Permutationally Invariant Polynomial Potential Energy Surfaces for Tropolone and H and D atom Tunneling Dynamics

We report permutationally invariant polynomial (PIP) fits to energies and gradients for 15-atom tropolone. These include standard, augmented, and fragmented PIP bases. Approximately 6600 energies and associated gradients are obtained from direct-dynamics calculations using DFT/B3LYP/6-31+G(d) supplemented by grid calculations spanning an energy range up to roughly 35 000 cm-1. Three fragmentation schemes are investigated with respect to efficiency and fit precision. In addition several fits are done with reduced weight for gradient data relative to energies. These do result in more precision for the H-transfer barrier height. Properties of the fits such as stationary points, harmonic frequencies and the barrier to H-atom transfer are reported and compared to direct calculations. A 1-d model to obtain the tunneling splitting for the ground vibrational state and qualitative predictions for excited vibrational states is employed. Several 1-d double well fits to the PES are developed and used to extrapolate H and D atom tunneling splittings to values at the CCSD(T)-F12 barrier. The level of agreement is within expectations for the method adapted and the level of the electronic structure theory employed

Meta-analysis across Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) consortium provides evidence for an association of serum Vitamin D with pulmonary function

The role that vitamin D plays in pulmonary function remains uncertain. Epidemiological studies reported mixed findings for serum 25-hydroxyvitamin D (25(OH)D)-pulmonary function association. We conducted the largest cross-sectional meta-analysis of the 25(OH)D-pulmonary function association to date, based on nine European ancestry (EA) cohorts (n 22 838) and five African ancestry (AA) cohorts (n 4290) in the Cohorts for Heart and Aging Research in Genomic Epidemiology Consortium. Data were analysed using linear models by cohort and ancestry. Effect modification by smoking status (current/former/never) was tested. Results were combined using fixed-effects meta-analysis. Mean serum 25(OH)D was 68 (sd 29) nmol/l for EA and 49 (sd 21) nmol/l for AA. For each 1 nmol/l higher 25(OH)D, forced expiratory volume in the 1st second (FEV1) was higher by 1·1 ml in EA (95 % CI 0·9, 1·3; P<0·0001) and 1·8 ml (95 % CI 1·1, 2·5; P<0·0001) in AA (P race difference=0·06), and forced vital capacity (FVC) was higher by 1·3 ml in EA (95 % CI 1·0, 1·6; P<0·0001) and 1·5 ml (95 % CI 0·8, 2·3; P=0·0001) in AA (Prace difference=0·56). Among EA, the 25(OH)D-FVC association was stronger in smokers: per 1 nmol/l higher 25(OH)D, FVC was higher by 1·7 ml (95 % CI 1·1, 2·3) for current smokers and 1·7 ml (95 % CI 1·2, 2·1) for former smokers, compared with 0·8 ml (95 % CI 0·4, 1·2) for never smokers. In summary, the 25(OH)D associations with FEV1 and FVC were positive in both ancestries. In EA, a stronger association was observed for smokers compared with never smokers, which supports the importance of vitamin D in vulnerable populations

Trajectory study of energy transfer and unimolecular dissociation of highly excited allyl with argon

The influence of rotational excitation on energy transfer in single collisions of allyl with argon and on allyl dissociation is investigated. About 90 000 classical scattering simulations are performed in order to determine collision-induced changes in internal energy and in allyl rotational angular momentum. Dissociation is studied by means of about 50 000 additional trajectories evolved for the isolated allyl under three different conditions: allyl with no angular momentum (J = 0); allyl with the same microcanonically sampled initial conditions used for the collisions (J 17); allyl evolving from the corresponding exit conditions after the collision. The potential energy surface is the sum of an intramolecular potential and an interaction one, and it has already been used in a previous work on allyl-argon scattering (Conte, R.; Houston, P. L.; Bowman, J. M. J. Phys. Chem. A 2013, 117, 14028-14041). Energy transfer data show that increased initial rotation favors, on average, increased relaxation of the excited molecule. The availability of a high-level intramolecular potential energy surface permits us to study the dependence of energy transfer on the type of starting allyl isomer. A turning point analysis is presented, and highly efficient collisions are detected. Collision-induced variations in the allyl rotational angular momentum may be quite large and are found to be distributed according to three regimes. The roles of rotational angular momentum, collision, and type of isomer on allyl unimolecular dissociation are considered by looking at dissociations times, kinetic energies of the fragments, and branching ratios. Generally, rotational angular momentum has a strong influence on the dissociation dynamics, while the single collision and the type of starting isomer are less influential

Reliability of human cryopreserved hepatocytes and liver microsomes as in vitro systems to predict metabolic clearance

A total of 110 drugs, selected to cover a range of physicochemical and pharmacokinetic properties, were used to explore standard approaches to the prediction of in vivo metabolic clearance using drug-depletion profiles from human liver microsomes (HLMs) and cyropreserved hepatocytes. A total of 41 drugs (37% of the compounds tested) showed measurable depletion rates using HLMs (depletion by 20% or more over the time course). The most reliable correlations in terms of bias (average fold error (AFE) = 2.32) and precision (root mean square error (RMSE) = 3501) were observed by comparing in vivo intrinsic clearance (CLint), calculated using the parallel-tube model and incorporating the fraction unbound in blood, with in vitro CLint adjusted for microsomal binding. For these reference drugs, 29% of predictions were within two-fold of the observed values and 66% were within five-fold. Compared with HLMs, clearance predictions with cryopreserved hepatocytes (57 drugs) were of similar precision (RMSE = 3608) but showed more bias (AFE = 5.21) with 18% of predictions within two-fold of the observed values and 46% within five-fold. However, with a broad complement of drug-metabolizing enzymes, hepatocytes catalysed measurable CLint values for a greater proportion (52%) of the reference compounds and were particularly proficient at defining metabolic rates for drugs with predominantly phase 2 metabolic routes.Peer reviewe

Classical trajectory study of energy transfer in collisions of highly excited allyl radical with argon

Predicting the results of collisions of polyatomic molecules with a bath of atoms is a research area that has attracted substantial interest in both experimental and theoretical chemistry. Energy transfer, which is the consequence of such collisions, plays an important role in gas-phase kinetics and relaxation of excited molecules. We present a study of energy transfer in single collisions of highly vibrationally excited allyl radical in argon. We evolve a total of 52 000 classical trajectories on a potential energy surface, which is the sum of an ab initio intramolecular potential for the allyl and a pairwise interaction potential describing the argon's effect on the allyl. The former is described by means of a permutationally invariant full-dimensional potential, whereas the interaction potential between allyl and argon is obtained by means of a sum of pairwise potentials dependent on nonlinear parameters that have been fit to a set of MP2/avtz counterpoise corrected ab initio energies. Results are reported for energy transfers and related probability densities at different collisional energies. The sensitivity of results to the interaction potential is considered and the potential is shown to be suitable for future applications involving different isomers of the allyl. The impact of highly efficient collisions in the energy transfer process is examined. \ua9 2013 American Chemical Society

Communication: A benchmark-quality, full-dimensional ab initio potential energy surface for Ar-HOCO

A full-dimensional, global ab initio potential energy surface (PES) for the Ar-HOCO system is presented. The PES consists of a previous intramolecular ab initio PES for HOCO [J. Li, C. Xie, J. Ma, Y. Wang, R. Dawes, D. Xie, J. M. Bowman, and H. Guo, J. Phys. Chem. A 116, 5057 (2012)], plus a new permutationally invariant interaction potential based on fitting 12 432 UCCSD(T)-F12a/aVDZ counterpoise-corrected energies. The latter has a total rms fitting error of about 25 cm-1 for fitted interaction energies up to roughly 12 000 cm-1. Two additional fits are presented. One is a novel very compact permutational invariant representation, which contains terms only involving the Ar-atom distances. The rms fitting error for this fit is 193 cm-1. The other fit is the widely used pairwise one. The pairwise fit to the entire data set has an rms fitting error of 427 cm-1. All of these potentials are used in preliminary classical trajectory calculations of energy transfer with a focus on comparisons with the results using the benchmark potential. \ua9 2014 AIP Publishing LLC

Trajectory and Model Studies of Collisions of Highly Excited Methane with Water Using an ab Initio Potential

Quasi-classical trajectory studies have been performed for the collision of internally excited methane with water using an accurate methane-water potential based on a full-dimensional, permutationally invariant analytical representation of energies calculated at a high level of theory. The results suggest that most energy transfer takes place at impact parameters smaller than about 8 Bohr; collisions at higher impact parameters are mostly elastic. Overall, energy transfer is fairly facile, with values for \uab\u394Edown\uab and \uab\u394Eup\uab approaching almost 2% of the total excitation energy. A classical model previously developed for the collision of internally excited molecules with atoms (Houston, P. L.; Conte, R.; Bowman, J. M. J. Phys. Chem. A 2015, 119, 4695-4710) has been extended to cover collisions of internally excited molecules with other molecules. For high initial rotational levels, the agreement with the trajectory results is quite good (R2 48 0.9), whereas for low initial rotational levels it is only fair (R2 48 0.7). Both the model and the trajectories can be characterized by a four-dimensional joint probability distribution, P(J1,f,\u394E1,J2,f,\u394E2), where J1,f and J2,f are the final rotational levels of molecules 1 and 2 and \u394E1 and \u394E2 are the respective changes in internal energy. A strong anticorrelation between \u394E1 and \u394E2 is observed in both the model and trajectory results and can be explained by the model. There is evidence in the trajectory results for a small amount of V \u8660 V energy transfer from the water, which has low internal energy, to the methane, which has substantial internal energy. This observation suggests that V \u8660 V energy transfer in the other direction also occurs

Neutral photodissociation of superexcited states of molecular iodine

The formation of high-n Rydberg atoms from the neutral dissociation of superexcited states of I2 formed by resonant two-photon excitation of molecular iodine using an ArF laser has been investigated. The high-n Rydberg atoms I* are formed by predissociation of the optically excited molecular Rydberg states I2 * RB 2g + converging on the I2 +B 2g + state of the ion. Measurement of the kinetic energy release of the Rydberg I* fragments allowed the identification of the asymptotic channels as I*R3PJ+I2P3/2, where the I*R3PJ are Rydberg atoms converging on the I+3PJ states of the ion with J=2, 1, and 0. In the case of the I*R3P2 fragments, the average Rydberg lifetime is observed to be 325±25 s. Based on experiments on the variation of the Rydberg atom signal with the field ionizing strength, the distribution of Rydberg levels peaks at about 25–50 cm−1 below the ionization limit

Collisional energy transfer in highly excited molecules

The excitation/de-excitation step in the Lindemann mechanism is investigated in detail using model development and classical trajectory studies based on a realistic potential energy surface. The model, based on a soft-sphere/line-of-centers approach and using elements of Landau-Teller theory and phase space theory, correctly predicts most aspects of the joint probability distribution P(\u394E,\u394J) for the collisional excitation and de-excitation process in the argon-allyl system. The classical trajectories both confirm the validity of the model and provide insight into the energy transfer. The potential employed was based on a previously available ab initio intramolecular potential for the allyl fit to 97418 allyl electronic energies and an intermolecular potential fit to 286 Ar-allyl energies. Intramolecular energies were calculated at the CCSD(T)/AVTZ level of theory, while intermolecular energies were calculated at the MP2/AVTZ level of theory. Trajectories were calculated for each of four starting allyl isomers and for an initial rotational level of Ji = 0 as well as for Ji taken from a microcanonical distribution. Despite a dissimilarity in Ar-allyl potentials for fixed Ar-allyl geometries, energy transfer properties starting from four different isomers were found to be remarkably alike. A contributing factor appears to be that the orientation-averaged potentials are almost identical. The model we have developed suggests that most hydrocarbons should have similar energy transfer properties, scaled by differences in the potential offset of the atom-hydrogen interaction. Available data corroborate this suggestion

Perspective: Advanced particle imaging

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