopamine (DA) response to psychological stress: contextual fear conditioning (CFC) in the rat prefrontal cortex (PFC) and dorsolateral striatum (DLS). Rats that received five footshocks (shock intensity, 0.5 mA; shock duration, 2 sec) were subjected to CFC and dynamic changes in DA and GABA in both PFC and DLS were examined using dual-probe microdialysis. Extracellular levels of DA in the PFC were enhanced during exposure to CFC, whereas the levels in the DLS were not affected by this stimulus. Extracellular levels of GABA in the PFC, but not in the DLS, were markedly enhanced by CFC. Freezing behavior observed during exposure to CFC was attenuated by the GABA(A) receptor antagonist bicuculline (10(-3) M), which was perfused into the PFC. Intracortical application of bicuculline (10(-3) M) furthermore caused sustained increases in DA levels in the DLS by CFC. These data suggest that cortical GABA(A) receptors contribute to modulation of DA release in the DLS in response to CFC. Thus, the GABAergic neuronal system in the PFC appears to play a key role in the regional differences of the DAergic response to psychological stress.