Diatom Systems Research Articles

Noncovalently bound molecular complexes beyond diatom-diatom systems: full-dimensional, fully coupled quantum calculations of rovibrational states.

The methodological advances made in recent years have significantly extended the range and dimensionality of noncovalently bound, hydrogen-bonded and van der Waals, molecular complexes for which full-dimensional and fully coupled quantum calculations of their rovibrational states are feasible. They exploit the unexpected implication that the weak coupling between the inter- and intramolecular rovibrational degrees of freedom (DOFs) of the complexes has for the ease of computing the high-energy eigenstates of the latter. This is done very effectively by using contracted eigenstate bases to cover both intra- and intermolecular DOFs. As a result, it is now possible to calculate rigorously all intramolecular rovibrational fundamentals, together with the low-lying intermolecular rovibrational states, of complexes involving two small molecules beyond diatomics, binary polyatomic molecule-large (rigid) molecule complexes, and endohedral complexes of light polyatomic molecules confined inside (rigid) fullerene cages. In this Perspective these advances are reviewed in considerable depth. The progress made thanks to them is illustrated by a number of representative applications. Whenever possible, direct comparison is made with the available infrared, far-infrared, and microwave spectroscopic data.

Rethinking the description of water product in polyatomic OH/OD + XH (X ≡ D, Br, NH2 and GeH3) reactions: theory/experimental comparison

Davis’ group and Setser’s group using different experimental techniques measured water vibrational distribution for OH/OD + XH → H2O/HOD + X hydrogen abstraction reactions (X ≡ D, Br, NH2, GeH3). Theoretically, this issue has been studied by several groups: different potential energy surfaces (PESs) have been developed for each system, and quasi-classical trajectory (QCT) and quantum mechanics (QM) calculations have been performed. However, important experimental/theoretical controversies still exist. In the present work, we have revisited and performed new kinetics and dynamics calculations, comparing the theoretical and experimental results on the same footing. In general, theoretical results reproduce reasonably well experimental rate constants and total vibrational energy released to water, ~ 50–60%, although they underestimate water bending excitation. In the present work, we analyse different causes of this theory/experiment discrepancy and propose different mechanisms to explain the water bending excitation for diatom–diatom and polyatomic systems. Finally, we reflect on the ability of QCT and QM calculations to provide reasonable (although not quantitative) predictions for polyatomic reactions and observe that even using full-dimensional QM calculations on very accurate PESs, agreement with the experiment is far from that reached in the case of triatomic systems.

Using a marine microalga as a chassis for polyethylene terephthalate (PET) degradation

BackgroundThe biological degradation of plastics is a promising method to counter the increasing pollution of our planet with artificial polymers and to develop eco-friendly recycling strategies. Polyethylene terephthalate (PET) is a thermoplast industrially produced from fossil feedstocks since the 1940s, nowadays prevalently used in bottle packaging and textiles. Although established industrial processes for PET recycling exist, large amounts of PET still end up in the environment—a significant portion thereof in the world’s oceans. In 2016, Ideonella sakaiensis, a bacterium possessing the ability to degrade PET and use the degradation products as a sole carbon source for growth, was isolated. I. sakaiensis expresses a key enzyme responsible for the breakdown of PET into monomers: PETase. This hydrolase might possess huge potential for the development of biological PET degradation and recycling processes as well as bioremediation approaches of environmental plastic waste.ResultsUsing the photosynthetic microalga Phaeodactylum tricornutum as a chassis we generated a microbial cell factory capable of producing and secreting an engineered version of PETase into the surrounding culture medium. Initial degradation experiments using culture supernatant at 30 °C showed that PETase possessed activity against PET and the copolymer polyethylene terephthalate glycol (PETG) with an approximately 80-fold higher turnover of low crystallinity PETG compared to bottle PET. Moreover, we show that diatom produced PETase was active against industrially shredded PET in a saltwater-based environment even at mesophilic temperatures (21 °C). The products resulting from the degradation of the PET substrate were mainly terephthalic acid (TPA) and mono(2-hydroxyethyl) terephthalic acid (MHET) estimated to be formed in the micromolar range under the selected reaction conditions.ConclusionWe provide a promising and eco-friendly solution for biological decomposition of PET waste in a saltwater-based environment by using a eukaryotic microalga instead of a bacterium as a model system. Our results show that via synthetic biology the diatom P. tricornutum indeed could be converted into a valuable chassis for biological PET degradation. Overall, this proof of principle study demonstrates the potential of the diatom system for future biotechnological applications in biological PET degradation especially for bioremediation approaches of PET polluted seawater.

To the creation of diatom system on the basis of molecular and morphological data

Main problems for creation of diatom system on the basis of morphological and molecular methods are discussed.

Silicon consumption in two shallow-water sponges with contrasting biological features

There is growing awareness that to improve the understanding of the biological control of silicon (Si) cycling in the oceans, the biogeochemical models need to incorporate Si users other than diatoms. In the last decades, siliceous sponges are coming into sight as important Si users, but the scarce quantitative information on how they use Si is hindering the assessment of their role. We are here investigating Si consumption kinetics in two demosponge species (Tethya citrina and Hymeniacidon perlevis) that have contrasting biological features while inhabiting at the same sublittoral habitat. In laboratory experiments, we have determined that both species share some common traits when incorporating Si from seawater: (1) saturable Michaelis-Menten kinetics; (2) maximum velocity of Si consumption occurring at high silicic acid (DSi) concentrations (∼150 μM) that are not available in shallow waters of the modern oceans; (3) the ability to increase consumption rates rapidly and predictably in response to increasing DSi availability; and (4) half-saturation constants that indicate an affinity for DSi lower than those of diatom systems. Across the four sponge species investigated to date, the affinity for DSi varies about 4.5 times. Our results also suggest that at least part of that between-species variability reflects the skeletonization level of the species. Within a given species, there are also between-individual differences in the DSi demand, which appear to reflect the particular physiological condition of each individual (i.e., body size, reproductive vs. non-reproductive stage).

How to define a diatom genus? Notes on the creation and recognition of taxa, and a call for revisionary studies of diatoms

AbstractWe highlight the increase in the number of diatom genera being described, and suggest that their description be based on the concept of monophyly. That is, a new genus will contain the ancestor and all its descendants. Past criteria or guidance on how to circumscribe genera are reviewed and discussed, with conceptual and actual exemplars presented. While there is an increase in the rate of genus descriptions in diatoms, and there are many journal and series dedicated to facilitating this important activity, we call for revisionary works on diatom groups, to assess and establish monophyletic groups at all levels of hierarchy in the diatom system.

Design and implementation of a Grid application for direct calculations of reactive rates

A detailed description of a new hybrid computational machinery devoted to the semiclassical direct calculation of atom–diatom reaction rate coefficients implemented on the production computing Grid of European Grid Infrastructures is given. Related validation and performance tests are reported and discussed. State to state reactive scattering computational results obtained for the N+N2 atom–diatom system are compared with those obtained using a HPC cluster.

Comparison of the multi-configuration, time-dependent Hartree (MCTDH) method with the Arthurs and Dalgarno coupled-channel method for rotationally inelastic scattering

Calculations of rotationally inelastic scattering at thermal energies for a model atom–diatom system have been performed using two completely different methodologies. The first method is the multi-configuration time-dependent Hartree (MCTDH) wave packet method, and the second is the well known, time-independent, Arthurs and Dalgarno coupled channel formalism. Excellent agreement is obtained between the two calculations. The advantages and drawbacks of these two methods are somewhat complementary, so that the decision to use one or the other approach will depend on what type of computational results are desired.

Cell to substratum and cell to cell interactions of microalgae

This paper reports the cell to substratum and cell to cell interactions of a diverse group of microalgae based on the Extended Derjaguin, Landau, Verwey, Overbeek (XDLVO) approach using the previously reported physico-chemical surface properties. The microalgae included 10 different species of green algae and diatoms from both freshwater and saltwater environments while the substrata included glass, indium-tin oxide (ITO), stainless steel, polycarbonate, polyethylene, and polystryrene. The results indicated that acid–base interactions were the dominating mechanism of interaction for microalgae. For green algae, if at least one of the interacting surfaces was hydrophobic, adhesion at primary minimum was predicted without any energy barrier. However, most diatom systems featured energy barriers for adhesion due to repulsive van der Waals interactions. The results reported in this study are expected to provide useful data and insight into the interaction mechanisms of microalgae cells with each other and with substrata for a number of practical applications including prevention of biofouling of photobioreactors and other man-made surfaces, promotion of biofilm formation in algal biofilm photobioreactors, and developing bioflocculation strategies for energy efficient harvesting of algal biomass. Particularly, Botryococcus braunii and Cerithiopsis fusiformis were identified as promising species for biofloccuation and biofilm formation in freshwater and saltwater aquatic systems, respectively. Finally, based on the observed trends in this study, use of hydrophilic algae and hydrophilic coatings over surfaces are recommended for minimizing biofouling in aquatic systems.

Maximum Limit of Rotational energy transfers in C2 - He system and Power gap law

Theoretical importance of the classical limit of the maximum rotational energy transfer, (∆E)max, it has been reviewed for a two dimensional hard ellipsoid potential model over a wide range of energies, reduced mass of the system. It has been found that (∆E)max, is comparable with a well-known parameter lΔEl * given by the two parameter Power- gap law. The numerical equivalence of (∆E)max and lΔEl * has been verified for different collision energy of the atom - diatom system. Such equivalence suggests that the value of (∆E)max can be used as one parameter lΔEl * of the power -gap law. The salient feature of the research helps to develop

Three-dimensional intermolecular potential energy surfaces of the Kr–OH complex

Pure rotational transitions of the Kr–OH van der Waals complex and its deuterated analog in the ground electronic state with resolved fine and hyperfine structures were observed by Fourier-transform microwave spectroscopy. Three-dimensional potential energy surfaces of Kr–OH, average V Π and difference V 2 potentials, were determined by a simultaneous analysis utilizing all the observed data for 82Kr–OH, 84Kr–OH, 86Kr–OH, and 84Kr–OD, where all the freedom of motions for an atom–diatom system in the Jacobi coordinates, R, θ, and r, were considered. The dependence of the intermolecular interaction energy on the bond length of the OH monomer is compared with those of Ar–OH and Ne–OH.

Landau-Zener Transitions in Frozen Pairs of Rydberg Atoms

We have induced adiabatic transitions in pairs of frozen Rydberg sodium atoms of a supersonic beam. The diatomic ns+ns-->np+(n-1)p transition takes place in a time-dependent electric field and originates from the adiabatic change of the internal state of the pair induced by the dipole-dipole interaction. This is experimentally achieved by sweeping an electric field across the energy degeneracy ns ns-np(n-1)p. Our results fully agree with a two-level Landau-Zener model in the diatom system.

GriF: A Grid framework for a Web Service approach to reactive scattering

Abstract Grid empowered calculations are becoming an important advanced tool indispensable for scientific advances. The possibility of simplifying and harmonizing the work carried out by computational scientists using a Web Service approach is considered here. To this end, a new Collaborative Grid Framework has been developed and tested. As a study case a three dimensional reactive scattering code dealing with atom–diatom systems has been considered. To this end an extended study of the energy dependence of the electronically adiabatic reactivity of N + N 2 has been performed on the EGEE Grid.

A study of the impact of long range interactions on the reactivity of N + N<SUB align=right>2 using the Grid Empowered Molecular Simulator GEMS

The Potential Energy Surface (PES) of the N + N2 atom diatom system has been reformulated using the Largest Angle Generalisation of the Rotating Bond Order (LAGROBO) functional form for interpolating ab initio points in the short distance region and using a modified Lennard-Jones functional form to model the van der Waals interaction at long range. On the proposed surface extended quantum calculations have been performed using the Dynamics module of the Grid Empowered Molecular Simulator (GEMS) on the European Grid platform. The values of the calculated thermal rate coefficients fairly well reproduce the experimental results.

Feshbach projection calculations of compound state resonances in atom-diatom scattering

The Feshbach projection operator formalism has been employed to calculate the energies of compound slate resonances in some collinear atom—diatom systems. Comparison with available close-coupled scattering calculations for the same systems shows the energies to lie within about ± Γ of the resonance centers. Beyond the preliminary results reported, the determination of the width Γp and energy shift Δp of each resonance is proposed using a method which makes the determination of all the parameters computationally self-contained. Extension to 2- and 3-dimensional systems is also suggested.

-related Quantum Interference of 2 [Case(a)] Diatom on Rotational Energy Transfer

To study theoretically the relationship between the integral interference angle and the scattering angle in collisional quantum interference, the integral interference angle of atom-2[case(a)] diatomic molecules system is described. To simulate the experiment theoretically, the theoretical model on collision-induced rotational energy transfer in an atom-2[case(a)]diatom system is presented based on the first order Born approximation taking into account of the long-range interaction potential. For the 2 electronic state in the Hund's case(a) diatom, the degree of the interference is discussed. The interference angles of collision-induced rotational energy transfer of CN(A2) in Hund's case(a) with He, Ne, and Ar are calculated quantitatively. The key parameters in the determination of integral interference angles are obtained.

Quantum mechanical limits to the control of atom–diatom chemical reactions through the polarisation of the reactants

This article considers the extent to which one can control the reactivity of atom-diatom systems through reactant polarisation. Three different limits for reactivity manipulation are defined: "absolute" limits that do not depend on the reaction dynamics but can only be obtained for particular combinations of quantum numbers, "unconstrained" limits that depend on dynamics but not on constraints imposed by any particular experimental setup, and "constrained" limits that depend on dynamics and also on the constraints imposed by a particular experimental setup. Methods for calculation of these limits are presented and applied to the benchmark F + H2 reaction. The variations of the maximum and minimum reactivity one can obtain are analysed in terms of reaction mechanisms and steric constraints. Tables listing the minimum and maximum values of angular momentum polarisation moments of rank up to 4, and integer and half-integer quantum numbers up to 5, are also presented.

The molecular Hamiltonian with two-rotational-angle embedding

Our approach for the derivation of the exact (non-relativistic) translational–rovibronic Hamiltonian, based on the Hamiltonian operator in tensor form, is now extended to cases in which a body-fixed frame is defined via the introduction of two Euler angles (two-rotational-angle embedding). Diatomic molecules and diatom–diatom systems are considered as examples for this general formulation. For comparison, the three-rotational-angle embedding version of the diatom–diatom Hamiltonian is also derived.

Collisional quantum interference on rotational energy transfer: physical interpretation of the differential interference angle

Collisional quantum interference (CQI) on the intramolecular rotational energy transfer is observed in an experiment with a static cell, and the integral interference angles are measured. To obtain more accurate information, an experiment with a molecular beam is carried out, and thereby the relationship between the differential interference angle and the scattering angle is obtained. Based on the first-Born approximation of time-dependent perturbation theory, the theoretical model of CQI is developed in an atom–diatom system in the condition of the molecular beam, with the long-range interaction potential taken into account. The method of measuring correctly the differential interference angle is presented. The tendencies of the differential interference angle changing with the impact parameter and relative velocity are discussed. The theoretical model presented here is important for understanding or performing the experiment in the molecular beam.

How Reactants Polarization Can Be Used to Change and Unravel Chemical Reactivity

This article presents theoretical methods for the description of the directional effect of reactant rotation on the reactivity of atom-diatom systems and suggests an experiment that could be used to test theoretical predictions. The theory can be used in conjunction with both quantum reactive scattering and quasiclassical trajectory calculations, and is stated in general terms, which allows it to deal with arbitrary reactant polarizations. The illustrative results obtained for the benchmark H + D2 reaction are also presented and show that under experimentally achievable conditions one can largely control reactive cross sections and product state distributions, while at the same time gaining valuable and at times surprising information on the reaction mechanism.