Does the Symbiotic Relationship Between Hydra Viridissima and Photoautotrophic Alga Provide an Evolutionary Advantage in Protecting DNA against Damage by the Cytotoxic or Genotoxic Mode of Action of Environmental Stressors?

The aim of this paper was to evaluate whether symbiotic cooperation between green hydra (Hydra viridissima) and photoautotrophic alga gives higher resistance of the preservation of DNA integrity compared to brown hydra (Hydra oligactis). Norflurazon concentrations were 0.061 or 0.61 mg/L and UV-B light 254 nm, 0.023mWcm- 2 applied separately or simultaneously. By alkaline comet assay primary DNA damage was assessed and cytotoxicity by fluorescent staining. Norflurazon at 0.61 mg L- 1 significantly increased DNA damage in brown hydras compared to the control (6.17 ± 0.6 µm, 5.2 ± 1.7% vs. 2.9 ± 0.2 µm, 1.2 ± 0.2%). Cytotoxicity was significantly elevated, being higher in brown hydras (25.7 ± 3.5% vs. 8.2 ± 0.2%). UV-B irradiation induced significant DNA damage in brown hydras (13.5 ± 1.0 µm, 4.1 ± 1.0%). Simultaneous exposure to UV-B and norflurazon led to a synergistic DNA damaging. The frequency of cytotoxicity and hedgehog nucleoids was more pronounced in brown (78.3 ± 9.4%; 56.4 ± 6.0%) than in green hydras (34.7 ± 2.5%; 24.2 ± 0.6%). Evolutionary established symbiotic cooperation proved to provide resistance against cyto/genotoxicity.

Expansion of multicenter Coulomb integrals in terms of two-center integrals.

Three- and four-center Coulomb integrals in the solid spherical harmonic Gaussian basis are solved by expansion in terms of two-center integrals. The two-electron Gaussian product rule, coupled with the addition theorem for solid spherical harmonics, reduces four-center Coulomb integrals into a linear combination of two-center Coulomb integrals and one-center overlap integrals. With this approach, three- and four-center Coulomb integrals can be reduced to the same form of two-center integrals. Resulting two-center Coulomb integrals can be further simplified into a simpler form, which can be related to the Boys function. Multi-center Coulomb integrals are solved hierarchically: simple two-center Coulomb integrals are used for calculation of more complicated two-center Coulomb integrals, which are used in the calculation of multicenter integrals.

Gaussian product rule for two-electron wave functions.

The Gaussian product rule for two-electron wave functions is introduced. The two-electron Gaussian product rule enables a new way for solving two-electron integrals. The solution is demonstrated with an example of the two-center two-electron integral in solid harmonic Gaussian basis. The solution is obtained by expanding inverse inter-electron separation and integrating in spherical coordinates. The resulting integral separates into four integrals, three of which are straightforward to solve. The remaining integral can be solved with Boys-like functions. It is demonstrated that the solution can deliver results with accuracy comparable with that of the McMurchie-Davidson scheme.

OpenMolcas: From Source Code to Insight.

In this Article we describe the OpenMolcas environment and invite the computational chemistry community to collaborate. The open-source project already includes a large number of new developments realized during the transition from the commercial MOLCAS product to the open-source platform. The paper initially describes the technical details of the new software development platform. This is followed by brief presentations of many new methods, implementations, and features of the OpenMolcas program suite. These developments include novel wave function methods such as stochastic complete active space self-consistent field, density matrix renormalization group (DMRG) methods, and hybrid multiconfigurational wave function and density functional theory models. Some of these implementations include an array of additional options and functionalities. The paper proceeds and describes developments related to explorations of potential energy surfaces. Here we present methods for the optimization of conical intersections, the simulation of adiabatic and nonadiabatic molecular dynamics, and interfaces to tools for semiclassical and quantum mechanical nuclear dynamics. Furthermore, the Article describes features unique to simulations of spectroscopic and magnetic phenomena such as the exact semiclassical description of the interaction between light and matter, various X-ray processes, magnetic circular dichroism, and properties. Finally, the paper describes a number of built-in and add-on features to support the OpenMolcas platform with postcalculation analysis and visualization, a multiscale simulation option using frozen-density embedding theory, and new electronic and muonic basis sets.

Reactions in silicon-nitrogen plasma.

Reaction mechanisms that lead to creation of silicon-nitrogen bonds are studied in detail. These reactions are of fundamental importance for silicon nitride synthesis by plasma enhanced chemical vapour deposition from the gas mixture of silane (SiH4) and ammonia (NH3). All reactions in SiH4-NH3 plasma can be categorised as some of the basic types of reactions: bond dissociation, neutral nucleophilic substitution, radical neutralisation, neutral-radical addition, silylene addition, silylene rearrangement, radical nucleophilic addition or hydrogen abstraction reaction. Energetics of these reactions is analysed in detail for a great number of reactions belonging to these categories, by using theoretical modelling. Geometry optimisations are carried out with the MP2/aug-cc-pVTZ level of theory and energetics is further determined with high level ab initio calculations at the CASPT2/aug-cc-pVTZ level, which enabled confirmation of relevance of several mechanisms as reactions that lead to silicon nitride growth from plasma enhanced chemical vapour deposition, as well as introduction of new, energetically favourable mechanisms. Besides amine radical assisted eliminative addition and proton transfer reactions, silylene addition reactions are thermodynamically and kinetically favourable since they lack energy barriers. A new reaction pathway for synthesis of silicon nitride from plasma is proposed. This pathway is enabled by the ability of silylene to create two weak dative bonds, which enables silylene-amine complexes to stick to the silicon nitride surface. Upon dissociation of amine from the surface-bound complex, silylene remains on the surface, available for reaction with other reactive species from plasma.

Atmospheric oxidation of halogenated aromatics: comparative analysis of reaction mechanisms and reaction kinetics.

Atmospheric transport is the major route for global distribution of semi-volatile compounds such as halogenated aromatics as well as their major exposure route for humans. Their major atmospheric removal process is oxidation by hydroxyl radicals. There is very little information on the reaction mechanism or reaction-path dynamics of atmospheric degradation of halogenated benzenes. Furthermore, the measured reaction rate constants are missing for the range of environmentally relevant temperatures, i.e. 230-330 K. A series of recent theoretical studies have provided those valuable missing information for fluorobenzene, chlorobenzene, hexafluorobenzene and hexachlorobenzene. Their comparative analysis has provided additional and more general insight into the mechanism of those important tropospheric degradation processes as well as into the mobility, transport and atmospheric fate of halogenated aromatic systems. It was demonstrated for the first time that the addition of hydroxyl radicals to monohalogenated as well as to perhalogenated benzenes proceeds indirectly, via a prereaction complex and its formation and dynamics have been characterized including the respective transition-state. However, in fluorobenzene and chlorobenzene reactions hydroxyl radical hydrogen is pointing approximately to the center of the aromatic ring while in the case of hexafluorobenzene and hexachlorobenzene, unexpectedly, the oxygen is directed towards the center of the aromatic ring. The reliable rate constants are now available for all environmentally relevant temperatures for the tropospheric oxidation of fluorobenzene, chlorobenzene, hexafluorobenzene and hexachlorobenzene while pentachlorophenol, a well-known organic micropollutant, seems to be a major stable product of tropospheric oxidation of hexachlorobenzene. Their calculated tropospheric lifetimes show that fluorobenzene and chlorobenzene are easily removed from the atmosphere and do not have long-range transport potential while hexafluorobenzene seems to be a potential POP chemical and hexachlorobenzene is clearly a typical persistent organic pollutant.

Atmospheric oxidation of hexachlorobenzene: New global source of pentachlorophenol.

Hexachlorobenzene is highly persistent, bioaccumulative, toxic and globally distributed, a model persistent organic pollutant. The major atmospheric removal process for hexachlorobenzene is its oxidation by hydroxyl radicals. Unfortunately, there is no information on the reaction mechanism of this important atmospheric process and the respective degradation rates were measured in a narrow temperature range not of environmental relevance. Thus, the geometries and energies of all stationary points significant for the atmospheric oxidation of hexachlorobenzene are optimized using MP2/6-311G(d,p) method. Furthermore, the single point energies were calculated with G3 method on the optimized minima and transition-states. It was demonstrated for the first time that the addition of hydroxyl radicals to hexachlorobenzene proceeds indirectly, via a prereaction complex. In the prereaction complex the hydroxyl radical is almost perpendicular to the aromatic ring while oxygen is pointing to its center. In contrast, in the transition state it is nearly parallel with the aromatic ring. The reliable rate constants are calculated for the first time for the atmospheric oxidation of hexachlorobenzene for all environmentally relevant temperatures. It was also demonstrated for the first time that pentachlorophenol is the major stable product in the addition of hydroxyl radicals to hexachlorobenzene and that atmosphere seems to be a new global secondary source of pentachlorophenol.

Waveguide design parameters impact on absorption in graphene coated silicon photonic integrated circuits.

In this paper, we propose a new way of estimating the absorption in graphene coated silicon wire waveguides based on a self-developed, modified 2D Finite Difference Method, and use it to obtain a detailed absorption dependency of the waveguide design. For the first time, we observe peaks in the TM mode absorption curves, as well as the reversals of the dominantly absorbed mode with waveguide design variation, both of which have not been predicted previously theoretically, but have been implied through experimental results. We also provide a qualitative explanation of our novel numerical results, and explain how these results can be utilized in optimization of various graphene based integrated devices like optical modulators, photodetectors and optical polarizers.

Algal endosymbionts in European Hydra strains reflect multiple origins of the zoochlorella symbiosis.

Symbiotic associations are of broad significance in evolution and biodiversity. Green Hydra is a classic example of endosymbiosis. In its gastrodermal myoepithelial cells it harbors endosymbiotic unicellular green algae, most commonly from the genus Chlorella. We reconstructed the phylogeny of cultured algal endosymbionts isolated and maintained in laboratory conditions for years from green Hydra strains collected from four different geographical sites within Croatia, one from Germany and one from Israel. Nuclear (18S rDNA, ITS region) and chloroplast markers (16S, rbcL) for maximum likelihood phylogenetic analyses were used. We focused on investigating the positions of these algal endosymbiotic strains within the chlorophyte lineage. Molecular analyses established that different genera and species of unicellular green algae are present as endosymbionts in green Hydra, showing that endosymbiotic algae growing within green Hydra sampled from four Croatian localities are not monophyletic. Our results indicate that the intracellular algal endosymbionts of green Hydra have become established several times independently in evolution.

The effects of CaCl2 and CaBr2 on the reproduction of Daphnia magna Straus.

Concentrated CaCl2 and CaBr2 salt solutions of densities up to 2.3 kg L-1 are regularly used to control hydrostatic pressure in oil wells during special operations in the exploration and production of natural gas and crude oil. Various concentrations of high density salts are frequently left in mud pits near the drilling site as waste, polluting fresh and ground waters by spillage and drainage. The toxic effects of these salts have already been observed. This study investigated the effects of CaCl2 and CaBr2 on water flea Daphnia magna Straus in a 21-day reproduction test. The three tested concentrations of CaCl2 (240, 481, and 1925 mg L-1) caused a significant dose-response decrease of reproduction (p<0.001). With CaBr2 (533 and 1066 mg L-1), only aborted eggs were produced, demonstrating the embryotoxicity of the substance. The results suggest that high concentrations of the tested chemicals are harmful to Daphnia's reproduction and could reduce its abundance.

Luscus: molecular viewer and editor for MOLCAS.

The novel program for graphical display and editing of molecular systems, luscus, is described. The program allows fast and easy building and/or editing different molecular structures, up to several thousands of atoms large. Luscus is able to visualise dipole moments, normal modes, molecular orbitals, electron densities and electrostatic potentials. In addition, simple geometrical objects can be rendered in order to reveal a geometrical feature or a physical quantity. The program is developed as a graphical interface for the MOLCAS program package, however its adaptive nature makes possible to use luscus with other computational program packages and chemical formats. All data files are opened via simple plug-ins which makes easy to implement a new file format in luscus. The easiness of editing molecular geometries makes luscus suitable for teaching students chemical concepts and molecular modelling. Graphical AbstractScreenshot of luscus program showing molecular orbital.

The exploration of hydrogen bonding properties of 2,6- and 3,5-diethynylpyridine by IR spectroscopy.

Hydrogen bonding properties of 2,6- and 3,5-diethynylpyridine were analyzed by exploring of their interactions with trimethylphosphate, as hydrogen bond acceptor, or phenol, as hydrogen bond donor, in tetrachloroethene C2Cl4. The employment of IR spectroscopy enabled unravelling of their interaction pattern as well as the determination of their association constants (Kc) and standard reaction enthalpies (ΔrH(⦵)). The association of diethynylpyridines with trimethylphosphate in stoichiometry 1:1 is established through CH⋯O hydrogen bond, accompanied by the secondary interaction between CC moiety and CH3 group of trimethylphosphate. In the complexes with phenol, along with the expected OH⋯N interaction, CC⋯HO interaction is revealed. In contrast to 2,6-diethynylpyridine where the spatial arrangement of hydrogen bond accepting groups enables the simultaneous involvement of phenol OH group in both OH⋯N and OH⋯CC hydrogen bond, in the complex between phenol and 3,5-diethynylpyridine this is not possible. It is postulated that cooperativity effects, arisen from the certain type of resonance-assisted hydrogen bonds, contribute the stability gain of the latter. Associations of diethynylpyridines with trimethylphosphate are characterized as weak (Kc≈0.8-0.9mol(-1)dm(3); -ΔrH(⦵)≈5-8kJmol(-1)), while their complexes with phenol as medium strong (Kc≈5mol(-1)dm(3); -ΔrH(⦵)≈15-35kJmol(-1)). Experimental findings on the studied complexes are supported with the calculations conducted at B3LYP/6-311++G(d,p) level of theory in the gas phase. Two conformers of diethynylpyridine⋯trimethylphosphate dimers are formed via CH⋯O interaction, whereas dimers between phenol and diethynylpyridines are established through OH⋯N interaction.

The study of secondary effects in vibrational and hydrogen bonding properties of 2- and 3-ethynylpyridine and ethynylbenzene by IR spectroscopy.

Weak hydrogen bonds formed by 2- and 3-ethynylpyridine and ethynylbenzene with trimethylphosphate and phenol were characterized by IR spectroscopy and DFT calculations (B3LYP/6-311++G(d, p)). The structure and stability of ethynylpyridines and ethynylbenzene in the gas phase and in the complexes with trimethylphosphate and phenol are discussed in terms of geometry and electronic charge redistribution. Anharmonic effects are taken into account when calculating vibrational wavenumbers of these systems what lead to partial improvement of agreement with experiment. The changes in the electronic charge distribution are behind the frequency shifts of the CC stretching in opposite direction depending on the role the ethyne molecule has in a hydrogen bonded complex (Δν̃=+9 cm(-1) in trimethylphosphate complexes, Δν̃=-3 cm(-1) in phenol complexes). The association constants were determined by keeping the concentrations of proton donors approximately constant and low enough to avoid self-association and the proton acceptors were present in excess. The values obtained for the association constants and enthalpy changes in C2Cl4 (for trimethylphosphate complexes K≈0.5-1.0 mol(-1)dm(3) and -ΔrH≈6-8 kJ mol(-1), for phenol complexes K≈20-40 mol(-1) dm3-ΔrH≈17-22 kJ mol(-1)) are in good agreement with literature data.

Behavioral, morphological and histopathological effects of sublethal doses of quercetin on the species Polycelis felina (Dalyell).

The effect of quercetin was studied on the multi-eyed flatworm Polycelis felina (Daly.) in laboratory conditions. This is a very suitable test-organism available year-round in nature, easily maintained in the laboratory. The results showed that depending on the dose and recovery period quercetin caused locomotory (behavioral) changes in treated animals including aggregation in groups, resting and unsynchronized movements and twisting of particular body parts. Morphological changes in the form of depigmentation of certain body parts were the result of damage or deterioration ofreticular and parenchymal cells. Numerous basophilic bodies representing parts of damaged and decomposed cells were determined in the gastroderm between the third and seventh day after treatment. All histological preparations revealed significant deterioration of cellular material, and therefore a damaging effect of quercetin on the multi-eyed flatworm Polycelis felina (Daly.). We found an increased number of neoblasts and reticular cells on the third day after treatment, so we concluded that quercetin in the applied doses had a stimulating effect on cell division of neoblasts and reticular cells of treated flatworms.

Mechanisms and reaction-path dynamics of hydroxyl radical reactions with aromatic hydrocarbons: the case of chlorobenzene.

All geometries and energies significant for the first step of tropospheric degradation of chlorobenzene were characterized using the MP2/6-31+G(d,p) and G3 methods. A pre-reaction complex for the addition of OH radical to chlorobenzene was found and the associated transition state was determined for the first time. The reaction path for the association of OH radical and chlorobenzene into the pre-reaction complex was extrapolated from the selected low frequency normal mode of pre-reaction complex. The reaction rate constant for addition of OH radical to chlorobenzene was determined for the temperature range 230-330K, using RRKM theory and G3 energies. The calculated rate constants are in agreement with the experimental results. Regioselectivity was also determined for the title reaction from the ratio of respective reaction rates and our results are in very good agreement with the experimental results, which show the dominance of the ortho and para channels as well as a negligible contribution by the ipso channel.

Theoretical study on the mechanism and kinetics of addition of hydroxyl radicals to fluorobenzene.

Geometries, frequencies, reaction barriers, and reaction rates were calculated for the addition of OH radical to fluorobenzene using Möller-Plesset second-order perturbation (MP2) and G3 methods. Four stationary points were found along each reaction path: reactants, prereaction complex, transition state, and product. A potential for association of OH radical and fluorobenzene into prereaction complex was calculated, and the associated transition state was determined for the first time. G3 calculations give higher reaction barriers than MP2, but also a significantly deeper prereaction complex minimum. The rate constants, calculated with Rice-Ramsperger-Kassel-Marcus (RRKM) theory using G3 energies, are much faster and in much better agreement with the experiment than those calculated with MP2 method, as the deeper well favors the formation of prereaction complex and also increases the final relative populations of adducts. The discrepancies between the experimental and calculated rate constants are attributed to the errors in calculated frequencies as well as to the overestimated G3 reaction barriers and underestimated prereaction complex well depth. It was possible to rectify those errors and to reproduce the experimental reaction rates in the temperature range 230-310 K by treating the relative translation of OH radical and fluorobenzene as a two-dimensional particle-in-the-box approximation and by downshifting the prereaction complex well and reaction barriers by 0.7 kcal mol(-1). The isomeric distribution of fluorohydroxycyclohexadienyl radicals is calculated from the reaction rates to be 30.9% ortho, 22.6% meta, 38.4% para, and 8.3% ipso. These results are in agreement with experiment that also shows dominance of ortho and para channels.

Value of the Hydra model system for studying symbiosis.

Green Hydra is used as a classical example for explaining symbiosis in schools as well as an excellent research model. Indeed the cosmopolitan green Hydra (Hydra viridissima) provides a potent experimental framework to investigate the symbiotic relationships between a complex eumetazoan organism and a unicellular photoautotrophic green algae named Chlorella. Chlorella populates a single somatic cell type, the gastrodermal myoepithelial cells (also named digestive cells) and the oocyte at the time of sexual reproduction. This symbiotic relationship is stable, well-determined and provides biological advantages to the algal symbionts, but also to green Hydra over the related non-symbiotic Hydra i.e. brown hydra. These advantages likely result from the bidirectional flow of metabolites between the host and the symbiont. Moreover genetic flow through horizontal gene transfer might also participate in the establishment of these selective advantages. However, these relationships between the host and the symbionts may be more complex. Thus, Jolley and Smith showed that the reproductive rate of the algae increases dramatically outside of Hydra cells, although this endosymbiont isolation is debated. Recently it became possible to keep different species of endosymbionts isolated from green Hydra in stable and permanent cultures and compare them to free-living Chlorella species. Future studies testing metabolic relationships and genetic flow should help elucidate the mechanisms that support the maintenance of symbiosis in a eumetazoan species.

2-(4-Amino-phen-yl)-3,4,5,6-tetra-hydro-pyrimidin-1-ium chloride.

In the title compound, C(10)H(14)N(3) (+)·Cl(-), the tetra-hydro-pyridinium ring of the cation, which adopts a slightly distorted envelope conformation, is disordered over two orientations with an occupancy ratio of 0.653 (5):0.347 (5). The amidinium fragment of the major conformer is twisted relative to the benzene ring by 22.5 (6)° and the two C-N bond lengths of this fragment are similar [1.3228 (16) and 1.319 (2) Å]. In the crystal, the chloride anions are involved in three N-H⋯Cl hydrogen bonds, which link the components into a two-dimensional hydrogen-bonded network parallel to (010).

Fragmentation of diamide derivatives of 3,4-ethylenedioxythiophene.

The sequential product ion (MS(n)) fragmentation of four symmetric diamide derivatives of 3,4-ethylenedioxythiophene were characterized using ion trap mass spectrometry with electrospray ionization and their fragmentation patterns were studied. The experimental data consists of mass spectra obtained by tandem mass spectrometry, and calculations were obtained by the M06-2X/6-31 G (d,p) method. Investigated compounds represent building blocks in synthesis of compounds used in different areas of chemistry and industry such as in medicinal chemistry, as potential anticancer and anticonvulsant agents, in organic chemistry as linkers for solid-phase synthesis, and in the synthesis of a variety of materials in polymer chemistry. We present herein the investigation of the fragmentation pathway of protonated diamide derivatives of 3,4-ethylenedioxythiophene that involves the identification of fragments, influence of proton transfer on direction of fragmentation and mechanisms of reactions by which the fragmentation process occurs. Data obtained from product ion spectra of these protonated compounds and density functional theory (DFT) calculations indicate that the fragmentation process takes place via four main reactions: amido-iminol proton transfer, reverse cycloaddition, cleavage of the amide bond, and isocyanic acid elimination. The 3,4-ethylenedioxythiophene-2,5-dicarboxamide was observed as an intermediate in the fragmentation of its alkyl derivatives. To our knowledge, this work brings the first correct description of the mechanism of elimination of isocyanic acid.