Dimetal-Binding Scaffold 2-(Pyridin-2-yl)imidazo [1,5-b]pyridazine-7-ylidene: Synthesis of Trinuclear Heterobimetallic Complexes Involving Gold-Metal Interactions.

As a dimetal-binding rigid scaffold, 2-(pyridin-2-yl)imidazo[1,5-b]pyridazine-7-ylidene was introduced. The scaffold was first converted into a meridional Au,N,N-tridentate ligand through binding of a Au(I)Cl moiety at the carbene center. The Au(I) center and the N,N-chelating moiety were expected to function as metallophilic and 4e-σ-donative interaction sites, respectively, in the binding of the second metal center. In this manner, various trinuclear heterobimetallic complexes were synthesized with different 3d-metal sources, such as cationic CuI , CuII , NiII , and CoII salts. SC-XRD analysis showed that the mono-3d-metal di-gold(I) trinuclear heterobimetallic complexes were constructed through gold(I)-metal interactions. Metallophilic interactions were also investigated by quantum chemical calculations including the AIM and IGMH methods.

Nonylphenol reduced the number of haploids in in vitro spermatogenesis of the endangered cyprinid Gnathopogon caerulescens.

Nonylphenol (NP), an endocrine disrupting chemical, is widely used in industrial and agricultural processes, causing NP influx into aquatic environments. NP induces hormonal imbalance, and male feminization, and reduces germ cell production during spermatogenesis; however, the mechanism by which it affects spermatogenesis remains unknown. Here, we investigated the effect of NP on spermatogenesis in honmoroko (Gnathopogon caerulescens), an endangered fish endemic to Lake Biwa, Japan, using an in vitro differentiation system. We collected spermatogonia from the testes of non-spawning G. caerulescens and subjected them to suspension culture. The spermatogonia differentiated into flagellated spermatozoa in 3 weeks, regardless of the presence of NP. NP concentrations as low as 1 nM caused a decrease in the number of germ cells in a dose-dependent manner, whereas the number of somatic cells decreased only at a high concentration of 1 µM. Flow cytometric analysis revealed that the decrease in germ cell number was attributed to haploids (spermatids and spermatozoa); the number of spermatogonia and spermatocytes was not affected by NP treatment. This result is consistent with the hypothesis that NP might repress the second meiosis or induce apoptosis in haploids. This study demonstrated that the combination of in vitro germ cell differentiation and flow cytometric analysis is useful for evaluating the direct effects of NP on germ cell differentiation in endangered endemic fish.

Multi-state Energy Landscape for Photoreaction of Stilbene and Dimethyl-stilbene.

We have recently developed the reaction space projector (ReSPer) method, which constructs a reduced-dimensionality reaction space uniquely determined from reference reaction paths for a polyatomic molecular system and projects classical trajectories into the same reaction space. In this paper, we extend ReSPer to the analysis of photoreaction dynamics and relaxation processes of stilbene and present the concept of a "multi-state energy landscape," incorporating the ground- and excited-state reaction subspaces. The multi-state energy landscape successfully explains the previously established photoreaction processes of cis-stilbene, such as the cis-trans photoisomerization and photocyclization. In addition, we discuss the difference in the excited-state reaction dynamics between stilbene and 1,1'-dimethyl stilbene based on a common reaction subspace determined from the framework part of reference structures with different number of atoms. This approach allows us to target any molecule with a common framework, greatly expanding the applicability of the ReSPer analysis. The multi-state energy landscape provides fruitful insight into photochemical reactions, exploring the excited- and ground-state potential energy surfaces, as well as comprehensive reaction processes with nonradiative transitions between adiabatic states, within the stage of a reduced-dimensionality reaction space.

Reaction Space Projector (ReSPer) for Visualizing Dynamic Reaction Routes Based on Reduced-Dimension Space.

To analyze chemical reaction dynamics based on a reaction path network, we have developed the "Reaction Space Projector" (ReSPer) method with the aid of the dimensionality reduction method. This program has two functions: the construction of a reduced-dimensionality reaction space from a molecular structure dataset, and the projection of dynamic trajectories into the low-dimensional reaction space. In this paper, we apply ReSPer to isomerization and bifurcation reactions of the Au5 cluster and succeed in analyzing dynamic reaction routes involved in multiple elementary reaction processes, constructing complicated networks (called "closed islands") of nuclear permutation-inversion (NPI) isomerization reactions, and elucidating dynamic behaviors in bifurcation reactions with reference to bundles of trajectories. Interestingly, in the second application, we find a correspondence between the contribution ratios in the ability to visualize and the symmetry of the morphology of closed islands. In addition, the third application suggests the existence of boundaries that determine the selectivity in bifurcation reactions, which was discussed in the phase space. The ReSPer program is a versatile and robust tool to clarify dynamic reaction mechanisms based on the reduced-dimensionality reaction space without prior knowledge of target reactions.

Visualization of reaction route map and dynamical trajectory in reduced dimension.

In the quantum chemical approach, chemical reaction mechanisms are investigated based on a potential energy surface (PES). Automated reaction path search methods enable us to construct a global reaction route map containing multiple reaction paths corresponding to a series of elementary reaction processes. The on-the-fly molecular dynamics (MD) method provides a classical trajectory exploring the full-dimensional PES based on electronic structure calculations. We have developed two reaction analysis methods, the on-the-fly trajectory mapping method and the reaction space projector (ReSPer) method, by introducing a structural similarity to a pair of geometric structures and revealed dynamic aspects affecting chemical reaction mechanisms. In this review, we will present the details of these analysis methods and discuss the dynamics effects of reaction path curvature and reaction path bifurcation with applications to the CH3OH + OH- collision reaction and the Au5 cluster branching and isomerization reactions.

Randomized Controlled Trial of Simple Salt Reduction Instructions by Physician for Patients with Type 2 Diabetes Consuming Excessive Salt.

Objectives: We verified the clinical usefulness of an approach method in which a physician gives simple salt reduction instructions during outpatient visits to patients with type 2 diabetes. Methods: This study was an open-blind, randomized controlled trial. Subjects were outpatients with type 2 diabetes whose estimated salt intake using spot morning urine sample exceeded the target of salt intake. The control group (CG) was notified only of the current salt intake, whereas the intervention group (IG) was given the brief salt reduction instruction by a physician in addition to the information regarding their current salt intake. Results: The change in estimated salt intake was -0.6 g (from 10.1 to 9.5 g, p = 0.029) in the CG after 8 weeks, and -0.9 g (from 10.1 to 9.2 g, p = 0.001) in the IG, although there were no significant differences between them (p = 0.47). After 24 weeks, both groups no longer differed significantly from the baseline. In addition, multivariate linear regression analyses indicated that high salt intake and low estimated glomerular filtration rate at baseline were significantly associated with salt reduction after 8 weeks. Conclusions: Salt-reducing effects were observed after 8 weeks in both the IG and CG, but no significant difference was observed. Moreover, patients with high salt intake and renal disfunction may be more effective in accepting salt reduction instructions. Making patients aware of the importance of salt reduction through a physician is effective for continuous salt reduction, and it is important to continue regular and repetitive guidance.

Visualization of the Dynamics Effect: Projection of on-the-Fly Trajectories to the Subspace Spanned by the Static Reaction Path Network.

Following our recent work to reduce a dimension of a set of reference structures along the intrinsic reaction coordinate (IRC) by a classical multidimensional scaling (CMDS) approach (J. Chem. Theory Comput. 2018, 14, 4263-4270), we propose the method to project on-the-fly trajectories into a reduced-dimension subspace determined by the IRC network, using the out-of-sample extension of CMDS. The method was applied to the SN2 reaction, OH- + CH3F, in which trajectories show a bifurcating nature around the highly curved region of the IRC path, and to the structural transformation of Au5 cluster in which the global reaction path network consists of five equilibrium structures and 14 IRCs. It was demonstrated that the present analysis can visualize the dynamics effect by showing a dynamic reaction route on the basis of the static reaction paths.

Transcriptome analysis revealed bisphenol A and nonylphenol affect reproduction.

Effects of endocrine disrupting chemicals (EDCs) on reproduction have not been fully explained comprehensively. In this study, we tried to validate the common effect of Bisphenol A (BPA) and Nonylphenol (NP) on the differentiation of embryonic stem (ES) cells and found that they modify the expression of germ cell specific genes. To elucidate functional significance on biological process, we performed Gene Ontology (GO)-based microarray analysis comparing with published GeneChip data of primordial germ cell development in vivo. Cluster analysis of gene expression profile revealed that EDC treatment and primordial germ cell (PGC) development shared characteristic cluster consists of GO terms related to "germ cell development" and "reproduction". In the GO term "reproduction", meiosis related genes showed high expression level by EDC exposure. These results suggest that BPA and NP affect not only some of the germ cell specific genes, but functionally interferes germ cell development and reproduction.

Visualization of the Intrinsic Reaction Coordinate and Global Reaction Route Map by Classical Multidimensional Scaling.

A classical multidimensional scaling (CMDS) method is employed to visualize an intrinsic reaction coordinate (IRC) and a global reaction route map consisting of the equilibrium minima and transition state structures connected by the IRC network. As demonstrations, the method was applied to the IRCs of the intramolecular proton transfer in malonaldehyde and the SN2 reaction of OH- + CH3F → CH3OH + F-, which are both well described by two principal coordinates. Next, the method was applied to the global reaction route map of the Au5 cluster; the resulting map shows appropriate positions of five minima and 14 transition states in a reduced 2- or 3-dimensional coordinate space successfully.

Analyses of trajectory on-the-fly based on the global reaction route map.

A methodology to analyze a trajectory on-the-fly (TOF) based on a global reaction route map consisting of intrinsic reaction coordinate (IRC) pathways is proposed. By using the distance functions in the configurational space, the location of each point on the trajectories is detected, providing a dynamical picture that the molecular system goes over several minima and transition states in the reaction path network. In its application to structural transformations of an Au5 cluster, a variety of reaction routes are obtained, and the hopping from one IRC to another IRC (IRC-jump) is analyzed. The branching of trajectories over many minima on the potential energy surface via valley-ridge transition points is also discussed.

Fundamental peak disappears upon binding of a noble gas: a case of the vibrational spectrum of PtCO in an argon matrix.

Anharmonic vibrational state calculations were performed for PtCO and Ar-PtCO via the direct vibrational configuration interaction (VCI) method based on CCSD(T) energies and CCSD dipole moments at tens of thousands of grids, to get insights into the anomalous effect of a solid argon matrix on the vibrational spectra of PtCO. It was shown that, through the binding of Ar to PtCO via a strong van der Waals interaction, the Pt-C-O bending fundamental level drastically loses the infrared intensity although the corresponding overtone band shows a relatively large intensity. The origin of this phenomenon was analyzed based on the dipole moment surfaces and electron densities around the equilibrium structure. The present computations have solved the inconsistency between the gas-phase and the matrix-isolation experiments for PtCO.

Implementation and performance of the artificial force induced reaction method in the GRRM17 program.

This article reports implementation and performance of the artificial force induced reaction (AFIR) method in the upcoming 2017 version of GRRM program (GRRM17). The AFIR method, which is one of automated reaction path search methods, induces geometrical deformations in a system by pushing or pulling fragments defined in the system by an artificial force. In GRRM17, three different algorithms, that is, multicomponent algorithm (MC-AFIR), single-component algorithm (SC-AFIR), and double-sphere algorithm (DS-AFIR), are available, where the MC-AFIR was the only algorithm which has been available in the previous 2014 version. The MC-AFIR does automated sampling of reaction pathways between two or more reactant molecules. The SC-AFIR performs automated generation of global or semiglobal reaction path network. The DS-AFIR finds a single path between given two structures. Exploration of minimum energy structures within the hypersurface in which two different electronic states degenerate, and an interface with the quantum mechanics/molecular mechanics method, are also described. A code termed SAFIRE will also be available, as a visualization software for complicated reaction path networks. © 2017 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.

Nontotally symmetric trifurcation of an SN 2 reaction pathway.

A new type of reaction pathway which involves a nontotally symmetric trifurcation was found and investigated for a typical SN 2-type reaction, NC(-) + CH3 X → NC-CH3 + X(-) (X = F, Cl). A nontotally symmetric valley-ridge inflection (VRI) point was located along the C3 v reaction path. For X = F, the minimum energy path (MEP) starting from the transition state (TS) leads to a second-order saddle point with C3v symmetry, which connects three product minima of Cs symmetry. For X = Cl, four product minima have been observed, of which three belong to Cs symmetry and one to C3v symmetry. The branching path from the VRI point to the lower symmetry minima was determined by a linear interpolation technique. The branching mechanism is discussed based on the reaction path curvature and net atomic charges, and the possibility of a nonotally symmetric n-furcation is discussed.

Response to "Comment on 'Analyses of bifurcation of reaction pathways on a global reaction route map: A case study of gold cluster Au5"' [J. Chem. Phys. 143, 177101 (2015)].

The existence of a valley-ridge transition (VRT) point along the intrinsic reaction coordinate does not always indicate the existence of two minima in the product side, but VRT is a sign of bifurcating nature of dynamical trajectories running on the potential energy surface. It is demonstrated by molecular dynamics simulations.

Analyses of bifurcation of reaction pathways on a global reaction route map: a case study of gold cluster Au5.

A global reaction route map is generated for Au5 by the anharmonic downward distortion following method in which 5 minima and 14 transition states (TSs) are located. Through vibrational analyses in the 3N - 7 (N = 5) dimensional space orthogonal to the intrinsic reaction coordinate (IRC), along all the IRCs, four IRCs are found to have valley-ridge transition (VRT) points on the way where a potential curvature changes its sign from positive to negative in a direction orthogonal to the IRC. The detailed mechanisms of bifurcations related to the VRTs are discussed by surveying a landscape of the global reaction route map, and the connectivity of VRT points and minima is clarified. Branching of the products through bifurcations is confirmed by ab initio molecular dynamics simulations starting from the TSs. A new feature of the reaction pathways, unification, is found and discussed.

Vibrational shifts of HXeCl in matrix environments.

The hybrid quantum-classical simulations are performed to investigate the unusual vibrational spectral shifts of a noble-gas hydride HXeCl in matrix environments (in Ne, Ar, Kr, and Xe matrixes). The high-level ab initio calculations at the CCSD(T) level are employed to construct interaction potential energy surfaces between HXeCl and noble-gas atoms (Ne, Ar, Kr, and Xe). The configurations of noble-gas atoms are sampled by the Monte Carlo simulations and the vibrational levels of HXeCl in the presence of the surrounding noble-gas atoms are solved by the DVR approach. It is found that the H-Xe stretching frequencies are blue-shifted from the isolated gas-phase value in all matrix environments and that the relative blue shifts are in good agreement with the experimental results (Ne < Xe < Kr), demonstrating that the explicit treatment of matrix environments around HXeCl is essential to reproduce the observed unusual vibrational shifts.

Response to fish specific reproductive hormones and endocrine disrupting chemicals of a Sertoli cell line expressing endogenous receptors from an endemic cyprinid Gnathopogon caerulescens.

Fish Sertoli cells play a critical role in spermatogenesis by mediating androgen and progestogen signaling. Their hormonal response, however, considerably differ among species. Therefore it would be ideal to use Sertoli cells originated from the fish of interest to investigate the effects of hormones as well as endocrine disrupting chemicals (EDCs). The aim of this study was to investigate the responses to reproductive hormones and EDCs of a Sertoli cell line that we established from an endemic cyprinid Gnathopogon caerulescens. As the Sertoli cell line expressed endogenous androgen and progestogen receptors, we were able to detect hormone responses by transfecting only a reporter vector (pGL4.36) expressing luciferase under the control of the mouse mammary tumor virus-long terminal repeat (MMTV-LTR) promoter into the cell line. Unlike previous reporter gene assays using fish steroid hormone receptors expressed in mammalian cell lines, luciferase activities were induced by the fish specific androgen (11-ketotestosterone) and progestogen (17α,20ß-dihydroxy-4-pregnen-3-one), but not by testosterone and progesterone, at physiologically relevant concentrations. Furthermore, we found 4-nonylphenol (NP) but not bisphenol A showed strong anti-androgenic effects, implying that NP may have direct anti-androgenic effects on fish Sertoli cells in vivo. This is the first evidence, to the best of our knowledge, of anti-androgenic effects of NP in a fish Sertoli cell line. In addition, neither NP nor BPA showed anti-progestogenic effects. These results suggest that the Sertoli cell line established from the fish of interest can be a useful in vitro tool for investigating the mechanisms of reproductive hormones and EDCs in the specific fish.

Risk factor analysis of vasovagal reaction from blood donation.

BACKGROUND: Vasovagal reaction (VVR) is the most frequent side effect at blood collection sites. AIMS: To protect donors, factors contributing to VVR were analysed. MATERIALS AND METHODS: Complications following whole blood and apheresis donations have been recorded and accumulated by the Japanese Red Cross Tokyo Blood Centre. A dataset of 43,948 donors who had no complications was prepared as a control by randomly selecting days in each season in the 2006 and 2007 fiscal years. Factors contributing to 4924 VVR incidents in the 2006 and 2007 fiscal years were analysed by univariate and multivariate logistic regression. RESULTS: The age, weight, body mass index (BMI), predonation systolic and diastolic pressure, and circulating blood volume were lower, and the pulse was higher, for the VVR group compared to the control group (p<0.0001). The VVR group had more female donors, less sleep, and more time since a meal than the control. In multivariate analysis, significant risk factors for 400 ml whole blood donors, which are the majority of donors, were an age <50 years, being female, a BMI <25, pulse ≥90/min, sleep duration <8 h, the time after eating ≥4 h, a first time donation and circulating blood volume of <4.3 l. Sleep duration of <6 h was shown to be a VVR risk as much as a first time donation. CONCLUSION: From our analysis, the amount of sleep obtained the previous night should be considered at the reception of donors.

Competing effects of rare gas atoms in matrix isolation spectroscopy: a case study of vibrational shift of BeO in Xe and Ar matrices.

We investigate the vibrational shift of beryllium oxide (BeO) in Xe matrix as well as in Ar matrix environments by mixed quantum-classical simulation and examine the origin of spectral shift in details. BeO is known to form strong chemical complex with single rare gas atom, and it is predicted from the gas phase calculations that vibrational frequencies are blueshifted by 78 cm(-1) and 80 cm(-1) upon formation of XeBeO and ArBeO, respectively. When the effects of other surrounding rare gas atoms are included by Monte Carlo simulations, it is found that the vibrational frequencies are redshifted by 21 cm(-1) and 8 cm(-1) from the isolated XeBeO and ArBeO complexes, respectively. The vibrational shift of XeBeO in Ar matrix is also calculated and compared with experimental data. In all simulations examined in this paper, the calculated vibrational frequency shifts from the isolated BeO molecule are in reasonable agreement with experimental values. The spectral shift due to the rare-gas-complex formation of RgBeO (Rg = Xe or Ar) is not negligible as seen in the previous studies, but it is shown in this paper that the effects of other surrounding rare gas atoms should be carefully taken into account for quantitative description of the spectral shifts and that these two effects are competing in vibrational spectroscopy of BeO in matrix environments.

NtPolI-like1 and NtPolI-like2, bacterial DNA polymerase I homologs isolated from BY-2 cultured tobacco cells, encode DNA polymerases engaged in DNA replication in both plastids and mitochondria.

Two cDNAs encoding homologs of bacterial DNA polymerase I were isolated from cultured tobacco (Nicotiana tabacum) BY-2 cells, and the corresponding genes were named NtPolI-like1 and NtPolI-like2. High sequence similarity suggested that they are orthologous genes each derived from respective parental species of N. tabacum, an allotetraploid plant. Each of the NtPolI-like1/2 gene products had a putative transit peptide for plastid localization at the N-terminus, followed by a 3'-5' exonuclease domain in the internal region, and a DNA polymerase domain in the C-terminal region. Among family A DNA polymerases, NtPolI-like proteins formed, together with other plant DNA polymerase I homologs, a phylogenetic group distinct from mitochondrial DNA polymerase gamma in animals and fungi, as well as eukaryotic cell nuclear-localized repair enzymes. In contrast to computer predictions, experiments with green fluorescent protein (GFP) fusion protein and Western blotting analysis suggested dual targeting of the gene products to both plastids and mitochondria. The recombinant NtPolI-like2 protein exhibited DNA polymerase activity in vitro. Their biochemical character roughly coincided with those of the 116 kDa DNA polymerases found in the plastid and mitochondrial nuclei (nucleoids) isolated from BY-2 cells. Pre-treatment of the organelle nuclear extracts with anti-NtPolI-like antibody removed most of the DNA polymerase activity. Reverse transcription-PCR (RT-PCR) and Western blotting analyses demonstrated transient activation of NtPolI-like gene expression in the initial phase of cell proliferation, exactly when the 116 kDa DNA polymerases in the isolated organelle nuclei were activated and preferential synthesis of organelle DNAs occurred. Taken together, our results suggest that NtPolI-like1/2 genes encode DNA polymerases engaged in DNA replication in both plastids and mitochondria.