Nonadiabatic excited-state molecular dynamics: Numerical tests of convergence and parameters

Nonadiabatic molecular dynamics simulations, involving multiple Born-Oppenheimer potential energy surfaces, often require a large number of independent trajectories in order to achieve the desired convergence of the results, and simulation relies on different parameters that should be tested and compared. In addition to influencing the speed of the simulation, the chosen parameters combined with the frequently reduced number of trajectories can sometimes lead to unanticipated changes in the accuracy of the simulated dynamics. We have previously developed a nonadiabatic excited state molecular dynamics methodology employing Tullys fewest switches surface hopping algorithm. In this study, we seek to investigate the impact of the number of trajectories and the various parameters on the simulation of the photoinduced dynamics of distyrylbenzene (a small oligomer of polyphenylene vinylene) within our developed framework. Various user-defined parameters are analyzed: classical and quantum integration time steps, the value of the friction coefficient for Langevin dynamics, and the initial seed used for stochastic thermostat and hopping algorithms. Common approximations such as reduced number of nonadiabatic coupling terms and the classical path approximation are also investigated. Our analysis shows that, at least for the considered molecular system, a minimum of ∼400 independent trajectories should be calculated in order to achieve statistical averaging necessary for convergence of the calculated relaxation timescales.Fil: Nelson, Tammie. Los Alamos National Laboratory; Estados UnidosFil: Fernández Alberti, Sebastián. Universidad Nacional de Quilmes; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Chernyak, Vladimir. Wayne State University (wayne State University); Estados UnidosFil: Roitberg, Adrián. University of Florida; Estados UnidosFil: Tretiak, Sergei. Los Alamos National High Magnetic Field Laboratory; Estados Unido

Sex differences in contaminant concentrations of fish: a synthesis

Abstract A comparison of whole-fish polychlorinated biphenyl (PCB) and total mercury (Hg) concentrations in mature males with those in mature females may provide insights into sex differences in behavior, metabolism, and other physiological processes. In eight species of fish, we observed that males exceeded females in whole-fish PCB concentration by 17 to 43 %. Based on results from hypothesis testing, we concluded that these sex differences were most likely primarily driven by a higher rate of energy expenditure, stemming from higher resting metabolic rate (or standard metabolic rate (SMR)) and higher swimming activity, in males compared with females. A higher rate of energy expenditure led to a higher rate of food consumption, which, in turn, resulted in a higher rate of PCB accumulation. For two fish species, the growth dilution effect also made a substantial contribution to the sex difference in PCB concentrations, although the higher energy expenditure rate for males was still the primary driver. Hg concentration data were available for five of the eight species. For four of these five species, the ratio of PCB concentration in males to PCB concentration in females was substantially greater than the ratio of Hg concentration in males to Hg concentration in females. In sea lamprey (Petromyzon marinus), a very primitive fish, the two ratios were nearly identical. The most plausible explanation for this pattern was that certain androgens, such as testosterone and 11-ketotestosterone, enhanced Hg-elimination rate in males. In contrast, long-term elimination of PCBs is negligible for both sexes. According to this explanation, males not only ingest Hg at a higher rate than females but also eliminate Hg at a higher rate than females, in fish species other than sea lamprey. Male sea lamprey do not possess either of the above-specified androgens. These apparent sex differences in SMRs, activities, and Hg-elimination rates in teleost fishes may also apply, to some degree, to higher vertebrates including humans. Our synthesis findings will be useful in (1) developing sex-specific bioenergetics models for fish, (2) developing sex-specific risk assessment models for exposure of humans and wildlife to contaminants, and (3) refining Hg mass balance models for fish and higher vertebrates.http://deepblue.lib.umich.edu/bitstream/2027.42/134637/1/13293_2016_Article_90.pd

PAHs, nitro‐PAHs, hopanes, and steranes in lake trout from Lake Michigan

The present study examines concentrations and risks of polycyclic aromatic hydrocarbons (PAHs), nitro‐PAHs (NPAHs), steranes, and hopanes in lake trout collected in Lake Michigan. A total of 74 fish were collected in 2 seasons at 3 offshore sites. The total PAH concentration (Σ 9 PAH) in whole fish ranged from 223 pg/g to 1704 pg/g wet weight, and PAH concentrations and profiles were similar across season, site, and sex. The total NPAH (Σ 9 NPAH) concentrations ranged from 0.2 pg/g to 31 pg/g wet weight, and carcinogenic compounds, including 1‐nitropyrene and 6‐nitrochrysene, were detected. In the fall, NPAH concentrations were low at the Illinois site (0.2–0.5 pg/g wet wt), and site profiles differed considerably; in the spring, concentrations and profiles were similar across sites, possibly reflecting changes in fish behavior. In the fall, the total sterane (Σ 5 Sterane) and total hopane (Σ 2 Hopane) levels reached 808 pg/g and 141 pg/g wet weight, respectively, but concentrations in the spring were 10 times lower. Concentrations in eggs (fall only) were on the same order of magnitude as those in whole fish. These results demonstrate the presence of target semivolatile organic compounds in a top predator fish, and are consistent with PAH biodilution observed previously. Using the available toxicity information for PAHs and NPAHs, the expected cancer risk from consumption of lake trout sampled are low. However, NPAHs contributed a significant portion of the toxic equivalencies in some samples. The present study provides the first measurements of NPAHs in freshwater fish, and results suggest that additional assessment is warranted. Environ Toxicol Chem 2014;33:1792–1801 . © 2014 SETACPeer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/108087/1/etc2620.pd

Development and comparison of methods using MS scan and selective ion monitoring modes for a wide range of airborne VOCs

Adsorbent sampling with analysis by thermal desorption, gas chromatography and mass spectrometry (TD/GC/MS) offers many advantages for volatile organic compounds (VOCs) and thus is increasingly used in many applications. For environmental samples and other complex mixtures, the MS detector typically is operated in the scan mode to aid identification of co-eluting compounds. However, scan mode does not achieve the optimal sensitivity, thus compounds occurring at low concentrations may not be detected. This paper develops and evaluates the application of a more sensitive TD/GC/MS method using selective ion monitoring (SIM) that is applicable to VOC mixtures found in ambient and indoor air. Based on toxicity and prevalence, 94 VOCs (including terpenes, aromatic, halogenated and aliphatic compounds) were selected as target compounds. Two analytical methods were developed: a conventional full scan method for ions from 29 to 270 m/z; and a SIM method using 16 time windows and different ions selected for the compounds in each window. Both methods used the same Tenax GR adsorbent sampling tubes, TD and GC parameters, and target and qualifier ions. Laboratory tests determined calibrations, method detection limits (MDLs), precisions, recoveries and storage stability. Field tests compared scan and SIM mode analyses for duplicate samples of indoor air in 51 houses and outdoor air at 41 sites. Statistical analyses included the development of error/precision models. The laboratory tests showed that most compounds demonstrated excellent precision (\u3c10% for concentrations exceeding ∼0.5 μg m-3), good linearity, near identical calibrations for scan and SIM modes, a wide dynamic range (up to 1500 μg m-3), and negligible storage losses after 1 month (7 compounds showed moderate losses). SIM mode MDLs ranged from 0.004 to 0.27 μg m-3, representing a modest (1.1 to 22-fold) improvement compared to scan mode. However, in field tests the SIM method detected significantly more compounds (e.g., styrene and chloroform). Error models fit most compounds and allow quantification of errors at selected percentiles. Overall, while the new SIM method is somewhat time-consuming to develop, it offers greater sensitivity and maintains the high selectivity of traditional scan methods. © The Royal Society of Chemistry 2006