Scattering resonances in the rotational excitation of HDO by Ne and normal-H2: theory and experiment.

The rotational excitation of a singly deuterated water molecule (HDO) by a heavy atom (Ne) and a light diatomic molecule (H2) is investigated theoretically and experimentally in the near-threshold regime. Crossed-molecular-beam measurements with a variable crossing angle are compared to close-coupling calculations based on high-accuracy potential energy surfaces. The two lowest rotational transitions, 000 → 101 and 000 → 111, are probed in detail and a good agreement between theory and experiment is observed for both transitions in the case of HDO + Ne, where scattering resonances are however blurred out experimentally. In the case of HDO + H2, the predicted theoretical overlapping resonances are faithfully reproduced by experiment for the 000 → 111 transition, while the calculated strong signal for the 000 → 101 transition is not detected. Future work is needed to reconcile this discrepancy.

Quantum study of the rovibrational relaxation of HF by collision with 4He on a new potential energy surface.

The HF molecule is considered the main reservoir of fluorine in the interstellar medium (ISM). Also, the interactions of this molecule with the most common atoms and molecules in the ISM have attracted great interest from the astrochemical community. Collisions between HF and helium have recently caused controversy following a study using a two-dimensional SAPT potential energy surface (PES) that exhibited large discrepancies with previous scattering calculations based on more recent ab initio potentials. To address this issue, our current work aims to develop the most precise three-dimensional PES for the HF+He system. We employ the size-consistent CCSD(T) method in conjunction with the aug-cc-pV6Z basis set. The main features of the new PES as well as the bound states of the He-HF complex are compared to the existing data. The new PES is then utilised to conduct close coupling calculations that demonstrate He-HF as a good instance of vibration-rotation near resonant energy transfer. The novel rate coefficients will be accessible via the BASECOL database, and the use of the new PES is advised when describing HF in helium droplets.

A Rigid Bender Study of the Bending Relaxation of H2O and D2O by Collisions with Ar.

The bending relaxation of H2O and D2O by collisions with Ar is studied at the Close Coupling level. Two new 4D PES are developed for these two systems. They are tested by performing rigid rotor calculations as well as by computing the D2O-Ar bound states. The results are compared with available theoretical and experimental data. Propensity rules for the dynamics are discussed and compared to those of H2O colliding with Ne or He. The bending relaxation cross sections and rates are then calculated for these two systems. The results are analysed and compared with available experimental data.

A Comparative Study of the Cold Collisions of H2O and D2O with Ne.

The present work is dedicated to the first theoretical study of the rotationally inelastic collisions of Ne with H2O and its isotopologue D2O in an attempt to analyze the effect on the dynamics of H substitution by deuterium. To this aim two new potential energy surfaces are developed. Their quality is tested by computing the bound states of the complexes and comparing them with those most recently reported by other teams. System-specific collisional propensity rules are inferred for these two systems by analyzing the computed state-to-state cross sections at low and higher collision energy. The application of the Alexander parity index propensity rule is also discussed, and the present results are compared with those obtained for the collisions with other noble gases.

Hyperthermal Dynamics and Kinetics of the C(3P) + N2(X1Σg+) → CN(X2Σ+) + N(4S) Reaction.

The hyperthermal dynamics and kinetics of the title reaction, which plays an important role in hypersonic chemistry for atmospheric entry vehicles, are investigated using quasi-classical trajectory methods on a recently developed ground electronic state potential energy surface. The dynamics calculations indicated that the reaction follows a complex-forming mechanism, despite its large endoergicity. The calculated differential cross section is forward-backward symmetric, consistent with a long-lived reaction intermediate supported by the NCN potential well. The lifetime of the reaction complex is sufficiently long that the vibrational distribution of the CN product can be predicted by the phase space theory. The calculated vibrational state specific and thermal rate coefficients follow the Arrhenius behavior, and the agreement with existing low-temperature experimental thermal rate coefficients is satisfactory. Extrapolations to high temperatures relevant to hypersonic conditions are provided.

An explicitly correlated six-dimensional potential energy surface for the SiCSi + H2 complex.

The first six-dimensional potential energy surface (PES) for the SiCSi + H2 complex is presented in this work. This surface is developed from a large number of ab initio energies computed at the explicitly correlated coupled-cluster level of theory together with the augmented correlation-consistent polarized valence triple zeta basis set (CCSD(T)-F12/aug-cc-pVTZ). These energies are fitted to an analytical function through a procedure that combines spline, least-squares, and kernel-based methods. Two minimums of similar depths were found at the equilibrium geometry of the SiCSi molecule. The dependence of the PES on the bending angle is analyzed. Furthermore, a reduced four-dimensional PES averaged over the H2 orientation is presented. Finally, the six-dimensional PES is used for computing the second virial coefficient of the SiCSi + H2 pair using classical and semi-classical methods.

Study of the CN(X2Σ+) + N(4S) Reaction at High Temperatures: Potential Energy Surface and Thermal Rate Coefficients.

Reactions involving C and N play an essential role in the chemistry around the surface of a hypersonic spacecraft during its atmospheric re-entry. The collision of CN with other molecules and atoms has particular interest in aerothermodynamic modeling. This work focuses on the study of the CN + N → N2 + C reaction in the triplet manifold 3A″ of CN2. A high-level full-dimensional potential energy surface for this system is developed from ab initio calculations at the MRCI-F12 + Q level of theory. This surface is employed in quasiclassical trajectory calculations, and thermal rate coefficients from 100 to 20,000 K are computed. The rates for the formation of N2 are compared with the available experimental data, and good agreement is found. At low and intermediate temperatures, the N2 formation is more efficient than the N-exchange process, while at high temperatures, the rates for both processes are comparable. Finally, analytically modified Arrhenius expressions for the reaction rates of N2 formation and N-exchange are reported.

A close coupling study of the bending relaxation of H2O by collision with He.

We present a close coupling study of the bending relaxation of H2O by collision with He, taking explicitly into account the bending-rotation coupling within the rigid-bender close-coupling method. A 4D potential energy surface is developed based on a large grid of ab initio points calculated at the coupled-cluster single double triple level of theory. The bound states energies of the He-H2O complex are computed and found to be in excellent agreement with previous theoretical calculations. The dynamics results also compare very well with the rigid-rotor results available in the Basecol database and with experimental data for both rotational transitions and bending relaxation. The bending-rotation coupling is also demonstrated to be very efficient in increasing bending relaxation when the rotational excitation of H2O increases.

Rotational Transitions of HOC+ Induced by Collision with He at Low Temperatures.

The HOC+ molecule has for long been detected in several regions of the interstellar medium (ISM). The collisional ro-vibrational rate coefficients of this molecule with the most common colliders in the ISM are then required for applying nonlocal thermal equilibrium models. However, this molecule has a low bending frequency (249 cm-1), and the use of the rigid rotor approximation is therefore limited to low collision energies. Also, the complete determination of the ro-vibrational rate coefficients of HOC+ in collision with He requires including the bending motion in the analytical model of the potential energy surface (PES) of the system. The first goal of this work is then to develop the first rigid bender four-dimensional PES for the interaction between HOC+ and He. To this aim, a large grid of ab initio energies are computed at the CCSD(T)-F12b/aug-cc-pVQZ level of theory and an analytical representation of the PES is obtained using a combination of least square and reproducing kernel Hilbert space procedures. The global minimum of this PES is found to be reached for a linear configuration of the complex. In the second part of this study, rigid rotor close-coupling calculations are performed at low collision energy, and the calculated rate coefficients are compared to those previously determined for the collisions of He with its HCO+ isomer.

Rigid-Bender Close-Coupling Treatment of the Inelastic Collisions of H2O with para-H2.

We present a new method taking explicitly into account the coupling between rotation and bending of a nonlinear triatomic molecule colliding with an atom. This approach based on a rigid-bender treatment of the triatomic molecule was originally developed for the case of triatomic molecule linear at equilibrium. It is here extended to the case of a colliding bent triatomic molecule at equilibrium and applied to the case of the para-H2 + H2O inelastic collision using a new H2O-para-H2 adiabatically reduced 4D potential. The results of the method for purely rotational transitions are compared to those of rigid-rotor calculations while vibrational quenching rates of the first exited bending level are calculated for the first time at the close-coupling level.

A benchmark for the size of the QM system required for accurate hybrid QM/MM calculations on the metal site of the protein copper, zinc superoxide dismutase.

The protein superoxide dismutase 1 (SOD1) is a copper and zinc-binding protein that has been implicated in the pathogenesis of amyotrophic lateral sclerosis (ALS). The Zn(II) binding to SOD1 is critical for the stability of the protein, and has been by itself implicated in ALS pathogenesis. Hence, the quantum mechanical (QM) study of the Zn(II)-site of SOD1 is relevant for understanding ALS. The hybrid QM-molecular mechanics (QM/MM) approach commonly employed for the QM study of proteins is highly dependent on the size of the sub-system treated quantum-mechanically. The size of the QM system also determines the computational feasibility of a given method. In the present work, we compare optimized geometries for the metal site and Zn(II) dissociation energies obtained with a QM/MM methodology employing different sizes for the QM sub-system. We find that geometries converge rapidly to RMSDs of around 0.3 Å, and fails to converge further, while a QM system of 480 atoms was required for converging the Zn(II) interaction energy of SOD1 to within 5 kcal*mol-1, and a 611-atoms QM system for a 1 kcal*mol-1 convergence with respect to our reference, 1280 QM-atoms system. Graphical Abstract The size of the QM system is critical for both the accuracy and the computational cost of a QM/MM calculation. We have identified a optimum balance for the study of the active site of the coppper, zinc superoxide dismutase.

Quantum and quasiclassical trajectory studies of rotational relaxation in Ar-N2+ collisions.

The collision of N2+ with Ar is studied using quantum and classical methods. The dynamics was followed on a new potential energy surface based on ab initio energies computed at the UCCSD(T)-F12a/aug-cc-pVTZ level, using the correct analytical long range behaviour and a reproducing kernel representation. Comparison with multi-reference MRCI+Q calculations establish that UCCSD(T)-F12a is a sufficiently high level of theory for this problem. Results from quantum close coupling and quasiclassical trajectory calculations agree favourably with each other and the rates for inelastic collisions are lower than those from Langevin theory. This differs from previous calculations on a zero point-corrected potential energy surface (PES) and indicates that such corrections, although potentially useful, should not be applied in the present case. Despite the rather large differences between the potential energy surfaces, the computed rates are within one order of magnitude of one another which suggests that the quality of the PES is not the main reason for the remaining disagreement between computation and experiment. Also, the fraction of inelastic rotational collisions exceeds 20% in all cases irrespective of whether quantum or classical dynamics is used. Previous experimental rate coefficients for N2+(ν = 0, j = 6) colliding with Ar suggest that the rotational quantum number is largely conserved. This can not be confirmed from any of the simulations and calls for new single molecule experiments.

Communication: Vibrational relaxation of CO(1Σ) in collision with Ar(1S) at temperatures relevant to the hypersonic flight regime.

Vibrational energy relaxation (VER) of diatomics following collisions with the surrounding medium is an important elementary process for modeling high-temperature gas flow. VER is characterized by two parameters: the vibrational relaxation time τvib and the state relaxation rates. Here the vibrational relaxation of CO(ν=0←ν=1) in Ar is considered for validating a computational approach to determine the vibrational relaxation time parameter (pτvib) using an accurate, fully dimensional potential energy surface. For lower temperatures, comparison with experimental data shows very good agreement whereas at higher temperatures (up to 25 000 K), comparisons with an empirically modified model due to Park confirm its validity for CO in Ar. Additionally, the calculations provide insight into the importance of Δν>1 transitions that are ignored in typical applications of the Landau-Teller framework.

Reactive collisions for NO(2Π) + N(4S) at temperatures relevant to the hypersonic flight regime.

The NO(X2Π) + N(4S) reaction which occurs entirely in the triplet manifold of N2O is investigated using quasiclassical trajectories and quantum simulations. Fully-dimensional potential energy surfaces for the 3A' and 3A'' states are computed at the MRCI+Q level of theory and are represented using a reproducing kernel Hilbert space. The N-exchange and N2-formation channels are followed by using the multi-state adiabatic reactive molecular dynamics method. Up to 5000 K these reactions occur predominantly on the N2O 3A'' surface. However, for higher temperatures the contributions of the 3A' and 3A'' states are comparable and the final state distributions are far from thermal equilibrium. From the trajectory simulations a new set of thermal rate coefficients of up to 20 000 K is determined. Comparison of the quasiclassical trajectory and quantum simulations shows that a classical description is a good approximation as determined from the final state analysis.

Heavy metal levels in dune sands from Matanzas urban resorts and Varadero beach (Cuba): Assessment of contamination and ecological risks.

Concentrations of chromium (Cr), nickel (Ni), copper (Cu), zinc (Zn) and lead (Pb) in dune sands from six urban and suburban Matanzas (Cuba) resorts and Varadero beach were estimated by X-ray fluorescence analysis. Ranges of metal contents in dune sands show a strong variation across the studied locations (in mg/kg(-1)): 20-2964 for Cr, 17-183 for Ni, 17-51 for Cu, 18-88 for Zn and 5-29 for Pb. The values of contamination factors and contamination degrees how that two of the studied Matanzas's resorts (Judio and Chirry) are strongly polluted. The comparison with Sediment Quality Guidelines shows that dune sands from Judio resort represent a serious risk for humans, due to polluted Cr and Ni levels, while sands from the rest of the studied resorts, including Varadero beach, do not represent any risk for public use.

Rotational excitation of HCN by para- and ortho-H2.

Rotational excitation of the hydrogen cyanide (HCN) molecule by collisions with para-H2(j = 0, 2) and ortho-H2(j = 1) is investigated at low temperatures using a quantum time independent approach. Both molecules are treated as rigid rotors. The scattering calculations are based on a highly correlated ab initio 4-dimensional (4D) potential energy surface recently published. Rotationally inelastic cross sections among the 13 first rotational levels of HCN were obtained using a pure quantum close coupling approach for total energies up to 1200 cm(-1). The corresponding thermal rate coefficients were computed for temperatures ranging from 5 to 100 K. The HCN rate coefficients are strongly dependent on the rotational level of the H2 molecule. In particular, the rate coefficients for collisions with para-H2(j = 0) are significantly lower than those for collisions with ortho-H2(j = 1) and para-H2(j = 2). Propensity rules in favor of even Δj transitions were found for HCN in collisions with para-H2(j = 0) whereas propensity rules in favor of odd Δj transitions were found for HCN in collisions with H2(j ⩾ 1). The new rate coefficients were compared with previously published HCN-para-H2(j = 0) rate coefficients. Significant differences were found due the inclusion of the H2 rotational structure in the scattering calculations. These new rate coefficients will be crucial to improve the estimation of the HCN abundance in the interstellar medium.

Rovibrational energy transfer in the He-C3 collision: potential energy surface and bound states.

We present a four-dimensional potential energy surface (PES) for the collision of C3 with He. Ab initio calculations were carried out at the coupled-cluster level with single and double excitations and a perturbative treatment of triple excitations, using a quadruple-zeta basis set and mid-bond functions. The global minimum of the potential energy is found to be -26.9 cm(-1) and corresponds to an almost T-shaped structure of the van der Waals complex along with a slightly bent configuration of C3. This PES is used to determine the rovibrational energy levels of the He-C3 complex using the rigid monomer approximation (RMA) and the recently developed atom-rigid bender approach at the Close Coupling level (RB-CC). The calculated dissociation energies are -9.56 cm(-1) and -9.73 cm(-1), respectively at the RMA and RB-CC levels. This is the first theoretical prediction of the bound levels of the He-C3 complex with the bending motion.

Rotational relaxation of CS by collision with ortho- and para-H2 molecules.

Quantum mechanical investigation of the rotationally inelastic collisions of CS with ortho- and para-H2 molecules is reported. The new global four-dimensional potential energy surface presented in our recent work is used. Close coupling scattering calculations are performed in the rigid rotor approximation for ortho- and para-H2 colliding with CS in the j = 0-15 rotational levels and for collision energies ranging from 10(-2) to 10(3) cm(-1). The cross sections and rate coefficients for selected rotational transitions of CS are compared with the ones previously reported for the collision of CS with He. The largest discrepancies are observed at low collision energy, below 1 cm(-1). Above 10 cm(-1), the approximation using the square root of the relative mass of the colliders to calculate the cross sections between a molecule and H2 from the data available with (4)He is found to be a good qualitative approximation. The rate coefficients calculated with the electron gas model for the He-CS system show more discrepancy with our accurate results. However, scaling up these rates by a factor of 2 gives a qualitative agreement.

A new ab initio potential energy surface for the collisional excitation of HCN by para- and ortho-H2.

We present a new four-dimensional potential energy surface for the collisional excitation of HCN by H2. Ab initio calculations of the HCN-H2 van der Waals complex, considering both molecules as rigid rotors, were carried out at the explicitly correlated coupled cluster with single, double, and perturbative triple excitations [CCSD(T)-F12a] level of theory using an augmented correlation-consistent triple zeta (aVTZ) basis set. The equilibrium structure is linear HCN-H2 with the nitrogen pointing towards H2 at an intermolecular separation of 7.20 a0. The corresponding well depth is -195.20 cm(-1). A secondary minimum of -183.59 cm(-1) was found for a T-shape configuration with the H of HCN pointing to the center of mass of H2. We also determine the rovibrational energy levels of the HCN-para-H2 and HCN-ortho-H2 complexes. The calculated dissociation energies for the para and ortho complexes are 37.79 cm(-1) and 60.26 cm(-1), respectively. The calculated ro-vibrational transitions in the HCN-H2 complex are found to agree by more than 0.5% with the available experimental data, confirming the accuracy of the potential energy surface.

Bioaccumulation of zinc in crops and its contribution to Zn intake by Cuban population / Bioacumulación de zinc en cultivos y su contribución a la ingestión de Zn por la población cubana

Zinc content and Zn bioaccumulation in crops (rice and some vegetables and condiments) cultivated in 18 Cuban urban and suburban areas are reported. Zinc content in food and the corresponding farming soil samples was determined by X-Ray Fluorescence analysis and by Atomic Absorption spectrometry. The quality of the analysis was verified using the Certified Reference Materials IAEA 393 «Algae¼, MA-B-3/TM «Fish Tissue Lyophilised¼, IAEA V-10 «Hay¼ and IAEA Soil-7. The obtained results show rice, of the studied crops, as the major Zn bioaccumulator and important Zn source in Cuban human diet.

Se reportan los contenidos de zinc y su bioacumulación en cultivos (arroz, vegetales y condimentos) procedentes de 18 áreas de agricultura urbana y suburbana. El contenido de zinc en los alimentos, así como en sus correspondientes suelos de cultivo, fue determinado por Fluorescencia de Rayos X y por Espectrometría de Absorción Atómica. La calidad del estudio se verificó mediante el análisis de los Materiales de Referencia Certificados IAEA 393 «Algae¼, MA-B-3/TM «Fish Tissue Lyophilised¼, IAEA V-10 «Hay¼ e IAEA Soil-7. Los resultados mostraron al arroz, de los cultivos estudiados, como el cultivo de mayor bioacumulación de zinc y como fuente importante de Zn en la dieta de nuestra población.