Highly Efficient Intramolecular Proton Transfer in p-Aminobenzoic Acid by a Single Ammonia Molecule as a Vehicle.

Proton transfer is classified into two mechanisms: the Grotthuss (proton-relay) and vehicle mechanisms. It has been well studied on gas-phase proton transfer by a proton relay involving multiple molecules. However, a vehicle mechanism in which a single molecule transports a proton has rarely been reported. Here, we have obtained clear evidence that the proton transfers efficiently between the two protonation sites in protonated p-aminobenzoic acid (PABA·H+) by a single ammonia molecule as a vehicle. The gaseous PABA·H+ ions were reacted with NH3 or ND3 under single-collision conditions in a cold ion trap, and the proton-transferred ions were identified by cryogenic ion mobility-mass spectrometry. A reaction intermediate PABA·H+·NH3 was also detected for the first time. The reaction pathway search calculations and ab initio molecular dynamics simulations supported the present experimental finding that intramolecular proton transfer occurs very efficiently by the vehicle mechanism.

A Structure-Based Gaussian Expansion for Quantum Reaction Dynamics in Molecules: Application to Hydrogen Tunneling in Malonaldehyde.

We developed an approximate method for quantum reaction dynamics simulations, namely, a structure-based Gaussian (SBG) expansion approach, where SBG bases for the expansion of the wave function Ψ, expressed by a product of single-atom Cartesian Gaussians centered at the positions of respective nuclei, are mainly placed around critical structures on reaction pathways such as on the intrinsic reaction coordinate (IRC) through a transition state. In the present approach, the "pseudo-lattice points" at which SBGs are deployed are selected in a perturbative manner so as to make moderate the expansion length. We first applied the SBG idea to a two-dimensional quadruple-well model and obtained accurate tunneling splitting values between the lowest four states. We then applied it to hydrogen tunneling in malonaldehyde and achieved a tunneling splitting of 27.1 cm-1 with only 875 SBGs at the MP2/6-31G(d,p) level of theory, in good agreement with 25 cm-1 by the more elaborate multiconfiguration time-dependent Hartree method. Reasonable results were also obtained for singly and doubly deuterated malonaldehyde. We analyzed the tunneling states by utilizing expansion coefficients of individual SBGs and found that 40-45% of the SBGs in Ψ are nonplanar structures and SBGs away from the IRC contribute a little to hydrogen transfer.

Identification of an ultrafast internal conversion pathway of pyrazine by time-resolved vacuum ultraviolet photoelectron spectrum simulations.

The internal conversion from the optically bright S2 (1B2u, ππ*) state to the dark S1 (1B3u, nπ*) 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 S3 (1Au, nπ*) and S4 (1B2g, nπ*) to the decay of S2. We have previously reported the results of nuclear wave packet simulations [Kanno et al., Phys. Chem. Chem. Phys. 17, 2012 (2015)] and photoelectron spectrum calculations [Mignolet et al., 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 S2 to S1. The present results reproduce almost all the characteristic features of the corresponding experimental time-resolved spectrum [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 (S2 → S1) of ultrafast internal conversion in pyrazine.

Ultrafast Ring-Opening Reaction of 1,3-Cyclohexadiene: Identification of Nonadiabatic Pathway via Doubly Excited State.

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.

A fast and robust trajectory surface hopping method: Application to the intermolecular photodissociation of a carbon dioxide dimer cation (CO2)2.

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.

N-terminal deletion of Swi3 created by the deletion of a dubious ORF YJL175W mitigates protein burden effect in S. cerevisiae.

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.

Capturing the photo-induced dynamics of nano-molecules by X-ray free electron laser induced Coulomb explosion.

We performed reaction dynamics simulations to demonstrate that the vibrational dynamics of C60 induced by infrared (IR) pulses can be traced by triggering Coulomb explosion with intense femtosecond X-ray free electron laser (XFEL) probe pulses. The time series of the angular anisotropy ß(t) of fast C+ and C2+ fragments of C60 60+ produced by such an XFEL pulse reflects the instantaneous structure of C60 vibrationally excited by IR pulses. The phases and amplitudes of excited vibrational modes and the coupling between excited modes can be successfully extracted from the expansion of ß(t) in terms of vibrational modes. This proof-of-principle simulation clearly demonstrates that various information of the structures and reaction dynamics of large clusters or biomolecules can be retrieved by decomposing the experimentally determined ß(t) into vibrational modes.

Identification and characterization of levulinyl-CoA synthetase from Pseudomonas citronellolis, which differs phylogenetically from LvaE of Pseudomonas putida.

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.

Real-time observation of X-ray-induced intramolecular and interatomic electronic decay in CH2I2.

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.

Diffractive Imaging of C_{60} Structural Deformations Induced by Intense Femtosecond Midinfrared Laser Fields.

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.

Visible photodissociation of the CO2 dimer cation: fast and slow dissociation dynamics in the excited state.

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 ßfast = 1.52 ± 0.14 and ßslow = 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.

Draft Genome Sequence of Pseudomonas citronellolis LA18T, a Bacterium That Uses Levulinic Acid.

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.

An efficient approximate algorithm for nonadiabatic molecular dynamics.

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.

Single-active-electron analysis of laser-polarization effects on atomic/molecular multiphoton excitation.

We theoretically explore the effects of optical ellipticity on single-active-electron multiphoton excitation in atoms and (nearly) spherical molecules irradiated by intense polarized laser fields. This work was motivated by the experimental and theoretical studies of Hertel et al. [Phys. Rev. Lett. 102, 023003 (2009) and Phys. Rev. A 79, 053414 (2009)], who reported pronounced changes in the near-infrared-induced ion yields of xenon and C60 as a function of ellipticity (in particular, yield reduction for circular polarization) at low light intensities and derived a perturbative cross section formula to describe such polarization effects by assuming that the excited-state energies and radial transition electric dipole moments of the system are independent of the azimuthal quantum number l. First, by reformulating the N-photon absorption cross section of a single active electron, we prove that their assumptions reduce the network of optically allowed transition pathways into what we call the "Pascal triangle" consisting of (N + 1) (N + 2)/2 states only. Next, nonperturbative analytical and numerical solutions of the time-dependent Schrödinger equation for a simple model of two-photon excitation are presented not only in the low-intensity regime but also in the high-intensity regime. The results show that the determining factor of ellipticity-dependent multiphoton excitation probability is transition moment magnitudes and that the detailed energetic structure of the system also becomes important at high intensities. The experimentally observed flattening of the ion yields of xenon and C60 with increasing intensity can be explained without a saturation effect, which was previously deemed to be responsible for it. We also argue the applicability range of the cross section formula by Hertel et al. and the identity of the "doorway state" for ionization of C60.

Ultrafast Coulomb explosion of a diiodomethane molecule induced by an X-ray free-electron laser pulse.

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.

Electrodialytic separation of levulinic acid catalytically synthesized from woody biomass for use in microbial conversion.

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.

Draft Genome Sequence of Burkholderia stabilis LA20W, a Trehalose Producer That Uses Levulinic Acid as a Substrate.

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.

Detection and isolation of plant-associated bacteria scavenging atmospheric molecular hydrogen.

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.

pH-induced change in cell susceptibility to butanol in a high butanol-tolerant bacterium, Enterococcus faecalis strain CM4A.

BACKGROUND: Though butanol is considered as a potential biofuel, its toxicity toward microorganisms is the main bottleneck for the biological butanol production. Recently, butanol-tolerant bacteria have been proposed as alternative butanol production hosts overcoming the end product inhibition. One remaining key issue to be addressed is how physicochemical properties such as pH and temperature affect microbial butanol tolerance during cultivation and fermentation. RESULTS: We investigated the pH effect on butanol tolerance of a high butanol-tolerant bacterium, Enterococcus faecalis strain CM4A. The strain grew over a broad pH range (pH 4.0 to 12.0) and preferred alkaline pH (pH 8.0 and 10.0) in the absence of butanol. However, in the presence of butanol, strain CM4A grew better under acidic and neutral pH conditions (pH 6.0 and 6.8). Membrane fatty acid analysis revealed that the cells exposed to butanol exhibited increased cyclopropane and saturated fatty acids, which contribute to butanol tolerance of the strain by decreasing membrane fluidity, more evidently at acidic and neutral pH than at alkaline pH. Meanwhile, the strain grown under alkaline pH without butanol increased short chain fatty acids, which is involved in increasing membrane fluidity for alkaline adaptation. Such a change was not observed in the cells grown under alkaline pH with butanol. These results suggested that strain CM4A simultaneously exposed to butanol and alkali stresses was not likely able to properly adjust membrane fluidity due to the opposite response to each stress and thereby showed low butanol tolerance under alkaline pH. Indeed, the cells exposed to butanol at alkaline pH showed an irregular shape with disrupted membrane structure under transmission electron microscopy observation, which also indicated the impact of butanol and alkali stresses on functioning of cellular membrane. CONCLUSION: The study clearly demonstrated the alkaline pH-induced increase of cell susceptibility to butanol in the tested strain. Our findings indicate the non-negligible impact of pH on microbial butanol tolerance, providing a new insight into efficient butanol production.

Catenisphaera adipataccumulans gen. nov., sp. nov., a member of the family Erysipelotrichaceae isolated from an anaerobic digester.

An obligately anaerobic bacterium, designated strain GK12(T), was isolated from an anaerobic digester in Fukagawa, Hokkaido Prefecture, Japan. The cells of strain GK12(T) were non-motile, non-spore-forming cocci that commonly occurred in chains. 16S rRNA gene sequence analysis revealed that strain GK12(T) was affiliated with the family Erysipelotrichaceae in the phylum Firmicutes and 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 : 0 1,1-dimethoxyalkane (DMA), C16 : 0 DMA and C18 : 0 DMA 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 adipataccumulans gen. nov., sp. nov., is proposed to accommodate strain GK12(T) ( = NBRC 108915(T) = DSM 25799(T)).